Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008032.1 Hibiscus syriacus cultivar Beakdansim tig00110514_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: 1200719
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:1035846 original size:18 final size:18
Alignment explanation
Indices: 1035825--1035873 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
1035815 CTCCACTTCG
1035825 AGAGCCATCACCTCACCC
1 AGAGCCATCACCTCACCC
*
1035843 AGAGCTATCACCTCACCC
1 AGAGCCATCACCTCACCC
1035861 AGAGCCATCACCT
1 AGAGCCATCACCT
1035874 GATCGACCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.29, C:0.45, G:0.12, T:0.14
Consensus pattern (18 bp):
AGAGCCATCACCTCACCC
Found at i:1036433 original size:20 final size:20
Alignment explanation
Indices: 1036408--1036453 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1036398 TAGTTTACTT
1036408 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
1036428 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
1036448 TCGCAA
1 TCGCAA
1036454 TGCGATAGCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:1036479 original size:20 final size:20
Alignment explanation
Indices: 1036454--1036518 Score: 103
Period size: 20 Copynumber: 3.2 Consensus size: 20
1036444 GCTATCGCAA
* *
1036454 TGCGATAGCCATTTCCGTGT
1 TGCGATAGTCATTTCCGCGT
1036474 TGCGATAGTCATTTCCGCGT
1 TGCGATAGTCATTTCCGCGT
*
1036494 TGCGATAGTCATTTTCGCGT
1 TGCGATAGTCATTTCCGCGT
1036514 TGCGA
1 TGCGA
1036519 AAGTAAGTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.15, C:0.23, G:0.26, T:0.35
Consensus pattern (20 bp):
TGCGATAGTCATTTCCGCGT
Found at i:1036529 original size:20 final size:20
Alignment explanation
Indices: 1036489--1036544 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1036479 TAGTCATTTC
* * *
1036489 CGCGTTGCGATAGTCATTTT
1 CGCGTTGCGAAAGTAAGTTT
1036509 CGCGTTGCGAAAGTAAGTTT
1 CGCGTTGCGAAAGTAAGTTT
*
1036529 CGTGTTGCGAAAGTAA
1 CGCGTTGCGAAAGTAA
1036545 ACTATTCTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.32
Consensus pattern (20 bp):
CGCGTTGCGAAAGTAAGTTT
Found at i:1036536 original size:40 final size:40
Alignment explanation
Indices: 1036454--1036538 Score: 100
Period size: 40 Copynumber: 2.1 Consensus size: 40
1036444 GCTATCGCAA
* * *
1036454 TGCGATAGCCATTTCCGTGTTGCGATAGTCATTTCCGCGT
1 TGCGATAGCCATTTCCGCGTTGCGAAAGTAATTTCCGCGT
* * *
1036494 TGCGATAGTCATTTTCGCGTTGCGAAAGTAAGTTT-CGTGT
1 TGCGATAGCCATTTCCGCGTTGCGAAAGTAA-TTTCCGCGT
1036534 TGCGA
1 TGCGA
1036539 AAGTAAACTA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 35 0.92
41 3 0.08
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.35
Consensus pattern (40 bp):
TGCGATAGCCATTTCCGCGTTGCGAAAGTAATTTCCGCGT
Found at i:1036919 original size:21 final size:21
Alignment explanation
Indices: 1036888--1036946 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
1036878 CTCACCTGTC
*
1036888 ATCCCTCAAGAGTCCCCTCTA
1 ATCCCTCAAGAGTCCCCTATA
** * *
1036909 ATCGTTCAAGAGGCCCCTATC
1 ATCCCTCAAGAGTCCCCTATA
1036930 ATCCCTCAAGAGTCCCC
1 ATCCCTCAAGAGTCCCC
1036947 CCACCGTTCA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.24, C:0.41, G:0.14, T:0.22
Consensus pattern (21 bp):
ATCCCTCAAGAGTCCCCTATA
Found at i:1036972 original size:40 final size:42
Alignment explanation
Indices: 1036883--1036972 Score: 130
Period size: 40 Copynumber: 2.2 Consensus size: 42
1036873 CCCGACTCAC
* *
1036883 CTGTCATCCCTCAAGAGTCCCCTCTAATCGTTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCTAACCGTTCAAGAGGCCA
* *
1036925 CTATCATCCCTCAAGAGTCCCC-C-CACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCTAACCGTTCAAGAGGCCA
1036965 CTGTCATC
1 CTGTCATC
1036973 GTTGAAGAGG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
40 21 0.49
41 1 0.02
42 21 0.49
ACGTcount: A:0.22, C:0.40, G:0.16, T:0.22
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCTAACCGTTCAAGAGGCCA
Found at i:1036981 original size:40 final size:42
Alignment explanation
Indices: 1036886--1037002 Score: 114
Period size: 42 Copynumber: 2.8 Consensus size: 42
1036876 GACTCACCTG
** * *
1036886 TCATCCCTCAAGA-GTCCCCTCTAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGGT-CCCTCCCACCGTTCAAGAGGCCACTA
*
1036928 TCATCCCTCAAGA-GTCCC-CCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGGTCCCTCCCACCGTTCAAGAGGCCACTA
** * * *
1036968 TCATCGTTGAAGAGGTCCCTCCCACCATTCCAGAG
1 TCATCCCTCAAGAGGTCCCTCCCACCGTTCAAGAG
1037003 CCCGATTCAC
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
40 27 0.43
41 8 0.13
42 28 0.44
ACGTcount: A:0.23, C:0.38, G:0.17, T:0.21
Consensus pattern (42 bp):
TCATCCCTCAAGAGGTCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:1038602 original size:20 final size:20
Alignment explanation
Indices: 1038577--1038623 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1038567 TCGCATTGCG
*
1038577 ATTTTCTAGTCGCGATAGCC
1 ATTTTCGAGTCGCGATAGCC
* *
1038597 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGAGTCGCGATAGCC
1038617 ATTTTCG
1 ATTTTCG
1038624 CGTTGCGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.17, C:0.23, G:0.21, T:0.38
Consensus pattern (20 bp):
ATTTTCGAGTCGCGATAGCC
Found at i:1038624 original size:20 final size:20
Alignment explanation
Indices: 1038588--1038632 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
1038578 TTTTCTAGTC
1038588 GCGATAGCCATTTTCGCGTT
1 GCGATAGCCATTTTCGCGTT
1038608 GCGATAGCCATTTTCGCGTT
1 GCGATAGCCATTTTCGCGTT
1038628 GCGAT
1 GCGAT
1038633 TTCCCCGTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.16, C:0.24, G:0.27, T:0.33
Consensus pattern (20 bp):
GCGATAGCCATTTTCGCGTT
Found at i:1038882 original size:20 final size:20
Alignment explanation
Indices: 1038857--1038953 Score: 149
Period size: 20 Copynumber: 4.8 Consensus size: 20
1038847 ATTGCTATTT
* *
1038857 TCAGAATCTCGTTGTGAAAG
1 TCAGAATCGCGTTGCGAAAG
*
1038877 TCAGAATCTCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
1038897 TCAGAATCGCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
*
1038917 TCAGAATCGCATTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
*
1038937 TCAGTATCGCGTTGCGA
1 TCAGAATCGCGTTGCGA
1038954 TTTTGTATTA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 72 1.00
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.25
Consensus pattern (20 bp):
TCAGAATCGCGTTGCGAAAG
Found at i:1038995 original size:20 final size:20
Alignment explanation
Indices: 1038866--1038994 Score: 125
Period size: 20 Copynumber: 6.4 Consensus size: 20
1038856 TTCAGAATCT
* * *
1038866 CGTTGTGAAAGTCAGAATCT
1 CGTTGCGAAAGTCAGTATCG
*
1038886 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGTATCG
*
1038906 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGTATCG
*
1038926 CATTGCGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGTATCG
** * *
1038946 CGTTGCGATTTTGT-ATTATCT
1 CGTTGCGA--AAGTCAGTATCG
*
1038967 CGTTGCGATAGTCAGTATCG
1 CGTTGCGAAAGTCAGTATCG
*
1038987 CATTGCGA
1 CGTTGCGA
1038995 TTTTTCAAAT
Statistics
Matches: 93, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
19 3 0.03
20 75 0.81
21 13 0.14
22 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGTATCG
Found at i:1039014 original size:41 final size:43
Alignment explanation
Indices: 1038923--1039016 Score: 117
Period size: 41 Copynumber: 2.3 Consensus size: 43
1038913 AAAGTCAGAA
* * *
1038923 TCGCATTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATTATC
1 TCGCATTGCGATAGTCAGTATCGCATTGCGATTTTGTATAATC
1038966 TCG--TTGCGATAGTCAGTATCGCATTGCGATTTT-TCA-AAT-
1 TCGCATTGCGATAGTCAGTATCGCATTGCGATTTTGT-ATAATC
1039005 TCGCATTGCGAT
1 TCGCATTGCGAT
1039017 TTACTTATTC
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
39 3 0.07
40 3 0.07
41 36 0.80
43 3 0.07
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCATTGCGATAGTCAGTATCGCATTGCGATTTTGTATAATC
Found at i:1039028 original size:20 final size:21
Alignment explanation
Indices: 1038984--1039035 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1038974 ATAGTCAGTA
*
1038984 TCGCATTGCGATTTTTCAAAT
1 TCGCATTGCGATTTTACAAAT
**
1039005 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
1039025 TCGCATTGCGA
1 TCGCATTGCGA
1039036 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:1039252 original size:12 final size:12
Alignment explanation
Indices: 1039233--1039266 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1039223 CTCTCCGGCG
1039233 ACATCCGTTCCT
1 ACATCCGTTCCT
*
1039245 ATATCCGTTCCT
1 ACATCCGTTCCT
1039257 ACATCC-TTCC
1 ACATCCGTTCC
1039267 CCATCCGACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:1039848 original size:24 final size:24
Alignment explanation
Indices: 1039821--1039874 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1039811 GTATTCGAAA
*
1039821 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
1039845 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
1039869 TTTGAT
1 TTTGAT
1039875 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:1042436 original size:33 final size:33
Alignment explanation
Indices: 1042394--1042516 Score: 183
Period size: 33 Copynumber: 3.7 Consensus size: 33
1042384 ATTACTATCA
*
1042394 CAATGCGAAATGAAAATCGCAACGAGATAATCG
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCG
* *
1042427 CAATGCGAAATGAAAATAGTAACGAGAGAATCG
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCG
* * *
1042460 CAATGTGAAATGAAAATCACAACGAGGGAATCG
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCG
*
1042493 CAAAGCGAAATGAAAATCGCAACG
1 CAATGCGAAATGAAAATCGCAACG
1042517 CGAATTTAGT
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.47, C:0.16, G:0.23, T:0.14
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGAGAGAATCG
Found at i:1042568 original size:33 final size:33
Alignment explanation
Indices: 1042526--1042638 Score: 199
Period size: 33 Copynumber: 3.4 Consensus size: 33
1042516 GCGAATTTAG
* *
1042526 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTATCTCGTTGCGATTTTCA
*
1042559 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTATCTCGTTGCGATTTTCA
1042592 TTTCGCATTGCGATTATCTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTATCTCGTTGCGATTTTCA
1042625 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
1042639 AGTAATTTTT
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 77 1.00
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.46
Consensus pattern (33 bp):
TTTCGCATTGCGATTATCTCGTTGCGATTTTCA
Found at i:1042571 original size:19 final size:19
Alignment explanation
Indices: 1042547--1042638 Score: 96
Period size: 19 Copynumber: 5.4 Consensus size: 19
1042537 GATTTTGTCG
1042547 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1042566 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1042580 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1042599 TTGCGA--TT-ATCTCG--
1 TTGCGATTTTCATTTCGCA
1042613 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1042632 TTGCGAT
1 TTGCGAT
1042639 AGTAATTTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 12 0.20
16 14 0.24
17 14 0.24
19 19 0.32
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1042764 original size:14 final size:14
Alignment explanation
Indices: 1042745--1042781 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1042735 CATCAATTAA
1042745 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1042759 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1042773 ACAAATCAA
1 ACAAATCAA
1042782 TTAAACAATC
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:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1044187 original size:21 final size:21
Alignment explanation
Indices: 1044121--1044187 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1044111 GTGAATCGGG
*
1044121 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1044141 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1044163 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1044184 CTCT
1 CTCT
1044188 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1044206 original size:42 final size:41
Alignment explanation
Indices: 1044121--1044243 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
1044111 GTGAATCGGG
* * * *
1044121 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
1044163 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
1044205 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
1044244 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:1044642 original size:91 final size:90
Alignment explanation
Indices: 1044461--1044645 Score: 282
Period size: 91 Copynumber: 2.0 Consensus size: 90
1044451 ATTTCAAACT
*
1044461 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
*
1044526 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGACAGCAACCGAATAAATTTAC
1044554 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
* *
1044618 GTATTGACAGCAACCGGATAAATTTAC
64 GAATTGACAGCAACCGAATAAATTTAC
1044645 T
1 T
1044646 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
91 40 0.47
93 19 0.22
95 27 0.31
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGACAGCAACCGAATAAATTTAC
Found at i:1046368 original size:20 final size:19
Alignment explanation
Indices: 1046338--1046489 Score: 93
Period size: 14 Copynumber: 8.7 Consensus size: 19
1046328 TCTTTTGGTT
*
1046338 GAAATGGAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
1046357 GATAATGAAAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
1046378 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
1046397 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
**
1046411 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
1046430 G--A-G--AATCGCAACGCA
1 GAAATGAAAATCGCAACG-A
1046445 -AAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
1046463 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
1046477 GAAATGAAAATCG
1 GAAATGAAAATCG
1046490 TAATGCGATT
Statistics
Matches: 103, Mismatches: 11, Indels: 38
0.68 0.07 0.25
Matches are distributed among these distances:
14 30 0.29
15 1 0.01
16 6 0.06
17 6 0.06
18 1 0.01
19 28 0.27
20 29 0.28
21 2 0.02
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:1046420 original size:33 final size:33
Alignment explanation
Indices: 1046366--1046483 Score: 200
Period size: 33 Copynumber: 3.5 Consensus size: 33
1046356 AGATAATGAA
1046366 AATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGC-GAAATGACTATCGCAACGAGAG
1046400 AATCGCAACGCGAAATGACTATCGCAACGAGAG
1 AATCGCAACGCGAAATGACTATCGCAACGAGAG
* **
1046433 AATCGCAACGCAAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGACTATCGCAACGAGAG
1046466 AATCGCAACGCGAAATGA
1 AATCGCAACGCGAAATGA
1046484 AAATCGTAAT
Statistics
Matches: 80, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
33 69 0.86
34 11 0.14
ACGTcount: A:0.42, C:0.23, G:0.24, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGACTATCGCAACGAGAG
Found at i:1046541 original size:33 final size:32
Alignment explanation
Indices: 1046493--1046585 Score: 123
Period size: 33 Copynumber: 2.8 Consensus size: 32
1046483 AAAATCGTAA
*
1046493 TGCGATTTTGGTTTCGCGTTGCGATTATCTCGT
1 TGCGATTTT-ATTTCGCGTTGCGATTATCTCGT
*
1046526 TGCGATTTTCATTTCGCGTTGCGATTTTCTCGT
1 TGCGATTTT-ATTTCGCGTTGCGATTATCTCGT
*
1046559 TGCGATAGTTATTTCCGCGTTGCGATT
1 TGCGAT-TTTATTT-CGCGTTGCGATT
1046586 TTCATTCTCG
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
33 40 0.74
34 14 0.26
ACGTcount: A:0.11, C:0.19, G:0.25, T:0.45
Consensus pattern (32 bp):
TGCGATTTTATTTCGCGTTGCGATTATCTCGT
Found at i:1046547 original size:19 final size:19
Alignment explanation
Indices: 1046523--1046591 Score: 69
Period size: 19 Copynumber: 3.8 Consensus size: 19
1046513 GCGATTATCT
1046523 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
1046542 CGTTGCGATTTTC---T--
1 CGTTGCGATTTTCATTTCG
*
1046556 CGTTGCGATAGTT-ATTTCCG
1 CGTTGCGAT-TTTCATTT-CG
1046576 CGTTGCGATTTTCATT
1 CGTTGCGATTTTCATT
1046592 CTCGAAACTA
Statistics
Matches: 40, Mismatches: 2, Indels: 15
0.70 0.04 0.26
Matches are distributed among these distances:
14 9 0.22
15 2 0.05
16 1 0.03
17 1 0.03
19 15 0.38
20 12 0.30
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1047200 original size:20 final size:20
Alignment explanation
Indices: 1047129--1047222 Score: 82
Period size: 20 Copynumber: 4.5 Consensus size: 20
1047119 ATAGTAAGAT
1047129 TCGCATTGCGATTTAC-TGACTA
1 TCGCATTGCGATTTACGT-A--A
* * * *
1047151 TCGCAATGCAATTTTCCTAA
1 TCGCATTGCGATTTACGTAA
*
1047171 TTCGCATTGCGATTTACTTAA
1 -TCGCATTGCGATTTACGTAA
* *
1047192 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAA
1047212 TCGCATTGCGA
1 TCGCATTGCGA
1047223 ATTATGAAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
20 28 0.47
21 16 0.27
22 14 0.24
23 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAA
Found at i:1047235 original size:41 final size:41
Alignment explanation
Indices: 1047190--1047360 Score: 132
Period size: 41 Copynumber: 4.2 Consensus size: 41
1047180 CGATTTACTT
* *
1047190 AATCGCGTTGCGATTTACGTATTCGCATTGCGAATTATGAA
1 AATCGCATTGCGATTTACGTATTCGCATTGCGAATTAGGAA
** * * * * *
1047231 AATCGCAACGCGA-ATACATAAATCGCAATACGAATTAGGAA
1 AATCGCATTGCGATTTACGT-ATTCGCATTGCGAATTAGGAA
* * * ***
1047272 AATTGCATTGCGATAGT-CAGTA-TCGCATTGCGATTTTCCAA
1 AATCGCATTGCGAT-TTAC-GTATTCGCATTGCGAATTAGGAA
* * *
1047313 ATTCGCATTGCGATTTACTTATTCGCATTGCGAATTGGGAA
1 AATCGCATTGCGATTTACGTATTCGCATTGCGAATTAGGAA
1047354 AATCGCA
1 AATCGCA
1047361 ACGCAAAATT
Statistics
Matches: 95, Mismatches: 29, Indels: 12
0.70 0.21 0.09
Matches are distributed among these distances:
40 7 0.07
41 84 0.88
42 2 0.02
43 2 0.02
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Consensus pattern (41 bp):
AATCGCATTGCGATTTACGTATTCGCATTGCGAATTAGGAA
Found at i:1047338 original size:20 final size:21
Alignment explanation
Indices: 1047294--1047345 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1047284 ATAGTCAGTA
*
1047294 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
1047315 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
1047335 TCGCATTGCGA
1 TCGCATTGCGA
1047346 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:1048394 original size:41 final size:41
Alignment explanation
Indices: 1048349--1048550 Score: 316
Period size: 41 Copynumber: 4.9 Consensus size: 41
1048339 ACGCGATAGT
*
1048349 CGAAGTTCACGTTGCGATTCATTCCAATTCGTTGCGACAGG
1 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
* *
1048390 CGAAGTTCGCATTGCGATTCATTCCAATTTGTTGCGACAGG
1 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
* *
1048431 CGAAGTTCGCATTACGATTCATTCCAATTCGTTGCGACAGG
1 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
*
1048472 CGAAGTTC-CTGTTGCGATTCAGTCCAATTCGTTGCGACAGG
1 CGAAGTTCGC-GTTGCGATTCATTCCAATTCGTTGCGACAGG
*
1048513 CGAAGTTCGCGTTGCGATTCTTTCCAAATTCGTTGCGA
1 CGAAGTTCGCGTTGCGATTCATTCC-AATTCGTTGCGA
1048551 TAGTCCAAAT
Statistics
Matches: 148, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
40 1 0.01
41 134 0.91
42 13 0.09
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.31
Consensus pattern (41 bp):
CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
Found at i:1048642 original size:6 final size:6
Alignment explanation
Indices: 1048631--1048673 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
1048621 GACACGTATT
1048631 ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1048674 CGGGACGGCG
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.27
6 27 0.73
ACGTcount: A:0.30, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1049491 original size:21 final size:21
Alignment explanation
Indices: 1049465--1049576 Score: 74
Period size: 21 Copynumber: 5.4 Consensus size: 21
1049455 TATTTGGACT
*
1049465 ATCGCAACGAATTTGGAATGA
1 ATCGCAACGAACTTGGAATGA
* **
1049486 ATCGCAACGCGAACTTCGCCT--
1 ATCGCAA--CGAACTTGGAATGA
1049507 ATCGCAACGAA-TTGGAATGA
1 ATCGCAACGAACTTGGAATGA
* *
1049527 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATGA
*
1049548 ATCGCAACG-ATTTGGAATGA
1 ATCGCAACGAACTTGGAATGA
*
1049568 ATTGCAACG
1 ATCGCAACG
1049577 CGAACTTCGC
Statistics
Matches: 69, Mismatches: 13, Indels: 19
0.68 0.13 0.19
Matches are distributed among these distances:
18 10 0.14
19 6 0.09
20 15 0.22
21 21 0.30
22 4 0.06
23 13 0.19
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATGA
Found at i:1049532 original size:41 final size:42
Alignment explanation
Indices: 1049463--1049627 Score: 271
Period size: 41 Copynumber: 4.0 Consensus size: 42
1049453 AATATTTGGA
1049463 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
*
1049505 CTATCGCAACGAA-TTGGAATGAATCGCAACGCGAACTTCGA
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
*
1049546 CTATCGCAACG-ATTTGGAATGAATTGCAACGCGAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
* * *
1049587 CTATCGCAACGAATTTGTAATAAATCGCAATGCGAACTTCG
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCG
1049628 ACTCTCGCGT
Statistics
Matches: 114, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
40 1 0.01
41 75 0.66
42 38 0.33
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (42 bp):
CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
Found at i:1049575 original size:82 final size:84
Alignment explanation
Indices: 1049461--1049635 Score: 291
Period size: 83 Copynumber: 2.1 Consensus size: 84
1049451 GCAATATTTG
1049461 GACTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTATCGCAACGAA-TTGGAAT
1 GACTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTATCGCAACGAATTTGGAAT
*
1049525 GAATCGCAACGCGAACTTC
66 AAATCGCAACGCGAACTTC
* *
1049544 GACTATCGCAACG-ATTTGGAATGAATTGCAACGCGAACTTCGCCTATCGCAACGAATTTGTAAT
1 GACTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTATCGCAACGAATTTGGAAT
*
1049608 AAATCGCAATGCGAACTTC
66 AAATCGCAACGCGAACTTC
*
1049627 GACTCTCGC
1 GACTATCGC
1049636 GTTGCGAATC
Statistics
Matches: 86, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
82 42 0.49
83 44 0.51
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (84 bp):
GACTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTATCGCAACGAATTTGGAAT
AAATCGCAACGCGAACTTC
Found at i:1049597 original size:21 final size:21
Alignment explanation
Indices: 1049486--1049556 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
1049476 TTTGGAATGA
*
1049486 ATCGCAACGCGAACTTCGCCT
1 ATCGCAACGCGAACTTCGACT
* *
1049507 ATCGCAA--CGAA-TTGGAAT
1 ATCGCAACGCGAACTTCGACT
1049525 GAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTCGACT
1049548 ATCGCAACG
1 ATCGCAACG
1049557 ATTTGGAATG
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
18 4 0.10
19 4 0.10
20 7 0.17
21 16 0.40
22 4 0.10
23 5 0.12
ACGTcount: A:0.31, C:0.30, G:0.21, T:0.18
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:1050321 original size:29 final size:29
Alignment explanation
Indices: 1050263--1050321 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
1050253 GTTTTTCTTA
* * * *
1050263 AATTAATTTTGGACTTAAATTGAAGTTTT
1 AATTAAATTTGGAATCAAATTGAAGATTT
1050292 AATTAAATTTGGAATCAAATTTGAA-ATTT
1 AATTAAATTTGGAATCAAA-TTGAAGATTT
1050321 A
1 A
1050322 GGAATTTTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.41, C:0.03, G:0.12, T:0.44
Consensus pattern (29 bp):
AATTAAATTTGGAATCAAATTGAAGATTT
Found at i:1052390 original size:18 final size:18
Alignment explanation
Indices: 1052367--1052460 Score: 88
Period size: 18 Copynumber: 5.3 Consensus size: 18
1052357 TGTTACATAT
1052367 ATGACATTGCATGCTAAC
1 ATGACATTGCATGCTAAC
* * *
1052385 ATGACAATGC-TAC-ATAT
1 ATGACATTGCATGCTA-AC
1052402 ATGACATTGCATGCTAAC
1 ATGACATTGCATGCTAAC
* * *
1052420 ATGACAATGC-TAC-ATAT
1 ATGACATTGCATGCTA-AC
1052437 ATGACATTGCATGCTAAC
1 ATGACATTGCATGCTAAC
1052455 ATGACA
1 ATGACA
1052461 ATGCTACATA
Statistics
Matches: 58, Mismatches: 12, Indels: 12
0.71 0.15 0.15
Matches are distributed among these distances:
16 2 0.03
17 24 0.41
18 30 0.52
19 2 0.03
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (18 bp):
ATGACATTGCATGCTAAC
Found at i:1052406 original size:35 final size:35
Alignment explanation
Indices: 1052360--1052472 Score: 226
Period size: 35 Copynumber: 3.2 Consensus size: 35
1052350 TTTAGGGTGT
1052360 TACATATATGACATTGCATGCTAACATGACAATGC
1 TACATATATGACATTGCATGCTAACATGACAATGC
1052395 TACATATATGACATTGCATGCTAACATGACAATGC
1 TACATATATGACATTGCATGCTAACATGACAATGC
1052430 TACATATATGACATTGCATGCTAACATGACAATGC
1 TACATATATGACATTGCATGCTAACATGACAATGC
1052465 TACATATA
1 TACATATA
1052473 CGAAGATGCT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 78 1.00
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.29
Consensus pattern (35 bp):
TACATATATGACATTGCATGCTAACATGACAATGC
Found at i:1052415 original size:21 final size:21
Alignment explanation
Indices: 1052391--1052452 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
1052381 TAACATGACA
1052391 ATGCTACATATATGACATTGC
1 ATGCTACATATATGACATTGC
*
1052412 ATGCT--A-ACATGACA----
1 ATGCTACATATATGACATTGC
1052426 ATGCTACATATATGACATTGC
1 ATGCTACATATATGACATTGC
1052447 ATGCTA
1 ATGCTA
1052453 ACATGACAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.16
16 1 0.03
17 7 0.22
18 7 0.22
19 1 0.03
21 11 0.34
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (21 bp):
ATGCTACATATATGACATTGC
Found at i:1052556 original size:16 final size:15
Alignment explanation
Indices: 1052532--1052561 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1052522 CATGGAAACG
1052532 AAAAATATTTTTTAA
1 AAAAATATTTTTTAA
1052547 AAAAAGTATTTTTTA
1 AAAAA-TATTTTTTA
1052562 TTTAATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
AAAAATATTTTTTAA
Found at i:1058793 original size:20 final size:18
Alignment explanation
Indices: 1058758--1058814 Score: 51
Period size: 21 Copynumber: 2.9 Consensus size: 18
1058748 GTTGGAATCC
* *
1058758 AAGGGATCAATCCTTTTA
1 AAGGGATCGATTCTTTTA
1058776 CAAGGGGATCGATTCTTTAGTTA
1 -AA-GGGATCGATTC-TT--TTA
1058799 AAGGGATCGATTCTTT
1 AAGGGATCGATTCTTT
1058815 GAGCCAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
18 1 0.03
19 2 0.06
20 11 0.34
21 13 0.41
22 2 0.06
23 3 0.09
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (18 bp):
AAGGGATCGATTCTTTTA
Found at i:1064587 original size:34 final size:33
Alignment explanation
Indices: 1064538--1064616 Score: 131
Period size: 34 Copynumber: 2.4 Consensus size: 33
1064528 TAAAAGAGAA
* *
1064538 AAAATAAAATAAAATGTATAAATGTTAAATTTC
1 AAAAGAAAAAAAAATGTATAAATGTTAAATTTC
1064571 AAAAGCAAAAAAAAATGTATAAATGTTAAATTTC
1 AAAAG-AAAAAAAAATGTATAAATGTTAAATTTC
1064605 AAAAGAAAAAAA
1 AAAAGAAAAAAA
1064617 TAAAAATTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
33 11 0.26
34 32 0.74
ACGTcount: A:0.63, C:0.04, G:0.08, T:0.25
Consensus pattern (33 bp):
AAAAGAAAAAAAAATGTATAAATGTTAAATTTC
Found at i:1065908 original size:21 final size:21
Alignment explanation
Indices: 1065887--1065927 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1065877 AATAAATAAA
1065887 TAAATAATAATAATAATAAAAT
1 TAAATAATAAT-ATAATAAAAT
* *
1065909 TATATATTAATATAATAAA
1 TAAATAATAATATAATAAA
1065928 TGAAATATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
TAAATAATAATATAATAAAAT
Found at i:1065998 original size:39 final size:40
Alignment explanation
Indices: 1065951--1066194 Score: 250
Period size: 39 Copynumber: 6.5 Consensus size: 40
1065941 CAAAAAAAGC
* *
1065951 ATTTTTAAAACTATATA-ATATATATGTTTTTCAAAAATT
1 ATTTTCAAAACTATATATATATATATATTTTTCAAAAATT
* * * *
1065990 ATTTTTAAAAATATAATATATATATATATATTT-AAAAATC
1 ATTTTCAAAACTAT-ATATATATATATATTTTTCAAAAATT
*
1066030 ATTTTCAAAACTATATATATATATATATATTT-AAAAA-T
1 ATTTTCAAAACTATATATATATATATATTTTTCAAAAATT
1066068 ATTTTTCAAAAC------TATATATATA-TTTTCAAAAATT
1 A-TTTTCAAAACTATATATATATATATATTTTTCAAAAATT
* * *
1066102 GTTTTCAAAAC--TA-ATATATATATA-TGTTCAAAAATA
1 ATTTTCAAAACTATATATATATATATATTTTTCAAAAATT
*
1066138 ATTTTCAAAACTATATA-ATATATATATTTTTCAAAAATC
1 ATTTTCAAAACTATATATATATATATATTTTTCAAAAATT
*
1066177 ATTTTCAAAAGTATATAT
1 ATTTTCAAAACTATATAT
1066195 TATGTTTTCA
Statistics
Matches: 177, Mismatches: 15, Indels: 25
0.82 0.07 0.12
Matches are distributed among these distances:
32 3 0.02
33 25 0.14
34 1 0.01
36 30 0.17
38 12 0.07
39 73 0.41
40 21 0.12
41 12 0.07
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.45
Consensus pattern (40 bp):
ATTTTCAAAACTATATATATATATATATTTTTCAAAAATT
Found at i:1066124 original size:34 final size:34
Alignment explanation
Indices: 1066048--1066233 Score: 168
Period size: 34 Copynumber: 5.3 Consensus size: 34
1066038 AACTATATAT
1066048 ATATATATATATTT-AAAAAT-ATTTTTCAAAACT-
1 ATATATATAT-TTTCAAAAATCA-TTTTCAAAACTA
**
1066081 ATATATATATTTTCAAAAATTGTTTTCAAAACTA
1 ATATATATATTTTCAAAAATCATTTTCAAAACTA
*
1066115 ATATATATATATGTTCAAAAATAATTTTCAAAACTATATA
1 ATATATATAT-T-TTCAAAAATCATTTTCAAAAC----TA
*
1066155 ATATATATATTTTTCAAAAATCATTTTCAAAAGT-
1 ATATATATA-TTTTCAAAAATCATTTTCAAAACTA
* * *
1066189 ATATATTATGTTTTCAAAAACCGTTTTCTAAAA--A
1 ATATA-TATATTTTCAAAAATCATTTTC-AAAACTA
1066223 ATATATATATT
1 ATATATATATT
1066234 ATATTTTTCC
Statistics
Matches: 131, Mismatches: 9, Indels: 26
0.79 0.05 0.16
Matches are distributed among these distances:
32 3 0.02
33 32 0.24
34 36 0.27
35 9 0.07
36 19 0.15
39 19 0.15
40 12 0.09
41 1 0.01
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.44
Consensus pattern (34 bp):
ATATATATATTTTCAAAAATCATTTTCAAAACTA
Found at i:1066174 original size:108 final size:108
Alignment explanation
Indices: 1066007--1066238 Score: 319
Period size: 108 Copynumber: 2.1 Consensus size: 108
1065997 AAAATATAAT
* *
1066007 ATATATATATATATTTAAAAATCATTTTCAAAACTATATATATATATATATATTTAAAAAT-ATT
1 ATATATATATATATTCAAAAATAATTTTCAAAACTATATATATATATATATATTTAAAAATCA-T
**
1066071 TTTCAAAACTATATA-TATATTTTCAAAAATTGTTTTC-AAAACTA
65 TTTCAAAACTATATATTATATTTTCAAAAACCGTTTTCTAAAA--A
* *
1066115 ATATATATATATGTTCAAAAATAATTTTCAAAACTATATA-ATATATATATTTTTCAAAAATCAT
1 ATATATATATATATTCAAAAATAATTTTCAAAACTATATATATATATATATATTT-AAAAATCAT
* *
1066179 TTTCAAAAGTATATATTATGTTTTCAAAAACCGTTTTCTAAAAA
65 TTTCAAAACTATATATTATATTTTCAAAAACCGTTTTCTAAAAA
1066223 ATATATATATTATATT
1 ATATATATA-TATATT
1066239 TTTCCAATTT
Statistics
Matches: 110, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
107 13 0.12
108 68 0.62
109 25 0.23
110 4 0.04
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (108 bp):
ATATATATATATATTCAAAAATAATTTTCAAAACTATATATATATATATATATTTAAAAATCATT
TTCAAAACTATATATTATATTTTCAAAAACCGTTTTCTAAAAA
Found at i:1075743 original size:32 final size:34
Alignment explanation
Indices: 1075698--1075766 Score: 108
Period size: 32 Copynumber: 2.1 Consensus size: 34
1075688 TAACCTTATA
1075698 AAAAGAAATATGAGAAAGTTCAAAAAA-AAGTTGC
1 AAAAGAAATATGAGAAAGTTCAAAAAACAAGTT-C
1075732 AAAA-AAA-ATGAGAAAGTTCAAAAAACAAGTTC
1 AAAAGAAATATGAGAAAGTTCAAAAAACAAGTTC
1075764 AAA
1 AAA
1075767 CAGGATGTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
32 22 0.65
33 8 0.24
34 4 0.12
ACGTcount: A:0.62, C:0.07, G:0.14, T:0.16
Consensus pattern (34 bp):
AAAAGAAATATGAGAAAGTTCAAAAAACAAGTTC
Found at i:1079021 original size:5 final size:5
Alignment explanation
Indices: 1079011--1079078 Score: 63
Period size: 5 Copynumber: 14.0 Consensus size: 5
1079001 TTAAAAGAGA
* * *
1079011 AAAAT AAAAT AAAAT AAAAT AAAAT AAGAT -GAAT AAAAT ATTAA- AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A-AAAT AAAAT
1079060 -AAA- AAAAT AAAAAT AAAAT
1 AAAAT AAAAT -AAAAT AAAAT
1079079 GTATAAATGT
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
4 10 0.20
5 34 0.67
6 7 0.14
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:1079074 original size:29 final size:29
Alignment explanation
Indices: 1079003--1079078 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
1078993 ACAAAATGTT
*
1079003 AAAAGAGAAAAATAAAATAAAATAAAATA
1 AAAAAAGAAAAATAAAATAAAATAAAATA
* ** *
1079032 AAATAAGATGAATAAAATATTAA-AAAATA
1 AAAAAAGAAAAATAAAATA-AAATAAAATA
*
1079061 AAAAAATAAAAATAAAAT
1 AAAAAAGAAAAATAAAAT
1079079 GTATAAATGT
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
29 35 0.95
30 2 0.05
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.18
Consensus pattern (29 bp):
AAAAAAGAAAAATAAAATAAAATAAAATA
Found at i:1080341 original size:19 final size:20
Alignment explanation
Indices: 1080313--1080364 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
1080303 AAAGAAAATA
*
1080313 AATAAATAAATAA-ATGAA-T
1 AATAATTAAATAATAT-AATT
1080332 AATAATTAAA-AATATAATT
1 AATAATTAAATAATATAATT
1080351 AAT-ATTAAATAATA
1 AATAATTAAATAATA
1080365 AAAGAAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
18 10 0.34
19 19 0.66
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
AATAATTAAATAATATAATT
Found at i:1080431 original size:39 final size:39
Alignment explanation
Indices: 1080371--1080529 Score: 175
Period size: 35 Copynumber: 4.1 Consensus size: 39
1080361 AATAAAAGAA
* * *
1080371 ATATGTTTTAAAAAAGCATTTTTAAAACTATATA-ATAT
1 ATATGTTTTTAAAAATCATTTTCAAAACTATATATATAT
* *
1080409 ATATGTTTTTCAAAAATTATTTTCAAAAGTATAATATATAT
1 ATATGTTTTT-AAAAATCATTTTCAAAACTAT-ATATATAT
* *
1080450 ATATATATATTTAAAAATCATTTTCAAAGCTATATA-ATAT
1 ATATGT-T-TTTAAAAATCATTTTCAAAACTATATATATAT
*
1080490 ATA--TTTTT-AAAATAATTTTCAAAACTATATATATAT
1 ATATGTTTTTAAAAATCATTTTCAAAACTATATATATAT
1080526 ATAT
1 ATAT
1080530 ATATATATAT
Statistics
Matches: 103, Mismatches: 11, Indels: 15
0.80 0.09 0.12
Matches are distributed among these distances:
35 21 0.20
36 10 0.10
37 1 0.01
38 10 0.10
39 17 0.17
40 10 0.10
41 12 0.12
42 19 0.18
43 3 0.03
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.45
Consensus pattern (39 bp):
ATATGTTTTTAAAAATCATTTTCAAAACTATATATATAT
Found at i:1080448 original size:44 final size:42
Alignment explanation
Indices: 1080399--1080535 Score: 128
Period size: 42 Copynumber: 3.3 Consensus size: 42
1080389 TTTTTAAAAC
* *
1080399 TATATAATATATATGTTTTTCAAAAATTATTTTCAAAAGTATAA
1 TATATAATATATAT-TTTTT-AAAAATAATTTTCAAAACTATAA
* * *
1080443 TATAT-ATATATATATATTTAAAAATCATTTTCAAAGC-----
1 TATATAATATATAT-TTTTTAAAAATAATTTTCAAAACTATAA
1080480 TATATAATATATA-TTTTT-AAAATAATTTTCAAAACTATATA
1 TATATAATATATATTTTTTAAAAATAATTTTCAAAACTATA-A
1080521 TATATATATATATAT
1 TATATA-ATATATAT
1080536 ATATATATAT
Statistics
Matches: 76, Mismatches: 8, Indels: 19
0.74 0.08 0.18
Matches are distributed among these distances:
35 15 0.20
36 4 0.05
37 5 0.07
38 7 0.09
41 6 0.08
42 22 0.29
43 12 0.16
44 5 0.07
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (42 bp):
TATATAATATATATTTTTTAAAAATAATTTTCAAAACTATAA
Found at i:1080467 original size:42 final size:41
Alignment explanation
Indices: 1080443--1080658 Score: 140
Period size: 44 Copynumber: 5.1 Consensus size: 41
1080433 AAAAGTATAA
* *
1080443 TATATATATATATATATTTAAAAATCATTTTC-AAAG-CTA
1 TATATATATATATATATTTAAAAATAATTTTCAAAAGTATA
*
1080482 TATA-ATATATAT-T-TTT-AAAATAATTTTCAAAACTATA
1 TATATATATATATATATTTAAAAATAATTTTCAAAAGTATA
* * * * *
1080519 TATATATATATATATATATATATAT-ATATTCAAAATTCATTTTCAAAA
1 TATATATATATATATATTTAAAAATAATTTTCAAAAGT-A---T----A
* * *
1080567 CTATAATATATATATATATACTCAAGAATAATTTTCAAAACTATA
1 -TAT-ATATATATATATAT--TTAAAAATAATTTTCAAAAGTATA
*
1080612 TAATATATATATATATATTTTCAAAAATCATTTTCAAAAGTATA
1 T-ATATATATATATATA-TTT-AAAAATAATTTTCAAAAGTATA
1080656 TAT
1 TAT
1080659 TATGTTTTCA
Statistics
Matches: 136, Mismatches: 19, Indels: 40
0.70 0.10 0.21
Matches are distributed among these distances:
35 11 0.08
36 6 0.04
37 7 0.05
38 16 0.12
39 5 0.04
40 12 0.09
41 4 0.03
43 3 0.02
44 35 0.26
45 4 0.03
48 1 0.01
49 4 0.03
50 14 0.10
52 4 0.03
53 10 0.07
ACGTcount: A:0.48, C:0.07, G:0.01, T:0.44
Consensus pattern (41 bp):
TATATATATATATATATTTAAAAATAATTTTCAAAAGTATA
Found at i:1080483 original size:81 final size:78
Alignment explanation
Indices: 1080381--1080657 Score: 261
Period size: 81 Copynumber: 3.3 Consensus size: 78
1080371 ATATGTTTTA
* * *
1080381 AAAAAGCATTTTTAAAACTATATAATATATATGTTTTTCAAAAATTATTTTCAAAAGTATA-ATA
1 AAAAAGCATTTTCAAAACTATATAATATATA--TTTTT--AAAATAATTTTCAAAACTATATATA
1080445 TATATATATATATATTT
62 TATATATATATATATTT
* *
1080462 AAAAATCATTTTCAAAGCTATATAATATATATTTTTAAAATAATTTTCAAAACTATATATATATA
1 AAAAAGCATTTTCAAAACTATATAATATATATTTTTAAAATAATTTTCAAAAC----TATATATA
1080527 TATATATATATATATATAT
62 TATATATATATATAT-T-T
* * *
1080546 ATTCAAAATTCATTTTCAAAACTATAATATATATATATATACTCAAGAATAATTTTCAAAACTAT
1 A---AAAA-GCATTTTCAAAACTAT-ATA-ATATATAT-T-TTTAA-AATAATTTTCAAAACTAT
1080611 ATA-ATATATATATATATATTTT
57 ATATATATATATATATATA-TTT
* *
1080633 CAAAAATCATTTTCAAAAGTATATA
1 -AAAAAGCATTTTCAAAACTATATA
1080658 TTATGTTTTC
Statistics
Matches: 169, Mismatches: 9, Indels: 34
0.80 0.04 0.16
Matches are distributed among these distances:
77 15 0.09
79 5 0.03
81 32 0.19
82 18 0.11
83 4 0.02
84 17 0.10
85 4 0.02
87 5 0.03
88 32 0.19
89 10 0.06
90 8 0.05
91 1 0.01
92 3 0.02
93 15 0.09
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (78 bp):
AAAAAGCATTTTCAAAACTATATAATATATATTTTTAAAATAATTTTCAAAACTATATATATATA
TATATATATATTT
Found at i:1080522 original size:2 final size:2
Alignment explanation
Indices: 1080515--1080547 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1080505 TTTTCAAAAC
1080515 TA TA 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 TA TA T
1080548 TCAAAATTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1080559 original size:88 final size:92
Alignment explanation
Indices: 1080438--1080629 Score: 288
Period size: 88 Copynumber: 2.1 Consensus size: 92
1080428 TTTTCAAAAG
* * * *
1080438 TATA-ATATATATATATATATATTTAAAAATCATTTTCAAAGCTAT-ATA-ATATATAT-T-TTT
1 TATATATATATATATATATATATTCAAAAATCATTTTCAAAACTATAATATATATATATATACTC
1080498 AA-AATAATTTTCAAAACTATATATATA
66 AAGAATAATTTTCAAAACTATATA-ATA
*
1080525 TATATATATATATATATATATATTCAAAATTCATTTTCAAAACTATAATATATATATATATACTC
1 TATATATATATATATATATATATTCAAAAATCATTTTCAAAACTATAATATATATATATATACTC
1080590 AAGAATAATTTTCAAAACTATATAATA
66 AAGAATAATTTTCAAAACTATATAATA
1080617 TATATATATATAT
1 TATATATATATAT
1080630 TTTCAAAAAT
Statistics
Matches: 94, Mismatches: 5, Indels: 7
0.89 0.05 0.07
Matches are distributed among these distances:
87 4 0.04
88 38 0.40
89 3 0.03
90 8 0.09
91 1 0.01
92 19 0.20
93 21 0.22
ACGTcount: A:0.48, C:0.07, G:0.01, T:0.44
Consensus pattern (92 bp):
TATATATATATATATATATATATTCAAAAATCATTTTCAAAACTATAATATATATATATATACTC
AAGAATAATTTTCAAAACTATATAATA
Found at i:1080669 original size:34 final size:35
Alignment explanation
Indices: 1080616--1080734 Score: 127
Period size: 34 Copynumber: 3.3 Consensus size: 35
1080606 ACTATATAAT
1080616 ATATATATATATATTTTCAAAAATCATTTTCAAAA
1 ATATATATATATATTTTCAAAAATCATTTTCAAAA
* * * *
1080651 GTATATAT-TATGTTTTCAAAAACCGTTTTCAAAAAA
1 ATATATATATATATTTTCAAAAATCATTTTC--AAAA
*
1080687 ATATATATTATATTTTTTCCAAAAAT-ATTTTCAAAA
1 ATATATA-TATATATTTT-CAAAAATCATTTTCAAAA
1080723 AT-TATACTATAT
1 ATATATA-TATAT
1080735 TATCACATAC
Statistics
Matches: 70, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
34 19 0.27
35 16 0.23
36 16 0.23
37 1 0.01
38 12 0.17
39 6 0.09
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.44
Consensus pattern (35 bp):
ATATATATATATATTTTCAAAAATCATTTTCAAAA
Found at i:1087148 original size:20 final size:20
Alignment explanation
Indices: 1087123--1087160 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1087113 TGGCCGAAGG
*
1087123 CATGAATCTTCATTAAAAGA
1 CATGAATCTTCATCAAAAGA
1087143 CATGAATCTTCATCAAAA
1 CATGAATCTTCATCAAAA
1087161 CCATGTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.18, G:0.08, T:0.29
Consensus pattern (20 bp):
CATGAATCTTCATCAAAAGA
Found at i:1088876 original size:37 final size:37
Alignment explanation
Indices: 1088825--1088929 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
1088815 CCTTTTCGTC
*
1088825 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* *
1088862 TTACTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** * *
1088899 CTACTATTATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
1088930 CCACAAGCAT
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:1089588 original size:24 final size:24
Alignment explanation
Indices: 1089572--1089674 Score: 89
Period size: 23 Copynumber: 4.5 Consensus size: 24
1089562 ATTTATTTTC
1089572 ATTTATTTATTATTA-TTATTACT
1 ATTTATTTATTATTATTTATTACT
1089595 ATTTA-TT-TTATTATTATATTACAT
1 ATTTATTTATTATTATT-TATTAC-T
*
1089619 ACATT-TTTA-TATT-TTTATATA-T
1 A-TTTATTTATTATTATTTAT-TACT
1089641 ATTT-TTTATTATTTATTTA-TACT
1 ATTTATTTATTA-TTATTTATTACT
1089664 ATTTATTTATT
1 ATTTATTTATT
1089675 TTCATATTTT
Statistics
Matches: 66, Mismatches: 2, Indels: 23
0.73 0.02 0.25
Matches are distributed among these distances:
21 12 0.18
22 9 0.14
23 21 0.32
24 16 0.24
25 8 0.12
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (24 bp):
ATTTATTTATTATTATTTATTACT
Found at i:1089643 original size:12 final size:11
Alignment explanation
Indices: 1089622--1089673 Score: 54
Period size: 10 Copynumber: 4.6 Consensus size: 11
1089612 ATTACATACA
1089622 TTTTTATAT-T
1 TTTTTATATAT
*
1089632 TTTATATATAT
1 TTTTTATATAT
1089643 TTTTTAT-TAT
1 TTTTTATATAT
1089653 TTATTTATACTAT
1 TT-TTTATA-TAT
1089666 TTATTTAT
1 TT-TTTAT
1089674 TTTCATATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
10 13 0.36
11 12 0.33
13 11 0.31
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTTTATATAT
Found at i:1089644 original size:20 final size:20
Alignment explanation
Indices: 1089541--1089675 Score: 75
Period size: 20 Copynumber: 6.7 Consensus size: 20
1089531 TGATTACTAT
*
1089541 TTTTTTAGTTAATTTATGTATA
1 TTTTTTA-TT-ATTTATATATA
*
1089563 TTTATTT-TCATTTAT-T-TA
1 TTT-TTTATTATTTATATATA
* *
1089581 -TTATTATTA-TTACTATTTA
1 TTTTTTATTATTTA-TATATA
* *
1089600 TTTTATTATTATATTACATACA
1 TTTT-TTATTAT-TTATATATA
1089622 TTTTTATATT-TTTATATATA
1 TTTTT-TATTATTTATATATA
*
1089642 TTTTTTATTATTTATTTATA
1 TTTTTTATTATTTATATATA
* *
1089662 CTATTTATTTATTT
1 TTTTTTA-TTATTT
1089676 TCATATTTTT
Statistics
Matches: 89, Mismatches: 12, Indels: 25
0.71 0.10 0.20
Matches are distributed among these distances:
16 5 0.06
17 5 0.06
18 3 0.03
19 7 0.08
20 34 0.38
21 15 0.17
22 14 0.16
23 6 0.07
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.67
Consensus pattern (20 bp):
TTTTTTATTATTTATATATA
Found at i:1089648 original size:21 final size:22
Alignment explanation
Indices: 1089572--1089681 Score: 68
Period size: 21 Copynumber: 4.9 Consensus size: 22
1089562 ATTTATTTTC
*
1089572 ATTTATTTATTATTATTAT-TACT
1 ATTT-TTTA-TATTTTTATATACT
*
1089595 ATTTATTT-TATTATTATATTACAT
1 ATTT-TTTATATTTTTATA-TAC-T
*
1089619 ACATTTTTATATTTTTATATA-T
1 A-TTTTTTATATTTTTATATACT
1089641 ATTTTTTATTATTTATT-TATACT
1 ATTTTTTA-TATTT-TTATATACT
* *
1089664 ATTTATT-TATTTTCATAT
1 ATTTTTTATATTTTTATAT
1089682 TTTTAGTTTC
Statistics
Matches: 73, Mismatches: 5, Indels: 20
0.74 0.05 0.20
Matches are distributed among these distances:
20 1 0.01
21 23 0.32
22 11 0.15
23 20 0.27
24 7 0.10
25 11 0.15
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (22 bp):
ATTTTTTATATTTTTATATACT
Found at i:1094119 original size:16 final size:14
Alignment explanation
Indices: 1094098--1094147 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
1094088 AAAGGGCAAA
1094098 AACAAAAAAGAAAAG
1 AACAAAAAAG-AAAG
1094113 AAGCAAAAAAG-AAG
1 AA-CAAAAAAGAAAG
1094127 AA-AAAAAAGAAAG
1 AACAAAAAAGAAAG
1094140 AACAAAAA
1 AACAAAAA
1094148 TCAAAAAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
12 7 0.22
13 5 0.16
14 10 0.31
15 2 0.06
16 8 0.25
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (14 bp):
AACAAAAAAGAAAG
Found at i:1095887 original size:106 final size:106
Alignment explanation
Indices: 1095757--1097031 Score: 1890
Period size: 106 Copynumber: 12.0 Consensus size: 106
1095747 ATATCGTGCC
* * * * * * *
1095757 ACTCGAGACAACACAAGTTTAACTTCACAATGAAGGGA-TGACTGGTTGTCAACAAAAAACTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCC
1095821 C-ATATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAAT-TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
1095863 GCTCTAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGATTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1095928 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* ** * *
1095969 ACTCCAGACAATGCAAGTTCAACTTCACGTTGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1096034 AATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
1096075 ACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAATAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1096140 AATTTCAGAGCCAATTTCAACTTAACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
1096181 ACTCCAGACAACGCAAGTTCAACTTCATGATGAAGGGACCGCTGGGTGTCAACAAACACCTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
1096246 AATTTCAAAGCCAATTTCAACATCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
**
1096287 ACTCCAGACAACTTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1096352 AATTTCAGAGCCAATTTTAACTTCACAGTGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
1096393 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
1096458 AATTTCTGAGCCAATTTCAATTTCACAGCGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
1096499 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAAGGACCGCTGGTTGTCAACAAAAAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1096564 AATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
1096605 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1096670 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
1096711 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1096776 AATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
1096817 ACTCGAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTATCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
1096882 AATTTTAGAGCCAATTTCAATTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
** * * ** *
1096923 ACTTGAGACAACACAAGTTCAACTTCACAACGAAGGGAGGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
1096988 GATTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
1097029 ACT
1 ACT
1097032 TGGAACAATG
Statistics
Matches: 1064, Mismatches: 102, Indels: 6
0.91 0.09 0.01
Matches are distributed among these distances:
106 1061 1.00
107 3 0.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:1097767 original size:37 final size:37
Alignment explanation
Indices: 1097716--1097820 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
1097706 ACTTTTCGTC
*
1097716 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
1097753 TTACTAGGATTCAAACTCCTAAAAGTAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** * *
1097790 CTACTATTATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
1097821 CCACAAGCAT
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:1098123 original size:165 final size:166
Alignment explanation
Indices: 1097848--1098178 Score: 655
Period size: 165 Copynumber: 2.0 Consensus size: 166
1097838 AGTCATTGTA
1097848 ACTCACTATTGTAACACATTCGGAGGAGGATATACGAAATAGCAAGCAAAAGATTGCAAGCAACT
1 ACTCACTATTGTAACACATTCGGAGGAGGATATACGAAATAGCAAGCAAAAGATTGCAAGCAACT
1097913 CGTAGCCATTTTTCGAAGCATTTATATTTTGAAAGGTAAAGTTCATACCTTCGCATGTTATTTTT
66 CGTAGCCATTTTTCGAAGCATTTATATTTTGAAAGGTAAAGTTCATACCTTCGCATGTTATTTTT
1097978 CCTTACCCTTGCTGTGTTTTGATTTCGAAAGAAAAC
131 CCTTACCCTTGCTGTGTTTTGATTTCGAAAGAAAAC
1098014 ACTCACTATTGTAACACATTCGGAGGAGGATATACGAAATAGCAAGCAAAAGATT-CAAGCAACT
1 ACTCACTATTGTAACACATTCGGAGGAGGATATACGAAATAGCAAGCAAAAGATTGCAAGCAACT
1098078 CGTAGCCATTTTTCGAAGCATTTATATTTTGAAAGGTAAAGTTCATACCTTCGCATGTTATTTTT
66 CGTAGCCATTTTTCGAAGCATTTATATTTTGAAAGGTAAAGTTCATACCTTCGCATGTTATTTTT
1098143 CCTTACCCTTGCTGTGTTTTGATTTCGAAAGAAAAC
131 CCTTACCCTTGCTGTGTTTTGATTTCGAAAGAAAAC
1098179 TGAGAGAAGT
Statistics
Matches: 165, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
165 110 0.67
166 55 0.33
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (166 bp):
ACTCACTATTGTAACACATTCGGAGGAGGATATACGAAATAGCAAGCAAAAGATTGCAAGCAACT
CGTAGCCATTTTTCGAAGCATTTATATTTTGAAAGGTAAAGTTCATACCTTCGCATGTTATTTTT
CCTTACCCTTGCTGTGTTTTGATTTCGAAAGAAAAC
Found at i:1098657 original size:20 final size:20
Alignment explanation
Indices: 1098634--1098684 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
1098624 TTACTATTAG
1098634 TATTTTATTATATATACATA
1 TATTTTATTATATATACATA
*
1098654 TATTTTA-TATTATATATATA
1 TATTTTATTA-TATATACATA
*
1098674 TGTTTTATTAT
1 TATTTTATTAT
1098685 TTTATTTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 2 0.07
20 23 0.85
21 2 0.07
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (20 bp):
TATTTTATTATATATACATA
Found at i:1098672 original size:18 final size:18
Alignment explanation
Indices: 1098634--1098684 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 18
1098624 TTACTATTAG
1098634 TATTTTATTATATATACATA
1 TATTTTA-TAT-TATACATA
*
1098654 TATTTTATATTATATATA
1 TATTTTATATTATACATA
1098672 TATGTTT-TATTAT
1 TAT-TTTATATTAT
1098685 TTTATTTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 16 0.55
19 6 0.21
20 7 0.24
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (18 bp):
TATTTTATATTATACATA
Found at i:1098694 original size:21 final size:21
Alignment explanation
Indices: 1098661--1098729 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
1098651 ATATATTTTA
* *
1098661 TATTATATATATATGTTTTA-T
1 TATTTTATTTATAT-TTTTAGT
* *
1098682 TATTTTATTTATACTATTTATT
1 TATTTTATTTATA-TTTTTAGT
1098704 TATTTTCA-TTATATTTTTAGT
1 TATTTT-ATTTATATTTTTAGT
1098725 TATTT
1 TATTT
1098730 GCTCTTATTA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
21 26 0.65
22 13 0.32
23 1 0.03
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (21 bp):
TATTTTATTTATATTTTTAGT
Found at i:1098715 original size:22 final size:20
Alignment explanation
Indices: 1098612--1098729 Score: 55
Period size: 21 Copynumber: 5.6 Consensus size: 20
1098602 TATTTTTCAT
1098612 TATTTATTATTATTACTATTAGTA
1 TATTTATTATT-TTA-T-TTA-TA
* **
1098636 T-TTTATTA-TATATACATA
1 TATTTATTATTTTATTTATA
* *
1098654 TATTT-TATATTATATATATA
1 TATTTAT-TATTTTATTTATA
*
1098674 TGTTTTATTATTTTATTTATA
1 T-ATTTATTATTTTATTTATA
1098695 CTATTTATTTATTTTCA-TTATA
1 -TATTTA-TTATTTT-ATTTATA
*
1098717 TTTTTAGTTATTT
1 TATTTA-TTATTT
1098730 GCTCTTATTA
Statistics
Matches: 76, Mismatches: 10, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.05
19 6 0.08
20 11 0.14
21 31 0.41
22 15 0.20
23 8 0.11
24 1 0.01
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (20 bp):
TATTTATTATTTTATTTATA
Found at i:1100781 original size:17 final size:17
Alignment explanation
Indices: 1100740--1100811 Score: 83
Period size: 17 Copynumber: 4.2 Consensus size: 17
1100730 ATTCATGCAT
1100740 CTAGTTCATTGAA-TAAA
1 CTAGTTCATT-AATTAAA
*
1100757 GTTAGTTCATTAATTAAA
1 -CTAGTTCATTAATTAAA
* *
1100775 CTAGTTCATTCATCAAA
1 CTAGTTCATTAATTAAA
*
1100792 CTAGTTCATTTATTAAA
1 CTAGTTCATTAATTAAA
1100809 CTA
1 CTA
1100812 ACTCTTAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
17 34 0.72
18 13 0.28
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:1114473 original size:39 final size:39
Alignment explanation
Indices: 1114430--1114534 Score: 149
Period size: 39 Copynumber: 2.7 Consensus size: 39
1114420 CTTGTTAAGG
* *
1114430 AGTTTTGACAAGACTAGATATTGGGTTGTATTCCCAAGA
1 AGTTTTGACAAGACTAGATATTGGGTTATAGTCCCAAGA
* *
1114469 AGTTTTGACAAGACTAGATATTGGGTTATCGTCCCAAGG
1 AGTTTTGACAAGACTAGATATTGGGTTATAGTCCCAAGA
* *
1114508 ATTTTTCA-AAGACTAGATATTGGGTTA
1 AGTTTTGACAAGACTAGATATTGGGTTA
1114535 AAATATTCTC
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
38 19 0.32
39 41 0.68
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.34
Consensus pattern (39 bp):
AGTTTTGACAAGACTAGATATTGGGTTATAGTCCCAAGA
Found at i:1116671 original size:13 final size:13
Alignment explanation
Indices: 1116655--1116679 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1116645 AAAGAGAACT
1116655 TTGTAAATTAATC
1 TTGTAAATTAATC
1116668 TTGTAAATTAAT
1 TTGTAAATTAAT
1116680 GATCCAACAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (13 bp):
TTGTAAATTAATC
Found at i:1122375 original size:20 final size:20
Alignment explanation
Indices: 1122350--1122390 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1122340 TATATTGGGA
1122350 TGATCTTTTGATAGGGGAAG
1 TGATCTTTTGATAGGGGAAG
1122370 TGATCTTTTGATAGGGGAAG
1 TGATCTTTTGATAGGGGAAG
1122390 T
1 T
1122391 TTAGTGAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.05, G:0.34, T:0.37
Consensus pattern (20 bp):
TGATCTTTTGATAGGGGAAG
Found at i:1133622 original size:2 final size:2
Alignment explanation
Indices: 1133615--1133647 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1133605 TAAAACATTT
1133615 TA TA 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 TA TA T
1133648 CGATTAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1134832 original size:6 final size:6
Alignment explanation
Indices: 1134823--1134847 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1134813 TATGTTACTA
1134823 TTTTAT TTTTAT TTTTAT TTTTAT T
1 TTTTAT TTTTAT TTTTAT TTTTAT T
1134848 ATATGTATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:1134923 original size:21 final size:21
Alignment explanation
Indices: 1134899--1134949 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1134889 TCTACACGTT
*
1134899 TTTTTCAACCTTC-TTTTCAAC
1 TTTTTCAACCTTCATTCT-AAC
**
1134920 TTTTTCAATTTTCATTCTAAC
1 TTTTTCAACCTTCATTCTAAC
1134941 TTTTTCAAC
1 TTTTTCAAC
1134950 TTTTCAACCT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.22, C:0.24, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTTCAACCTTCATTCTAAC
Found at i:1134931 original size:8 final size:9
Alignment explanation
Indices: 1134912--1134964 Score: 54
Period size: 9 Copynumber: 5.6 Consensus size: 9
1134902 TTCAACCTTC
1134912 TTTTCAACT
1 TTTTCAACT
*
1134921 TTTTCAATT
1 TTTTCAACT
1134930 TTCATTCTAACT
1 TT--TTC-AACT
1134942 TTTTCAAC-
1 TTTTCAACT
1134950 TTTTCAACCT
1 TTTTCAA-CT
1134960 TTTTC
1 TTTTC
1134965 TTTTAGCCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
8 7 0.19
9 14 0.38
10 8 0.22
11 3 0.08
12 5 0.14
ACGTcount: A:0.21, C:0.23, G:0.00, T:0.57
Consensus pattern (9 bp):
TTTTCAACT
Found at i:1146319 original size:74 final size:73
Alignment explanation
Indices: 1146185--1146327 Score: 164
Period size: 74 Copynumber: 1.9 Consensus size: 73
1146175 CTCGAGAGTA
* * * * *
1146185 GATTTCAACTTCACGACGGAGGATATCTAGCTTTAAGCCAAACTTCACAATAAAGAGGTCATTCA
1 GATTTCAACTTCACGACGAAGGATATCAAGC-TCAAGCCAAACTTCACAACAAAGAGGTCATCCA
1146250 CGATACTTG
65 CGATACTTG
* * *
1146259 GATTTCAACTTCACGACGAAGGATATTCAAG-TCAAGGCTC-AACTTCACGACGAAGGGGTCATC
1 GATTTCAACTTCACGACGAAGGATA-TCAAGCTCAA-GC-CAAACTTCACAACAAAGAGGTCATC
1146322 CACGAT
63 CACGAT
1146328 TTCAACTCCA
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
73 3 0.05
74 50 0.86
75 5 0.09
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (73 bp):
GATTTCAACTTCACGACGAAGGATATCAAGCTCAAGCCAAACTTCACAACAAAGAGGTCATCCAC
GATACTTG
Found at i:1147077 original size:35 final size:35
Alignment explanation
Indices: 1147038--1147111 Score: 87
Period size: 35 Copynumber: 2.1 Consensus size: 35
1147028 TCTTTTATTT
*
1147038 TATTTTGGTTTTTATTTATTACTATTATAT-TATAC
1 TATTTTAGTTTTTA-TTATTACTATTATATGTATAC
* * * *
1147073 TATTTTATTTTTTATTGTTATTATTATATGTATTC
1 TATTTTAGTTTTTATTATTACTATTATATGTATAC
1147108 TATT
1 TATT
1147112 ATCATAAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
34 13 0.39
35 20 0.61
ACGTcount: A:0.24, C:0.04, G:0.05, T:0.66
Consensus pattern (35 bp):
TATTTTAGTTTTTATTATTACTATTATATGTATAC
Found at i:1147213 original size:21 final size:21
Alignment explanation
Indices: 1147189--1147238 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1147179 TTATTCTAAC
1147189 TTTTTCAAC-TTTTTAATCTTT
1 TTTTTCAACTTTTTTAA-CTTT
* * *
1147210 TTTTTTAGCTTTTTTGACTTT
1 TTTTTCAACTTTTTTAACTTT
1147231 TTTTTCAA
1 TTTTTCAA
1147239 TATAAAATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.16, C:0.12, G:0.04, T:0.68
Consensus pattern (21 bp):
TTTTTCAACTTTTTTAACTTT
Found at i:1147394 original size:24 final size:26
Alignment explanation
Indices: 1147356--1147404 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
1147346 TTGTTTCATC
*
1147356 TTCCTCATTTTATTCT-T-TTATTTT
1 TTCCTCATTTGATTCTATCTTATTTT
*
1147380 TTCCTCCTTTGATTCTATCTTATTT
1 TTCCTCATTTGATTCTATCTTATTT
1147405 AATAAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 14 0.67
25 1 0.05
26 6 0.29
ACGTcount: A:0.12, C:0.20, G:0.02, T:0.65
Consensus pattern (26 bp):
TTCCTCATTTGATTCTATCTTATTTT
Found at i:1149012 original size:12 final size:12
Alignment explanation
Indices: 1148980--1149019 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1148970 TGCGGGAAAA
1148980 TTAAAATC-A-T
1 TTAAAATCTATT
1148990 TT-AAATCTATT
1 TTAAAATCTATT
*
1149001 TTAAAATTTATT
1 TTAAAATCTATT
1149013 TTAAAAT
1 TTAAAAT
1149020 ATAGATTGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
9 5 0.19
10 3 0.12
11 3 0.12
12 15 0.58
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (12 bp):
TTAAAATCTATT
Found at i:1149379 original size:22 final size:22
Alignment explanation
Indices: 1149006--1149370 Score: 574
Period size: 22 Copynumber: 16.6 Consensus size: 22
1148996 CTATTTTAAA
*
1149006 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
1149028 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
1149050 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
1149072 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
1149094 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* *
1149116 ATTTATTTTAAAATATGAAAAT-
1 ATTTATTTTAAAATATG-GATTG
*
1149138 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
***
1149160 ATTTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATGGATTG
1149182 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
1149204 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
1149226 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
1149248 ATTTATTTTAAAATATGGGA--A
1 ATTTATTTTAAAATAT-GGATTG
1149269 ATTTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATGGATTG
**
1149292 ATTTATTTTAAAATATAAATTG
1 ATTTATTTTAAAATATGGATTG
1149314 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
1149336 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
*
1149358 ATTTATTTAAAAA
1 ATTTATTTTAAAA
1149371 ATATTATTGT
Statistics
Matches: 318, Mismatches: 19, Indels: 12
0.91 0.05 0.03
Matches are distributed among these distances:
21 7 0.02
22 305 0.96
23 6 0.02
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:1149471 original size:17 final size:17
Alignment explanation
Indices: 1149436--1149471 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1149426 GTTTAAAAAA
*
1149436 TCAGTTTATTTTATATT
1 TCAGTTTATTTTAGATT
*
1149453 TCAGTTTATTTTAGCTT
1 TCAGTTTATTTTAGATT
1149470 TC
1 TC
1149472 TGCAGACGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.08, T:0.61
Consensus pattern (17 bp):
TCAGTTTATTTTAGATT
Found at i:1153109 original size:13 final size:14
Alignment explanation
Indices: 1153091--1153128 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
1153081 TAAGGTCTTT
1153091 AATCTAATCT-ATG
1 AATCTAATCTAATG
1153104 AATCTAATCTAATG
1 AATCTAATCTAATG
1153118 -ATCTAAT-TAAT
1 AATCTAATCTAAT
1153129 AAAGTTCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 4 0.17
13 17 0.71
14 3 0.12
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.39
Consensus pattern (14 bp):
AATCTAATCTAATG
Found at i:1153402 original size:17 final size:17
Alignment explanation
Indices: 1153380--1153420 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
1153370 CAATCATGTA
*
1153380 TAATAACTAAATACATT
1 TAATAAATAAATACATT
1153397 TAATAAATAAATACATT
1 TAATAAATAAATACATT
1153414 TAATAAA
1 TAATAAA
1153421 AATTAAACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (17 bp):
TAATAAATAAATACATT
Found at i:1156094 original size:14 final size:14
Alignment explanation
Indices: 1156077--1156127 Score: 59
Period size: 14 Copynumber: 3.4 Consensus size: 14
1156067 CCTGAACCTG
1156077 AAAAGGTAATAATT
1 AAAAGGTAATAATT
1156091 AAAAGGGTGAACT-ATT
1 AAAA-GGT-AA-TAATT
1156107 GAAAAGGTAATAATT
1 -AAAAGGTAATAATT
1156122 AAAAGG
1 AAAAGG
1156128 GTGAACTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
14 11 0.34
15 8 0.25
16 8 0.25
17 5 0.16
ACGTcount: A:0.53, C:0.02, G:0.22, T:0.24
Consensus pattern (14 bp):
AAAAGGTAATAATT
Found at i:1156110 original size:31 final size:31
Alignment explanation
Indices: 1156075--1156137 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
1156065 AACCTGAACC
1156075 TGAAAAGGTAATAATTAAAAGGGTGAACTAT
1 TGAAAAGGTAATAATTAAAAGGGTGAACTAT
1156106 TGAAAAGGTAATAATTAAAAGGGTGAACTAT
1 TGAAAAGGTAATAATTAAAAGGGTGAACTAT
1156137 T
1 T
1156138 AAGCCCAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.48, C:0.03, G:0.22, T:0.27
Consensus pattern (31 bp):
TGAAAAGGTAATAATTAAAAGGGTGAACTAT
Found at i:1156555 original size:36 final size:36
Alignment explanation
Indices: 1156508--1156905 Score: 408
Period size: 36 Copynumber: 11.1 Consensus size: 36
1156498 TGAGTAAAAG
* * *
1156508 ATCATGCATATAACCACCAATAGAAAGAACATGTAT
1 ATCATGCATATAATCATCAATAGAAAGCACATGTAT
* **
1156544 ATCATGCATATAATCATTAATATCAAGCACATGTAT
1 ATCATGCATATAATCATCAATAGAAAGCACATGTAT
* **
1156580 ATCATGTATATAATCATCGGTAGTAAA-CACATGTAT
1 ATCATGCATATAATCATCAATAG-AAAGCACATGTAT
* * *
1156616 ATCATACATATAATCATTAATA-ACAAGTACATGTAT
1 ATCATGCATATAATCATCAATAGA-AAGCACATGTAT
* * * *
1156652 ATCATGCATATTATAATCAGTAGGAAGCACATGTAT
1 ATCATGCATATAATCATCAATAGAAAGCACATGTAT
* * * *
1156688 ATCATGCATAT-TTCATCAGTAGCAAGCACATTTAT
1 ATCATGCATATAATCATCAATAGAAAGCACATGTAT
* * *
1156723 ATCATGCATAT-TTCATCAGTAGAAAACACATGTAT
1 ATCATGCATATAATCATCAATAGAAAGCACATGTAT
** * *
1156758 ATCATGCATATGTTCATCAATAGCAAGCACATTTAT
1 ATCATGCATATAATCATCAATAGAAAGCACATGTAT
* * * * *
1156794 ATTATGTATATAATCCTCAATAGCAAGAACATGTAT
1 ATCATGCATATAATCATCAATAGAAAGCACATGTAT
* * *
1156830 ATCATGCATATAATCATCAGTCGCAAGCACATGTAT
1 ATCATGCATATAATCATCAATAGAAAGCACATGTAT
* * *
1156866 ATCTTGCATATAATCATCATTAGAAAGCGCATGTAT
1 ATCATGCATATAATCATCAATAGAAAGCACATGTAT
1156902 ATCA
1 ATCA
1156906 CACATAGGAA
Statistics
Matches: 302, Mismatches: 55, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
34 1 0.00
35 65 0.22
36 234 0.77
37 2 0.01
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (36 bp):
ATCATGCATATAATCATCAATAGAAAGCACATGTAT
Found at i:1156828 original size:178 final size:179
Alignment explanation
Indices: 1156508--1156905 Score: 465
Period size: 178 Copynumber: 2.2 Consensus size: 179
1156498 TGAGTAAAAG
* * * * * * * ** *
1156508 ATCATGCATATAACCACCAATAGAAAGAACATGTATATCATGCATATAATCATTAATATCAAGCA
1 ATCATGCATATAATCATCAGTAGAAAGCACATGTATATCATGCATAT-TTCATCAGTAGAAAACA
* ** * *
1156573 CATGTATATCATGTATATAATCATCGGTAGTAAACACATGTATATCATACATATAATCATTAATA
65 CATGTATATCATGCATATAATCATCAATAGCAAACACATGTATATCATACATATAATCATCAATA
* * *
1156638 ACAAGTACATGTATATCATGCATATTATAATCAGTAGGAAGCACATGTAT
130 ACAAGAACATGTATATCATGCATATAATAATCAGTAGCAAGCACATGTAT
* * *
1156688 ATCATGCATAT-TTCATCAGTAGCAAGCACATTTATATCATGCATATTTCATCAGTAGAAAACAC
1 ATCATGCATATAATCATCAGTAGAAAGCACATGTATATCATGCATATTTCATCAGTAGAAAACAC
** * * * ** * *
1156752 ATGTATATCATGCATATGTTCATCAATAGCAAGCACATTTATATTATGTATATAATCCTCAATAG
66 ATGTATATCATGCATATAATCATCAATAGCAAACACATGTATATCATACATATAATCATCAATAA
* *
1156817 CAAGAACATGTATATCATGCATATAATCATCAGTCGCAAGCACATGTAT
131 CAAGAACATGTATATCATGCATATAATAATCAGTAGCAAGCACATGTAT
* * *
1156866 ATCTTGCATATAATCATCATTAGAAAGCGCATGTATATCA
1 ATCATGCATATAATCATCAGTAGAAAGCACATGTATATCA
1156906 CACATAGGAA
Statistics
Matches: 179, Mismatches: 38, Indels: 3
0.81 0.17 0.01
Matches are distributed among these distances:
178 117 0.65
179 51 0.28
180 11 0.06
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (179 bp):
ATCATGCATATAATCATCAGTAGAAAGCACATGTATATCATGCATATTTCATCAGTAGAAAACAC
ATGTATATCATGCATATAATCATCAATAGCAAACACATGTATATCATACATATAATCATCAATAA
CAAGAACATGTATATCATGCATATAATAATCAGTAGCAAGCACATGTAT
Found at i:1157407 original size:2 final size:2
Alignment explanation
Indices: 1157400--1157431 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1157390 GCATTACAGA
1157400 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
1157432 CTTTTATAAA
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:1157757 original size:19 final size:19
Alignment explanation
Indices: 1157705--1157825 Score: 98
Period size: 19 Copynumber: 6.4 Consensus size: 19
1157695 AGACTTACAC
* *
1157705 CCTAAAATGTAATTTCCAA
1 CCTAAAATTTAGTTTCCAA
** **
1157724 CAAAAAATCCAGTTTCCAA
1 CCTAAAATTTAGTTTCCAA
* * *
1157743 TCTAAAATTTGGTTTTCAA
1 CCTAAAATTTAGTTTCCAA
*
1157762 CCTAAAATTTAGTTGCCAA
1 CCTAAAATTTAGTTTCCAA
* * *
1157781 CCTAAAATCTAGTTACTAA
1 CCTAAAATTTAGTTTCCAA
** *
1157800 CAAAAAATTTAGTTGCCAA
1 CCTAAAATTTAGTTTCCAA
1157819 CCTAAAA
1 CCTAAAA
1157826 AACCTGGTTG
Statistics
Matches: 76, Mismatches: 26, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
19 76 1.00
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (19 bp):
CCTAAAATTTAGTTTCCAA
Found at i:1165938 original size:21 final size:22
Alignment explanation
Indices: 1165914--1165956 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1165904 TAATTCAATG
*
1165914 GTATCAATA-TCAAATGTAGGA
1 GTATCAATACTCAAATGGAGGA
*
1165935 GTATCGATACTCAAATGGAGGA
1 GTATCAATACTCAAATGGAGGA
1165957 TTCAAGTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.40, C:0.12, G:0.23, T:0.26
Consensus pattern (22 bp):
GTATCAATACTCAAATGGAGGA
Found at i:1167170 original size:38 final size:38
Alignment explanation
Indices: 1167042--1167335 Score: 378
Period size: 39 Copynumber: 7.7 Consensus size: 38
1167032 CTACATAACG
* * * *
1167042 TATATAATATATAGTGTTGAAAGCATTTTTTTCGAAAGTA
1 TATATAATATATAGTTTTGAAAACA--TTTTTCAAAAATA
*
1167082 TATATAATATATAGTTTTGAAAACATTTTTGAAAATATA
1 TATATAATATATAGTTTTGAAAACATTTTTCAAAA-ATA
1167121 TATATAATATATAGTTTTGAAAACATTTTTCAAAAATA
1 TATATAATATATAGTTTTGAAAACATTTTTCAAAAATA
* * **
1167159 TATATAATATATAATTTT-AAAACGTTTTTTGAAAATA
1 TATATAATATATAGTTTTGAAAACATTTTTCAAAAATA
*
1167196 TATATAATATATAGTTTTGAAAACATTTTTGAAAATATA
1 TATATAATATATAGTTTTGAAAACATTTTTCAAAA-ATA
*
1167235 TACATAATATATAGTTTTGAAAACATTTTTCAAAAATA
1 TATATAATATATAGTTTTGAAAACATTTTTCAAAAATA
* * ***
1167273 TATATAATATATAGGTTT-AAAACGTTTTTTGGAAA-A
1 TATATAATATATAGTTTTGAAAACATTTTTCAAAAATA
1167309 TATATAATATATAGTTTTGGAAAACAT
1 TATATAATATATAGTTTT-GAAAACAT
1167336 ATATTATATA
Statistics
Matches: 225, Mismatches: 24, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
36 18 0.08
37 46 0.20
38 66 0.29
39 72 0.32
40 23 0.10
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.43
Consensus pattern (38 bp):
TATATAATATATAGTTTTGAAAACATTTTTCAAAAATA
Found at i:1167215 original size:114 final size:114
Alignment explanation
Indices: 1167042--1167335 Score: 466
Period size: 114 Copynumber: 2.6 Consensus size: 114
1167032 CTACATAACG
* * *
1167042 TATATAATATAT-AGTGTTGAAAGCATTTTTTTCGAAAGTATATATAATATATAGTTTTGAAAAC
1 TATATAATATATAAGT-TT-AAAAC-GTTTTTT-GAAAATATATATAATATATAGTTTTGAAAAC
*
1167106 ATTTTTGAAAATATATATATAATATATAGTTTTGAAAACATTTTTCAAAAATA
62 ATTTTTGAAAATATATACATAATATATAGTTTTGAAAACATTTTTCAAAAATA
*
1167159 TATATAATATATAATTTTAAAACGTTTTTTGAAAATATATATAATATATAGTTTTGAAAACATTT
1 TATATAATATATAAGTTTAAAACGTTTTTTGAAAATATATATAATATATAGTTTTGAAAACATTT
1167224 TTGAAAATATATACATAATATATAGTTTTGAAAACATTTTTCAAAAATA
66 TTGAAAATATATACATAATATATAGTTTTGAAAACATTTTTCAAAAATA
* *
1167273 TATATAATATATAGGTTTAAAACGTTTTTTGGAAA-ATATATAATATATAGTTTTGGAAAACAT
1 TATATAATATATAAGTTTAAAACGTTTTTTGAAAATATATATAATATATAGTTTT-GAAAACAT
1167336 ATATTATATA
Statistics
Matches: 167, Mismatches: 8, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
113 19 0.11
114 122 0.73
115 6 0.04
116 4 0.02
117 14 0.08
118 2 0.01
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.43
Consensus pattern (114 bp):
TATATAATATATAAGTTTAAAACGTTTTTTGAAAATATATATAATATATAGTTTTGAAAACATTT
TTGAAAATATATACATAATATATAGTTTTGAAAACATTTTTCAAAAATA
Found at i:1167327 original size:24 final size:24
Alignment explanation
Indices: 1167299--1167345 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1167289 TTAAAACGTT
*
1167299 TTTTGGAAAATATATAATATATAG
1 TTTTGGAAAACATATAATATATAG
*
1167323 TTTTGGAAAACATATATTATATA
1 TTTTGGAAAACATATAATATATA
1167346 ATTTCAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.43
Consensus pattern (24 bp):
TTTTGGAAAACATATAATATATAG
Found at i:1169896 original size:17 final size:18
Alignment explanation
Indices: 1169863--1169897 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1169853 TTTTATTGAC
1169863 TTGTTCTCCTTTCATTTT
1 TTGTTCTCCTTTCATTTT
*
1169881 TTGTTCT-CTTTTATTTT
1 TTGTTCTCCTTTCATTTT
1169898 ATCATTTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.06, C:0.17, G:0.06, T:0.71
Consensus pattern (18 bp):
TTGTTCTCCTTTCATTTT
Found at i:1180193 original size:15 final size:15
Alignment explanation
Indices: 1180173--1180202 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1180163 AATTACCACC
1180173 CAACCTAATTTATAG
1 CAACCTAATTTATAG
1180188 CAACCTAATTTATAG
1 CAACCTAATTTATAG
1180203 GTGAGAAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (15 bp):
CAACCTAATTTATAG
Found at i:1180786 original size:39 final size:38
Alignment explanation
Indices: 1180733--1180951 Score: 248
Period size: 38 Copynumber: 5.7 Consensus size: 38
1180723 TCTCCATAAC
*
1180733 ATATATAATATATAGTGTTGAAAGA-ATTTTTTCGAAAGT
1 ATATATAATATATAGT-TTGAAA-ACATTTTTTCGAAAAT
* ***
1180772 ATATATAATATATAGTTTTGAAAATATTTTTGAAAAAAT
1 ATATATAATATATAG-TTTGAAAACATTTTTTCGAAAAT
*
1180811 ATATATGATATATAGTTTTGAAAACA-TTTTTCGAAAAT
1 ATATATAATATATAG-TTTGAAAACATTTTTTCGAAAAT
* * * *
1180849 ATATATAATATACAGTTTTAAAACGTTTTTTTGAAAAT
1 ATATATAATATATAGTTTGAAAACATTTTTTCGAAAAT
*
1180887 ATATACAATATATAGTTTGGAAAACA-TTTTT-GAAAAT
1 ATATATAATATATAGTTT-GAAAACATTTTTTCGAAAAT
1180924 ATATATAATATATAGTTTTGGAAAACAT
1 ATATATAATATATAG-TTT-GAAAACAT
1180952 ATATTATATA
Statistics
Matches: 155, Mismatches: 19, Indels: 12
0.83 0.10 0.06
Matches are distributed among these distances:
37 28 0.18
38 66 0.43
39 60 0.39
40 1 0.01
ACGTcount: A:0.44, C:0.04, G:0.11, T:0.42
Consensus pattern (38 bp):
ATATATAATATATAGTTTGAAAACATTTTTTCGAAAAT
Found at i:1180860 original size:38 final size:37
Alignment explanation
Indices: 1180733--1180951 Score: 271
Period size: 39 Copynumber: 5.7 Consensus size: 37
1180723 TCTCCATAAC
* *
1180733 ATATATAATATATAGTGTTGAAAGA-ATTTTTTCGAAAGT
1 ATATATAATATATAGTTTTGAAA-ACA-TTTTT-GAAAAT
*
1180772 ATATATAATATATAGTTTTGAAAATATTTTTGAAAAAAT
1 ATATATAATATATAGTTTTGAAAACATTTTTG--AAAAT
*
1180811 ATATATGATATATAGTTTTGAAAACATTTTTCGAAAAT
1 ATATATAATATATAGTTTTGAAAACATTTTT-GAAAAT
* *
1180849 ATATATAATATACAGTTTT-AAAACGTTTTTTTGAAAAT
1 ATATATAATATATAGTTTTGAAAAC--ATTTTTGAAAAT
* *
1180887 ATATACAATATATAGTTTGGAAAACATTTTTGAAAAT
1 ATATATAATATATAGTTTTGAAAACATTTTTGAAAAT
1180924 ATATATAATATATAGTTTTGGAAAACAT
1 ATATATAATATATAGTTTT-GAAAACAT
1180952 ATATTATATA
Statistics
Matches: 159, Mismatches: 13, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
37 34 0.21
38 58 0.36
39 66 0.42
40 1 0.01
ACGTcount: A:0.44, C:0.04, G:0.11, T:0.42
Consensus pattern (37 bp):
ATATATAATATATAGTTTTGAAAACATTTTTGAAAAT
Found at i:1180972 original size:24 final size:24
Alignment explanation
Indices: 1180926--1180972 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
1180916 TTGAAAATAT
***
1180926 ATATAATATATAGTTTTGGAAAAC
1 ATATAATATATAGTTTCAAAAAAC
*
1180950 ATATATTATATAGTTTCAAAAAA
1 ATATAATATATAGTTTCAAAAAA
1180973 AAATTGAACA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (24 bp):
ATATAATATATAGTTTCAAAAAAC
Found at i:1181116 original size:3 final size:3
Alignment explanation
Indices: 1181098--1181130 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
1181088 TAATTCATTT
1181098 TTA TT- TTA TT- TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1181131 TTAGTTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 24 0.86
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (3 bp):
TTA
Found at i:1181397 original size:22 final size:23
Alignment explanation
Indices: 1181358--1181407 Score: 84
Period size: 22 Copynumber: 2.2 Consensus size: 23
1181348 GAGATTTTCG
1181358 GCACCGGAATCCGAAAAATCACA
1 GCACCGGAATCCGAAAAATCACA
*
1181381 GCACCGGAAT-CGAAAAATCATA
1 GCACCGGAATCCGAAAAATCACA
1181403 GCACC
1 GCACC
1181408 CTGGGACTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 16 0.62
23 10 0.38
ACGTcount: A:0.42, C:0.30, G:0.18, T:0.10
Consensus pattern (23 bp):
GCACCGGAATCCGAAAAATCACA
Found at i:1183054 original size:94 final size:92
Alignment explanation
Indices: 1182938--1183118 Score: 211
Period size: 94 Copynumber: 1.9 Consensus size: 92
1182928 TACTAAAAGG
* * * * * * * **
1182938 GAAAGTATGATACCATGGATTACATAATGCCAACATTGTATCGATATTGAAAGGGAGTATTGGTA
1 GAAAGTATGATACCATGAATTACAGAATACAAAAATGGTATCGATACTGAAAGGGAGTATCAGTA
*
1183003 CCATAGTGTAGTAGTAT-GATACTGAGA
66 CCATAGT-TAGAAGTATCGATACTGAGA
* * *
1183030 GAAAGGTATCGATACCATGAATTACAGAATATAAAAATGGTATTGATACTGAAAGGGGGTATCAG
1 GAAA-GTAT-GATACCATGAATTACAGAATACAAAAATGGTATCGATACTGAAAGGGAGTATCAG
1183095 TACCATAGTTAGAAGTATCGATAC
64 TACCATAGTTAGAAGTATCGATAC
1183119 CAGGGTAGGG
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
92 4 0.05
93 12 0.16
94 57 0.78
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (92 bp):
GAAAGTATGATACCATGAATTACAGAATACAAAAATGGTATCGATACTGAAAGGGAGTATCAGTA
CCATAGTTAGAAGTATCGATACTGAGA
Found at i:1183605 original size:45 final size:45
Alignment explanation
Indices: 1183541--1183640 Score: 164
Period size: 45 Copynumber: 2.2 Consensus size: 45
1183531 AAATGAATGA
* *
1183541 ATAAATTAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCC
1 ATAAATGAAATGCATAACGGTGAATTAAAGGCATGAAAGGATGCC
*
1183586 ATAAATGAAATGTATAACGGTGAATTAAAGGCATGAAAGGATGCC
1 ATAAATGAAATGCATAACGGTGAATTAAAGGCATGAAAGGATGCC
*
1183631 CTAAATGAAA
1 ATAAATGAAA
1183641 ATAATGAATA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.45, C:0.11, G:0.22, T:0.22
Consensus pattern (45 bp):
ATAAATGAAATGCATAACGGTGAATTAAAGGCATGAAAGGATGCC
Found at i:1188058 original size:20 final size:21
Alignment explanation
Indices: 1188021--1188060 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1188011 AAATTAAGTT
1188021 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
1188042 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
1188061 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:1188304 original size:17 final size:18
Alignment explanation
Indices: 1188284--1188324 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
1188274 GAAACATCGA
1188284 ATGCATTC-CATGCACCG
1 ATGCATTCACATGCACCG
*
1188301 ATGCATTCTACATGCATCG
1 ATGCATTC-ACATGCACCG
1188320 ATGCA
1 ATGCA
1188325 CTCTGAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.38
19 13 0.62
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (18 bp):
ATGCATTCACATGCACCG
Found at i:1188362 original size:38 final size:37
Alignment explanation
Indices: 1188319--1188402 Score: 98
Period size: 38 Copynumber: 2.2 Consensus size: 37
1188309 TACATGCATC
1188319 GATGCACTC-TGAATATTTTCAAAACAACGAATGCATTT
1 GATGCA-TCATGAATATTTTC-AAACAACGAATGCATTT
** *
1188357 GATGCATCGATGGCTATTTTCAAACATCGAATGCATTT
1 GATGCATC-ATGAATATTTTCAAACAACGAATGCATTT
*
1188395 CATGCATC
1 GATGCATC
1188403 GATGCATACT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
37 2 0.05
38 29 0.73
39 9 0.22
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.32
Consensus pattern (37 bp):
GATGCATCATGAATATTTTCAAACAACGAATGCATTT
Found at i:1188362 original size:65 final size:65
Alignment explanation
Indices: 1188226--1188368 Score: 157
Period size: 65 Copynumber: 2.2 Consensus size: 65
1188216 TTATTTGAGG
* * * *
1188226 TGATGCACCGATGCATCAACCATGCATCGATGCATTAGTGAATTAATTGAAACATCGAATGCATT
1 TGATGCACCGATGCATCAACCATGCATCGATGCACTACTGAATTAATTAAAACAACGAATGCATT
** * *
1188291 CCATGCACCGATGCATTCTA-CATGCATCGATGCACT-CTGAA-TATTTTCAAAACAACGAATGC
1 TGATGCACCGATGCA-TCAACCATGCATCGATGCACTACTGAATTA-ATT-AAAACAACGAATGC
1188353 ATT
63 ATT
*
1188356 TGATGCATCGATG
1 TGATGCACCGATG
1188369 GCTATTTTCA
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
63 2 0.03
64 6 0.09
65 53 0.83
66 3 0.05
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.28
Consensus pattern (65 bp):
TGATGCACCGATGCATCAACCATGCATCGATGCACTACTGAATTAATTAAAACAACGAATGCATT
Found at i:1188402 original size:18 final size:17
Alignment explanation
Indices: 1188349--1188409 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 17
1188339 AAAACAACGA
*
1188349 ATGCATTTGATGCATCG
1 ATGCATTTCATGCATCG
**
1188366 ATGGCTATTTTCAAACATCG
1 AT-GC-A-TTTCATGCATCG
1188386 AATGCATTTCATGCATCG
1 -ATGCATTTCATGCATCG
1188404 ATGCAT
1 ATGCAT
1188410 ACTTGGTGCA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
17 8 0.23
18 12 0.34
19 2 0.06
20 11 0.31
21 2 0.06
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (17 bp):
ATGCATTTCATGCATCG
Found at i:1188403 original size:38 final size:39
Alignment explanation
Indices: 1188332--1188406 Score: 125
Period size: 38 Copynumber: 1.9 Consensus size: 39
1188322 GCACTCTGAA
*
1188332 TATTTTCAAAACAACGAATGCATTTGATGCATCGATGGC
1 TATTTTCAAAACAACGAATGCATTTCATGCATCGATGGC
*
1188371 TATTTTC-AAACATCGAATGCATTTCATGCATCGATG
1 TATTTTCAAAACAACGAATGCATTTCATGCATCGATG
1188407 CATACTTGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 27 0.79
39 7 0.21
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (39 bp):
TATTTTCAAAACAACGAATGCATTTCATGCATCGATGGC
Found at i:1194395 original size:42 final size:41
Alignment explanation
Indices: 1194263--1194397 Score: 98
Period size: 42 Copynumber: 3.2 Consensus size: 41
1194253 GCTAAAAGAA
* *
1194263 CACTTGGCTTTCCCGTGAAGGGGATTCATCCAAAGACCATCT
1 CACTTGGATTTCCCGTGAAGGGGA-TCATCCAAAGATCATCT
* * * *
1194305 CAC-TCGATTTAGACCCGCGAAGGGGAACCA-CCTAAGGAAT-ATAC-
1 CACTTGGATTT---CCCGTGAAGGGG-ATCATCC-AAAG-ATCAT-CT
*
1194349 CACTTGGATTTCCCGTGAAGGGGAGTCGTCCAAAGATCATCT
1 CACTTGGATTTCCCGTGAAGGGGA-TCATCCAAAGATCATCT
1194391 CACTTGG
1 CACTTGG
1194398 TTCAGACCCA
Statistics
Matches: 70, Mismatches: 11, Indels: 24
0.67 0.10 0.23
Matches are distributed among these distances:
41 9 0.13
42 27 0.39
43 4 0.06
44 21 0.30
45 9 0.13
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.23
Consensus pattern (41 bp):
CACTTGGATTTCCCGTGAAGGGGATCATCCAAAGATCATCT
Found at i:1194417 original size:86 final size:86
Alignment explanation
Indices: 1194263--1194463 Score: 267
Period size: 86 Copynumber: 2.3 Consensus size: 86
1194253 GCTAAAAGAA
* * * * * *
1194263 CACTTGGCTTTCCCGTGAAGGGGATTCATCCAAAGACCATCTCACTCGATTTAGACCCGCGAAGG
1 CACTTGGATTTCCCGTGAAGGGGAGTCATCCAAAGACCATCTCACTCGATTCAGACCCACAAAAG
1194328 GGAACCACCTAAGGAATATAC
66 GGAACCACCTAAGGAATATAC
* * * *
1194349 CACTTGGATTTCCCGTGAAGGGGAGTCGTCCAAAGATCATCTCACTTGGTTCAGACCCACAAAAG
1 CACTTGGATTTCCCGTGAAGGGGAGTCATCCAAAGACCATCTCACTCGATTCAGACCCACAAAAG
*
1194414 GGAACCACCTGAGGAATATAC
66 GGAACCACCTAAGGAATATAC
* * * *
1194435 TACTTAGTTTTCCCGTGAAAGGGAGTCAT
1 CACTTGGATTTCCCGTGAAGGGGAGTCAT
1194464 TTAAAGAATT
Statistics
Matches: 99, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
86 99 1.00
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (86 bp):
CACTTGGATTTCCCGTGAAGGGGAGTCATCCAAAGACCATCTCACTCGATTCAGACCCACAAAAG
GGAACCACCTAAGGAATATAC
Found at i:1195850 original size:18 final size:18
Alignment explanation
Indices: 1195827--1195869 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1195817 CTTTAGATTA
*
1195827 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
* *
1195845 TTTATTCAATTCTTATCT
1 TTTATTTAATTATTATCT
1195863 TTTATTT
1 TTTATTT
1195870 TAAAAACAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:1196034 original size:23 final size:23
Alignment explanation
Indices: 1196008--1196112 Score: 56
Period size: 23 Copynumber: 4.5 Consensus size: 23
1195998 TTTATTTCTC
1196008 TTTTAACATTTTTTATATTTTTA
1 TTTTAACATTTTTTATATTTTTA
* * * *
1196031 TTTT-TC-TTTTCTGAAATTTAATA
1 TTTTAACATTTT-TTATATTT-TTA
** *
1196054 TTTTCTTCATTTATTT-TATTTTTC
1 TTTT-AACATTT-TTTATATTTTTA
*
1196078 TTTTAACATTTTTTATATAATTT-
1 TTTTAACATTTTTTATAT-TTTTA
*
1196101 TTTTAAAATTTT
1 TTTTAACATTTT
1196113 AAATTTCCTT
Statistics
Matches: 62, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
21 4 0.06
22 10 0.16
23 29 0.47
24 8 0.13
25 6 0.10
26 4 0.06
27 1 0.02
ACGTcount: A:0.25, C:0.07, G:0.01, T:0.68
Consensus pattern (23 bp):
TTTTAACATTTTTTATATTTTTA
Done.