Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001094.1 Hibiscus syriacus cultivar Beakdansim tig00002168_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: 103829
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:153 original size:12 final size:12
Alignment explanation
Indices: 136--169 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
126 CTATAATCCT
136 GAAGAAAAAGAA
1 GAAGAAAAAGAA
148 GAAGAAAAAGAA
1 GAAGAAAAAGAA
160 GAAGAAAAAG
1 GAAGAAAAAG
170 TCCCCGAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
GAAGAAAAAGAA
Found at i:2448 original size:20 final size:19
Alignment explanation
Indices: 2418--2473 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
2408 CAATCATCTT
*
2418 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAACGC-GA
* *
2438 AATTACTATCGCAATGCGA
1 AATGACTATCGCAACGCGA
**
2457 AATGAAAATCGCAACGC
1 AATGACTATCGCAACGC
2474 TAATTTCGCG
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.20
Consensus pattern (19 bp):
AATGACTATCGCAACGCGA
Found at i:2648 original size:14 final size:14
Alignment explanation
Indices: 2629--2665 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2619 CATCAATTAA
2629 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2643 ACAAATCACCTTTT
1 ACAAATCAACTTTT
2657 ACAAATCAA
1 ACAAATCAA
2666 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:4071 original size:21 final size:21
Alignment explanation
Indices: 4002--4071 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
3992 CATGTGAATC
*
4002 GGACTCTTGAATGGTGGGA-G
1 GGACTCTTGAACGGTGGGAGG
* * ** *
4022 GGACCTCTTCAACGATGACAGT
1 GGA-CTCTTGAACGGTGGGAGG
*
4044 GGCCTCTTGAACGGTGGGAGG
1 GGACTCTTGAACGGTGGGAGG
4065 GGACTCT
1 GGACTCT
4072 CGAGGAATGA
Statistics
Matches: 35, Mismatches: 13, Indels: 3
0.69 0.25 0.06
Matches are distributed among these distances:
20 3 0.09
21 30 0.86
22 2 0.06
ACGTcount: A:0.20, C:0.20, G:0.37, T:0.23
Consensus pattern (21 bp):
GGACTCTTGAACGGTGGGAGG
Found at i:4523 original size:89 final size:89
Alignment explanation
Indices: 4343--4524 Score: 278
Period size: 89 Copynumber: 2.0 Consensus size: 89
4333 ATTTCAAACT
* *
4343 TTCAACCAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCA
1 TTCAACCAAAGACAAAACAAAGACAAATACTAACTTCACAATGTT--A-AATAAACAGTTTAGCA
4408 GAATTGGCAGCAACCGAATAAATTTAC
63 GAATTGGCAGCAACCGAATAAATTTAC
4435 TTCAACCAAAAGAC-AAACAAAAGACAAATACTAACTTCACAATGTT-AATAAACAGTTTAGCAG
1 TTCAACC-AAAGACAAAAC-AAAGACAAATACTAACTTCACAATGTTAAATAAACAGTTTAGCAG
*
4498 TATTGGCAGCAACCGAATAAATTTAC
64 AATTGGCAGCAACCGAATAAATTTAC
4524 T
1 T
4525 AAGCAATCTA
Statistics
Matches: 85, Mismatches: 3, Indels: 7
0.89 0.03 0.07
Matches are distributed among these distances:
89 42 0.49
92 11 0.13
93 32 0.38
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (89 bp):
TTCAACCAAAGACAAAACAAAGACAAATACTAACTTCACAATGTTAAATAAACAGTTTAGCAGAA
TTGGCAGCAACCGAATAAATTTAC
Found at i:6235 original size:20 final size:19
Alignment explanation
Indices: 6204--6325 Score: 84
Period size: 20 Copynumber: 6.8 Consensus size: 19
6194 TCTTTTGGTT
6204 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
6223 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
6244 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
6263 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
**
6277 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
6296 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
6310 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
6326 TGCGATTTTC
Statistics
Matches: 80, Mismatches: 11, Indels: 24
0.70 0.10 0.21
Matches are distributed among these distances:
14 20 0.25
16 4 0.05
17 4 0.05
19 21 0.26
20 29 0.36
21 2 0.03
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:6272 original size:14 final size:14
Alignment explanation
Indices: 6253--6308 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
6243 GGAAATGACT
6253 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
6267 ATCGCAACGCGAAATGA
1 ATCGCAA--CGAGA-GA
6284 CTATCGCAACGAGAGA
1 --ATCGCAACGAGAGA
6300 ATCGCAACG
1 ATCGCAACG
6309 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 16 0.46
16 6 0.17
17 6 0.17
19 7 0.20
ACGTcount: A:0.39, C:0.25, G:0.25, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:6286 original size:33 final size:33
Alignment explanation
Indices: 6229--6325 Score: 167
Period size: 33 Copynumber: 2.9 Consensus size: 33
6219 ACGAGATAAT
6229 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
6263 GAGAATCGCAACGCGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
6296 GAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGACTATCGCAA
6326 TGCGATTTTC
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
33 47 0.77
34 14 0.23
ACGTcount: A:0.41, C:0.23, G:0.25, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:6362 original size:19 final size:19
Alignment explanation
Indices: 6326--6370 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
6316 AAAATCGCAA
*
6326 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTACGCGT
*
6345 TGCGATTTTTATTACGCGT
1 TGCGATTTTCATTACGCGT
*
6364 TGTGATT
1 TGCGATT
6371 CTCTCGTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.13, C:0.16, G:0.22, T:0.49
Consensus pattern (19 bp):
TGCGATTTTCATTACGCGT
Found at i:6990 original size:21 final size:20
Alignment explanation
Indices: 6944--6993 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
6934 CGATAATAAG
* *
6944 ATTCACATTGCGATTTACGT
1 ATTCGCATTGCGATTTACCT
*
6964 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACCT
6984 AATTCGCATT
1 -ATTCGCATT
6994 CGTAACGCGA
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:0.14, T:0.42
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACCT
Found at i:7098 original size:20 final size:21
Alignment explanation
Indices: 7054--7105 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
7044 ATAGTCAGTA
*
7054 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
7075 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
7095 TCGCATTGCGA
1 TCGCATTGCGA
7106 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:7120 original size:41 final size:41
Alignment explanation
Indices: 7012--7120 Score: 96
Period size: 41 Copynumber: 2.7 Consensus size: 41
7002 GAATACGTAA
* * *
7012 ATCGCAATGCGAATTAGGAAAATTGCATTGCGATAGTCAGT
1 ATCGCATTGCGAATTAGGAAAATCGCATTGCGATACTCAGT
* *** * *
7053 ATCGCATTGCGATTTTCCAAATTCGCATTGCGATTTACTTA-T
1 ATCGCATTGCGAATTAGGAAAATCGCATTGCGA--TACTCAGT
*
7095 -TCGCATTGCGAATTGGGAAAATCGCA
1 ATCGCATTGCGAATTAGGAAAATCGCA
7121 ACGCGAAATT
Statistics
Matches: 52, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
41 47 0.90
42 1 0.02
43 4 0.08
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.31
Consensus pattern (41 bp):
ATCGCATTGCGAATTAGGAAAATCGCATTGCGATACTCAGT
Found at i:7147 original size:21 final size:22
Alignment explanation
Indices: 7095--7147 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
7085 ATTTACTTAT
*
7095 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGAAAAA
**
7116 TCGCAACGCGAAATT-GAAAAA
1 TCGCATTGCGAAATTGGAAAAA
7137 TCGCATTGCGA
1 TCGCATTGCGA
7148 TAGTCATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGAAAAA
Found at i:9103 original size:13 final size:13
Alignment explanation
Indices: 9085--9110 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9075 TTTAGTCGCG
9085 TGATGATGAGAAA
1 TGATGATGAGAAA
9098 TGATGATGAGAAA
1 TGATGATGAGAAA
9111 GACCGTCTAT
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:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (13 bp):
TGATGATGAGAAA
Found at i:11267 original size:18 final size:17
Alignment explanation
Indices: 11246--11284 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
11236 ATTGTTATTG
*
11246 TTATTATAATTTTGGTTA
1 TTATTATAAGTTTGG-TA
11264 TTATTATAAGTTTGGTA
1 TTATTATAAGTTTGGTA
11281 TTAT
1 TTAT
11285 GTAGTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.59
Consensus pattern (17 bp):
TTATTATAAGTTTGGTA
Found at i:12350 original size:29 final size:29
Alignment explanation
Indices: 12275--12350 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 29
12265 TATTAAAATT
12275 TTTAAAAAT-TCAAAAATATATTCTATTA
1 TTTAAAAATATCAAAAATATATTCTATTA
12303 TTTCAAAATTATAT-AAAAA-ATATT-TATTTA
1 TTT-AAAA--ATATCAAAAATATATTCTA-TTA
12333 TTTAAAAATATCAGAAAA
1 TTTAAAAATATCA-AAAA
12351 GAACTTCTAG
Statistics
Matches: 41, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
27 4 0.10
28 4 0.10
29 14 0.34
30 11 0.27
31 7 0.17
32 1 0.02
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (29 bp):
TTTAAAAATATCAAAAATATATTCTATTA
Found at i:12546 original size:20 final size:21
Alignment explanation
Indices: 12523--12563 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
12513 TATTATATAT
**
12523 ATATTTATGAATAT-ATAAAA
1 ATATTTAACAATATAATAAAA
12543 ATATTTAACAATATAATAAAA
1 ATATTTAACAATATAATAAAA
12564 TAAAAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATTTAACAATATAATAAAA
Found at i:13541 original size:9 final size:9
Alignment explanation
Indices: 13521--13558 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
13511 TTTGTCTCTC
13521 TTTCTGTTTT
1 TTTCT-TTTT
13531 TTTCTTTTT
1 TTTCTTTTT
13540 TTTCTTCTTT
1 TTTCTT-TTT
13550 TTT-TTTTT
1 TTTCTTTTT
13558 T
1 T
13559 CAGGTTCGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 4 0.15
9 12 0.44
10 11 0.41
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.87
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:13547 original size:12 final size:12
Alignment explanation
Indices: 13507--13554 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
13497 GTCTCTCTCT
13507 TTTTTTTGTCTCTC
1 TTTTTTT-TCT-TC
*
13521 TTTCTGTTTTTTTC
1 TTT-T-TTTTCTTC
13535 TTTTTTTTCTTC
1 TTTTTTTTCTTC
13547 TTTTTTTT
1 TTTTTTTT
13555 TTTTCAGGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
12 15 0.50
13 1 0.03
14 8 0.27
15 3 0.10
16 3 0.10
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.81
Consensus pattern (12 bp):
TTTTTTTTCTTC
Found at i:13988 original size:14 final size:15
Alignment explanation
Indices: 13969--14003 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
13959 GGTCTGTAAT
13969 TATTTATTT-ATATA
1 TATTTATTTAATATA
13983 TATTTATTTAATATA
1 TATTTATTTAATATA
13998 TATTTA
1 TATTTA
14004 ATAATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TATTTATTTAATATA
Found at i:14010 original size:3 final size:3
Alignment explanation
Indices: 14002--14078 Score: 145
Period size: 3 Copynumber: 25.7 Consensus size: 3
13992 AATATATATT
*
14002 TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
14050 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
14079 TGGATAAAAA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:14640 original size:113 final size:113
Alignment explanation
Indices: 14397--14950 Score: 1029
Period size: 113 Copynumber: 4.9 Consensus size: 113
14387 AGAGTCATTC
* * *
14397 AAAAGGTTGAATAAATTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
14462 TATGAAC-TTCTCTGGAAAAGATAATCCATCAATTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
*
14509 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTGTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
14574 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
14622 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
14687 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
14735 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
14800 TATGAACTTTCTCTGGAAAAGATGATCCATCAATTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
14848 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
14913 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGAT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGAT
14951 AGATTTGAAT
Statistics
Matches: 431, Mismatches: 10, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
112 68 0.16
113 363 0.84
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
Found at i:16300 original size:83 final size:83
Alignment explanation
Indices: 15675--16298 Score: 1099
Period size: 83 Copynumber: 7.5 Consensus size: 83
15665 GTTCCTACCA
*
15675 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCACATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATT
* *
15740 CAATGATTGGTTCTGCCA
66 CAATGATTGGTTCTGTCT
15758 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATT
* *
15823 CAATGATTGGTTCTGCCA
66 CAATGATTGGTTCTGTCT
15841 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATT
15906 CAATGATTGGTTCTGTCT
66 CAATGATTGGTTCTGTCT
* * * *
15924 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTCTAAAC
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTCCAAAT
15988 TCAATGATTGGTTCTGTCT
65 TCAATGATTGGTTCTGTCT
16007 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATT
16072 CAATGATTGGTTCTGTCT
66 CAATGATTGGTTCTGTCT
16090 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATT
16155 CAATGATTGGTTCTGTCT
66 CAATGATTGGTTCTGTCT
* * * *
16173 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTCTAAAC
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTCCAAAT
16237 TCAATGATTGGTTCTGTCT
65 TCAATGATTGGTTCTGTCT
16256 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
16299 TGAGTCTCTT
Statistics
Matches: 523, Mismatches: 15, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
82 3 0.01
83 516 0.99
84 4 0.01
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.27
Consensus pattern (83 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATT
CAATGATTGGTTCTGTCT
Found at i:16664 original size:12 final size:12
Alignment explanation
Indices: 16647--16673 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
16637 AGTGCTGAAA
16647 ATGGAATCTAGT
1 ATGGAATCTAGT
16659 ATGGAATCTAGT
1 ATGGAATCTAGT
16671 ATG
1 ATG
16674 CCACCTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.26, T:0.33
Consensus pattern (12 bp):
ATGGAATCTAGT
Found at i:17365 original size:6 final size:6
Alignment explanation
Indices: 17354--17399 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
17344 CTTGACCCTC
*
17354 CTTTTT CTTTTT CTTTTCT CTTTTT -TCCTTT -TTTTT CTTTTT CTTT
1 CTTTTT CTTTTT CTTTT-T CTTTTT CT-TTTT CTTTTT CTTTTT CTTT
17400 CTTTTCTTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
5 4 0.11
6 25 0.71
7 6 0.17
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
CTTTTT
Found at i:17389 original size:10 final size:9
Alignment explanation
Indices: 17355--17404 Score: 55
Period size: 10 Copynumber: 5.1 Consensus size: 9
17345 TTGACCCTCC
17355 TTTTTCTTTT
1 TTTTTC-TTT
17365 TCTTTTCTCTT
1 T-TTTTCT-TT
*
17376 TTTTCCTTT
1 TTTTTCTTT
17385 TTTTTCTTT
1 TTTTTCTTT
17394 TTCTTTCTTT
1 TT-TTTCTTT
17404 T
1 T
17405 CTTCAAGCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 12 0.34
10 15 0.43
11 8 0.23
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:28464 original size:29 final size:29
Alignment explanation
Indices: 28389--28464 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 29
28379 TATTAAAATT
28389 TTTAAAAAT-TCAAAAATATATTCTATTA
1 TTTAAAAATATCAAAAATATATTCTATTA
28417 TTTCAAAATTATAT-AAAAA-ATATT-TATTTA
1 TTT-AAAA--ATATCAAAAATATATTCTA-TTA
28447 TTTAAAAATATCAGAAAA
1 TTTAAAAATATCA-AAAA
28465 GAACTTCTAG
Statistics
Matches: 41, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
27 4 0.10
28 4 0.10
29 14 0.34
30 11 0.27
31 7 0.17
32 1 0.02
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (29 bp):
TTTAAAAATATCAAAAATATATTCTATTA
Found at i:28659 original size:20 final size:21
Alignment explanation
Indices: 28636--28676 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
28626 TATTATATAT
**
28636 ATATTTATGAATAT-ATAAAA
1 ATATTTAACAATATAATAAAA
28656 ATATTTAACAATATAATAAAA
1 ATATTTAACAATATAATAAAA
28677 TAAAAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATTTAACAATATAATAAAA
Found at i:28732 original size:19 final size:19
Alignment explanation
Indices: 28708--28746 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
28698 AACAATATAT
28708 TTAAAATCA-ATAAAATAAA
1 TTAAAA-CATATAAAATAAA
28727 TTAAAACATATAAAATAAA
1 TTAAAACATATAAAATAAA
28746 T
1 T
28747 GACTAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 2 0.11
19 17 0.89
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (19 bp):
TTAAAACATATAAAATAAA
Found at i:29652 original size:12 final size:12
Alignment explanation
Indices: 29637--29668 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
29627 TCTCTGTCTG
29637 TTTTTTTCTTTT
1 TTTTTTTCTTTT
*
29649 TTTTCTTCTTTT
1 TTTTTTTCTTTT
29661 TTTTTTTC
1 TTTTTTTC
29669 AGGTTCGGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (12 bp):
TTTTTTTCTTTT
Found at i:30097 original size:14 final size:15
Alignment explanation
Indices: 30078--30112 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
30068 GGTCTGTAAT
30078 TATTTATTT-ATATA
1 TATTTATTTAATATA
30092 TATTTATTTAATATA
1 TATTTATTTAATATA
30107 TATTTA
1 TATTTA
30113 ATAATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TATTTATTTAATATA
Found at i:30119 original size:3 final size:3
Alignment explanation
Indices: 30111--30229 Score: 220
Period size: 3 Copynumber: 39.7 Consensus size: 3
30101 AATATATATT
* *
30111 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
30159 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
30207 TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
30230 TGGATAAAAA
Statistics
Matches: 112, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 112 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:33940 original size:6 final size:6
Alignment explanation
Indices: 33929--33967 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
33919 ATTAACACCT
*
33929 TTTGCA TTTGCA TTTAGCA TTTGCA TTTGCA TATGCA TT
1 TTTGCA TTTGCA TTT-GCA TTTGCA TTTGCA TTTGCA TT
33968 ACATTCATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.21, C:0.15, G:0.15, T:0.49
Consensus pattern (6 bp):
TTTGCA
Found at i:36050 original size:2 final size:2
Alignment explanation
Indices: 36043--36077 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
36033 ATCCCTTCAA
36043 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 A
36078 CTCCTTGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39170 original size:36 final size:37
Alignment explanation
Indices: 39077--39172 Score: 104
Period size: 37 Copynumber: 2.6 Consensus size: 37
39067 AGCAAAATCA
* ** **
39077 ATCTTAAGCCTTTACCGAAGAGTAGTGAAGCAAGTTG
1 ATCTTAAGCCTTCACAAAAGAGTAGTGAAGCAAGTCC
* *
39114 ATCTTAAGCCTTCACTAAAGAGTAGTGAAGTAA-TCC
1 ATCTTAAGCCTTCACAAAAGAGTAGTGAAGCAAGTCC
* *
39150 ATTTTAAGCCTTCTCAAAAGAGT
1 ATCTTAAGCCTTCACAAAAGAGT
39173 GTTGGAGCAA
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
36 21 0.42
37 29 0.58
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (37 bp):
ATCTTAAGCCTTCACAAAAGAGTAGTGAAGCAAGTCC
Found at i:39841 original size:111 final size:108
Alignment explanation
Indices: 39445--39849 Score: 444
Period size: 108 Copynumber: 3.7 Consensus size: 108
39435 TAGTGAAGCA
* * **
39445 AAGAAGATTGTTCAAGTTCCATACTCCTTAAAGAAAGAGGGAGCGAACCCGT--TTGAAGATGTT
1 AAGAAGA-TGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGAAGAAGATGTT
* * *
39508 CGAGTTCTATACTCCCT-AGAGAAAGAGGGAGCGAACCAATAAG
65 CGAGTTCTATACTACCTGAAAGAAAGAGGGAGCGAACCCATAAG
* * ** *
39551 AAGAAGATGTTCGAGTTCCCTACTCCCTAGAGAAAGAATGAGCTAACCCGTAAGAAGAAGATGTT
1 AAGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGT-AGAAGAAGATGTT
*
39616 CGAGTTCTATACTACCTG-AAGAAAGAGGGAGTGAACCCATAAG
65 CGAGTTCTATACTACCTGAAAGAAAGAGGGAGCGAACCCATAAG
* * * * *
39659 AAGATGATGTTCGAGTTCCATACTTCCTGAAAGAAAGAGGGAGCAAACCCGTTTGCAGAAGAT-T
1 AAGAAGATGTTCGAGTTCCATACTCCCT-AAAGAAAGAGGGAGCGAACCCG-TAGAAGAAGATGT
* ** **
39723 ATCCGAGTTCTATACTTCCTGAAAGAAAGAGAAAGCGAACCCATTCG
64 -T-CGAGTTCTATACTACCTGAAAGAAAGAGGGAGCGAACCCATAAG
* * *
39770 CAGAAGATTATTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCTGTAGGAAGAAGATTG
1 AAGAAGA-TGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTA-GAAGAAGA-TG
39835 TTCGAG-TCTTATACT
63 TTCGAGTTC-TATACT
39850 CTCTGAATAA
Statistics
Matches: 249, Mismatches: 36, Indels: 23
0.81 0.12 0.07
Matches are distributed among these distances:
105 37 0.15
106 7 0.03
108 73 0.29
109 27 0.11
110 21 0.08
111 62 0.25
112 21 0.08
113 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.22
Consensus pattern (108 bp):
AAGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGAAGAAGATGTTC
GAGTTCTATACTACCTGAAAGAAAGAGGGAGCGAACCCATAAG
Found at i:39850 original size:55 final size:54
Alignment explanation
Indices: 39445--39841 Score: 388
Period size: 54 Copynumber: 7.3 Consensus size: 54
39435 TAGTGAAGCA
* *
39445 AAGAAGATTGTTCAAGTTCCATACTCCTTAAAGAAAGAGGGAGCGAACCCGT---
1 AAGAAGA-TGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAG
** * * **
39497 TTGAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCAATAAG
1 AAGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAG
* * ** *
39551 AAGAAGATGTTCGAGTTCCCTACTCCCTAGAGAAAGAATGAGCTAACCCGTAAG
1 AAGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAG
* * * * *
39605 AAGAAGATGTTCGAGTTCTATACTACCTGAAGAAAGAGGGAGTGAACCCATAAG
1 AAGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAG
* * * **
39659 AAGATGATGTTCGAGTTCCATACTTCCTGAAAGAAAGAGGGAGCAAACCCGTTTG
1 AAGAAGATGTTCGAGTTCCATACTCCCT-AAAGAAAGAGGGAGCGAACCCGTAAG
* * * ** * **
39714 CAGAAGAT-TATCCGAGTTCTATACTTCCTGAAAGAAAGAGAAAGCGAACCCATTCG
1 AAGAAGATGT-T-CGAGTTCCATACTCCCT-AAAGAAAGAGGGAGCGAACCCGTAAG
* * * *
39770 CAGAAGATTATTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCTGTAGG
1 AAGAAGA-TGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAG
39825 AAGAAGATTGTTCGAGT
1 AAGAAGA-TGTTCGAGT
39842 CTTATACTCT
Statistics
Matches: 283, Mismatches: 54, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
51 38 0.13
52 5 0.02
54 115 0.41
55 62 0.22
56 60 0.21
57 2 0.01
58 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (54 bp):
AAGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAG
Found at i:39886 original size:55 final size:55
Alignment explanation
Indices: 39827--40719 Score: 1224
Period size: 55 Copynumber: 16.3 Consensus size: 55
39817 CCTGTAGGAA
* * * *
39827 GAAGATTGTTCGAGTCTTATACTCTCTGAATAAATAGAGAACAGACACGATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
* *
39882 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGTAGACACGATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
* * *
39937 GAAGATTATTCGAGTCTTATACTCTCTGAATG-AATAGAGATCAGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAA-GAAATAGGGAGCAGACACGATTGTT
* * *
39992 GAAGATTGTTCGAGTCTTATACTCTCTAAAAAAATAGGGAGCAGACACGATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
*
40047 GAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGA-TGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
* * * * *
40101 GAAGATTGTTCGAGTCTTATACTCTCTGAAAAAATAGGGAACATACATGATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
* * * * **
40156 GAAGATTATTCGAGT-TCTATACT-TCCTGAAAGAAAGAGGGAGC-GAACCCGTTTGCA
1 GAAGATTGTTCGAGTCT-TATACTCT-CTG-AAGAAATAGGGAGCAG-ACACGATTGTT
* *
40212 GAAGATTATTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGA-TGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
* * *
40266 GAAGATTGCTCGAGTCTTATACTCTCTGAAAAAATAGGGAGCAAACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
* * * * * * *
40321 AAAGATTATTCGAGTCTTATACTCTATGAAAAAATAAGGAGTAGACACGATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
* *
40376 GAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAAACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
*
40431 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
* *
40486 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCTGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
* * *
40541 GAAGATTGTTCGAGTGTTATACTCTCTGAAGGAATAGGGAGCAGACATGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
* *
40596 GAAGATTGTTCGAGTCTTATACTCTATGAAGGAATAGGGAGCAGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
* ** * *
40651 GAAGATTGTTCAAGTCTTATACTCTCTGAAG-AATACAGAGCAGAGACGTTTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
*
40705 GAAGATTGTGCGAGT
1 GAAGATTGTTCGAGT
40720 TCCATGCACC
Statistics
Matches: 745, Mismatches: 82, Indels: 23
0.88 0.10 0.03
Matches are distributed among these distances:
54 129 0.17
55 573 0.77
56 41 0.06
57 2 0.00
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.29
Consensus pattern (55 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
Found at i:41041 original size:18 final size:17
Alignment explanation
Indices: 41020--41058 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
41010 ATTGTTATTG
*
41020 TTATTATAATTTTGGTTA
1 TTATTATAAGTTTGG-TA
41038 TTATTATAAGTTTGGTA
1 TTATTATAAGTTTGGTA
41055 TTAT
1 TTAT
41059 GTAGTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.59
Consensus pattern (17 bp):
TTATTATAAGTTTGGTA
Found at i:44011 original size:33 final size:33
Alignment explanation
Indices: 43973--44052 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
43963 CTTTCAGTGA
*
43973 CAGCAACAATTGTTCAACAATTACTTTCGGTGG
1 CAGCAACAATTGTTCAACAATTACTTTCGATGG
* *
44006 TAGCAACAATTGTTCAACAATTGCTTTCGATGG
1 CAGCAACAATTGTTCAACAATTACTTTCGATGG
44039 CAGCAACAATTGTT
1 CAGCAACAATTGTT
44053 GAATTTGGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Consensus pattern (33 bp):
CAGCAACAATTGTTCAACAATTACTTTCGATGG
Found at i:49822 original size:20 final size:20
Alignment explanation
Indices: 49797--49864 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
49787 AAGAATCAGG
49797 AAGAACAGAAATAGGGTGGC
1 AAGAACAGAAATAGGGTGGC
* * * * *
49817 AAGAACAGTAACACTGCTAG-
1 AAGAACAGAAATA-GGGTGGC
* *
49837 AAGAGCGGAAATAGGGTGGC
1 AAGAACAGAAATAGGGTGGC
49857 AAGAACAG
1 AAGAACAG
49865 TAACACTGCT
Statistics
Matches: 32, Mismatches: 14, Indels: 4
0.64 0.28 0.08
Matches are distributed among these distances:
19 3 0.09
20 26 0.81
21 3 0.09
ACGTcount: A:0.44, C:0.13, G:0.32, T:0.10
Consensus pattern (20 bp):
AAGAACAGAAATAGGGTGGC
Found at i:49851 original size:40 final size:40
Alignment explanation
Indices: 49804--49880 Score: 154
Period size: 40 Copynumber: 1.9 Consensus size: 40
49794 AGGAAGAACA
49804 GAAATAGGGTGGCAAGAACAGTAACACTGCTAGAAGAGCG
1 GAAATAGGGTGGCAAGAACAGTAACACTGCTAGAAGAGCG
49844 GAAATAGGGTGGCAAGAACAGTAACACTGCTAGAAGA
1 GAAATAGGGTGGCAAGAACAGTAACACTGCTAGAAGA
49881 TCAGATCAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.42, C:0.14, G:0.31, T:0.13
Consensus pattern (40 bp):
GAAATAGGGTGGCAAGAACAGTAACACTGCTAGAAGAGCG
Found at i:54628 original size:20 final size:20
Alignment explanation
Indices: 54603--54670 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
54593 AAGAATCAGG
54603 AAGAACAGAAATAGGGTGGC
1 AAGAACAGAAATAGGGTGGC
* * * * *
54623 AAGAACAGTAACACTGCTAG-
1 AAGAACAGAAATA-GGGTGGC
* *
54643 AAGAGCGGAAATAGGGTGGC
1 AAGAACAGAAATAGGGTGGC
54663 AAGAACAG
1 AAGAACAG
54671 TAACACTGCT
Statistics
Matches: 32, Mismatches: 14, Indels: 4
0.64 0.28 0.08
Matches are distributed among these distances:
19 3 0.09
20 26 0.81
21 3 0.09
ACGTcount: A:0.44, C:0.13, G:0.32, T:0.10
Consensus pattern (20 bp):
AAGAACAGAAATAGGGTGGC
Found at i:54657 original size:40 final size:40
Alignment explanation
Indices: 54610--54686 Score: 154
Period size: 40 Copynumber: 1.9 Consensus size: 40
54600 AGGAAGAACA
54610 GAAATAGGGTGGCAAGAACAGTAACACTGCTAGAAGAGCG
1 GAAATAGGGTGGCAAGAACAGTAACACTGCTAGAAGAGCG
54650 GAAATAGGGTGGCAAGAACAGTAACACTGCTAGAAGA
1 GAAATAGGGTGGCAAGAACAGTAACACTGCTAGAAGA
54687 TCAGATCAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.42, C:0.14, G:0.31, T:0.13
Consensus pattern (40 bp):
GAAATAGGGTGGCAAGAACAGTAACACTGCTAGAAGAGCG
Found at i:61407 original size:22 final size:22
Alignment explanation
Indices: 61379--61447 Score: 138
Period size: 22 Copynumber: 3.1 Consensus size: 22
61369 GATAATGCTC
61379 AATCCACTAATATTGAGTGTTA
1 AATCCACTAATATTGAGTGTTA
61401 AATCCACTAATATTGAGTGTTA
1 AATCCACTAATATTGAGTGTTA
61423 AATCCACTAATATTGAGTGTTA
1 AATCCACTAATATTGAGTGTTA
61445 AAT
1 AAT
61448 GCATGAGGTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (22 bp):
AATCCACTAATATTGAGTGTTA
Found at i:62946 original size:22 final size:23
Alignment explanation
Indices: 62893--62946 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
62883 TTTTCTCTTT
*
62893 TCTTCTCTCCACGTATGGCTTCTC
1 TCTTC-CTCCACGTATGACTTCTC
62917 TCTTTTCCT-CACGTATGACTTCTC
1 TC--TTCCTCCACGTATGACTTCTC
62941 TCTTCC
1 TCTTCC
62947 CCCTCCCTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 4 0.15
24 18 0.67
25 2 0.07
26 3 0.11
ACGTcount: A:0.09, C:0.37, G:0.09, T:0.44
Consensus pattern (23 bp):
TCTTCCTCCACGTATGACTTCTC
Found at i:63142 original size:6 final size:6
Alignment explanation
Indices: 63133--63797 Score: 1267
Period size: 6 Copynumber: 110.8 Consensus size: 6
63123 AGTGCTTGAG
* * * * * *
63133 TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA TAATAC TAATAC
1 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC
63181 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC
1 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC
63229 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC
1 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC
63277 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC
1 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC
63325 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC
1 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC
63373 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC
1 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC
63421 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC
1 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC
63469 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC
1 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC
63517 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC
1 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC
63565 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC
1 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC
63613 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC
1 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC
63661 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC
1 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC
63709 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC
1 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC
*
63757 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAA TAATA
1 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATA
63798 TTTAATAATA
Statistics
Matches: 657, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 657 1.00
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.33
Consensus pattern (6 bp):
TAATAC
Found at i:64368 original size:36 final size:37
Alignment explanation
Indices: 64278--64369 Score: 98
Period size: 36 Copynumber: 2.5 Consensus size: 37
64268 TTCAAAGGTT
* * *
64278 TTATGTTTCAAGGGAAACCGTCTTAAGGGAGACAAAATT
1 TTAT-TTT-AAGGGAAACTGTCTCAAGGGAGACAAAATC
* * *
64317 TTGTTTTAA-GAAAACTGTCTCACGGGAGACAAAA-C
1 TTATTTTAAGGGAAACTGTCTCAAGGGAGACAAAATC
64352 TTATTTTAAGGGAAACTG
1 TTATTTTAAGGGAAACTG
64370 ATTCAAAGAT
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
35 8 0.18
36 28 0.64
37 2 0.05
38 3 0.07
39 3 0.07
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (37 bp):
TTATTTTAAGGGAAACTGTCTCAAGGGAGACAAAATC
Found at i:64470 original size:36 final size:36
Alignment explanation
Indices: 64413--64801 Score: 286
Period size: 36 Copynumber: 10.6 Consensus size: 36
64403 TCAAAGTTTA
* * * * *
64413 TGTTTCAAGAGAAATTGTCTCAAGGGAGAAAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGAAAAATTT
64449 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGA-AAAATTT
* * *
64485 CGTTCCAAGGGAAACTATCTCAAAAGAGATAAAA-TT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGA-AAAATTT
* *
64521 CGTTTCAAGGGAAACGT-TTTC-A-A-AG-----TTT
1 TGTTTCAAGGGAAAC-TATCTCAAGAGAGAAAAATTT
* * *
64549 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TT
1 -TGTTTCAAGGGAAACTATCTCAAGAGAGA-AAAATTT
64586 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATCTTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGA-AAAA--TTT
* * *
64625 TGTTTCGA-GGAAACTATCTCATGCGAGATAAAATCTTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGA-AAAA--TTT
* * *
64663 TATTTCGAGGGAAACTATCTTC-AGTGAGATAAAATCTTT
1 TGTTTCAAGGGAAACTATC-TCAAGAGAGA-AAAA--TTT
* *
64702 TGTTTCGAGGGAAACTATCTCAAGCG-GATAAAATCTTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGA-AAAA--TTT
*
64740 TGTTTCAAGGGAAACTATCTCAAGCGAGACAAAATCTTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGA-AAAA--TTT
64779 TGTTTCAAGGGAAACTATCTCAA
1 TGTTTCAAGGGAAACTATCTCAA
64802 ACGAGATACA
Statistics
Matches: 304, Mismatches: 28, Indels: 39
0.82 0.08 0.11
Matches are distributed among these distances:
28 3 0.01
29 16 0.05
30 1 0.00
32 2 0.01
33 2 0.01
34 1 0.00
35 1 0.00
36 107 0.35
37 7 0.02
38 73 0.24
39 89 0.29
40 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGAAAAATTT
Found at i:64571 original size:137 final size:136
Alignment explanation
Indices: 64221--64620 Score: 458
Period size: 137 Copynumber: 2.9 Consensus size: 136
64211 TGGGTGTTTT
* * * * * * *
64221 AGGGAAACTGTCTCAAGAGAGACAAAACTCATTTCAAGGGGAAAAG-ATTCAAAGGTTTTATGTT
1 AGGGAAACTATCTCAAAAGAGATAAAATTCGTTTCAA-GGGAAACGTTTTCAAA-G-TTTATGTT
* * * * * * * * *
64285 TCAAGGGAAACCGTCTTAAGGGAGACAAAATTTTGTTTTAA-GAAAACTGTCTCACGGGAGACAA
63 TCAAGAGAAACTGTCTCAAGGGAGA-AAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGACAA
**
64349 AACTTATTTTA
127 AA-TTATTCCA
* *
64360 AGGGAAACTGAT-TC--AA-AGAT---TTTGTGTTTCAAGGGAAACGTTTTCAAAGTTTATGTTT
1 AGGGAAACT-ATCTCAAAAGAGATAAAATT-CGTTTCAAGGGAAACGTTTTCAAAGTTTATGTTT
*
64418 CAAGAGAAATTGTCTCAAGGGAGAAAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA
64 CAAGAGAAACTGTCTCAAGGGAGAAAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA
*
64483 TTCGTTCCA
129 TT-ATTCCA
64492 AGGGAAACTATCTCAAAAGAGATAAAATTCGTTTCAAGGGAAACGTTTTCAAAGTTTATGTTTCA
1 AGGGAAACTATCTCAAAAGAGATAAAATTCGTTTCAAGGGAAACGTTTTCAAAGTTTATGTTTCA
*
64557 AGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAT
66 AGAGAAACTGTCTCAAGGGAGAAAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAT
64621 CTTTTGTTTC
Statistics
Matches: 223, Mismatches: 26, Indels: 26
0.81 0.09 0.09
Matches are distributed among these distances:
131 17 0.08
132 64 0.29
133 9 0.04
134 14 0.06
135 4 0.02
136 3 0.01
137 98 0.44
138 2 0.01
139 11 0.05
140 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (136 bp):
AGGGAAACTATCTCAAAAGAGATAAAATTCGTTTCAAGGGAAACGTTTTCAAAGTTTATGTTTCA
AGAGAAACTGTCTCAAGGGAGAAAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
ATTCCA
Found at i:64692 original size:39 final size:39
Alignment explanation
Indices: 64550--64809 Score: 343
Period size: 39 Copynumber: 6.8 Consensus size: 39
64540 TCAAAGTTTA
* * * *
64550 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA---TT
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTT
* *
64586 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATCTTT
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTT
* *
64625 TGTTTCGA-GGAAACTATCTCATGCGAGATAAAATCTTT
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTT
* * *
64663 TATTTCGAGGGAAACTATCTTC-AGTGAGATAAAATCTTT
1 TGTTTCAAGGGAAACTATC-TCAAGCGAGATAAAATCTTT
*
64702 TGTTTCGAGGGAAACTATCTCAAGCG-GATAAAATCTTT
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTT
*
64740 TGTTTCAAGGGAAACTATCTCAAGCGAGACAAAATCTTT
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTT
*
64779 TGTTTCAAGGGAAACTATCTCAAACGAGATA
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATA
64810 CAATGTTCTT
Statistics
Matches: 201, Mismatches: 16, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
36 31 0.15
38 73 0.36
39 95 0.47
40 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.30
Consensus pattern (39 bp):
TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTT
Found at i:64697 original size:77 final size:78
Alignment explanation
Indices: 64550--64809 Score: 343
Period size: 77 Copynumber: 3.4 Consensus size: 78
64540 TCAAAGTTTA
* * * * * *
64550 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA---TTTGTTTCAAGGGAAACTATCTCAAGAG
1 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTTTATTTCAAGGGAAACTATCTCAAGAG
64612 AGACAAAATCTTT
66 AGACAAAATCTTT
* * *
64625 TGTTTCGA-GGAAACTATCTCATGCGAGATAAAATCTTTTATTTCGAGGGAAACTATCTTC-AGT
1 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTTTATTTCAAGGGAAACTATC-TCAAGA
*
64688 GAGATAAAATCTTT
65 GAGACAAAATCTTT
* *
64702 TGTTTCGAGGGAAACTATCTCAAGCG-GATAAAATCTTTTGTTTCAAGGGAAACTATCTCAAGCG
1 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTTTATTTCAAGGGAAACTATCTCAAGAG
64766 AGACAAAATCTTT
66 AGACAAAATCTTT
* *
64779 TGTTTCAAGGGAAACTATCTCAAACGAGATA
1 TGTTTCGAGGGAAACTATCTCAAGCGAGATA
64810 CAATGTTCTT
Statistics
Matches: 161, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
74 20 0.12
75 7 0.04
76 2 0.01
77 110 0.68
78 22 0.14
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.30
Consensus pattern (78 bp):
TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTTTATTTCAAGGGAAACTATCTCAAGAG
AGACAAAATCTTT
Found at i:64969 original size:76 final size:75
Alignment explanation
Indices: 64880--65056 Score: 196
Period size: 75 Copynumber: 2.3 Consensus size: 75
64870 TCAAGTGAGA
* * ** *
64880 AAAAACAATCTTGAGTGAAATAAATCTTCATGTTTTTAGTGAAAACTGTCTTAAGCGAGAAAAA-
1 AAAAACAATCTTGAGTGAAATAAATCGTCATCTTTCGAGT-AAAACTGTCTCAAGCGAGAAAAAT
64944 TCTTCTTTTAAG
65 TC-TCTTTTAAG
* * * *
64956 AAAAACAATCTTGAGTCAAATGAAAT-GTCTTCTTTCGAGTAAAACTGTCTCAAGGGAGACAAAT
1 AAAAACAATCTTGAGTGAAAT-AAATCGTCATCTTTCGAGTAAAACTGTCTCAAGCGAGAAAAAT
*
65020 TCTGTTTTAAG
65 TCTCTTTTAAG
** *
65031 AAAAACAATCTCAAGTGAGATAAATC
1 AAAAACAATCTTGAGTGAAATAAATC
65057 CTATTTATTA
Statistics
Matches: 84, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
74 4 0.05
75 45 0.54
76 31 0.37
77 4 0.05
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.31
Consensus pattern (75 bp):
AAAAACAATCTTGAGTGAAATAAATCGTCATCTTTCGAGTAAAACTGTCTCAAGCGAGAAAAATT
CTCTTTTAAG
Found at i:70554 original size:14 final size:12
Alignment explanation
Indices: 70535--70568 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 12
70525 CATGATGATT
70535 ATGCAAATACGAA
1 ATGCAAATAC-AA
70548 GATGCAAATACAA
1 -ATGCAAATACAA
70561 ATGCAAAT
1 ATGCAAAT
70569 GTGATGATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.40
13 2 0.10
14 10 0.50
ACGTcount: A:0.53, C:0.15, G:0.15, T:0.18
Consensus pattern (12 bp):
ATGCAAATACAA
Found at i:72091 original size:30 final size:29
Alignment explanation
Indices: 71973--72091 Score: 82
Period size: 30 Copynumber: 3.9 Consensus size: 29
71963 TAGATCTAGA
* *
71973 AAAAACATG-AACTTAAAGGATTAAGAATGGT
1 AAAAACA-GAAACTT-AAGGACTAA-AATAGT
* * * *
72004 AAGAACATAAACTTAAAAGACTAAAACAGAT
1 AAAAACAGAAACTT-AAGGACTAAAATAG-T
*
72035 AAAAA-AGAAATTTAAAGGAC-ATAAATAGT
1 AAAAACAGAAACTT-AAGGACTA-AAATAGT
72064 AAAAACAGAAACTTAAGTGACTAAAATA
1 AAAAACAGAAACTTAAG-GACTAAAATA
72092 AAATAACTGA
Statistics
Matches: 70, Mismatches: 12, Indels: 13
0.74 0.13 0.14
Matches are distributed among these distances:
29 10 0.14
30 35 0.50
31 25 0.36
ACGTcount: A:0.59, C:0.08, G:0.13, T:0.19
Consensus pattern (29 bp):
AAAAACAGAAACTTAAGGACTAAAATAGT
Found at i:72659 original size:3 final size:3
Alignment explanation
Indices: 72651--72730 Score: 160
Period size: 3 Copynumber: 26.7 Consensus size: 3
72641 AGTGCTTGAC
72651 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
72699 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
72731 TTTTTTGACC
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:77008 original size:22 final size:22
Alignment explanation
Indices: 76942--77001 Score: 111
Period size: 22 Copynumber: 2.7 Consensus size: 22
76932 GATAATGCTC
*
76942 AATCCACTAATATTGAGTGTTA
1 AATCCACTAGTATTGAGTGTTA
76964 AATCCACTAGTATTGAGTGTTA
1 AATCCACTAGTATTGAGTGTTA
76986 AATCCACTAGTATTGA
1 AATCCACTAGTATTGA
77002 ATATTAATTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
AATCCACTAGTATTGAGTGTTA
Found at i:79987 original size:2 final size:2
Alignment explanation
Indices: 79980--80016 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
79970 TTTTATTGGT
79980 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
80017 CTTCAAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:81283 original size:24 final size:25
Alignment explanation
Indices: 81223--81307 Score: 72
Period size: 24 Copynumber: 3.5 Consensus size: 25
81213 TCGGGCCGGG
81223 TATATA-TATA-TATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
*
81246 TATATATT-TTTTATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
* * *
81270 T-T-TATTAATATTATATATATATATA
1 TATATATT-ATATTATTTAAAT-TAAA
81295 TATATATATATAT
1 TATATAT-TATAT
81308 ATAAATAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
22 4 0.08
23 8 0.16
24 24 0.49
25 4 0.08
26 1 0.02
27 7 0.14
28 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TATATATTATATTATTTAAATTAAA
Found at i:81288 original size:2 final size:2
Alignment explanation
Indices: 81277--81310 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
81267 AAATTTATTA
81277 AT AT -T 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 A
81311 AATAATTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:81347 original size:12 final size:13
Alignment explanation
Indices: 81331--81375 Score: 58
Period size: 12 Copynumber: 3.5 Consensus size: 13
81321 TTTAATATTT
81331 ATCGGGTCGGGT-
1 ATCGGGTCGGGTA
*
81343 ATCGGGGCGGGTA
1 ATCGGGTCGGGTA
81356 ATCGGGGT-GGGTA
1 ATC-GGGTCGGGTA
81369 ATCGGGT
1 ATCGGGT
81376 AATCGGGGCG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 15 0.52
13 11 0.38
14 3 0.10
ACGTcount: A:0.13, C:0.13, G:0.51, T:0.22
Consensus pattern (13 bp):
ATCGGGTCGGGTA
Found at i:81387 original size:13 final size:13
Alignment explanation
Indices: 81331--81374 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
81321 TTTAATATTT
*
81331 ATCGGGTCGGGT-
1 ATCGGGGCGGGTA
81343 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
*
81356 ATCGGGGTGGGTA
1 ATCGGGGCGGGTA
81369 ATCGGG
1 ATCGGG
81375 TAATCGGGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.14, C:0.14, G:0.52, T:0.20
Consensus pattern (13 bp):
ATCGGGGCGGGTA
Found at i:81655 original size:2 final size:2
Alignment explanation
Indices: 81648--81682 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
81638 ACAAATAGAT
* *
81648 TA TA TA TA TA TA TA TA TA TA TG TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
81683 TTCCTCATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (2 bp):
TA
Found at i:82263 original size:22 final size:22
Alignment explanation
Indices: 82238--82313 Score: 125
Period size: 22 Copynumber: 3.5 Consensus size: 22
82228 AGCACAATAG
82238 ATGTCAAGAGTGTGAAAATTCA
1 ATGTCAAGAGTGTGAAAATTCA
*
82260 ATGTCAAGATTGTGAAAATTCA
1 ATGTCAAGAGTGTGAAAATTCA
**
82282 ATGTCAAGAGTGTGAACGTTCA
1 ATGTCAAGAGTGTGAAAATTCA
82304 ATGTCAAGAG
1 ATGTCAAGAG
82314 ATTAAAAGTT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.28
Consensus pattern (22 bp):
ATGTCAAGAGTGTGAAAATTCA
Found at i:87025 original size:12 final size:12
Alignment explanation
Indices: 86997--87033 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
86987 TTTGGTAATC
86997 CCCGCCCCGATTA
1 CCCGCCCCGA-TA
87010 CCCGCCCCGATA
1 CCCGCCCCGATA
*
87022 CCCGACCCGATA
1 CCCGCCCCGATA
87034 AATTAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.19, C:0.54, G:0.16, T:0.11
Consensus pattern (12 bp):
CCCGCCCCGATA
Found at i:87048 original size:2 final size:2
Alignment explanation
Indices: 87041--87156 Score: 111
Period size: 2 Copynumber: 61.5 Consensus size: 2
87031 ATAAATTAAA
87041 AT AT AT AT AT AT AT AT AT AT AT AT -T 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
* * * * *
87082 AT AT AT AT AT AT AT AA AT AT -T A- AT AA AT TT A- AT TT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
87121 A- AA AT AT AT AT -T A- AT TT AA AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
87157 CCTGACCCGA
Statistics
Matches: 92, Mismatches: 15, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
1 7 0.08
2 85 0.92
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:87120 original size:21 final size:22
Alignment explanation
Indices: 87095--87153 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 22
87085 TATATATATA
*
87095 TAAATATTAATAAAT-TTAATT
1 TAAATATAAATAAATATTAATT
*
87116 TAAATA-AAATATATATTAATT
1 TAAATATAAATAAATATTAATT
* *
87137 TAAATATATATATATAT
1 TAAATATAAATAAATAT
87154 ATACCTGACC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.18
21 18 0.55
22 9 0.27
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TAAATATAAATAAATATTAATT
Found at i:87187 original size:23 final size:24
Alignment explanation
Indices: 87154--87205 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 24
87144 ATATATATAT
* *
87154 ATACCTGACCCGATTCCCGGCCCA
1 ATACCTGACCCAATACCCGGCCCA
87178 ATACC-GACCCAATACCCGGCCCA
1 ATACCTGACCCAATACCCGGCCCA
87201 ATACC
1 ATACC
87206 CGTTTAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.27, C:0.46, G:0.13, T:0.13
Consensus pattern (24 bp):
ATACCTGACCCAATACCCGGCCCA
Found at i:87202 original size:12 final size:12
Alignment explanation
Indices: 87169--87207 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
87159 TGACCCGATT
87169 CCCGGCCCAATA
1 CCCGGCCCAATA
*
87181 -CCGACCCAATA
1 CCCGGCCCAATA
87192 CCCGGCCCAATA
1 CCCGGCCCAATA
87204 CCCG
1 CCCG
87208 TTTAAATAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.26, C:0.51, G:0.15, T:0.08
Consensus pattern (12 bp):
CCCGGCCCAATA
Found at i:87418 original size:5 final size:5
Alignment explanation
Indices: 87408--87432 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
87398 ACAAGAAATA
87408 TTATT TTATT TTATT TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT
87433 ATATATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTATT
Found at i:87503 original size:14 final size:11
Alignment explanation
Indices: 87472--87519 Score: 60
Period size: 11 Copynumber: 4.2 Consensus size: 11
87462 CTTGCAAATA
87472 AAATTTTTATT
1 AAATTTTTATT
87483 AAATTTTTATT
1 AAATTTTTATT
87494 ATGAATTTTTATT
1 A--AATTTTTATT
* *
87507 CAATTTTTTTT
1 AAATTTTTATT
87518 AA
1 AA
87520 TTATTTCATC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
11 22 0.69
13 10 0.31
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (11 bp):
AAATTTTTATT
Done.