Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008316.1 Hibiscus syriacus cultivar Beakdansim tig00111013_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: 2380696
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 12
Found at i:2232001 original size:33 final size:33
Alignment explanation
Indices: 2231964--2232034 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
2231954 AGAATGACTG
**
2231964 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
2231997 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
2232030 TCGCA
1 TCGCA
2232035 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:2232071 original size:14 final size:14
Alignment explanation
Indices: 2232052--2232141 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
2232042 TTTGGTTTCG
2232052 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2232066 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2232085 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2232099 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
2232116 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
2232132 CGTTGCGATT
1 CGTTGCGATT
2232142 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2232077 original size:33 final size:33
Alignment explanation
Indices: 2232035--2232149 Score: 194
Period size: 33 Copynumber: 3.5 Consensus size: 33
2232025 CAAAATCGCA
**
2232035 TTGCGATTTTGGTTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2232068 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
2232101 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2232134 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
2232150 AACCAAAAGA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:2234151 original size:93 final size:93
Alignment explanation
Indices: 2233848--2234316 Score: 894
Period size: 93 Copynumber: 5.1 Consensus size: 93
2233838 TAGATTGCTT
2233848 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAAC-GTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2233912 -TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
2233939 AGT-AATTTGTTCGGTTGCTGCCAATTCTGCTAAATTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2234002 -TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2234029 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2234094 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2234122 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2234187 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2234215 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2234280 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2234308 AGTAAATTT
1 AGTAAATTT
2234317 ATCCATTCAA
Statistics
Matches: 372, Mismatches: 2, Indels: 6
0.98 0.01 0.02
Matches are distributed among these distances:
90 63 0.17
91 85 0.23
92 2 0.01
93 222 0.60
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2234400 original size:19 final size:19
Alignment explanation
Indices: 2234360--2234488 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
2234350 TAGTTTACTT
* *
2234360 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
2234380 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
2234399 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
2234418 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
2234432 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
2234451 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
2234465 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
2234484 TCGCA
1 TCGCA
2234489 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:2234439 original size:33 final size:32
Alignment explanation
Indices: 2234396--2234488 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
2234386 CGCGAAACCA
**
2234396 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
2234428 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
2234461 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
2234489 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:2234486 original size:52 final size:52
Alignment explanation
Indices: 2234360--2234488 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
2234350 TAGTTTACTT
**
2234360 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
2234412 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
2234465 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
2234489 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:2234506 original size:19 final size:19
Alignment explanation
Indices: 2234484--2234618 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
2234474 GAAACCAAAA
*
2234484 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2234503 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
2234519 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
2234536 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
2234552 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
2234569 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
2234588 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
2234608 TCGTGTTGCGA
1 TCGCGTTGCGA
2234619 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2234525 original size:14 final size:14
Alignment explanation
Indices: 2234506--2234562 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2234496 TTTCATTTCG
2234506 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
2234520 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
2234537 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
2234553 CGTTGCGATT
1 CGTTGCGATT
2234563 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:2234531 original size:33 final size:33
Alignment explanation
Indices: 2234489--2234581 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
2234479 CAAAATCGCA
*
2234489 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
2234522 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
2234555 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
2234582 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:2236527 original size:14 final size:14
Alignment explanation
Indices: 2236508--2236543 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2236498 GATGTTTAAT
2236508 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
2236522 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
2236536 TGATTTGT
1 TGATTTGT
2236544 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2236667 original size:19 final size:19
Alignment explanation
Indices: 2236651--2236752 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
2236641 AAAAATGACT
2236651 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2236670 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2236689 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2236703 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2236722 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
2236742 ATCGCAATGCG
1 ATCGCAATGCG
2236753 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2236771 original size:19 final size:18
Alignment explanation
Indices: 2236743--2237057 Score: 238
Period size: 19 Copynumber: 17.9 Consensus size: 18
2236733 GAAATGAAAA
* *
2236743 TCGCAATGCGTTTATAATT
1 TCGCATTGCGTTT-TCATT
* *
2236762 TCGCATTGCG-ATT-ATC
1 TCGCATTGCGTTTTCATT
2236778 TCG--TTGCGATTTTCATT
1 TCGCATTGCG-TTTTCATT
2236795 TCGCATTGCGATTTTCATT
1 TCGCATTGCG-TTTTCATT
*
2236814 TCGCATTGCG-ATTC-TT
1 TCGCATTGCGTTTTCATT
2236830 TCG--TTGCGATTTTCATT
1 TCGCATTGCG-TTTTCATT
*
2236847 TCGCATTGCGATTTCATT
1 TCGCATTGCGTTTTCATT
2236865 TCGCATTGCGATTTTCATT
1 TCGCATTGCG-TTTTCATT
* * *
2236884 TCGTATTGCGATTTAATT
1 TCGCATTGCGTTTTCATT
* *
2236902 TCGCATTGCG-ATT-ATG
1 TCGCATTGCGTTTTCATT
*
2236918 TCG-GTT-CGATTTTCATT
1 TCGCATTGCG-TTTTCATT
2236935 TCGCATTGCGATTTTCATT
1 TCGCATTGCG-TTTTCATT
* *
2236954 TCGCATTGCG-ATTC-TC
1 TCGCATTGCGTTTTCATT
2236970 TCG--TTGCGATTTTCATT
1 TCGCATTGCG-TTTTCATT
2236987 TCGCATTGCGATTTTCATT
1 TCGCATTGCG-TTTTCATT
* *
2237006 TCGCATTGCG-ATTC-TC
1 TCGCATTGCGTTTTCATT
2237022 TCG--TTGCGATTTTCATT
1 TCGCATTGCG-TTTTCATT
2237039 TCCGCATTGCGATTTTCAT
1 T-CGCATTGCG-TTTTCAT
2237058 GTTGGGATTT
Statistics
Matches: 242, Mismatches: 27, Indels: 53
0.75 0.08 0.16
Matches are distributed among these distances:
14 22 0.09
15 2 0.01
16 36 0.15
17 33 0.14
18 37 0.15
19 99 0.41
20 13 0.05
ACGTcount: A:0.16, C:0.21, G:0.17, T:0.46
Consensus pattern (18 bp):
TCGCATTGCGTTTTCATT
Found at i:2236801 original size:33 final size:33
Alignment explanation
Indices: 2236759--2237085 Score: 201
Period size: 33 Copynumber: 9.5 Consensus size: 33
2236749 TGCGTTTATA
2236759 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
*
2236792 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
*
2236828 -TTTCG--TTGCGATTTTCATTTCGCATTGCGA-TTTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
* *
2236862 ATTTCGCATTGCGATTTTCATTTCGTATTGCGA-TTTA
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
*
2236899 ATTTCGCATTGCGATTATGTCGGTT-CGATTTTC
1 ATTTCGCATTGCGATTATCTC-GTTGCGATTTTC
*
2236932 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATT-T-TC
* * * * *
2236972 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTATCTCGTTGCGATTTTC
*
2237003 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
* *
2237036 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTATC-TCGTTGCGATTTTC
*
2237070 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
2237086 GTATTTTCCG
Statistics
Matches: 249, Mismatches: 20, Indels: 50
0.78 0.06 0.16
Matches are distributed among these distances:
31 9 0.04
32 8 0.03
33 95 0.38
34 36 0.14
35 21 0.08
36 12 0.05
37 45 0.18
38 11 0.04
39 3 0.01
40 9 0.04
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
Found at i:2237024 original size:52 final size:52
Alignment explanation
Indices: 2236781--2237057 Score: 352
Period size: 52 Copynumber: 5.2 Consensus size: 52
2236771 GATTATCTCG
*
2236781 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* *
2236833 TTGCGATTTTCATTTCGCATTGCGATTTCATTTCGCATTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCATTGCGA-TTC-TCTCG--TTGCGATTTTCATTTCGCA
* * *
2236889 TTGCGA-TTTAATTTCGCATTGCGATTATGTCGGTT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTC-GTTGCGATTTTCATTTCGCA
2236940 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
2236992 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCA
2237045 TTGCGATTTTCAT
1 TTGCGATTTTCAT
2237058 GTTGGGATTT
Statistics
Matches: 209, Mismatches: 7, Indels: 17
0.90 0.03 0.07
Matches are distributed among these distances:
51 42 0.20
52 113 0.54
53 23 0.11
54 8 0.04
55 17 0.08
56 6 0.03
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:2237772 original size:20 final size:20
Alignment explanation
Indices: 2237747--2237956 Score: 287
Period size: 20 Copynumber: 10.5 Consensus size: 20
2237737 TACAACTACA
2237747 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
*
2237767 CGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACG
*
2237787 CGTTGCGGTTTACGGATACG
1 CGTTGCGATTTACGGATACG
2237807 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
*
2237827 CGTTGCGATATACGGATACG
1 CGTTGCGATTTACGGATACG
* **
2237847 CATTGCGATTTACCCATACG
1 CGTTGCGATTTACGGATACG
*
2237867 CGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACG
2237887 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
* *
2237907 CGTTGCGATTTATGTG-TTCG
1 CGTTGCGATTTACG-GATACG
* ** *
2237927 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTACGGATACG
2237947 CGTTGCGATT
1 CGTTGCGATT
2237957 ATGGAAAATC
Statistics
Matches: 168, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
20 167 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (20 bp):
CGTTGCGATTTACGGATACG
Found at i:2239513 original size:20 final size:20
Alignment explanation
Indices: 2239488--2239527 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2239478 AGATTGTGCA
2239488 GGGGGTA-CAGATTCCCCCTT
1 GGGGGTATC-GATTCCCCCTT
2239508 GGGGGTATCGATTCCCCCTT
1 GGGGGTATCGATTCCCCCTT
2239528 AAAGAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.12, C:0.30, G:0.30, T:0.28
Consensus pattern (20 bp):
GGGGGTATCGATTCCCCCTT
Found at i:2240257 original size:18 final size:17
Alignment explanation
Indices: 2240230--2240263 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2240220 TGACATAAGA
*
2240230 GAAAGAACAAGTGATAT
1 GAAAGAACAAATGATAT
2240247 GAAATGAACAAATGATA
1 GAAA-GAACAAATGATA
2240264 ATGCCCATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.56, C:0.06, G:0.21, T:0.18
Consensus pattern (17 bp):
GAAAGAACAAATGATAT
Found at i:2240356 original size:21 final size:21
Alignment explanation
Indices: 2240330--2240386 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
2240320 GGGTTTCATA
2240330 GGTCCTTCGGGACAATACAGT
1 GGTCCTTCGGGACAATACAGT
*
2240351 GGTCCTTCTGGACAATACAGT
1 GGTCCTTCGGGACAATACAGT
*
2240372 GGTCCCTCGGGACAA
1 GGTCCTTCGGGACAA
2240387 ATTTCATATG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.23, C:0.26, G:0.28, T:0.23
Consensus pattern (21 bp):
GGTCCTTCGGGACAATACAGT
Found at i:2240733 original size:26 final size:24
Alignment explanation
Indices: 2240704--2240751 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
2240694 TACGATAGGT
*
2240704 ATAAATGATAAGTATATGATAATATG
1 ATAAAAGAT-AGTA-ATGATAATATG
*
2240730 ATAAAAGATATTAATGATAATA
1 ATAAAAGATAGTAATGATAATA
2240752 ATAGGATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 9 0.45
25 3 0.15
26 8 0.40
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.33
Consensus pattern (24 bp):
ATAAAAGATAGTAATGATAATATG
Found at i:2242901 original size:2 final size:2
Alignment explanation
Indices: 2242894--2242971 Score: 156
Period size: 2 Copynumber: 39.0 Consensus size: 2
2242884 TTGACTGGAA
2242894 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
2242936 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
2242972 GGATAGTTTG
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2246418 original size:18 final size:17
Alignment explanation
Indices: 2246391--2246424 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2246381 ACAGAGAAGA
*
2246391 GAAAGAACAAGTGATAT
1 GAAAGAACAAATGATAT
2246408 GAAATGAACAAATGATA
1 GAAA-GAACAAATGATA
2246425 ATGCCCATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.56, C:0.06, G:0.21, T:0.18
Consensus pattern (17 bp):
GAAAGAACAAATGATAT
Found at i:2247266 original size:21 final size:22
Alignment explanation
Indices: 2247240--2247283 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2247230 TGTAGCAGCA
*
2247240 CTGTAGCA-TGGTATCGATTCC
1 CTGTAGCAGTGGGATCGATTCC
*
2247261 CTGTAGCAGTGGGATCGGTTCC
1 CTGTAGCAGTGGGATCGATTCC
2247283 C
1 C
2247284 CTATTACAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.16, C:0.25, G:0.30, T:0.30
Consensus pattern (22 bp):
CTGTAGCAGTGGGATCGATTCC
Found at i:2250035 original size:2 final size:2
Alignment explanation
Indices: 2250022--2250052 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2250012 ATATTCTAAG
*
2250022 TA TA TA TG 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 T
2250053 TCTAAACTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2253781 original size:20 final size:20
Alignment explanation
Indices: 2253756--2253811 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 20
2253746 TTAAATTATT
2253756 TAAATAATACTTTTTTAAGC
1 TAAATAATACTTTTTTAAGC
*
2253776 TAAATACTAC-TTTTTAAGC
1 TAAATAATACTTTTTTAAGC
*
2253795 TAAATAATACTTATTTA
1 TAAATAATACTTTTTTA
2253812 TTGATAAGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.45
Consensus pattern (20 bp):
TAAATAATACTTTTTTAAGC
Found at i:2258189 original size:13 final size:11
Alignment explanation
Indices: 2258158--2258186 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
2258148 TTATTTTAAT
2258158 AAAAAAATTGA
1 AAAAAAATTGA
2258169 AAAAAAATTGA
1 AAAAAAATTGA
2258180 AAAAAAA
1 AAAAAAA
2258187 AATCAACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (11 bp):
AAAAAAATTGA
Found at i:2259058 original size:29 final size:29
Alignment explanation
Indices: 2259016--2259076 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
2259006 TTGGAGTGAA
*
2259016 AGGATTAGAGATTTGTGTATCATAGATTT
1 AGGATTAGAGATTTGTGTATAATAGATTT
*
2259045 AGGATTAGAGATTTGTGTATAATATATTT
1 AGGATTAGAGATTTGTGTATAATAGATTT
2259074 AGG
1 AGG
2259077 GATTTGAGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.33, C:0.02, G:0.25, T:0.41
Consensus pattern (29 bp):
AGGATTAGAGATTTGTGTATAATAGATTT
Found at i:2267097 original size:2 final size:2
Alignment explanation
Indices: 2267090--2267114 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2267080 ACTATGTACT
2267090 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 T
2267115 CTTCCTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2270244 original size:33 final size:31
Alignment explanation
Indices: 2270207--2270268 Score: 72
Period size: 33 Copynumber: 1.9 Consensus size: 31
2270197 ACTTTATCGG
*
2270207 AGATA-ATAATATAATTATACATCATATATTTAA
1 AGATATATAATA-AATAATA-AT-ATATATTTAA
*
2270240 AGATATATATTAAATAATAATATATATTT
1 AGATATATAATAAATAATAATATATATTT
2270269 TTTTGTATCC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
31 8 0.31
32 2 0.08
33 11 0.42
34 5 0.19
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (31 bp):
AGATATATAATAAATAATAATATATATTTAA
Found at i:2276860 original size:13 final size:12
Alignment explanation
Indices: 2276842--2276884 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
2276832 AAATATAGGC
2276842 TATATAATTATAG
1 TATATAA-TATAG
2276855 TATATAATATAG
1 TATATAATATAG
* *
2276867 TATGT-ATATAT
1 TATATAATATAG
2276878 TATATAA
1 TATATAA
2276885 CATAATACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
11 9 0.35
12 10 0.38
13 7 0.27
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (12 bp):
TATATAATATAG
Found at i:2276875 original size:16 final size:14
Alignment explanation
Indices: 2276842--2276883 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 14
2276832 AAATATAGGC
2276842 TATATAAT-TATAG
1 TATATAATATATAG
2276855 TATATAATATAGTATG
1 TATATAATATA-TA-G
*
2276871 TATATATTATATA
1 TATATAATATATA
2276884 ACATAATACA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 8 0.32
14 2 0.08
15 4 0.16
16 11 0.44
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (14 bp):
TATATAATATATAG
Found at i:2279829 original size:25 final size:25
Alignment explanation
Indices: 2279797--2279844 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
2279787 TTTCTATACG
2279797 ATTTTTT-AATAATAAAAGTTTTCT
1 ATTTTTTAAATAATAAAAGTTTTCT
*
2279821 ATTTCTTTAAATAATAAAATTTTT
1 ATTT-TTTAAATAATAAAAGTTTT
2279845 AGAGGGTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.19
25 3 0.14
26 14 0.67
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (25 bp):
ATTTTTTAAATAATAAAAGTTTTCT
Found at i:2283418 original size:19 final size:19
Alignment explanation
Indices: 2283394--2283445 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
2283384 GAATGCAATT
2283394 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
*
2283413 AGTGCATCAATGCATAAGG
1 AGTGCATCGATGCATAAGG
2283432 AGTGCATCGATGCA
1 AGTGCATCGATGCA
2283446 CATGCTAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (19 bp):
AGTGCATCGATGCATAAGG
Found at i:2283992 original size:21 final size:22
Alignment explanation
Indices: 2283968--2284011 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
2283958 GTCTATGAAG
2283968 AGTCATAGGAGAAT-AAATATA
1 AGTCATAGGAGAATGAAATATA
* *
2283989 AGTCATATGATAATGAAATATA
1 AGTCATAGGAGAATGAAATATA
2284011 A
1 A
2284012 TACTATGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.52, C:0.05, G:0.16, T:0.27
Consensus pattern (22 bp):
AGTCATAGGAGAATGAAATATA
Found at i:2285021 original size:23 final size:23
Alignment explanation
Indices: 2284991--2285076 Score: 118
Period size: 23 Copynumber: 3.7 Consensus size: 23
2284981 AATCTTATAT
2284991 GGCACTACGGTGCATTTCTACAC
1 GGCACTACGGTGCATTTCTACAC
2285014 GGCACTACGGTGCATTTCTACAC
1 GGCACTACGGTGCATTTCTACAC
* * **
2285037 GGTACTACGGTGCAATTCTACGT
1 GGCACTACGGTGCATTTCTACAC
* *
2285060 GACACTTCGGTGCATTT
1 GGCACTACGGTGCATTT
2285077 ATACGAGTTG
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.29
Consensus pattern (23 bp):
GGCACTACGGTGCATTTCTACAC
Found at i:2288608 original size:20 final size:22
Alignment explanation
Indices: 2288570--2288611 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
2288560 TTTCAATGTA
*
2288570 TAAAATTAATTTTTTAATAATT
1 TAAAATTAATTTTTAAATAATT
2288592 TAAAATT-A-TTTTAAATAATT
1 TAAAATTAATTTTTAAATAATT
2288612 ATATTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 1 0.05
22 7 0.37
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TAAAATTAATTTTTAAATAATT
Found at i:2288628 original size:18 final size:17
Alignment explanation
Indices: 2288600--2288637 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
2288590 TTTAAAATTA
2288600 TTTTAAATAATTAT-ATT
1 TTTTAAATAA-TATCATT
2288617 TTTTACAATAATATCATT
1 TTTTA-AATAATATCATT
2288635 TTT
1 TTT
2288638 CACCTCATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTAAATAATATCATT
Found at i:2290744 original size:25 final size:25
Alignment explanation
Indices: 2290715--2290764 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
2290705 GATTAGGGGT
2290715 ACTGAAGCATAAACATGTAGGGATA
1 ACTGAAGCATAAACATGTAGGGATA
*
2290740 ACTGAAGCATAAACATGTAGTGATA
1 ACTGAAGCATAAACATGTAGGGATA
2290765 TGGTGCTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.22
Consensus pattern (25 bp):
ACTGAAGCATAAACATGTAGGGATA
Found at i:2293059 original size:21 final size:21
Alignment explanation
Indices: 2293033--2293077 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2293023 GATTTATGGG
* *
2293033 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2293054 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2293075 CAA
1 CAA
2293078 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:2294937 original size:103 final size:103
Alignment explanation
Indices: 2294753--2294965 Score: 347
Period size: 103 Copynumber: 2.1 Consensus size: 103
2294743 GGGTCTACGC
* *
2294753 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATATATTCTTTGAAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* *
2294818 CCTTGGCATATGTATATAATTCTTAAGGAATGATATGT
66 CCTTAGCATATATATATAATTCTTAAGGAATGATATGT
2294856 GGTCCTTCGGGACATATATATATTCTTTGAAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATATATTCTTTGAAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* *
2294921 -CTCTAGTATATATATATGATTCTTAAGGAATGATATGT
66 CCT-TAGCATATATATATAATTCTTAAGGAATGATATGT
*
2294959 AGTCCTT
1 GGTCCTT
2294966 ATGGACATTA
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
102 2 0.02
103 100 0.98
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.37
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATATATTCTTTGAAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCTTAGCATATATATATAATTCTTAAGGAATGATATGT
Found at i:2295015 original size:23 final size:23
Alignment explanation
Indices: 2294982--2295049 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
2294972 ATTATTATAT
2294982 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
2295005 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* * *
2295028 GGCACTTCAGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
2295050 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:2298061 original size:21 final size:21
Alignment explanation
Indices: 2298035--2298079 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2298025 GATTTATGGG
* *
2298035 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2298056 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2298077 CAA
1 CAA
2298080 ACGAACAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:2299944 original size:103 final size:104
Alignment explanation
Indices: 2299761--2299971 Score: 343
Period size: 103 Copynumber: 2.0 Consensus size: 104
2299751 GGTCTACGCG
* * *
2299761 GTCTTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACATATACTTGAT-
1 GTCTTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATC
* * *
2299825 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGTA
66 CCTAGACATATATATATGATTCTTAAGGAATGATATGTA
2299864 GTCTTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATC
1 GTCTTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATC
*
2299929 CCTAGTATATATATATATGATTCTTAAGGAATGATATGTA
66 CCTAG-ACATATATATATGATTCTTAAGGAATGATATGTA
2299969 GTC
1 GTC
2299972 CTTATGGACA
Statistics
Matches: 99, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
103 61 0.62
104 4 0.04
105 34 0.34
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (104 bp):
GTCTTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATC
CCTAGACATATATATATGATTCTTAAGGAATGATATGTA
Found at i:2300027 original size:23 final size:23
Alignment explanation
Indices: 2299991--2300058 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
2299981 ATTATTATAT
2299991 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* * **
2300014 GGCACTCCGATGCAATTCTACAT
1 GGCACTACGGTGCAATTCTACGC
* *
2300037 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
2300059 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:2300797 original size:26 final size:25
Alignment explanation
Indices: 2300751--2300799 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
2300741 CATCACATGT
* *
2300751 TCACATATCTCTTATTCTCATAGGA
1 TCACATAGCTCATATTCTCATAGGA
2300776 TCACATAGCTCATACTTCTCATAG
1 TCACATAGCTCATA-TTCTCATAG
2300800 ACATATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.29, C:0.27, G:0.08, T:0.37
Consensus pattern (25 bp):
TCACATAGCTCATATTCTCATAGGA
Found at i:2301888 original size:15 final size:15
Alignment explanation
Indices: 2301865--2301906 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
2301855 ATCTTAAATT
*
2301865 TAACAAGAAACTAAC
1 TAACCAGAAACTAAC
2301880 TAACCAGAAACTAAC
1 TAACCAGAAACTAAC
2301895 TAACCAGAAACT
1 TAACCAGAAACT
2301907 CACCTTTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.55, C:0.24, G:0.07, T:0.14
Consensus pattern (15 bp):
TAACCAGAAACTAAC
Found at i:2304189 original size:18 final size:18
Alignment explanation
Indices: 2304168--2304206 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2304158 AGAACAACAC
* * *
2304168 GAGGTACAAGCTCTACCA
1 GAGGAACAAGCACGACCA
2304186 GAGGAACAAGCACGACCA
1 GAGGAACAAGCACGACCA
2304204 GAG
1 GAG
2304207 CATCAAATGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.26, G:0.28, T:0.08
Consensus pattern (18 bp):
GAGGAACAAGCACGACCA
Found at i:2313169 original size:12 final size:13
Alignment explanation
Indices: 2313153--2313197 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
2313143 TTTAATATTT
2313153 ATCGGGTCGGGT-
1 ATCGGGTCGGGTA
*
2313165 ATCGGGCCGGGTA
1 ATCGGGTCGGGTA
* *
2313178 ATCGGGGCAGGTA
1 ATCGGGTCGGGTA
2313191 ATCGGGT
1 ATCGGGT
2313198 AATCGGGGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 11 0.39
13 17 0.61
ACGTcount: A:0.16, C:0.18, G:0.47, T:0.20
Consensus pattern (13 bp):
ATCGGGTCGGGTA
Found at i:2314040 original size:2 final size:2
Alignment explanation
Indices: 2314033--2314076 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2314023 TTGTGAAATC
2314033 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
2314075 AT
1 AT
2314077 GTGTGTGTGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2314081 original size:2 final size:2
Alignment explanation
Indices: 2314076--2314120 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2314066 TATATATATA
2314076 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2314118 TG T
1 TG T
2314121 ATTGGTTATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:2314879 original size:182 final size:180
Alignment explanation
Indices: 2314572--2315053 Score: 761
Period size: 182 Copynumber: 2.7 Consensus size: 180
2314562 GGGGTGTTAC
2314572 ACTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCGGTCTCTA
1 ACTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCGGTCTCTA
* *
2314637 TAGGACAAAATCGGTACAA-AGCGACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATA
66 AAGGACAAAACCGGTA-AAGAGCGACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATA
2314701 GACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGAT
130 GACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCG-C-ATAAAGTGTCGAT
* *
2314754 ACTTTATAACAATGTATCGATCCACAACGATATAATAGGTAAAAATATGAAAAAACCGGTCTCTA
1 ACTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCGGTCTCTA
* * * * *
2314819 AAGGAAAAAACCGGTATAGAGCGACTGAATATATTGAAAGTGTCGATACTTTAATATAAGTATCG
66 AAGGACAAAACCGGTAAAGAGCGACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATAG
2314884 ACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCATAAAGTGTCGAT
131 ACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCATAAAGTGTCGAT
* * * *
2314934 ACTTTATAA-AAAGTATCGATCCATAACGATATAACAGGTAAAAATATGACAAAACCGATCTCAA
1 ACTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCGGTCTCTA
* * * * *
2314998 AATGACAAAACCAGTAAAGCGCTACCGGATATATTGAAAGTGTTGATACTTTAATA
66 AAGGACAAAACCGGTAAAGAGCGACCGGATATATTGAAAGTGTCGATACTTTAATA
2315054 AGTACACGTA
Statistics
Matches: 275, Mismatches: 24, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
179 96 0.35
180 22 0.08
181 2 0.01
182 155 0.56
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (180 bp):
ACTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCGGTCTCTA
AAGGACAAAACCGGTAAAGAGCGACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATAG
ACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCATAAAGTGTCGAT
Found at i:2317449 original size:21 final size:21
Alignment explanation
Indices: 2317425--2317469 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
2317415 AAGACAATCA
*
2317425 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAAAGAAACTTGAG
*
2317446 AGAGTCGAAAAGACACTTGAG
1 AGAGTCGAAAAGAAACTTGAG
2317467 AGA
1 AGA
2317470 CATAAGGGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.11, G:0.31, T:0.13
Consensus pattern (21 bp):
AGAGTCGAAAAGAAACTTGAG
Found at i:2317615 original size:66 final size:66
Alignment explanation
Indices: 2317489--2317615 Score: 148
Period size: 66 Copynumber: 1.9 Consensus size: 66
2317479 GAAGTGGAAG
** * *
2317489 GAAAAAATAGATGGAGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGAACTTAAGATGGTGACGGG
1 GAAAAAATAGATGGAGTGGTGAAAGAAGTTGAGGAATTGAGGGGTAAACTTAAGAGGGTGACGGG
2317554 T
66 T
* * ** * *
2317555 GAAAAAATTA-ATGGAGTGGTGAAGGAGGTTGCTGAATTGAGGGGTAAACTTACGGGGGTGA
1 GAAAAAA-TAGATGGAGTGGTGAAAGAAGTTGAGGAATTGAGGGGTAAACTTAAGAGGGTGA
2317616 AGATGGTGGT
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
66 48 0.96
67 2 0.04
ACGTcount: A:0.33, C:0.04, G:0.40, T:0.23
Consensus pattern (66 bp):
GAAAAAATAGATGGAGTGGTGAAAGAAGTTGAGGAATTGAGGGGTAAACTTAAGAGGGTGACGGG
T
Found at i:2321456 original size:199 final size:200
Alignment explanation
Indices: 2321005--2321482 Score: 680
Period size: 200 Copynumber: 2.4 Consensus size: 200
2320995 ACGTAAATAT
*
2321005 GTGTCGATACATTT-TCTAAAAGTATCGA-CCCAAAAAACATCGAAACCAATAATTATAATGTAA
1 GTGTCGATACATTTAT-TAAAAGTATCGATCCC-AAAAACATCGAAACCGATAATTATAATGTAA
* * * *
2321068 TAGGTAAATTAACAATGTAACTGGTATAAATATACTGGTTAATTAGAAAACAGGTCAACATAATG
64 TAGGTAAATTTACAATGTAACTGGTATAAATATACCGGTTAATGAGAAAACAGGTCAACATAAAG
* *
2321133 TATCGACACTTGTGAAATTTGTGTCGATACTTATTGTCCAGAATAAATGTCCAAACTAGGTGCAC
129 TATCGACACTTGTGAAATTTGTGTCAATACTTATTGCCCAGAATAAATGTCCAAACTAGGTGCAC
2321198 ACATAAA
194 ACATAAA
2321205 GTGTCGATACATTTATTAAAAGTATCGATCCCAATAAA-ATCGAAACCGATAATTATAATGTAAT
1 GTGTCGATACATTTATTAAAAGTATCGATCCCAA-AAACATCGAAACCGATAATTATAATGTAAT
* * * * * *
2321269 ATGTAAATTTACAATGTAACTGGTATAAATATACCGATTTTATGAGAAAATAGGTTAGCATAAAG
65 AGGTAAATTTACAATGTAACTGGTATAAATATACCG-GTTAATGAGAAAACAGGTCAACATAAAG
* * *
2321334 TATCGACACTTGTTAAATTTGTGTCAATACATT-TTGCCCATAATAAATG-CCAAAC-GGGTGCA
129 TATCGACACTTGTGAAATTTGTGTCAATAC-TTATTGCCCAGAATAAATGTCCAAACTAGGTGCA
*
2321396 CGCATAAA
193 CACATAAA
* * * *
2321404 GTGTCGATACATTTATTAAAAGTATCGATCTCAAAAACATCGAAATCGATAATTACAATGTGATA
1 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
2321469 GGTAAATTTACAAT
66 GGTAAATTTACAAT
2321483 ATACCTAATA
Statistics
Matches: 250, Mismatches: 22, Indels: 13
0.88 0.08 0.05
Matches are distributed among these distances:
198 3 0.01
199 83 0.33
200 92 0.37
201 70 0.28
202 2 0.01
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (200 bp):
GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
GGTAAATTTACAATGTAACTGGTATAAATATACCGGTTAATGAGAAAACAGGTCAACATAAAGTA
TCGACACTTGTGAAATTTGTGTCAATACTTATTGCCCAGAATAAATGTCCAAACTAGGTGCACAC
ATAAA
Found at i:2321904 original size:23 final size:23
Alignment explanation
Indices: 2321854--2321915 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
2321844 TTCTGATTAA
*
2321854 ATACCTATTTTATTATACAAGCG
1 ATACCTATTATATTATACAAGCG
* * **
2321877 CTACCTATTATATTATATAAGTT
1 ATACCTATTATATTATACAAGCG
*
2321900 ATACCTAATATATTAT
1 ATACCTATTATATTAT
2321916 TGTACTTGAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.37, C:0.15, G:0.05, T:0.44
Consensus pattern (23 bp):
ATACCTATTATATTATACAAGCG
Found at i:2322723 original size:34 final size:34
Alignment explanation
Indices: 2322678--2322762 Score: 91
Period size: 34 Copynumber: 2.4 Consensus size: 34
2322668 AGTATTTTTT
* * *
2322678 TAAATAGTTATTATTTT-TTATATTAATATATTATG
1 TAAATA-TTATTATTTTATTAAAATAATAT-TTATA
*
2322713 TAAATATTATTTTTTTATTAAAATAATATTTATA
1 TAAATATTATTATTTTATTAAAATAATATTTATA
*
2322747 TAATTATTATTTATTT
1 TAAATATTA-TTATTT
2322763 AGAATTATTA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
34 21 0.50
35 21 0.50
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (34 bp):
TAAATATTATTATTTTATTAAAATAATATTTATA
Found at i:2322724 original size:31 final size:31
Alignment explanation
Indices: 2322686--2322760 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
2322676 TTTAAATAGT
* *
2322686 TATTATTTTTTATATTAATATATTATGTAAA
1 TATTATTTTTTATATTAAAATAATATGTAAA
* *
2322717 TATTATTTTTT-TATTAAAATAATATTTATA
1 TATTATTTTTTATATTAAAATAATATGTAAA
*
2322747 TAATTATTATTTAT
1 T-ATTATTTTTTAT
2322761 TTAGAATTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 16 0.43
31 20 0.54
32 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (31 bp):
TATTATTTTTTATATTAAAATAATATGTAAA
Found at i:2322923 original size:17 final size:17
Alignment explanation
Indices: 2322901--2322954 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
2322891 AATGTTAATA
2322901 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
2322918 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
2322935 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
2322952 TTT
1 TTT
2322955 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:2324512 original size:21 final size:21
Alignment explanation
Indices: 2324482--2324529 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
2324472 GCAGGGGTAC
* *
2324482 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
2324503 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
2324524 ATGCCA
1 ATGCCA
2324530 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:2324559 original size:21 final size:21
Alignment explanation
Indices: 2324533--2324626 Score: 120
Period size: 21 Copynumber: 4.5 Consensus size: 21
2324523 TATGCCATCT
* * *
2324533 CCGCAGGGATACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
2324554 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
2324575 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
2324596 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
2324617 CCGCAGGGTT
1 CCGCAGGGTT
2324627 TTATACCATA
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
20 2 0.03
21 64 0.94
22 2 0.03
ACGTcount: A:0.19, C:0.35, G:0.27, T:0.19
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:2325207 original size:33 final size:34
Alignment explanation
Indices: 2325170--2325238 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 34
2325160 ATATTATTCG
*
2325170 AAATTTAAAATAAAAATAATATTATTC-AAATTT
1 AAATTTAAAATAAAAATAATAGTATTCAAAATTT
* *
2325203 AAATTTAAAATATAAATTATAGTATTCAAAATTT
1 AAATTTAAAATAAAAATAATAGTATTCAAAATTT
2325237 AA
1 AA
2325239 CATTAAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 24 0.75
34 8 0.25
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (34 bp):
AAATTTAAAATAAAAATAATAGTATTCAAAATTT
Found at i:2325234 original size:28 final size:28
Alignment explanation
Indices: 2325145--2325247 Score: 100
Period size: 28 Copynumber: 3.5 Consensus size: 28
2325135 GATAAATGTT
* *
2325145 TTTAAAATACAAATTATATTATTCGAAA
1 TTTAAAATATAAATTATATTATTCAAAA
* *
2325173 TTTAAAATAAAAATAATATTATTCAAATTTAAA
1 TTTAAAATATAAATTATATTATTC--A---AAA
*
2325206 TTTAAAATATAAATTATAGTATTCAAAA
1 TTTAAAATATAAATTATATTATTCAAAA
*
2325234 TTTAACAT-TAAATT
1 TTTAAAATATAAATT
2325248 TCAACTTAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 11
0.78 0.09 0.14
Matches are distributed among these distances:
27 6 0.10
28 32 0.51
31 1 0.02
33 24 0.38
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (28 bp):
TTTAAAATATAAATTATATTATTCAAAA
Found at i:2325938 original size:127 final size:128
Alignment explanation
Indices: 2325639--2326136 Score: 957
Period size: 127 Copynumber: 3.9 Consensus size: 128
2325629 TTACCTGATT
2325639 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
2325704 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
2325767 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
2325832 TGACGAAATAATGGAAGGCGC-CCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
2325894 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
2325959 TGACGAAATAATGGAAGGCGCGCCCCCGAGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
2326022 TACTGATATATCTAGTGT-CCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
2326086 TGACGAAATAATGGAAGGCGCG-CCCCGGGAACGCGCCTTCATGTGAATAGT
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
2326137 ACTCCGATTA
Statistics
Matches: 366, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
126 28 0.08
127 194 0.53
128 144 0.39
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:2326218 original size:8 final size:8
Alignment explanation
Indices: 2326205--2326245 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
2326195 TCACAATCTT
2326205 TCAAATTC
1 TCAAATTC
2326213 TCAAATTC
1 TCAAATTC
* *
2326221 CCAAACTC
1 TCAAATTC
2326229 T-AAATTC
1 TCAAATTC
2326236 TCAAATTC
1 TCAAATTC
2326244 TC
1 TC
2326246 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:2334305 original size:54 final size:54
Alignment explanation
Indices: 2334238--2334342 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 54
2334228 ATCATATTCG
* * *
2334238 TATGTCCTCGGTGGCGGTGACCGGGAGTCATCTCGTCCACCATATCTATCATCA
1 TATGGCCTCGGTGGCGGTGACCGGAAATCATCTCGTCCACCATATCTATCATCA
* ** * *
2334292 TATGGCCTCGGTGGTGGTGATTGGAAATTATCTCGTCCACCGTATCTATCA
1 TATGGCCTCGGTGGCGGTGACCGGAAATCATCTCGTCCACCATATCTATCA
2334343 ACATTACCCC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.30
Consensus pattern (54 bp):
TATGGCCTCGGTGGCGGTGACCGGAAATCATCTCGTCCACCATATCTATCATCA
Found at i:2337597 original size:120 final size:120
Alignment explanation
Indices: 2337384--2337623 Score: 480
Period size: 120 Copynumber: 2.0 Consensus size: 120
2337374 AGGAGTGGTT
2337384 GGAGTAGAAAGGATTAGAAAGGATTAGAGATTTGTGTACCATAGGCTTAGGAATTTACGGGTTAA
1 GGAGTAGAAAGGATTAGAAAGGATTAGAGATTTGTGTACCATAGGCTTAGGAATTTACGGGTTAA
2337449 GGAGATTTATGTATTTAAGTTTAGGGATTTTGGGGATTGGGGCAACGATGAGAGA
66 GGAGATTTATGTATTTAAGTTTAGGGATTTTGGGGATTGGGGCAACGATGAGAGA
2337504 GGAGTAGAAAGGATTAGAAAGGATTAGAGATTTGTGTACCATAGGCTTAGGAATTTACGGGTTAA
1 GGAGTAGAAAGGATTAGAAAGGATTAGAGATTTGTGTACCATAGGCTTAGGAATTTACGGGTTAA
2337569 GGAGATTTATGTATTTAAGTTTAGGGATTTTGGGGATTGGGGCAACGATGAGAGA
66 GGAGATTTATGTATTTAAGTTTAGGGATTTTGGGGATTGGGGCAACGATGAGAGA
2337624 ATGACCAATT
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 120 1.00
ACGTcount: A:0.32, C:0.05, G:0.33, T:0.30
Consensus pattern (120 bp):
GGAGTAGAAAGGATTAGAAAGGATTAGAGATTTGTGTACCATAGGCTTAGGAATTTACGGGTTAA
GGAGATTTATGTATTTAAGTTTAGGGATTTTGGGGATTGGGGCAACGATGAGAGA
Found at i:2339150 original size:21 final size:21
Alignment explanation
Indices: 2339124--2339166 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2339114 TTTATGGGTT
* *
2339124 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
2339145 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
2339166 A
1 A
2339167 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:2339242 original size:67 final size:67
Alignment explanation
Indices: 2339146--2339296 Score: 191
Period size: 67 Copynumber: 2.3 Consensus size: 67
2339136 ACCCATTCAA
* * *
2339146 GGGGAACCGATACCCCTTCAACGAATATGATTTCCAG-TATGC-TAGAGGGGAATCGGTACCCCC
1 GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAT-TGCTTA-AGGGGAATCGATA-CCCC
2339209 A-GGG
63 AGGGG
* **
2339213 GGGGAACCGATACCCCCTCATCGTTTATGAATTCCAGATTGCTTAAGGGGAATCGATACCCCAGG
1 GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGATTGCTTAAGGGGAATCGATACCCCAGG
2339278 GG
66 GG
*
2339280 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
2339297 ATGAGAAAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
66 5 0.07
67 66 0.89
68 3 0.04
ACGTcount: A:0.25, C:0.27, G:0.28, T:0.20
Consensus pattern (67 bp):
GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGATTGCTTAAGGGGAATCGATACCCCAGG
GG
Found at i:2339636 original size:29 final size:29
Alignment explanation
Indices: 2339602--2339673 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
2339592 CATATTATGA
**
2339602 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
* *
2339631 TACATGACATGAATTCATCTTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
2339660 TACATGACATGAAT
1 TACATGACATGAAT
2339674 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:2339751 original size:29 final size:32
Alignment explanation
Indices: 2339687--2339751 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 32
2339677 CAGAAAAGTT
*
2339687 CTATGCACTATGTGATAAAAGTATGTAAATGA
1 CTATGCACTATGTGATAAAAGTATGGAAATGA
* *
2339719 -TATGC-CTATGTG-TTAAGGTATGGAAAT-A
1 CTATGCACTATGTGATAAAAGTATGGAAATGA
2339747 CTATG
1 CTATG
2339752 TCTACGCGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
28 1 0.03
29 16 0.55
30 7 0.24
31 5 0.17
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.34
Consensus pattern (32 bp):
CTATGCACTATGTGATAAAAGTATGGAAATGA
Found at i:2346037 original size:21 final size:21
Alignment explanation
Indices: 2346011--2346053 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2346001 TTTATGGGTT
* *
2346011 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
2346032 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
2346053 A
1 A
2346054 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:2346114 original size:66 final size:66
Alignment explanation
Indices: 2346011--2346180 Score: 195
Period size: 66 Copynumber: 2.6 Consensus size: 66
2346001 TTTATGGGTT
* * * *
2346011 AGGGGAATCGGTACCCATTCA-AGGGGAACCGATACCCCTTCAACGAATATGATTTCCAG-TATG
1 AGGGGAATCGGTACCC--CCAGGGGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAT-TG
2346074 C-TA
63 CTTA
* **
2346077 GAGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCATCGTTTATGAATTCCAGATTGCT
1 -AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCAACGAATATGAATTCCAGATTGCT
2346142 TA
65 TA
* *
2346144 AGGGGAATCGATA-CCCCAGGGGGGAACCGATTCCCCC
1 AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCC
2346181 ATGAGAAAAA
Statistics
Matches: 91, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
65 25 0.27
66 47 0.52
67 19 0.21
ACGTcount: A:0.26, C:0.27, G:0.26, T:0.20
Consensus pattern (66 bp):
AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCAACGAATATGAATTCCAGATTGCTT
A
Found at i:2346519 original size:29 final size:29
Alignment explanation
Indices: 2346485--2346556 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
2346475 CATATTATGA
**
2346485 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
* *
2346514 TACATGACATGAATTCATCTTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
2346543 TACATGACATGAAT
1 TACATGACATGAAT
2346557 GCAGAAAAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:2346609 original size:30 final size:31
Alignment explanation
Indices: 2346569--2346627 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
2346559 AGAAAAGTTC
*
2346569 TATGCACTATGTGATAAAAGTATGTAAATGA
1 TATGCACTATGTGATAAAAGTATGGAAATGA
* *
2346600 TATGC-CTATGTGTTAAAGGTATGGAAAT
1 TATGCACTATGTGATAAAAGTATGGAAAT
2346628 ACTATGTCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (31 bp):
TATGCACTATGTGATAAAAGTATGGAAATGA
Found at i:2346921 original size:22 final size:22
Alignment explanation
Indices: 2346847--2346913 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
2346837 TTATGGACAA
2346847 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
2346869 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
2346891 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
2346913 A
1 A
2346914 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:2348583 original size:25 final size:25
Alignment explanation
Indices: 2348555--2348602 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
2348545 ATAACATTTT
* *
2348555 TTATTATAATGACGAAAAGTAATAC
1 TTATTATAATGACAAAAAATAATAC
2348580 TTATTATAATGACAAAAAATAAT
1 TTATTATAATGACAAAAAATAAT
2348603 GATACTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.33
Consensus pattern (25 bp):
TTATTATAATGACAAAAAATAATAC
Found at i:2348744 original size:27 final size:27
Alignment explanation
Indices: 2348699--2348750 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
2348689 TGTTGACGCT
* * *
2348699 ATATTTTAATTAATATGATTAATATCA
1 ATATTTGAATGAATATGATGAATATCA
*
2348726 ATATTTGAATGAATGTGATGAATAT
1 ATATTTGAATGAATATGATGAATAT
2348751 TAATTCAACT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.42, C:0.02, G:0.12, T:0.44
Consensus pattern (27 bp):
ATATTTGAATGAATATGATGAATATCA
Found at i:2350701 original size:14 final size:14
Alignment explanation
Indices: 2350682--2350716 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
2350672 GAGGAGGGAC
2350682 CACAGCTGGACATG
1 CACAGCTGGACATG
2350696 CACAGCTGGACATG
1 CACAGCTGGACATG
2350710 CACAGCT
1 CACAGCT
2350717 TCGCTGCTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (14 bp):
CACAGCTGGACATG
Found at i:2352532 original size:15 final size:16
Alignment explanation
Indices: 2352449--2352546 Score: 85
Period size: 16 Copynumber: 6.2 Consensus size: 16
2352439 AATTTTTGTT
* * *
2352449 GAACCGAAAACCATCC
1 GAACCGAAATCAACCC
*
2352465 GAACCGAAAGT-AACAC
1 GAACCGAAA-TCAACCC
*
2352481 GAACC-AATAGCAACCC
1 GAACCGAA-ATCAACCC
*
2352497 GAACCAAAATCAACCC
1 GAACCGAAATCAACCC
2352513 GAACCGAAATC-ACCC
1 GAACCGAAATCAACCC
* *
2352528 AAACCGAAAACAACCC
1 GAACCGAAATCAACCC
2352544 GAA
1 GAA
2352547 TTTAATTTAC
Statistics
Matches: 66, Mismatches: 11, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
15 15 0.23
16 49 0.74
17 2 0.03
ACGTcount: A:0.48, C:0.35, G:0.12, T:0.05
Consensus pattern (16 bp):
GAACCGAAATCAACCC
Found at i:2355781 original size:3 final size:3
Alignment explanation
Indices: 2355773--2355842 Score: 117
Period size: 3 Copynumber: 23.7 Consensus size: 3
2355763 TGCATTGATC
2355773 TCT TCT TCT TCT TCT TCT TC- TCT CTCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT -TCT TCT TCT TCT TCT TCT TCT
2355818 TCT TCT TC- TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
2355843 CTTTCCTGTT
Statistics
Matches: 64, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.06
3 57 0.89
4 3 0.05
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
TCT
Found at i:2359138 original size:71 final size:71
Alignment explanation
Indices: 2359022--2359165 Score: 288
Period size: 71 Copynumber: 2.0 Consensus size: 71
2359012 TACGTACTCC
2359022 AATGAACATCATCTAGTTTCCTTTTGCAAAATTATACGAAATGTAAAAGGTAATTACAAATTAAA
1 AATGAACATCATCTAGTTTCCTTTTGCAAAATTATACGAAATGTAAAAGGTAATTACAAATTAAA
2359087 AGTAGA
66 AGTAGA
2359093 AATGAACATCATCTAGTTTCCTTTTGCAAAATTATACGAAATGTAAAAGGTAATTACAAATTAAA
1 AATGAACATCATCTAGTTTCCTTTTGCAAAATTATACGAAATGTAAAAGGTAATTACAAATTAAA
2359158 AGTAGA
66 AGTAGA
2359164 AA
1 AA
2359166 ATAGCTTAAT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 73 1.00
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.31
Consensus pattern (71 bp):
AATGAACATCATCTAGTTTCCTTTTGCAAAATTATACGAAATGTAAAAGGTAATTACAAATTAAA
AGTAGA
Found at i:2363994 original size:17 final size:17
Alignment explanation
Indices: 2363972--2364006 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2363962 TTCATGTTAT
2363972 TGTTTTA-TTTTCTATCA
1 TGTTTTAGTTTT-TATCA
2363989 TGTTTTAGTTTTTATCA
1 TGTTTTAGTTTTTATCA
2364006 T
1 T
2364007 AATTCTCTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.17, C:0.09, G:0.09, T:0.66
Consensus pattern (17 bp):
TGTTTTAGTTTTTATCA
Found at i:2379209 original size:20 final size:20
Alignment explanation
Indices: 2379172--2379228 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
2379162 AATCATATTC
*
2379172 CTGGTAATCTT-TATTCCCA
1 CTGGTAATCTTACATTCCCA
2379191 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
2379211 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
2379229 GTGAACCAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
19 11 0.31
20 25 0.69
ACGTcount: A:0.23, C:0.28, G:0.11, T:0.39
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:2380385 original size:151 final size:154
Alignment explanation
Indices: 2380156--2380460 Score: 426
Period size: 158 Copynumber: 2.0 Consensus size: 154
2380146 ATTCGTCCTG
* * *
2380156 TGATAGATAATATATTGTGAGCATCGAACGTGTATTATTATAAGAAGTCACGTCAGTATTATTAA
1 TGATAGATAATATATTGTGAGCATCGAACGTGTATTATTATAAAAAGTCACATCAATATTATTAA
* *
2380221 AAGTTAAATTTTAATC-TAC-TTCATTT-AAA-AATTTTATCATTTCT-TGTTGATGGTCAAAA-
66 AAGTTAAACTTTAATCATACTTTCATTTAAAATAATTTTATAATTTCTAT-TTGAT-GTCAAAAT
2380280 TTAGGTAAAAATTAAGAACTATATGT
129 TTAGGTAAAAATTAAGAACTATATGT
2380306 TGATAGATAATATA-TGTGAGCATCGAACGTGTATTATTATACAAAATGTCACATCAATATTATT
1 TGATAGATAATATATTGTGAGCATCGAACGTGTATTATTATA-AAAA-GTCACATCAATATTATT
* *
2380370 AAAAGTTAAACTTTAATCAATACTTTTATTTAAAAAATAATTTTATAATTTCTATTTTATGTCAA
64 AAAAGTTAAACTTTAATC-ATACTTTCATTT--AAAATAATTTTATAATTTCTATTTGATGTCAA
*
2380435 AATTTAGGTAAAAATTAATAACTATA
126 AATTTAGGTAAAAATTAAGAACTATA
2380461 AAATATAATA
Statistics
Matches: 136, Mismatches: 8, Indels: 14
0.86 0.05 0.09
Matches are distributed among these distances:
149 27 0.20
150 17 0.12
151 32 0.24
153 3 0.02
154 6 0.04
157 10 0.07
158 40 0.29
159 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.40
Consensus pattern (154 bp):
TGATAGATAATATATTGTGAGCATCGAACGTGTATTATTATAAAAAGTCACATCAATATTATTAA
AAGTTAAACTTTAATCATACTTTCATTTAAAATAATTTTATAATTTCTATTTGATGTCAAAATTT
AGGTAAAAATTAAGAACTATATGT
Done.