Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007921.1 Hibiscus syriacus cultivar Beakdansim tig00110325_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: 892961
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:878 original size:21 final size:21
Alignment explanation
Indices: 838--892 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
828 GATTCTTGAC
838 AATCGCAATGCGATAGTACA-
1 AATCGCAATGCGATAGTACAG
* **
858 AATTCGCATTGCGATTTTACAG
1 AA-TCGCAATGCGATAGTACAG
*
880 AATCGCAACGCGA
1 AATCGCAATGCGA
893 ATATGAAATC
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (21 bp):
AATCGCAATGCGATAGTACAG
Found at i:904 original size:19 final size:18
Alignment explanation
Indices: 880--949 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 18
870 GATTTTACAG
*
880 AATCGCAACGCGAATATGA
1 AATCGCAACGCGAACAT-A
899 AATCGCAACGCGAACACATA
1 AATCGCAACGCG-A-ACATA
*
919 AATCGCAACGCGAACACA
1 AATCGCAACGCGAACATA
937 TAATCGCAACGCG
1 -AATCGCAACGCG
950 TATCCGTAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.09
19 25 0.54
20 14 0.30
21 3 0.07
ACGTcount: A:0.41, C:0.29, G:0.19, T:0.11
Consensus pattern (18 bp):
AATCGCAACGCGAACATA
Found at i:992 original size:20 final size:20
Alignment explanation
Indices: 880--1126 Score: 236
Period size: 20 Copynumber: 12.4 Consensus size: 20
870 GATTTTACAG
* **
880 AATCGCAACGCGAATATG-A
1 AATCGCAACGCGTATCCGTA
* *
899 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
* *
919 AATCGCAACGCG-AACACAT-
1 AATCGCAACGCGTATC-CGTA
938 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
958 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
978 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
998 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1018 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1038 AATCGCAACG-ATAATCAGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1058 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1078 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1098 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1118 AATCACAAC
1 AATCGCAAC
1127 ACTGAAATTT
Statistics
Matches: 196, Mismatches: 24, Indels: 15
0.83 0.10 0.06
Matches are distributed among these distances:
18 1 0.01
19 27 0.14
20 168 0.86
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1847 original size:23 final size:24
Alignment explanation
Indices: 1804--1849 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
1794 AAATTTGGTC
1804 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1828 TTGGTCAATA-CCGGATTTTGAT
1 TTGGTCAATATCCGGACTTTGAT
1850 GATGTTCAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.39
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:4278 original size:33 final size:33
Alignment explanation
Indices: 4227--4444 Score: 136
Period size: 34 Copynumber: 6.2 Consensus size: 33
4217 CGGAAATTAC
* *
4227 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGCGAAATGAA
* *
4260 AATCCCAACAAGAAAATCGCAATGCGGAACTGAA
1 AATCGCAACAAGAAAATCGCAATGC-GAAATGAA
* * * *
4294 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCAC
1 AATCGCAA--C--AA-GAAAATCGCAATGCGA-AATGAA
* *
4333 AATGCGGAA-ATGAAAATCGCAATGCGAAATGAA
1 AAT-CGCAACAAGAAAATCGCAATGCGAAATGAA
* * *
4366 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-C
1 AATCGCAA--C--AA-GAAAATCGCAATGCGA-AAT-GAA
* *
4405 AATGCGGAA-ATGAAAATCGCAATGCGAAATGAA
1 AAT-CGCAACAAGAAAATCGCAATGCGAAATGAA
4438 AATCGCA
1 AATCGCA
4445 TTGCGATTCT
Statistics
Matches: 140, Mismatches: 27, Indels: 37
0.69 0.13 0.18
Matches are distributed among these distances:
32 8 0.06
33 35 0.25
34 42 0.30
35 2 0.01
36 1 0.01
37 1 0.01
38 18 0.13
39 24 0.17
40 9 0.06
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (33 bp):
AATCGCAACAAGAAAATCGCAATGCGAAATGAA
Found at i:4368 original size:72 final size:72
Alignment explanation
Indices: 4271--4450 Score: 324
Period size: 72 Copynumber: 2.5 Consensus size: 72
4261 ATCCCAACAA
*
4271 GAAAATCGCAATGCGGAACTGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCACAAT
1 GAAAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCACAAT
4336 GCGGAAAT
65 GCGGAAAT
*
4344 GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATG
1 GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCACAATG
4409 CGGAAAT
66 CGGAAAT
*
4416 GAAAATCGCAATGCGAAATGAAAATCGCATTGCGA
1 GAAAATCGCAATGCGAAATGAAAATCGCAATGCGA
4451 TTCTCTCGTT
Statistics
Matches: 104, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
72 90 0.87
73 14 0.13
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.14
Consensus pattern (72 bp):
GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCACAATG
CGGAAAT
Found at i:4427 original size:53 final size:53
Alignment explanation
Indices: 4227--4444 Score: 229
Period size: 53 Copynumber: 4.1 Consensus size: 53
4217 CGGAAATTAC
* *
4227 AATCGCAACGA-GAGAATCGCAATGCGAAATGAAAATCCCAA--C--AA-GAA
1 AATCGCAACGATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
* * * *
4274 AATCGCAATGCGGAACTGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCAC
1 AATCGCAA--C-G-A-TGAAAATCGCAATGCGAAATGAAAATCGCAATGCGA-AATGAA
*
4333 AATGCGGAA--ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AAT-CGCAACGATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
4385 AATCGCAACGA-GAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
4438 AATCGCA
1 AATCGCA
4445 TTGCGATTCT
Statistics
Matches: 143, Mismatches: 12, Indels: 26
0.79 0.07 0.14
Matches are distributed among these distances:
47 8 0.06
49 1 0.01
50 1 0.01
51 5 0.03
52 20 0.14
53 97 0.68
54 1 0.01
58 2 0.01
59 4 0.03
60 4 0.03
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (53 bp):
AATCGCAACGATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:4484 original size:53 final size:52
Alignment explanation
Indices: 4421--4536 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 52
4411 GAAATGAAAA
*
4421 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
** ** **
4473 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
4526 TCGCATTGCGA
1 TCGCATTGCGA
4537 TTTTCATTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
52 11 0.20
53 45 0.80
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:4499 original size:19 final size:19
Alignment explanation
Indices: 4459--4546 Score: 123
Period size: 19 Copynumber: 4.8 Consensus size: 19
4449 GATTCTCTCG
4459 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
4479 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
4498 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
4512 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4531 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
4547 AACATAATGC
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.10
16 7 0.11
17 7 0.11
19 26 0.43
20 15 0.25
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:4655 original size:14 final size:14
Alignment explanation
Indices: 4631--4670 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
4621 TTCACATCAA
4631 TTACAAAATCAACTT
1 TTAC-AAATCAACTT
*
4646 TTACAAATCATCTT
1 TTACAAATCAACTT
4660 TTACAAATCAA
1 TTACAAATCAA
4671 TTAAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 19 0.83
15 4 0.17
ACGTcount: A:0.45, C:0.20, G:0.00, T:0.35
Consensus pattern (14 bp):
TTACAAATCAACTT
Found at i:6617 original size:19 final size:19
Alignment explanation
Indices: 6575--6728 Score: 130
Period size: 19 Copynumber: 8.6 Consensus size: 19
6565 TAGTTTACTT
* *
6575 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
* *
6595 TCGCAACGTGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
6614 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
6633 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
6652 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
6666 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
6685 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
6699 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
6718 TCGCAATGCGA
1 TCGCAACGCGA
6729 TTTTGGTTTC
Statistics
Matches: 108, Mismatches: 16, Indels: 21
0.74 0.11 0.14
Matches are distributed among these distances:
14 18 0.17
15 1 0.01
16 7 0.06
17 7 0.06
18 1 0.01
19 63 0.58
20 11 0.10
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:6669 original size:14 final size:14
Alignment explanation
Indices: 6650--6706 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
6640 GCGAAATGAA
*
6650 AATCGCAACGACAG
1 AATCGCAACGAAAG
6664 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
6681 AAAATCGCAACGAGAG
1 --AATCGCAACGAAAG
6697 AATCGCAACG
1 AATCGCAACG
6707 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
16 5 0.14
17 5 0.14
19 8 0.22
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:6677 original size:33 final size:33
Alignment explanation
Indices: 6593--6723 Score: 172
Period size: 33 Copynumber: 3.8 Consensus size: 33
6583 CGAAACTTAA
* * *
6593 AATCGCAACGTGAAATGAGAATCGCAACGAGAAACCAA
1 AATCGCAACGCGAAATGAAAATCGCAAC--G--A-CAG
6631 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* *
6664 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
6697 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
6724 TGCGATTTTG
Statistics
Matches: 87, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
33 59 0.68
34 1 0.01
36 1 0.01
38 26 0.30
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:6720 original size:52 final size:51
Alignment explanation
Indices: 6592--6728 Score: 132
Period size: 52 Copynumber: 2.6 Consensus size: 51
6582 ACGAAACTTA
* * * * *
6592 AAATCGCAACGTGAAATGAGAATCGCAACGAGAAACCAAAATCGCAACGCG
1 AAATCGCAACGCGAAATGAAAATCGCAATGCGAAACCAAAATCGCAACGAG
* ** * * **
6643 AAAT-GAAAATCGCAACGACAGAATCGCAATGCGAAATGAAAATCGCAACGAG
1 AAATCGCAACGCGAAATGA-A-AATCGCAATGCGAAACCAAAATCGCAACGAG
6695 AGAATCGCAACGCGAAATGAAAATCGCAATGCGA
1 A-AATCGCAACGCGAAATGAAAATCGCAATGCGA
6729 TTTTGGTTTC
Statistics
Matches: 65, Mismatches: 17, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
50 8 0.12
51 4 0.06
52 40 0.62
53 4 0.06
54 9 0.14
ACGTcount: A:0.46, C:0.21, G:0.22, T:0.11
Consensus pattern (51 bp):
AAATCGCAACGCGAAATGAAAATCGCAATGCGAAACCAAAATCGCAACGAG
Found at i:6759 original size:14 final size:14
Alignment explanation
Indices: 6740--6798 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
6730 TTTGGTTTCG
6740 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
6754 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
6771 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
6787 CGTTGCGATTTT
1 CGTTGCGATTTT
6799 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:6766 original size:33 final size:33
Alignment explanation
Indices: 6724--6847 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
6714 AAAATCGCAA
*
6724 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
6757 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
6790 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* *
6823 TGCGATTTTATGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
6848 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.08, C:0.18, G:0.27, T:0.47
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:6778 original size:19 final size:18
Alignment explanation
Indices: 6724--6815 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 18
6714 AAAATCGCAA
6724 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
6743 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
6757 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
6776 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
6790 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
6809 TGCGATT
1 TGCGATT
6816 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 23 0.38
15 1 0.02
16 2 0.03
17 2 0.03
18 2 0.03
19 30 0.50
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:6825 original size:14 final size:14
Alignment explanation
Indices: 6773--6829 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
6763 TTTGGTTTCG
*
6773 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
6787 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
6806 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
6820 CGTTGCGATT
1 CGTTGCGATT
6830 TTATGTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:7225 original size:93 final size:93
Alignment explanation
Indices: 6945--7259 Score: 596
Period size: 93 Copynumber: 3.4 Consensus size: 93
6935 TCAGGGTATT
6945 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
7010 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
7038 AGTTTAGCAGAATTGGTAGCAACCGAAC-AATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
7102 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
7130 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
7195 GACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
7223 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
7260 AAGCAATCTA
Statistics
Matches: 217, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
92 91 0.42
93 126 0.58
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (93 bp):
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACAC
Found at i:8970 original size:20 final size:20
Alignment explanation
Indices: 8939--9002 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
8929 TTTTGGTTGA
8939 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
8959 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
8979 AAATGAAAATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
9000 AAT
1 AAT
9003 CGCAACGCGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.47, C:0.16, G:0.25, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:8991 original size:21 final size:21
Alignment explanation
Indices: 8937--9001 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
8927 TCTTTTGGTT
8937 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
8958 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
8978 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
8999 GAA
1 GAA
9002 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:9139 original size:41 final size:40
Alignment explanation
Indices: 9054--9145 Score: 123
Period size: 42 Copynumber: 2.3 Consensus size: 40
9044 GTTGCGATTC
** * *
9054 TCTCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATAGTCATTTCACGTTGCGATTTTCATTTA
9094 TCTCGTTGCAGATAGTCATTTTCACGTTGCGATTTTCA-TTA
1 TCTCGTTGC-GATAGTCA-TTTCACGTTGCGATTTTCATTTA
9135 TCTCGTTGCGA
1 TCTCGTTGCGA
9146 CTCTTCTGCA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
40 11 0.24
41 17 0.37
42 18 0.39
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (40 bp):
TCTCGTTGCGATAGTCATTTCACGTTGCGATTTTCATTTA
Found at i:9267 original size:33 final size:33
Alignment explanation
Indices: 9225--9295 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
9215 AATACTAACT
9225 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
9258 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
9291 TGAAA
1 TGAAA
9296 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:9747 original size:60 final size:60
Alignment explanation
Indices: 9671--9862 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
9661 CTTTAAAAAT
* *
9671 CGCGTTGCGATTTACGGATACGCATTGCGATTTACTGATTA-TCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATACGCATTGCGATTTACGGA-TACGCGTTGCGATTTACAGATA
* *
9731 CGCGTTGCGATATACGGATACGCATTGCGATTTACGGATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCATTGCGATTTACGGATACGCGTTGCGATTTACAGATA
* * * * * * * *
9791 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-TTCGCGTTGCAATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCATTGCGATTTACG-GATACGCGTTGCGATTTACAGATA
9851 CGCGTTGCGATT
1 CGCGTTGCGATT
9863 CTTGAAAATC
Statistics
Matches: 115, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
59 2 0.02
60 112 0.97
61 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCATTGCGATTTACGGATACGCGTTGCGATTTACAGATA
Found at i:9837 original size:40 final size:40
Alignment explanation
Indices: 9670--9862 Score: 226
Period size: 40 Copynumber: 4.8 Consensus size: 40
9660 GCTTTAAAAA
* *
9670 TCGCGTTGCGATTTACGGATACGCATTGCGATTTACTGAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGAT
** * *
9710 TATCGTTGCGATTTACAGATACGCGTTGCGATATACGGAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGAT
* *
9750 ACGCATTGCGATTTACGGATACGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGAT
* * *
9790 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTACG-GAT
* * ** *
9830 TCGCGTTGCAATTTTCATATTCGCGTTGCGATT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATT
9863 CTTGAAAATC
Statistics
Matches: 130, Mismatches: 22, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
40 129 0.99
41 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGAT
Found at i:9838 original size:20 final size:20
Alignment explanation
Indices: 9671--9824 Score: 229
Period size: 20 Copynumber: 7.7 Consensus size: 20
9661 CTTTAAAAAT
9671 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
9691 CGCATTGCGATTTACTGATTA
1 CGCGTTGCGATTTACGGA-TA
* *
9712 -TCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
*
9731 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
9751 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
9771 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
9791 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
9811 CGCGTTGCGATTTA
1 CGCGTTGCGATTTA
9825 TGTGTTCGCG
Statistics
Matches: 119, Mismatches: 13, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
19 2 0.02
20 115 0.97
21 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:28599 original size:21 final size:21
Alignment explanation
Indices: 28575--28616 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
28565 AATGAGTATG
28575 GATATAGATGGGAGGTGATCA
1 GATATAGATGGGAGGTGATCA
*
28596 GATATAGATGGGCGGTGATCA
1 GATATAGATGGGAGGTGATCA
28617 TAAATAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.07, G:0.38, T:0.24
Consensus pattern (21 bp):
GATATAGATGGGAGGTGATCA
Found at i:46509 original size:36 final size:34
Alignment explanation
Indices: 46428--46509 Score: 85
Period size: 35 Copynumber: 2.3 Consensus size: 34
46418 GAAATTCAAT
46428 TTTTTTTTAAATTTTAAATTATTTTATTAATTATA
1 TTTTTTTTAAATTTTAAATTATTTTATTAATTA-A
* * * *
46463 TTTATTTTAAATTTT-TATTTTATTTATTCATATAA
1 TTTTTTTTAAATTTTAAATTAT-TTTATTAAT-TAA
46498 TTTTTTATTAAA
1 TTTTTT-TTAAA
46510 CTAAAGTAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
34 4 0.10
35 28 0.72
36 7 0.18
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (34 bp):
TTTTTTTTAAATTTTAAATTATTTTATTAATTAA
Found at i:46822 original size:23 final size:21
Alignment explanation
Indices: 46774--46828 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 21
46764 TTATAGATTT
*
46774 AATTTTTATTTTTAATCTAAT
1 AATTTTTATTTTTAATCTAAC
* *
46795 TATTTTTAATTTTATAATTTAAC
1 AATTTTT-ATTTT-TAATCTAAC
*
46818 AATTTATATTT
1 AATTTTTATTT
46829 GAATGTGACC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
21 6 0.22
22 9 0.33
23 12 0.44
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (21 bp):
AATTTTTATTTTTAATCTAAC
Found at i:51126 original size:16 final size:17
Alignment explanation
Indices: 51105--51144 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
51095 GATCCGGATA
*
51105 TTCGGATATCTGA-ATT
1 TTCGGATATCCGATATT
*
51121 TTCGGATATCCGATTTT
1 TTCGGATATCCGATATT
51138 TTCGGAT
1 TTCGGAT
51145 CGGATACAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.45
Consensus pattern (17 bp):
TTCGGATATCCGATATT
Found at i:52447 original size:21 final size:21
Alignment explanation
Indices: 52421--52461 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
52411 GGTAAAAAAT
*
52421 TACCTAAAACATTATTATTTC
1 TACCTAAAACATTAATATTTC
*
52442 TACCTAAAATATTAATATTT
1 TACCTAAAACATTAATATTT
52462 TTTAACATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (21 bp):
TACCTAAAACATTAATATTTC
Found at i:57617 original size:20 final size:20
Alignment explanation
Indices: 57592--57684 Score: 105
Period size: 20 Copynumber: 4.6 Consensus size: 20
57582 TAGTTGAAAA
57592 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
*
57612 TCGCGTTACGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * * ** **
57632 TCGTGTTGCTATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
57653 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
57673 TCGCGTTGCGAT
1 TCGCGTTGCGAT
57685 AGTCTACAAT
Statistics
Matches: 56, Mismatches: 16, Indels: 2
0.76 0.22 0.03
Matches are distributed among these distances:
20 43 0.77
21 13 0.23
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.42
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:57634 original size:61 final size:61
Alignment explanation
Indices: 57567--57684 Score: 218
Period size: 61 Copynumber: 1.9 Consensus size: 61
57557 ATTCGTGTTG
57567 CATTTCGTGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTACGATTTTC
1 CATTTCGTGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTACGATTTTC
* *
57628 CATTTCGTGTTGCTATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGAT
1 CATTTCGTGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTACGAT
57685 AGTCTACAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.18, C:0.19, G:0.22, T:0.41
Consensus pattern (61 bp):
CATTTCGTGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTACGATTTTC
Found at i:57701 original size:41 final size:41
Alignment explanation
Indices: 57612--57732 Score: 133
Period size: 41 Copynumber: 3.0 Consensus size: 41
57602 ATTTTCCATT
* * * *
57612 TCGCGTTACGATTTTCCATTTCGTGTTGCTATAGT-TGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCT-ACAA
57653 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAA
* *
57694 T-GTCGTTGCGATTTTCCAAATT--CGTTGCGATGGTCTACA
1 TCG-CGTTGCGATTTTCC-ATTTCGCGTTGCGATAGTCTACA
57733 GTTGTTGTTG
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
40 17 0.24
41 50 0.70
42 4 0.06
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAA
Found at i:57744 original size:22 final size:22
Alignment explanation
Indices: 57676--57768 Score: 86
Period size: 22 Copynumber: 4.4 Consensus size: 22
57666 TTCCATTTCG
*
57676 CGTTGCGATAGTCTACA-ATGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
57697 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
*
57716 CGTTGCGATGGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* *
57738 TGTTGCGAAAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
57760 CGTTGCGAT
1 CGTTGCGAT
57769 TTTCCAAATT
Statistics
Matches: 57, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
19 14 0.25
20 2 0.04
21 14 0.25
22 27 0.47
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:57745 original size:41 final size:40
Alignment explanation
Indices: 57656--57732 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
57646 TTGAAAATCG
*
57656 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAATGT
1 CGTTGCGATTTTCCAATTC-CGTTGCGATAGTCTACAATGT
*
57697 CGTTGCGATTTTCCAAATT-CGTTGCGATGGTCTACA
1 CGTTGCGATTTTCC-AATTCCGTTGCGATAGTCTACA
57733 GTTGTTGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
40 16 0.48
41 14 0.42
42 3 0.09
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (40 bp):
CGTTGCGATTTTCCAATTCCGTTGCGATAGTCTACAATGT
Found at i:57881 original size:6 final size:6
Alignment explanation
Indices: 57870--57974 Score: 203
Period size: 6 Copynumber: 17.7 Consensus size: 6
57860 CGTATTACCA
57870 CGACCG CGACCG CGACCG CGACCG CGACCG CGACCG CGACCG CGACCG
1 CGACCG CGACCG CGACCG CGACCG CGACCG CGACCG CGACCG CGACCG
57918 CGACCG CGACCG CGACCG CGACCG CGACCG CGACCG CGACCG CGACCG
1 CGACCG CGACCG CGACCG CGACCG CGACCG CGACCG CGACCG CGACCG
57966 CGACC- CGAC
1 CGACCG CGAC
57975 GGACGGCGGC
Statistics
Matches: 99, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 4 0.04
6 95 0.96
ACGTcount: A:0.17, C:0.50, G:0.32, T:0.00
Consensus pattern (6 bp):
CGACCG
Found at i:58462 original size:6 final size:6
Alignment explanation
Indices: 58453--58477 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
58443 GCCGTCCGTC
58453 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
58478 AATACGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:58617 original size:20 final size:20
Alignment explanation
Indices: 58592--58643 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
58582 ACTGTAGACT
*
58592 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAAATGGAAA
58612 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
58632 ATCGCAACGCGA
1 ATCGCAACGCGA
58644 TTTTCAACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.40, C:0.25, G:0.25, T:0.10
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:58658 original size:21 final size:21
Alignment explanation
Indices: 58632--58681 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
58622 GAAATGGAAA
58632 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
*
58653 ATCGCAACGCGATTTTCAATT
1 ATCGCAACGCGATTTTCAACT
58674 ATCGCAAC
1 ATCGCAAC
58682 TTGAAATGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:59145 original size:21 final size:20
Alignment explanation
Indices: 59092--59161 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 20
59082 AACTTAAACC
*
59092 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
59112 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
59130 AAAATAATTT-AT-ATAATAT
1 AAAATAATTTAATAAT-ATAT
59149 AAAATAAATTTAA
1 AAAAT-AATTTAA
59162 AAAATTAATA
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
17 5 0.12
18 13 0.30
19 11 0.26
20 13 0.30
21 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:59150 original size:19 final size:19
Alignment explanation
Indices: 59092--59166 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 19
59082 AACTTAAACC
*
59092 AAAATAATTAAAATAAATAT
1 AAAATAATT-TAATAAATAT
59112 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAA-ATAT
59130 AAAATAATTT-ATATAATAT
1 AAAATAATTTAATA-AATAT
*
59149 AAAATAAATTTAAAAAAT
1 AAAAT-AATTTAATAAAT
59167 TAATATTTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
17 5 0.11
18 11 0.23
19 12 0.26
20 17 0.36
21 2 0.04
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAATAATTTAATAAATAT
Found at i:59177 original size:28 final size:27
Alignment explanation
Indices: 59146--59202 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
59136 ATTTATATAA
59146 TATAAAATAA-ATTTAAAAAATTAATATT
1 TATAAAATAATA-TT-AAAAATTAATATT
*
59174 TATAATATAATATTAAAAATTAATATT
1 TATAAAATAATATTAAAAATTAATATT
59201 TA
1 TA
59203 ATTTATTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 15 0.56
28 11 0.41
29 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
TATAAAATAATATTAAAAATTAATATT
Found at i:59184 original size:47 final size:47
Alignment explanation
Indices: 59095--59184 Score: 119
Period size: 48 Copynumber: 1.9 Consensus size: 47
59085 TTAAACCAAA
**
59095 ATAATTAAAATAAATATAAAATTTTAATAATATATAAAATAATTTAT
1 ATAATTAAAATAAATATAAAAAATTAATAATATATAAAATAATTTAT
* * *
59142 ATAATATAAAATAAATTTAAAAAATTAAT-ATTTATAATATAAT
1 ATAAT-TAAAATAAATATAAAAAATTAATAATATATAAAATAAT
59185 ATTAAAAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
47 17 0.46
48 20 0.54
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (47 bp):
ATAATTAAAATAAATATAAAAAATTAATAATATATAAAATAATTTAT
Found at i:59186 original size:14 final size:13
Alignment explanation
Indices: 59162--59232 Score: 62
Period size: 13 Copynumber: 5.6 Consensus size: 13
59152 ATAAATTTAA
59162 AAAATTAATATTT
1 AAAATTAATATTT
* *
59175 ATAATATAATATTA
1 AAAAT-TAATATTT
59189 AAAATTAATATTT
1 AAAATTAATATTT
59202 --AATT--TATTT
1 AAAATTAATATTT
59211 AAAATATTAATA-TT
1 -AAA-ATTAATATTT
59225 AAAATTAA
1 AAAATTAA
59233 AATTACATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 15
0.71 0.06 0.23
Matches are distributed among these distances:
9 5 0.11
11 4 0.09
12 6 0.13
13 17 0.36
14 13 0.28
15 2 0.04
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AAAATTAATATTT
Found at i:59199 original size:18 final size:19
Alignment explanation
Indices: 59176--59247 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 19
59166 TTAATATTTA
59176 TAATA-TAATATTAAAAAT
1 TAATATTAATATTAAAAAT
59194 TAATATTTAATTTATTTAAAATAT
1 TAATA-TTAA--TA-TTAAAA-AT
*
59218 TAATATTAAAATT-AAAAT
1 TAATATTAATATTAAAAAT
59236 TACATA-TAATAT
1 TA-ATATTAATAT
59248 AATATAAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
18 14 0.31
19 6 0.13
20 5 0.11
21 1 0.02
22 2 0.04
23 10 0.22
24 7 0.16
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATATTAATATTAAAAAT
Found at i:60741 original size:14 final size:14
Alignment explanation
Indices: 60722--60753 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
60712 TAATATCCAC
60722 GTCAACGGTCATAA
1 GTCAACGGTCATAA
60736 GTCAACGGTCATAA
1 GTCAACGGTCATAA
60750 GTCA
1 GTCA
60754 CGTTTTTGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (14 bp):
GTCAACGGTCATAA
Found at i:68735 original size:26 final size:26
Alignment explanation
Indices: 68689--68740 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
68679 TAATTAATTC
* * *
68689 CTCTTTTATCAATTATTTGATTTAGT
1 CTCTTTTATCAATGATGTGATCTAGT
68715 CTCTTTTATCAATGATGTGATCTAGT
1 CTCTTTTATCAATGATGTGATCTAGT
68741 TTAATAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.23, C:0.13, G:0.12, T:0.52
Consensus pattern (26 bp):
CTCTTTTATCAATGATGTGATCTAGT
Found at i:72088 original size:18 final size:18
Alignment explanation
Indices: 72031--72088 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
72021 CATAAATATG
* * *
72031 TAAAAAAATTATTTTTAT
1 TAAAAAAATGAATATTAT
*
72049 TAGAAAAATATGAATATAAT
1 TA-AAAAA-ATGAATATTAT
*
72069 TAAAAAAATGAGTATTAT
1 TAAAAAAATGAATATTAT
72087 TA
1 TA
72089 TAATTATCTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
18 13 0.41
19 10 0.31
20 9 0.28
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (18 bp):
TAAAAAAATGAATATTAT
Found at i:77862 original size:29 final size:29
Alignment explanation
Indices: 77820--77879 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
77810 GTAGATCATA
77820 AGGTTTTTAACCTTGAAGTCGTGGGATCG
1 AGGTTTTTAACCTTGAAGTCGTGGGATCG
77849 AGGTTTTTAACCTTGAAGTCGTGGGATCG
1 AGGTTTTTAACCTTGAAGTCGTGGGATCG
77878 AG
1 AG
77880 TCACACGGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.22, C:0.13, G:0.32, T:0.33
Consensus pattern (29 bp):
AGGTTTTTAACCTTGAAGTCGTGGGATCG
Found at i:87244 original size:43 final size:43
Alignment explanation
Indices: 87196--87278 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
87186 ATTATGTAAG
87196 CTTAGTGAGATTGGAGTCCAAATACTTCTAGTTGGCCAAAAAC
1 CTTAGTGAGATTGGAGTCCAAATACTTCTAGTTGGCCAAAAAC
** *
87239 CTTAGTGAGATTGGAGTCCACGTCCTTCTAGTTGGCCAAA
1 CTTAGTGAGATTGGAGTCCAAATACTTCTAGTTGGCCAAA
87279 CCTTATCTCC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (43 bp):
CTTAGTGAGATTGGAGTCCAAATACTTCTAGTTGGCCAAAAAC
Found at i:88195 original size:2 final size:2
Alignment explanation
Indices: 88188--88213 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
88178 AAAGTTAAAT
88188 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
88214 ATTTTATGCG
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):
TA
Found at i:88721 original size:19 final size:22
Alignment explanation
Indices: 88680--88721 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 22
88670 ATGTGTCACC
*
88680 TTTTAATTGGAGATTAAATTTA
1 TTTTAATTGGAGATTAAAATTA
88702 TTTTAATT-GA-A-TAAAATTA
1 TTTTAATTGGAGATTAAAATTA
88721 T
1 T
88722 GATCAAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 8 0.42
20 1 0.05
21 2 0.11
22 8 0.42
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (22 bp):
TTTTAATTGGAGATTAAAATTA
Found at i:89297 original size:2 final size:2
Alignment explanation
Indices: 89290--89319 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
89280 TGTTTCCTTT
*
89290 TA TA TA TA TA TG 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
89320 CGCACCAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:96384 original size:21 final size:22
Alignment explanation
Indices: 96360--96417 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
96350 ATTTCGCAAC
96360 GCGAATATGT-AAATTCGCGTT
1 GCGAATATGTCAAATTCGCGTT
* *
96381 GCG-ATTTTTCAAATTCGCGTT
1 GCGAATATGTCAAATTCGCGTT
96402 GCG-ATAT-TCTAAATTC
1 GCGAATATGTC-AAATTC
96418 ACAACTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 6 0.19
21 26 0.81
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (22 bp):
GCGAATATGTCAAATTCGCGTT
Found at i:96436 original size:19 final size:20
Alignment explanation
Indices: 96412--96499 Score: 137
Period size: 19 Copynumber: 4.5 Consensus size: 20
96402 GCGATATTCT
*
96412 AAATTCACAAC-TGAATTTC
1 AAATTCGCAACGTGAATTTC
96431 AAATTCGCAAC-TGAATTTC
1 AAATTCGCAACGTGAATTTC
96450 AAATTCGCAACGTGAATTTC
1 AAATTCGCAACGTGAATTTC
96470 AAATTCGCAACGTGAATTT-
1 AAATTCGCAACGTGAATTTC
*
96489 AATTTCGCAAC
1 AAATTCGCAAC
96500 AGGTTTTAGT
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
19 39 0.59
20 27 0.41
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (20 bp):
AAATTCGCAACGTGAATTTC
Found at i:96473 original size:39 final size:38
Alignment explanation
Indices: 96411--96499 Score: 135
Period size: 39 Copynumber: 2.3 Consensus size: 38
96401 TGCGATATTC
*
96411 TAAATTCACAACTGAATTTCAAATTCGCAAC-TGAATT
1 TAAATTCGCAACTGAATTTCAAATTCGCAACGTGAATT
96448 TCAAATTCGCAACGTGAATTTCAAATTCGCAACGTGAATT
1 T-AAATTCGCAAC-TGAATTTCAAATTCGCAACGTGAATT
*
96488 TAATTTCGCAAC
1 TAAATTCGCAAC
96500 AGGTTTTAGT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
37 1 0.02
38 10 0.21
39 29 0.62
40 7 0.15
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.31
Consensus pattern (38 bp):
TAAATTCGCAACTGAATTTCAAATTCGCAACGTGAATT
Found at i:97266 original size:12 final size:12
Alignment explanation
Indices: 97245--97278 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
97235 ACCACATTTC
*
97245 CAATACCAAACA
1 CAATATCAAACA
97257 CAATATCAAACA
1 CAATATCAAACA
*
97269 CAATCTCAAA
1 CAATATCAAA
97279 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:97431 original size:24 final size:24
Alignment explanation
Indices: 97404--97457 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
97394 GTATTCGAAA
97404 TTTGATCTTGGTCAATACTCGGAC
1 TTTGATCTTGGTCAATACTCGGAC
*
97428 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACTCGGAC
97452 TTTGAT
1 TTTGAT
97458 GATGTGATGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACTCGGAC
Found at i:100035 original size:20 final size:20
Alignment explanation
Indices: 100010--100051 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
100000 GCAACGCTTA
100010 TTTCGCATTGCGAATTTACC
1 TTTCGCATTGCGAATTTACC
*
100030 TTTCGCGTTGCGAATTTACC
1 TTTCGCATTGCGAATTTACC
100050 TT
1 TT
100052 CAACAGGTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.43
Consensus pattern (20 bp):
TTTCGCATTGCGAATTTACC
Found at i:100569 original size:18 final size:18
Alignment explanation
Indices: 100548--100584 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
100538 GTAATTGGAG
100548 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
100566 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
100584 T
1 T
100585 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:100591 original size:24 final size:24
Alignment explanation
Indices: 100540--100592 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
100530 TTTCATATGT
* * *
100540 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
100564 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
100588 AATTT
1 AATTT
100593 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:100929 original size:39 final size:39
Alignment explanation
Indices: 100886--100972 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
100876 TCCGATGCTC
100886 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
* *
100925 ATCAAAATCCAAATCTCATGTGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
100964 ATCAAAATC
1 ATCAAAATC
100973 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.46, C:0.21, G:0.16, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:101220 original size:20 final size:21
Alignment explanation
Indices: 101176--101220 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
101166 CAAACCGAAA
*
101176 ATCGCGTTGCGAATTTGACTT
1 ATCGCGTTACGAATTTGACTT
101197 -TCGCGTTACGAATTTGA-TT
1 ATCGCGTTACGAATTTGACTT
101216 ATCGC
1 ATCGC
101221 AACGCTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (21 bp):
ATCGCGTTACGAATTTGACTT
Found at i:102832 original size:21 final size:20
Alignment explanation
Indices: 102808--102904 Score: 70
Period size: 21 Copynumber: 4.7 Consensus size: 20
102798 GGCGGGACCA
102808 CTTGAACGATGACAGGGGCCT
1 CTTGAACGATGA-AGGGGCCT
* * *
102829 CTTGAACGGTGGGAGGGGCTT
1 CTTGAACGAT-GAAGGGGCCT
*
102850 CTTCG-ATGATGATAGGGGCCT
1 CTT-GAACGATGA-AGGGGCCT
* * *
102871 CTTAAACGATAGAATGCGCCT
1 CTTGAACGAT-GAAGGGGCCT
*
102892 CTTGAATGATGAA
1 CTTGAACGATGAA
102905 AGGTGCATCG
Statistics
Matches: 58, Mismatches: 13, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
20 4 0.07
21 50 0.86
22 4 0.07
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.25
Consensus pattern (20 bp):
CTTGAACGATGAAGGGGCCT
Found at i:105435 original size:22 final size:22
Alignment explanation
Indices: 105375--105436 Score: 115
Period size: 22 Copynumber: 2.8 Consensus size: 22
105365 GATGGAGATA
*
105375 GACGGATTTCGTCGGAAATGGG
1 GACGGATTTCGTCGGAGATGGG
105397 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
105419 GACGGATTTCGTCGGAGA
1 GACGGATTTCGTCGGAGA
105437 GAGTGAGAGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.21, C:0.15, G:0.42, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:112762 original size:12 final size:12
Alignment explanation
Indices: 112745--112770 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
112735 TGAAATAGAA
112745 ATAATAAAATAT
1 ATAATAAAATAT
112757 ATAATAAAATAT
1 ATAATAAAATAT
112769 AT
1 AT
112771 CAGTAATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
ATAATAAAATAT
Found at i:117404 original size:15 final size:15
Alignment explanation
Indices: 117384--117413 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
117374 TTTTATTAAT
117384 ATAAAATAAATAAAA
1 ATAAAATAAATAAAA
*
117399 ATAAAATATATAAAA
1 ATAAAATAAATAAAA
117414 GTATAGATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
ATAAAATAAATAAAA
Found at i:125225 original size:19 final size:21
Alignment explanation
Indices: 125183--125239 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
125173 AGAGAACCGA
*
125183 CGGTTCACACCGGGTTTCAGC
1 CGGTTCACACCCGGTTTCAGC
*
125204 CGGTTCAC-CCCGGTTTTA-C
1 CGGTTCACACCCGGTTTCAGC
* *
125223 CGGTTCTCAGCCGGTTT
1 CGGTTCACACCCGGTTT
125240 TGAAAGTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 8 0.26
20 15 0.48
21 8 0.26
ACGTcount: A:0.11, C:0.33, G:0.26, T:0.30
Consensus pattern (21 bp):
CGGTTCACACCCGGTTTCAGC
Found at i:125572 original size:2 final size:2
Alignment explanation
Indices: 125567--125592 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
125557 AACTAAACTA
125567 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
125593 TTGGAGGTTT
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:139487 original size:18 final size:18
Alignment explanation
Indices: 139464--139498 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
139454 ACGTAATATT
139464 GTAATT-TACTTTTTAAAA
1 GTAATTATA-TTTTTAAAA
139482 GTAATTATATTTTTAAA
1 GTAATTATATTTTTAAA
139499 TTACGAATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (18 bp):
GTAATTATATTTTTAAAA
Found at i:141716 original size:23 final size:23
Alignment explanation
Indices: 141673--141718 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
141663 ATATCAAGAC
*
141673 ATATATAAGACATAAACATATAT
1 ATATATAAGACAGAAACATATAT
*
141696 ATATATTAGATCAGAAA-ATATAT
1 ATATATAAGA-CAGAAACATATAT
141719 GCAGGAAAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.54, C:0.07, G:0.07, T:0.33
Consensus pattern (23 bp):
ATATATAAGACAGAAACATATAT
Found at i:164439 original size:19 final size:19
Alignment explanation
Indices: 164403--164441 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
164393 ATGTTGGGAT
** *
164403 AAAATTAAATCATCAATAA
1 AAAATTAAAAAATAAATAA
164422 AAAATTAAAAAATAAATAA
1 AAAATTAAAAAATAAATAA
164441 A
1 A
164442 TTATACACGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (19 bp):
AAAATTAAAAAATAAATAA
Found at i:164851 original size:4 final size:4
Alignment explanation
Indices: 164842--164867 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
164832 TTCTCACCTA
164842 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
164868 CGTAGGTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:191393 original size:29 final size:29
Alignment explanation
Indices: 191348--191405 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
191338 GTGTTGGCCG
*
191348 TAGGTCGCCATGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
* *
191377 TAGGTCGCCATGTCTTCCCGGCGAGCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
191406 AAGAGATTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.14, C:0.36, G:0.28, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGCGACCTAC
Found at i:191541 original size:23 final size:24
Alignment explanation
Indices: 191490--191542 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
191480 ATCCGATACC
*
191490 ATCCGAACGAGCTATGCGAGAGCA
1 ATCCGAGCGAGCTATGCGAGAGCA
*
191514 A-CCGAGCGAGCTATGCGAG-GGA
1 ATCCGAGCGAGCTATGCGAGAGCA
191536 ATCCGAG
1 ATCCGAG
191543 GGAAGCCGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 3 0.12
23 22 0.85
24 1 0.04
ACGTcount: A:0.30, C:0.25, G:0.34, T:0.11
Consensus pattern (24 bp):
ATCCGAGCGAGCTATGCGAGAGCA
Found at i:191593 original size:29 final size:29
Alignment explanation
Indices: 191560--191615 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
191550 GAGCGAGGGT
*
191560 AGGTCG-CGCGGAGTGCATGGCGACCTACA
1 AGGTCGTC-CGGAGGGCATGGCGACCTACA
191589 AGGTCGTCCGGAGGGCATGGCGACCTA
1 AGGTCGTCCGGAGGGCATGGCGACCTA
191616 TGTGTTGGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 24 0.96
30 1 0.04
ACGTcount: A:0.20, C:0.27, G:0.39, T:0.14
Consensus pattern (29 bp):
AGGTCGTCCGGAGGGCATGGCGACCTACA
Found at i:191661 original size:12 final size:12
Alignment explanation
Indices: 191644--191668 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
191634 TTCCATGCAA
191644 CACGTTCATTCT
1 CACGTTCATTCT
191656 CACGTTCATTCT
1 CACGTTCATTCT
191668 C
1 C
191669 TCTGTTTGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (12 bp):
CACGTTCATTCT
Found at i:194502 original size:22 final size:24
Alignment explanation
Indices: 194456--194503 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 24
194446 ATACATTGAC
* *
194456 AAATTATATAAATGCAATAACATT
1 AAATTATATAAATACAAAAACATT
194480 AAATTAT-TAAA-ACAAAAACATT
1 AAATTATATAAATACAAAAACATT
194502 AA
1 AA
194504 TTGAAATACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 11 0.50
23 4 0.18
24 7 0.32
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.29
Consensus pattern (24 bp):
AAATTATATAAATACAAAAACATT
Found at i:197884 original size:128 final size:128
Alignment explanation
Indices: 197480--197959 Score: 809
Period size: 128 Copynumber: 3.7 Consensus size: 128
197470 ACTATTCACA
* *
197480 TGAAGACGCGTTCCCGGGCGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
197545 TTATATCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
* * * * *
197608 TGAAGGCGCGTTCCCGGGGACGCACCTTCCATTATTTTGTCAGATAATATGTTATTATTGCTCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* *
197673 TTATGTCACTCATGTCCCCTCGGGGACACTAGAT-ATATCAGTACCTATTATTTTTCAGGGGACT
66 TTATGTCACTCATGT-CCCTCGGGGACACTA-TTCATATCAGTACCTATTATTTCTCAGGGGACT
*
197737 TGAAGGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
197802 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGAACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
* *
197865 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAAAGAATATGTTATCATTGCCATA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
197930 TTATGTCACTCATGTCCCTCGGGGACACTA
66 TTATGTCACTCATGTCCCTCGGGGACACTA
197960 AATATATCAG
Statistics
Matches: 327, Mismatches: 22, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
127 1 0.00
128 207 0.63
129 118 0.36
130 1 0.00
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (128 bp):
TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
Found at i:197942 original size:257 final size:256
Alignment explanation
Indices: 197480--197971 Score: 860
Period size: 257 Copynumber: 1.9 Consensus size: 256
197470 ACTATTCACA
197480 TGAAGACGCGTTCCCGGGCGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGACGCGTTCCCGGGCGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
197545 TTATATCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTG
66 TTATATCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGAACTTG
* * *
197610 AAGGCGCGTTCCCGGGGACGCACCTTCCATTATTTTGTCAGATAATATGTTATTATTGCTCTATT
131 AAGGCGCGTTCCCGGGGACGCACCTTCCATTATTTTGTCAAAGAATATGTTATCATTGCTCTATT
*
197675 ATGTCACTCATGTCCCCTCGGGGACACTAGATATATCAGTACCTATTATTTTTCAGGGGACT
196 ATGTCACTCATGT-CCCTCGGGGACACTAAATATATCAGTACCTATTATTTTTCAGGGGACT
* * *
197737 TGAAGGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGACGCGTTCCCGGGCGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
197802 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGAACTTG
66 TTATATCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGAACTTG
* *
197867 AAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAAAGAATATGTTATCATTGC-CATAT
131 AAGGCGCGTTCCCGGGGACGCACCTTCCATTATTTTGTCAAAGAATATGTTATCATTGCTC-TAT
197931 TATGTCACTCATGTCCCTCGGGGACACTAAATATATCAGTA
195 TATGTCACTCATGTCCCTCGGGGACACTAAATATATCAGTA
197972 AATCAGGTAA
Statistics
Matches: 223, Mismatches: 11, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
256 27 0.12
257 196 0.88
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (256 bp):
TGAAGACGCGTTCCCGGGCGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
TTATATCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGAACTTG
AAGGCGCGTTCCCGGGGACGCACCTTCCATTATTTTGTCAAAGAATATGTTATCATTGCTCTATT
ATGTCACTCATGTCCCTCGGGGACACTAAATATATCAGTACCTATTATTTTTCAGGGGACT
Found at i:198363 original size:34 final size:34
Alignment explanation
Indices: 198324--198430 Score: 151
Period size: 34 Copynumber: 3.1 Consensus size: 34
198314 TAAGTTGAAA
* *
198324 TTTAATGTTAAATTTCGAATACTATAATTTATAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
* * *
198358 TTTAATTTTAAATTTTGAATAATATTATTTTTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
* *
198392 TTTTATTTTAAATTTCGAATAATATAATTTGTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
198426 TTTAA
1 TTTAA
198431 AAACATTTAT
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 63 1.00
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (34 bp):
TTTAATTTTAAATTTCGAATAATATAATTTATAT
Found at i:198982 original size:21 final size:20
Alignment explanation
Indices: 198953--199037 Score: 98
Period size: 21 Copynumber: 4.1 Consensus size: 20
198943 GGTATTAAAC
*
198953 CCTGCGGGCTAGGCATGTAA
1 CCTGCGGGCTAGGAATGTAA
* *
198973 CATGGCGGGCAAGGAATGTAA
1 CCT-GCGGGCTAGGAATGTAA
*
198994 CCCTGCGGGCTCGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
*
199015 CCTTGCGGGCTCGGAATGTAA
1 CC-TGCGGGCTAGGAATGTAA
199036 CC
1 CC
199038 CTGCAGAGAT
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
20 4 0.07
21 50 0.89
22 2 0.04
ACGTcount: A:0.22, C:0.25, G:0.34, T:0.19
Consensus pattern (20 bp):
CCTGCGGGCTAGGAATGTAA
Found at i:199013 original size:42 final size:42
Alignment explanation
Indices: 198950--199041 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 42
198940 TATGGTATTA
*
198950 AACCCTGCGGGCTAGGCATGTAACATGGCGGGCAAGGAATGT
1 AACCCTGCGGGCTAGGAATGTAACATGGCGGGCAAGGAATGT
* * * **
198992 AACCCTGCGGGCTCGGAATGTAACCTTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGTAACATGGCGGGCAAGGAATGT
199034 AACCCTGC
1 AACCCTGC
199042 AGAGATGGCA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.23, C:0.26, G:0.33, T:0.18
Consensus pattern (42 bp):
AACCCTGCGGGCTAGGAATGTAACATGGCGGGCAAGGAATGT
Found at i:199073 original size:21 final size:21
Alignment explanation
Indices: 199047--199094 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
199037 CCTGCAGAGA
*
199047 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
199068 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
199089 GGGCAT
1 TGGCAT
199095 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:200067 original size:21 final size:21
Alignment explanation
Indices: 200041--200085 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
200031 GATTTCTGGG
* *
200041 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
200062 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
200083 CAA
1 CAA
200086 ACGAACAAGA
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:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:201815 original size:13 final size:13
Alignment explanation
Indices: 201797--201859 Score: 61
Period size: 13 Copynumber: 5.5 Consensus size: 13
201787 TCTACAGGCA
201797 CTACGGTGCAATT
1 CTACGGTGCAATT
201810 CTACGG-GC-A--
1 CTACGGTGCAATT
201819 CTACGGTGCAATT
1 CTACGGTGCAATT
201832 CTACGG-GC-A--
1 CTACGGTGCAATT
*
201841 CTTCGGTGCAATT
1 CTACGGTGCAATT
201854 CTACGG
1 CTACGG
201860 GCACTTCGGT
Statistics
Matches: 40, Mismatches: 2, Indels: 16
0.69 0.03 0.28
Matches are distributed among these distances:
9 11 0.28
10 4 0.10
11 4 0.10
12 4 0.10
13 17 0.43
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:201880 original size:22 final size:22
Alignment explanation
Indices: 201785--201872 Score: 149
Period size: 22 Copynumber: 4.0 Consensus size: 22
201775 TATGGACATC
*
201785 ATTCTACAGGCACTACGGTGCA
1 ATTCTACGGGCACTACGGTGCA
201807 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTACGGTGCA
*
201829 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTACGGTGCA
*
201851 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTACGGTGCA
201873 TTTATACGAG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 64 1.00
ACGTcount: A:0.22, C:0.27, G:0.26, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTACGGTGCA
Found at i:204086 original size:32 final size:34
Alignment explanation
Indices: 204025--204103 Score: 99
Period size: 32 Copynumber: 2.4 Consensus size: 34
204015 AATTCTAAAT
*
204025 AAATAATAATTATATAAATATTATTTTAATAAAAA
1 AAATAATAATTACATAAATATTA-TTTAATAAAAA
* *
204060 AAATAATATTTACATAAATA-TA-TTAATATAAA
1 AAATAATAATTACATAAATATTATTTAATAAAAA
*
204092 ATATAATAATTA
1 AAATAATAATTA
204104 TTTTAAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
32 19 0.49
34 2 0.05
35 18 0.46
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (34 bp):
AAATAATAATTACATAAATATTATTTAATAAAAA
Found at i:216329 original size:37 final size:36
Alignment explanation
Indices: 216259--216331 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 36
216249 TCATTAAACC
* *
216259 TTTTTATATTTTTAATTTTGTAAAAAAATTATATAA
1 TTTTTATAATTTAAATTTTGTAAAAAAATTATATAA
*
216295 TTTTTATGAATTTAAATTTTTTAAAGAAAA-TATATAA
1 TTTTTAT-AATTTAAATTTTGTAAA-AAAATTATATAA
216332 ATATTTTTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 7 0.22
37 21 0.66
38 4 0.12
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (36 bp):
TTTTTATAATTTAAATTTTGTAAAAAAATTATATAA
Found at i:216503 original size:16 final size:16
Alignment explanation
Indices: 216478--216513 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
216468 ACATTACCAA
*
216478 TAATTATATTTCCTGG
1 TAATTATATTGCCTGG
*
216494 TAATTTTATTGCCTGG
1 TAATTATATTGCCTGG
216510 TAAT
1 TAAT
216514 CTTACATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.25, C:0.11, G:0.14, T:0.50
Consensus pattern (16 bp):
TAATTATATTGCCTGG
Found at i:221571 original size:20 final size:20
Alignment explanation
Indices: 221546--221583 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
221536 ATGTAGGATG
* *
221546 TTATTACATTATTTTTATAT
1 TTATTAAATGATTTTTATAT
221566 TTATTAAATGATTTTTAT
1 TTATTAAATGATTTTTAT
221584 TTAAAATACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (20 bp):
TTATTAAATGATTTTTATAT
Found at i:221931 original size:17 final size:17
Alignment explanation
Indices: 221889--221931 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
221879 ACATATTTTC
*
221889 AATTTAAAATATATAAA
1 AATTTTAAATATATAAA
* * *
221906 AAATCTAAATATATAAT
1 AATTTTAAATATATAAA
221923 AATTTTAAA
1 AATTTTAAA
221932 ATTTTAAGGG
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (17 bp):
AATTTTAAATATATAAA
Found at i:222070 original size:19 final size:19
Alignment explanation
Indices: 222046--222090 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
222036 CGGTGTTAGT
* *
222046 GAACCGTTTTGAACTGTTC
1 GAACCGCTTTGAACAGTTC
222065 GAACCGGCTTTGAACAGTTC
1 GAACC-GCTTTGAACAGTTC
*
222085 AAACCG
1 GAACCG
222091 GATCGGACCG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (19 bp):
GAACCGCTTTGAACAGTTC
Found at i:222078 original size:20 final size:20
Alignment explanation
Indices: 222053--222091 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
222043 AGTGAACCGT
* *
222053 TTTGAACTGTTCGAACCGGC
1 TTTGAACAGTTCAAACCGGC
222073 TTTGAACAGTTCAAACCGG
1 TTTGAACAGTTCAAACCGG
222092 ATCGGACCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (20 bp):
TTTGAACAGTTCAAACCGGC
Found at i:222151 original size:10 final size:11
Alignment explanation
Indices: 222126--222152 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
222116 AACCTAAATT
222126 TTTTTATTTAA
1 TTTTTATTTAA
222137 TTTTTATTTAA
1 TTTTTATTTAA
222148 TTTTT
1 TTTTT
222153 TATATAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTATTTAA
Found at i:222152 original size:12 final size:12
Alignment explanation
Indices: 222125--222161 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
222115 CAACCTAAAT
222125 TTTTTTATTTAA
1 TTTTTTATTTAA
222137 -TTTTTATTTAA
1 TTTTTTATTTAA
*
222148 TTTTTTATATAA
1 TTTTTTATTTAA
222160 TT
1 TT
222162 ATGACGTCGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.48
12 12 0.52
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTTTATTTAA
Found at i:225056 original size:8 final size:9
Alignment explanation
Indices: 225038--225073 Score: 54
Period size: 10 Copynumber: 3.8 Consensus size: 9
225028 TTTTTATTAA
225038 TAAATTATTT
1 TAAATT-TTT
225048 TAAATTTTT
1 TAAATTTTT
225057 TAAATTTTT
1 TAAATTTTT
225066 ATAAATTT
1 -TAAATTT
225074 ATACTAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 12 0.48
10 13 0.52
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
TAAATTTTT
Found at i:225075 original size:41 final size:41
Alignment explanation
Indices: 224997--225075 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 41
224987 ATTAAAATTC
* **
224997 TAAATTATTATATATTTTAAATATTTTTATATTTTTATTAA
1 TAAATTATTATAAATTTTAAATATTTTTATAAATTTATTAA
* *
225038 TAAATTATTTTAAATTTTTTAA-ATTTTTATAAATTTAT
1 TAAATTATTATAAA-TTTTAAATATTTTTATAAATTTAT
225076 ACTAATATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
41 26 0.81
42 6 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (41 bp):
TAAATTATTATAAATTTTAAATATTTTTATAAATTTATTAA
Found at i:232567 original size:31 final size:31
Alignment explanation
Indices: 232528--232590 Score: 76
Period size: 30 Copynumber: 2.0 Consensus size: 31
232518 CTTTACAAGG
*
232528 AAAAAATTATTTTAATTAAC-AATA-AATTAT
1 AAAAAATTA-TATAATTAACAAATATAATTAT
*
232558 AAAATAATTATATAATTTACAAATATAATTAT
1 AAAA-AATTATATAATTAACAAATATAATTAT
232590 A
1 A
232591 TTAGCTAACG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 12 0.43
31 9 0.32
32 7 0.25
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (31 bp):
AAAAAATTATATAATTAACAAATATAATTAT
Found at i:234772 original size:24 final size:24
Alignment explanation
Indices: 234745--234793 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
234735 ACTGTTAATC
234745 AAACTAAATTATTAATCGAATTGA
1 AAACTAAATTATTAATCGAATTGA
234769 AAACTAAATTATTAATCGAATTGA
1 AAACTAAATTATTAATCGAATTGA
234793 A
1 A
234794 CAAAGTTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.33
Consensus pattern (24 bp):
AAACTAAATTATTAATCGAATTGA
Found at i:238104 original size:60 final size:59
Alignment explanation
Indices: 237977--238119 Score: 151
Period size: 60 Copynumber: 2.4 Consensus size: 59
237967 TATTTTTACG
* * * * * * *** *
237977 CTTTTGTATATTTTAATTTTATCATCAAATTATGACTTTTATTTCAAATTAGTCTTTATA
1 CTTTTGAATA-TTTAATTTCATCATCAAACTATAACTTTCATTCCAAATTAGTCCCCAAA
* *
238037 CTATTGAATATTGTAATTTCATCCTCAAACTATAACTTTCATTCCAAATTAGTCCCCAAA
1 CTTTTGAATATT-TAATTTCATCATCAAACTATAACTTTCATTCCAAATTAGTCCCCAAA
238097 CTTTTGAATATTTCAATTTCATC
1 CTTTTGAATATTT-AATTTCATC
238120 TCCAAATTCA
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
59 3 0.04
60 65 0.96
ACGTcount: A:0.31, C:0.17, G:0.05, T:0.47
Consensus pattern (59 bp):
CTTTTGAATATTTAATTTCATCATCAAACTATAACTTTCATTCCAAATTAGTCCCCAAA
Found at i:238474 original size:59 final size:59
Alignment explanation
Indices: 238304--238476 Score: 166
Period size: 59 Copynumber: 3.1 Consensus size: 59
238294 TATTAAATTT
* *
238304 AAATTAAATTAATTAGAGTCCTATTTAATTTTAAATTTAGCTATAATTTTATCTCTTCAA
1 AAATTAAATTAATTAGAGTCTTATTTAATTTTAAATTTAACTATAATTTTATCTCTTC-A
* * * ** * * **
238364 AAATT---TT-A-TA-A-TTTTA-TTAAATAT-AATTTATTTATAATTCTATTTTATCA
1 AAATTAAATTAATTAGAGTCTTATTTAATTTTAAATTTAACTATAATTTTATCTCTTCA
*
238414 AAATTAAATTAATTAGAGTCTTATTTAATTTTAAAATTAACTATAATTTTATCTCTTCA
1 AAATTAAATTAATTAGAGTCTTATTTAATTTTAAATTTAACTATAATTTTATCTCTTCA
238473 AAAT
1 AAAT
238477 CTTATAAATT
Statistics
Matches: 84, Mismatches: 20, Indels: 19
0.68 0.16 0.15
Matches are distributed among these distances:
50 6 0.07
51 19 0.23
52 6 0.07
53 5 0.06
54 2 0.02
55 4 0.05
56 2 0.02
57 6 0.07
58 6 0.07
59 23 0.27
60 5 0.06
ACGTcount: A:0.40, C:0.08, G:0.03, T:0.49
Consensus pattern (59 bp):
AAATTAAATTAATTAGAGTCTTATTTAATTTTAAATTTAACTATAATTTTATCTCTTCA
Found at i:239111 original size:29 final size:29
Alignment explanation
Indices: 239071--239163 Score: 107
Period size: 29 Copynumber: 3.2 Consensus size: 29
239061 AGGTCATAGA
*
239071 TTGAGAATGAAAATGAAATATTCAAAAAT
1 TTGAGGATGAAAATGAAATATTCAAAAAT
* * *
239100 TCGAGGATGAAAAT-AAAAATTCAAAATT
1 TTGAGGATGAAAATGAAATATTCAAAAAT
* ** *
239128 TTAAACATGAAAATGAAATATTCAAAAGT
1 TTGAGGATGAAAATGAAATATTCAAAAAT
239157 TTGAGGA
1 TTGAGGA
239164 CTAATTTAGA
Statistics
Matches: 50, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
28 22 0.44
29 28 0.56
ACGTcount: A:0.53, C:0.05, G:0.15, T:0.27
Consensus pattern (29 bp):
TTGAGGATGAAAATGAAATATTCAAAAAT
Found at i:243583 original size:41 final size:41
Alignment explanation
Indices: 243528--243611 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
243518 TATAAATCTA
243528 GTACCTCTTGTACGCAAGACTTGTGACCTGAGATGAAAATC
1 GTACCTCTTGTACGCAAGACTTGTGACCTGAGATGAAAATC
*
243569 GTACCTCTTTTACGCAAGACTTGTGACCTGAGATGAAAATC
1 GTACCTCTTGTACGCAAGACTTGTGACCTGAGATGAAAATC
243610 GT
1 GT
243612 GGAACTCGTA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (41 bp):
GTACCTCTTGTACGCAAGACTTGTGACCTGAGATGAAAATC
Found at i:244604 original size:13 final size:15
Alignment explanation
Indices: 244580--244611 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
244570 AATACTGTCA
244580 TTTGTCTATTATT-T
1 TTTGTCTATTATTAT
244594 TTTGT-TATTATTAT
1 TTTGTCTATTATTAT
244608 TTTG
1 TTTG
244612 GATAAATTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.16, C:0.03, G:0.09, T:0.72
Consensus pattern (15 bp):
TTTGTCTATTATTAT
Found at i:245860 original size:20 final size:18
Alignment explanation
Indices: 245835--245879 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
245825 TCTCAAGTTC
245835 CTTCTTTAAATTATCTATTT
1 CTTCTTTAAA-TATCT-TTT
*
245855 CTTCTTTCAATATCTTTT
1 CTTCTTTAAATATCTTTT
*
245873 CCTCTTT
1 CTTCTTT
245880 GGTTTCTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 9 0.39
19 5 0.22
20 9 0.39
ACGTcount: A:0.18, C:0.22, G:0.00, T:0.60
Consensus pattern (18 bp):
CTTCTTTAAATATCTTTT
Found at i:247028 original size:214 final size:215
Alignment explanation
Indices: 246716--247138 Score: 584
Period size: 214 Copynumber: 2.0 Consensus size: 215
246706 TTCTCATTCA
* ** *
246716 ACAAGCCCCAATGCTTATATGGTAACATAACCAAGAATGGATTTAAGTCACAATTCAGTTGGCTG
1 ACAAGCCCCAATGCTTATATGGTAAAATAACCAAGAATACATTTAAGTCAAAATTCAGTTGGCTG
* * * * * *
246781 TGTATTCATAAATGAAATAAATTTTGGAATACAATAGTGCATGTTAATTTAATGCATGAAAAAGC
66 TGTATTCATAAATAAAATAAATTTTAGAATACAACAGTACATGTGAATTTAATGCATGAAAAAGA
** * * * * *
246846 TGCAAAAGCTTGATTCAGAAGCCAAACCTCTGTTCTGAACTCGGTCAAAAATT-CATTTCTAAGA
131 TGCAAAAGCTCAACTCAGAAGCCAAACATCTGTTCGGAACTCAGTAAAAAATTCCA-TTCTAAGA
*
246910 T-GAAGCCCTATACTCCAACTC
195 TGGAA-CCCTAAACTCCAACTC
* *
246931 ACAAGTCCCAATGC-T-TATGGTAAAATAACCAAGAATACATTTTAGTCAAAATTCAGTTGGCTT
1 ACAAGCCCCAATGCTTATATGGTAAAATAACCAAGAATACATTTAAGTCAAAATTCAGTTGGC-T
* *
246994 GTGTGTTCATAAATAAAATAAATTTTATAATACAACAGTACATGTGAATTTAATGCATGAAAAAG
65 GTGTATTCATAAATAAAATAAATTTTAGAATACAACAGTACATGTGAATTTAATGCATGAAAAAG
*
247059 ATGCAAAAGCTCAACTCAGAAGCCAAATATCTGTTCGGAACTCAGTAAAAAATTCCATTCTAAGA
130 ATGCAAAAGCTCAACTCAGAAGCCAAACATCTGTTCGGAACTCAGTAAAAAATTCCATTCTAAGA
247124 TGGAACCCTAAACTC
195 TGGAACCCTAAACTC
247139 AATTCCCAGC
Statistics
Matches: 182, Mismatches: 23, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
213 41 0.23
214 123 0.68
215 18 0.10
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (215 bp):
ACAAGCCCCAATGCTTATATGGTAAAATAACCAAGAATACATTTAAGTCAAAATTCAGTTGGCTG
TGTATTCATAAATAAAATAAATTTTAGAATACAACAGTACATGTGAATTTAATGCATGAAAAAGA
TGCAAAAGCTCAACTCAGAAGCCAAACATCTGTTCGGAACTCAGTAAAAAATTCCATTCTAAGAT
GGAACCCTAAACTCCAACTC
Found at i:255194 original size:16 final size:16
Alignment explanation
Indices: 255173--255205 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
255163 TAATAAATAG
255173 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
255189 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
255205 A
1 A
255206 AAATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:255286 original size:10 final size:10
Alignment explanation
Indices: 255271--255361 Score: 56
Period size: 10 Copynumber: 9.7 Consensus size: 10
255261 CATTTAATAA
255271 ATAAACGAAC
1 ATAAACGAAC
255281 ATAAACGAAC
1 ATAAACGAAC
255291 ----ACGAAC
1 ATAAACGAAC
255297 ATAAACGAAC
1 ATAAACGAAC
255307 ----ACGAAC
1 ATAAACGAAC
255313 ATAAACGAAC
1 ATAAACGAAC
** *
255323 ACGAAC-ATAA
1 ATAAACGA-AC
255333 ATGAACACGAAC
1 AT-AA-ACGAAC
*
255345 ATAAACAAAC
1 ATAAACGAAC
255355 ATAAACG
1 ATAAACG
255362 TTGGAGACCC
Statistics
Matches: 61, Mismatches: 8, Indels: 24
0.66 0.09 0.26
Matches are distributed among these distances:
6 12 0.20
9 1 0.02
10 39 0.64
11 3 0.05
12 5 0.08
13 1 0.02
ACGTcount: A:0.58, C:0.22, G:0.11, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:255296 original size:16 final size:16
Alignment explanation
Indices: 255275--255355 Score: 144
Period size: 16 Copynumber: 5.1 Consensus size: 16
255265 TAATAAATAA
255275 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
255291 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
255307 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
255323 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
*
255339 ACGAACATAAACAAAC
1 ACGAACATAAACGAAC
255355 A
1 A
255356 TAAACGTTGG
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 62 1.00
ACGTcount: A:0.58, C:0.23, G:0.11, T:0.07
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:256114 original size:14 final size:14
Alignment explanation
Indices: 256097--256142 Score: 83
Period size: 14 Copynumber: 3.3 Consensus size: 14
256087 AATGAACATA
*
256097 AACGAACATAATCG
1 AACGAACATAACCG
256111 AACGAACATAACCG
1 AACGAACATAACCG
256125 AACGAACATAACCG
1 AACGAACATAACCG
256139 AACG
1 AACG
256143 TTCACGAACG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.50, C:0.26, G:0.15, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:256117 original size:24 final size:24
Alignment explanation
Indices: 256077--256127 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
256067 GATTGGGTTA
*
256077 AACATAAATGAATGAACATAAACG
1 AACATAAATGAACGAACATAAACG
*
256101 AACAT-AATCGAACGAACATAACCG
1 AACATAAAT-GAACGAACATAAACG
256125 AAC
1 AAC
256128 GAACATAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.55, C:0.20, G:0.12, T:0.14
Consensus pattern (24 bp):
AACATAAATGAACGAACATAAACG
Found at i:259763 original size:3 final size:3
Alignment explanation
Indices: 259757--259789 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
259747 ATTGAAAAAG
259757 ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
259790 AAAGCTACCT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:259779 original size:14 final size:14
Alignment explanation
Indices: 259760--259788 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
259750 GAAAAAGATA
259760 ATAATAATAATAAT
1 ATAATAATAATAAT
259774 ATAATAATAATAAT
1 ATAATAATAATAAT
259788 A
1 A
259789 AAAAGCTACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:259779 original size:17 final size:17
Alignment explanation
Indices: 259757--259789 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
259747 ATTGAAAAAG
259757 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
259774 ATAATAATAATAATAA
1 ATAATAATAATAATAA
259790 AAAGCTACCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATAATAATAATAATAAT
Found at i:263204 original size:5 final size:5
Alignment explanation
Indices: 263194--263222 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
263184 CACTAATTAT
263194 AATAG AATAG AATAG AATAG AATAG AATA
1 AATAG AATAG AATAG AATAG AATAG AATA
263223 TTAGAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.21
Consensus pattern (5 bp):
AATAG
Found at i:270816 original size:18 final size:18
Alignment explanation
Indices: 270793--270833 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
270783 CTACGTTAAT
270793 GAATTGAAATATGTGAAG
1 GAATTGAAATATGTGAAG
270811 GAATTGAAATATGTGAAG
1 GAATTGAAATATGTGAAG
270829 GAATT
1 GAATT
270834 TGATATCAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.27, T:0.29
Consensus pattern (18 bp):
GAATTGAAATATGTGAAG
Found at i:271359 original size:33 final size:33
Alignment explanation
Indices: 271311--271433 Score: 156
Period size: 33 Copynumber: 3.6 Consensus size: 33
271301 CCCTAAACCC
271311 AAACCCGGCCCGACCCGAATATCACACTTAAAA
1 AAACCCGGCCCGACCCGAATATCACACTTAAAA
* * *
271344 AAACCTGGCCTGACCCAAATATCACACTTAAAA
1 AAACCCGGCCCGACCCGAATATCACACTTAAAA
*
271377 AAACCCGACCCGACTCGACCCGAATATCACACTTAAAA
1 AAACCCG----G-CCCGACCCGAATATCACACTTAAAA
*
271415 AAACCCGACCCGACCCGAA
1 AAACCCGGCCCGACCCGAA
271434 CAAAATAAAG
Statistics
Matches: 76, Mismatches: 9, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
33 46 0.61
37 1 0.01
38 29 0.38
ACGTcount: A:0.40, C:0.37, G:0.11, T:0.12
Consensus pattern (33 bp):
AAACCCGGCCCGACCCGAATATCACACTTAAAA
Found at i:271403 original size:38 final size:38
Alignment explanation
Indices: 271321--271428 Score: 154
Period size: 38 Copynumber: 3.0 Consensus size: 38
271311 AAACCCGGCC
* *
271321 CGACCCGAATATCACACTTAAAAAAACCTG----GCCT
1 CGACCCGAATATCACACTTAAAAAAACCCGACCCGACT
*
271355 -GACCCAAATATCACACTTAAAAAAACCCGACCCGACT
1 CGACCCGAATATCACACTTAAAAAAACCCGACCCGACT
271392 CGACCCGAATATCACACTTAAAAAAACCCGACCCGAC
1 CGACCCGAATATCACACTTAAAAAAACCCGACCCGAC
271429 CCGAACAAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
33 27 0.42
37 3 0.05
38 35 0.54
ACGTcount: A:0.41, C:0.35, G:0.10, T:0.14
Consensus pattern (38 bp):
CGACCCGAATATCACACTTAAAAAAACCCGACCCGACT
Done.