Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004660.1 Hibiscus syriacus cultivar Beakdansim tig00010451_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: 84323
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:889 original size:200 final size:198
Alignment explanation
Indices: 540--1246 Score: 883
Period size: 199 Copynumber: 3.6 Consensus size: 198
530 GTAAATAGAT
* * ** *
540 GTGTCGATACATTTTATAAAAGTATCGACCCCAAAAACATCGAAACTAATGATTATAATGTAATA
1 GTGTCGATACA-TTTAAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* * *
605 GGTAAATTAACAATATAACCGGTATAAAAATACCGG-TTAATTACAAAA-C-ATGTCAACATAAT
65 GGTAAATTTACAATATAACCGGTATAAATATACCGGTTTAATTAGAAAAGCGA--TCAACATAAT
* **
667 GTATCGACACTTGTGGAATTTGTGTCGATACTTTTTGTCCAGAATGAATACCCAACCGAGGTGCA
128 GTATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAAT-CCCAA-CGAGGTGCA
732 CGCATAAA
191 CGCATAAA
* *
740 GTGTCGATATATTTATAAAAAGTATCCATCCCAAAAACATCGAAA-CGATAATTATAATGTAATA
1 GTGTCGATACATTTA-AAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
*
804 GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTAATTAGAAAAGCGATCAACATAATGT
65 GGTAAATTTACAATATAACCGGTATAAATATACCGGTTTAATTAGAAAAGCGATCAACATAATGT
* * * * * *
869 ATCGATACTTTTTAAATTTGTGT-TATACTTGTTGTCCAGAATCAATGCCCAAACGAGGTGTATG
130 ATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAAT-CCC-AACGAGGTGCACG
933 CATAAA
193 CATAAA
** * *
939 GTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCAAAACCGATAATTATAATGTAGTAG
1 GTGTCGATACATTTAAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAG
* * * * * * *
1004 GTATATTTGCAATGTAACCGGTATAAATATACTGATTTTATGAGAGAATAG-G-TCAACATAATG
66 GTAAATTTACAATATAACCGGTATAAATATACCGGTTTAATTAGA-AA-AGCGATCAACATAATG
* *
1067 TATCGACACTTTTTAAATTTGTGTCGATACTTTTT-TCCAGAATGAATGCCAACGAGGTGCACAC
129 TATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATCCCAACGAGGTGCACGC
1131 ATAAA
194 ATAAA
* **
1136 GTGTCGATATATTTAAAATTGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA-
1 GTGTCGATACATTTAAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAG
* * * * * *
1200 GTAAATTTGCATTATTACCGGTATAAATAAATCGGTTTAGTTAGAAA
66 GTAAATTTACAATATAACCGGTATAAATATACCGGTTTAATTAGAAA
1247 TAGGTCAATA
Statistics
Matches: 443, Mismatches: 55, Indels: 23
0.85 0.11 0.04
Matches are distributed among these distances:
195 2 0.00
196 34 0.08
197 77 0.17
198 27 0.06
199 208 0.47
200 91 0.21
201 3 0.01
202 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (198 bp):
GTGTCGATACATTTAAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAG
GTAAATTTACAATATAACCGGTATAAATATACCGGTTTAATTAGAAAAGCGATCAACATAATGTA
TCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATCCCAACGAGGTGCACGCAT
AAA
Found at i:1387 original size:23 final size:23
Alignment explanation
Indices: 1337--1381 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1327 TGCCTATTTT
* *
1337 ATTATATAAACGCTACCTATTAC
1 ATTATATAAACACTACCTAATAC
*
1360 ATTATATAAGCACTACCTAATA
1 ATTATATAAACACTACCTAATA
1382 TGTTATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.42, C:0.20, G:0.04, T:0.33
Consensus pattern (23 bp):
ATTATATAAACACTACCTAATAC
Found at i:2804 original size:23 final size:26
Alignment explanation
Indices: 2760--2809 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
2750 TGTGAAATCC
2760 AACCTAAAAAAAGATAACAAAAATGT
1 AACCTAAAAAAAGATAACAAAAATGT
*
2786 AACC-AAAAATAGA-AA-AAAAATGT
1 AACCTAAAAAAAGATAACAAAAATGT
2809 A
1 A
2810 TAAACGGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 9 0.39
24 2 0.09
25 8 0.35
26 4 0.17
ACGTcount: A:0.68, C:0.10, G:0.08, T:0.14
Consensus pattern (26 bp):
AACCTAAAAAAAGATAACAAAAATGT
Found at i:6920 original size:20 final size:20
Alignment explanation
Indices: 6895--6967 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
6885 TAATACAAAA
*
6895 TCGCAACGAGATACTGACTT
1 TCGCAACGAGATTCTGACTT
6915 TCGCAACGCA-ATTCTGACTT
1 TCGCAACG-AGATTCTGACTT
*
6935 TCGCAACGCGATTCTGACTT
1 TCGCAACGAGATTCTGACTT
*
6955 TCGCAACGCGATT
1 TCGCAACGAGATT
6968 TATAAAGCGC
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
20 48 0.98
21 1 0.02
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (20 bp):
TCGCAACGAGATTCTGACTT
Found at i:7536 original size:19 final size:19
Alignment explanation
Indices: 7483--7549 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
7473 TTCGAGAATG
7483 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
** * *
7503 ACTATCACAAAGCGAAATA
1 AAAATCGCAACGCGAAATA
**
7522 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
7541 AAAATCGCA
1 AAAATCGCA
7550 TTGCGATTTT
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
19 28 0.76
20 9 0.24
ACGTcount: A:0.51, C:0.24, G:0.15, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:7567 original size:19 final size:19
Alignment explanation
Indices: 7545--7690 Score: 114
Period size: 19 Copynumber: 8.1 Consensus size: 19
7535 GAAACCAAAA
*
7545 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
7564 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
7583 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
7597 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
7616 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
7630 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
7649 TCCACGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
7669 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
7689 TC
1 TC
7691 AACCAAAAGA
Statistics
Matches: 103, Mismatches: 12, Indels: 24
0.74 0.09 0.17
Matches are distributed among these distances:
14 20 0.19
16 4 0.04
17 5 0.05
19 42 0.41
20 31 0.30
21 1 0.01
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:7605 original size:14 final size:14
Alignment explanation
Indices: 7586--7641 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
7576 TTTCATTTCG
7586 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
7600 CGTTGCGATAGTCATTTCG
1 CGTTGCGAT--TC---TCT
7619 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
7633 CGTTGCGAT
1 CGTTGCGAT
7642 AGTCATTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 20 0.57
16 2 0.06
17 2 0.06
19 11 0.31
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:7615 original size:33 final size:33
Alignment explanation
Indices: 7567--7665 Score: 162
Period size: 33 Copynumber: 3.0 Consensus size: 33
7557 TTTCATTTCG
**
7567 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
7600 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
*
7633 CGTTGCGATAGTCATTTCCACGTTGCGATTCTC
1 CGTTGCGATAGTCATTT-CGCGTTGCGATTCTC
7666 ATTATCTCGT
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
33 48 0.77
34 14 0.23
ACGTcount: A:0.12, C:0.25, G:0.22, T:0.40
Consensus pattern (33 bp):
CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
Found at i:7667 original size:20 final size:20
Alignment explanation
Indices: 7633--7690 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
7623 GCGATTCTCT
**
7633 CGTTGCGATAGTCATTTCCA
1 CGTTGCGATTCTCATTTCCA
*
7653 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCA
*
7673 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
7691 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.16, C:0.24, G:0.17, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCA
Found at i:9858 original size:21 final size:21
Alignment explanation
Indices: 9834--9900 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
9824 TCATTCCTCG
9834 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
9855 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
9876 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
9897 AGAG
1 AGAG
9901 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:9858 original size:42 final size:42
Alignment explanation
Indices: 9807--9900 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 42
9797 CCACTTCTAT
* *
9807 CGTTGAAGAGGCCCCTATCATTCCTCG-AGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCACTATCA-TCCTCGAAGAGGT-CCCTCCCAC
* * *
9849 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCAC
*
9891 CATTCAAGAG
1 CGTTCAAGAG
9901 CCCGATTCAC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
41 4 0.09
42 38 0.86
43 2 0.05
ACGTcount: A:0.22, C:0.35, G:0.21, T:0.21
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCAC
Found at i:11277 original size:14 final size:14
Alignment explanation
Indices: 11258--11293 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
11248 ATTATTTAAT
11258 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
11272 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
11286 TGATTTGT
1 TGATTTGT
11294 TTAATTGATG
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:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:11423 original size:19 final size:19
Alignment explanation
Indices: 11399--11464 Score: 105
Period size: 19 Copynumber: 3.5 Consensus size: 19
11389 AAAATGTACT
* *
11399 ATCGCAATGCGAAATAAAA
1 ATCGCAACGCGAAATGAAA
11418 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
11437 ATCGCAAGGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
11456 ATCGCAACG
1 ATCGCAACG
11465 AGAGAATCGC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.47, C:0.20, G:0.21, T:0.12
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:11482 original size:33 final size:36
Alignment explanation
Indices: 11399--11493 Score: 97
Period size: 33 Copynumber: 2.7 Consensus size: 36
11389 AAAATGTACT
*
11399 ATCGCAATGCGAAATAAAAATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATAAAAATCGCAAC-CG-AATGAAA
* * *
11437 ATCGCAAGGCGAAATGAAAATCGCAA-CG-A-GAGA
1 ATCGCAACGCGAAATAAAAATCGCAACCGAATGAAA
* *
11470 ATCGCAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATAAAAATCGC
11494 GTTGCGATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
33 24 0.47
34 1 0.02
36 2 0.04
38 24 0.47
ACGTcount: A:0.45, C:0.20, G:0.21, T:0.14
Consensus pattern (36 bp):
ATCGCAACGCGAAATAAAAATCGCAACCGAATGAAA
Found at i:11511 original size:19 final size:19
Alignment explanation
Indices: 11489--11639 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
11479 CGAAATTAAA
11489 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
11508 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
11523 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
11541 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
11555 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
11574 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
11589 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
11607 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
11626 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
11640 AGACATTAAG
Statistics
Matches: 95, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 28 0.29
16 6 0.06
17 6 0.06
19 45 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:11535 original size:33 final size:32
Alignment explanation
Indices: 11493--11619 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
11483 ATTAAATTCG
11493 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
11526 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
11559 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
11592 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
11620 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:11571 original size:66 final size:66
Alignment explanation
Indices: 11486--11618 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
11476 ACGCGAAATT
*
11486 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
11551 G
66 G
*
11552 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
11617 G
66 G
11618 A
1 A
11619 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:13933 original size:12 final size:12
Alignment explanation
Indices: 13916--13942 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
13906 CGGGGACTTT
13916 TTCTTTTTCTTC
1 TTCTTTTTCTTC
13928 TTCTTTTTCTTC
1 TTCTTTTTCTTC
13940 TTC
1 TTC
13943 AGGATTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTCTTTTTCTTC
Found at i:14151 original size:24 final size:24
Alignment explanation
Indices: 14116--14170 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
14106 TCTGAAACAT
14116 GATCAAAATCCGAGTATTGACCAA
1 GATCAAAATCCGAGTATTGACCAA
* * *
14140 TATCAAAGTCCGGGTATTGACCAA
1 GATCAAAATCCGAGTATTGACCAA
14164 GATCAAA
1 GATCAAA
14171 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Consensus pattern (24 bp):
GATCAAAATCCGAGTATTGACCAA
Found at i:14980 original size:20 final size:21
Alignment explanation
Indices: 14955--15006 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
14945 TTTTCCTAAT
*
14955 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
14975 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
14996 TCGCAATGCGA
1 TCGCAATGCGA
15007 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:15020 original size:20 final size:20
Alignment explanation
Indices: 14995--15052 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
14985 AATTTGGAAA
* *
14995 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
*
15015 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATACTGACT
* *
15035 TTCGCAACGAGATTCTGA
1 ATCGCAACGAGATACTGA
15053 AAATCGCAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:15059 original size:20 final size:20
Alignment explanation
Indices: 14991--15061 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
14981 TGCGAATTTG
* * *
14991 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATTCT
**
15011 GACTATCGCAACGAGATTCT
1 GAAAATCGCAACGAGATTCT
***
15031 GACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATTCT
15051 GAAAATCGCAA
1 GAAAATCGCAA
15062 TCATCTTCAA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (20 bp):
GAAAATCGCAACGAGATTCT
Found at i:15370 original size:20 final size:20
Alignment explanation
Indices: 15279--15362 Score: 98
Period size: 20 Copynumber: 4.2 Consensus size: 20
15269 GGGGAAATCA
15279 CAACGCGAAAATGGCTATCG
1 CAACGCGAAAATGGCTATCG
*
15299 CAACGCGAAACTGGCTATCG
1 CAACGCGAAAATGGCTATCG
** ***
15319 CAATTCG-AAATGAAAAATCG
1 CAACGCGAAAATG-GCTATCG
15339 CAACGCGAAAATGGCTATCG
1 CAACGCGAAAATGGCTATCG
15359 CAAC
1 CAAC
15363 TAGAAAATCG
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
19 4 0.08
20 41 0.82
21 5 0.10
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.15
Consensus pattern (20 bp):
CAACGCGAAAATGGCTATCG
Found at i:15413 original size:33 final size:33
Alignment explanation
Indices: 15376--15446 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
15366 AAAATCGCAA
*
15376 TGCGAAATGAAAATCGCATTGTGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
15409 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
15442 TGCGA
1 TGCGA
15447 TAGTCAGTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.41
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:15417 original size:14 final size:14
Alignment explanation
Indices: 15398--15447 Score: 55
Period size: 14 Copynumber: 3.2 Consensus size: 14
15388 ATCGCATTGT
15398 GATTTTCTCGTTGC
1 GATTTTCTCGTTGC
15412 GATTTTCATTTCGCATTGC
1 GATTTTC---TCG--TTGC
15431 GATTTTCTCGTTGC
1 GATTTTCTCGTTGC
15445 GAT
1 GAT
15448 AGTCAGTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
14 14 0.45
16 3 0.10
17 3 0.10
19 11 0.35
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
GATTTTCTCGTTGC
Found at i:15593 original size:14 final size:14
Alignment explanation
Indices: 15574--15610 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
15564 CATCAATTAA
15574 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
15588 ACAAATCATCTTTT
1 ACAAATCAACATTT
15602 ACAAATCAA
1 ACAAATCAA
15611 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:17074 original size:21 final size:20
Alignment explanation
Indices: 17050--17109 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
17040 AACGGTGAGG
17050 GGGGACTCTTGAGGGA-GGATA
1 GGGGACTCTTGAGGGATGG--A
* **
17071 GGGGCCTCTTGAACGATTGGA
1 GGGGACTCTTGAGGGA-TGGA
17092 GGGGACTCTTGAGGGATG
1 GGGGACTCTTGAGGGATG
17110 ACAGGTGAGT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
23 2 0.06
ACGTcount: A:0.20, C:0.13, G:0.45, T:0.22
Consensus pattern (20 bp):
GGGGACTCTTGAGGGATGGA
Found at i:17490 original size:20 final size:20
Alignment explanation
Indices: 17475--17578 Score: 89
Period size: 20 Copynumber: 5.6 Consensus size: 20
17465 CACGAAACTT
17475 AAAATCGCAACGCGAAAATG
1 AAAATCGCAACGCGAAAATG
**
17495 ACTATCGCAACGCGAAAATG
1 AAAATCGCAACGCGAAAATG
*** *
17515 GCTATCGCAATGCG-AAATG
1 AAAATCGCAACGCGAAAATG
17534 AAAATCGCAA--C--AAA--
1 AAAATCGCAACGCGAAAATG
*
17548 AAAATCGCAATGCG-AAATG
1 AAAATCGCAACGCGAAAATG
17567 AAAATCGCAACG
1 AAAATCGCAACG
17579 ACAAAATCGC
Statistics
Matches: 71, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
14 10 0.14
16 4 0.06
17 4 0.06
19 23 0.32
20 30 0.42
ACGTcount: A:0.46, C:0.21, G:0.19, T:0.13
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:17553 original size:14 final size:14
Alignment explanation
Indices: 17534--17623 Score: 54
Period size: 14 Copynumber: 5.8 Consensus size: 14
17524 ATGCGAAATG
17534 AAAATCGCAACAAA
1 AAAATCGCAACAAA
17548 AAAATCGCAATGCGAAA
1 AAAATCGCAA--C-AAA
* *
17565 TGAAAATCGCAACGAC
1 --AAAATCGCAACAAA
17581 AAAATCGCAATGCGAAA
1 AAAATCGCAA--C-AAA
* * *
17598 TGAAATCGCAACGAC
1 -AAAATCGCAACAAA
17613 AAAATCGCAAC
1 AAAATCGCAAC
17624 GCGAAACACA
Statistics
Matches: 59, Mismatches: 8, Indels: 18
0.69 0.09 0.21
Matches are distributed among these distances:
14 30 0.51
15 1 0.02
16 4 0.07
17 5 0.08
18 9 0.15
19 10 0.17
ACGTcount: A:0.51, C:0.22, G:0.16, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACAAA
Found at i:17609 original size:32 final size:33
Alignment explanation
Indices: 17518--17629 Score: 190
Period size: 33 Copynumber: 3.4 Consensus size: 33
17508 GAAAATGGCT
* *
17518 ATCGCAATGCGAAATGAAAATCGCAACAAAAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
17551 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
17584 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
17616 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
17630 CACAAATCGC
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
32 29 0.38
33 47 0.62
ACGTcount: A:0.49, C:0.21, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:17624 original size:14 final size:14
Alignment explanation
Indices: 17567--17624 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
17557 ATGCGAAATG
17567 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
17581 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
17597 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
17613 AAAATCGCAACG
1 AAAATCGCAACG
17625 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:17637 original size:65 final size:66
Alignment explanation
Indices: 17518--17640 Score: 187
Period size: 65 Copynumber: 1.9 Consensus size: 66
17508 GAAAATGGCT
* *
17518 ATCGCAATGCGAAATGAAAATCGCAACAAAAAAATCGCAATGCGAAATGAAAATCGCAACGACAA
1 ATCGCAATGCGAAATGAAAATCGCAACAAAAAAATCGCAACGCGAAATCAAAATCGCAACGACAA
17583 A
66 A
* *
17584 ATCGCAATGCGAAATG-AAATCGCAACGACAAAATCGCAACGCGAAA-CACAAATCGCA
1 ATCGCAATGCGAAATGAAAATCGCAACAAAAAAATCGCAACGCGAAATCA-AAATCGCA
17641 TTACGATTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
64 1 0.02
65 35 0.67
66 16 0.31
ACGTcount: A:0.49, C:0.23, G:0.17, T:0.11
Consensus pattern (66 bp):
ATCGCAATGCGAAATGAAAATCGCAACAAAAAAATCGCAACGCGAAATCAAAATCGCAACGACAA
A
Found at i:17658 original size:19 final size:19
Alignment explanation
Indices: 17636--17702 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 19
17626 GAAACACAAA
*
17636 TCGCATTACGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
17655 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
17671 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
17688 TCGCATTGCGATTTT
1 TCGCATTGCGATTTT
17703 GTCGTTGCGA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
14 6 0.15
15 3 0.08
16 4 0.10
17 4 0.10
18 3 0.08
19 19 0.49
ACGTcount: A:0.13, C:0.19, G:0.19, T:0.48
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:17677 original size:14 final size:14
Alignment explanation
Indices: 17658--17716 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
17648 TTTCATTTCG
17658 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
17672 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
17689 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
17705 CGTTGCGATTTT
1 CGTTGCGATTTT
17717 CATTTCGTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 18 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:17686 original size:33 final size:33
Alignment explanation
Indices: 17644--17728 Score: 152
Period size: 33 Copynumber: 2.6 Consensus size: 33
17634 AATCGCATTA
*
17644 CGATTTTCATTTCGCGTTGCGATTTTGTCGTTG
1 CGATTTTCATTTCGCATTGCGATTTTGTCGTTG
17677 CGATTTTCATTTCGCATTGCGATTTTGTCGTTG
1 CGATTTTCATTTCGCATTGCGATTTTGTCGTTG
*
17710 CGATTTTCATTTCGTATTG
1 CGATTTTCATTTCGCATTG
17729 TGATAGCCAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.12, C:0.18, G:0.21, T:0.49
Consensus pattern (33 bp):
CGATTTTCATTTCGCATTGCGATTTTGTCGTTG
Found at i:17759 original size:20 final size:20
Alignment explanation
Indices: 17730--17771 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
17720 TTCGTATTGT
17730 GATAGCCATTTCCGCGTTGC
1 GATAGCCATTTCCGCGTTGC
* * *
17750 GATAGTCATTTTCGTGTTGC
1 GATAGCCATTTCCGCGTTGC
17770 GA
1 GA
17772 AAGTAAACTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.36
Consensus pattern (20 bp):
GATAGCCATTTCCGCGTTGC
Found at i:18279 original size:18 final size:18
Alignment explanation
Indices: 18253--18297 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
18243 GTCGATCAGA
*
18253 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
18271 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
18289 TGATGGCTC
1 TGATGGCTC
18298 CCGAAGTAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:19660 original size:20 final size:20
Alignment explanation
Indices: 19616--19670 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
19606 TAATAGTTTC
19616 TGAAAATGAAAATCGCAACA
1 TGAAAATGAAAATCGCAACA
* ** *
19636 CGAAAATGACTATCGCAACG
1 TGAAAATGAAAATCGCAACA
*
19656 TGAAACT-AAAATCGC
1 TGAAAATGAAAATCGC
19671 GTTGCGATTT
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
19 6 0.22
20 21 0.78
ACGTcount: A:0.47, C:0.20, G:0.16, T:0.16
Consensus pattern (20 bp):
TGAAAATGAAAATCGCAACA
Found at i:20145 original size:21 final size:21
Alignment explanation
Indices: 20115--20230 Score: 80
Period size: 20 Copynumber: 5.7 Consensus size: 21
20105 CGCTTTGAAA
20115 ATCGCATTGCGATTATGTATT
1 ATCGCATTGCGATTATGTATT
* * *
20136 ATCGCGTTGCGA--AAGTCAGT
1 ATCGCATTGCGATTATGT-ATT
* * *
20156 ATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGATTATGTATT
* *
20177 ATCACATTGCGA-TA-GTAAGT
1 ATCGCATTGCGATTATGT-ATT
* * *
20197 ATCGCATTGCGATAAT-CAGT
1 ATCGCATTGCGATTATGTATT
20217 ATCGCATTGCGATT
1 ATCGCATTGCGATT
20231 TTCCCAATTC
Statistics
Matches: 74, Mismatches: 15, Indels: 13
0.73 0.15 0.13
Matches are distributed among these distances:
19 5 0.07
20 43 0.58
21 24 0.32
22 2 0.03
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (21 bp):
ATCGCATTGCGATTATGTATT
Found at i:20178 original size:41 final size:41
Alignment explanation
Indices: 20115--20209 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 41
20105 CGCTTTGAAA
* * *
20115 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTATGTATTATCACATTGCGAAAGTAAGT
* * * *
20156 ATCTCGTTGCGATTTTGTATTATCACATTGCGATAGTAAGT
1 ATCGCATTGCGATTATGTATTATCACATTGCGAAAGTAAGT
20197 ATCGCATTGCGAT
1 ATCGCATTGCGAT
20210 AATCAGTATC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCACATTGCGAAAGTAAGT
Found at i:20204 original size:20 final size:20
Alignment explanation
Indices: 20176--20229 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
20166 GATTTTGTAT
* *
20176 TATCACATTGCGATAGTAAG
1 TATCGCATTGCGATAATAAG
*
20196 TATCGCATTGCGATAATCAG
1 TATCGCATTGCGATAATAAG
20216 TATCGCATTGCGAT
1 TATCGCATTGCGAT
20230 TTTCCCAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAATAAG
Found at i:20247 original size:21 final size:21
Alignment explanation
Indices: 20218--20273 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
20208 ATAATCAGTA
*
20218 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
20239 TCGCGTTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
*
20260 TTGCGTTGCGATTT
1 TCGCGTTGCGATTT
20274 ACTTATTCGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.14, C:0.25, G:0.20, T:0.41
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCCAAT
Found at i:20361 original size:21 final size:21
Alignment explanation
Indices: 20321--20361 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
20311 ACTGTAGACC
** *
20321 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
20342 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
20362 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:20751 original size:18 final size:18
Alignment explanation
Indices: 20728--20775 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
20718 AAATTGTACT
*
20728 TATTATATATTTGTATAA
1 TATTATATATTTGTAAAA
*
20746 TATTATA-AATTGTAAAA
1 TATTATATATTTGTAAAA
20763 TATTTATATATTT
1 TA-TTATATATTT
20776 TCTTTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 10 0.40
18 12 0.48
19 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (18 bp):
TATTATATATTTGTAAAA
Found at i:20801 original size:36 final size:38
Alignment explanation
Indices: 20751--20824 Score: 107
Period size: 37 Copynumber: 2.0 Consensus size: 38
20741 TATAATATTA
20751 TAAATTGTAAAATATTTATATA-TTTTCTTTAAAAAAT
1 TAAATTGTAAAATATTTATATAGTTTTCTTTAAAAAAT
* * *
20788 TAAATT-TATAATATTTATATAGTTTTTTTTACAAAAT
1 TAAATTGTAAAATATTTATATAGTTTTCTTTAAAAAAT
20825 AAAAAATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
36 14 0.42
37 19 0.58
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (38 bp):
TAAATTGTAAAATATTTATATAGTTTTCTTTAAAAAAT
Found at i:20835 original size:37 final size:36
Alignment explanation
Indices: 20761--20835 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 36
20751 TAAATTGTAA
* **
20761 AATATTTATATATTTTCTTTAAAAAATTAAATTTAT
1 AATATTTATATATTTTCTTTAAAAAATAAAAAATAT
* *
20797 AATATTTATATAGTTTTTTTTACAAAATAAAAAATAT
1 AATATTTATATA-TTTTCTTTAAAAAATAAAAAATAT
20834 AA
1 AA
20836 AAAAGGTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
36 12 0.36
37 21 0.64
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (36 bp):
AATATTTATATATTTTCTTTAAAAAATAAAAAATAT
Found at i:22080 original size:20 final size:19
Alignment explanation
Indices: 22057--22102 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
22047 CGATATACCA
22057 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
22077 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
22097 GGTAAA
1 GGTAAA
22103 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:24516 original size:21 final size:21
Alignment explanation
Indices: 24489--24552 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
24479 CAAGACAATC
* *
24489 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTCGAG
* *
24510 CGAGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
24531 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
24552 A
1 A
24553 TGCATAAGGG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.39, C:0.16, G:0.30, T:0.16
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:24627 original size:32 final size:31
Alignment explanation
Indices: 24586--24645 Score: 93
Period size: 32 Copynumber: 1.9 Consensus size: 31
24576 AAATAGATGG
*
24586 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGTGA
1 AGTGGTGAAAGAAGTAG-GGTGTTAAGGGTGA
*
24618 AGTGGTGAAAGAAGTTGGGTGTTAAGGG
1 AGTGGTGAAAGAAGTAGGGTGTTAAGGG
24646 ATGATATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 10 0.38
32 16 0.62
ACGTcount: A:0.30, C:0.00, G:0.47, T:0.23
Consensus pattern (31 bp):
AGTGGTGAAAGAAGTAGGGTGTTAAGGGTGA
Found at i:26469 original size:19 final size:19
Alignment explanation
Indices: 26445--26493 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
26435 AATGTAGGGT
26445 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
26464 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
26483 TATTTTTGTAT
1 TAATTTTGTAT
26494 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:27136 original size:197 final size:199
Alignment explanation
Indices: 26612--27185 Score: 1044
Period size: 197 Copynumber: 2.9 Consensus size: 199
26602 CAATATGGCC
* *
26612 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAAACATCGAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCG-AA
* * * *
26677 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTCTACCGGTTTTAAGAG
64 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
*
26742 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGA
129 AGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGA
26807 ATGGAA
194 ATGGAA
*
26813 AACAGTGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
26878 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
26943 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAAT
131 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
27007 GGAA
196 GGAA
27011 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
27075 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
27140 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
131 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
27186 CTAATTTAAA
Statistics
Matches: 364, Mismatches: 9, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
197 124 0.34
198 72 0.20
199 110 0.30
200 24 0.07
201 34 0.09
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (199 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
GGAA
Found at i:27172 original size:23 final size:23
Alignment explanation
Indices: 27146--27197 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 23
27136 AGAGAATATG
27146 TATAAATAATGTGTCGACACTAA
1 TATAAATAATGTGTCGACACTAA
* * *
27169 TAT-AGT-TTGTGTCGATACTAA
1 TATAAATAATGTGTCGACACTAA
*
27190 TTTAAATA
1 TATAAATA
27198 TCAAGTGTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 4
0.71 0.16 0.13
Matches are distributed among these distances:
21 15 0.68
22 4 0.18
23 3 0.14
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (23 bp):
TATAAATAATGTGTCGACACTAA
Found at i:28828 original size:25 final size:25
Alignment explanation
Indices: 28800--28859 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
28790 TTATCATTAA
28800 ATTTAGGTATGTAAAATAACTACAT
1 ATTTAGGTATGTAAAATAACTACAT
****
28825 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTAAAATAACTACAT
28850 ATTTAGGTAT
1 ATTTAGGTAT
28860 ATACATCTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (25 bp):
ATTTAGGTATGTAAAATAACTACAT
Found at i:29240 original size:23 final size:23
Alignment explanation
Indices: 29209--29357 Score: 217
Period size: 23 Copynumber: 6.5 Consensus size: 23
29199 ATAGGTAAAC
*
29209 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
29232 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
29255 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
29278 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
29301 ATATAATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
29324 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
29347 ATATATTGTAA
1 ATATAATGTAA
29358 AGTATCTATC
Statistics
Matches: 112, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 112 1.00
ACGTcount: A:0.35, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:29268 original size:46 final size:46
Alignment explanation
Indices: 29209--29357 Score: 271
Period size: 46 Copynumber: 3.2 Consensus size: 46
29199 ATAGGTAAAC
*
29209 ATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTT
*
29255 ATATAATGTAATAGGTAGTGCTTATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTT
29301 ATATAATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTT
*
29347 ATATATTGTAA
1 ATATAATGTAA
29358 AGTATCTATC
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 99 1.00
ACGTcount: A:0.35, C:0.05, G:0.19, T:0.40
Consensus pattern (46 bp):
ATATAATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTT
Found at i:29801 original size:18 final size:18
Alignment explanation
Indices: 29780--29816 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
29770 GTAATTGGAG
29780 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
29798 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
29816 T
1 T
29817 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:29824 original size:24 final size:24
Alignment explanation
Indices: 29772--29818 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
29762 TTTCATATGT
* *
29772 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
29796 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
29819 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:30115 original size:39 final size:39
Alignment explanation
Indices: 30072--30158 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
30062 TCCGATGCTC
*
30072 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
* *
30111 ATCAAAATTCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
30150 ATCAAAATC
1 ATCAAAATC
30159 TACAACTTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.48, C:0.20, G:0.14, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:30627 original size:22 final size:22
Alignment explanation
Indices: 30584--30649 Score: 96
Period size: 23 Copynumber: 2.9 Consensus size: 22
30574 AAAAATATGG
*
30584 TGTAATAGGTAGCGCTTATATAA
1 TGTAATAGGTATCG-TTATATAA
30607 TGTAATAGGTATCGTTATATAA
1 TGTAATAGGTATCGTTATATAA
*
30629 TGTAATAGGTAGTGGTTATAT
1 TGTAATAGGTA-TCGTTATAT
30650 TGTAAAGTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
22 19 0.47
23 21 0.52
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.39
Consensus pattern (22 bp):
TGTAATAGGTATCGTTATATAA
Found at i:33415 original size:22 final size:21
Alignment explanation
Indices: 33390--33432 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
33380 AAAAGAAATA
33390 ATTTTTTTGTAA-GTTTTCTTTT
1 ATTTTTTT-TAATGTTTT-TTTT
33412 ATTTTTTTTAATGTTTTTTTT
1 ATTTTTTTTAATGTTTTTTTT
33433 CCTACAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.14, C:0.02, G:0.07, T:0.77
Consensus pattern (21 bp):
ATTTTTTTTAATGTTTTTTTT
Found at i:33417 original size:21 final size:21
Alignment explanation
Indices: 33392--33432 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
33382 AAGAAATAAT
33392 TTTTTTGTAA-GTTTTCTTTTA
1 TTTTTTGTAATGTTTT-TTTTA
*
33413 TTTTTTTTAATGTTTTTTTT
1 TTTTTTGTAATGTTTTTTTT
33433 CCTACAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.12, C:0.02, G:0.07, T:0.78
Consensus pattern (21 bp):
TTTTTTGTAATGTTTTTTTTA
Found at i:34941 original size:22 final size:22
Alignment explanation
Indices: 34879--34938 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 22
34869 ATGTATATAA
* *
34879 AATTTTTATAAATGGTATATTTT
1 AATTTATATAAAT-TTATATTTT
34902 AATTTATATAAATTTATATTTT
1 AATTTATATAAATTTATATTTT
34924 AACTTTGATA-AAATT
1 AA-TTT-ATATAAATT
34939 ATAATATACA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 10 0.30
23 20 0.61
24 3 0.09
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (22 bp):
AATTTATATAAATTTATATTTT
Found at i:39644 original size:31 final size:31
Alignment explanation
Indices: 39606--39700 Score: 102
Period size: 31 Copynumber: 3.1 Consensus size: 31
39596 GAACCTCGGC
* *
39606 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* ** *
39637 AACTGTCCATATGTTCCTTAGAACATAAGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* *
39668 TACTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATATGTC-CCAAAGAACATAGGTA
39699 AA
1 AA
39701 ACCCTCGACT
Statistics
Matches: 50, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
31 47 0.94
32 3 0.06
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (31 bp):
AACTGTCCATATGTCCCAAAGAACATAGGTA
Found at i:39866 original size:17 final size:19
Alignment explanation
Indices: 39834--39869 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
39824 CATATATCTC
39834 ATATCATATCACATGTATT
1 ATATCATATCACATGTATT
39853 ATAT-ATAT-ACATGTATT
1 ATATCATATCACATGTATT
39870 CATGTAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (19 bp):
ATATCATATCACATGTATT
Found at i:40464 original size:64 final size:65
Alignment explanation
Indices: 40353--40503 Score: 191
Period size: 64 Copynumber: 2.3 Consensus size: 65
40343 TCTTTCAATG
* * * * * *
40353 AAGGTATGCATCGATGCACTA-CTTGTGCATCGGTGCATAAAATGCATTCGATGTTTTTATTTTA
1 AAGGAATGCATCGATGCATTATCTTATGCATCGATGCATAAAAGGCATTCGATGTTCTTATTTT-
40417 A
65 A
* *
40418 AAGG-ATGCATCGATGCATTATC-TATGCATCGATGCATCAAAGGCATTCGATGTTCTTCTTTTA
1 AAGGAATGCATCGATGCATTATCTTATGCATCGATGCATAAAAGGCATTCGATGTTCTTATTTTA
40481 AAGGAATGCATCGATGCACTTAT
1 AAGGAATGCATCGATGCA-TTAT
40504 GAATGTGCAT
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
63 5 0.07
64 62 0.82
65 9 0.12
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.34
Consensus pattern (65 bp):
AAGGAATGCATCGATGCATTATCTTATGCATCGATGCATAAAAGGCATTCGATGTTCTTATTTTA
Found at i:41734 original size:3 final size:3
Alignment explanation
Indices: 41726--41819 Score: 75
Period size: 3 Copynumber: 31.7 Consensus size: 3
41716 CTGTAATATG
* * * *
41726 TAA TAA TAA TATT TAT TAA TAA AAA T-A TAA TAA TAA TAG TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
41771 TTA TAA TAA TTA TAA CAA TTA TAA TAA TAA AAA TAA TAA AAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
41818 TA
1 TA
41820 GGAAAAAAAT
Statistics
Matches: 70, Mismatches: 18, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
2 4 0.06
3 64 0.91
4 2 0.03
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:42186 original size:58 final size:58
Alignment explanation
Indices: 42091--42207 Score: 189
Period size: 58 Copynumber: 2.0 Consensus size: 58
42081 TCTGAAAATG
* * *
42091 TTGATGCTAATCTATCTCCTTCTATGATAGATTATACAAAATGTTGAACAAGCTTTTC
1 TTGATGCTAATCTATCTCCTTCTATGATAGATCATACAAAAGGTTGAACAAGCTCTTC
* *
42149 TTGATGCTAATCTATCTCCTTCTGTGATAGATCATACAAAAGGTTGAGCAAGCTCTTC
1 TTGATGCTAATCTATCTCCTTCTATGATAGATCATACAAAAGGTTGAACAAGCTCTTC
42207 T
1 T
42208 CATTATGAAC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (58 bp):
TTGATGCTAATCTATCTCCTTCTATGATAGATCATACAAAAGGTTGAACAAGCTCTTC
Found at i:42458 original size:248 final size:248
Alignment explanation
Indices: 42149--42772 Score: 1063
Period size: 248 Copynumber: 2.5 Consensus size: 248
42139 CAAGCTTTTC
* * * *
42149 TTGATGCTAATCTATCTCCTTCTGTGATAGA-TCATACAAAAGGTTGAGCAAGCTCTTCTCATTA
1 TTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTA
42213 TGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGTTGATA
66 TGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGTTGATA
*
42278 CTGATCTATCTCATTCTTTGATAGAGTCATACAAAAAGGATGAACAAGCTCTTCTCATTATGAAC
131 CTGATCTATCTCATTCTGTGATAGAGTCATACAAAAAGGATGAACAAGCTCTTCTCATTATGAAC
* *
42343 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTTTGAACTTCTCTGGAAAAG
196 TTATTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTCTGGAAAAG
42396 TTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTA
1 TTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTA
* * * * *
42461 TGAACTTCTTATTCCTTCTTCATATGAGTTCTTCTTATTATGAACTTTCTCTAGAAAAATTGATG
66 TGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGTTGATA
* * * *
42526 TTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
131 CTGATCTATCTCATTCTGTGATAGAGTCATACAAAAAGGATGAACAAGCTCTTCTCATTATGAAC
42591 TTATTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTCTGGAAAAG
196 TTATTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTCTGGAAAAG
42644 TTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTA
1 TTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTA
* *
42709 TGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTT-TCTGGAAATGTTGAT
66 TGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACT-TTCTCTGGAAAAGTTGAT
42773 CCATCGAATG
Statistics
Matches: 353, Mismatches: 22, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
247 29 0.08
248 322 0.91
249 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (248 bp):
TTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTA
TGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGTTGATA
CTGATCTATCTCATTCTGTGATAGAGTCATACAAAAAGGATGAACAAGCTCTTCTCATTATGAAC
TTATTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTCTGGAAAAG
Found at i:42498 original size:123 final size:123
Alignment explanation
Indices: 42149--42772 Score: 1025
Period size: 123 Copynumber: 5.0 Consensus size: 123
42139 CAAGCTTTTC
* * * *
42149 TTGATGCTAATCTATCTCCTTCTGTGATAGA-TCATACAAAAGGTTGAGCAAGCTCTTCTCATTA
1 TTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTA
42213 TGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAG
66 TGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAAC-TTCTCTGGAAAAG
** * * * *
42272 TTGATACTGATCTATCTCATTCTTTGATAGAGTCATACAAAAAGGATGAACAAGCTCTTCTCATT
1 TTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGC-AAAAGGTTGAACAAGCTCTTCTCATT
*
42337 ATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTTTGAACTTCTCTGGAAAAG
65 ATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTCTGGAAAAG
42396 TTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTA
1 TTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTA
* * * *
42461 TGAACTTCTTATTCCTTCTTCATATGAGTTCTTCTTATTATGAACTTTCTCTAGAAAAA
66 TGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAAC-TTCTCTGGAAAAG
42520 TTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAAGGTTGAACAAGCTCTTCTCATT
1 TTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGC-AAAAGGTTGAACAAGCTCTTCTCATT
*
42585 ATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTCTGGAAAAG
65 ATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTCTGGAAAAG
42644 TTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTA
1 TTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTA
* * *
42709 TGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTCTGGAAATG
66 TGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACT-TCTCTGGAAAAG
42768 TTGAT
1 TTGAT
42773 CCATCGAATG
Statistics
Matches: 469, Mismatches: 27, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
123 166 0.35
124 165 0.35
125 138 0.29
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (123 bp):
TTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTA
TGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTCTGGAAAAG
Found at i:43969 original size:18 final size:18
Alignment explanation
Indices: 43946--43980 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
43936 TATATGAAAC
43946 AAATTGAATTTCAAAAAT
1 AAATTGAATTTCAAAAAT
43964 AAATTGAATTTCAAAAA
1 AAATTGAATTTCAAAAA
43981 GATAAACTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (18 bp):
AAATTGAATTTCAAAAAT
Found at i:44367 original size:11 final size:11
Alignment explanation
Indices: 44353--44406 Score: 56
Period size: 11 Copynumber: 4.6 Consensus size: 11
44343 TTTTTCAACA
44353 TTTTTTCTCTT
1 TTTTTTCTCTT
44364 TTTTTTCT-TT
1 TTTTTTCTCTT
*
44374 TTTTCTTCATTTTT
1 TTTT-TTC--TCTT
44388 TCTTTTTCTCTT
1 T-TTTTTCTCTT
44400 TTTTTTC
1 TTTTTTC
44407 CAGCATAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
10 6 0.16
11 17 0.46
12 4 0.11
13 1 0.03
14 6 0.16
15 3 0.08
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTTTCTCTT
Found at i:44375 original size:19 final size:18
Alignment explanation
Indices: 44353--44406 Score: 76
Period size: 17 Copynumber: 3.0 Consensus size: 18
44343 TTTTTCAACA
44353 TTTTTTCTCTTTTTTTTC
1 TTTTTTCTCTTTTTTTTC
44371 TTTTTT-TCTTCATTTTTTC
1 TTTTTTCTCTT--TTTTTTC
44390 -TTTTTCTCTTTTTTTTC
1 TTTTTTCTCTTTTTTTTC
44407 CAGCATAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
17 11 0.33
18 11 0.33
19 11 0.33
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTTTCTCTTTTTTTTC
Found at i:44376 original size:30 final size:28
Alignment explanation
Indices: 44327--44394 Score: 82
Period size: 30 Copynumber: 2.4 Consensus size: 28
44317 CTGACCCTCC
*
44327 TTTTCTATTTTTTTATTTTTTCAACATT
1 TTTTCTTTTTTTTTATTTTTTCAACATT
* **
44355 TTTTCTCTTTTTTTTCTTTTTTTCTTCATT
1 TTTTCT-TTTTTTTT-ATTTTTTCAACATT
44385 TTTTCTTTTT
1 TTTTCTTTTT
44395 CTCTTTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 6 0.18
29 11 0.32
30 17 0.50
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.78
Consensus pattern (28 bp):
TTTTCTTTTTTTTTATTTTTTCAACATT
Found at i:44405 original size:30 final size:29
Alignment explanation
Indices: 44334--44406 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 29
44324 TCCTTTTCTA
*
44334 TTTTTTTATTTTTTCAACATTTTTTCTCT
1 TTTTTTTTTTTTTTCAACATTTTTTCTCT
**
44363 TTTTTTTCTTTTTTTCTTCATTTTTTCT-T
1 TTTTTTT-TTTTTTTCAACATTTTTTCTCT
* *
44392 TTTCTCTTTTTTTTC
1 TTTTTTTTTTTTTTC
44407 CAGCATAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
28 8 0.21
29 13 0.34
30 17 0.45
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (29 bp):
TTTTTTTTTTTTTTCAACATTTTTTCTCT
Found at i:52840 original size:21 final size:21
Alignment explanation
Indices: 52814--52855 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
52804 CAAGAATGGG
*
52814 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
*
52835 GGGAATCGATACCTCTTCATA
1 GGGAATCGATACCCCTTCATA
52856 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:52978 original size:30 final size:31
Alignment explanation
Indices: 52931--53021 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
52921 AAATTTTGAA
52931 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
52960 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
52991 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
53022 CCTTAAATTG
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.18
30 11 0.18
31 38 0.63
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:55714 original size:30 final size:29
Alignment explanation
Indices: 55675--55732 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
55665 ACATTAATAA
55675 AATAATATATATATA-AATATTATGAAAAT
1 AATAATATATATATATAA-ATTATGAAAAT
*
55704 AATAAGTATATATATATAAATTTTGAAAA
1 AATAA-TATATATATATAAATTATGAAAA
55733 GAAAGAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 5 0.19
30 19 0.73
31 2 0.08
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (29 bp):
AATAATATATATATATAAATTATGAAAAT
Found at i:56490 original size:26 final size:27
Alignment explanation
Indices: 56461--56513 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
56451 AATAATTTAT
*
56461 ATAAAGGATTTAATAA-AATAA-AATAA
1 ATAAAAGATTT-ATAATAATAATAATAA
*
56487 ATAAAATATTTATAATAATAATAATAA
1 ATAAAAGATTTATAATAATAATAATAA
56514 TTTAAATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 4 0.17
26 14 0.61
27 5 0.22
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (27 bp):
ATAAAAGATTTATAATAATAATAATAA
Found at i:57702 original size:16 final size:16
Alignment explanation
Indices: 57681--57721 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
57671 GGCTGCGTGT
57681 CCCTAGGGTATCATAA
1 CCCTAGGGTATCATAA
57697 CCCTAGGGTATCATAA
1 CCCTAGGGTATCATAA
57713 CCCTAGGGT
1 CCCTAGGGT
57722 TTCAGCTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (16 bp):
CCCTAGGGTATCATAA
Found at i:57932 original size:3 final size:3
Alignment explanation
Indices: 57924--58017 Score: 66
Period size: 3 Copynumber: 31.7 Consensus size: 3
57914 CTGTAATATG
* * * *
57924 TAA TAA TAA TATT TAT TAA TAA AAA T-A TAA TAA TAA TAG TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * * *
57969 TTA TAA TAA TTA TAA CAG TTA TAA TAA TTA TAA TAA TAA AAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
58016 TA
1 TA
58018 GGTAAAAATT
Statistics
Matches: 68, Mismatches: 20, Indels: 6
0.72 0.21 0.06
Matches are distributed among these distances:
2 4 0.06
3 62 0.91
4 2 0.03
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:64963 original size:19 final size:20
Alignment explanation
Indices: 64926--64965 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
64916 ACTCTTTAAG
64926 TTATTATAATAACAATTGTA
1 TTATTATAATAACAATTGTA
64946 TTATTA-AATTAA-AATTGTA
1 TTATTATAA-TAACAATTGTA
64965 T
1 T
64966 ATACATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (20 bp):
TTATTATAATAACAATTGTA
Found at i:69737 original size:10 final size:10
Alignment explanation
Indices: 69718--69767 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
69708 TTCATCGCAC
*
69718 CAAATCCTCT
1 CAAATACTCT
* *
69728 AAAATTCTCT
1 CAAATACTCT
69738 CAAATACTCT
1 CAAATACTCT
* *
69748 CAACTTCTCT
1 CAAATACTCT
69758 CAAATACTCT
1 CAAATACTCT
69768 TATATTCTAT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
10 32 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (10 bp):
CAAATACTCT
Found at i:69747 original size:20 final size:20
Alignment explanation
Indices: 69718--69767 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
69708 TTCATCGCAC
*
69718 CAAATCCTCTAAAATTCTCT
1 CAAATACTCTAAAATTCTCT
* *
69738 CAAATACTCTCAACTTCTCT
1 CAAATACTCTAAAATTCTCT
69758 CAAATACTCT
1 CAAATACTCT
69768 TATATTCTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (20 bp):
CAAATACTCTAAAATTCTCT
Found at i:69831 original size:23 final size:26
Alignment explanation
Indices: 69797--69851 Score: 73
Period size: 23 Copynumber: 2.3 Consensus size: 26
69787 TTAAGGTATA
*
69797 TTTT-ATTATATTTAA-TATTT-TAT
1 TTTTAATTATATTTAAGTATTTAAAT
69820 TTTTAATT-TATTTAAGTATTTAAAT
1 TTTTAATTATATTTAAGTATTTAAAT
69845 TTTTAAT
1 TTTTAAT
69852 ATTTTATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 11 0.39
24 8 0.29
25 9 0.32
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (26 bp):
TTTTAATTATATTTAAGTATTTAAAT
Found at i:69847 original size:24 final size:23
Alignment explanation
Indices: 69796--69862 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
69786 TTTAAGGTAT
*
69796 ATTTTATTATATTTAATATTTTA
1 ATTTTATTATATTTAATATTTAA
*
69819 TTTTTAATT-TATTTAAGTATTTAA
1 ATTTT-ATTATATTTAA-TATTTAA
*
69843 ATTTT-TAATATTT--TATTTAA
1 ATTTTATTATATTTAATATTTAA
69863 TTAATTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
20 7 0.19
22 1 0.03
23 16 0.43
24 13 0.35
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (23 bp):
ATTTTATTATATTTAATATTTAA
Found at i:71926 original size:18 final size:18
Alignment explanation
Indices: 71903--71939 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
71893 AGCTGCTCAC
71903 GACGACGACGATGACGAT
1 GACGACGACGATGACGAT
* *
71921 GACGACTACGATGATGAT
1 GACGACGACGATGACGAT
71939 G
1 G
71940 GTGATGATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.19, G:0.32, T:0.16
Consensus pattern (18 bp):
GACGACGACGATGACGAT
Found at i:72170 original size:33 final size:34
Alignment explanation
Indices: 72133--72206 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 34
72123 TAATACTTAC
72133 TTTATTTCATT-AATTTGGTTGGA-TTTATT-TTAA
1 TTTATTTCATTAAATTT-GTTGGACTTT-TTGTTAA
**
72166 TTTATTTTGTTAAATTTGTTGGACTTTTTGTTAA
1 TTTATTTCATTAAATTTGTTGGACTTTTTGTTAA
*
72200 TGTATTT
1 TTTATTT
72207 TGGTTAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
33 17 0.49
34 18 0.51
ACGTcount: A:0.22, C:0.03, G:0.14, T:0.62
Consensus pattern (34 bp):
TTTATTTCATTAAATTTGTTGGACTTTTTGTTAA
Found at i:72200 original size:34 final size:34
Alignment explanation
Indices: 72144--72220 Score: 95
Period size: 34 Copynumber: 2.2 Consensus size: 34
72134 TTATTTCATT
*
72144 AATTTGGTTGGATTTATTTTAATTTATTTT-GTTA
1 AATTT-GTTGGATTTATTTTAATGTATTTTGGTTA
72178 AATTTGTTGGACTTT-TTGTTAATGTATTTTGGTTA
1 AATTTGTTGGA-TTTATT-TTAATGTATTTTGGTTA
*
72213 ATTTTGTT
1 AATTTGTT
72221 TATTACCATT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
33 8 0.21
34 19 0.50
35 11 0.29
ACGTcount: A:0.21, C:0.01, G:0.17, T:0.61
Consensus pattern (34 bp):
AATTTGTTGGATTTATTTTAATGTATTTTGGTTA
Found at i:72250 original size:35 final size:31
Alignment explanation
Indices: 72215--72295 Score: 81
Period size: 38 Copynumber: 2.3 Consensus size: 31
72205 TTTGGTTAAT
72215 TTTGTTTATTACCATTTAATATCAGTTATTGTAA
1 TTTGTTTATTACCATTTAATAT---TTATTGTAA
72249 TTTGTTTACCATTTACCATTTAATATTTATTGTAA
1 TTTGTTT---A-TTACCATTTAATATTTATTGTAA
72284 GTTTGTTGTATT
1 -TTTGTT-TATT
72296 TAAAATTATA
Statistics
Matches: 41, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
33 2 0.05
34 8 0.20
35 9 0.22
36 6 0.15
37 2 0.05
38 14 0.34
ACGTcount: A:0.26, C:0.09, G:0.10, T:0.56
Consensus pattern (31 bp):
TTTGTTTATTACCATTTAATATTTATTGTAA
Found at i:74021 original size:51 final size:51
Alignment explanation
Indices: 73902--74022 Score: 143
Period size: 51 Copynumber: 2.4 Consensus size: 51
73892 ACTTAACATG
* **
73902 TACTTACACCAATGTAAGTGAATAAAATAAAAAAGAATAGTAATTAACAAA
1 TACTTACACCAGTGTAAGTGAATAAAATAAAAAAGAATAACAATTAACAAA
* * * ** * *
73953 TACTTACATCGGTGTAAGTGAATAAAATAAGAAAGTGTAACATTTAACACA
1 TACTTACACCAGTGTAAGTGAATAAAATAAAAAAGAATAACAATTAACAAA
*
74004 TACTTACACCAGCGTAAGT
1 TACTTACACCAGTGTAAGT
74023 ATGTACATCT
Statistics
Matches: 57, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (51 bp):
TACTTACACCAGTGTAAGTGAATAAAATAAAAAAGAATAACAATTAACAAA
Found at i:74498 original size:38 final size:38
Alignment explanation
Indices: 74412--74498 Score: 90
Period size: 38 Copynumber: 2.3 Consensus size: 38
74402 GTAACATTAG
* **
74412 TATATTTTAAAATAATAAATGTTATTAATTATATTAGT
1 TATATTTTAAAATAATAAATGTTATTAATTATAATAAA
*
74450 TA-ATTATTAAAATAATATTATGTTA-T-ATTATCAATAAA
1 TATATT-TTAAAATAATA-AATGTTATTAATTAT-AATAAA
74488 TATATTTTAAA
1 TATATTTTAAA
74499 TATTTTACTA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
37 8 0.20
38 24 0.59
39 9 0.22
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.48
Consensus pattern (38 bp):
TATATTTTAAAATAATAAATGTTATTAATTATAATAAA
Found at i:74574 original size:26 final size:27
Alignment explanation
Indices: 74545--74612 Score: 68
Period size: 30 Copynumber: 2.4 Consensus size: 27
74535 ACAAATAATA
74545 TTATTTATTATAACAATCA-ATAAATT
1 TTATTTATTATAACAATCATATAAATT
* *
74571 TTATTTTATCAATATAATAATCATTTAAATT
1 TTA-TTTAT---TATAACAATCATATAAATT
74602 TTATTT-TTATA
1 TTATTTATTATA
74613 TTTTTAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
26 7 0.20
27 5 0.14
29 1 0.03
30 13 0.37
31 9 0.26
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (27 bp):
TTATTTATTATAACAATCATATAAATT
Found at i:78185 original size:38 final size:38
Alignment explanation
Indices: 78141--78254 Score: 228
Period size: 38 Copynumber: 3.0 Consensus size: 38
78131 AATTTTCAAA
78141 CATACTTCTCCCCTGTTATATAAAAAATAATTCAAACT
1 CATACTTCTCCCCTGTTATATAAAAAATAATTCAAACT
78179 CATACTTCTCCCCTGTTATATAAAAAATAATTCAAACT
1 CATACTTCTCCCCTGTTATATAAAAAATAATTCAAACT
78217 CATACTTCTCCCCTGTTATATAAAAAATAATTCAAACT
1 CATACTTCTCCCCTGTTATATAAAAAATAATTCAAACT
78255 TTAAGTTTCA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 76 1.00
ACGTcount: A:0.39, C:0.24, G:0.03, T:0.34
Consensus pattern (38 bp):
CATACTTCTCCCCTGTTATATAAAAAATAATTCAAACT
Found at i:79250 original size:20 final size:20
Alignment explanation
Indices: 79201--79238 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
79191 TTGAAAGCTC
79201 AAAATTATT-TTTCAAAATAA
1 AAAATT-TTCTTTCAAAATAA
79221 AAAATTTTCTTTCAAAAT
1 AAAATTTTCTTTCAAAAT
79239 CAATCATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (20 bp):
AAAATTTTCTTTCAAAATAA
Found at i:84206 original size:35 final size:35
Alignment explanation
Indices: 84167--84283 Score: 121
Period size: 34 Copynumber: 3.3 Consensus size: 35
84157 GTCTCCTTTC
* *
84167 GTTCTACTTGAATTGAAAGTGCGATGCTTTCTTCT
1 GTTCTACTTGAATTGAAAGTGTGATGCTTACTTCT
* * *
84202 GTTCTACTTTAGGGATATTG-AAGTGTTATGCCTCCTTC-
1 GTTCTAC-TT---GA-ATTGAAAGTGTGATGCTTACTTCT
*
84240 GTTCTACTTGAATCGAAAGTGTGATGCTTACTTCT
1 GTTCTACTTGAATTGAAAGTGTGATGCTTACTTCT
84275 GTTCTACTT
1 GTTCTACTT
84284 TATACGAGAA
Statistics
Matches: 67, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
33 3 0.04
34 17 0.25
35 16 0.24
36 2 0.03
37 2 0.03
38 7 0.10
39 16 0.24
40 4 0.06
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.43
Consensus pattern (35 bp):
GTTCTACTTGAATTGAAAGTGTGATGCTTACTTCT
Done.