Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009597.1 Hibiscus syriacus cultivar Beakdansim tig00116976_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: 1557931
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 6 of 7
Found at i:1117415 original size:19 final size:19
Alignment explanation
Indices: 1117391--1117489 Score: 109
Period size: 19 Copynumber: 5.4 Consensus size: 19
1117381 GTTGCTTTGT
1117391 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTGGTTTCG
*
1117410 CGTTGCGATTCT-G--T--
1 CGTTGCGATTTTGGTTTCG
**
1117424 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTGGTTTCG
1117443 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTGGTTTCG
*
1117462 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTT-GGTTTCG
*
1117482 TGTTGCGA
1 CGTTGCGA
1117490 AAGTAAACTA
Statistics
Matches: 67, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
14 11 0.16
16 1 0.01
17 1 0.01
18 1 0.01
19 40 0.60
20 13 0.19
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTGGTTTCG
Found at i:1117430 original size:33 final size:32
Alignment explanation
Indices: 1117364--1117453 Score: 139
Period size: 33 Copynumber: 2.8 Consensus size: 32
1117354 AAAATCGCAA
1117364 TGCGATTTTGGTTTCGCGTTGC--TTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTTGTCGT
1117394 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATT-TGTCGT
**
1117427 TGCGATTTTCATTTCGCGTTGCGATTT
1 TGCGATTTTGGTTTCGCGTTGCGATTT
1117454 TGGTTTCGCG
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
30 22 0.40
32 3 0.05
33 30 0.55
ACGTcount: A:0.07, C:0.18, G:0.28, T:0.48
Consensus pattern (32 bp):
TGCGATTTTGGTTTCGCGTTGCGATTTGTCGT
Found at i:1117703 original size:91 final size:93
Alignment explanation
Indices: 1117533--1117998 Score: 849
Period size: 91 Copynumber: 5.1 Consensus size: 93
1117523 TTGAATGGAT
1117533 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1117598 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
1117626 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTA-TTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1117689 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1117717 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCAC---GTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1117779 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
1117807 AAATTTACTTTCAACCAAAAGACAAAACAAAAACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1117871 AGTTTAGCAGAATTGGCAGCAA-CGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1117898 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTG-TAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1117962 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1117990 AAATTTACT
1 AAATTTACT
1117999 AAGCAATCTA
Statistics
Matches: 361, Mismatches: 5, Indels: 15
0.95 0.01 0.04
Matches are distributed among these distances:
89 8 0.02
90 79 0.22
91 160 0.44
92 75 0.21
93 39 0.11
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1117899 original size:181 final size:182
Alignment explanation
Indices: 1117533--1117998 Score: 839
Period size: 181 Copynumber: 2.5 Consensus size: 182
1117523 TTGAATGGAT
1117533 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACA--GTTAAAGAATACAC
*
1117598 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAT
64 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAAACAAT
*
1117663 ACTATTCACAGTGTTATAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
129 ACTATTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1117717 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCAC-GTTAAAGAATACACAG
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTTAAAGAATACACAG
1117781 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAAACAAATA
66 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAAAC-AATA
1117846 -TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAA-CGAAC
130 CTA-TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1117898 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTAAAGAATACACA
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGT-TAAAGAATACACA
*
1117963 GTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
65 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
1117999 AAGCAATCTA
Statistics
Matches: 275, Mismatches: 3, Indels: 9
0.96 0.01 0.03
Matches are distributed among these distances:
181 130 0.47
182 49 0.18
183 48 0.17
184 48 0.17
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (182 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTTAAAGAATACACAG
TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAAACAATAC
TATTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1119713 original size:19 final size:18
Alignment explanation
Indices: 1119689--1119786 Score: 86
Period size: 19 Copynumber: 5.7 Consensus size: 18
1119679 TCGCAACGAG
1119689 AATCGCAACGCGAGATGA
1 AATCGCAACGCGAGATGA
1119707 CAATCGCAA--CGAGA-G-
1 -AATCGCAACGCGAGATGA
*
1119722 AATCGCAACGCGAAATGA
1 AATCGCAACGCGAGATGA
1119740 CAATCGCAA--CGAGA-G-
1 -AATCGCAACGCGAGATGA
*
1119755 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAGATG-A
*
1119774 AATCGCAATGCGA
1 AATCGCAACGCGA
1119787 TTTTGGTTTC
Statistics
Matches: 65, Mismatches: 4, Indels: 20
0.73 0.04 0.22
Matches are distributed among these distances:
14 16 0.25
16 10 0.15
17 11 0.17
19 28 0.43
ACGTcount: A:0.42, C:0.23, G:0.24, T:0.10
Consensus pattern (18 bp):
AATCGCAACGCGAGATGA
Found at i:1119727 original size:14 final size:14
Alignment explanation
Indices: 1119677--1119764 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
1119667 TTGAAATGAA
1119677 AATCGCAAC--GAG
1 AATCGCAACGAGAG
1119689 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
1119706 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
1119722 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
1119741 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1119755 AATCGCAACG
1 AATCGCAACG
1119765 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 22
0.72 0.02 0.26
Matches are distributed among these distances:
12 8 0.13
14 21 0.34
15 1 0.02
16 5 0.08
17 8 0.13
18 1 0.02
19 18 0.29
ACGTcount: A:0.41, C:0.25, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1119728 original size:33 final size:33
Alignment explanation
Indices: 1119669--1119781 Score: 185
Period size: 33 Copynumber: 3.5 Consensus size: 33
1119659 TCTTTTGGTT
1119669 GAAATGAAAATCGCAAC--GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1119700 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
1119733 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1119766 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1119782 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 15 0.20
33 61 0.80
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1119817 original size:14 final size:15
Alignment explanation
Indices: 1119798--1119855 Score: 64
Period size: 15 Copynumber: 3.7 Consensus size: 15
1119788 TTTGGTTTCG
1119798 CGTTGCGA-TTCTCT
1 CGTTGCGATTTCTCT
*
1119812 CGTTGCGATTTTCATTTCG
1 CGTTGCGA-TTTC---TCT
1119831 CGTTGCGATTTCTCT
1 CGTTGCGATTTCTCT
1119846 CGTTGCGATT
1 CGTTGCGATT
1119856 GTCATTTCTC
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
14 8 0.22
15 12 0.32
16 3 0.08
18 4 0.11
19 10 0.27
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.45
Consensus pattern (15 bp):
CGTTGCGATTTCTCT
Found at i:1119830 original size:33 final size:34
Alignment explanation
Indices: 1119782--1119903 Score: 138
Period size: 33 Copynumber: 3.4 Consensus size: 34
1119772 AAAATCGCAA
**
1119782 TGCGATTTTGGTTTCGCGTTGCGA-TTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTTCTCTCGT
1119815 TGCGATTTTCATTTCGCGTTGCGATTTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTTCTCTCGT
* *
1119849 TGCGATTGTCATTTCTCTCGTTGCGACAGTCATTCTCTCGT
1 TGCGATTTTCA-TT-TCGCGTTGCG--A-T--TTCTCTCGT
1119890 TGCGATTTTCATTT
1 TGCGATTTTCATTT
1119904 ATCTCTGCGA
Statistics
Matches: 76, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
33 22 0.29
34 19 0.25
35 2 0.03
36 9 0.12
38 1 0.01
39 2 0.03
40 2 0.03
41 19 0.25
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (34 bp):
TGCGATTTTCATTTCGCGTTGCGATTTCTCTCGT
Found at i:1119864 original size:21 final size:21
Alignment explanation
Indices: 1119838--1119908 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
1119828 TCGCGTTGCG
1119838 ATTTCTCTCGTTGCGATTGTC
1 ATTTCTCTCGTTGCGATTGTC
**
1119859 ATTTCTCTCGTTGCGACAGTC
1 ATTTCTCTCGTTGCGATTGTC
*
1119880 A-TTCTCTCGTTGCGATTTTC
1 ATTTCTCTCGTTGCGATTGTC
*
1119900 ATTTATCTC
1 ATTTCTCTC
1119909 TGCGACTCTT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.40
21 26 0.60
ACGTcount: A:0.13, C:0.25, G:0.15, T:0.46
Consensus pattern (21 bp):
ATTTCTCTCGTTGCGATTGTC
Found at i:1120029 original size:32 final size:33
Alignment explanation
Indices: 1119993--1120062 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
1119983 AATACTAACT
* *
1119993 TGAAAATCGGAAC-AGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1120025 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1120058 TGAAA
1 TGAAA
1120063 TCTAAGTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
32 12 0.36
33 21 0.64
ACGTcount: A:0.49, C:0.17, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:1120295 original size:22 final size:22
Alignment explanation
Indices: 1120243--1120297 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1120233 TGGTTGTGAG
**
1120243 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1120265 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1120287 GGATTTCTTCG
1 GGATTTCTTCG
1120298 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1120463 original size:39 final size:40
Alignment explanation
Indices: 1120420--1120501 Score: 96
Period size: 40 Copynumber: 2.1 Consensus size: 40
1120410 TACGCGTAGC
*
1120420 GATTATAATGGCGCTTTA-A-ATATCGCGTTGCGATTTACG
1 GATTATAATGGCGATTTACAGAT-TCGCGTTGCGATTTACG
** * *
1120459 GATTATCGTTGCGATTTACAGATTCTCGTTGCGATTTACG
1 GATTATAATGGCGATTTACAGATTCGCGTTGCGATTTACG
1120499 GAT
1 GAT
1120502 ACGCGTTGCG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
39 14 0.39
40 20 0.56
41 2 0.06
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.38
Consensus pattern (40 bp):
GATTATAATGGCGATTTACAGATTCGCGTTGCGATTTACG
Found at i:1120470 original size:20 final size:20
Alignment explanation
Indices: 1120443--1120635 Score: 219
Period size: 20 Copynumber: 9.7 Consensus size: 20
1120433 CTTTAAATAT
1120443 CGCGTTGCGATTTACGGATTA
1 CGCGTTGCGATTTACGGA-TA
* * *
1120464 -TCGTTGCGATTTACAGATT
1 CGCGTTGCGATTTACGGATA
*
1120483 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1120503 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1120523 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1120543 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1120563 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1120583 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1120603 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1120623 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1120636 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
19 1 0.01
20 145 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1120629 original size:60 final size:60
Alignment explanation
Indices: 1120442--1120757 Score: 200
Period size: 60 Copynumber: 5.2 Consensus size: 60
1120432 GCTTTAAATA
* * * **
1120442 TCGCGTTGCGATTTACGGATTATCG--TTGCGATTTACAG-ATTCTCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGA-TA-CGCATTGCGATTTA-TGTATTCGCGTTGCGATTTTCATAT
* * *** * * **
1120502 ACGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCATAT
* * * *
1120562 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCATAT
* * * * * *
1120622 TCGCGTTGCGATTT-TGGAAAATCGCAATGCGAATT-TGTACTATCGCATTGCGATTTTCAATAA
1 TCGCGTTGCGATTTACGG-ATA-CGCATTGCGATTTATGTA-T-TCGCGTTGCGATTTTC-ATAT
* * ** * *
1120685 TCGCGTTGCGATTT-TGGAAACTG-ATTTGCGATTCTGGGGA-TCGCGTTGCGATTTTTAT-T
1 TCGCGTTGCGATTTACGGATAC-GCA-TTGCGATT-TATGTATTCGCGTTGCGATTTTCATAT
1120744 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
1120758 TGTTGGTCAT
Statistics
Matches: 210, Mismatches: 34, Indels: 25
0.78 0.13 0.09
Matches are distributed among these distances:
58 2 0.01
59 18 0.09
60 115 0.55
61 27 0.13
62 25 0.12
63 21 0.10
64 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (60 bp):
TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCATAT
Found at i:1120652 original size:21 final size:21
Alignment explanation
Indices: 1120622--1120704 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
1120612 ATTTTCATAT
*
1120622 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1120643 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
1120664 TCGCATTGCGATTTT-CAATAA
1 TCGCATTGCGATTTTGGAA-AA
*
1120685 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1120705 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:1120695 original size:42 final size:43
Alignment explanation
Indices: 1120602--1120700 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
1120592 ATTTATGTGT
* *
1120602 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
1120643 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAATAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
1120685 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
1120701 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.38
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:1132161 original size:30 final size:31
Alignment explanation
Indices: 1132122--1132251 Score: 86
Period size: 31 Copynumber: 4.2 Consensus size: 31
1132112 GAAGGACCTA
* * * *
1132122 TCCAGAGGTCATAAAGATCCTCGGT-AACTG
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
* *
1132152 TCCATAGGTCCCGAAGAACCTAGGTAAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
* ** * *
1132183 TCCATATGTTC-CTTAGAACATAGGTATACTG
1 TCCATA-GGTCACAAAGAACCTAGGTAAACTG
* * *
1132214 TCCATATGTCTCGAAAG-ACATAGGTAAAACTG
1 TCCATAGGTCAC-AAAGAACCTAGGT-AAACTG
1132246 TCCATA
1 TCCATA
1132252 TGTTCCGTAG
Statistics
Matches: 79, Mismatches: 16, Indels: 8
0.77 0.16 0.08
Matches are distributed among these distances:
30 21 0.27
31 42 0.53
32 16 0.20
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.26
Consensus pattern (31 bp):
TCCATAGGTCACAAAGAACCTAGGTAAACTG
Found at i:1132257 original size:63 final size:61
Alignment explanation
Indices: 1132144--1132272 Score: 188
Period size: 63 Copynumber: 2.1 Consensus size: 61
1132134 AAAGATCCTC
* *
1132144 GGTAACTGTCCATAGGTCCCGAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATA
* *
1132205 GGTATACTGTCCATATGTCTCGAA-AGACATAGGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGTA-ACTGTCCATAGGTCCCGAAGA-ACATAGGT-AAACTGTCCATATGTTCCGTAGAACATA
1132268 GGTAA
1 GGTAA
1132273 ACCCTCGACT
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
61 5 0.08
62 25 0.41
63 31 0.51
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (61 bp):
GGTAACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATA
Found at i:1132267 original size:32 final size:31
Alignment explanation
Indices: 1132147--1132274 Score: 152
Period size: 31 Copynumber: 4.1 Consensus size: 31
1132137 GATCCTCGGT
* * * *
1132147 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
*
1132178 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
* *
1132209 TACTGTCCATATG-TCTCG-AAAGACATAGGTAA
1 AACTGTCCATATGTTC-CGTAGA-ACATAGGT-A
1132241 AACTGTCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
1132272 AAC
1 AAC
1132275 CCTCGACTCT
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
30 4 0.05
31 51 0.62
32 23 0.28
33 4 0.05
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTA
Found at i:1133011 original size:22 final size:21
Alignment explanation
Indices: 1132967--1133008 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1132957 TAAATCAATT
1132967 TCATATAACTCCTCTAATCTTC
1 TCATATAACT-CTCTAATCTTC
1132989 TCATATAACT-TCATAATCTT
1 TCATATAACTCTC-TAATCTT
1133009 TCTTATGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 2 0.11
21 7 0.37
22 10 0.53
ACGTcount: A:0.31, C:0.26, G:0.00, T:0.43
Consensus pattern (21 bp):
TCATATAACTCTCTAATCTTC
Found at i:1133482 original size:21 final size:21
Alignment explanation
Indices: 1133458--1133502 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1133448 TGTTGTTCGT
* *
1133458 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1133479 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1133500 TTG
1 TTG
1133503 CCCATAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1136641 original size:30 final size:30
Alignment explanation
Indices: 1136607--1136679 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
1136597 CCCGAATGAC
1136607 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1136637 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
1136667 CTGTCCATAGGTC
1 CTATCCAGAGGTC
1136680 CCGAAGAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1136703 original size:31 final size:31
Alignment explanation
Indices: 1136665--1136792 Score: 141
Period size: 31 Copynumber: 4.1 Consensus size: 31
1136655 GATCCTCGGT
* *
1136665 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* **
1136696 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* * *
1136727 TACTGTCCATATATCTCGAA-AGACATAGGTAA
1 AACTGTCCATATGTCCCGAAGA-ACATAGGT-A
* *
1136759 AACTGTCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
1136790 AAC
1 AAC
1136793 CCTCGACTCT
Statistics
Matches: 78, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
30 1 0.01
31 52 0.67
32 24 0.31
33 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTCCCGAAGAACATAGGTA
Found at i:1137530 original size:22 final size:21
Alignment explanation
Indices: 1137486--1137527 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1137476 TAAATCAATT
1137486 TCATATAACTCCTCTAATCTTC
1 TCATATAACT-CTCTAATCTTC
1137508 TCATATAACT-TCATAATCTT
1 TCATATAACTCTC-TAATCTT
1137528 TCTTATGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 2 0.11
21 7 0.37
22 10 0.53
ACGTcount: A:0.31, C:0.26, G:0.00, T:0.43
Consensus pattern (21 bp):
TCATATAACTCTCTAATCTTC
Found at i:1138001 original size:21 final size:21
Alignment explanation
Indices: 1137977--1138021 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1137967 TGTTGTTCGT
* *
1137977 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1137998 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1138019 TTG
1 TTG
1138022 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1146813 original size:40 final size:40
Alignment explanation
Indices: 1146725--1146817 Score: 109
Period size: 39 Copynumber: 2.3 Consensus size: 40
1146715 GATTTGACAT
* * **
1146725 TTAGCGGCGTTTTTACAAAAAATGTCGCAATAGGGTGGTTTA
1 TTAGCGGCGTTTTT--AAAAAACGTCGCAATAGAGTGGTAAA
1146767 TT-GCGGCGTTTGTT-AAAAACGTCGCAATAGAGTGGTAAA
1 TTAGCGGCGTTT-TTAAAAAACGTCGCAATAGAGTGGTAAA
1146806 TTAGCGGCGTTT
1 TTAGCGGCGTTT
1146818 ATACCACAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
39 23 0.51
40 9 0.20
41 9 0.20
42 4 0.09
ACGTcount: A:0.27, C:0.13, G:0.28, T:0.32
Consensus pattern (40 bp):
TTAGCGGCGTTTTTAAAAAACGTCGCAATAGAGTGGTAAA
Found at i:1146837 original size:42 final size:42
Alignment explanation
Indices: 1146791--1146913 Score: 132
Period size: 41 Copynumber: 3.0 Consensus size: 42
1146781 AAAAACGTCG
1146791 CAATAGAGTGGTAAATTAGCGGCGTTTATACCACAAACGCCA
1 CAATAGAGTGGTAAATTAGCGGCGTTTATACCACAAACGCCA
* * * *
1146833 CAAT--AGT-TTAACATATAGTGGCGTTT-TAGCTA-AAACGCCG
1 CAATAGAGTGGTAA-AT-TAGCGGCGTTTATA-CCACAAACGCCA
1146873 CAATAGA-TCGGTAAATTAGCGGCGTTTATACCACAAACGCC
1 CAATAGAGT-GGTAAATTAGCGGCGTTTATACCACAAACGCC
1146914 GTAATATATA
Statistics
Matches: 65, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
39 3 0.05
40 18 0.28
41 25 0.38
42 16 0.25
43 3 0.05
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.24
Consensus pattern (42 bp):
CAATAGAGTGGTAAATTAGCGGCGTTTATACCACAAACGCCA
Found at i:1146914 original size:42 final size:41
Alignment explanation
Indices: 1146783--1146919 Score: 147
Period size: 42 Copynumber: 3.3 Consensus size: 41
1146773 CGTTTGTTAA
*
1146783 AAACGTCGCAATAGAGTGGTAAATTAGCGGCGTTTATACCAC
1 AAACGCCGCAATAGA-TGGTAAATTAGCGGCGTTTATACCAC
* * * *
1146825 AAACGCCACAATAG-T-TTAACATATAGTGGCGTTT-TAGCTA-
1 AAACGCCGCAATAGATGGTAA-AT-TAGCGGCGTTTATA-CCAC
1146865 AAACGCCGCAATAGATCGGTAAATTAGCGGCGTTTATACCAC
1 AAACGCCGCAATAGAT-GGTAAATTAGCGGCGTTTATACCAC
*
1146907 AAACGCCGTAATA
1 AAACGCCGCAATA
1146920 TATACCACAT
Statistics
Matches: 77, Mismatches: 10, Indels: 16
0.75 0.10 0.16
Matches are distributed among these distances:
39 3 0.04
40 18 0.23
41 25 0.32
42 28 0.36
43 3 0.04
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (41 bp):
AAACGCCGCAATAGATGGTAAATTAGCGGCGTTTATACCAC
Found at i:1147001 original size:41 final size:41
Alignment explanation
Indices: 1146953--1147133 Score: 197
Period size: 41 Copynumber: 4.4 Consensus size: 41
1146943 TTCTTAAAAT
* * *
1146953 GCCGCAATAGTGATAATAAATAGTGGCCTTTTTAAATAAAC
1 GCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAAATAAAC
1146994 GCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGAA-AAAC
1 GCCGCAATAGTGTTAATCAATAGTGGCGTTTTTA-AATAAAC
* * * *
1147035 GCCGTAATAGTTTTAATCAATAGTGGCGTTTTTTAACAAAC
1 GCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAAATAAAC
* * * *
1147076 ACCACAATAGTG-TAATCAATAGTGGCTTTTTTTTTATATAAAC
1 GCCGCAATAGTGTTAATCAATAGTGGC---GTTTTTAAATAAAC
*
1147119 GCCGCAA-AATGTTAA
1 GCCGCAATAGTGTTAA
1147134 ATATATAGTC
Statistics
Matches: 117, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
40 16 0.14
41 78 0.67
42 5 0.04
43 18 0.15
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (41 bp):
GCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAAATAAAC
Found at i:1148606 original size:124 final size:123
Alignment explanation
Indices: 1148378--1148702 Score: 367
Period size: 124 Copynumber: 2.6 Consensus size: 123
1148368 TTGTATCCAT
* * *
1148378 AAACGCCGCTATAG-GTACGTACTTTAGTGGCATTTTTATACAAACGCCGCTATAGAA-TCGTAC
1 AAACGCCGCTATAGACTA-GTACTTTAGTGGCGTTTTTATACAAACGCTGCTATA-AACTCGTAC
* * * *
1148441 TTTAGTGGCGTTTTTATACAAACGCCGCTATATACTAGTACTTTAGTGGTGTTTCTATAC
64 TTTAGTGGCGTTTTAATACAAACGCCGCTATAGACTAGTACTTTAGTAGCGTTTCTATAC
* *
1148501 AAACGCCGCTATATACTCA-TACTTTAGTGGCGTTTTGA-ATCTAAACGCTGCTATAAACTCGTA
1 AAACGCCGCTATAGACT-AGTACTTTAGTGGCGTTTTTATA-C-AAACGCTGCTATAAACTCGTA
* * * *
1148564 CTTTAGTGGTGTTTTGAATGA-AAA-GCCGCT-TAAGACTTGTACTTTAGTAGCGTTTTTATAT
63 CTTTAGTGGCGTTTT-AAT-ACAAACGCCGCTAT-AGACTAGTACTTTAGTAGCGTTTCTATAC
* * *
1148625 AAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTTTATACAAACGTTGCTATAGACTCGTACCC
1 AAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTTTATACAAACGCTGCTATAAACTCGTA-CT
*
1148690 TTAGTGGCATTTT
65 TTAGTGGCGTTTT
1148703 TAGATAAATG
Statistics
Matches: 171, Mismatches: 20, Indels: 21
0.81 0.09 0.10
Matches are distributed among these distances:
122 1 0.01
123 54 0.32
124 108 0.63
125 7 0.04
126 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (123 bp):
AAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTTTATACAAACGCTGCTATAAACTCGTACTT
TAGTGGCGTTTTAATACAAACGCCGCTATAGACTAGTACTTTAGTAGCGTTTCTATAC
Found at i:1148677 original size:41 final size:41
Alignment explanation
Indices: 1148378--1148722 Score: 342
Period size: 41 Copynumber: 8.4 Consensus size: 41
1148368 TTGTATCCAT
* *
1148378 AAACGCCGCTATAG-GTACGTACTTTAGTGGCATTTTTATAC
1 AAACGCCGCTATAGACTA-GTACTTTAGTGGCGTTTTTATAC
* *
1148419 AAACGCCGCTATAGAATCGTACTTTAGTGGCGTTTTTATAC
1 AAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTTTATAC
* * *
1148460 AAACGCCGCTATATACTAGTACTTTAGTGGTGTTTCTATAC
1 AAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTTTATAC
* *
1148501 AAACGCCGCTATATACTCA-TACTTTAGTGGCGTTTTGA-ATC
1 AAACGCCGCTATAGACT-AGTACTTTAGTGGCGTTTTTATA-C
* * * * *
1148542 TAAACGCTGCTATAAACTCGTACTTTAGTGGTGTTTTGAATGA-
1 -AAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTT-TAT-AC
* * *
1148585 AAA-GCCGCT-TAAGACTTGTACTTTAGTAGCGTTTTTATAT
1 AAACGCCGCTAT-AGACTAGTACTTTAGTGGCGTTTTTATAC
1148625 AAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTTTATAC
1 AAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTTTATAC
** * * * * *
1148666 AAACGTTGCTATAGACTCGTACCCTTAGTGGCATTTTTAGAT
1 AAACGCCGCTATAGACTAGTA-CTTTAGTGGCGTTTTTATAC
* *
1148708 AAATGCCGCAATAGA
1 AAACGCCGCTATAGA
1148723 TATAATATTT
Statistics
Matches: 255, Mismatches: 36, Indels: 25
0.81 0.11 0.08
Matches are distributed among these distances:
39 1 0.00
40 7 0.03
41 181 0.71
42 64 0.25
43 1 0.00
45 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (41 bp):
AAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTTTATAC
Found at i:1150999 original size:102 final size:102
Alignment explanation
Indices: 1150876--1151105 Score: 451
Period size: 102 Copynumber: 2.3 Consensus size: 102
1150866 TCGCCAGAGA
*
1150876 TTATTCATTTTTCATTTAACCAGTTCCTTTTTTAAATGTTATGAACCTAAATTTAAGAAATTTTG
1 TTATTCATTTATCATTTAACCAGTTCCTTTTTTAAATGTTATGAACCTAAATTTAAGAAATTTTG
1150941 GTTTTCATTTAAAGGTTAAAATTAGTTCTTTATTTCT
66 GTTTTCATTTAAAGGTTAAAATTAGTTCTTTATTTCT
1150978 TTATTCATTTATCATTTAACCAGTTCCTTTTTTAAATGTTATGAACCTAAATTTAAGAAATTTTG
1 TTATTCATTTATCATTTAACCAGTTCCTTTTTTAAATGTTATGAACCTAAATTTAAGAAATTTTG
1151043 GTTTTCATTTAAAGGTTAAAATTAGTTCTTTATTTCT
66 GTTTTCATTTAAAGGTTAAAATTAGTTCTTTATTTCT
1151080 TTATTCATTTATCATTTAACCAGTTC
1 TTATTCATTTATCATTTAACCAGTTC
1151106 TTTAGTTATT
Statistics
Matches: 127, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 127 1.00
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.50
Consensus pattern (102 bp):
TTATTCATTTATCATTTAACCAGTTCCTTTTTTAAATGTTATGAACCTAAATTTAAGAAATTTTG
GTTTTCATTTAAAGGTTAAAATTAGTTCTTTATTTCT
Found at i:1156839 original size:21 final size:21
Alignment explanation
Indices: 1156815--1156867 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1156805 ATGAAGCTAG
1156815 AGAAGCAGAGAGAGCAGCAAC
1 AGAAGCAGAGAGAGCAGCAAC
* *
1156836 AGAAGCA-ACCAGAGCAGCAGC
1 AGAAGCAGA-GAGAGCAGCAAC
*
1156857 GGAAGCAGAGA
1 AGAAGCAGAGA
1156868 AAGAAGCAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 1 0.04
21 24 0.92
22 1 0.04
ACGTcount: A:0.45, C:0.21, G:0.34, T:0.00
Consensus pattern (21 bp):
AGAAGCAGAGAGAGCAGCAAC
Found at i:1156875 original size:21 final size:21
Alignment explanation
Indices: 1156846--1156917 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
1156836 AGAAGCAACC
* * *
1156846 AGAGCAGCAGCGGAAGCAGAG
1 AGAGAAGCAGCGGCAGCACAG
* * *
1156867 AAAGAAGCAGTGGCAGTACAG
1 AGAGAAGCAGCGGCAGCACAG
1156888 AGAGAAGCAGCGGCAGCACAG
1 AGAGAAGCAGCGGCAGCACAG
1156909 AGAGAAGCA
1 AGAGAAGCA
1156918 TCATATCAGC
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.42, C:0.18, G:0.38, T:0.03
Consensus pattern (21 bp):
AGAGAAGCAGCGGCAGCACAG
Found at i:1157469 original size:129 final size:129
Alignment explanation
Indices: 1157332--1157583 Score: 314
Period size: 129 Copynumber: 1.9 Consensus size: 129
1157322 TTTTTAACAG
*
1157332 AAACGCCGCAAAACATCAACACCTACTGCGGCG-TTTTAACAAA-AAAACACCGCTAAACATC-A
1 AAACGCCGCAAAACATCAA-ACCTACTGCGGCGTTTTTAA-AAATAAAACACCACTAAACATCAA
* * *
1157394 TAACATATTGTGGCGTTTGTCTGAGAAACGCTGCTAAATATTAACACATATTGC-GCGTTTTTAT
64 T-ACATATTGTGGCGTTTAT-TGAAAAACGCTGCTAAATATCAACACATATTGCGGCGTTTTTAT
1157458 GAC
127 GAC
* * ** * * *
1157461 AAACGCCGCTAAATATCAAACCTTTTGCGGTGTTTTTTAAAAATAAAACGCCACTAAATATCAAT
1 AAACGCCGCAAAACATCAAACCTACTGCGGCG-TTTTTAAAAATAAAACACCACTAAACATCAAT
* *
1157526 ACCTATTGTGGCGTTTATTGAAAAACGCTGCTAAATATCAACACCTATTGCGGCGTTT
65 ACATATTGTGGCGTTTATTGAAAAACGCTGCTAAATATCAACACATATTGCGGCGTTT
1157584 GTATCAACAC
Statistics
Matches: 105, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
128 10 0.10
129 50 0.48
130 43 0.41
131 2 0.02
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (129 bp):
AAACGCCGCAAAACATCAAACCTACTGCGGCGTTTTTAAAAATAAAACACCACTAAACATCAATA
CATATTGTGGCGTTTATTGAAAAACGCTGCTAAATATCAACACATATTGCGGCGTTTTTATGAC
Found at i:1157496 original size:42 final size:43
Alignment explanation
Indices: 1157332--1157583 Score: 197
Period size: 42 Copynumber: 5.8 Consensus size: 43
1157322 TTTTTAACAG
* * * * **
1157332 AAACGCCGCAAAACATCAACACCTACTGCGGCGTTTTAACAAAA
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTA-TGAA
* * * * * * *
1157376 AAACACCGCTAAACATCATA-ACATATTGTGGCGTTTGTCTGAG
1 AAACGCCGCTAAATATCA-ACACCTATTGCGGCGTTTTTATGAA
* * * *
1157419 AAACGCTGCTAAATATTAACACATATTGC-GCGTTTTTATGAC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATGAA
* * **
1157461 AAACGCCGCTAAATATCAA-ACCTTTTGCGGTGTTTTTTAAAAATA
1 AAACGCCGCTAAATATCAACACCTATTGCGGCG-TTTTT-ATGA-A
* * * *
1157506 AAACGCCACTAAATATCAATACCTATTGTGGCGTTTAT-TGAA
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATGAA
*
1157548 AAACGCTGCTAAATATCAACACCTATTGCGGCGTTT
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTT
1157584 GTATCAACAC
Statistics
Matches: 163, Mismatches: 38, Indels: 16
0.75 0.18 0.07
Matches are distributed among these distances:
41 7 0.04
42 63 0.39
43 29 0.18
44 31 0.19
45 23 0.14
46 10 0.06
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (43 bp):
AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATGAA
Found at i:1157652 original size:43 final size:43
Alignment explanation
Indices: 1157585--1157695 Score: 127
Period size: 43 Copynumber: 2.6 Consensus size: 43
1157575 GCGGCGTTTG
*
1157585 TATCAACACCTATTGC-A-GTATTTTTATAACAAACACCACTAAA
1 TATCAACACCTATTGCGACGT-TTTTCA-AACAAACACCACTAAA
* * * *
1157628 TATCAACACTTATTGCGACGTTTTTCACACAAACGCCGCTAAA
1 TATCAACACCTATTGCGACGTTTTTCAAACAAACACCACTAAA
* *
1157671 TATCAATACCTATTGCGGCGTTTTT
1 TATCAACACCTATTGCGACGTTTTT
1157696 TGTGAAAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
43 50 0.86
44 6 0.10
45 2 0.03
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.32
Consensus pattern (43 bp):
TATCAACACCTATTGCGACGTTTTTCAAACAAACACCACTAAA
Found at i:1158295 original size:2 final size:2
Alignment explanation
Indices: 1158288--1158343 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1158278 TATGATTATG
1158288 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1158330 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
1158344 ATGAGAGAGA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1158959 original size:18 final size:17
Alignment explanation
Indices: 1158925--1158957 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1158915 CAATTGATAT
1158925 ATTTAAATATATAAAAG
1 ATTTAAATATATAAAAG
1158942 ATTTATAATAT-TAAAA
1 ATTTA-AATATATAAAA
1158958 AGTAAATTAA
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:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
ATTTAAATATATAAAAG
Found at i:1168211 original size:2 final size:2
Alignment explanation
Indices: 1168204--1168250 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1168194 GTCCAAATAA
1168204 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1168246 AT AT A
1 AT AT A
1168251 GGTGATAAGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1172951 original size:16 final size:17
Alignment explanation
Indices: 1172922--1172959 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
1172912 ATATACATAT
*
1172922 ATAATAATACATGAATA
1 ATAATAATAAATGAATA
1172939 ATAA-AATAAATGAATA
1 ATAATAATAAATGAATA
1172955 A-AATA
1 ATAATA
1172960 TCCATATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 2 0.11
16 13 0.68
17 4 0.21
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAAATGAATA
Found at i:1174255 original size:105 final size:105
Alignment explanation
Indices: 1173955--1174996 Score: 1531
Period size: 105 Copynumber: 10.0 Consensus size: 105
1173945 CATTGTTCCA
* * * * ** *
1173955 AGTCCAATATCCTCCGTCGTGAAGTTAAAATTGGCTATG-GAACCGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACAA
* * * * *
1174019 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
** * *
1174061 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTTA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
*
1174121 AGCGGTCCATTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
1174161 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTTGACAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
*
1174226 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1174266 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1174326 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1174366 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
* *
1174431 AGCGATCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
1174471 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1174536 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1174576 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
*
1174640 AGCGGTCCCTTCGTCGTGAAGTTGAAC-TGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
1174679 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAG-TGTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1174743 AGC-GT-CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
1174781 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGG-AAGTTG-TTGTTGACAA
1174846 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
64 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
1174888 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAAG
** * * *
1174953 CAGCCTTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
1174994 AGT
1 AGT
1174997 GCCACGATAT
Statistics
Matches: 855, Mismatches: 63, Indels: 36
0.90 0.07 0.04
Matches are distributed among these distances:
100 169 0.20
101 27 0.03
102 67 0.08
103 76 0.09
104 50 0.06
105 300 0.35
106 88 0.10
107 78 0.09
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:1174311 original size:205 final size:206
Alignment explanation
Indices: 1173955--1175027 Score: 1539
Period size: 205 Copynumber: 5.2 Consensus size: 206
1173945 CATTGTTCCA
* * * ** *
1173955 AGTCCAATATCCTCCGTCGTGAAGTTAAAATTGGCTATG-GAACCGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACAA
* * * ** *
1174019 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAA
64 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAA
** * * *
1174084 GTTGAAATTGAATCTTAA-TGAAATTTTGTTGACAAGCAGCGGTCCATTCGTCGTGAAGTTGAAC
129 GTTGAAATTGGCTCTGAATTGAAATTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
1174148 TTGCGTTGTCTGG
194 TTGCGTTGTCTGG
* * * *
1174161 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTTGACAAAC
1 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
*
1174226 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
*
1174291 TGAAATTGGCTCTGAA-TGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
131 TGAAATTGGCTCTGAATTGAAATTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
1174355 GCGTTGTCTGG
196 GCGTTGTCTGG
*
1174366 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
*
1174431 AGCGATCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
*
1174496 TGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
131 TGAAATTGGCTCTGA-ATT--GAAATT-TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
1174561 ACTTGCGTTGTCTGG
192 ACTTGCGTTGTCTGG
*
1174576 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTT-TTGTTGACAAGC
1 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1174640 AGCGGTCCCTTCGTCGTGAAGTTGAAC-TGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
* *
1174704 TGAAATTGGCTCTGAGATTGGGAAGTGTTGTTGACAACCAGC-GT-CCTTCGTCGTGAAGTTGAA
131 TGAAATTGGCTCTGA-ATT--GAAATTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
1174767 CTTGCGTTGTCTGG
193 CTTGCGTTGTCTGG
* * * * *
1174781 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTGACAA
1 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGG-AAGTTG-TTGTTGACAA
*
1174846 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
64 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAA
** *
1174911 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCTTCCCTTCGTTGTGAAGT
129 GTTGAAATTGGCTCTG-AATTGA-AA--T-TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
* *
1174976 TGAACTTGTGTTGTCTCG
189 TGAACTTGCGTTGTCTGG
* * *
1174994 AGTGCCACGATATTCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTCCGTTGTGAAGTTGAAAT
1175028 CGCGGATGGC
Statistics
Matches: 799, Mismatches: 48, Indels: 30
0.91 0.05 0.03
Matches are distributed among these distances:
205 355 0.44
206 50 0.06
207 19 0.02
208 102 0.13
209 96 0.12
210 105 0.13
211 15 0.02
212 1 0.00
213 33 0.04
214 3 0.00
216 20 0.03
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (206 bp):
AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
TGAAATTGGCTCTGAATTGAAATTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
GCGTTGTCTGG
Found at i:1174507 original size:310 final size:312
Alignment explanation
Indices: 1173955--1175027 Score: 1540
Period size: 310 Copynumber: 3.4 Consensus size: 312
1173945 CATTGTTCCA
* * * * *
1173955 AGTCCAATATCCTCCGTCGTGAAGTTAAAATTGGCTATGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCT-GAA-C-TGAAAGTGTTTGTTGACAAC
* * *
1174020 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAG
63 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTCCGTTGTGAAG
** * *
1174085 TTGAAATTGAATCTTA-A-T-GAAA-TT-TTGTTGACAAGCAGCGGTCCATTCGTCGTGAAGTTG
128 TTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGC-GTCCCTTCGTCGTGAAGTTG
* *
1174145 AACTTGCGTTGTCTGGAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAA
192 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAA
*
1174210 GTTGTTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
257 GTTGTTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
1174266 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAA-TGAAA-T-TTTGTTGACAAGCAG
1 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAACTGAAAGTGTTTGTTGACAACCAG
* *
1174328 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTCCGTTGTGAAGTTG
66 CCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTCCGTTGTGAAGTTG
1174393 AAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGATCCCTTCGTCGTGAAGTTGAAC
131 AAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCG-TCCCTTCGTCGTGAAGTTGAAC
*
1174458 TTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTT
195 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTT
*
1174523 GTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
260 GTTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1174576 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGT-TTTGTTGACAAGC
1 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGA-ACT-GAAAGTGTTTGTTGACAACC
* * * *
1174640 AGCGGTCCCTTCGTCGTGAAGTTGAAC-TGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
64 AGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTCCGTTGTGAAGT
* *
1174704 TGAAATTGGCTCTGAGATTGGGAAG-TGTTGTTGACAACCAGCGT-CCTTCGTCGTGAAGTTGAA
129 TGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGTCCCTTCGTCGTGAAGTTGAA
* * *
1174767 CTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAA
194 CTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGG-AAG
* *
1174832 TTGTTTATTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
258 TTG-TTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1174888 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTG-AACTGA-AAG-TGTTTGTTGACAAC
* * * * *
1174953 CAGCCTTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCCACGATATTCTCCGTCGTG
63 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGT-CCA--ATATCCTCCGTTGTG
*
1175018 GAGTTGAAAT
125 AAGTTGAAAT
1175028 CGCGGATGGC
Statistics
Matches: 697, Mismatches: 45, Indels: 33
0.90 0.06 0.04
Matches are distributed among these distances:
305 84 0.12
306 2 0.00
307 5 0.01
308 4 0.01
309 3 0.00
310 267 0.38
311 42 0.06
312 112 0.16
313 65 0.09
314 77 0.11
315 12 0.02
316 3 0.00
318 21 0.03
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (312 bp):
AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAACTGAAAGTGTTTGTTGACAACCAG
CCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTCCGTTGTGAAGTTG
AAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGTCCCTTCGTCGTGAAGTTGAACT
TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG
TTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:1175805 original size:65 final size:65
Alignment explanation
Indices: 1175735--1175889 Score: 208
Period size: 65 Copynumber: 2.4 Consensus size: 65
1175725 GAAACGAAAT
* *
1175735 TTTGTTTTAAGGGAGATA-AAT-TCAAAGATTTTGTGTTTCAAGAAAACTGTCTCATAGGAGAC-
1 TTTGTTTCAAGGGA-A-ACAATCTCAAAGATTTTGTGTTTC-AGAAAACTGTCTCAAAGGAGACA
1175797 AAA
63 AAA
* *
1175800 TTTGTTTCGAGGGAAACAATCTCAAAGATTTTGTGTTTCAGAGAACTGTCTCAAAGGAGACAAAA
1 TTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAGAAAACTGTCTCAAAGGAGACAAAA
**
1175865 TTTGTTTCAAGGGAAATTATCTCAA
1 TTTGTTTCAAGGGAAACAATCTCAA
1175890 GAGAGACGAA
Statistics
Matches: 80, Mismatches: 7, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
63 1 0.01
64 24 0.30
65 55 0.69
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (65 bp):
TTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAGAAAACTGTCTCAAAGGAGACAAAA
Found at i:1175888 original size:36 final size:36
Alignment explanation
Indices: 1175848--1175917 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
1175838 CAGAGAACTG
**
1175848 TCTCAA-AGGAGACAAAATTTGTTTCAAGGGAAATTA
1 TCTCAAGA-GAGACAAAATTCATTTCAAGGGAAATTA
*
1175884 TCTCAAGAGAGACGAAATTCATTTCAAGGGAAAT
1 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAAT
1175918 GTTTTTCAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 29 0.97
37 1 0.03
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (36 bp):
TCTCAAGAGAGACAAAATTCATTTCAAGGGAAATTA
Found at i:1176011 original size:34 final size:35
Alignment explanation
Indices: 1175943--1176030 Score: 133
Period size: 34 Copynumber: 2.5 Consensus size: 35
1175933 TGTTTCAGGA
*
1175943 GAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAAG
1 GAAACTGTCTCAA--GAGACAAAAGTTTGTTTCAAAG
*
1175980 GAAACTGTCTCAAGAGAC-AAAGTTTGTTTCAAGG
1 GAAACTGTCTCAAGAGACAAAAGTTTGTTTCAAAG
1176014 GAAACTGTCTCAAGAGA
1 GAAACTGTCTCAAGAGA
1176031 GACAATGGTG
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
34 31 0.63
35 5 0.10
37 13 0.27
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.25
Consensus pattern (35 bp):
GAAACTGTCTCAAGAGACAAAAGTTTGTTTCAAAG
Found at i:1176012 original size:101 final size:98
Alignment explanation
Indices: 1175768--1176018 Score: 265
Period size: 101 Copynumber: 2.5 Consensus size: 98
1175758 AAAGATTTTG
* * *
1175768 TGTTTC-AAGAAAACTGTCTCATAGGAGACAAATTTGTTTCGAGGGAAACAATCTCAAAGATTTT
1 TGTTTCAAAGGAAACTGTCTCAGA-GAGACAAATTTGTTTCAAGGGAAACAATCTCAAAGA-TTT
*
1175832 GTGTTTCAGAGAACTGTCTCAAAGGAGACAAAATT
64 ATGTTTCAGAGAACTGTCTCAAAGGAGACAAAATT
* * * ** *** * *
1175867 TGTTTCAAGGGAAATTATCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTTCAATG-TT
1 TGTTTCAAAGGAAACTGTCTC-AGAGAGAC-AAATTTGTTTCAAGGGAAA-CAATCTCAAAGATT
*
1175931 TATGTTTCAGGAGAAACTGTCTCAAGGGAGACAAAATTT
63 TATGTTTCA-GAG-AACTGTCTCAAAGGAGACAAAA-TT
1175970 TGTTTCAAAGGAAACTGTCTCA-AGAGACAAAGTTTGTTTCAAGGGAAAC
1 TGTTTCAAAGGAAACTGTCTCAGAGAGACAAA-TTTGTTTCAAGGGAAAC
1176019 TGTCTCAAGA
Statistics
Matches: 123, Mismatches: 21, Indels: 15
0.77 0.13 0.09
Matches are distributed among these distances:
99 6 0.05
100 28 0.23
101 41 0.33
102 28 0.23
103 20 0.16
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (98 bp):
TGTTTCAAAGGAAACTGTCTCAGAGAGACAAATTTGTTTCAAGGGAAACAATCTCAAAGATTTAT
GTTTCAGAGAACTGTCTCAAAGGAGACAAAATT
Found at i:1176462 original size:24 final size:24
Alignment explanation
Indices: 1176435--1176484 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
1176425 ATTATCTCTC
1176435 GAACTCGTCTGAAGTTGATTCTAA
1 GAACTCGTCTGAAGTTGATTCTAA
1176459 GAACTCGTCTGAAGTTGATTCTAA
1 GAACTCGTCTGAAGTTGATTCTAA
1176483 GA
1 GA
1176485 TCTGTCGATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (24 bp):
GAACTCGTCTGAAGTTGATTCTAA
Found at i:1177282 original size:22 final size:22
Alignment explanation
Indices: 1177205--1177275 Score: 106
Period size: 22 Copynumber: 3.2 Consensus size: 22
1177195 TTGTGTGTGG
*
1177205 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
*
1177227 TCAAAGGTTTAACATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
* *
1177249 TTAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTTGATGC
1177271 TCAAA
1 TCAAA
1177276 AGATTGATGG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGACATTTGATGC
Found at i:1177928 original size:22 final size:22
Alignment explanation
Indices: 1177903--1177944 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1177893 TTGCATGTGC
1177903 TTTTGTCCCTTTTT-CTTTTGAT
1 TTTTG-CCCTTTTTCCTTTTGAT
*
1177925 TTTTGCTCTTTTTCCTTTTG
1 TTTTGCCCTTTTTCCTTTTG
1177945 TTCTTGTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.02, C:0.19, G:0.10, T:0.69
Consensus pattern (22 bp):
TTTTGCCCTTTTTCCTTTTGAT
Found at i:1177943 original size:15 final size:17
Alignment explanation
Indices: 1177925--1177977 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 17
1177915 TTCTTTTGAT
1177925 TTTTGCTCTT-TTTC-C
1 TTTTGCTCTTGTTTCTC
*
1177940 TTTTGTTCTTGTTTCTC
1 TTTTGCTCTTGTTTCTC
*
1177957 TTTT-CT-TTGTTT-TT
1 TTTTGCTCTTGTTTCTC
1177971 TTTTGCT
1 TTTTGCT
1177978 TTTTTGCTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
14 5 0.16
15 17 0.53
16 5 0.16
17 5 0.16
ACGTcount: A:0.00, C:0.17, G:0.09, T:0.74
Consensus pattern (17 bp):
TTTTGCTCTTGTTTCTC
Found at i:1181629 original size:17 final size:17
Alignment explanation
Indices: 1181609--1181650 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
1181599 ATATATACAT
*
1181609 ATAATAATAATACATGA
1 ATAATAATAATAAATGA
*
1181626 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
1181643 ATAA-AATA
1 ATAATAATA
1181651 TCCATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 3 0.14
17 19 0.86
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:1182912 original size:41 final size:42
Alignment explanation
Indices: 1182855--1182934 Score: 126
Period size: 41 Copynumber: 1.9 Consensus size: 42
1182845 TCCACTGAAA
1182855 AAGTTATATAAATTTATAA-TGTTTTTATTATAATTAAATTT
1 AAGTTATATAAATTTATAATTGTTTTTATTATAATTAAATTT
* * *
1182896 AAGTTATATGAATTTATAATTTTTTTTGTTATAATTAAA
1 AAGTTATATAAATTTATAATTGTTTTTATTATAATTAAA
1182935 AAGTTATATT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
41 18 0.51
42 17 0.49
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (42 bp):
AAGTTATATAAATTTATAATTGTTTTTATTATAATTAAATTT
Found at i:1182939 original size:39 final size:38
Alignment explanation
Indices: 1182852--1182943 Score: 121
Period size: 41 Copynumber: 2.3 Consensus size: 38
1182842 GTTTCCACTG
1182852 AAAAAGTTATATAAATTTATAATGTTTTTATTATAATT
1 AAAAAGTTATATAAATTTATAATGTTTTTATTATAATT
* * *
1182890 AAATTTAAGTTATATGAATTTATAATTTTTTTTGTTATAATT
1 AAA---AAGTTATATAAATTTATAA-TGTTTTTATTATAATT
1182932 AAAAAGTTATAT
1 AAAAAGTTATAT
1182944 TAGGGGTTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
38 3 0.06
39 9 0.19
41 18 0.38
42 17 0.36
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (38 bp):
AAAAAGTTATATAAATTTATAATGTTTTTATTATAATT
Found at i:1191710 original size:2 final size:2
Alignment explanation
Indices: 1191703--1191732 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1191693 GTCTGAGGAG
1191703 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1191733 ATGGTAACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1199683 original size:27 final size:27
Alignment explanation
Indices: 1199599--1199684 Score: 68
Period size: 27 Copynumber: 3.2 Consensus size: 27
1199589 TACTGGTGGA
*
1199599 GGTGGAGACTGATGCTCAGAAGATGAC
1 GGTGGAGACTGATGCTCATAAGATGAC
* * ** * * *
1199626 GGTGGTGGA-TGGTATTC-TACTGGTGAA
1 GGTGG-AGACTGATGCTCATA-AGATGAC
1199653 GGTGGAGACTGATGCTCATAAGATGAC
1 GGTGGAGACTGATGCTCATAAGATGAC
1199680 GGTGG
1 GGTGG
1199685 TGGATGGTAT
Statistics
Matches: 40, Mismatches: 15, Indels: 8
0.63 0.24 0.13
Matches are distributed among these distances:
26 3 0.08
27 33 0.82
28 4 0.10
ACGTcount: A:0.24, C:0.12, G:0.40, T:0.24
Consensus pattern (27 bp):
GGTGGAGACTGATGCTCATAAGATGAC
Found at i:1199687 original size:30 final size:30
Alignment explanation
Indices: 1199653--1199742 Score: 77
Period size: 30 Copynumber: 3.2 Consensus size: 30
1199643 TACTGGTGAA
1199653 GGTGGAGACTGATGCTCATAAGATGACGGT
1 GGTGGAGACTGATGCTCATAAGATGACGGT
* * ** *
1199683 GGTGGATG-GT-AT--TC-T-A-CTGGGGGA
1 GGTGGA-GACTGATGCTCATAAGATGACGGT
1199707 GGTGGAGACTGATGCTCATAAGATGACGGT
1 GGTGGAGACTGATGCTCATAAGATGACGGT
1199737 GGTGGA
1 GGTGGA
1199743 TGGTATTCTG
Statistics
Matches: 42, Mismatches: 10, Indels: 16
0.62 0.15 0.24
Matches are distributed among these distances:
23 1 0.02
24 11 0.26
25 3 0.07
26 1 0.02
27 4 0.10
28 1 0.02
29 3 0.07
30 17 0.40
31 1 0.02
ACGTcount: A:0.23, C:0.11, G:0.41, T:0.24
Consensus pattern (30 bp):
GGTGGAGACTGATGCTCATAAGATGACGGT
Found at i:1199849 original size:54 final size:54
Alignment explanation
Indices: 1199572--1199850 Score: 432
Period size: 54 Copynumber: 5.2 Consensus size: 54
1199562 TGACTCCTTG
* *
1199572 GGTGGTGGATGATATTCTACTGGTGGAGGTGGAGACTGATGCTCAGAAGATGAC
1 GGTGGTGGATGGTATTCTACTGGTGGAGGTGGAGACTGATGCTCATAAGATGAC
*
1199626 GGTGGTGGATGGTATTCTACTGGTGAAGGTGGAGACTGATGCTCATAAGATGAC
1 GGTGGTGGATGGTATTCTACTGGTGGAGGTGGAGACTGATGCTCATAAGATGAC
*
1199680 GGTGGTGGATGGTATTCTACTGGGGGAGGTGGAGACTGATGCTCATAAGATGAC
1 GGTGGTGGATGGTATTCTACTGGTGGAGGTGGAGACTGATGCTCATAAGATGAC
* * **
1199734 GGTGGTGGATGGTATTCTGCTGGTGGAGGTGGAGACTGATGCTCGTAAGATGGT
1 GGTGGTGGATGGTATTCTACTGGTGGAGGTGGAGACTGATGCTCATAAGATGAC
* * * * *
1199788 GGTGGTGGATGGTATTCTACTGGTAGAGGCGGAGACTGATGTTCATTAGTTGAC
1 GGTGGTGGATGGTATTCTACTGGTGGAGGTGGAGACTGATGCTCATAAGATGAC
*
1199842 GGAGGTGGA
1 GGTGGTGGA
1199851 GGGGGGCTTG
Statistics
Matches: 205, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 205 1.00
ACGTcount: A:0.22, C:0.10, G:0.41, T:0.28
Consensus pattern (54 bp):
GGTGGTGGATGGTATTCTACTGGTGGAGGTGGAGACTGATGCTCATAAGATGAC
Found at i:1208395 original size:123 final size:123
Alignment explanation
Indices: 1208176--1208419 Score: 470
Period size: 123 Copynumber: 2.0 Consensus size: 123
1208166 GGTCTGTTTA
1208176 TTTCCAAAATCGTTGGCCCCTTTTGACTGAGCATTATTCTGGACACCAAAACCAAAAGGATTTGG
1 TTTCCAAAATCGTTGGCCCCTTTTGACTGAGCATTATTCTGGACACCAAAACCAAAAGGATTTGG
*
1208241 CTTTTGTTGTTGGTTTGAATTGGATTGAGTGCCAAATCCGAATGCATTAGACTTTGGC
66 CTTTTGTTGTTGGTTTGAATTGGATTGAGTGCCAAATCCAAATGCATTAGACTTTGGC
*
1208299 TTTCCAAAATCGTTGGCCCCTTTTGACTGAGCATTATTCTGGACTCCAAAACCAAAAGGATTTGG
1 TTTCCAAAATCGTTGGCCCCTTTTGACTGAGCATTATTCTGGACACCAAAACCAAAAGGATTTGG
1208364 CTTTTGTTGTTGGTTTGAATTGGATTGAGTGCCAAATCCAAATGCATTAGACTTTG
66 CTTTTGTTGTTGGTTTGAATTGGATTGAGTGCCAAATCCAAATGCATTAGACTTTG
1208420 ACTGTTGCGG
Statistics
Matches: 119, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
123 119 1.00
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.35
Consensus pattern (123 bp):
TTTCCAAAATCGTTGGCCCCTTTTGACTGAGCATTATTCTGGACACCAAAACCAAAAGGATTTGG
CTTTTGTTGTTGGTTTGAATTGGATTGAGTGCCAAATCCAAATGCATTAGACTTTGGC
Found at i:1217399 original size:10 final size:10
Alignment explanation
Indices: 1217384--1217411 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1217374 TTTACACTAT
1217384 TAAAATGTTG
1 TAAAATGTTG
1217394 TAAAATGTTG
1 TAAAATGTTG
1217404 TAAAATGT
1 TAAAATGT
1217412 AGACTTGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.18, T:0.39
Consensus pattern (10 bp):
TAAAATGTTG
Found at i:1220712 original size:17 final size:18
Alignment explanation
Indices: 1220680--1220730 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 18
1220670 AATAAAGATA
* *
1220680 AAAAAAATAAGTAAAA-T
1 AAAAATATAAGAAAAAGT
*
1220697 GAAAATATAAGAAAAAGT
1 AAAAATATAAGAAAAAGT
*
1220715 AAAAATA-AAGACAAAG
1 AAAAATATAAGAAAAAG
1220731 AGAATAGAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
17 21 0.75
18 7 0.25
ACGTcount: A:0.73, C:0.02, G:0.12, T:0.14
Consensus pattern (18 bp):
AAAAATATAAGAAAAAGT
Found at i:1222550 original size:99 final size:99
Alignment explanation
Indices: 1222414--1222612 Score: 344
Period size: 99 Copynumber: 2.0 Consensus size: 99
1222404 GAAATTGTTT
* * * *
1222414 GTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTC
1 GTTGACAGTCAGCCGCCCCTTCGCTGTGAAATTGAGCTTGTGCTATCTTGAGTCCAACATCCTTC
*
1222479 GTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA
66 GTTGTGAAGTTGAAATTGGCTATGAAATTGGGAA
*
1222513 GTTGACATTCAGCCGCCCCTTCGCTGTGAAATTGAGCTTGTGCTATCTTGAGTCCAACATCCTTC
1 GTTGACAGTCAGCCGCCCCTTCGCTGTGAAATTGAGCTTGTGCTATCTTGAGTCCAACATCCTTC
1222578 GTTGTGAAGTTGAAATTGGCTATGAAATTGGGAA
66 GTTGTGAAGTTGAAATTGGCTATGAAATTGGGAA
1222612 G
1 G
1222613 CCCCTTCGTC
Statistics
Matches: 94, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
99 94 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.33
Consensus pattern (99 bp):
GTTGACAGTCAGCCGCCCCTTCGCTGTGAAATTGAGCTTGTGCTATCTTGAGTCCAACATCCTTC
GTTGTGAAGTTGAAATTGGCTATGAAATTGGGAA
Found at i:1223722 original size:8 final size:7
Alignment explanation
Indices: 1223700--1223745 Score: 65
Period size: 8 Copynumber: 6.1 Consensus size: 7
1223690 CTTATTTTTC
1223700 TTTTCTT
1 TTTTCTT
1223707 TTTTCTT
1 TTTTCTT
1223714 TTGTTCTT
1 TT-TTCTT
1223722 TTGTTCTT
1 TT-TTCTT
1223730 TTTTCTCT
1 TTTTCT-T
1223738 TTTTCTT
1 TTTTCTT
1223745 T
1 T
1223746 CTTCAATTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
7 15 0.41
8 22 0.59
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.80
Consensus pattern (7 bp):
TTTTCTT
Found at i:1223722 original size:15 final size:14
Alignment explanation
Indices: 1223700--1223745 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 14
1223690 CTTATTTTTC
1223700 TTTTCTTTTTTCTT
1 TTTTCTTTTTTCTT
1223714 TTGTTCTTTTGTTCTT
1 TT-TTCTTTT-TTCTT
1223730 TTTTCTCTTTTTCTT
1 TTTTCT-TTTTTCTT
1223745 T
1 T
1223746 CTTCAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
14 2 0.07
15 17 0.59
16 10 0.34
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.80
Consensus pattern (14 bp):
TTTTCTTTTTTCTT
Found at i:1223731 original size:23 final size:23
Alignment explanation
Indices: 1223702--1223745 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
1223692 TATTTTTCTT
1223702 TTCTTTTTTCT-TTTGTTCTTTTG
1 TTCTTTTTTCTCTTT-TTCTTTTG
1223725 TTCTTTTTTCTCTTTTTCTTT
1 TTCTTTTTTCTCTTTTTCTTT
1223746 CTTCAATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.80
Consensus pattern (23 bp):
TTCTTTTTTCTCTTTTTCTTTTG
Found at i:1234214 original size:23 final size:23
Alignment explanation
Indices: 1234175--1234236 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 23
1234165 TAACACTAAT
1234175 AATAA-TAAAGATAAAAAAAATAA-
1 AATAAGTAAA-AT-AAAAAAATAAG
* *
1234198 AATAAGTAAAATGAAAATATAAG
1 AATAAGTAAAATAAAAAAATAAG
*
1234221 AAAAAGTAAAAATAAA
1 AATAAGT-AAAATAAA
1234237 GACAAAGAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
22 8 0.25
23 13 0.41
24 11 0.34
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (23 bp):
AATAAGTAAAATAAAAAAATAAG
Found at i:1237269 original size:16 final size:15
Alignment explanation
Indices: 1237248--1237279 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
1237238 TTTGTTCCTA
1237248 TCTCTCTCCGAATCTG
1 TCTCTCTCCG-ATCTG
1237264 TCTCTCTCCGATCTG
1 TCTCTCTCCGATCTG
1237279 T
1 T
1237280 AACCATAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.09, C:0.38, G:0.12, T:0.41
Consensus pattern (15 bp):
TCTCTCTCCGATCTG
Found at i:1242578 original size:16 final size:16
Alignment explanation
Indices: 1242557--1242587 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1242547 AGTTGGTCTG
1242557 AAGGCCGTGCAACTCA
1 AAGGCCGTGCAACTCA
1242573 AAGGCCGTGCAACTC
1 AAGGCCGTGCAACTC
1242588 TTTCGTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.32, G:0.26, T:0.13
Consensus pattern (16 bp):
AAGGCCGTGCAACTCA
Found at i:1262342 original size:11 final size:11
Alignment explanation
Indices: 1262326--1262384 Score: 66
Period size: 11 Copynumber: 5.5 Consensus size: 11
1262316 TGTTTTTTTT
1262326 AAATACAATTA
1 AAATACAATTA
1262337 AAATACAATTA
1 AAATACAATTA
* *
1262348 AAAAATAATTA
1 AAATACAATTA
*
1262359 AAATTCAA-TA
1 AAATACAATTA
* *
1262369 AAATTCAATAA
1 AAATACAATTA
1262380 AAATA
1 AAATA
1262385 TAATGTAATG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
10 10 0.25
11 30 0.75
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (11 bp):
AAATACAATTA
Found at i:1262370 original size:10 final size:10
Alignment explanation
Indices: 1262357--1262381 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1262347 AAAAAATAAT
1262357 TAAAATTCAA
1 TAAAATTCAA
1262367 TAAAATTCAA
1 TAAAATTCAA
1262377 TAAAA
1 TAAAA
1262382 ATATAATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (10 bp):
TAAAATTCAA
Found at i:1262388 original size:32 final size:33
Alignment explanation
Indices: 1262326--1262388 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 33
1262316 TGTTTTTTTT
1262326 AAATACAATTAAAATACAATTAAAAAATAATTA
1 AAATACAATTAAAATACAATTAAAAAATAATTA
* *
1262359 AAATTCAA-TAAAATTCAA-TAAAAATATAAT
1 AAATACAATTAAAATACAATTAAAAA-ATAAT
1262389 GTAATGCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 6 0.22
32 14 0.52
33 7 0.26
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (33 bp):
AAATACAATTAAAATACAATTAAAAAATAATTA
Found at i:1262523 original size:30 final size:26
Alignment explanation
Indices: 1262451--1262523 Score: 67
Period size: 26 Copynumber: 2.6 Consensus size: 26
1262441 TTTTAAAAAA
*
1262451 TATTAAATAAATATTAAAATTTAATTT
1 TATTAAA-AAATAATAAAATTTAATTT
*
1262478 TA-TCAAAAATGAATAAACATTATTAATTGT
1 TATTAAAAAAT-AATAAA-A-T-TTAATT-T
1262508 TATTAAAAAATAATAA
1 TATTAAAAAATAATAA
1262524 TTAATGAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
25 4 0.11
26 8 0.22
27 3 0.08
28 1 0.03
29 6 0.16
30 8 0.22
31 7 0.19
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (26 bp):
TATTAAAAAATAATAAAATTTAATTT
Found at i:1263588 original size:18 final size:18
Alignment explanation
Indices: 1263555--1263597 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
1263545 TAAAGAGGTG
1263555 ATATTTTTTAGCTTTACATT
1 ATATTTTTTA-CTTTA-ATT
1263575 ATATTTTTTA-TTTAATT
1 ATATTTTTTACTTTAATT
*
1263592 TTATTT
1 ATATTT
1263598 ATTTTTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 8 0.36
18 4 0.18
20 10 0.45
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (18 bp):
ATATTTTTTACTTTAATT
Found at i:1263600 original size:21 final size:20
Alignment explanation
Indices: 1263576--1263635 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
1263566 CTTTACATTA
*
1263576 TATTTTTTATTTAATTTTATT
1 TATTTTTTATTTATTTTTA-T
* *
1263597 TATTTTTAATTCATTTTTAT
1 TATTTTTTATTTATTTTTAT
*
1263617 TATATATTTATTTATTTTT
1 TAT-TTTTTATTTATTTTT
1263636 TAAAAAAATG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 4 0.12
21 28 0.88
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (20 bp):
TATTTTTTATTTATTTTTAT
Found at i:1263637 original size:11 final size:11
Alignment explanation
Indices: 1263576--1263637 Score: 58
Period size: 11 Copynumber: 5.8 Consensus size: 11
1263566 CTTTACATTA
1263576 TATTTTTTATT
1 TATTTTTTATT
*
1263587 TA-ATTTTATT
1 TATTTTTTATT
*
1263597 TATTTTTAATT
1 TATTTTTTATT
*
1263608 CA-TTTTTA-T
1 TATTTTTTATT
*
1263617 TATATATTTATT
1 TAT-TTTTTATT
1263629 TATTTTTTA
1 TATTTTTTA
1263638 AAAAAATGAA
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
9 2 0.05
10 14 0.36
11 19 0.49
12 4 0.10
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.73
Consensus pattern (11 bp):
TATTTTTTATT
Found at i:1268566 original size:209 final size:209
Alignment explanation
Indices: 1268206--1268832 Score: 1220
Period size: 209 Copynumber: 3.0 Consensus size: 209
1268196 ATTTGTTGAA
*
1268206 CAGGTTAATGTGGAAAACAACACCAATCACTCTTCTTTTTCTGGTTTCTATGATTCCTTTCCTTG
1 CAGGTTAATGTGGAAAACAACACCAATCACTCTGCTTTTTCTGGTTTCTATGATTCCTTTCCTTG
1268271 ATCCCCCGGGTGTGCTCGCCTTCCATTGGAGCTTCAACAATACATCGGCAATCCTCTTATCAGCT
66 ATCCCCCGGGTGTGCTCGCCTTCCATTGGAGCTTCAACAATACATCGGCAATCCTCTTATCAGCT
1268336 TTTCTCGGCTTCTTGCTTCAGTGGTCGGGAGCTTTGCACTTGGGTAATACATCTTTTCTCCGCTT
131 TTTCTCGGCTTCTTGCTTCAGTGGTCGGGAGCTTTGCACTTGGGTAATACATCTTTTCTCCGCTT
1268401 TTTGTATGCTTGTC
196 TTTGTATGCTTGTC
* *
1268415 CAGGTTAATGTGGAAAACAACACCAGTCACTCTGCTTTTTCTGGCTTCTATGATTCCTTTCCTTG
1 CAGGTTAATGTGGAAAACAACACCAATCACTCTGCTTTTTCTGGTTTCTATGATTCCTTTCCTTG
1268480 ATCCCCCGGGTGTGCTCGCCTTCCATTGGAGCTTCAACAATACATCGGCAATCCTCTTATCAGCT
66 ATCCCCCGGGTGTGCTCGCCTTCCATTGGAGCTTCAACAATACATCGGCAATCCTCTTATCAGCT
1268545 TTTCTCGGCTTCTTGCTTCAGTGGTCGGGAGCTTTGCACTTGGGTAATACATCTTTTCTCCGCTT
131 TTTCTCGGCTTCTTGCTTCAGTGGTCGGGAGCTTTGCACTTGGGTAATACATCTTTTCTCCGCTT
1268610 TTTGTATGCTTGTC
196 TTTGTATGCTTGTC
1268624 CAGGTTAATGTGGAAAACAACACCAATCACTCTGCTTTTTCTGGTTTCTATGATTCCTTTCCTTG
1 CAGGTTAATGTGGAAAACAACACCAATCACTCTGCTTTTTCTGGTTTCTATGATTCCTTTCCTTG
1268689 AT-CCCCGGGTGTGCTCGCCTTCCATTGGAGCTTCAACAATACATCGGCAATCCTCTTATCAGCT
66 ATCCCCCGGGTGTGCTCGCCTTCCATTGGAGCTTCAACAATACATCGGCAATCCTCTTATCAGCT
1268753 TTTCTCGGCTTCTTGCTTCAGTGGTCGGGAGCTTTGCACTTGGGTAATACATCTTTTCTCCGCTT
131 TTTCTCGGCTTCTTGCTTCAGTGGTCGGGAGCTTTGCACTTGGGTAATACATCTTTTCTCCGCTT
1268818 TTTGTATGCTTGTC
196 TTTGTATGCTTGTC
1268832 C
1 C
1268833 TGCCTGGCCA
Statistics
Matches: 413, Mismatches: 5, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
208 142 0.34
209 271 0.66
ACGTcount: A:0.17, C:0.26, G:0.19, T:0.37
Consensus pattern (209 bp):
CAGGTTAATGTGGAAAACAACACCAATCACTCTGCTTTTTCTGGTTTCTATGATTCCTTTCCTTG
ATCCCCCGGGTGTGCTCGCCTTCCATTGGAGCTTCAACAATACATCGGCAATCCTCTTATCAGCT
TTTCTCGGCTTCTTGCTTCAGTGGTCGGGAGCTTTGCACTTGGGTAATACATCTTTTCTCCGCTT
TTTGTATGCTTGTC
Found at i:1272015 original size:8 final size:8
Alignment explanation
Indices: 1272002--1272029 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
1271992 GATTAAAGTA
1272002 TAATAGTT
1 TAATAGTT
1272010 TAATAGTT
1 TAATAGTT
1272018 TAATAGTT
1 TAATAGTT
1272026 TAAT
1 TAAT
1272030 GATTTATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (8 bp):
TAATAGTT
Found at i:1272234 original size:11 final size:12
Alignment explanation
Indices: 1272212--1272240 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
1272202 AAATGGATTT
1272212 TTAAGTGAAAGC
1 TTAAGTGAAAGC
1272224 TTAAG-GAAAGC
1 TTAAGTGAAAGC
1272235 TTAAGT
1 TTAAGT
1272241 TATCTTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.41, C:0.07, G:0.24, T:0.28
Consensus pattern (12 bp):
TTAAGTGAAAGC
Found at i:1273965 original size:31 final size:31
Alignment explanation
Indices: 1273927--1274022 Score: 97
Period size: 31 Copynumber: 3.1 Consensus size: 31
1273917 AGAGTCGAGG
1273927 GTTTACCTATGTCTTTCGAGACATATGGACA
1 GTTTACCTATGTCTTTCGAGACATATGGACA
***
1273958 GTTTACCTATGTTCTAAGGA-ACATATGGACA
1 GTTTACCTATG-TCTTTCGAGACATATGGACA
* * * *
1273989 ATTTACCTAGGT-TCTTCGGGACCTATGGACA
1 GTTTACCTATGTCT-TTCGAGACATATGGACA
1274020 GTT
1 GTT
1274023 GTCGAGGTTC
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
29 1 0.02
30 2 0.04
31 43 0.84
32 5 0.10
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTCTTTCGAGACATATGGACA
Found at i:1275711 original size:23 final size:23
Alignment explanation
Indices: 1275678--1275745 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
1275668 ATTATTATAT
1275678 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
1275701 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
1275724 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
1275746 AGCTGTGGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:1282604 original size:23 final size:23
Alignment explanation
Indices: 1282571--1282638 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
1282561 ATTATTATAT
*
1282571 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
1282594 GGCACTCCGGTGCAATTATACGT
1 GGCACTACGGTGCAATTATACGC
*
1282617 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
1282639 AGCTGTGGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.22, C:0.26, G:0.26, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:1284012 original size:19 final size:21
Alignment explanation
Indices: 1283965--1284016 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
1283955 GTATTGTTCA
**
1283965 TCACTGTTCATACGGTATTGT
1 TCACTGTTCATACCATATTGT
1283986 TCACTGTTCATACCATATT-T
1 TCACTGTTCATACCATATTGT
1284006 T-ACTGTTCATA
1 TCACTGTTCATA
1284017 AAACATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 10 0.34
20 2 0.07
21 17 0.59
ACGTcount: A:0.23, C:0.21, G:0.12, T:0.44
Consensus pattern (21 bp):
TCACTGTTCATACCATATTGT
Found at i:1285911 original size:32 final size:32
Alignment explanation
Indices: 1285874--1285944 Score: 142
Period size: 32 Copynumber: 2.2 Consensus size: 32
1285864 GATTCAAGAA
1285874 CACATTAAGGGCGTGTTTGGTTCAAGTCATCT
1 CACATTAAGGGCGTGTTTGGTTCAAGTCATCT
1285906 CACATTAAGGGCGTGTTTGGTTCAAGTCATCT
1 CACATTAAGGGCGTGTTTGGTTCAAGTCATCT
1285938 CACATTA
1 CACATTA
1285945 TCGGGGGAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.34
Consensus pattern (32 bp):
CACATTAAGGGCGTGTTTGGTTCAAGTCATCT
Found at i:1286371 original size:11 final size:11
Alignment explanation
Indices: 1286357--1286382 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1286347 TATATAAATT
1286357 AATTATAGTAG
1 AATTATAGTAG
1286368 AATTATAGTAG
1 AATTATAGTAG
1286379 AATT
1 AATT
1286383 CAACTTGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (11 bp):
AATTATAGTAG
Found at i:1287073 original size:12 final size:12
Alignment explanation
Indices: 1287056--1287106 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
1287046 TTCAAAGAGG
1287056 TTTTATATTTAA
1 TTTTATATTTAA
1287068 TTTTATA-TTATA
1 TTTTATATTTA-A
*
1287080 TTTGAT-TTTAA
1 TTTTATATTTAA
1287091 TTTTA-ATATTAA
1 TTTTATAT-TTAA
1287103 TTTT
1 TTTT
1287107 TTAAATAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
11 9 0.27
12 24 0.73
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (12 bp):
TTTTATATTTAA
Found at i:1287122 original size:24 final size:27
Alignment explanation
Indices: 1287089--1287222 Score: 94
Period size: 24 Copynumber: 4.7 Consensus size: 27
1287079 ATTTGATTTT
*
1287089 AATTTTAATATTAATTTTTTAA-A-TA
1 AATTATAATATTAATTTTTTAATATTA
*
1287114 AATTA-AATATTACTTTTTTAATATTA
1 AATTATAATATTAATTTTTTAATATTA
* *
1287140 TATTATAGATATTAATTTTAATAATAATTTTTA
1 AATTATA-ATATTAATTTT--T--TAA-TATTA
*
1287173 AATAAATTAAATATTAATTTTTTAATATTA
1 AAT-TA-T-AATATTAATTTTTTAATATTA
*
1287203 TATTATAGATATTTAATTTT
1 AATTATA-ATA-TTAATTTT
1287223 ATATCATATA
Statistics
Matches: 85, Mismatches: 10, Indels: 24
0.71 0.08 0.20
Matches are distributed among these distances:
24 15 0.18
25 5 0.06
26 6 0.07
27 2 0.02
28 14 0.16
29 9 0.11
30 7 0.08
31 3 0.04
32 3 0.04
33 7 0.08
34 1 0.01
35 12 0.14
36 1 0.01
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (27 bp):
AATTATAATATTAATTTTTTAATATTA
Found at i:1287169 original size:12 final size:12
Alignment explanation
Indices: 1287064--1287223 Score: 71
Period size: 14 Copynumber: 12.8 Consensus size: 12
1287054 GGTTTTATAT
1287064 TTAATTTT-ATA
1 TTAATTTTAATA
* *
1287075 TT-ATATTTGATT
1 TTAAT-TTTAATA
1287087 TTAATTTTAATA
1 TTAATTTTAATA
1287099 TTAATTTTTTAA-A
1 TTAA--TTTTAATA
* *
1287112 -TAAATTAAATA
1 TTAATTTTAATA
*
1287123 TTACTTTTTTAATA
1 TTA--ATTTTAATA
*
1287137 TTATATTATAGATA
1 TTA-ATTTTA-ATA
1287151 TTAATTTTAATA
1 TTAATTTTAATA
*
1287163 ATAATTTTTAA-A
1 TTAA-TTTTAATA
* *
1287175 -TAAATTAAATA
1 TTAATTTTAATA
1287186 TTAATTTTTTAATA
1 TTAA--TTTTAATA
*
1287200 TTATATTATAGATA
1 TTA-ATTTTA-ATA
1287214 TTTAATTTTA
1 -TTAATTTTA
1287224 TATCATATAA
Statistics
Matches: 113, Mismatches: 18, Indels: 33
0.69 0.11 0.20
Matches are distributed among these distances:
10 10 0.09
11 10 0.09
12 28 0.25
13 23 0.20
14 38 0.34
15 4 0.04
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (12 bp):
TTAATTTTAATA
Found at i:1287194 original size:63 final size:64
Alignment explanation
Indices: 1287068--1287223 Score: 248
Period size: 63 Copynumber: 2.5 Consensus size: 64
1287058 TTATATTTAA
* * *
1287068 TTTT-ATATTATATT-T-GATTTTAATTTTAATATTAATTTTTTAAATAAATTAAATATTACTT
1 TTTTAATATTATATTATAGATATTAATTTTAATAATAATTTTTTAAATAAATTAAATATTAATT
1287129 TTTTAATATTATATTATAGATATTAATTTTAATAATAA-TTTTTAAATAAATTAAATATTAATT
1 TTTTAATATTATATTATAGATATTAATTTTAATAATAATTTTTTAAATAAATTAAATATTAATT
1287192 TTTTAATATTATATTATAGATATTTAATTTTA
1 TTTTAATATTATATTATAGATA-TTAATTTTA
1287224 TATCATATAA
Statistics
Matches: 88, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
61 4 0.05
62 10 0.11
63 47 0.53
64 27 0.31
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (64 bp):
TTTTAATATTATATTATAGATATTAATTTTAATAATAATTTTTTAAATAAATTAAATATTAATT
Found at i:1287783 original size:31 final size:31
Alignment explanation
Indices: 1287746--1287806 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
1287736 GTAGTTGTAT
* *
1287746 AAATTATTTAAATTTCAGTATTGTAAAACTA
1 AAATTATTTAAATCTCAGTATTGCAAAACTA
1287777 AAATTATTTAAATCTCAGTATTGCAAAACT
1 AAATTATTTAAATCTCAGTATTGCAAAACT
1287807 CTTTTAAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.39
Consensus pattern (31 bp):
AAATTATTTAAATCTCAGTATTGCAAAACTA
Found at i:1292566 original size:60 final size:60
Alignment explanation
Indices: 1292502--1292620 Score: 159
Period size: 60 Copynumber: 2.0 Consensus size: 60
1292492 TGTTAAATCG
* * * * *
1292502 GTCCTTAAACTTTTAGATATTTTAATTCCATCCTTGAACTATGA-ATCTCATTCTAAATTA
1 GTCCTTAAACTTTTAAACATTCTAATTCCATCCCTAAACTATGATA-CTCATTCTAAATTA
* *
1292562 GTCCTTAAACTTTTAAACATTCTAATTTCATCCCTAAACTATGATACTCTTTCTAAATT
1 GTCCTTAAACTTTTAAACATTCTAATTCCATCCCTAAACTATGATACTCATTCTAAATT
1292621 GATCCCCAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 50 0.98
61 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (60 bp):
GTCCTTAAACTTTTAAACATTCTAATTCCATCCCTAAACTATGATACTCATTCTAAATTA
Found at i:1292846 original size:31 final size:31
Alignment explanation
Indices: 1292810--1292910 Score: 91
Period size: 31 Copynumber: 3.3 Consensus size: 31
1292800 ATGTTCAAAA
*
1292810 AGTTTGGGGACCAATTTAGAATGTATGTCAT
1 AGTTTGGGGACTAATTTAGAATGTATGTCAT
* ** * *
1292841 AGTTTGGGGATTAAAATAAAATG--T-TCAAA
1 AGTTTGGGGACTAATTTAGAATGTATGTC-AT
* *
1292870 AGTTTGAGTACTAATTTAGAATGTATGTCAT
1 AGTTTGGGGACTAATTTAGAATGTATGTCAT
*
1292901 AGTTTAGGGA
1 AGTTTGGGGA
1292911 TGAAATTGGA
Statistics
Matches: 50, Mismatches: 16, Indels: 8
0.68 0.22 0.11
Matches are distributed among these distances:
28 2 0.04
29 19 0.38
31 27 0.54
32 2 0.04
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.36
Consensus pattern (31 bp):
AGTTTGGGGACTAATTTAGAATGTATGTCAT
Found at i:1292946 original size:60 final size:59
Alignment explanation
Indices: 1292779--1292947 Score: 155
Period size: 60 Copynumber: 2.8 Consensus size: 59
1292769 GTTTATACGT
** * * *
1292779 ATAGTTTGGGATGAAATTGGAATGTTCAAAAAGTTTGGGGACCAATTTAGAATGTATGTC
1 ATAGTTTGGGATGAAATTGGAAAATTTAAAAA-TGTAGGGACCAATTTAGAATGTATGTC
* * * * * *
1292839 ATAGTTTGGGGATTAAAAT--AAAATGTTCAAAA-GTTTGAGTACTAATTTAGAATGTATGTC
1 ATAGTTT-GGGATGAAATTGGAAAAT-TTAAAAATG-TAG-GGACCAATTTAGAATGTATGTC
*
1292899 ATAGTTTAGGGATGAAATTGGAACATTTAAAAATGTAGGGACCAATTTA
1 ATAGTTT-GGGATGAAATTGGAAAATTTAAAAATGTAGGGACCAATTTA
1292948 AAACAAAGGT
Statistics
Matches: 84, Mismatches: 18, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
59 5 0.06
60 57 0.68
61 17 0.20
62 5 0.06
ACGTcount: A:0.37, C:0.06, G:0.23, T:0.34
Consensus pattern (59 bp):
ATAGTTTGGGATGAAATTGGAAAATTTAAAAATGTAGGGACCAATTTAGAATGTATGTC
Found at i:1293855 original size:13 final size:14
Alignment explanation
Indices: 1293839--1293868 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1293829 AAATTGATTA
1293839 TTTAATTT-AATAT
1 TTTAATTTAAATAT
1293852 TTTAATTTAAATAT
1 TTTAATTTAAATAT
1293866 TTT
1 TTT
1293869 CAAATTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTAATTTAAATAT
Found at i:1295396 original size:18 final size:17
Alignment explanation
Indices: 1295361--1295412 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 17
1295351 TTTATTTGAA
*
1295361 AAATAATATATACGTAT
1 AAATAATATATACATAT
*
1295378 AAATAA-ATATATATAT
1 AAATAATATATACATAT
* *
1295394 ATATATATATATCCATAT
1 AAATA-ATATATACATAT
1295412 A
1 A
1295413 TTAATATTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
16 12 0.43
17 7 0.25
18 9 0.32
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (17 bp):
AAATAATATATACATAT
Found at i:1311433 original size:152 final size:144
Alignment explanation
Indices: 1311225--1311513 Score: 416
Period size: 152 Copynumber: 2.0 Consensus size: 144
1311215 TTGGATTCGG
* *
1311225 GTTTTAAAGCTCTTAGGTTGGTAATTGGACACGTTTTAGGATGGATTAACAAGTTGAACATGAAG
1 GTTTTAAAGCTCTTAGATTGGTAATTGGACACGTTTTAGGACGGATTAACAAGTTGAACATGAAG
* *
1311290 CATTTGTTGATCTACTATCTACTTTTATATTCGTAAAGCACGAGTGTTCTTCAAATGTGAGTTTA
66 CATTTGTTGATC-A--A--T--TTTTATATTCGTAAAGCACGAGTATTCTTCAAATGTCAGTTTA
* *
1311355 TGTTTATAGTGAATGATTGTA
124 TGATTACAGTGAATGATTGTA
* * *
1311376 GTTTTAAAGCTCTTTTGATTGGTAATTGGACATGTTTTAGGACGGATTAGCAAGTTGAACATGAA
1 GTTTTAAAGCTC-TTAGATTGGTAATTGGACACGTTTTAGGACGGATTAACAAGTTGAACATGAA
*
1311441 GCATTTGTTGATCAATTTTTATATTCGTAAATCACGAGTATTCTTCAAATGTCAGTTTATGATTA
65 GCATTTGTTGATCAATTTTTATATTCGTAAAGCACGAGTATTCTTCAAATGTCAGTTTATGATTA
1311506 CAGTGAAT
130 CAGTGAAT
1311514 ATGGTCTATC
Statistics
Matches: 127, Mismatches: 10, Indels: 8
0.88 0.07 0.06
Matches are distributed among these distances:
145 52 0.41
147 1 0.01
149 1 0.01
151 13 0.10
152 60 0.47
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (144 bp):
GTTTTAAAGCTCTTAGATTGGTAATTGGACACGTTTTAGGACGGATTAACAAGTTGAACATGAAG
CATTTGTTGATCAATTTTTATATTCGTAAAGCACGAGTATTCTTCAAATGTCAGTTTATGATTAC
AGTGAATGATTGTA
Found at i:1316016 original size:15 final size:15
Alignment explanation
Indices: 1315996--1316026 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1315986 TATTTTGATC
1315996 ACTCATCCTTAAAAA
1 ACTCATCCTTAAAAA
1316011 ACTCATCCTTAAAAA
1 ACTCATCCTTAAAAA
1316026 A
1 A
1316027 TTAAAAGTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (15 bp):
ACTCATCCTTAAAAA
Found at i:1317821 original size:2 final size:2
Alignment explanation
Indices: 1317814--1317839 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1317804 AGTTTGAATA
1317814 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
1317840 TTATTGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1319538 original size:69 final size:65
Alignment explanation
Indices: 1319447--1319604 Score: 192
Period size: 65 Copynumber: 2.4 Consensus size: 65
1319437 CGATTAACGG
*
1319447 TCAAAT-AATTTCGGTTCGATTAATAGTTAAAGAAAAAAAATCGGTTGATTTGGTTCAGTTAATA
1 TCAAATAAATTTCGGTTCGATTAATAGTTAAAGAAAAAAAAT---TT-ATTTGATTCAGTTAATA
1319511 ATTT
62 ATTT
* * ** * * *
1319515 TCAAATAAATTTTGGTTTGATTAACGGTTAAAGAAAAATAATTTATTTTATTCGGTTAATAATTT
1 TCAAATAAATTTCGGTTCGATTAATAGTTAAAGAAAAAAAATTTATTTGATTCAGTTAATAATTT
*
1319580 TCAAATAAATTTGGGTTCGATTAAT
1 TCAAATAAATTTCGGTTCGATTAAT
1319605 GGTCAAATAA
Statistics
Matches: 78, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
65 40 0.51
66 2 0.03
68 6 0.08
69 30 0.38
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.41
Consensus pattern (65 bp):
TCAAATAAATTTCGGTTCGATTAATAGTTAAAGAAAAAAAATTTATTTGATTCAGTTAATAATTT
Found at i:1319597 original size:95 final size:91
Alignment explanation
Indices: 1319515--1319876 Score: 381
Period size: 95 Copynumber: 4.0 Consensus size: 91
1319505 TTAATAATTT
* * * *
1319515 TCAAATAAATTTTGGTTTGATTAACGGTTAAAGAAAAATAAT-TT-ATTTTATTCGGTTAATAAT
1 TCAAAT-AATTTCGGTTCGATTAA-TGTTAAAGAAAAA-AATGTTAATTTGATTCGGTTAATAAT
*
1319578 TTTCAAATAAATTTGGGTTCGATTAATGG
63 TTTCAAATAAATTTGGGTTCGAATAATGG
*
1319607 TCAAATAATTTCAGTTCGATTAATTGTTAAAG---AAAA----AA-TT--TT-GGTTAATAATTT
1 TCAAATAATTTCGGTTCGATTAA-TGTTAAAGAAAAAAATGTTAATTTGATTCGGTTAATAATTT
* **
1319661 TCAAATAAATTTGGGTTCGATTAACAG
65 TCAAATAAATTTGGGTTCGAATAATGG
*
1319688 TCAAATAATTTCGGTTCGATTAATGTTAAAGAAAAAAAATTTGGTTAATTTGGTTCGGTTAATAA
1 TCAAATAATTTCGGTTCGATTAATGTTAAAG-AAAAAAA--T-GTTAATTTGATTCGGTTAATAA
* ** * *
1319753 TTTTCAAATAAATCTAAGTTCGATTAACGG
62 TTTTCAAATAAATTTGGGTTCGAATAATGG
*
1319783 TCAAATAATTTCGGTTGGATTAATGTTAAAGAAAAAAATCGGTTAATTTGATTCGGTTAATAATT
1 TCAAATAATTTCGGTTCGATTAATGTTAAAGAAAAAAAT--GTTAATTTGATTCGGTTAATAATT
* *
1319848 TTCAAATAAATTTCGGTTCGATTAATGG
64 TTCAAATAAATTTGGGTTCGAATAATGG
1319876 T
1 T
1319877 TAAAGAAAAA
Statistics
Matches: 235, Mismatches: 18, Indels: 33
0.82 0.06 0.12
Matches are distributed among these distances:
80 8 0.03
81 59 0.25
82 2 0.01
84 6 0.03
85 1 0.00
87 2 0.01
88 2 0.01
91 23 0.10
92 9 0.04
93 49 0.21
94 9 0.04
95 65 0.28
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.40
Consensus pattern (91 bp):
TCAAATAATTTCGGTTCGATTAATGTTAAAGAAAAAAATGTTAATTTGATTCGGTTAATAATTTT
CAAATAAATTTGGGTTCGAATAATGG
Found at i:1319604 original size:27 final size:27
Alignment explanation
Indices: 1319574--1319711 Score: 113
Period size: 26 Copynumber: 5.1 Consensus size: 27
1319564 ATTCGGTTAA
*
1319574 TAATTTTCAAATAAATTTGGGTTCGAT
1 TAATTTTCAAATAAATTTCGGTTCGAT
** *
1319601 TAATGGTCAAAT-AATTTCAGTTCGAT
1 TAATTTTCAAATAAATTTCGGTTCGAT
* * * *
1319627 TAATTGTTAAAGAAAAAATTTTGGTT--AA
1 TAATT-TT-CA-AATAAATTTCGGTTCGAT
*
1319655 TAATTTTCAAATAAATTTGGGTTCGAT
1 TAATTTTCAAATAAATTTCGGTTCGAT
***
1319682 TAACAGTCAAAT-AATTTCGGTTCGAT
1 TAATTTTCAAATAAATTTCGGTTCGAT
1319708 TAAT
1 TAAT
1319712 GTTAAAGAAA
Statistics
Matches: 85, Mismatches: 20, Indels: 13
0.72 0.17 0.11
Matches are distributed among these distances:
25 12 0.14
26 33 0.39
27 23 0.27
28 7 0.08
29 2 0.02
30 8 0.09
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (27 bp):
TAATTTTCAAATAAATTTCGGTTCGAT
Found at i:1319705 original size:81 final size:81
Alignment explanation
Indices: 1319568--1319736 Score: 286
Period size: 81 Copynumber: 2.1 Consensus size: 81
1319558 TATTTTATTC
**
1319568 GGTTAATAATTTTCAAATAAATTTGGGTTCGATTAATGGTCAAATAATTTCAGTTCGATTAATTG
1 GGTTAATAATTTTCAAATAAATTTGGGTTCGATTAACAGTCAAATAATTTCAGTTCGATTAA-TG
*
1319633 TTAAAG-AAAAAATTTT
65 TTAAAGAAAAAAAATTT
*
1319649 GGTTAATAATTTTCAAATAAATTTGGGTTCGATTAACAGTCAAATAATTTCGGTTCGATTAATGT
1 GGTTAATAATTTTCAAATAAATTTGGGTTCGATTAACAGTCAAATAATTTCAGTTCGATTAATGT
1319714 TAAAGAAAAAAAATTT
66 TAAAGAAAAAAAATTT
1319730 GGTTAAT
1 GGTTAAT
1319737 TTGGTTCGGT
Statistics
Matches: 83, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
80 8 0.10
81 75 0.90
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (81 bp):
GGTTAATAATTTTCAAATAAATTTGGGTTCGATTAACAGTCAAATAATTTCAGTTCGATTAATGT
TAAAGAAAAAAAATTT
Found at i:1319912 original size:24 final size:24
Alignment explanation
Indices: 1319833--1319913 Score: 72
Period size: 25 Copynumber: 3.1 Consensus size: 24
1319823 GGTTAATTTG
1319833 ATTCGGTTAATAATTTTCAAATAA
1 ATTCGGTTAATAATTTTCAAATAA
* ** *
1319857 ATTTCGGTTCGATTAATGGTTAAAGAAAAA
1 A-TTCGGTT--AATAAT--TTTCA-AATAA
1319887 ATTCGGTTAATAATTTTCAAATAA
1 ATTCGGTTAATAATTTTCAAATAA
1319911 ATT
1 ATT
1319914 ATTTTTTCCT
Statistics
Matches: 43, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
24 8 0.19
25 10 0.23
27 10 0.23
29 10 0.23
30 5 0.12
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.40
Consensus pattern (24 bp):
ATTCGGTTAATAATTTTCAAATAA
Found at i:1321603 original size:39 final size:40
Alignment explanation
Indices: 1321560--1321643 Score: 100
Period size: 39 Copynumber: 2.1 Consensus size: 40
1321550 AGTTAAATAT
* *
1321560 GAAGACT-ACACGATTGTATGACGTATTCAGAAAAATAGA
1 GAAGACTCACACGACTGTATGACATATTCAGAAAAATAGA
* * * *
1321599 GAAGA-TCCCACGACTGTATGGCATATTCAGACAAGTAGA
1 GAAGACTCACACGACTGTATGACATATTCAGAAAAATAGA
1321638 GAAGAC
1 GAAGAC
1321644 CCTAAAAGTG
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
38 1 0.03
39 36 0.97
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.20
Consensus pattern (40 bp):
GAAGACTCACACGACTGTATGACATATTCAGAAAAATAGA
Found at i:1326941 original size:75 final size:75
Alignment explanation
Indices: 1326818--1326962 Score: 254
Period size: 75 Copynumber: 1.9 Consensus size: 75
1326808 TGCAAAAAAG
*
1326818 CAACCATCCAATGCTGTTAGCAGTGTAATGACATGTGCTGCTGCAGCTGCTCATTCTGTGATCAC
1 CAACCATCCAATGCTGTTAGCAGCGTAATGACATGTGCTGCTGCAGCTGCTCATTCTGTGATCAC
1326883 CGATGCAAAT
66 CGATGCAAAT
* *
1326893 CAACCATCCAATTCTGTTAGCAGCGTAATGACATGTGCTGCTGTAGCTGCTCATTCTGTGATCAC
1 CAACCATCCAATGCTGTTAGCAGCGTAATGACATGTGCTGCTGCAGCTGCTCATTCTGTGATCAC
*
1326958 TGATG
66 CGATG
1326963 ATAATCCATC
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 66 1.00
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (75 bp):
CAACCATCCAATGCTGTTAGCAGCGTAATGACATGTGCTGCTGCAGCTGCTCATTCTGTGATCAC
CGATGCAAAT
Found at i:1368996 original size:31 final size:30
Alignment explanation
Indices: 1368961--1369024 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
1368951 TATATATAAT
* *
1368961 AAATTAAGTATCAT-ATTATACATAAATATTA
1 AAATTAAATA-CATCATTATACA-AAAAATTA
*
1368992 AAATTAAATACCTCATTATACAAAAAATTA
1 AAATTAAATACATCATTATACAAAAAATTA
1369022 AAA
1 AAA
1369025 CACCACATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 12 0.41
31 17 0.59
ACGTcount: A:0.56, C:0.09, G:0.02, T:0.33
Consensus pattern (30 bp):
AAATTAAATACATCATTATACAAAAAATTA
Found at i:1370060 original size:18 final size:17
Alignment explanation
Indices: 1370023--1370061 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
1370013 CGAATAAAAA
1370023 TATATTTTATATAAATG
1 TATATTTTATATAAATG
* *
1370040 TATATTTATATTTAGATG
1 TATATTT-TATATAAATG
1370058 TATA
1 TATA
1370062 AATAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (17 bp):
TATATTTTATATAAATG
Found at i:1370124 original size:16 final size:18
Alignment explanation
Indices: 1370092--1370125 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1370082 TATTAATGTA
1370092 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
1370110 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
1370126 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:1370830 original size:132 final size:131
Alignment explanation
Indices: 1370593--1370842 Score: 403
Period size: 132 Copynumber: 1.9 Consensus size: 131
1370583 AATTTTCTTC
* *
1370593 TAATTAGGTGGTGACATATGTCACCAATAACGTATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATATGTCACCAATAACG-ATATCATGATCATATGCTAACACATGTCAGAT
** *
1370658 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
65 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
1370723 TA
130 TA
* *
1370725 TAATTAGGTGGTGACATGTGTCACCAATGACACG-TGTCATGATCATATGCTAACACATGTCAGA
1 TAATTAGGTGGTGACATATGTCACCAAT-A-ACGATATCATGATCATATGCTAACACATGTCAGA
1370789 TCCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
64 TCCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
1370843 TATATAAATA
Statistics
Matches: 109, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
132 105 0.96
133 1 0.01
134 3 0.03
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (131 bp):
TAATTAGGTGGTGACATATGTCACCAATAACGATATCATGATCATATGCTAACACATGTCAGATC
CTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAAT
A
Found at i:1371291 original size:35 final size:35
Alignment explanation
Indices: 1371240--1371315 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
1371230 AATTGAATTT
*
1371240 AATTGAATTATATTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTATATTGGAAATTAGGGTTTAGAATGA
*
1371275 AATTGAATTACT-TTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTA-TATTGGAAATTAGGGTTTAGAATGA
1371310 AATTGA
1 AATTGA
1371316 GGACTGTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 37 0.97
36 1 0.03
ACGTcount: A:0.37, C:0.01, G:0.24, T:0.38
Consensus pattern (35 bp):
AATTGAATTATATTGGAAATTAGGGTTTAGAATGA
Found at i:1373749 original size:169 final size:169
Alignment explanation
Indices: 1373437--1373749 Score: 400
Period size: 169 Copynumber: 1.9 Consensus size: 169
1373427 GTGGACAGTT
* *
1373437 GTCGTCGTTCACCGAAATAGAGCCCTTGAAGTTTCACCGAAAACTCACACCGATGCCTCGGATTT
1 GTCGTCGTTCACCGAAATAGAGCCCTTGAAGTTTCACCGAAAACCCACACCGATGCCTCAGATTT
* * *
1373502 TGGATGATGCCGACCACCTTGGACCTCTGTTTGCCTCACCGCAACCATAGTTAGCTTCCTCGTCA
66 TGGACGATGCCGACCACCTCGGACCTCTGTTCGCCTCACCGCAACCATAGTTAGCTTCCTCGTCA
*
1373567 CCATTATCTCAAAAGCCCCAAAACAATTCGAGGATAGCC
131 CCATTAGCTCAAAAGCCCCAAAACAATTCGAGGATAGCC
** * ** **
1373606 GTCGTCGTTCGTCGAAATCGATTCCTTGAAGTTTCGTCGAAAACCCA-ACCCGATGCCTCAGATT
1 GTCGTCGTTCACCGAAATAGAGCCCTTGAAGTTTCACCGAAAACCCACA-CCGATGCCTCAGATT
* * * *
1373670 TTGGACGATTCCGACCGCCTCGGACCT-TCGTTCGCCTCACCGCCACCATA-TATAGTTTCCTCG
65 TTGGACGATGCCGACCACCTCGGACCTCT-GTTCGCCTCACCGCAACCATAGT-TAGCTTCCTCG
*
1373733 TCGCCATCT-GCTCAAAA
128 TCACCAT-TAGCTCAAAA
1373750 CCCAACCAGT
Statistics
Matches: 122, Mismatches: 18, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
168 3 0.02
169 118 0.97
170 1 0.01
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.26
Consensus pattern (169 bp):
GTCGTCGTTCACCGAAATAGAGCCCTTGAAGTTTCACCGAAAACCCACACCGATGCCTCAGATTT
TGGACGATGCCGACCACCTCGGACCTCTGTTCGCCTCACCGCAACCATAGTTAGCTTCCTCGTCA
CCATTAGCTCAAAAGCCCCAAAACAATTCGAGGATAGCC
Found at i:1374275 original size:19 final size:20
Alignment explanation
Indices: 1374250--1374300 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1374240 AAATAACCAA
*
1374250 TAAATTCGCAACACGATCTC
1 TAAATTCGCAACACGAACTC
1374270 -AAATTCGCAACACGAACTC
1 TAAATTCGCAACACGAACTC
*
1374289 TAATTTCGCAAC
1 TAAATTCGCAAC
1374301 TCAGTTTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 18 0.64
20 10 0.36
ACGTcount: A:0.37, C:0.29, G:0.10, T:0.24
Consensus pattern (20 bp):
TAAATTCGCAACACGAACTC
Found at i:1374355 original size:40 final size:39
Alignment explanation
Indices: 1374306--1374387 Score: 92
Period size: 39 Copynumber: 2.1 Consensus size: 39
1374296 GCAACTCAGT
** *
1374306 TTTGAAATTCACAACTCGAATTTCCTTTTCGCAACGCGAA
1 TTTGAAATTCACAAAGCGAATTT-ATTTTCGCAACGCGAA
* * **
1374346 TTTGGAATTCGCAAAGCGCGTTTATTTTCGCAACGCGAA
1 TTTGAAATTCACAAAGCGAATTTATTTTCGCAACGCGAA
1374385 TTT
1 TTT
1374388 TATTTTCAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
39 18 0.51
40 17 0.49
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (39 bp):
TTTGAAATTCACAAAGCGAATTTATTTTCGCAACGCGAA
Found at i:1374391 original size:20 final size:20
Alignment explanation
Indices: 1374317--1374394 Score: 61
Period size: 20 Copynumber: 4.0 Consensus size: 20
1374307 TTGAAATTCA
* **
1374317 CAACTCGAATTTCCTTTTCG
1 CAACGCGAATTTTATTTTCG
* *
1374337 CAACGCGAATTTGGA-ATTCG
1 CAACGCGAATTT-TATTTTCG
* **
1374357 CAAAGCG-CGTTTATTTTCG
1 CAACGCGAATTTTATTTTCG
1374376 CAACGCGAATTTTATTTTC
1 CAACGCGAATTTTATTTTC
1374395 AAATTCGAAA
Statistics
Matches: 43, Mismatches: 12, Indels: 6
0.70 0.20 0.10
Matches are distributed among these distances:
18 1 0.02
19 12 0.28
20 30 0.70
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (20 bp):
CAACGCGAATTTTATTTTCG
Found at i:1374658 original size:25 final size:25
Alignment explanation
Indices: 1374630--1374705 Score: 77
Period size: 25 Copynumber: 3.0 Consensus size: 25
1374620 AAATGGAAAC
1374630 TTTTGTATTATTATTAGATTTTGCA
1 TTTTGTATTATTATTAGATTTTGCA
* * *
1374655 TTTT-TAAGTATT-TT-TATTTTGAAA
1 TTTTGT-ATTATTATTAGATTTTG-CA
1374679 TTTTTGTATTATTATTAGATTTTGCA
1 -TTTTGTATTATTATTAGATTTTGCA
1374705 T
1 T
1374706 ATTTAAATTG
Statistics
Matches: 39, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
23 6 0.15
24 4 0.10
25 19 0.49
26 4 0.10
27 6 0.15
ACGTcount: A:0.25, C:0.03, G:0.11, T:0.62
Consensus pattern (25 bp):
TTTTGTATTATTATTAGATTTTGCA
Found at i:1374665 original size:28 final size:28
Alignment explanation
Indices: 1374634--1374711 Score: 80
Period size: 24 Copynumber: 3.0 Consensus size: 28
1374624 GGAAACTTTT
1374634 GTATTATTATTAGATTTTGCATTTTTAA
1 GTATTATTATTAGATTTTGCATTTTTAA
*
1374662 GTA-T-TT-TT--ATTTTGAAATTTTT--
1 GTATTATTATTAGATTTTG-CATTTTTAA
*
1374684 GTATTATTATTAGATTTTGCATATTTAA
1 GTATTATTATTAGATTTTGCATTTTTAA
1374712 ATTGATGATA
Statistics
Matches: 39, Mismatches: 3, Indels: 16
0.67 0.05 0.28
Matches are distributed among these distances:
22 3 0.08
23 7 0.18
24 8 0.21
25 4 0.10
26 7 0.18
27 7 0.18
28 3 0.08
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.59
Consensus pattern (28 bp):
GTATTATTATTAGATTTTGCATTTTTAA
Found at i:1375291 original size:18 final size:18
Alignment explanation
Indices: 1375268--1375304 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1375258 TTTTGGGAAC
1375268 TATGATAAAATAATGACT
1 TATGATAAAATAATGACT
*
1375286 TATGATAGAATAATGACT
1 TATGATAAAATAATGACT
1375304 T
1 T
1375305 GGGTGAATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.05, G:0.14, T:0.35
Consensus pattern (18 bp):
TATGATAAAATAATGACT
Found at i:1376605 original size:42 final size:42
Alignment explanation
Indices: 1376546--1376698 Score: 198
Period size: 42 Copynumber: 3.6 Consensus size: 42
1376536 TGAGCACCCC
* *
1376546 CCACTCCGACACCGAGAGCCATCACCTTATCGAGCCTCTTCT
1 CCACTTCGACACCGAGAGCCATCACCTCATCGAGCCTCTTCT
* *
1376588 CCACTTCGACACCGAGAGCAATCACCTCATCAAGCCTCTTCT
1 CCACTTCGACACCGAGAGCCATCACCTCATCGAGCCTCTTCT
* * * * **
1376630 CCACTTCAACACCGAGAGTCATCACCTGATTGAGCCAATTCT
1 CCACTTCGACACCGAGAGCCATCACCTCATCGAGCCTCTTCT
* *
1376672 ACACCTCGACACCGAGAGCCATCACCT
1 CCACTTCGACACCGAGAGCCATCACCT
1376699 ATTCCATCAC
Statistics
Matches: 95, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 95 1.00
ACGTcount: A:0.26, C:0.40, G:0.14, T:0.20
Consensus pattern (42 bp):
CCACTTCGACACCGAGAGCCATCACCTCATCGAGCCTCTTCT
Found at i:1376837 original size:21 final size:21
Alignment explanation
Indices: 1376813--1376865 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
1376803 GTTAGGGGAG
1376813 TTACGTGATGAGGTCAATGCT
1 TTACGTGATGAGGTCAATGCT
* **
1376834 TTACGTAATGAGGTCGGTGCT
1 TTACGTGATGAGGTCAATGCT
1376855 TTACGTGATGA
1 TTACGTGATGA
1376866 TAATTGTGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.23, C:0.13, G:0.30, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGGTCAATGCT
Done.