Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009577.1 Hibiscus syriacus cultivar Beakdansim tig00116945_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: 348734
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 1 of 2
Found at i:550 original size:18 final size:18
Alignment explanation
Indices: 529--573 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
519 TCCACTTCGG
* *
529 GAGCCATCACCTCGCCTA
1 GAGCCATCACCTCACCCA
*
547 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
565 GAGCCATCA
1 GAGCCATCA
574 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1072 original size:20 final size:20
Alignment explanation
Indices: 1047--1092 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1037 TAGTTTACTT
*
1047 TCGCAACATGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
1067 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
1087 TCGCAA
1 TCGCAA
1093 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:1101 original size:19 final size:20
Alignment explanation
Indices: 1058--1102 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1048 CGCAACATGA
1058 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
1078 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
1097 AAATGA
1 AAATGA
1103 AAATTGCAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.18
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:1111 original size:19 final size:19
Alignment explanation
Indices: 1086--1144 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
1076 GGAAATGGCT
1086 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
1105 ATTGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
1119 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1138 ATCGCAA
1 ATCGCAA
1145 CGACAAATTG
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 9 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 16 0.52
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1152 original size:19 final size:19
Alignment explanation
Indices: 1066--1146 Score: 55
Period size: 19 Copynumber: 4.5 Consensus size: 19
1056 GAAAATGACT
***
1066 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGAAA
*
1086 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
* *
1105 ATTGCAA--CG--A-CAAA
1 ATCGCAACGCGAAATGAAA
*
1119 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
1138 ATCGCAACG
1 ATCGCAACG
1147 ACAAATTGCA
Statistics
Matches: 47, Mismatches: 9, Indels: 11
0.70 0.13 0.16
Matches are distributed among these distances:
14 9 0.19
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 23 0.49
20 9 0.19
ACGTcount: A:0.42, C:0.21, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:1163 original size:32 final size:33
Alignment explanation
Indices: 1086--1169 Score: 143
Period size: 33 Copynumber: 2.6 Consensus size: 33
1076 GGAAATGGCT
*
1086 ATCGCAATGCGAAATGAAAATTGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1119 ATCGCAATGCGAAATGAAAATCGCAACGAC-AA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1151 ATTGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1170 GTCGTATGCG
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 20 0.41
33 29 0.59
ACGTcount: A:0.48, C:0.18, G:0.19, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1211 original size:14 final size:14
Alignment explanation
Indices: 1192--1281 Score: 72
Period size: 14 Copynumber: 5.8 Consensus size: 14
1182 TTGTGTTTCG
1192 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1206 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
1222 CACATTGCGATTTTGT
1 --CGTTGCGATTTTGT
*
1238 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
1255 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
1271 CGTTGCGATTT
1 CGTTGCGATTT
1282 GCATTTCGCA
Statistics
Matches: 61, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
14 27 0.44
15 3 0.05
16 8 0.13
17 4 0.07
18 13 0.21
19 6 0.10
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1233 original size:32 final size:32
Alignment explanation
Indices: 1187--1298 Score: 188
Period size: 33 Copynumber: 3.4 Consensus size: 32
1177 GCGATTTGTG
*
1187 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTCA
*
1219 TTTCACATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGA-TTTCA
1252 TTTCGCATTGCGATTTTGTCGTTGCGATTTGCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTT-CA
1285 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
1299 AGCCATTTCC
Statistics
Matches: 75, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
32 28 0.37
33 47 0.63
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.46
Consensus pattern (32 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTCA
Found at i:1256 original size:65 final size:67
Alignment explanation
Indices: 1170--1298 Score: 201
Period size: 65 Copynumber: 2.0 Consensus size: 67
1160 CGAAATGAAA
* *
1170 GTCGTATGCGATTTGTGTTTCGCGTTGCGATTTTGTCGTTGCGATTT-CATTTCACATTGCGATT
1 GTCGTATGCGATTTGTATTTCGCATTGCGATTTTGTCGTTGCGATTTGCATTTCACATTGCGATT
1234 TT
66 TT
*
1236 GTCGT-TGCGATTT-TCATTTCGCATTGCGATTTTGTCGTTGCGATTTGCATTTCGCATTGCGAT
1 GTCGTATGCGATTTGT-ATTTCGCATTGCGATTTTGTCGTTGCGATTTGCATTTCACATTGCGAT
1299 AGCCATTTCC
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
64 1 0.02
65 37 0.64
66 20 0.34
ACGTcount: A:0.12, C:0.18, G:0.24, T:0.46
Consensus pattern (67 bp):
GTCGTATGCGATTTGTATTTCGCATTGCGATTTTGTCGTTGCGATTTGCATTTCACATTGCGATT
TT
Found at i:1317 original size:20 final size:19
Alignment explanation
Indices: 1283--1338 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
1273 TTGCGATTTG
*
1283 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1302 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
1322 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
1339 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:3221 original size:14 final size:14
Alignment explanation
Indices: 3187--3225 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
3177 TTTATTGTTT
3187 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
3201 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
3215 TGTTGATTTGT
1 AATTGATTTGT
3226 TTAATTGGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:3421 original size:20 final size:20
Alignment explanation
Indices: 3396--3471 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
3386 TCGCATTGCG
*
3396 ATTTTCTAGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
* ***
3416 ATTTTCGCGTTGCGATTTTTC
1 ATTTTCGAGTTGCGA-TAGCC
*
3437 A-TTTCGAATTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
*
3456 ATTTTCGCGTTGCGAT
1 ATTTTCGAGTTGCGAT
3472 TTCCCCGTTG
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
19 3 0.07
20 36 0.86
21 3 0.07
ACGTcount: A:0.17, C:0.20, G:0.21, T:0.42
Consensus pattern (20 bp):
ATTTTCGAGTTGCGATAGCC
Found at i:3429 original size:34 final size:34
Alignment explanation
Indices: 3384--3487 Score: 109
Period size: 40 Copynumber: 2.9 Consensus size: 34
3374 GCGATTTTCA
*
3384 TTTCGCATTGCGATTTTCTAGTTGCGATAGCCAT
1 TTTCGCGTTGCGATTTTCTAGTTGCGATAGCCAT
*
3418 TTTCGCGTTGCGATTTTTCATTTCGAATTGCGATAGCCAT
1 TTTCGCGTTGCGA-TTTTC---T--AGTTGCGATAGCCAT
* **
3458 TTTCGCGTTGCGATTTCCCCGTTGCGATAG
1 TTTCGCGTTGCGATTTTCTAGTTGCGATAG
3488 TCAAATGAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
34 21 0.36
35 5 0.09
38 1 0.02
39 4 0.07
40 27 0.47
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.40
Consensus pattern (34 bp):
TTTCGCGTTGCGATTTTCTAGTTGCGATAGCCAT
Found at i:3710 original size:20 final size:20
Alignment explanation
Indices: 3685--3734 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
3675 TTGAAGATGA
3685 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
3705 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
3725 TTGCGATTTT
1 TTGCGATTTT
3735 GTATTATCTC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:3789 original size:21 final size:20
Alignment explanation
Indices: 3763--3812 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
3753 AGTCAGTATT
*
3763 GCATTGCGATTTTCCAAATTC
1 GCATTGCGA-TTTACAAATTC
**
3784 GCATTGCGATTTACTTATTC
1 GCATTGCGATTTACAAATTC
3804 GCATTGCGA
1 GCATTGCGA
3813 ATTAGGAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (20 bp):
GCATTGCGATTTACAAATTC
Found at i:4028 original size:12 final size:12
Alignment explanation
Indices: 4009--4043 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
3999 CTCTCCGGCG
4009 ACATCCGTTCCT
1 ACATCCGTTCCT
*
4021 ATATCCGTTCCT
1 ACATCCGTTCCT
*
4033 ACATCCTTTCC
1 ACATCCGTTCC
4044 CATCCGGCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.17, C:0.40, G:0.06, T:0.37
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:4624 original size:24 final size:24
Alignment explanation
Indices: 4597--4650 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
4587 GTATTCGAAA
*
4597 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
4621 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
4645 TTTGAT
1 TTTGAT
4651 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:4842 original size:12 final size:12
Alignment explanation
Indices: 4825--4849 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4815 ATATAATCCT
4825 GAAGAAGAAAAA
1 GAAGAAGAAAAA
4837 GAAGAAGAAAAA
1 GAAGAAGAAAAA
4849 G
1 G
4850 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:6568 original size:19 final size:19
Alignment explanation
Indices: 6546--6634 Score: 72
Period size: 19 Copynumber: 5.2 Consensus size: 19
6536 AGAAATTACT
6546 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
6565 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
6579 ATCACAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
6598 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
6612 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
6631 ATCG
1 ATCG
6635 TAACACGAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 20
0.65 0.10 0.25
Matches are distributed among these distances:
14 18 0.35
15 2 0.04
16 4 0.08
17 4 0.08
18 2 0.04
19 22 0.42
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:6592 original size:33 final size:33
Alignment explanation
Indices: 6550--6634 Score: 152
Period size: 33 Copynumber: 2.6 Consensus size: 33
6540 ATTACTATCG
6550 CAATGCGAAATGAAAATCGCAACGAGAGAATCA
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCA
* *
6583 CAATGCGAAATGAAAATCGCAACGAGGGAATCG
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCA
6616 CAATGCGAAATGAAAATCG
1 CAATGCGAAATGAAAATCG
6635 TAACACGAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.13
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGAGAGAATCA
Found at i:6673 original size:14 final size:14
Alignment explanation
Indices: 6654--6710 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
6644 TTTAATTTCG
6654 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
6668 CGTTGCGATTTTCATTTCA
1 CGTTGCGA--TTC---TCT
6687 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
6701 CGTTGCGATT
1 CGTTGCGATT
6711 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:6691 original size:33 final size:33
Alignment explanation
Indices: 6648--6728 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
6638 CACGAATTTA
6648 ATTTCGCGTTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTCTCTCGTTGCGATTTTC
*
6681 ATTTCACGTTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTCTCTCGTTGCGATTTTC
*
6714 ATTTCGCATTGCGAT
1 ATTTCGCGTTGCGAT
6729 AGTACTTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.44
Consensus pattern (33 bp):
ATTTCGCGTTGCGATTCTCTCGTTGCGATTTTC
Found at i:6692 original size:19 final size:19
Alignment explanation
Indices: 6668--6728 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
6658 GCGATTCTCT
6668 CGTTGCGATTTTCATTTCA
1 CGTTGCGATTTTCATTTCA
*
6687 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCA
*
6701 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCA
*
6720 CATTGCGAT
1 CGTTGCGAT
6729 AGTACTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 10 0.29
16 3 0.09
17 3 0.09
19 18 0.53
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCA
Found at i:6854 original size:14 final size:14
Alignment explanation
Indices: 6835--6871 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
6825 CATCAATTAA
6835 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
6849 ACAAATCACCTTTT
1 ACAAATCAACTTTT
6863 ACAAATCAA
1 ACAAATCAA
6872 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:8293 original size:21 final size:21
Alignment explanation
Indices: 8227--8293 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
8217 GTGAATCGGG
*
8227 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
8247 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
8269 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
8290 CTCT
1 CTCT
8294 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:8743 original size:91 final size:90
Alignment explanation
Indices: 8567--8751 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 90
8557 ATTTCAAACT
*
8567 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
8632 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
8660 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
* *
8724 GTATTGGCAGCAACTGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
8751 T
1 T
8752 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 41 0.47
93 19 0.22
95 27 0.31
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:10522 original size:33 final size:34
Alignment explanation
Indices: 10465--10530 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 34
10455 ACAAGTTAAT
10465 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
10499 GAGAATCGCAACGC-GAAATGACTATCGCAACG
1 GAGAATCGCAACGCGGAAATGACTATCGCAACG
10531 CGAAATGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 18 0.56
34 14 0.44
ACGTcount: A:0.38, C:0.24, G:0.26, T:0.12
Consensus pattern (34 bp):
GAGAATCGCAACGCGGAAATGACTATCGCAACGA
Found at i:10549 original size:52 final size:52
Alignment explanation
Indices: 10462--10585 Score: 185
Period size: 52 Copynumber: 2.4 Consensus size: 52
10452 GCAACAAGTT
* **
10462 AATGAGAATCGCAACGCGGAAATGACTATCGCAACGAGAGAATCGCAACGCGA
1 AATGAAAATCGCAACGC-GAAATGAAAATCGCAACGAGAGAATCGCAACGCGA
**
10515 AATGACTATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGA
1 AATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGA
*
10567 AATGAAAATCGCAATGCGA
1 AATGAAAATCGCAACGCGA
10586 TTTTGGTTTC
Statistics
Matches: 64, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
52 49 0.77
53 15 0.23
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.12
Consensus pattern (52 bp):
AATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGA
Found at i:10578 original size:19 final size:19
Alignment explanation
Indices: 10440--10585 Score: 105
Period size: 19 Copynumber: 8.1 Consensus size: 19
10430 TCTTTTGGTT
**
10440 GAAATGAAAATCGCAACAA
1 GAAATGAAAATCGCAACGC
* *
10459 GTTAATGAGAATCGCAACGC
1 G-AAATGAAAATCGCAACGC
**
10479 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
10497 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
**
10513 GAAATGACTATCGCAACGC
1 GAAATGAAAATCGCAACGC
10532 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
10549 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
10565 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
10584 GA
1 GA
10586 TTTTGGTTTC
Statistics
Matches: 99, Mismatches: 16, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
14 19 0.19
15 2 0.02
16 4 0.04
17 3 0.03
18 3 0.03
19 41 0.41
20 26 0.26
21 1 0.01
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:10603 original size:19 final size:19
Alignment explanation
Indices: 10581--10628 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
10571 AAAATCGCAA
*
10581 TGCGATTTTGGTTT-CGCGT
1 TGCGATTTT-ATTTCCGCGT
*
10600 TGCGATAGTTATTTCCGCGT
1 TGCGAT-TTTATTTCCGCGT
10620 TGCGATTTT
1 TGCGATTTT
10629 CATTCTCGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.10, C:0.17, G:0.27, T:0.46
Consensus pattern (19 bp):
TGCGATTTTATTTCCGCGT
Found at i:11172 original size:20 final size:20
Alignment explanation
Indices: 11147--11197 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
11137 GCTATGTAAA
11147 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-GTAAGTAT
* * *
11167 TCGCATTGTGATTTACGTAT
1 TCGCATTGCGATGTAAGTAT
11187 TCGCATTGCGA
1 TCGCATTGCGA
11198 ATTATGAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 3 0.12
20 23 0.88
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.35
Consensus pattern (20 bp):
TCGCATTGCGATGTAAGTAT
Found at i:11218 original size:21 final size:21
Alignment explanation
Indices: 11194--11249 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
11184 TATTCGCATT
*
11194 GCGAATTATGAAAATCGCAAC
1 GCGAATTACGAAAATCGCAAC
* *
11215 GCGAA-TACGTAAATCGCAAT
1 GCGAATTACGAAAATCGCAAC
*
11235 GCGAATTAGGAAAAT
1 GCGAATTACGAAAAT
11250 TGCATTGCGA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (21 bp):
GCGAATTACGAAAATCGCAAC
Found at i:11258 original size:21 final size:21
Alignment explanation
Indices: 11187--11259 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
11177 ATTTACGTAT
* *
11187 TCGCATTGCGAATTATGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
11208 TCGCAACGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
*
11228 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
11249 TTGCATTGCGA
1 TCGCAATGCGA
11260 TAGTCAGTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.40
21 25 0.60
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:11362 original size:21 final size:22
Alignment explanation
Indices: 11314--11362 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
11304 ACTTATTCGT
11314 ATTGCG-AATTGGGAAAATCGC
1 ATTGCGAAATTGGGAAAATCGC
**
11335 AACGCGAAATT-GGAAAATCGC
1 ATTGCGAAATTGGGAAAATCGC
11356 ATTGCGA
1 ATTGCGA
11363 TAGTCATAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.37, C:0.16, G:0.27, T:0.20
Consensus pattern (22 bp):
ATTGCGAAATTGGGAAAATCGC
Found at i:12577 original size:23 final size:23
Alignment explanation
Indices: 12546--12593 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
12536 CAATCCAACC
12546 TTTAAATTTTATAAAA-ATTTAAT
1 TTTAAATTTTA-AAAATATTTAAT
* *
12569 TTTATATTTTAAAAATATTTGAT
1 TTTAAATTTTAAAAATATTTAAT
12592 TT
1 TT
12594 CGTCTCTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
TTTAAATTTTAAAAATATTTAAT
Found at i:18161 original size:18 final size:19
Alignment explanation
Indices: 18121--18161 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
18111 AAATTGATGG
18121 TTATAAAAATTCAAAAATA
1 TTATAAAAATTCAAAAATA
* *
18140 -TATAAAAA-TCAATATTA
1 TTATAAAAATTCAAAAATA
18157 TTATA
1 TTATA
18162 TCCCAATTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TTATAAAAATTCAAAAATA
Found at i:18441 original size:27 final size:27
Alignment explanation
Indices: 18403--18459 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
18393 ACATGTTCAA
*
18403 TTATTTCACTTTCAAATAATCTATAGG
1 TTATTTCACTTTCAAATAATCCATAGG
* *
18430 TTATTTTACTTTCAAATAATCCATGGG
1 TTATTTCACTTTCAAATAATCCATAGG
18457 TTA
1 TTA
18460 GTATGTAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.46
Consensus pattern (27 bp):
TTATTTCACTTTCAAATAATCCATAGG
Found at i:18799 original size:40 final size:40
Alignment explanation
Indices: 18744--18825 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 40
18734 TCAAATAAAT
* * *
18744 TTCACTATAAATTTAATTGTATGATGATAATTAGTTGTAA
1 TTCACTATAAATTTAATTGTATAATAATAATTACTTGTAA
* *
18784 TTCACTATAAGTTTAATTGTATAATAATACTTACTTGTAA
1 TTCACTATAAATTTAATTGTATAATAATAATTACTTGTAA
18824 TT
1 TT
18826 GCAGTTATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.46
Consensus pattern (40 bp):
TTCACTATAAATTTAATTGTATAATAATAATTACTTGTAA
Found at i:18900 original size:25 final size:27
Alignment explanation
Indices: 18841--18908 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 27
18831 TATATTTCAA
*
18841 ATTAT-ATATACAATTACAATCAATAC
1 ATTATAATATACAACTACAATCAATAC
18867 ATTCAT-ATAATTACAACTACAATCAA-AC
1 ATT-ATAAT-A-TACAACTACAATCAATAC
*
18895 ATTATAATACACAA
1 ATTATAATATACAA
18909 ACAAATGAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
26 7 0.19
27 7 0.19
28 8 0.22
29 14 0.39
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (27 bp):
ATTATAATATACAACTACAATCAATAC
Found at i:19585 original size:16 final size:16
Alignment explanation
Indices: 19564--19596 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
19554 TAATAAATAG
19564 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
19580 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
19596 A
1 A
19597 AATTTTTTTT
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:19681 original size:10 final size:10
Alignment explanation
Indices: 19662--19736 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
19652 CATTTAATAA
19662 ATAAACGAAC
1 ATAAACGAAC
*
19672 ATAAATGAAC
1 ATAAACGAAC
19682 ----ACGAAC
1 ATAAACGAAC
19688 ATAAACGAAC
1 ATAAACGAAC
** *
19698 ACGAAC-ATAA
1 ATAAACGA-AC
19708 ATGAACACGAAC
1 AT-AA-ACGAAC
19720 ATAAACGAAC
1 ATAAACGAAC
19730 ATAAACG
1 ATAAACG
19737 TTGGAGACCC
Statistics
Matches: 49, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
6 5 0.10
9 1 0.02
10 34 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.20, G:0.12, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:19687 original size:16 final size:16
Alignment explanation
Indices: 19658--19730 Score: 114
Period size: 16 Copynumber: 4.7 Consensus size: 16
19648 CGTTCATTTA
19658 ATAAAT-AA-ACGAAC
1 ATAAATGAACACGAAC
19672 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
*
19688 ATAAACGAACACGAAC
1 ATAAATGAACACGAAC
19704 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
*
19720 ATAAACGAACA
1 ATAAATGAACA
19731 TAAACGTTGG
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
14 6 0.11
15 2 0.04
16 46 0.85
ACGTcount: A:0.59, C:0.19, G:0.11, T:0.11
Consensus pattern (16 bp):
ATAAATGAACACGAAC
Found at i:19702 original size:32 final size:32
Alignment explanation
Indices: 19666--19730 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
19656 TAATAAATAA
19666 ACGAACATAAATGAACACGAACATAAACGAAC
1 ACGAACATAAATGAACACGAACATAAACGAAC
19698 ACGAACATAAATGAACACGAACATAAACGAAC
1 ACGAACATAAATGAACACGAACATAAACGAAC
19730 A
1 A
19731 TAAACGTTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.57, C:0.22, G:0.12, T:0.09
Consensus pattern (32 bp):
ACGAACATAAATGAACACGAACATAAACGAAC
Found at i:20499 original size:14 final size:14
Alignment explanation
Indices: 20482--20537 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 14
20472 AATGAACATA
20482 AACGAACATAATCG
1 AACGAACATAATCG
20496 AACGAACAT-A---
1 AACGAACATAATCG
* *
20506 AACAAACATAACCG
1 AACGAACATAATCG
*
20520 AACAAACATAATCG
1 AACGAACATAATCG
20534 AACG
1 AACG
20538 TTCACGAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 8 0.23
11 1 0.03
13 1 0.03
14 25 0.71
ACGTcount: A:0.55, C:0.23, G:0.11, T:0.11
Consensus pattern (14 bp):
AACGAACATAATCG
Found at i:20502 original size:24 final size:24
Alignment explanation
Indices: 20462--20536 Score: 89
Period size: 24 Copynumber: 3.1 Consensus size: 24
20452 GATTGAGTTA
*
20462 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
*
20486 AACATAATCGAACGAACATAAACA
1 AACATAATCGAACGAACATAAACG
* * *
20510 AACATAACCGAACAAACATAATCG
1 AACATAATCGAACGAACATAAACG
20534 AAC
1 AAC
20537 GTTCACGAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
23 3 0.07
24 41 0.93
ACGTcount: A:0.57, C:0.20, G:0.09, T:0.13
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:21115 original size:20 final size:20
Alignment explanation
Indices: 21090--21128 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
21080 AAAATGAGAG
*
21090 AATTAAAATAAATCTAATTA
1 AATTAAAATAAATATAATTA
*
21110 AATTAAATTAAATATAATT
1 AATTAAAATAAATATAATT
21129 TTTATTTAAG
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:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
AATTAAAATAAATATAATTA
Found at i:23904 original size:20 final size:21
Alignment explanation
Indices: 23879--23919 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
23869 CTTTACATAG
23879 TAGTATCGATACCAT-AGGCA
1 TAGTATCGATACCATCAGGCA
*
23899 TAGTATTGATACCATCAGGCA
1 TAGTATCGATACCATCAGGCA
23920 CCAACGGCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (21 bp):
TAGTATCGATACCATCAGGCA
Found at i:25854 original size:916 final size:905
Alignment explanation
Indices: 24086--25917 Score: 2180
Period size: 916 Copynumber: 2.0 Consensus size: 905
24076 CAACTTCATT
* *
24086 CCAACATATAAATACAAGTTCAAGACACTTGAAGAATGGTTAGAACACCTATCCAAGCAATCAAA
1 CCAAGATATAAATACAAGTTCAAGACACTTGAAGAAGGGTTAGAACACCTATCCAAGCAATCAAA
* *
24151 CACAAGAGAAGAGTTTTTCATTCGTATTTTCTATTCTCTTGTAAATATTGTGTTTTAGTGAGCTT
66 CACAAGAGAAGAATTTTTCATTCATATTTTCTATTCTCTTGTAAATATTGTGTTTTAGTGAGCTT
*
24216 CAATTTGTAAACACCTACCTTGTGAGGGTTTTCACTATCTTTCTTTTGTAAAAAAGGTTTGGTTA
131 CAATTTGTAAACACCTACCTTGTGAGGGTTTTCACTATCTTTCTTTTGTAAAAAAGGATTGGTTA
* * * * *
24281 TATCTTAGCTAAGTGAAAAGATAGGGAGTGTAAATGTTATCTCTCGATCATTTAAAAAGAATGAA
196 TATCTTAACAAAGTGAAAAGATAGGGAGTGTAAAGGTTATCTCTCGATCATATAAAAAGAAAGAA
* * * *
24346 CAAATTAGTGAATTTGTTAGAAAATCCAAAGTGATGAGCTTAGGTAGTGGATGTAGACTTGGTTG
261 CAAATTAGTGAATTTGTTAGAAAATCCAAAGTGAGGAGCTAAGGTAGTGGAGGTAGACTTAGTTG
* * *** *
24411 ATAAGTTAAACCACTATAAATCCTTATGCCAATTTTTTTTATCTTTTACTCTCCTCACTCCTTAA
326 AGAAGTCAAACCACTATAAATCCTTATGCCAAAACTTTCTATCTTTTACTCTCCTCACTCCTTAA
* * *
24476 TCAAATTATTGCCAATTAATCCACTTGTAACTCTTTTGGTTGTAAATTCGAGCTTTCGCAAATCC
391 TCAAATTATTACCAATTAATCCACTTGCAACACTTTTGGTTGTAAATTCGAGCTTTCG--AATCC
* * ** * * ** * *
24541 TAACAATTGATATCAGAGCTTGACTTGTTAGAATACCTCACATTTTTAACACGATCCTCGAAGAA
454 CAACAATTGATATAAGAGCTTGACTCATTAGAAGACCTAACACCTTGAACAC-ATCCTAGAAGAA
* * * * * *
24606 GCTCTACCGATTCCCGATGCAACCCACAAAAATATAGTTTTAACCTCCGGTGCTTATTACTTGGA
518 GCTATACCGATTCCCGACGCAACCCACAAAAATAGAGCTTCAACCTCCGATGCTTATTACTTGGA
* * *
24671 AAATTCTCAACCAGTTAACAAGCCACCCTATTTCAATGGAGCAAATTATGCATATTTAAAGAATA
583 AAATTCTCAACCAGTCAACAAGCCACCCTATTTCAATGAAGCAAATTATGCATATTGAAAGAATA
* * * *
24736 AAATGATGTTCTTAATTCAAGCCAACGATCTAGGAGCTTGGAACTCAATCATGAAGGGTTACTCC
648 AAATAATGCTCTTAATTCAACCCAACGATCTAGGAGCTTGAAACTCAATCATGAAGGGTTACTCC
* *
24801 ACTCCACCCGGTAAGATGGACGATTGGAGTGATGGAGATAAGAAAAAGTTCCAGCTCAATCCTAA
713 ACTCCACCCGGTAAGATGGACGATTGGAGTGATGGAGAGAAGAAAAAATTCCAGCTCAATCCTAA
* * * *
24866 GGGTATGCACATCATTTTTTGTGCATTAGGCCCGGATGAATATGGAAGAGTCTCATCTTGTTCTA
778 GGCTATGCACATCATCTTTTGTGCATTAGGCCCGGATGAATATGGAAGAGTCCCATCTTGTTCCA
* *
24931 ATGCCAAGGAGATATGAGACAAACTCCAAGTCACTCATTAAGGAACCGA-TGAAGTGAGGGAAA
843 ATGCCAAGGAGATATGAGACAAACTCCAAGTCACTCATGAAGGAACC-ATTAAAGTGAGGGAAA
* * *
24994 CCAAGATATAAATATAAGTTCAAGACACTTGAA-AAGGGGTTAGACCACCTATCCAAGCATTCAA
1 CCAAGATATAAATACAAGTTCAAGACACTTGAAGAA-GGGTTAGAACACCTATCCAAGCAATCAA
*
25058 ACACAAGAGAAGAATTTTTCATTCATATTTTACT-TTCTCTTGTAAATATTTTGTTCTT-GTGAG
65 ACACAAGAGAAGAATTTTTCATTCATATTTT-CTATTCTCTTGTAAATATTGTGTT-TTAGTGAG
* * * * *
25121 CTTTATTTTGTAAACAACCTACCTT-TGAGAGATTTTATTTGTTTACTTATTTTTACCTTTTGT-
128 CTTCAATTTGTAAAC-ACCTACCTTGTGAG-G------GTT-TTCAC-TATCTTT--CTTTTGTA
** * * *
25184 AAACGGGATTGGTTCTAGT-TTAACAAAGTGAAAA-ACTAGGGATTTGTAAAGGTTATCTCTTGA
181 AAAAAGGATTGGTTATA-TCTTAACAAAGTGAAAAGA-TAGGGA-GTGTAAAGGTTATCTCTCGA
* * * **
25247 TCCTATAAAAAGAAAGAGCAAATTAGTGAATTTGTTAGAAAATTCTTAGTGAGGAGCTAAGGTAG
243 TCATATAAAAAGAAAGAACAAATTAGTGAATTTGTTAGAAAATCCAAAGTGAGGAGCTAAGGTAG
* * *
25312 TGGAGGTAGACTTAGTTGAGAAGTCGAGCCACTATAAATCGC-TGTG-CAAAACTTTCTATCTTT
308 TGGAGGTAGACTTAGTTGAGAAGTCAAACCACTATAAATC-CTTATGCCAAAACTTTCTATCTTT
* * * * * *
25375 TATTTCTCCTTACTACC-TAAT-AATTTTTTTATCAATTCA-CTCATCTTGCAACACTTTTCGGT
372 TA-CTCTCCTCACT-CCTTAATCAA-ATTATTACCAATTAATC-CA-CTTGCAACACTTTT-GGT
* **
25437 TGTTAAATT-GAGCCTCTTCG-ATCCCAA-AATTGGTATAAGAGCTTGACTCATTAGAAGATTTA
431 TG-TAAATTCGAG-CT-TTCGAATCCCAACAATTGATATAAGAGCTTGACTCATTAGAAGACCTA
* * * * ** *
25499 ACCACCTTGAGACA-ATCCTAGAAGAAGCTATATCTATTCCTGACGCAACCGA-GTAGAT-GA-C
493 A-CACCTTGA-ACACATCCTAGAAGAAGCTATACCGATTCCCGACGCAACCCACAAAAATAGAGC
* * *
25560 TTCAACCTCCGATGCTTATTACTTGGAAAATTCTCAA-CTGATCAACAAGTCACCCTGTTTCAAT
556 TTCAACCTCCGATGCTTATTACTTGGAAAATTCTCAACCAG-TCAACAAGCCACCCTATTTCAAT
* * * *
25624 TAAGCAAATTATGTC-TATTGGAAA-AATAAGATAATGCTCTTCATTCGACCCAACGATCTAGGA
620 GAAGCAAATTATG-CATATT-GAAAGAATAAAATAATGCTCTTAATTCAACCCAACGATCTAGGA
* * *
25687 GCTTGAAACTTAATCATGAAGGGTTGCTCCACTCCACCCGGTGAGATGGACGATTGGAGTGATGG
683 GCTTGAAACTCAATCATGAAGGGTTACTCCACTCCACCCGGTAAGATGGACGATTGGAGTGATGG
* * * *
25752 AGAGAAGAAAAAATTCTAGCTCAATGCTAAGGCTATGCACATCCTCTTTTGTGCATTAGGCCTGG
748 AGAGAAGAAAAAATTCCAGCTCAATCCTAAGGCTATGCACATCATCTTTTGTGCATTAGGCCCGG
* *
25817 ATGAATATGGAAGAGTCCCCTCTTGTTCCAATGCCAAGGAGATATGAGATAAACTCCAAGTCACT
813 ATGAATATGGAAGAGTCCCATCTTGTTCCAATGCCAAGGAGATATGAGACAAACTCCAAGTCACT
*
25882 CATGAAGGAATCATTAAAGTGAGGGAAA
878 CATGAAGGAACCATTAAAGTGAGGGAAA
*
25910 CCATGATA
1 CCAAGATA
25918 AGTCTTCTCA
Statistics
Matches: 780, Mismatches: 110, Indels: 60
0.82 0.12 0.06
Matches are distributed among these distances:
907 2 0.00
908 127 0.16
909 14 0.02
915 5 0.01
916 316 0.41
917 12 0.02
918 53 0.07
919 202 0.26
920 26 0.03
921 11 0.01
922 8 0.01
923 4 0.01
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (905 bp):
CCAAGATATAAATACAAGTTCAAGACACTTGAAGAAGGGTTAGAACACCTATCCAAGCAATCAAA
CACAAGAGAAGAATTTTTCATTCATATTTTCTATTCTCTTGTAAATATTGTGTTTTAGTGAGCTT
CAATTTGTAAACACCTACCTTGTGAGGGTTTTCACTATCTTTCTTTTGTAAAAAAGGATTGGTTA
TATCTTAACAAAGTGAAAAGATAGGGAGTGTAAAGGTTATCTCTCGATCATATAAAAAGAAAGAA
CAAATTAGTGAATTTGTTAGAAAATCCAAAGTGAGGAGCTAAGGTAGTGGAGGTAGACTTAGTTG
AGAAGTCAAACCACTATAAATCCTTATGCCAAAACTTTCTATCTTTTACTCTCCTCACTCCTTAA
TCAAATTATTACCAATTAATCCACTTGCAACACTTTTGGTTGTAAATTCGAGCTTTCGAATCCCA
ACAATTGATATAAGAGCTTGACTCATTAGAAGACCTAACACCTTGAACACATCCTAGAAGAAGCT
ATACCGATTCCCGACGCAACCCACAAAAATAGAGCTTCAACCTCCGATGCTTATTACTTGGAAAA
TTCTCAACCAGTCAACAAGCCACCCTATTTCAATGAAGCAAATTATGCATATTGAAAGAATAAAA
TAATGCTCTTAATTCAACCCAACGATCTAGGAGCTTGAAACTCAATCATGAAGGGTTACTCCACT
CCACCCGGTAAGATGGACGATTGGAGTGATGGAGAGAAGAAAAAATTCCAGCTCAATCCTAAGGC
TATGCACATCATCTTTTGTGCATTAGGCCCGGATGAATATGGAAGAGTCCCATCTTGTTCCAATG
CCAAGGAGATATGAGACAAACTCCAAGTCACTCATGAAGGAACCATTAAAGTGAGGGAAA
Found at i:28364 original size:20 final size:20
Alignment explanation
Indices: 28339--28378 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
28329 TGTAGAGATT
28339 ACATCCCCAACAGCTAGAAA
1 ACATCCCCAACAGCTAGAAA
*
28359 ACATCCCCAACGGCTAGAAA
1 ACATCCCCAACAGCTAGAAA
28379 CGACCACAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.35, G:0.12, T:0.10
Consensus pattern (20 bp):
ACATCCCCAACAGCTAGAAA
Found at i:33078 original size:152 final size:149
Alignment explanation
Indices: 32773--33074 Score: 552
Period size: 151 Copynumber: 2.0 Consensus size: 149
32763 AATCAGATAT
32773 CAAAG-AAATAAAACATGGAAGTATTATGAAAATTATAAGTATTTTAAGAGTTTAGTTATTTAAA
1 CAAAGAAAATAAAACATGGAAGTATTATGAAAATTATAAGTATTTTAAGAGTTTAGTTATTTAAA
32837 GAGATATGCGGTGGTGGATGACAGATGACGGCAGCTACAGGACGACTACACGCGGGGAGCTGAGA
66 GAGATATGCGGTGGTGGATGACAGATGACGGCAGCTACAGGACGACTACACGCGGGGAGCTGAGA
32902 GATTAGACAGTCTGAAAAA
131 GATTAGACAGTCTGAAAAA
32921 CAAAGAAAATAAAACATGGAAGTATATTATGAAAATTATAAGTATTTTAAGAGTTTAGTTATTTA
1 CAAAGAAAATAAAACATGGAAG--TATTATGAAAATTATAAGTATTTTAAGAGTTTAGTTATTTA
32986 AAGAGATTATGCGGTGGTGGATGACAGATGACGGCAGCTACAGGACGACTACACCGCGGGGAGCT
64 AAGAGA-TATGCGGTGGTGGATGACAGATGACGGCAGCTACAGGACGACTACA-CGCGGGGAGCT
33051 GAGAGATTAGACAGATCTGAAAAA
127 GAGAGATTAGACAG-TCTGAAAAA
33075 AAGAGGAGGA
Statistics
Matches: 148, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
148 5 0.03
149 16 0.11
151 47 0.32
152 46 0.31
153 25 0.17
154 9 0.06
ACGTcount: A:0.39, C:0.11, G:0.26, T:0.24
Consensus pattern (149 bp):
CAAAGAAAATAAAACATGGAAGTATTATGAAAATTATAAGTATTTTAAGAGTTTAGTTATTTAAA
GAGATATGCGGTGGTGGATGACAGATGACGGCAGCTACAGGACGACTACACGCGGGGAGCTGAGA
GATTAGACAGTCTGAAAAA
Found at i:37366 original size:13 final size:13
Alignment explanation
Indices: 37348--37373 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
37338 GTAATACAGC
37348 ATGATATATATGT
1 ATGATATATATGT
37361 ATGATATATATGT
1 ATGATATATATGT
37374 CATGGTCATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
ATGATATATATGT
Found at i:39610 original size:10 final size:9
Alignment explanation
Indices: 39560--39610 Score: 50
Period size: 10 Copynumber: 5.3 Consensus size: 9
39550 ATCTAGCTTT
39560 TTTTATTTA
1 TTTTATTTA
39569 TTTATAATTTA
1 TTT-T-ATTTA
39580 TTTTATTTTA
1 TTTTA-TTTA
*
39590 TTTTA-TCA
1 TTTTATTTA
39598 TTTTGATTTA
1 TTTT-ATTTA
39608 TTT
1 TTT
39611 AATATTCCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
8 6 0.17
9 5 0.14
10 16 0.46
11 8 0.23
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (9 bp):
TTTTATTTA
Found at i:42634 original size:8 final size:8
Alignment explanation
Indices: 42623--42672 Score: 55
Period size: 8 Copynumber: 6.2 Consensus size: 8
42613 CAAAAAGGGC
42623 AAAAAGAA
1 AAAAAGAA
42631 AAAAAGAA
1 AAAAAGAA
* *
42639 AAGAAGCA
1 AAAAAGAA
*
42647 AAAAAGGA
1 AAAAAGAA
*
42655 AAAAAGGA
1 AAAAAGAA
*
42663 AAAAACAA
1 AAAAAGAA
42671 AA
1 AA
42673 GAACAAAAAG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 36 1.00
ACGTcount: A:0.80, C:0.04, G:0.16, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:42649 original size:16 final size:16
Alignment explanation
Indices: 42630--42685 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
42620 GGCAAAAAGA
42630 AAAAAAGAAAAGAAGC
1 AAAAAAGAAAAGAAGC
*
42646 AAAAAAGGAAAA-AAGG
1 AAAAAA-GAAAAGAAGC
*
42662 AAAAAACAAAAGAA-C
1 AAAAAAGAAAAGAAGC
42677 -AAAAAGAAA
1 AAAAAAGAAA
42686 GAACAAAGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
14 8 0.24
15 4 0.12
16 17 0.50
17 5 0.15
ACGTcount: A:0.79, C:0.05, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAAAGAAGC
Found at i:42649 original size:32 final size:31
Alignment explanation
Indices: 42609--42682 Score: 103
Period size: 32 Copynumber: 2.4 Consensus size: 31
42599 AGATTCAATC
* *
42609 AGAACAAAAAGGGCAAAAAGAAAAAAAGAAA
1 AGAACAAAAAGGGAAAAAAGAAAAAAACAAA
* *
42640 AGAAGCAAAAAAGGAAAAAAGGAAAAAACAAA
1 AGAA-CAAAAAGGGAAAAAAGAAAAAAACAAA
42672 AGAACAAAAAG
1 AGAACAAAAAG
42683 AAAGAACAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 10 0.27
32 27 0.73
ACGTcount: A:0.74, C:0.07, G:0.19, T:0.00
Consensus pattern (31 bp):
AGAACAAAAAGGGAAAAAAGAAAAAAACAAA
Found at i:42707 original size:21 final size:22
Alignment explanation
Indices: 42624--42707 Score: 79
Period size: 20 Copynumber: 3.9 Consensus size: 22
42614 AAAAAGGGCA
42624 AAAAGAA-AAAAAGAAAAGAAGC
1 AAAAGAACAAAAAGAAAAGAA-C
*
42646 AAAAAAGGAA-AAAAGGAAAA-AAC
1 --AAAA-GAACAAAAAGAAAAGAAC
42669 AAAAGAACAAAAAG-AAAGAAC
1 AAAAGAACAAAAAGAAAAGAAC
*
42690 -AAAGATCAAAAAGAAAAG
1 AAAAGAACAAAAAGAAAAG
42708 GGGATAAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
20 18 0.34
21 16 0.30
23 1 0.02
24 6 0.11
25 12 0.23
ACGTcount: A:0.76, C:0.06, G:0.17, T:0.01
Consensus pattern (22 bp):
AAAAGAACAAAAAGAAAAGAAC
Found at i:43337 original size:22 final size:22
Alignment explanation
Indices: 43309--43352 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
43299 AGCTACCCCA
*
43309 TCAAACCTTTGAACATCAAATG
1 TCAAACCATTGAACATCAAATG
*
43331 TCAAACCATTGAGCATCAAATG
1 TCAAACCATTGAACATCAAATG
43353 GACAAAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.41, C:0.23, G:0.11, T:0.25
Consensus pattern (22 bp):
TCAAACCATTGAACATCAAATG
Found at i:45002 original size:23 final size:23
Alignment explanation
Indices: 44976--45039 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
44966 CAGCTCATAT
44976 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
44999 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
45022 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
45040 TATAATAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:45229 original size:103 final size:103
Alignment explanation
Indices: 45050--45375 Score: 616
Period size: 103 Copynumber: 3.2 Consensus size: 103
45040 TATAATAATG
*
45050 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
1 TCCCGAAGGACCACATATCACTCCTTAAAAATCATATACATATACTAGGGATCAAGTATGTGTCT
45115 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
66 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
*
45153 TCCCGAAGGACCACATATCACTCCTTAATAATCATATACATATACTAGGGATCAAGTATGTGTCT
1 TCCCGAAGGACCACATATCACTCCTTAAAAATCATATACATATACTAGGGATCAAGTATGTGTCT
45218 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
66 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
*
45256 TCCCGAAGGACCACATATCACTCCTTAAAAATCATATACATATACTAGGGATCAAGTATGTATCT
1 TCCCGAAGGACCACATATCACTCCTTAAAAATCATATACATATACTAGGGATCAAGTATGTGTCT
*
45321 CACCAGACATCACACATGTTCCAAAGAATACATATATA
66 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
45359 TCCCGAAGGACCACATA
1 TCCCGAAGGACCACATA
45376 GACCCTCGAC
Statistics
Matches: 219, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 219 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (103 bp):
TCCCGAAGGACCACATATCACTCCTTAAAAATCATATACATATACTAGGGATCAAGTATGTGTCT
CACCAGACTTCACACATGTTCCAAAGAATACATATATA
Found at i:46235 original size:64 final size:64
Alignment explanation
Indices: 46127--46351 Score: 244
Period size: 64 Copynumber: 3.5 Consensus size: 64
46117 TAATGAAGGT
* * * * *
46127 ATGCATCGATGCACTACTGATGCATCGGTGCA-TAAAATGTATTCGATGTTGT-ATTATTACTGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACT-AATTGCATTCGATGTT-TCATTATTAATGG
46190 G
64 G
* * *
46191 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGTG
1 ATGCATCGATGCACT-ACTTATGCATCGATGCACTAATTGCATTCGATGTTTCATTATTAATGGG
* * **
46255 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGATGT-TTCATTATTAATGGG
**
46318 AGTGCATCGATGCACTACCAATGCATCGATGCAC
1 A-TGCATCGATGCACTACTTATGCATCGATGCAC
46352 CTTCAAACAA
Statistics
Matches: 139, Mismatches: 16, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
63 4 0.03
64 129 0.93
65 6 0.04
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGATGTTTCATTATTAATGGG
Found at i:50862 original size:23 final size:23
Alignment explanation
Indices: 50825--50888 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
50815 CATCTCATAT
*
50825 AATTGCATCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
50848 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
50871 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
50889 TATAATAATG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.27, C:0.25, G:0.28, T:0.20
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:51075 original size:103 final size:103
Alignment explanation
Indices: 50908--51327 Score: 795
Period size: 103 Copynumber: 4.1 Consensus size: 103
50898 GTCCCAAATA
50908 ACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACT
1 ACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACT
* *
50973 TCACACATGTTCCAAAGAATACATATATGTCCCGAATG
66 TCACACATGTTCCAAAGAATACATATATATCCCGAAGG
51011 ACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACT
1 ACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACT
51076 TCACACATGTTCCAAAGAATACATATATATCCCGAAGG
66 TCACACATGTTCCAAAGAATACATATATATCCCGAAGG
*
51114 ACCATATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACT
1 ACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACT
51179 TCACACATGTTCCAAAGAATACATATATATCCCGAAGG
66 TCACACATGTTCCAAAGAATACATATATATCCCGAAGG
51217 ACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACT
1 ACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACT
* *
51282 TCACACATGTTCCAAAGAATATATATATATCCCGAAGA
66 TCACACATGTTCCAAAGAATACATATATATCCCGAAGG
51320 ACCACATA
1 ACCACATA
51328 GACCCTCGAC
Statistics
Matches: 311, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 311 1.00
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (103 bp):
ACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACT
TCACACATGTTCCAAAGAATACATATATATCCCGAAGG
Found at i:52187 original size:64 final size:64
Alignment explanation
Indices: 52079--52303 Score: 251
Period size: 64 Copynumber: 3.5 Consensus size: 64
52069 TAATAAAGGT
* * * * * * *
52079 ATGCATTGATGCACTACTGATGCATCGGTGCATAAAATGTATTCGATGTTGT-ATTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTT-TCATTATTAATGGG
* * *
52143 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGG
1 ATGCATCGATGCACT-ACTTATGCATCGATGCACAAATTGCATTCGATGTTTCATTATTAATGGG
* **
52207 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGT-TTCATTATTAATGGG
**
52270 AGTGCATCGATGCACTACCAATGCATCGATGCAC
1 A-TGCATCGATGCACTACTTATGCATCGATGCAC
52304 CTTCAAACAA
Statistics
Matches: 138, Mismatches: 18, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
63 4 0.03
64 129 0.93
65 5 0.04
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTTTCATTATTAATGGG
Found at i:53974 original size:88 final size:88
Alignment explanation
Indices: 53820--53999 Score: 324
Period size: 88 Copynumber: 2.0 Consensus size: 88
53810 CAATTTCAAC
*
53820 TTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGG
1 TTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
53885 TTGTCAATAAACAACTTCCCAAT
66 TTGTCAATAAACAACTTCCCAAT
* * *
53908 TTCATAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
1 TTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
53973 TTGTCAATAAACAACTTCCCAAT
66 TTGTCAATAAACAACTTCCCAAT
53996 TTCA
1 TTCA
54000 GAACCAATTT
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
88 88 1.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (88 bp):
TTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
TTGTCAATAAACAACTTCCCAAT
Found at i:54072 original size:194 final size:200
Alignment explanation
Indices: 53734--54262 Score: 757
Period size: 194 Copynumber: 2.6 Consensus size: 200
53724 ATATCGTGCC
* * *
53734 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAACTTCTC
1 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
53799 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACT
* * * * *
53864 TCATGACGAAGGGACCGCTGGTTGTCAATAAACAAC-T-TC-CCAATTTC-A-T-AGCGAAGGAT
131 TCACGACAAAGGGACCGCTGGTTGTCAACAAACAACTTCTCACCAATTTCAACTCAACAAAGGAT
53923 ATTGG
196 ATTGG
53928 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
53993 AATTTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGATTTC-AGACAACGCAAGTTCAAC
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA-CTCAAGACAACGCAAGTTCAAC
54057 TTCACGACAAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTTAGAGCCAATTTCAACTT
130 TTCACGACAAAGGGACCGCTGGTTGTCAACAAACAACTTCTC--------A-CCAATTTCAAC-T
54122 CACAACAAAGGATATTGG
185 --CAACAAAGGATATTGG
* * *
54140 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTATCAACAAACAATTTCCC
1 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
54205 AATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAG
54263 GACGGCTGGT
Statistics
Matches: 298, Mismatches: 17, Indels: 22
0.88 0.05 0.07
Matches are distributed among these distances:
194 155 0.52
195 3 0.01
196 2 0.01
206 8 0.03
207 1 0.00
209 1 0.00
211 2 0.01
212 126 0.42
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (200 bp):
ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACT
TCACGACAAAGGGACCGCTGGTTGTCAACAAACAACTTCTCACCAATTTCAACTCAACAAAGGAT
ATTGG
Found at i:54102 original size:106 final size:106
Alignment explanation
Indices: 53908--54256 Score: 563
Period size: 106 Copynumber: 3.3 Consensus size: 106
53898 ACTTCCCAAT
*
53908 TTCATAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
1 TTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
* *
53973 TTGTCAATAAACAACTTCCCAATTTCAGAACCAATTTCAAC
66 TTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAAC
* * * *
54014 TTCACAGCGAAGGATATTGGATTTCAGACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGG
1 TTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
* *
54079 TTGTCAACAAACAACTTCTCAATTTTAGAGCCAATTTCAAC
66 TTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAAC
* *
54120 TTCACAACAAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
1 TTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
* * *
54185 TTATCAACAAACAATTTCCCAATTTCAGAGCCAATTTTAAC
66 TTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAAC
*
54226 TTCACAGCGAAGGATATTGGACTCAAGACAA
1 TTCACAGCGAAGGATATTGGACTCCAGACAA
54257 CACAAGGACG
Statistics
Matches: 220, Mismatches: 23, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
106 220 1.00
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (106 bp):
TTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGG
TTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAAC
Found at i:54327 original size:87 final size:87
Alignment explanation
Indices: 54175--54336 Score: 236
Period size: 87 Copynumber: 1.9 Consensus size: 87
54165 CACGACGAAG
* *
54175 GGACCGCTGGTTATCAACAAACAATTTCCCAATTTCAGAGCCAATTTTAACTTCACAGCGAAGGA
1 GGACCGCTGGTTATCAACAAACAATTTCCCAATTCCAGAGCCAATTTCAACTTCACAGCGAAGGA
54240 TATTGGACTCAAGACAACACAA
66 TATTGGACTCAAGACAACACAA
* * * ** *
54262 GGACGGCTGGTTGTCAATAAACAATTTCCCGGTTCCAGAGCCAATTTCAACTTCAC-GACGGAGG
1 GGACCGCTGGTTATCAACAAACAATTTCCCAATTCCAGAGCCAATTTCAACTTCACAG-CGAAGG
54326 ATATTGGACTC
65 ATATTGGACTC
54337 GGAACAATAC
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
86 1 0.02
87 65 0.98
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (87 bp):
GGACCGCTGGTTATCAACAAACAATTTCCCAATTCCAGAGCCAATTTCAACTTCACAGCGAAGGA
TATTGGACTCAAGACAACACAA
Found at i:64759 original size:15 final size:14
Alignment explanation
Indices: 64735--64764 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
64725 CTTCTACACT
64735 TCCTAGTACATAAA
1 TCCTAGTACATAAA
64749 TCCTCAGTACATAAA
1 TCCT-AGTACATAAA
64764 T
1 T
64765 AAGGGGACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30
Consensus pattern (14 bp):
TCCTAGTACATAAA
Found at i:71538 original size:20 final size:21
Alignment explanation
Indices: 71513--71564 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
71503 TTTTCCCAAT
*
71513 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
71533 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
71554 TCGCAATGCGA
1 TCGCAATGCGA
71565 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:71577 original size:41 final size:41
Alignment explanation
Indices: 71550--71647 Score: 142
Period size: 41 Copynumber: 2.4 Consensus size: 41
71540 GCGAATTGGG
* *
71550 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* *
71591 AAAATCGCAACGCGATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* *
71632 AGAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
71648 TTTCAAAGTT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.20
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:71599 original size:21 final size:21
Alignment explanation
Indices: 71551--71647 Score: 76
Period size: 20 Copynumber: 4.7 Consensus size: 21
71541 CGAATTGGGA
*
71551 AAATCGCAATGCGATACTGAC
1 AAATCGCAATGCGATAATGAC
*
71572 -TATCGCAATGCGATAAT-AC
1 AAATCGCAATGCGATAATGAC
* *
71591 AAAATCGCAACGCGATACTGAC
1 -AAATCGCAATGCGATAATGAC
** * *
71613 -TTTCGCAACGAGATAAT-AC
1 AAATCGCAATGCGATAATGAC
71632 AGAATCGCAATGCGAT
1 A-AATCGCAATGCGAT
71648 TTTCAAAGTT
Statistics
Matches: 58, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
19 4 0.07
20 28 0.48
21 24 0.41
22 2 0.03
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.21
Consensus pattern (21 bp):
AAATCGCAATGCGATAATGAC
Found at i:72614 original size:12 final size:12
Alignment explanation
Indices: 72597--72621 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
72587 ATATAATCCT
72597 GAAGAAGAAAAA
1 GAAGAAGAAAAA
72609 GAAGAAGAAAAA
1 GAAGAAGAAAAA
72621 G
1 G
72622 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:74934 original size:19 final size:19
Alignment explanation
Indices: 74912--74976 Score: 59
Period size: 19 Copynumber: 3.7 Consensus size: 19
74902 GGAAATTACT
74912 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
74931 ATCGTAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
74945 ATCGTAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
74964 ATCGCAACGCGAA
1 ATCGCAATGCGAA
74977 TTTCACAACG
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
14 10 0.28
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 20 0.56
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:75005 original size:47 final size:47
Alignment explanation
Indices: 74936--75026 Score: 164
Period size: 47 Copynumber: 1.9 Consensus size: 47
74926 TGAAAATCGT
*
74936 AACGAGAGAATCGTAATGCGAAATGAAAATCGCAACGCGAATTTCAC
1 AACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTCAC
*
74983 AACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
1 AACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
75027 AATTTCGCGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.42, C:0.19, G:0.23, T:0.16
Consensus pattern (47 bp):
AACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTCAC
Found at i:75051 original size:14 final size:14
Alignment explanation
Indices: 75034--75090 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
75024 TTTAATTTCG
75034 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
75048 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
75067 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
75081 CGTTGCGATT
1 CGTTGCGATT
75091 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:75070 original size:33 final size:33
Alignment explanation
Indices: 75019--75108 Score: 153
Period size: 33 Copynumber: 2.7 Consensus size: 33
75009 AAATCGCAAC
* *
75019 GCGAATTTAATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
75052 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
75085 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
75109 AGTACTTTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.43
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:75072 original size:19 final size:19
Alignment explanation
Indices: 75048--75108 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
75038 GCGATTCTCT
75048 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
75067 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
75081 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
75100 CATTGCGAT
1 CGTTGCGAT
75109 AGTACTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 10 0.29
16 3 0.09
17 3 0.09
19 18 0.53
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:75234 original size:14 final size:14
Alignment explanation
Indices: 75215--75251 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
75205 CATCAATTAA
75215 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
75229 ACAAATCACCTTTT
1 ACAAATCAACTTTT
75243 ACAAATCAA
1 ACAAATCAA
75252 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:77114 original size:91 final size:90
Alignment explanation
Indices: 76939--77123 Score: 300
Period size: 91 Copynumber: 2.0 Consensus size: 90
76929 ATTTCAAACT
*
76939 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
77004 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
77032 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
77096 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
77123 T
1 T
77124 AAGCAATCTA
Statistics
Matches: 88, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
91 42 0.48
93 19 0.22
95 27 0.31
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:78837 original size:20 final size:19
Alignment explanation
Indices: 78806--78927 Score: 75
Period size: 20 Copynumber: 6.8 Consensus size: 19
78796 TCTTTTGGTT
78806 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
78825 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
78846 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
78865 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
** *
78879 GAAATGACTATCGCGACGA
1 GAAATGAAAATCGCAACGA
*
78898 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
78912 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
78928 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 13, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
14 19 0.24
16 4 0.05
17 4 0.05
19 20 0.26
20 29 0.37
21 2 0.03
ACGTcount: A:0.43, C:0.20, G:0.25, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:78888 original size:33 final size:33
Alignment explanation
Indices: 78831--78927 Score: 158
Period size: 33 Copynumber: 2.9 Consensus size: 33
78821 ACGAGATAAT
78831 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
78865 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
78898 GAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGACTATCGCAA
78928 TGCGATTTTG
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.40, C:0.23, G:0.26, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:78961 original size:19 final size:19
Alignment explanation
Indices: 78928--79008 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
78918 AAAATCGCAA
**
78928 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
78947 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
78966 TGCGA---TTA--TCTCGT
1 TGCGATTTTTATTTCGCGT
**
78980 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
79000 TGCGATTTT
1 TGCGATTTT
79009 CATTCTCTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
14 10 0.20
16 3 0.06
17 3 0.06
19 23 0.46
20 11 0.22
ACGTcount: A:0.11, C:0.17, G:0.25, T:0.47
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:79609 original size:20 final size:20
Alignment explanation
Indices: 79524--79657 Score: 135
Period size: 20 Copynumber: 6.7 Consensus size: 20
79514 CGCTATGTAA
* * *
79524 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
79544 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * * *
79564 ATCTCGTTGTGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
79585 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
*
79605 ATCGCATTACGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
79625 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
79645 ATCGCATTGCGAT
1 ATCGCATTGCGAT
79658 TTTCCCAATT
Statistics
Matches: 97, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
19 3 0.03
20 81 0.84
21 11 0.11
22 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:79768 original size:21 final size:21
Alignment explanation
Indices: 79728--79768 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
79718 ACTGTAGACC
**
79728 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
79749 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
79769 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:84251 original size:102 final size:102
Alignment explanation
Indices: 84088--84275 Score: 313
Period size: 102 Copynumber: 1.8 Consensus size: 102
84078 CTACACATGA
* * * *
84088 AGAAGATATAACTCCATCGTATATATAAATAAAGAGACCATTTCATCGGTAATTCACGTTCAGTT
1 AGAAGATATAACTCAATCGTATATATAAATAAAGAGACAATTTCATCGATAATTCACGTTCAGAT
84153 TTGCATAACAAACGACACCTATAAAACCTAAACGTGG
66 TTGCATAACAAACGACACCTATAAAACCTAAACGTGG
* **
84190 AGAAGATATAACTCAATCGTATATATAAATATATCGACAATTTCATCGATAATTCACGTTCAGAT
1 AGAAGATATAACTCAATCGTATATATAAATAAAGAGACAATTTCATCGATAATTCACGTTCAGAT
84255 TTGCATAACAAACGACACCTA
66 TTGCATAACAAACGACACCTA
84276 AATCAAGAAT
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
102 79 1.00
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (102 bp):
AGAAGATATAACTCAATCGTATATATAAATAAAGAGACAATTTCATCGATAATTCACGTTCAGAT
TTGCATAACAAACGACACCTATAAAACCTAAACGTGG
Found at i:90635 original size:2 final size:2
Alignment explanation
Indices: 90628--90706 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
90618 TAGATATAAA
90628 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
90670 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
90707 ACATTATTAT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:91859 original size:29 final size:28
Alignment explanation
Indices: 91798--91873 Score: 109
Period size: 29 Copynumber: 2.6 Consensus size: 28
91788 GTCCACATCG
*
91798 AAAATTCCCAAATTGTCA-TTTTTTCACA
1 AAAATTCCCAAA-TGTCACATTTTTCACA
91826 AAAATTCCCAGAATGTCACATTTTTCACA
1 AAAATTCCCA-AATGTCACATTTTTCACA
91855 AAAATTCCCAAAATGTCAC
1 AAAATTCCC-AAATGTCAC
91874 TGGGTCGGGT
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
28 15 0.34
29 28 0.64
30 1 0.02
ACGTcount: A:0.39, C:0.24, G:0.05, T:0.32
Consensus pattern (28 bp):
AAAATTCCCAAATGTCACATTTTTCACA
Found at i:98778 original size:29 final size:29
Alignment explanation
Indices: 98718--98823 Score: 162
Period size: 29 Copynumber: 3.7 Consensus size: 29
98708 TCCACATTCG
98718 AAAATTCCCA-AATTGTCA-TTTTTTCACA
1 AAAATTCCCAGAA-TGTCACTTTTTTCACA
*
98746 AAAATTCCCAGAATGTCACTTTTTTTACA
1 AAAATTCCCAGAATGTCACTTTTTTCACA
* *
98775 AAAATTCCTAGAATGTCACCTTTTTCACA
1 AAAATTCCCAGAATGTCACTTTTTTCACA
98804 AAAATTCCCAGAATGTCACT
1 AAAATTCCCAGAATGTCACT
98824 GGATCGGGTC
Statistics
Matches: 70, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
28 15 0.21
29 55 0.79
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.35
Consensus pattern (29 bp):
AAAATTCCCAGAATGTCACTTTTTTCACA
Found at i:101283 original size:19 final size:19
Alignment explanation
Indices: 101246--101291 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
101236 AGAGAAGTTA
* * *
101246 AAAAATGATTGTGGGTTAG
1 AAAAGTGATTGAGGATTAG
101265 AAAAGTGATTGAGGATTAG
1 AAAAGTGATTGAGGATTAG
*
101284 TAAAGTGA
1 AAAAGTGA
101292 ATATAACAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.28
Consensus pattern (19 bp):
AAAAGTGATTGAGGATTAG
Found at i:113594 original size:30 final size:30
Alignment explanation
Indices: 113558--113617 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
113548 TCGGAGGATC
113558 TGCAGATAGTCAGCTTATCATCACAAGACG
1 TGCAGATAGTCAGCTTATCATCACAAGACG
113588 TGCAGATAGTCAGCTTATCATCACAAGACG
1 TGCAGATAGTCAGCTTATCATCACAAGACG
113618 GCCACTTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (30 bp):
TGCAGATAGTCAGCTTATCATCACAAGACG
Found at i:120160 original size:17 final size:16
Alignment explanation
Indices: 120132--120179 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
120122 ACAGTTAATA
*
120132 GTCAACTGGTTTGATTTC
1 GTCAA-TGGTTTG-GTTC
120150 GTCAATGGTTTGGTTC
1 GTCAATGGTTTGGTTC
*
120166 GATCAATGGGTTGG
1 G-TCAATGGTTTGG
120180 GTCAAACCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 4 0.15
17 18 0.67
18 5 0.19
ACGTcount: A:0.17, C:0.12, G:0.31, T:0.40
Consensus pattern (16 bp):
GTCAATGGTTTGGTTC
Found at i:127692 original size:23 final size:23
Alignment explanation
Indices: 127666--127730 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
127656 CAGCTCATAT
*
127666 AATTGCACCTTAGTGCCATGTAG
1 AATTGCACCGTAGTGCCATGTAG
* **
127689 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGTAGTGCCATGTAG
127712 AATTGCACCGTAGTGCCAT
1 AATTGCACCGTAGTGCCAT
127731 ATAATAATGT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.25
Consensus pattern (23 bp):
AATTGCACCGTAGTGCCATGTAG
Found at i:127916 original size:103 final size:103
Alignment explanation
Indices: 127749--127962 Score: 401
Period size: 103 Copynumber: 2.1 Consensus size: 103
127739 GTCCATAAGG
*
127749 ACCATATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACC
1 ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACC
127814 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGA
66 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGA
*
127852 ACCACATATTATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACC
1 ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACC
*
127917 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
66 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGA
127955 ACCACATA
1 ACCACATA
127963 GACCCTCTAC
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.26
Consensus pattern (103 bp):
ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACC
TCACACATGTTCCAAAGAATACATATATGTCCCGAAGA
Found at i:128533 original size:21 final size:21
Alignment explanation
Indices: 128509--128551 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
128499 TTCATATTCA
* * *
128509 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTACCAATTCCCC
*
128530 TTGAATGGGTACCAATTCCCC
1 TTGAAGGGGTACCAATTCCCC
128551 T
1 T
128552 AGCCTAGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCAATTCCCC
Found at i:134611 original size:23 final size:23
Alignment explanation
Indices: 134585--134648 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
134575 CAGCTCATAT
*
134585 AATTGCACCTTAGTGCCACGTAG
1 AATTGCACCGTAGTGCCACGTAG
* * *
134608 AATTACACCGGAGTGCCGCGTAG
1 AATTGCACCGTAGTGCCACGTAG
134631 AATTGCACCGTAGTGCCA
1 AATTGCACCGTAGTGCCA
134649 TATAATAATG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.27, C:0.27, G:0.25, T:0.22
Consensus pattern (23 bp):
AATTGCACCGTAGTGCCACGTAG
Found at i:145548 original size:22 final size:21
Alignment explanation
Indices: 145520--145570 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
145510 AATGTAAAGA
145520 ACACAAACAACAGGCTCTTTTC
1 ACACAAA-AACAGGCTCTTTTC
* * *
145542 ATACAAAATCATGCTCTTTTC
1 ACACAAAAACAGGCTCTTTTC
145563 ACACAAAA
1 ACACAAAA
145571 TCGTTTCCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 19 0.76
22 6 0.24
ACGTcount: A:0.41, C:0.27, G:0.06, T:0.25
Consensus pattern (21 bp):
ACACAAAAACAGGCTCTTTTC
Found at i:145558 original size:21 final size:21
Alignment explanation
Indices: 145533--145572 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
145523 CAAACAACAG
*
145533 GCTCTTTTCATACAAAATCAT
1 GCTCTTTTCACACAAAATCAT
145554 GCTCTTTTCACACAAAATC
1 GCTCTTTTCACACAAAATC
145573 GTTTCCATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.35
Consensus pattern (21 bp):
GCTCTTTTCACACAAAATCAT
Found at i:159114 original size:17 final size:18
Alignment explanation
Indices: 159092--159134 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
159082 AGTTTGAGCA
*
159092 TTTCAAGCCT-ATTTTTC
1 TTTCAAGACTCATTTTTC
* *
159109 TTTCAATATTCATTTTTC
1 TTTCAAGACTCATTTTTC
159127 TTTCAAGA
1 TTTCAAGA
159135 ACACTTATTG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.23, C:0.19, G:0.05, T:0.53
Consensus pattern (18 bp):
TTTCAAGACTCATTTTTC
Found at i:167654 original size:36 final size:36
Alignment explanation
Indices: 167606--167716 Score: 204
Period size: 36 Copynumber: 3.1 Consensus size: 36
167596 AAGCAAGTCA
* *
167606 ATCTCAAGCCTTCACCGAAGAGCAGTGAAGCAAATC
1 ATCTTAAGCCTTCACCGAAGAGCAGTGAAGCAAACC
167642 ATCTTAAGCCTTCACCGAAGAGCAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCGAAGAGCAGTGAAGCAAACC
167678 ATCTTAAGCCTTCACCGAAGAGCAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCGAAGAGCAGTGAAGCAAACC
167714 ATC
1 ATC
167717 CATAAAACTT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 73 1.00
ACGTcount: A:0.36, C:0.28, G:0.19, T:0.17
Consensus pattern (36 bp):
ATCTTAAGCCTTCACCGAAGAGCAGTGAAGCAAACC
Found at i:167920 original size:41 final size:41
Alignment explanation
Indices: 167828--167929 Score: 107
Period size: 41 Copynumber: 2.5 Consensus size: 41
167818 TTTCACAATT
* ** *
167828 TATAAGTCCTTCGGGCATCAGTAAGTCTTTCGAGCATGATG
1 TATAAGTCCTTCGGGCATCAGTAAGCCTTTAAAGCAAGATG
* * * *
167869 TTTAAATCCTTCGGGTCATCTGTAAGCCTTTAAATCAAGATG
1 TATAAGTCCTTCGGG-CATCAGTAAGCCTTTAAAGCAAGATG
167911 -ATAAGTCCTTCGGGACATC
1 TATAAGTCCTTCGGG-CATC
167930 CATAAAACCT
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
41 29 0.59
42 20 0.41
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (41 bp):
TATAAGTCCTTCGGGCATCAGTAAGCCTTTAAAGCAAGATG
Found at i:168136 original size:213 final size:215
Alignment explanation
Indices: 167712--168786 Score: 1696
Period size: 213 Copynumber: 5.0 Consensus size: 215
167702 GTGAAGCAAA
* * *
167712 CCATCCATAAAACTTTCAGGTAGGATGTTTTCATATTAATTTGAAAATG-AAAAATGATGTTTTA
1 CCATCCATAAAACCTTCAGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAAATGATGTTTTA
* *
167776 AGAAGATGGAATTTTTGAAAACGAAGAATGTGATTTTCAAAGTTTCACAATTTATAAGTCCTTCG
66 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCG
* * *
167841 GG-CATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTAAGCCTTTAAATC
131 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
167905 AAGATGATAAGTCCTTCGGG
196 AAGATGATAAGTCCTTCGGG
* * * * * *
167925 ACATCCATAAAACCTTCAAGTAGCATGTTTTCACAAGAATTTGAAAATGAAAAAACGACGTTTTA
1 CCATCCATAAAACCTTCAGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAAATGATGTTTTA
* * * *
167990 AGAAGATGAAATTTTTGAAAACTAAGAATGCGATTTT-AAAATTTCATAATTTATAAATCCTTCG
66 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCG
* *
168054 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTTATCTGTAAGCCTTTAG-GA
131 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
* *
168118 AAGATAATAAGCCCTTCGGG
196 AAGATGATAAGTCCTTCGGG
*
168138 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAAATGATGTTTTA
1 CCATCCATAAAACCTTCAGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAAATGATGTTTTA
168203 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCG
66 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCG
* * *
168268 GGCCATCATTAAGTCTTTCAAGCATGATGTTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
131 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
* *
168333 AAGATGATAAGTCATTCAGG
196 AAGATGATAAGTCCTTCGGG
* *
168353 CCATCCATAAAACTTTCGGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAAAAT-AGTGTTT
1 CCATCCATAAAACCTTCAGGTAGGATGTTTTCACATGAATTTGAAAATG-AAAAAATGA-TGTTT
* *
168417 TAAGAAGATGGAATTTTTGAAAAAGAAGAATGCGATTTTCAAAATTTCACGATTTATAAGTCCTT
64 TAAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTT
* *
168482 CGAGCCATCAGTAAGTCTTTCGAGCATGATGCTTATATCCTTCGGGTCATCTGTAAGCCTTTAGA
129 CGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGA
*
168547 GCAAGATGATAAG-CCCTCGGG
194 GCAAGATGATAAGTCCTTCGGG
*
168568 CCATCCATAAAACCTTCAGGTAGGATGTTTTCACATTAATTTGAAAATG-AAAAATGATGTTTTA
1 CCATCCATAAAACCTTCAGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAAATGATGTTTTA
* * * **
168632 AGAAGATGAAATTTTTGAAAATGAAGAATGCAATTTTCAAAATTTCATGATTTATAAGTCCTTCG
66 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCG
* *
168697 AGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
131 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
168762 AAGATGATAAGTCCTTCGGG
196 AAGATGATAAGTCCTTCGGG
168782 CCATC
1 CCATC
168787 AGTAAGTCTG
Statistics
Matches: 791, Mismatches: 63, Indels: 15
0.91 0.07 0.02
Matches are distributed among these distances:
213 327 0.41
214 199 0.25
215 117 0.15
216 148 0.19
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (215 bp):
CCATCCATAAAACCTTCAGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAAATGATGTTTTA
AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCG
GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
AAGATGATAAGTCCTTCGGG
Found at i:168736 original size:42 final size:41
Alignment explanation
Indices: 168677--168819 Score: 144
Period size: 42 Copynumber: 3.4 Consensus size: 41
168667 TTCAAAATTT
* *
168677 CATGAT-TTATAAGTCCTTCGAGCCATCAATAAGTCTTTCGAG
1 CATGATGTTA-AA-TCCTTCGGGCCATCAGTAAGTCTTTCGAG
* * * *
168719 CATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAG
1 CATGATG-TTAAATCCTTCGGGCCATCAGTAAGTCTTTCGAG
* * * *
168761 CAAGATGATAAGTCCTTCGGGCCATCAGTAAGTCTGTCGAG
1 CATGATGTTAAATCCTTCGGGCCATCAGTAAGTCTTTCGAG
*
168802 CATGATGATTAAAACCTT
1 CATGATG-TTAAATCCTT
168820 TGGGTAATTT
Statistics
Matches: 80, Mismatches: 18, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
41 33 0.41
42 42 0.52
43 2 0.03
44 3 0.04
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (41 bp):
CATGATGTTAAATCCTTCGGGCCATCAGTAAGTCTTTCGAG
Found at i:168833 original size:83 final size:83
Alignment explanation
Indices: 168685--168838 Score: 236
Period size: 83 Copynumber: 1.9 Consensus size: 83
168675 TTCATGATTT
* * * *
168685 ATAAGTCCTTCGAGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTA
1 ATAAGTCCTTCGAGCCATCAATAAGTCTGTCGAGCATGATGATTAAAACCTTCGGGTAATCTGTA
168750 AGCCTTTAGAGCAAGATG
66 AGCCTTTAGAGCAAGATG
* * * *
168768 ATAAGTCCTTCGGGCCATCAGTAAGTCTGTCGAGCATGATGATTAAAACCTTTGGGTAATTTGTA
1 ATAAGTCCTTCGAGCCATCAATAAGTCTGTCGAGCATGATGATTAAAACCTTCGGGTAATCTGTA
168833 AGCCTT
66 AGCCTT
168839 CACTGAAGAG
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
83 63 1.00
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.31
Consensus pattern (83 bp):
ATAAGTCCTTCGAGCCATCAATAAGTCTGTCGAGCATGATGATTAAAACCTTCGGGTAATCTGTA
AGCCTTTAGAGCAAGATG
Found at i:176120 original size:23 final size:23
Alignment explanation
Indices: 176078--176161 Score: 143
Period size: 23 Copynumber: 3.7 Consensus size: 23
176068 ATAGGGCAGA
* *
176078 GGGAATCGATACCCCC-TTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
176100 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
176123 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
176146 GGGAACCGATTCCCCC
1 GGGAACCGATTCCCCC
176162 CAGGGGAATC
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
22 14 0.24
23 45 0.76
ACGTcount: A:0.23, C:0.32, G:0.26, T:0.19
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:185890 original size:33 final size:33
Alignment explanation
Indices: 185843--185913 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
185833 CCAAAGTTTA
* *
185843 CGAT-AATTGAAATACTTAAATACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
*
185875 CGATAAATTCAAATACTTAAAAACTTTCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
*
185908 TGATAA
1 CGATAA
185914 TTGAAACAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 4 0.12
33 30 0.88
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (33 bp):
CGATAAATTCAAATACTTAAAAACTTCCAAGTT
Found at i:187313 original size:24 final size:24
Alignment explanation
Indices: 187277--187331 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
187267 AATCATAATC
* *
187277 TTTTAAGTTTTATGATTT-ATTTAA
1 TTTTAAATATTAT-ATTTGATTTAA
*
187301 TTTTAAATATTATATTTGTTTTAA
1 TTTTAAATATTATATTTGATTTAA
*
187325 TATTAAA
1 TTTTAAA
187332 CGACTTATCC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (24 bp):
TTTTAAATATTATATTTGATTTAA
Found at i:189083 original size:143 final size:142
Alignment explanation
Indices: 188923--189240 Score: 600
Period size: 143 Copynumber: 2.2 Consensus size: 142
188913 AAGCTAAGAC
188923 AATATTATTTTGTATGGGAAATCTATGGAAATGTGCCTTTACTGACAAGGGTCACATTCCCAATG
1 AATATTATTTTGTATGGGAAATCTATGGAAATGTGCCTTTACTGACAAGGGTCACATTCCCAATG
188988 ATTTCTCATACAAAGTAACACCTTTTTATATTTGATTTTTTAGAATTATTGTATGTATAATTTAT
66 ATTTCTCATACAAAGTAACACCTTTTTATATTTGATTTTTTAGAATTATTGTATGTATAATTTAT
189053 TAAAAATTTGGGT
131 T-AAAATTTGGGT
189066 AATATTATTTTGTATGGGAAATCTATGGAAATGTGCCTTTACTGACAAGGGTCACATTCCCAATG
1 AATATTATTTTGTATGGGAAATCTATGGAAATGTGCCTTTACTGACAAGGGTCACATTCCCAATG
189131 ATTTCTCATACAAAGTAACACCTTTTTATATTTGATTTTTTAGAATTATTGTATGTATAATTTAT
66 ATTTCTCATACAAAGTAACACCTTTTTATATTTGATTTTTTAGAATTATTGTATGTATAATTTAT
189196 TAAAATTTGGGT
131 TAAAATTTGGGT
* * *
189208 AATATTATTTTGTATGGGGAATCCATGAAAATG
1 AATATTATTTTGTATGGGAAATCTATGGAAATG
189241 CCCCCTTAAC
Statistics
Matches: 172, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
142 41 0.24
143 131 0.76
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (142 bp):
AATATTATTTTGTATGGGAAATCTATGGAAATGTGCCTTTACTGACAAGGGTCACATTCCCAATG
ATTTCTCATACAAAGTAACACCTTTTTATATTTGATTTTTTAGAATTATTGTATGTATAATTTAT
TAAAATTTGGGT
Found at i:203343 original size:42 final size:42
Alignment explanation
Indices: 203271--203352 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
203261 CCAAATTTGA
* * *
203271 TAAATCCTTCGGTCCATCAGTGAGTCTTTCGCGCATGATGCT
1 TAAATCCTTCGGTCCATCAGTAAGTCTTTCGAGCAAGATGCT
* *
203313 TAAATCCTTCGAGT-CATCTGTAAGTTTTTCGAGCAAGATG
1 TAAATCCTTCG-GTCCATCAGTAAGTCTTTCGAGCAAGATG
203353 ATAACTCATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 32 0.94
43 2 0.06
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (42 bp):
TAAATCCTTCGGTCCATCAGTAAGTCTTTCGAGCAAGATGCT
Found at i:203605 original size:231 final size:233
Alignment explanation
Indices: 203008--203913 Score: 1185
Period size: 231 Copynumber: 3.9 Consensus size: 233
202998 CAAGCGATCA
*
203008 CTTACCTAATAAACTATTTCCAAAATTGGTAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
1 CTTACCTAGTAAACTATTTCCAAAATTGGTAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
* * ** *
203073 GATACTTAAATCCTTTGGGTCATCTGTAAGTCTTTCGAGTTAGATGATAAGTCATTCGGGCAATC
66 GATACTTAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATGATAAGTCATTCGGGCCATC
* * * * * *
203138 CATAAGACTTTCGGG-AAGGATTTTTTCACACGTCTTTCGAAAAAATGAGAAAAATTTCTCATTT
131 CATAAGACCTTCGGGCAA-GATGTTTTCACATGTTTTTCAAAAAAATGAGAAAAGTTTCTCATTT
*
203202 AAATCTAAAAATTGAAAATTTTGAAAAGTAAGAAAAATTT
195 AAATCTGAAAATTGAAAATTTTGAAAAGTAA-AAAAATTT
* * * * * *
203242 CTTACCTAGTAAACTATTCCCAAATTTGATAAATCCTTCGGTCCATCAGTGAGTCTTTCGCGCAT
1 CTTACCTAGTAAACTATTTCCAAAATTGGTAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
* * * * *
203307 GATGCTTAAATCCTTCGAGTCATCTGTAAGTTTTTCGAGCAAGATGATAACTCATTCGGGCCATC
66 GATACTTAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATGATAAGTCATTCGGGCCATC
* * *
203372 CATAAGACCTT-GGGCAAGATGTTTCCACCTGTTTTTCAAAAAAATGAGAAAATTTTCTCATTTA
131 CATAAGACCTTCGGGCAAGATGTTTTCACATGTTTTTCAAAAAAATGAGAAAAGTTTCTCATTTA
* *
203436 AATCTGAAAATTGAAATTTTTGAAAAGTAAAAAAGTTT
196 AATCTGAAAATTGAAAATTTTGAAAAGTAAAAAAATTT
* * * *
203474 CTTACCTAGTAAACTATTTCGAAAA-TGGTAAGTCCTTTGGGCCATCAGTAAGTATTTCGAGCAT
1 CTTACCTAGTAAACTATTTCCAAAATTGGTAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
* * * *
203538 GATGCTTAAATCCTTCGGGTTATCCGTAAGTCTTTCAAGCAAGATGATAAGTCATTTGGGCCATC
66 GATACTTAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATGATAAGTCATTCGGGCCATC
* * *
203603 CATAAGACCTT-GGGCAGGATGTTTTCACATGCTTTT-AGAAAAATGAGAAAAGTTTCTCATTTA
131 CATAAGACCTTCGGGCAAGATGTTTTCACATGTTTTTCAAAAAAATGAGAAAAGTTTCTCATTTA
* * *
203666 AATATGAAAATTGAAAATTTTGAAAAGTAAGAAATTTT
196 AATCTGAAAATTGAAAATTTTGAAAAGTAAAAAAATTT
* * * * * *
203704 CTTTCGTAGTAAACTATTTCTAAAATTGGTAAGTCATTTGGGCCATCAGTAAGTCTTTCGAGCAT
1 CTTACCTAGTAAACTATTTCCAAAATTGGTAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
** ** ** ** * *
203769 GATAAGTAAATAATTATGGTCATCTACAAGCCTTTCAAGCAAGATGATAAGTCATTCGGACCATC
66 GATACTTAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATGATAAGTCATTCGGGCCATC
* *
203834 TATAAGACCTTCGGGCAAGATATTTTCACATGTTTTTTC-AAAAAATGAGAAAAGTTTCTCATTT
131 CATAAGACCTTCGGGCAAGATGTTTTCACATG-TTTTTCAAAAAAATGAGAAAAGTTTCTCATTT
*
203898 AAATTTGAAAATTGAA
195 AAATCTGAAAATTGAA
203914 TTTTTTTGAA
Statistics
Matches: 589, Mismatches: 78, Indels: 11
0.87 0.12 0.02
Matches are distributed among these distances:
230 81 0.14
231 220 0.37
232 47 0.08
233 114 0.19
234 127 0.22
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (233 bp):
CTTACCTAGTAAACTATTTCCAAAATTGGTAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
GATACTTAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATGATAAGTCATTCGGGCCATC
CATAAGACCTTCGGGCAAGATGTTTTCACATGTTTTTCAAAAAAATGAGAAAAGTTTCTCATTTA
AATCTGAAAATTGAAAATTTTGAAAAGTAAAAAAATTT
Found at i:204300 original size:3 final size:3
Alignment explanation
Indices: 204292--204318 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
204282 CAAAACATTT
204292 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
204319 AACATTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:205050 original size:135 final size:136
Alignment explanation
Indices: 204790--205051 Score: 327
Period size: 135 Copynumber: 1.9 Consensus size: 136
204780 ACCAAAGTGC
* * *
204790 CGAAATGGAAATTCACAAACTCATTAAGAATTCCATGGATACATCCATAATGCCTAAAGTACATA
1 CGAAATGGAAATTCACAAACTCATTAAGAATACCATGGATACATCCATAATGCCGAAAGTACACA
* * * *
204855 TAGTATTGATACAAAAATGCACCGTTATGCATTAAAAAATCGATCGATAACTTTTATACATAATG
66 TAGTACTAATACAAAAATGCACCATTATGCATTAAAAAATCGATCGATAACTTATATACATAATG
204920 GTATGT
131 GTATGT
* * * * * *
204926 CGAAATGGTAATTCATAAACTCATTATGAATACCATGGTTGCACAT-C-TAGTG-CGAAAGTATA
1 CGAAATGGAAATTCACAAACTCATTAAGAATACCATGGAT--ACATCCATAATGCCGAAAGTACA
*
204988 CATAGTACTAATACGAAAATGCACCATTATGCATTACATAAAATCGATCGATAAC-TAT-TACAT
64 CATAGTACTAATACAAAAATGCACCATTATGCATTA-A-AAAATCGATCGATAACTTATATACAT
205051 A
127 A
205052 CAATTTATGT
Statistics
Matches: 108, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
135 45 0.42
136 42 0.39
137 17 0.16
138 4 0.04
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.29
Consensus pattern (136 bp):
CGAAATGGAAATTCACAAACTCATTAAGAATACCATGGATACATCCATAATGCCGAAAGTACACA
TAGTACTAATACAAAAATGCACCATTATGCATTAAAAAATCGATCGATAACTTATATACATAATG
GTATGT
Found at i:205068 original size:136 final size:136
Alignment explanation
Indices: 204792--205068 Score: 319
Period size: 136 Copynumber: 2.0 Consensus size: 136
204782 CAAAGTGCCG
* * *
204792 AAATGGAAATTCACAAACTCATTAAGAATTCCATGGATACATCCATAATGCCTAAAGTACATATA
1 AAATGGAAATTCACAAACTCATTAAGAATACCATGGATACATCCATAATGCCGAAAGTACACATA
* * * * * *
204857 GTATTGATACAAAAATGCACCGTTATGCATTAAAAAATCGATCGATAACTTTTATACATAATGGT
66 GTACTAATACAAAAATGCACCATTATGCATTAAAAAATCGATCGATAACTATTACACACAATGGT
*
204922 ATGTCG
131 ATGTCA
* * * * * *
204928 AAATGGTAATTCATAAACTCATTATGAATACCATGGTTGCACAT-C-TAGTG-CGAAAGTATACA
1 AAATGGAAATTCACAAACTCATTAAGAATACCATGGAT--ACATCCATAATGCCGAAAGTACACA
* *
204990 TAGTACTAATACGAAAATGCACCATTATGCATTACATAAAATCGATCGATAACTATTACATACAA
64 TAGTACTAATACAAAAATGCACCATTATGCATTA-A-AAAATCGATCGATAACTATTACACACAA
*
205055 T-TTATGTCA
127 TGGTATGTCA
205064 AAATG
1 AAATG
205069 CACCTATGAC
Statistics
Matches: 118, Mismatches: 19, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
135 39 0.33
136 49 0.42
137 26 0.22
138 4 0.03
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.30
Consensus pattern (136 bp):
AAATGGAAATTCACAAACTCATTAAGAATACCATGGATACATCCATAATGCCGAAAGTACACATA
GTACTAATACAAAAATGCACCATTATGCATTAAAAAATCGATCGATAACTATTACACACAATGGT
ATGTCA
Found at i:206176 original size:26 final size:26
Alignment explanation
Indices: 206146--206203 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
206136 GTAAAAGTGT
*
206146 TATTATTTTAATAATTATTAAAATTA
1 TATTATATTAATAATTATTAAAATTA
*
206172 TATTATATTAATAATTTTTAAAA-TA
1 TATTATATTAATAATTATTAAAATTA
*
206197 AATTATA
1 TATTATA
206204 GTTATGAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 8 0.28
26 21 0.72
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
TATTATATTAATAATTATTAAAATTA
Found at i:214426 original size:24 final size:25
Alignment explanation
Indices: 214392--214439 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
214382 CCCTTTTACT
214392 TTTTTATTTTATTCATT-TTATTTTC
1 TTTTTATTTTATT-ATTATTATTTTC
214417 TTTTTA-TTTATTATTATTATTTT
1 TTTTTATTTTATTATTATTATTTT
214440 TATTATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 3 0.14
24 13 0.59
25 6 0.27
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (25 bp):
TTTTTATTTTATTATTATTATTTTC
Found at i:214440 original size:20 final size:20
Alignment explanation
Indices: 214398--214468 Score: 63
Period size: 22 Copynumber: 3.5 Consensus size: 20
214388 TACTTTTTTA
*
214398 TTTTATTCATTTTATTTTCT
1 TTTTATTCATTTTATTATCT
* *
214418 TTTTATTTATTATTATTATTT
1 TTTTATTCATT-TTATTATCT
**
214439 TTATTATTTTTGTTTATTATCT
1 TT-TTATTCAT-TTTATTATCT
214461 TTTT-TTCA
1 TTTTATTCA
214469 CTAACTTTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
20 12 0.29
21 11 0.27
22 17 0.41
23 1 0.02
ACGTcount: A:0.18, C:0.06, G:0.01, T:0.75
Consensus pattern (20 bp):
TTTTATTCATTTTATTATCT
Found at i:214449 original size:9 final size:9
Alignment explanation
Indices: 214398--214449 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
214388 TACTTTTTTA
214398 TTTTATTCAT
1 TTTTATT-AT
* *
214408 TTTATTTTCT
1 TTT-TATTAT
214418 TTTTATTTAT
1 TTTTA-TTAT
*
214428 TATTATTAT
1 TTTTATTAT
214437 TTTTATTAT
1 TTTTATTAT
214446 TTTT
1 TTTT
214450 GTTTATTATC
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
9 17 0.50
10 14 0.41
11 3 0.09
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTATTAT
Found at i:214463 original size:15 final size:13
Alignment explanation
Indices: 214407--214466 Score: 57
Period size: 15 Copynumber: 4.2 Consensus size: 13
214397 ATTTTATTCA
*
214407 TTTTATTTTCTTTT
1 TTTTATTAT-TTTT
214421 TATTTATTATTATTAT
1 T-TTTATTATT-TT-T
214437 TTTTATTATTTTT
1 TTTTATTATTTTT
*
214450 GTTTATTATCTTTT
1 TTTTATTAT-TTTT
214464 TTT
1 TTT
214467 CACTAACTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
13 9 0.23
14 10 0.26
15 18 0.46
16 2 0.05
ACGTcount: A:0.17, C:0.03, G:0.02, T:0.78
Consensus pattern (13 bp):
TTTTATTATTTTT
Found at i:215518 original size:18 final size:20
Alignment explanation
Indices: 215480--215520 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
215470 TTTGATCATG
*
215480 ATATTTCAATATGCATGTAT
1 ATATTTCAATATGCATATAT
215500 ATATTTC-ATATG-ATATAT
1 ATATTTCAATATGCATATAT
215518 ATA
1 ATA
215521 ACCAAGTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 5 0.25
20 7 0.35
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (20 bp):
ATATTTCAATATGCATATAT
Found at i:222423 original size:20 final size:20
Alignment explanation
Indices: 222383--222423 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
222373 TTTGATCATG
*
222383 ATATTTCAATATGCATGTAT
1 ATATTTCAATATGCATATAT
222403 ATATTTC-ATATGACATATAT
1 ATATTTCAATATG-CATATAT
222423 A
1 A
222424 ACCAAGTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (20 bp):
ATATTTCAATATGCATATAT
Found at i:224665 original size:10 final size:11
Alignment explanation
Indices: 224645--224673 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
224635 TCACTAACTC
224645 TTTTCATTTTA
1 TTTTCATTTTA
224656 TTTT-ATTTTA
1 TTTTCATTTTA
224666 TTTTCATT
1 TTTTCATT
224674 ACTTGCATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTCATTTTA
Done.