Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004445.1 Hibiscus syriacus cultivar Beakdansim tig00009754_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: 142015
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1121 original size:20 final size:21
Alignment explanation
Indices: 1098--1149 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
1088 TCTGAAACTT
1098 AAAATCGCAACAC-GAAAATG
1 AAAATCGCAACACGGAAAATG
1118 AAAATCGCAACACGGAAAATG
1 AAAATCGCAACACGGAAAATG
**
1139 ACTATCGCAAC
1 AAAATCGCAAC
1150 GCAAATTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.50, C:0.23, G:0.15, T:0.12
Consensus pattern (21 bp):
AAAATCGCAACACGGAAAATG
Found at i:1181 original size:14 final size:14
Alignment explanation
Indices: 1162--1203 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
1152 AAATTTGACT
*
1162 ATCGCAACGAGATA
1 ATCGCAACGAGAAA
*
1176 ATCGCAATGAGAAA
1 ATCGCAACGAGAAA
*
1190 ATCGCAACGCGAAA
1 ATCGCAACGAGAAA
1204 CTAAAATTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.12
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:1623 original size:22 final size:22
Alignment explanation
Indices: 1596--1653 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
1586 GATGGAGATA
1596 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1618 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1640 GACGGATGTCGCCG
1 GACGGATTTCGCCG
1654 TAGAGAGTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.17, C:0.19, G:0.45, T:0.19
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1847 original size:20 final size:20
Alignment explanation
Indices: 1822--1865 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1812 TATCGCAACG
1822 CGATAGTCAGAATCACGTTA
1 CGATAGTCAGAATCACGTTA
* * *
1842 CGATAGTTAGAATCGCGTTG
1 CGATAGTCAGAATCACGTTA
1862 CGAT
1 CGAT
1866 TATGTATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (20 bp):
CGATAGTCAGAATCACGTTA
Found at i:1883 original size:21 final size:21
Alignment explanation
Indices: 1853--1927 Score: 55
Period size: 21 Copynumber: 3.6 Consensus size: 21
1843 GATAGTTAGA
*
1853 ATCGCGTTGCGATTATGTATT
1 ATCGCATTGCGATTATGTATT
* **
1874 ATCGCATTGCTA-TA-GTCAGA
1 ATCGCATTGCGATTATGT-ATT
* *
1894 ATCGCATTTCAATTATGTATT
1 ATCGCATTGCGATTATGTATT
* *
1915 ATCACGTTGCGAT
1 ATCGCATTGCGAT
1928 AGTCAGAATC
Statistics
Matches: 39, Mismatches: 12, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
19 2 0.05
20 13 0.33
21 22 0.56
22 2 0.05
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (21 bp):
ATCGCATTGCGATTATGTATT
Found at i:1895 original size:41 final size:41
Alignment explanation
Indices: 1833--1948 Score: 142
Period size: 41 Copynumber: 2.8 Consensus size: 41
1823 GATAGTCAGA
* * *
1833 ATCACGTTACGATAGTTAGAATCGCGTTGCGATTATGTATT
1 ATCACATTGCGATAGTCAGAATCGCGTTGCGATTATGTATT
* * * * *
1874 ATCGCATTGCTATAGTCAGAATCGCATTTCAATTATGTATT
1 ATCACATTGCGATAGTCAGAATCGCGTTGCGATTATGTATT
* *
1915 ATCACGTTGCGATAGTCAGAATCGCGTTGGGATT
1 ATCACATTGCGATAGTCAGAATCGCGTTGCGATT
1949 TACATATTCG
Statistics
Matches: 60, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (41 bp):
ATCACATTGCGATAGTCAGAATCGCGTTGCGATTATGTATT
Found at i:1979 original size:82 final size:82
Alignment explanation
Indices: 1833--1983 Score: 189
Period size: 82 Copynumber: 1.8 Consensus size: 82
1823 GATAGTCAGA
* ** * *
1833 ATCACGTTACGATAGTTAGAATCGCGTTGCGATTATGTATTATCGCATTGCTATAGTCAGAATCG
1 ATCACGTTACGATAGTCAGAATCGCGTTGCGATTACATATTATCGCATTGCGATAGTCAAAATCG
1898 CATTTCAATTATGTATT
66 CATTTCAATTATGTATT
* * **
1915 ATCACGTTGCGATAGTCAGAATCGCGTTGGGATTTACATA-T-TCGCATTGCGATTTTCTAAAAT
1 ATCACGTTACGATAGTCAGAATCGCGTTGCGA-TTACATATTATCGCATTGCGATAGTC-AAAAT
1978 CGCATT
64 CGCATT
1984 GCGAATTTGG
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
81 13 0.22
82 40 0.69
83 5 0.09
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.36
Consensus pattern (82 bp):
ATCACGTTACGATAGTCAGAATCGCGTTGCGATTACATATTATCGCATTGCGATAGTCAAAATCG
CATTTCAATTATGTATT
Found at i:1981 original size:21 final size:20
Alignment explanation
Indices: 1956--2028 Score: 74
Period size: 21 Copynumber: 3.5 Consensus size: 20
1946 ATTTACATAT
1956 TCGCATTGCGATTTTCTAAAA
1 TCGCATTGCGATTTTC-AAAA
**
1977 TCGCATTGCGAATTTGGAAAA
1 TCGCATTGCG-ATTTTCAAAA
* **
1998 TCGCAATGCGATAGTCAAAA
1 TCGCATTGCGATTTTCAAAA
*
2018 TCGCGTTGCGA
1 TCGCATTGCGA
2029 ATCTGGAAAC
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
20 15 0.36
21 23 0.55
22 4 0.10
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (20 bp):
TCGCATTGCGATTTTCAAAA
Found at i:2558 original size:45 final size:45
Alignment explanation
Indices: 2494--2597 Score: 181
Period size: 45 Copynumber: 2.3 Consensus size: 45
2484 AATGAAAAAA
* * *
2494 AAATGCATATGAGTGCATTATCGGTATGAAAGGATGTCATAATTG
1 AAATGCATATGGGTGCATTATCGGCATGAAAGGATGCCATAATTG
2539 AAATGCATATGGGTGCATTATCGGCATGAAAGGATGCCATAATTG
1 AAATGCATATGGGTGCATTATCGGCATGAAAGGATGCCATAATTG
2584 AAATGCATATGGGT
1 AAATGCATATGGGT
2598 AGGGTTGTAA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 56 1.00
ACGTcount: A:0.35, C:0.11, G:0.26, T:0.29
Consensus pattern (45 bp):
AAATGCATATGGGTGCATTATCGGCATGAAAGGATGCCATAATTG
Found at i:2990 original size:16 final size:16
Alignment explanation
Indices: 2964--3003 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
2954 AATGACTCTA
*
2964 ATATTATCTGACTTGAT
1 ATATTACCTGACTT-AT
2981 AT-TTACCTGACTTAT
1 ATATTACCTGACTTAT
2996 ATATTACC
1 ATATTACC
3004 ATGGATGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 4 0.19
16 15 0.71
17 2 0.10
ACGTcount: A:0.30, C:0.17, G:0.07, T:0.45
Consensus pattern (16 bp):
ATATTACCTGACTTAT
Found at i:3182 original size:23 final size:23
Alignment explanation
Indices: 3135--3190 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
3125 AAATAGACCT
*
3135 ATTATATAAAATTATTTAATAAA
1 ATTAGATAAAATTATTTAATAAA
*
3158 ATTA-ATAAAA-TATTTAAATGTAA
1 ATTAGATAAAATTATTT-AAT-AAA
3181 ATTAGATAAA
1 ATTAGATAAA
3191 CATGATTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 5 0.17
22 9 0.31
23 10 0.34
24 5 0.17
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (23 bp):
ATTAGATAAAATTATTTAATAAA
Found at i:3611 original size:15 final size:15
Alignment explanation
Indices: 3587--3617 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3577 ATTTACCTTT
*
3587 TATAGTTTATATATA
1 TATAGGTTATATATA
3602 TATAGGTTATATATA
1 TATAGGTTATATATA
3617 T
1 T
3618 TATACATGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.52
Consensus pattern (15 bp):
TATAGGTTATATATA
Found at i:4006 original size:7 final size:7
Alignment explanation
Indices: 3994--4045 Score: 68
Period size: 7 Copynumber: 7.4 Consensus size: 7
3984 TCAATTTACA
3994 TTAGGGT
1 TTAGGGT
4001 TTAGGGT
1 TTAGGGT
4008 TTAGGGT
1 TTAGGGT
**
4015 TTATAGT
1 TTAGGGT
* *
4022 TTATGGA
1 TTAGGGT
4029 TTAGGGT
1 TTAGGGT
4036 TTAGGGT
1 TTAGGGT
4043 TTA
1 TTA
4046 TATAAATTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.46
Consensus pattern (7 bp):
TTAGGGT
Found at i:4154 original size:20 final size:21
Alignment explanation
Indices: 4129--4177 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
4119 TATATAGTTC
4129 ATATATATAT-TAGGTTATAT
1 ATATATATATATAGGTTATAT
*
4149 ATATATATATATAGTTTATAT
1 ATATATATATATAGGTTATAT
4170 ATACTATA
1 ATA-TATA
4178 CATGGTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 10 0.38
21 12 0.46
22 4 0.15
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (21 bp):
ATATATATATATAGGTTATAT
Found at i:4185 original size:20 final size:20
Alignment explanation
Indices: 4141--4193 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
4131 ATATATATTA
*
4141 GGTTATATATATA-TATATAT
1 GGTT-TATATATACTATACAT
*
4161 AGTTTATATATACTATACAT
1 GGTTTATATATACTATACAT
*
4181 GGTTTATACATAC
1 GGTTTATATATAC
4194 ATATTATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 8 0.29
20 20 0.71
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (20 bp):
GGTTTATATATACTATACAT
Found at i:4488 original size:13 final size:13
Alignment explanation
Indices: 4470--4494 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4460 TACATTAGTT
4470 TACATAAGCCCAA
1 TACATAAGCCCAA
4483 TACATAAGCCCA
1 TACATAAGCCCA
4495 CTCTTTTATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.32, G:0.08, T:0.16
Consensus pattern (13 bp):
TACATAAGCCCAA
Found at i:4669 original size:16 final size:15
Alignment explanation
Indices: 4639--4697 Score: 63
Period size: 15 Copynumber: 4.2 Consensus size: 15
4629 TAATTTACTT
*
4639 TATATAGTTTATATA
1 TATATAGTGTATATA
*
4654 TATATAG-GTGTATA
1 TATATAGTGTATATA
4668 TATATA---TATATA
1 TATATAGTGTATATA
*
4680 TATATAGTTTATATA
1 TATATAGTGTATATA
4695 TAT
1 TAT
4698 TGTACATTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
12 11 0.29
14 11 0.29
15 16 0.42
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (15 bp):
TATATAGTGTATATA
Found at i:4716 original size:2 final size:2
Alignment explanation
Indices: 4648--4697 Score: 55
Period size: 2 Copynumber: 24.5 Consensus size: 2
4638 TTATATAGTT
** * *
4648 TA TA TA TA TA TA GG TG TA TA TA TA TA TA TA TA TA TA TA GTT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
4691 TA TA TA T
1 TA TA TA T
4698 TGTACATTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
2 40 0.98
3 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4835 original size:2 final size:2
Alignment explanation
Indices: 4828--5037 Score: 179
Period size: 2 Copynumber: 107.0 Consensus size: 2
4818 TTCTATAAAC
4828 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
4870 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TT TA TA GA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
4911 T- TA CT- TA TA T- TA GT- TA TA CA TA CA TA TA TA TA CTA TA T-
1 TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * * *
4949 TA -A TA TA AA T- TA TA -A TT TA TA AA CTA AA TA T- TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * * *
4988 GTT TA TA CA TA TA TA GTT TA TA TA TA TA CA TA TA TA TA TA TA TA
1 -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5032 TA TA TA
1 TA TA TA
5038 ATTAAAAGTA
Statistics
Matches: 167, Mismatches: 25, Indels: 32
0.75 0.11 0.14
Matches are distributed among these distances:
1 10 0.06
2 150 0.90
3 7 0.04
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5000 original size:15 final size:15
Alignment explanation
Indices: 4982--5015 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
4972 CTAAATATTT
4982 TATATAGTTTATACA
1 TATATAGTTTATACA
*
4997 TATATAGTTTATATA
1 TATATAGTTTATACA
5012 TATA
1 TATA
5016 CATATATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (15 bp):
TATATAGTTTATACA
Found at i:5395 original size:12 final size:12
Alignment explanation
Indices: 5378--5413 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
5368 CACTTTGAAG
5378 AATATATATATA
1 AATATATATATA
*
5390 AATATATACATA
1 AATATATATATA
*
5402 AATTTATATATA
1 AATATATATATA
5414 TATAATTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (12 bp):
AATATATATATA
Found at i:6029 original size:2 final size:2
Alignment explanation
Indices: 6022--6075 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
6012 TGTGTACCAA
6022 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
6064 AT AT AT AT -T AT A
1 AT AT AT AT AT AT A
6076 GTTTATAAAC
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6136 original size:22 final size:22
Alignment explanation
Indices: 6073--6138 Score: 69
Period size: 24 Copynumber: 2.9 Consensus size: 22
6063 TATATATATT
* * **
6073 ATAGTTTATAAACTATATTTTTT
1 ATAGTTTATATA-TATAGTTTAC
6096 ATAGTTTATACCTATATAGTTTAC
1 ATAGTTTATA--TATATAGTTTAC
6120 ATAGTTTATATATATAGTT
1 ATAGTTTATATATATAGTT
6139 CATATAAACA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 9 0.24
23 10 0.27
24 17 0.46
25 1 0.03
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.52
Consensus pattern (22 bp):
ATAGTTTATATATATAGTTTAC
Found at i:6198 original size:18 final size:18
Alignment explanation
Indices: 6159--6212 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
6149 TAATTTTTAT
* *
6159 ATATAGCTTATAATA-ATT
1 ATATAGTTTATAATATA-A
6177 ATATAGTTTATAATATAA
1 ATATAGTTTATAATATAA
6195 ATATAGTTTAT-ATATAA
1 ATATAGTTTATAATATAA
6212 A
1 A
6213 CTTATATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
17 7 0.21
18 25 0.76
19 1 0.03
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (18 bp):
ATATAGTTTATAATATAA
Found at i:8338 original size:60 final size:60
Alignment explanation
Indices: 8196--8339 Score: 148
Period size: 60 Copynumber: 2.4 Consensus size: 60
8186 GTTTGGGGAC
* * * * * *
8196 TAATTTAGAATGAAG-GTTATAGTTTAGGGATGAAATTGAAATATTTAAAAAATTAAGGAA
1 TAATTTAAAAT-AAGAGTTATAATTTAAGGATAAAATTAAAATATTTAAAAAATTAAGAAA
* * * * *
8256 TAATTTGAAATAATAGTCATAATTTAAGGATAAAATTAAAATATTT-AAAATTTTAGAAA
1 TAATTTAAAATAAGAGTTATAATTTAAGGATAAAATTAAAATATTTAAAAAATTAAGAAA
*
8315 TCAATTTAAAATTAGAGTTATAATT
1 T-AATTTAAAATAAGAGTTATAATT
8340 GAAGACGTGT
Statistics
Matches: 67, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
59 13 0.19
60 54 0.81
ACGTcount: A:0.49, C:0.01, G:0.13, T:0.37
Consensus pattern (60 bp):
TAATTTAAAATAAGAGTTATAATTTAAGGATAAAATTAAAATATTTAAAAAATTAAGAAA
Found at i:12664 original size:37 final size:37
Alignment explanation
Indices: 12623--12699 Score: 100
Period size: 37 Copynumber: 2.1 Consensus size: 37
12613 AAAATAGGAT
12623 TCGTCAACTCCAATAACTCGAAAATTTTTAACTCGAC
1 TCGTCAACTCCAATAACTCGAAAATTTTTAACTCGAC
** * * * *
12660 TCGTCAACTTTAATCACTCGAAATTTTTTCACTTGAC
1 TCGTCAACTCCAATAACTCGAAAATTTTTAACTCGAC
12697 TCG
1 TCG
12700 ACCGAACACT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.35
Consensus pattern (37 bp):
TCGTCAACTCCAATAACTCGAAAATTTTTAACTCGAC
Found at i:13442 original size:9 final size:9
Alignment explanation
Indices: 13428--13480 Score: 63
Period size: 9 Copynumber: 5.6 Consensus size: 9
13418 TTCTTTTCAT
13428 TTATTTATA
1 TTATTTATA
13437 TTATTTATATTA
1 TTA-TT-TA-TA
13449 TTATTTATA
1 TTATTTATA
13458 TTATTTATA
1 TTATTTATA
13467 TTA-TTATTA
1 TTATTTA-TA
13476 TTATT
1 TTATT
13481 ATTACTACTA
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
8 3 0.08
9 22 0.56
10 5 0.13
11 4 0.10
12 5 0.13
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTATTTATA
Found at i:13453 original size:21 final size:21
Alignment explanation
Indices: 13428--13483 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
13418 TTCTTTTCAT
13428 TTATTTATATTATTTATATTA
1 TTATTTATATTATTTATATTA
13449 TTATTTATATTATTTATATTA
1 TTATTTATATTATTTATATTA
13470 TTA-TTATTATTATT
1 TTATTTA-TATTATT
13484 ACTACTAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 3 0.09
21 31 0.91
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TTATTTATATTATTTATATTA
Found at i:13484 original size:12 final size:12
Alignment explanation
Indices: 13435--13480 Score: 65
Period size: 12 Copynumber: 3.6 Consensus size: 12
13425 CATTTATTTA
13435 TATTATTTATAT
1 TATTATTTATAT
13447 TATTATTTATAT
1 TATTATTTATAT
13459 TATTTATATTATTAT
1 TA-TTAT-TTA-TAT
13474 TATTATT
1 TATTATT
13481 ATTACTACTA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
12 14 0.45
13 5 0.16
14 7 0.23
15 5 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TATTATTTATAT
Found at i:15333 original size:25 final size:24
Alignment explanation
Indices: 15305--15352 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
15295 TGTTTAACTT
15305 TATATGTTATAAATATTTTGTTTCG
1 TATATGTTATAAATA-TTTGTTTCG
* **
15330 TATATTTTATTTATATTTGTTTC
1 TATATGTTATAAATATTTGTTTC
15353 CATTGTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.25, C:0.04, G:0.08, T:0.62
Consensus pattern (24 bp):
TATATGTTATAAATATTTGTTTCG
Found at i:18516 original size:20 final size:20
Alignment explanation
Indices: 18491--18531 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
18481 ACATTCCCTC
18491 TCTTTGAGACCTTGAAACAT
1 TCTTTGAGACCTTGAAACAT
18511 TCTTTGAGACCTTGAAACAT
1 TCTTTGAGACCTTGAAACAT
18531 T
1 T
18532 GCATTTATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37
Consensus pattern (20 bp):
TCTTTGAGACCTTGAAACAT
Found at i:19149 original size:10 final size:10
Alignment explanation
Indices: 19131--19232 Score: 50
Period size: 10 Copynumber: 10.0 Consensus size: 10
19121 AAGAGAAAAG
19131 AAACAAAGAA
1 AAACAAAGAA
*
19141 AAACCAAGAAA
1 AAACAAAG-AA
*
19152 AAAGAAAAGAA
1 AAA-CAAAGAA
*
19163 AAGCAAA-AA
1 AAACAAAGAA
* *
19172 CAA-AAACAA
1 AAACAAAGAA
19181 AAACAAA-AA
1 AAACAAAGAA
* *
19190 CAA-AAACAA
1 AAACAAAGAA
*
19199 AAACAAAAACAA
1 AAAC--AAAGAA
19211 AAACAAAGAA
1 AAACAAAGAA
19221 AATAGCAAAGAA
1 AA-A-CAAAGAA
19233 CAAAAAGATG
Statistics
Matches: 71, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
8 6 0.08
9 15 0.21
10 20 0.28
11 10 0.14
12 20 0.28
ACGTcount: A:0.78, C:0.13, G:0.08, T:0.01
Consensus pattern (10 bp):
AAACAAAGAA
Found at i:19170 original size:6 final size:6
Alignment explanation
Indices: 19156--19217 Score: 106
Period size: 6 Copynumber: 10.3 Consensus size: 6
19146 AAGAAAAAAG
* *
19156 AAAAGA AAAGCA AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA
1 AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA
19204 AAAACA AAAACA AA
1 AAAACA AAAACA AA
19218 GAAAATAGCA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.82, C:0.15, G:0.03, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:19229 original size:18 final size:18
Alignment explanation
Indices: 19127--19236 Score: 86
Period size: 18 Copynumber: 6.2 Consensus size: 18
19117 ATCAAAGAGA
* *
19127 AAAGAAACAAAGAAAAAC
1 AAAGAAAAAAACAAAAAC
* *
19145 CAAGAAAAAAGA-AAAGA-
1 AAAGAAAAAA-ACAAAAAC
*
19162 AAAG-CAAAAACAAAAAC
1 AAAGAAAAAAACAAAAAC
19179 AAA-AACAAAAACAAAAAC
1 AAAGAA-AAAAACAAAAAC
19197 AAA-AACAAAAACAAAAAC
1 AAAGAA-AAAAACAAAAAC
* *
19215 AAAGAAAATAGCAAAGAAC
1 AAAGAAAAAAACAAA-AAC
19234 AAA
1 AAA
19237 AAGATGACAA
Statistics
Matches: 76, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
15 1 0.01
16 8 0.11
17 6 0.08
18 52 0.68
19 9 0.12
ACGTcount: A:0.78, C:0.13, G:0.08, T:0.01
Consensus pattern (18 bp):
AAAGAAAAAAACAAAAAC
Found at i:20439 original size:2 final size:2
Alignment explanation
Indices: 20432--20574 Score: 286
Period size: 2 Copynumber: 71.5 Consensus size: 2
20422 ATACATACAT
20432 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
20474 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
20516 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
20558 AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC A
20575 AAGATTAGGC
Statistics
Matches: 141, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 141 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:20847 original size:35 final size:37
Alignment explanation
Indices: 20798--20923 Score: 159
Period size: 35 Copynumber: 3.4 Consensus size: 37
20788 ACAGTTTCTT
20798 TTGAAAAACAAATTTTGTCTCGCTTGAGACAATTTTC
1 TTGAAAAACAAATTTTGTCTCGCTTGAGACAATTTTC
* *
20835 -T-AAAAACAAATTTTGTATCGTTTGAGACAA-TTTC
1 TTGAAAAACAAATTTTGTCTCGCTTGAGACAATTTTC
* *
20869 TTGAAAAACAAATTTTGTCTCGCTAGAGACATTTTTCC
1 TTGAAAAACAAATTTTGTCTCGCTTGAGACAATTTT-C
* *
20907 TTTGAGATACAAATTTT
1 -TTGAAAAACAAATTTT
20924 TGAATTTGTT
Statistics
Matches: 76, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
34 4 0.05
35 28 0.37
36 26 0.34
37 3 0.04
38 1 0.01
39 14 0.18
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (37 bp):
TTGAAAAACAAATTTTGTCTCGCTTGAGACAATTTTC
Found at i:21524 original size:33 final size:33
Alignment explanation
Indices: 21487--21551 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
21477 ATAACATTTA
21487 CCATCTGTGAGTCTATTTCCCTTGAAACAAAGC
1 CCATCTGTGAGTCTATTTCCCTTGAAACAAAGC
* * * **
21520 CCATCTTTGAGTGTTTTTCTTTTGAAACAAAG
1 CCATCTGTGAGTCTATTTCCCTTGAAACAAAG
21552 TTTTGTCTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (33 bp):
CCATCTGTGAGTCTATTTCCCTTGAAACAAAGC
Found at i:21683 original size:63 final size:60
Alignment explanation
Indices: 21611--21728 Score: 150
Period size: 63 Copynumber: 1.9 Consensus size: 60
21601 CTATAAGAAC
*
21611 AAAAATCTTTGA-TTCTGTTTC-TCTGAAAACAAATTTTTTGTCTCTTGAGACAATTTCTGTGGA
1 AAAAATCTTTGAGTT-TGTTTCTTCTG-AAACAAA-ATTTTGTCTC--GAGACAATTTCTGTGGA
* *
21674 AAAAATCTTTGAGTTTGTTTCTTTTGAAACAAAATTTTGTCTCGAGATAATTTCT
1 AAAAATCTTTGAGTTTGTTTCTTCTGAAACAAAATTTTGTCTCGAGACAATTTCT
21729 TTTGAAACAC
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
60 11 0.22
62 9 0.18
63 25 0.50
64 5 0.10
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.44
Consensus pattern (60 bp):
AAAAATCTTTGAGTTTGTTTCTTCTGAAACAAAATTTTGTCTCGAGACAATTTCTGTGGA
Found at i:21764 original size:30 final size:30
Alignment explanation
Indices: 21717--21797 Score: 90
Period size: 30 Copynumber: 2.7 Consensus size: 30
21707 ATTTTGTCTC
* * * *
21717 GAGATAATTTCTTTTGAAACACCTATCTTT
1 GAGATAGTTTCTATTGAAACACCCACCTTT
* *
21747 GAGTTAGTTTCTCTTGAAACACCCACCTTT
1 GAGATAGTTTCTATTGAAACACCCACCTTT
* *
21777 GAGATCGTTTCTATTAAAACA
1 GAGATAGTTTCTATTGAAACA
21798 ATTTTGTTTC
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (30 bp):
GAGATAGTTTCTATTGAAACACCCACCTTT
Found at i:22436 original size:27 final size:31
Alignment explanation
Indices: 22374--22450 Score: 76
Period size: 27 Copynumber: 2.6 Consensus size: 31
22364 TTTTCGAGAC
*
22374 AGTTGCTTTTGAAACACATTATCTTTGAGTCT
1 AGTTTCTTTTGAAACACA-TATCTTTGAGTCT
22406 -GTTTCTTTTGAAACA-A-AT-TTTGAGT-T
1 AGTTTCTTTTGAAACACATATCTTTGAGTCT
* *
22432 AGTTTATCTTGAAAC-CATA
1 AGTTTCTTTTGAAACACATA
22451 ATCCCTAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
26 1 0.03
27 20 0.51
28 3 0.08
30 1 0.03
31 14 0.36
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.44
Consensus pattern (31 bp):
AGTTTCTTTTGAAACACATATCTTTGAGTCT
Found at i:22568 original size:42 final size:40
Alignment explanation
Indices: 22471--22570 Score: 121
Period size: 40 Copynumber: 2.5 Consensus size: 40
22461 ATGGCCAACA
*
22471 GTCCTCATCACGTAGGAACCGTGTCATCCCTTGACCAGAC
1 GTCCTCATCACGTAGGAACCGTGTCATACCTTGACCAGAC
* * *
22511 CTCCTCATCACGTAGGAGCCGTGTCA-ACCTTGATAACTAGAC
1 GTCCTCATCACGTAGGAACCGTGTCATACCTTG---ACCAGAC
*
22553 GTCCTCATCATGTAGGAA
1 GTCCTCATCACGTAGGAA
22571 TCGAGTTATC
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
39 5 0.10
40 24 0.48
42 21 0.42
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (40 bp):
GTCCTCATCACGTAGGAACCGTGTCATACCTTGACCAGAC
Found at i:22675 original size:94 final size:93
Alignment explanation
Indices: 22503--22676 Score: 267
Period size: 94 Copynumber: 1.9 Consensus size: 93
22493 GTCATCCCTT
* * *
22503 GACCAGACCTCCTCATCACGTAGGAGCCGTGTCAACCTTGATAACTAGACGTCCTCATCATGTAG
1 GACCAGACCTCCTCATCACGTAGGAGCCGTGTCAACCTAGATAACCAGACGTCCTCATCACGTAG
*
22568 GAATCGAGTTATCACATTTCCTTTAAAC
66 GAACCGAGTTATCACATTTCCTTTAAAC
* * * *
22596 GACCAGTCCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGTCGTCCTCATCGCGTA
1 GACCAGACCTCCTCATCACGTAGGAGCCGTGTCA-ACCTAGATAACCAGACGTCCTCATCACGTA
22661 GGAACCGAGTTATCAC
65 GGAACCGAGTTATCAC
22677 CCTTCCTAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
93 33 0.46
94 39 0.54
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (93 bp):
GACCAGACCTCCTCATCACGTAGGAGCCGTGTCAACCTAGATAACCAGACGTCCTCATCACGTAG
GAACCGAGTTATCACATTTCCTTTAAAC
Found at i:22773 original size:135 final size:134
Alignment explanation
Indices: 22595--22907 Score: 479
Period size: 135 Copynumber: 2.3 Consensus size: 134
22585 TTCCTTTAAA
22595 CGACCAG-TCCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGTCGTCCTCATCGCG
1 CGACCAGAT-CTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGTCGTCCTCATCGCG
* * *
22659 TAGGAACCGAGTTATCACCCTTCCTAAAGATGGCCAAGAACTCTTCATCACTTATGATCCA-TGT
65 TAGAAACCGAGTTATCACCATTCCTAAAGATGGCC-AGAACTCTTCATCACGTATGA-CCAGTGT
22723 CATCCC-
128 CATCCCT
* *
22729 CTGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCCCTAGATAACCAGTCGTCCTCATCGCG
1 C-GACCAGATCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGTCGTCCTCATCGCG
*
22794 TAGAAACCGAGTTATCACCATTCCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCAGTGTCA
65 TAGAAACCGAGTTATCACCATTCCTAAAGATGGCCAGAACTCTTCATCACGTATGACCAGTGTCA
22859 TCCCT
130 TCCCT
* * * *
22864 CGACCATATTTCCTCATCACGTAGGAACCGTGTCACCCTTAGAT
1 CGACCAGATCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGAT
22908 GACTCGAACT
Statistics
Matches: 163, Mismatches: 12, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
133 2 0.01
134 67 0.41
135 93 0.57
136 1 0.01
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (134 bp):
CGACCAGATCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGTCGTCCTCATCGCGT
AGAAACCGAGTTATCACCATTCCTAAAGATGGCCAGAACTCTTCATCACGTATGACCAGTGTCAT
CCCT
Found at i:22790 original size:43 final size:43
Alignment explanation
Indices: 22597--22796 Score: 106
Period size: 43 Copynumber: 4.5 Consensus size: 43
22587 CCTTTAAACG
22597 ACCAGTCCTCCTCATCACGTAGGAGCCGTGTCA-CCCCTAGATA
1 ACCAGT-CTCCTCATCACGTAGGAGCCGTGTCACCCCCTAGATA
* * * *
22640 ACCAGTCGTCCTCATCGCGTAGGAACCGAGTTATCACCCTTCCTAAAGATG
1 ACCAGTC-TCCTCATCACGTAGGAGCC--G-TGTCACCC--CCT--AGATA
* * * * * * * *
22691 GCCAAGAACTCTTCATCACTTATGATCCATGTCATCCCCT-G---
1 ACC-AG-TCTCCTCATCACGTAGGAGCCGTGTCACCCCCTAGATA
* *
22732 ACCAGATCTCTTCATCACGTATGAGCCGTGTCA-CCCCTAGATA
1 ACCAG-TCTCCTCATCACGTAGGAGCCGTGTCACCCCCTAGATA
*
22775 ACCAGTCGTCCTCATCGCGTAG
1 ACCAGTC-TCCTCATCACGTAG
22797 AAACCGAGTT
Statistics
Matches: 119, Mismatches: 22, Indels: 32
0.69 0.13 0.18
Matches are distributed among these distances:
39 5 0.04
40 27 0.23
41 2 0.02
42 3 0.03
43 39 0.33
44 1 0.01
45 1 0.01
46 4 0.03
47 5 0.04
49 9 0.08
51 6 0.05
52 16 0.13
53 1 0.01
ACGTcount: A:0.24, C:0.34, G:0.17, T:0.24
Consensus pattern (43 bp):
ACCAGTCTCCTCATCACGTAGGAGCCGTGTCACCCCCTAGATA
Found at i:23114 original size:9 final size:9
Alignment explanation
Indices: 23100--23152 Score: 63
Period size: 9 Copynumber: 5.6 Consensus size: 9
23090 TTTTTTTCAT
23100 TTATTTATA
1 TTATTTATA
23109 TTATTTATATTA
1 TTA-TT-TA-TA
23121 TTATTTATA
1 TTATTTATA
23130 TTATTTATA
1 TTATTTATA
23139 TTA-TTATTA
1 TTATTTA-TA
23148 TTATT
1 TTATT
23153 ATTACTAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
8 3 0.08
9 22 0.56
10 5 0.13
11 4 0.10
12 5 0.13
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTATTTATA
Found at i:23125 original size:21 final size:21
Alignment explanation
Indices: 23100--23155 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
23090 TTTTTTTCAT
23100 TTATTTATATTATTTATATTA
1 TTATTTATATTATTTATATTA
23121 TTATTTATATTATTTATATTA
1 TTATTTATATTATTTATATTA
23142 TTA-TTATTATTATT
1 TTATTTA-TATTATT
23156 ACTAATTACA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 3 0.09
21 31 0.91
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TTATTTATATTATTTATATTA
Found at i:23156 original size:12 final size:12
Alignment explanation
Indices: 23107--23152 Score: 65
Period size: 12 Copynumber: 3.6 Consensus size: 12
23097 CATTTATTTA
23107 TATTATTTATAT
1 TATTATTTATAT
23119 TATTATTTATAT
1 TATTATTTATAT
23131 TATTTATATTATTAT
1 TA-TTAT-TTA-TAT
23146 TATTATT
1 TATTATT
23153 ATTACTAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
12 14 0.45
13 5 0.16
14 7 0.23
15 5 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TATTATTTATAT
Found at i:25019 original size:25 final size:24
Alignment explanation
Indices: 24991--25038 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
24981 TGTTTAACAT
24991 TATATGTTATAAATATTTTGTTTCG
1 TATATGTTATAAATA-TTTGTTTCG
* **
25016 TATATTTTATTTATATTTGTTTC
1 TATATGTTATAAATATTTGTTTC
25039 CATTGTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.25, C:0.04, G:0.08, T:0.62
Consensus pattern (24 bp):
TATATGTTATAAATATTTGTTTCG
Found at i:28704 original size:17 final size:17
Alignment explanation
Indices: 28678--28711 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28668 TTGGTATGTC
*
28678 ATTGTGGAAATTATATT
1 ATTGTGGAAAGTATATT
*
28695 ATTGTTGAAAGTATATT
1 ATTGTGGAAAGTATATT
28712 CTGGACAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (17 bp):
ATTGTGGAAAGTATATT
Found at i:30323 original size:26 final size:24
Alignment explanation
Indices: 30294--30346 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
30284 TATTATTAAA
30294 ATAAAAATATAATATCATATATTATT
1 ATAAAAATA-AATAT-ATATATTATT
*
30320 AT-AAAATAATTATATATATTATT
1 ATAAAAATAAATATATATATTATT
30343 ATAA
1 ATAA
30347 CACTGAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 12 0.48
24 5 0.20
25 6 0.24
26 2 0.08
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
ATAAAAATAAATATATATATTATT
Found at i:30336 original size:23 final size:23
Alignment explanation
Indices: 30302--30346 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
30292 AAATAAAAAT
30302 ATAATATCATATATTATTATAAA
1 ATAATATCATATATTATTATAAA
30325 ATAATTAT-ATATATTATTATAA
1 ATAA-TATCATATATTATTATAA
30347 CACTGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
ATAATATCATATATTATTATAAA
Found at i:32769 original size:19 final size:20
Alignment explanation
Indices: 32745--32792 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
32735 AATGATTTTC
* * *
32745 TTTTGAAAGCTAAAATG-GA
1 TTTTGAAAACCAAAATGAAA
32764 TTTTGAAAACCAAAATGAAA
1 TTTTGAAAACCAAAATGAAA
32784 TTTTGAAAA
1 TTTTGAAAA
32793 AGGATTTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.48, C:0.06, G:0.15, T:0.31
Consensus pattern (20 bp):
TTTTGAAAACCAAAATGAAA
Found at i:34187 original size:20 final size:20
Alignment explanation
Indices: 34162--34227 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
34152 CTTACAATAT
34162 CGATACCTCATGAATAGTAC
1 CGATACCTCATGAATAGTAC
* * * *
34182 CGATACTGTTC-T-TACAGTAT
1 CGATAC--CTCATGAATAGTAC
34202 CGATACCTCATGAATAGTAC
1 CGATACCTCATGAATAGTAC
34222 CGATAC
1 CGATAC
34228 TGTTCATATG
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
18 2 0.06
19 1 0.03
20 28 0.82
21 1 0.03
22 2 0.06
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (20 bp):
CGATACCTCATGAATAGTAC
Found at i:34203 original size:40 final size:40
Alignment explanation
Indices: 34139--34232 Score: 161
Period size: 40 Copynumber: 2.4 Consensus size: 40
34129 GGACAAGCAA
* *
34139 TACCAATATTGTTCTTACAATATCGATACCTCATGAATAG
1 TACCGATACTGTTCTTACAATATCGATACCTCATGAATAG
*
34179 TACCGATACTGTTCTTACAGTATCGATACCTCATGAATAG
1 TACCGATACTGTTCTTACAATATCGATACCTCATGAATAG
34219 TACCGATACTGTTC
1 TACCGATACTGTTC
34233 ATATGGTACA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34
Consensus pattern (40 bp):
TACCGATACTGTTCTTACAATATCGATACCTCATGAATAG
Found at i:35283 original size:2 final size:2
Alignment explanation
Indices: 35276--35305 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
35266 TAATGTTAAA
35276 AT AT AT AT AT AT AT AT AT AT AT AT AGT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
35306 ATAAAATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:42367 original size:16 final size:16
Alignment explanation
Indices: 42325--42366 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
42315 AAAAATAATT
42325 GAAAATGAAAATGATC
1 GAAAATGAAAATGATC
42341 GAAAATGAAAATGATC
1 GAAAATGAAAATGATC
42357 GAAAA-GAAAA
1 GAAAATGAAAA
42367 AAAAAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 5 0.19
16 21 0.81
ACGTcount: A:0.62, C:0.05, G:0.19, T:0.14
Consensus pattern (16 bp):
GAAAATGAAAATGATC
Found at i:47012 original size:3 final size:3
Alignment explanation
Indices: 47004--47061 Score: 73
Period size: 3 Copynumber: 19.0 Consensus size: 3
46994 TGTCCCGGTT
*
47004 TTA TTA TTA TTA TTA TTA -TA TTA TTTA TTA TATA TTT TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA T-TA TTA TTA TTA TTA
*
47050 ATA TTA TTA TTA
1 TTA TTA TTA TTA
47062 CAACCAGGCC
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 2 0.04
3 40 0.83
4 6 0.12
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:47165 original size:22 final size:22
Alignment explanation
Indices: 47140--47191 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
47130 AGCCATCCAC
47140 GCCCCAACCGAAGGCTCCAGAA
1 GCCCCAACCGAAGGCTCCAGAA
47162 GCCCCAACCGAAGGCTCCAGAA
1 GCCCCAACCGAAGGCTCCAGAA
*
47184 GCTCCAAC
1 GCCCCAAC
47192 GCCAGCCGTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.31, C:0.42, G:0.21, T:0.06
Consensus pattern (22 bp):
GCCCCAACCGAAGGCTCCAGAA
Found at i:48339 original size:13 final size:13
Alignment explanation
Indices: 48300--48340 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
48290 AATAATAATT
48300 TATTT-TTTTCAA
1 TATTTATTTTCAA
*
48312 TAAATTATTTT-AA
1 T-ATTTATTTTCAA
48325 TATTTATTTTCAA
1 TATTTATTTTCAA
48338 TAT
1 TAT
48341 CGAAGAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
12 9 0.38
13 11 0.46
14 4 0.17
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (13 bp):
TATTTATTTTCAA
Found at i:50285 original size:170 final size:171
Alignment explanation
Indices: 50003--50343 Score: 675
Period size: 170 Copynumber: 2.0 Consensus size: 171
49993 ATTGAAGAGT
50003 ACACAACTTTGTTACATATCGAAGGGGCTTTGGAGAATCGAATCTATTCAAAGTCAATTAAAACT
1 ACACAACTTTGTTACATATCGAAGGGGCTTTGGAGAATCGAATCTATTCAAAGTCAATTAAAACT
50068 CATCCCTTTCGAGTTAAATTAGAAAAGATTGACGGGGTACGAGAAGAATGGGT-GCATCCCGTAC
66 CATCCCTTTCGAGTTAAATTAGAAAAGATTGACGGGGTACGAGAAGAATGGGTGGCATCCCGTAC
50132 AAAACAAAAAGGCGAAAGCGAAGGCATTGCTTGGACCAACA
131 AAAACAAAAAGGCGAAAGCGAAGGCATTGCTTGGACCAACA
50173 ACACAACTTTGTTACATATCGAAGGGGCTTTGGAGAATCGAATCTATTCAAAGTCAATTAAAACT
1 ACACAACTTTGTTACATATCGAAGGGGCTTTGGAGAATCGAATCTATTCAAAGTCAATTAAAACT
50238 CATCCCTTTCGAGTTAAATTAGAAAAGATTGACGGGGTACGAGAAGAATGGGTGGCATCCCGTAC
66 CATCCCTTTCGAGTTAAATTAGAAAAGATTGACGGGGTACGAGAAGAATGGGTGGCATCCCGTAC
50303 AAAACAAAAAGGCGAAAGCGAAGGCATTGCTTGGACCAACA
131 AAAACAAAAAGGCGAAAGCGAAGGCATTGCTTGGACCAACA
50344 TTAAAGAACT
Statistics
Matches: 170, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
170 118 0.69
171 52 0.31
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (171 bp):
ACACAACTTTGTTACATATCGAAGGGGCTTTGGAGAATCGAATCTATTCAAAGTCAATTAAAACT
CATCCCTTTCGAGTTAAATTAGAAAAGATTGACGGGGTACGAGAAGAATGGGTGGCATCCCGTAC
AAAACAAAAAGGCGAAAGCGAAGGCATTGCTTGGACCAACA
Found at i:59612 original size:12 final size:11
Alignment explanation
Indices: 59576--59646 Score: 81
Period size: 12 Copynumber: 6.4 Consensus size: 11
59566 ATTATGCTTG
59576 AAAAAAAAAGA
1 AAAAAAAAAGA
* *
59587 AGAAAAAGAGA
1 AAAAAAAAAGA
*
59598 AAAAAGAAAG-
1 AAAAAAAAAGA
*
59608 AAAAAAAGAGA
1 AAAAAAAAAGA
59619 AAAGAAAAAAGA
1 AAA-AAAAAAGA
59631 AAAAGAAAAAGA
1 AAAA-AAAAAGA
59643 AAAA
1 AAAA
59647 GGGGGGTCAA
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
10 8 0.16
11 20 0.41
12 21 0.43
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:59641 original size:19 final size:19
Alignment explanation
Indices: 59577--59647 Score: 81
Period size: 21 Copynumber: 3.6 Consensus size: 19
59567 TTATGCTTGA
59577 AAAAAAAAGAAGAAAAAGAG
1 AAAAAAAA-AAGAAAAAGAG
*
59597 AAAAAAGAAAGAAAAAAAGAG
1 AAAAAA-AAA-AGAAAAAGAG
59618 AAAAGAAAAAAGAAAAAGA-
1 AAAA-AAAAAAGAAAAAGAG
*
59637 AAAAGAAAAAG
1 AAAAAAAAAAG
59648 GGGGGTCAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
18 6 0.13
19 4 0.09
20 15 0.33
21 18 0.40
22 2 0.04
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAGAAAAAGAG
Found at i:60931 original size:83 final size:83
Alignment explanation
Indices: 60799--61186 Score: 605
Period size: 83 Copynumber: 4.6 Consensus size: 83
60789 TGCAATGTAT
*
60799 TCATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAA
1 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAA
60864 TTTGAAAGATGAATGTGC
66 TTTGAAAGATGAATGTGC
* *
60882 TCATAGCATCTTCTGGAAGTGTTCTTTGATTTATCTAATCTGGTTTGGTAAAACCAATCATTGAA
1 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAA
60947 TTTGAAAGATGAATGTGC
66 TTTGAAAGATGAATGTGC
*
60965 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATAAAACCAATCATTGAA
1 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAA
61030 TTTGAAAGATGAATGTGC
66 TTTGAAAGATGAATGTGC
*
61048 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAATCA
1 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA--AA--AC-CAATC-
* *
61113 GTTATTGAATTTGGAAGAGGAATGTGC
60 ---ATTGAATTTGAAAGATGAATGTGC
* * *
61140 TAATAGCATCTTCTGGAAGTGTTCTTTGAGTTCTCTGATTTGGTTTG
1 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
61187 ATATAAAACC
Statistics
Matches: 283, Mismatches: 13, Indels: 9
0.93 0.04 0.03
Matches are distributed among these distances:
83 209 0.74
85 2 0.01
87 2 0.01
88 4 0.01
92 66 0.23
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.39
Consensus pattern (83 bp):
TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAA
TTTGAAAGATGAATGTGC
Found at i:61625 original size:52 final size:52
Alignment explanation
Indices: 61563--61667 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
61553 TACCGATATC
61563 TGTGAAATCATCTTGAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
1 TGTGAAATCATCTTGAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
61615 TGTGAAATCATCTTGAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
1 TGTGAAATCATCTTGAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
61667 T
1 T
61668 TAACATGTTG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.33
Consensus pattern (52 bp):
TGTGAAATCATCTTGAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
Found at i:62768 original size:113 final size:113
Alignment explanation
Indices: 61967--62755 Score: 1321
Period size: 113 Copynumber: 7.0 Consensus size: 113
61957 GCAAAGATTT
61967 AAATCCATCA-TTCGATGGATCAAAC-TTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGA
1 AAATCCATCACTT-GATGGATC-AACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGA
62030 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
64 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
62080 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACCCATCTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
62145 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
62193 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACCCATCTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
*
62258 AAGGAAGAAGAAGTTCATATTGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * *
62306 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAAAAAAACCCATCTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
62371 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* *
62419 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCAAGTTCATAATGAGAATAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
62484 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
62532 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATTTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
* * * * *
62597 AAGGAAGAATAAGTTCATAATGAGAAGAACTTGTTCAACGTTTTGATT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * *****
62645 GAATCCATCACTTGATGGATCAGCTTTTCCAAAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
* ** *
62710 AAAGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTTTTGC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
62756 AGGACTCTAT
Statistics
Matches: 643, Mismatches: 31, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
112 3 0.00
113 638 0.99
114 2 0.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (113 bp):
AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:62829 original size:33 final size:35
Alignment explanation
Indices: 62792--62857 Score: 82
Period size: 36 Copynumber: 1.9 Consensus size: 35
62782 TCATCATCAG
* *
62792 CATTTCCAGAAG-G-AGTTCATAATGAGAAGAACT
1 CATTTCAAGAAGAGAAGTTCACAATGAGAAGAACT
*
62825 CATTTGAAGAAGAAGAAGTTCACAATGAGAAGA
1 CATTTCAAGAAG-AGAAGTTCACAATGAGAAGA
62858 GTTTGTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 10 0.37
35 1 0.04
36 16 0.59
ACGTcount: A:0.44, C:0.12, G:0.23, T:0.21
Consensus pattern (35 bp):
CATTTCAAGAAGAGAAGTTCACAATGAGAAGAACT
Found at i:62885 original size:120 final size:123
Alignment explanation
Indices: 62663--62962 Score: 339
Period size: 120 Copynumber: 2.5 Consensus size: 123
62653 CACTTGATGG
* *
62663 ATCAGCTTTTCCAAAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCAT
1 ATCAGCATTTCCAAAGAAAGTTCATAATGAGAAGAACTCATCT-AAGAAAGAAGAAGAAGTTCAC
*
62728 AATGAGAAGAGCTTGTTCGACCTTTTGCAGGACTCTATCACAGAAAGAGATATATCATC
65 AATGAGAAGAGCTTGTTCGACCTTTTGCAGAACTCTATCACAGAAAGAGATATATCATC
* *
62787 ATCAGCATTTCCAGAAG-GAGTTCATAATGAGAAGAACTCAT-T-TG-AAGAAGAAGAAGTTCAC
1 ATCAGCATTTCCA-AAGAAAGTTCATAATGAGAAGAACTCATCTAAGAAAGAAGAAGAAGTTCAC
* * * * *
62848 AATGAGAAGAGTTTGTTC-AGTCTTTTGCATAATTCTATCACAGAAGGAGATATAT--T-
65 AATGAGAAGAGCTTGTTCGA-CCTTTTGCAGAACTCTATCACAGAAAGAGATATATCATC
* * ** ** *
62904 AGCATCATCCCCAGTGGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAAG-AGAAGAA
1 ATCAGCATTTCCA-AAGAAAGTTCATAATGAGAAGAACTCATCT-AAGAAAGAAGAAGAA
62963 TTTATTCAAC
Statistics
Matches: 150, Mismatches: 19, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
117 11 0.07
118 23 0.15
119 2 0.01
120 63 0.42
121 9 0.06
122 3 0.02
123 1 0.01
124 35 0.23
125 3 0.02
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (123 bp):
ATCAGCATTTCCAAAGAAAGTTCATAATGAGAAGAACTCATCTAAGAAAGAAGAAGAAGTTCACA
ATGAGAAGAGCTTGTTCGACCTTTTGCAGAACTCTATCACAGAAAGAGATATATCATC
Found at i:63108 original size:3 final size:3
Alignment explanation
Indices: 63100--63157 Score: 73
Period size: 3 Copynumber: 19.0 Consensus size: 3
63090 TATCCCGGTT
*
63100 TTA TTA TTA TTA TTA TTA -TA TTA TTTA TTA TATA TTT TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA T-TA TTA TTA TTA TTA
*
63146 ATA TTA TTA TTA
1 TTA TTA TTA TTA
63158 CAACCAGGCC
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 2 0.04
3 40 0.83
4 6 0.12
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:71411 original size:30 final size:30
Alignment explanation
Indices: 71376--71441 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
71366 TAATATTATT
*
71376 TATTTTGA-TCTTATCATAACTCATAAAATA
1 TATTTTGATTCTTACCATAACTCA-AAAATA
* *
71406 TATTTT-ATTCTTACCTTAACTTAAAAATA
1 TATTTTGATTCTTACCATAACTCAAAAATA
71435 TATTTTG
1 TATTTTG
71442 TTTTTATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 13 0.42
30 18 0.58
ACGTcount: A:0.36, C:0.12, G:0.03, T:0.48
Consensus pattern (30 bp):
TATTTTGATTCTTACCATAACTCAAAAATA
Found at i:71576 original size:31 final size:31
Alignment explanation
Indices: 71538--71663 Score: 110
Period size: 31 Copynumber: 4.3 Consensus size: 31
71528 TTACATATTA
71538 TTTATTCTTATCTTAATTTAAAAATATATAT
1 TTTATTCTTATCTTAATTTAAAAATATATAT
* *
71569 TTTA----T-TC-TAATTTCAAAATGTATAT
1 TTTATTCTTATCTTAATTTAAAAATATATAT
* *
71594 TTTATTCTTATTTTAATTTAAGAA-ATATAT
1 TTTATTCTTATCTTAATTTAAAAATATATAT
* *
71624 TTTATTTTTTATCTTAACTATAAAAATAT-T-T
1 TTTA-TTCTTATCTTAA-TTTAAAAATATATAT
71655 TTTA-TCTTA
1 TTTATTCTTA
71664 ATTTAAAATA
Statistics
Matches: 75, Mismatches: 11, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
25 20 0.27
26 2 0.03
27 1 0.01
29 5 0.07
30 10 0.13
31 28 0.37
32 7 0.09
33 2 0.03
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.56
Consensus pattern (31 bp):
TTTATTCTTATCTTAATTTAAAAATATATAT
Found at i:71579 original size:25 final size:25
Alignment explanation
Indices: 71551--71606 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
71541 ATTCTTATCT
71551 TAATTTAAAAATATATATTTTATTC
1 TAATTTAAAAATATATATTTTATTC
* *
71576 TAATTTCAAAATGTATATTTTATTC
1 TAATTTAAAAATATATATTTTATTC
*
71601 TTATTT
1 TAATTT
71607 TAATTTAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (25 bp):
TAATTTAAAAATATATATTTTATTC
Found at i:75419 original size:5 final size:5
Alignment explanation
Indices: 75409--75434 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
75399 CAACATGCAA
75409 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
75435 GGACTAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:76945 original size:22 final size:24
Alignment explanation
Indices: 76901--76945 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
76891 AAGGAAAACA
*
76901 AATAATAAATATTATAATTAAAAAT
1 AATAATAAATAATATAA-TAAAAAT
76926 AATAAT-AATAATATAA-AAAA
1 AATAATAAATAATATAATAAAA
76946 GGATAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
24 9 0.47
25 6 0.32
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (24 bp):
AATAATAAATAATATAATAAAAAT
Found at i:77322 original size:134 final size:134
Alignment explanation
Indices: 77151--77818 Score: 806
Period size: 134 Copynumber: 5.0 Consensus size: 134
77141 TATTAAAACG
* * * * *
77151 AGGCATACTTGTTTCACTGTTACTCAGAGAATATCAAATCTTGAAAGAGTGGGATCTGTTTCGCT
1 AGGCATACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCCACT
* * * *
77216 TTTTCTTGAGGGAAAATCAGATTTGGGGACGATGATTCATTCCATTGTTACTCAGAGAAGATTGA
66 TTTTCTTGAGGGAAAATCAGATTTGGGGACGTTGATTCATTCCACTGTCACTCAGGGAAGATTGA
77281 ATCA
131 ATCA
* * *
77285 AGGCATACTTGTTCCACTGTTACTCAGAGCATATCAAATCTTGAAAGAGAGGGATTTGTTCCACT
1 AGGCATACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCCACT
* * * * *
77350 TCTTGCAT-AGGGAAAATCAGATATGGGGACGTTGATCCATTCCACTGTTACTCAGGGAAGATTG
66 T-TTTCTTGAGGGAAAATCAGATTTGGGGACGTTGATTCATTCCACTGTCACTCAGGGAAGATTG
**
77414 -ATTG
130 AATCA
* * * * * * * *
77418 AGACATACTTGTTCCACTGTTACTTAGGGAATATCAAATATTGAAATATAGAGATCTATTCCGCT
1 AGGCATACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCCACT
* * *
77483 TCTTT-TTGTGGGAAAATCATATCTAGGGGA-GTTGATTCATTCCACTGTCACTCAGGGAAGATT
66 T-TTTCTTGAGGGAAAATCAGAT-TTGGGGACGTTGATTCATTCCACTGTCACTCAGGGAAGATT
77546 GAATCA
129 GAATCA
* * * * *
77552 AGGCAGACTTGTTCCACTGTTACTCAGGGAATATTAAATCTTGAAAGTGAGGGATATTTTCCACT
1 AGGCATACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCCACT
* * * * *
77617 TCTTCTTGAGGGAAAATCATATCTAGGGGA-GTTGATTCATTCTACCGTCACTCAGGGAAGATTG
66 TTTTCTTGAGGGAAAATCAGAT-TTGGGGACGTTGATTCATTCCACTGTCACTCAGGGAAGATTG
*
77681 AATCG
130 AATCA
* * * *
77686 AGGAAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGGAAGAGAGAGATCTGTTCCACT
1 AGGCATACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCCACT
* * * * **
77751 TTTTCTTGAGGAAAAATTAGATATGGGGACATTGATTCATTCCACTGTCACTCAGAAAAGATTGA
66 TTTTCTTGAGGGAAAATCAGATTTGGGGACGTTGATTCATTCCACTGTCACTCAGGGAAGATTGA
77816 ATC
131 ATC
77819 GAGTTCGATT
Statistics
Matches: 457, Mismatches: 71, Indels: 12
0.85 0.13 0.02
Matches are distributed among these distances:
132 1 0.00
133 111 0.24
134 341 0.75
135 4 0.01
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.32
Consensus pattern (134 bp):
AGGCATACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCCACT
TTTTCTTGAGGGAAAATCAGATTTGGGGACGTTGATTCATTCCACTGTCACTCAGGGAAGATTGA
ATCA
Found at i:77631 original size:267 final size:268
Alignment explanation
Indices: 77149--77818 Score: 874
Period size: 267 Copynumber: 2.5 Consensus size: 268
77139 AATATTAAAA
* * * *
77149 CGAGG-CATACTTGTTTCACTGTTACTCAGAGAATATCAAATCTTGAAAGAGT-GGGATCTGTTT
1 CGAGGACATACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGA-TAGAGATCTGTTC
* * *
77212 CGCTTTTTCTTGAGGGAAAATCAGATTTGGGGACGATGATTCATTCCATTGTTACTCAGAGAAGA
65 CGCTTTTTCTTGAGGGAAAATCAGA-TTGGGGACGTTGATTCATTCCACTGTCACTCAGAGAAGA
* *
77277 TTGAATCAAGGCATACTTGTTCCACTGTTACTCAGAGCATATCAAATCTTGAAAGAGAGGGATTT
129 TTGAATCAAGGCAGACTTGTTCCACTGTTACTCAGAGAATATCAAATCTTGAAAGAGAGGGATTT
* *
77342 GTTCCACTTCTTGCATAGGGAAAATCAGATAT-GGGGACGTTGATCCATTCCACTGTTACTCAGG
194 GTTCCACTTCTTGCATAGGGAAAATCAGATATAGGGGA-GTTGATCCATTCCACCGTCACTCAGG
77406 GAAGATTG-AT
258 GAAGATTGAAT
* * * * *
77416 TGA-GACATACTTGTTCCACTGTTACTTAGGGAATATCAAATATTGAAATATAGAGATCTATTCC
1 CGAGGACATACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGATAGAGATCTGTTCC
* * *
77480 GCTTCTTT-TTGTGGGAAAATCATATCTAGGGGA-GTTGATTCATTCCACTGTCACTCAGGGAAG
66 GCTT-TTTCTTGAGGGAAAATCAGAT-T-GGGGACGTTGATTCATTCCACTGTCACTCAGAGAAG
* * *
77543 ATTGAATCAAGGCAGACTTGTTCCACTGTTACTCAGGGAATATTAAATCTTGAAAGTGAGGGATA
128 ATTGAATCAAGGCAGACTTGTTCCACTGTTACTCAGAGAATATCAAATCTTGAAAGAGAGGGAT-
* * * * *
77608 TT-TTCCACTTCTT-CTTGAGGGAAAATCATATCTAGGGGAGTTGATTCATTCTACCGTCACTCA
192 TTGTTCCACTTCTTGCAT-AGGGAAAATCAGATATAGGGGAGTTGATCCATTCCACCGTCACTCA
77671 GGGAAGATTGAAT
256 GGGAAGATTGAAT
* * *
77684 CGAGGA-AGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGGAAGAGAGAGATCTGTTCC
1 CGAGGACATACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGATAGAGATCTGTTCC
* * * * *
77748 ACTTTTTCTTGAGGAAAAATTAGATATGGGGACATTGATTCATTCCACTGTCACTCAGAAAAGAT
66 GCTTTTTCTTGAGGGAAAATCAGAT-TGGGGACGTTGATTCATTCCACTGTCACTCAGAGAAGAT
77813 TGAATC
130 TGAATC
77819 GAGTTCGATT
Statistics
Matches: 347, Mismatches: 44, Indels: 23
0.84 0.11 0.06
Matches are distributed among these distances:
266 5 0.01
267 218 0.63
268 122 0.35
269 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.32
Consensus pattern (268 bp):
CGAGGACATACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGATAGAGATCTGTTCC
GCTTTTTCTTGAGGGAAAATCAGATTGGGGACGTTGATTCATTCCACTGTCACTCAGAGAAGATT
GAATCAAGGCAGACTTGTTCCACTGTTACTCAGAGAATATCAAATCTTGAAAGAGAGGGATTTGT
TCCACTTCTTGCATAGGGAAAATCAGATATAGGGGAGTTGATCCATTCCACCGTCACTCAGGGAA
GATTGAAT
Found at i:80092 original size:27 final size:28
Alignment explanation
Indices: 80052--80108 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
80042 CTAATCATTT
* *
80052 AAAGAGTTTTTAATT-CAAATGATATTC
1 AAAGAATTTCTAATTGCAAATGATATTC
**
80079 AAAGAATTTCTAATTGCAAATTTTATTC
1 AAAGAATTTCTAATTGCAAATGATATTC
80107 AA
1 AA
80109 TGCTCACCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 13 0.52
28 12 0.48
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (28 bp):
AAAGAATTTCTAATTGCAAATGATATTC
Found at i:82100 original size:11 final size:11
Alignment explanation
Indices: 82079--82115 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
82069 GTAATGTGAA
82079 AATGTAAATGC
1 AATGTAAATGC
**
82090 AATGTGGATGC
1 AATGTAAATGC
82101 AATGTAAATGC
1 AATGTAAATGC
82112 AATG
1 AATG
82116 CAAGGTGTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.41, C:0.08, G:0.24, T:0.27
Consensus pattern (11 bp):
AATGTAAATGC
Found at i:86214 original size:23 final size:25
Alignment explanation
Indices: 86188--86242 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 25
86178 AAATCCAGCA
*
86188 AAGAAAATCAAAGCAC-TCAAAA-G
1 AAGAAAATCAAAGCACTTAAAAAGG
* *
86211 AAGAAATTGAAAGCACTTAAAAAGG
1 AAGAAAATCAAAGCACTTAAAAAGG
86236 AAGAAAA
1 AAGAAAA
86243 AGAACAGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 14 0.54
24 5 0.19
25 7 0.27
ACGTcount: A:0.62, C:0.11, G:0.16, T:0.11
Consensus pattern (25 bp):
AAGAAAATCAAAGCACTTAAAAAGG
Found at i:86251 original size:11 final size:10
Alignment explanation
Indices: 86229--86282 Score: 56
Period size: 10 Copynumber: 5.3 Consensus size: 10
86219 GAAAGCACTT
*
86229 AAAAAGGAAG
1 AAAAAGAAAG
86239 AAAAAGAACAG
1 AAAAAGAA-AG
*
86250 AAAAGAAAAAG
1 AAAA-AGAAAG
86261 AAAAA-AAAG
1 AAAAAGAAAG
*
86270 AAAAATAAAG
1 AAAAAGAAAG
86280 AAA
1 AAA
86283 GTTGAAGCAC
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
9 9 0.23
10 15 0.38
11 12 0.31
12 3 0.08
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.02
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:86257 original size:16 final size:15
Alignment explanation
Indices: 86236--86274 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
86226 CTTAAAAAGG
*
86236 AAGAAAAAGAACAGAA
1 AAGAAAAAGAA-AAAA
86252 AAGAAAAAGAAAAAA
1 AAGAAAAAGAAAAAA
86267 AAGAAAAA
1 AAGAAAAA
86275 TAAAGAAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (15 bp):
AAGAAAAAGAAAAAA
Found at i:90124 original size:21 final size:21
Alignment explanation
Indices: 90098--90147 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
90088 ATGCATTCAT
90098 ATTAGCTCTTAAGCTTTATGC
1 ATTAGCTCTTAAGCTTTATGC
90119 ATTAGCTCTTAAGCTTTATGC
1 ATTAGCTCTTAAGCTTTATGC
90140 ATTAGCTC
1 ATTAGCTC
90148 ACACATATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (21 bp):
ATTAGCTCTTAAGCTTTATGC
Found at i:92753 original size:131 final size:131
Alignment explanation
Indices: 92452--92753 Score: 295
Period size: 131 Copynumber: 2.3 Consensus size: 131
92442 TCAAAACAAT
* * * * *
92452 CATTTATTACCCCAATTTAAAT-AAAGAGATATTACTATTTCGTCTTAAAATTCGATATCGATTC
1 CATTTATTACTCCAATTGAAATGAAA-AGATATTACTATTCCATCTTAAAATTCGATATCAATTC
* * ** * * * * *
92516 AAGTGAAAACGATAAAATTTAATAATTTCCAATCGAGAAGAAATTACCTCTCATATCTTAAAGTT
65 AAGAGAAAACGACAAAATCAAATAATTTCCAATCAAAAAGAAATGACCTCTCATACCTTAAAGAT
*
92581 GT
130 GC
* * * * *
92583 CATTTATTGCTCCAATTGAAATGAAGAA-ATGTCATTATTCCATCTTAAAATTCGATATTAATTC
1 CATTTATTACTCCAATTGAAATGAA-AAGATATTACTATTCCATCTTAAAATTCGATATCAATTC
* * * * * * *
92647 GAGAGAAAACGACAATATCAAATTATTTTCAATCAAAAATAAATGACCTCTCTTGCCTTAAAGCA
65 AAGAGAAAACGACAAAATCAAATAATTTCCAATCAAAAAGAAATGACCTCTCATACCTTAAAG-A
92712 T-C
129 TGC
**
92714 CATTTATTACTCCAAGCGAAATGAAAAGATATTACTATTC
1 CATTTATTACTCCAATTGAAATGAAAAGATATTACTATTC
92754 TCGTTATCGA
Statistics
Matches: 134, Mismatches: 33, Indels: 8
0.77 0.19 0.05
Matches are distributed among these distances:
130 2 0.01
131 127 0.95
132 4 0.03
133 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.34
Consensus pattern (131 bp):
CATTTATTACTCCAATTGAAATGAAAAGATATTACTATTCCATCTTAAAATTCGATATCAATTCA
AGAGAAAACGACAAAATCAAATAATTTCCAATCAAAAAGAAATGACCTCTCATACCTTAAAGATG
C
Found at i:93497 original size:3 final size:3
Alignment explanation
Indices: 93489--93526 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
93479 ATTTTATTTT
93489 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
93527 TATTGTTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:95919 original size:21 final size:21
Alignment explanation
Indices: 95894--95933 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
95884 AAGACTTTAT
95894 TTTCAAAATAAAAAAATGATA
1 TTTCAAAATAAAAAAATGATA
**
95915 TTTCAAAATTGAAAAATGA
1 TTTCAAAATAAAAAAATGA
95934 AAAGTCTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATAAAAAAATGATA
Found at i:99740 original size:22 final size:22
Alignment explanation
Indices: 99708--99768 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
99698 AGCGCTAGAA
* * *
99708 ATCGATACCCCCTTGCATGGGT
1 ATCGATTCCCCCTTGAATAGGT
99730 ATCGATTCCCCCTTTGAATAGGT
1 ATCGATTCCCCC-TTGAATAGGT
*
99753 ACCGATTCCCCCTTGA
1 ATCGATTCCCCCTTGA
99769 GGGAACTGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 15 0.44
23 19 0.56
ACGTcount: A:0.20, C:0.33, G:0.18, T:0.30
Consensus pattern (22 bp):
ATCGATTCCCCCTTGAATAGGT
Found at i:102026 original size:21 final size:21
Alignment explanation
Indices: 102000--102068 Score: 129
Period size: 21 Copynumber: 3.3 Consensus size: 21
101990 ATTTAACAAA
*
102000 AAGGGGGAGAAGTGTTATAGT
1 AAGGGGAAGAAGTGTTATAGT
102021 AAGGGGAAGAAGTGTTATAGT
1 AAGGGGAAGAAGTGTTATAGT
102042 AAGGGGAAGAAGTGTTATAGT
1 AAGGGGAAGAAGTGTTATAGT
102063 AAGGGG
1 AAGGGG
102069 GAGTAATTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.36, C:0.00, G:0.42, T:0.22
Consensus pattern (21 bp):
AAGGGGAAGAAGTGTTATAGT
Found at i:103567 original size:9 final size:9
Alignment explanation
Indices: 103553--103578 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
103543 AGAAGCTAAA
103553 AAAATAGAG
1 AAAATAGAG
103562 AAAATAGAG
1 AAAATAGAG
103571 AAAATAGA
1 AAAATAGA
103579 AGGATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.19, T:0.12
Consensus pattern (9 bp):
AAAATAGAG
Found at i:104058 original size:15 final size:16
Alignment explanation
Indices: 104034--104067 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
104024 AGCGTCATTT
*
104034 AAATT-TTTTTAAGAA
1 AAATTGTTTTCAAGAA
104049 AAATTGTTTTCAAGAA
1 AAATTGTTTTCAAGAA
104065 AAA
1 AAA
104068 AGTTGGTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.50, C:0.03, G:0.09, T:0.38
Consensus pattern (16 bp):
AAATTGTTTTCAAGAA
Found at i:106309 original size:40 final size:40
Alignment explanation
Indices: 106265--106406 Score: 110
Period size: 40 Copynumber: 3.5 Consensus size: 40
106255 AAATCTGGTG
*
106265 ATGATCTTACTCTTTTCTTTGAAAGACGTTGAGTCATGGA
1 ATGATCTTACTCTTTCCTTTGAAAGACGTTGAGTCATGGA
* * * * *
106305 ATGATTTTACTCATTCCTATAACT-AAAGGACCTTAAATC-TAGTG-
1 ATGATCTTACTCTTTCCT-T---TGAAA-GACGTTGAGTCAT-G-GA
* *
106349 TTGATCTTACTCTTTCCTTTGAAATACGTTGAGTCATGGA
1 ATGATCTTACTCTTTCCTTTGAAAGACGTTGAGTCATGGA
* *
106389 ATGATTTTACTCGTTCCT
1 ATGATCTTACTCTTTCCT
106407 CTCAAGGATG
Statistics
Matches: 76, Mismatches: 16, Indels: 20
0.68 0.14 0.18
Matches are distributed among these distances:
39 1 0.01
40 39 0.51
41 5 0.07
43 5 0.07
44 25 0.33
45 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (40 bp):
ATGATCTTACTCTTTCCTTTGAAAGACGTTGAGTCATGGA
Found at i:106385 original size:84 final size:84
Alignment explanation
Indices: 106244--106406 Score: 272
Period size: 84 Copynumber: 1.9 Consensus size: 84
106234 ATCCTTTTGA
* * *
106244 TAAAGGACGTTAAATCTGGTGATGATCTTACTCTTTTCTTTGAAAGACGTTGAGTCATGGAATGA
1 TAAAGGACCTTAAATCTAGTGATGATCTTACTCTTTCCTTTGAAAGACGTTGAGTCATGGAATGA
106309 TTTTACTCATTCCTATAAC
66 TTTTACTCATTCCTATAAC
* *
106328 TAAAGGACCTTAAATCTAGTGTTGATCTTACTCTTTCCTTTGAAATACGTTGAGTCATGGAATGA
1 TAAAGGACCTTAAATCTAGTGATGATCTTACTCTTTCCTTTGAAAGACGTTGAGTCATGGAATGA
*
106393 TTTTACTCGTTCCT
66 TTTTACTCATTCCT
106407 CTCAAGGATG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
84 73 1.00
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (84 bp):
TAAAGGACCTTAAATCTAGTGATGATCTTACTCTTTCCTTTGAAAGACGTTGAGTCATGGAATGA
TTTTACTCATTCCTATAAC
Found at i:106815 original size:40 final size:40
Alignment explanation
Indices: 106714--106816 Score: 125
Period size: 40 Copynumber: 2.6 Consensus size: 40
106704 GAATCTGGTG
* *
106714 ACGATCTCACTCTTTCCTCTGAAAGACCCTGAGTTATGAA
1 ACGATCTTACTCTTTCCTCTGAAAGACCCTGAGTCATGAA
* * **
106754 ACGATCTTACTCCTTCCTCTGAAAGACGCTGAGTCATGGG
1 ACGATCTTACTCTTTCCTCTGAAAGACCCTGAGTCATGAA
* * *
106794 ATGATCTTACTTTTTCTTCTGAA
1 ACGATCTTACTCTTTCCTCTGAA
106817 GGATGTTAAG
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (40 bp):
ACGATCTTACTCTTTCCTCTGAAAGACCCTGAGTCATGAA
Found at i:106828 original size:264 final size:264
Alignment explanation
Indices: 106380--106957 Score: 628
Period size: 264 Copynumber: 2.2 Consensus size: 264
106370 AAATACGTTG
** * * * * *
106380 AGTCATGGAATGATTTTACTCGTTCCTCTCAAGGATGTTAAGTCGTAATTCGGGGTCACTGAATC
1 AGTCATGGGCTGATCTTACTCCTTCCTCTAAAGGATGCTAAGTCGTAATTCGGGATCACTGAATC
* ** ** * *
106445 TAGTGACGATATCACTCTTTTCTATGAAAGATGATGAGTCATGGGATGATCTTACTCATTCCTTT
66 TAGTGACGATATCACTCTTTCCTATGAAAGACCATGAGTCATGAAACGATCTTACTCATTCCTTG
* *
106510 AAAGGATGCTAAGTCGAGGAACTATCTTACTCCTTTCTCTGAAAGGTATTAAGTTGTGATTAGGG
131 AAAGGACGCTAAGTCGAGGAACTATCTTACTCCTTTCTCTGAAAGGTATTAAGTTGTAATTAGGG
** * * ** * *
106575 TAATTCACTCCTTTTGTTGAAGGGTGAGAAATCTGGTGACGATCTCACTCTTTCCTCTTAAAGAC
196 TAATTCACTCCTTTTACTGAAGGATGAAAAATCTAATGACGATCTCACTCTTTCATATTAAAGAC
106640 GCTA
261 GCTA
* * * * *
106644 ATTTATGGGGC-GATCTTACTCTTTCCTCTAAAGGATGCTAAATCATAATTCGGGATCACTGAAT
1 AGTCAT-GGGCTGATCTTACTCCTTCCTCTAAAGGATGCTAAGTCGTAATTCGGGATCACTGAAT
* * * * * *
106708 CTGGTGACGATCTCACTCTTTCCTCTGAAAGACCCTGAGTTATGAAACGATCTTACTCCTTCCTC
65 CTAGTGACGATATCACTCTTTCCTATGAAAGACCATGAGTCATGAAACGATCTTACTCATTCCT-
* * * *
106773 TGAAA-GACGCTGAGTC-ATGGGA-TGATCTTACT-TTTTCTTCTG-AAGGATGTTAAGTTGTAA
129 TGAAAGGACGCTAAGTCGA-GGAACT-ATCTTACTCCTTTC-TCTGAAAGG-TATTAAGTTGTAA
* ** *
106833 TTGGGGTGGTTCACTTCTTTTACTGAAGGATGAAAAATCTAATGACGATCTCACTCTTTCATATT
190 TTAGGGTAATTCACTCCTTTTACTGAAGGATGAAAAATCTAATGACGATCTCACTCTTTCATATT
* *
106898 AAATATGCTA
255 AAAGACGCTA
* * *
106908 AGTCGTGGGCTGATCTTACTCCTTCCTCTGAAGGACGCTAAGTCGTAATT
1 AGTCATGGGCTGATCTTACTCCTTCCTCTAAAGGATGCTAAGTCGTAATT
106958 GAATGATTGT
Statistics
Matches: 255, Mismatches: 52, Indels: 14
0.79 0.16 0.04
Matches are distributed among these distances:
263 14 0.05
264 235 0.92
265 6 0.02
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (264 bp):
AGTCATGGGCTGATCTTACTCCTTCCTCTAAAGGATGCTAAGTCGTAATTCGGGATCACTGAATC
TAGTGACGATATCACTCTTTCCTATGAAAGACCATGAGTCATGAAACGATCTTACTCATTCCTTG
AAAGGACGCTAAGTCGAGGAACTATCTTACTCCTTTCTCTGAAAGGTATTAAGTTGTAATTAGGG
TAATTCACTCCTTTTACTGAAGGATGAAAAATCTAATGACGATCTCACTCTTTCATATTAAAGAC
GCTA
Found at i:107431 original size:45 final size:43
Alignment explanation
Indices: 107299--107438 Score: 124
Period size: 45 Copynumber: 3.1 Consensus size: 43
107289 AATCAGGTTG
* *
107299 AAGAAATACATCACTGAAAAGTTGACTCATC--TACGCAAGAAATTC
1 AAGAAAGACATCACT-AAAAGTTGACTCATCTTTA-G--AGAAAGTC
* * * *
107344 AAGAATGAAATCACTACAAGGTTGACTCCTCATTGTAG-GAAAGTC
1 AAGAAAGACATCACTA-AAAGTTGACTCATC-TT-TAGAGAAAGTC
107389 AAGAAAGACATCACTAAAAGATTGACTCATCTTTATGAGAAAGTC
1 AAGAAAGACATCACTAAAAG-TTGACTCATCTTTA-GAGAAAGTC
107434 AAGAA
1 AAGAA
107439 TGGCATACTT
Statistics
Matches: 77, Mismatches: 10, Indels: 16
0.75 0.10 0.16
Matches are distributed among these distances:
43 2 0.03
44 7 0.09
45 65 0.84
48 1 0.01
49 2 0.03
ACGTcount: A:0.44, C:0.17, G:0.16, T:0.23
Consensus pattern (43 bp):
AAGAAAGACATCACTAAAAGTTGACTCATCTTTAGAGAAAGTC
Found at i:110522 original size:20 final size:20
Alignment explanation
Indices: 110494--110531 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
110484 TGATACATTT
110494 AAAACATAAATAAAACAATC
1 AAAACATAAATAAAACAATC
*
110514 AAAAGATAAATAAAACAA
1 AAAACATAAATAAAACAA
110532 ACTCATATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.74, C:0.11, G:0.03, T:0.13
Consensus pattern (20 bp):
AAAACATAAATAAAACAATC
Found at i:111820 original size:29 final size:29
Alignment explanation
Indices: 111756--111813 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
111746 CAATAGACTG
111756 AAATAAATACAACATACAAATTAGAAACC
1 AAATAAATACAACATACAAATTAGAAACC
*
111785 AAATAAATACAAGATACAAATTAGAAACC
1 AAATAAATACAACATACAAATTAGAAACC
111814 GATTAAACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.62, C:0.16, G:0.05, T:0.17
Consensus pattern (29 bp):
AAATAAATACAACATACAAATTAGAAACC
Found at i:112086 original size:19 final size:20
Alignment explanation
Indices: 112053--112097 Score: 83
Period size: 19 Copynumber: 2.3 Consensus size: 20
112043 ATTTGTTTGT
112053 CCATCCGTTGTTTTTTTGCC
1 CCATCCGTTGTTTTTTTGCC
112073 CCATCCGTTG-TTTTTTGCC
1 CCATCCGTTGTTTTTTTGCC
112092 CCATCC
1 CCATCC
112098 CAATCACTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.07, C:0.36, G:0.13, T:0.44
Consensus pattern (20 bp):
CCATCCGTTGTTTTTTTGCC
Found at i:114891 original size:12 final size:12
Alignment explanation
Indices: 114874--114907 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
114864 GAATACCCGG
114874 GTATCGGGCCGA
1 GTATCGGGCCGA
*
114886 GTATCGGGCCGG
1 GTATCGGGCCGA
114898 GTATCGGGCC
1 GTATCGGGCC
114908 AGGTATTCGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.12, C:0.26, G:0.44, T:0.18
Consensus pattern (12 bp):
GTATCGGGCCGA
Found at i:114912 original size:12 final size:11
Alignment explanation
Indices: 114873--114918 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 11
114863 TGAATACCCG
114873 GGTATCGGGCC
1 GGTATCGGGCC
114884 GAGTATCGGGCC
1 G-GTATCGGGCC
114896 GGGTATCGGGCC
1 -GGTATCGGGCC
114908 AGGTATTCGGG
1 -GGTA-TCGGG
114919 GCGGGGATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
11 1 0.03
12 24 0.77
13 6 0.19
ACGTcount: A:0.13, C:0.22, G:0.46, T:0.20
Consensus pattern (11 bp):
GGTATCGGGCC
Found at i:114913 original size:24 final size:25
Alignment explanation
Indices: 114870--114923 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
114860 GTTTGAATAC
114870 CCGGGTATCGGGCCGAGTA-TCGGG
1 CCGGGTATCGGGCCGAGTATTCGGG
114894 CCGGGTATCGGGCC-AGGTATTCGGG
1 CCGGGTATCGGGCCGA-GTATTCGGG
*
114919 GCGGG
1 CCGGG
114924 GATTACCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 1 0.04
24 17 0.63
25 9 0.33
ACGTcount: A:0.11, C:0.24, G:0.48, T:0.17
Consensus pattern (25 bp):
CCGGGTATCGGGCCGAGTATTCGGG
Found at i:118009 original size:21 final size:22
Alignment explanation
Indices: 117983--118023 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
117973 GGCTATTTTC
117983 ATTTTTCAATTTTG-AAATATA
1 ATTTTTCAATTTTGTAAATATA
**
118004 ATTTTTGTATTTTGTAAATA
1 ATTTTTCAATTTTGTAAATA
118024 GAGTCTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.56
Consensus pattern (22 bp):
ATTTTTCAATTTTGTAAATATA
Found at i:120085 original size:65 final size:65
Alignment explanation
Indices: 119952--120108 Score: 169
Period size: 65 Copynumber: 2.4 Consensus size: 65
119942 ACTAAGAGTA
* * * * *
119952 CATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGGCAGAGTGCATCGATGTATGGCTGGTG
1 CATCGATGCAACAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTGGTG
* * * *
120016 CATCGATGCAACAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-TATG
1 CATCGATGCAACAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATGGCT-GG
120079 TG
64 TG
*
120081 CATCGATGCATA-AAACGCATTCGATGTT
1 CATCGATGCA-ACAAATGCATTCGATGTT
120109 CAATTTAATT
Statistics
Matches: 79, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
64 25 0.32
65 50 0.63
66 4 0.05
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (65 bp):
CATCGATGCAACAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTGGTG
Found at i:131667 original size:13 final size:13
Alignment explanation
Indices: 131651--131675 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
131641 TTAAAATTGG
131651 AAAATAAAGAAAT
1 AAAATAAAGAAAT
131664 AAAATAAAGAAA
1 AAAATAAAGAAA
131676 ACAAACACAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (13 bp):
AAAATAAAGAAAT
Found at i:137436 original size:20 final size:20
Alignment explanation
Indices: 137413--137457 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
137403 AAAACAAGAG
*
137413 AGCTTGCCTAGAAACTTTCA
1 AGCTTACCTAGAAACTTTCA
*
137433 AGCTTACTTAGAAACTTTCA
1 AGCTTACCTAGAAACTTTCA
137453 AGCTT
1 AGCTT
137458 CCTTAGGGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.33
Consensus pattern (20 bp):
AGCTTACCTAGAAACTTTCA
Found at i:137462 original size:20 final size:20
Alignment explanation
Indices: 137421--137463 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
137411 AGAGCTTGCC
137421 TAGAAACTTTCAAGCTTACT
1 TAGAAACTTTCAAGCTTACT
*
137441 TAGAAACTTTCAAGCTTCCT
1 TAGAAACTTTCAAGCTTACT
137461 TAG
1 TAG
137464 GGATAGACTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.35
Consensus pattern (20 bp):
TAGAAACTTTCAAGCTTACT
Found at i:139389 original size:20 final size:20
Alignment explanation
Indices: 139366--139409 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
139356 CAAGAGATGG
*
139366 GTATCGATACT-CAGGGTTCA
1 GTATCAATACTACAGGGTT-A
*
139386 GTATCAATATTACAGGGTTA
1 GTATCAATACTACAGGGTTA
139406 GTAT
1 GTAT
139410 TGGTAGCAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.34
Consensus pattern (20 bp):
GTATCAATACTACAGGGTTA
Done.