Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001487.1 Hibiscus syriacus cultivar Beakdansim tig00002890_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: 234512
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:8823 original size:14 final size:15
Alignment explanation
Indices: 8804--8835 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
8794 GAAAAAAAAT
8804 TTTGAAAT-AATTTA
1 TTTGAAATAAATTTA
8818 TTTGAAATAAATTTA
1 TTTGAAATAAATTTA
8833 TTT
1 TTT
8836 ATTATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (15 bp):
TTTGAAATAAATTTA
Found at i:10209 original size:3 final size:3
Alignment explanation
Indices: 10201--10318 Score: 116
Period size: 3 Copynumber: 38.7 Consensus size: 3
10191 TTATTTATTA
*
10201 AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAT AAAT AA- AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
* * * *
10247 AAT AAT AAT TAT TAT AAT AAT AA- AAT ACT AAT AAT ATTT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
*
10292 AAT AAAT AA- ATTT AAT AAT AAT AAT AA
1 AAT -AAT AAT A-AT AAT AAT AAT AAT AA
10319 ATTTAAATGA
Statistics
Matches: 97, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
2 5 0.05
3 80 0.82
4 12 0.12
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:10726 original size:75 final size:76
Alignment explanation
Indices: 10442--10852 Score: 758
Period size: 76 Copynumber: 5.5 Consensus size: 76
10432 GATGGAAATG
* *
10442 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
10507 CCCGAAGGCTT
66 CCCGAAGGCTT
10518 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
10583 CCCGAAGGC-T
66 CCCGAAGGCTT
10593 TTTGGAAACATCATGCACTG-AGGACTTACAGATGACCCGAAGGCTTTGAAAACATC-AAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
10656 CCCGAAGGCTT
66 CCCGAAGGCTT
10667 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
10732 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
10743 TTTGGAAACATCATGCACTGGAGGACTTACAGATGACCCGAAGGATTTG-AAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
10807 CCCGAAGGCTT
66 CCCGAAGGCTT
10818 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
10853 GGAAATAGTT
Statistics
Matches: 327, Mismatches: 5, Indels: 7
0.96 0.01 0.02
Matches are distributed among these distances:
73 16 0.05
74 57 0.17
75 117 0.36
76 137 0.42
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:10838 original size:225 final size:226
Alignment explanation
Indices: 10442--10852 Score: 763
Period size: 225 Copynumber: 1.8 Consensus size: 226
10432 GATGGAAATG
*
10442 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
10507 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAAC
10572 ATCAAAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTG-AGGACTTACAGATGACCCGAAGG
131 ATCAAAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
10636 CTTTGAAAACATCAAAAGCTCCCGAAGGCTT
196 CTTTGAAAACATCAAAAGCTCCCGAAGGCTT
*
10667 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
10732 CCCGAAGGCTTTTTGGAAACATCATGCACTGGAGGACTTACAGATGACCCGAAGGATTTG-AAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAAC
10796 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
131 ATCAAAAAGCTCCCGAAGGC-TTTTGGAAACATCATGCACTGAAGGACTTACAGATG
10853 GGAAATAGTT
Statistics
Matches: 180, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
224 24 0.13
225 142 0.79
226 14 0.08
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (226 bp):
TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAAC
ATCAAAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
CTTTGAAAACATCAAAAGCTCCCGAAGGCTT
Found at i:11549 original size:21 final size:22
Alignment explanation
Indices: 11525--11578 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
11515 CATAAAGCTT
*
11525 TCAT-TTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAACCTA
*
11546 TCATCTTTAAAAAGAGAACCTA
1 TCATCTTTGAAAAGAGAACCTA
11568 TCATCTTTGAA
1 TCATCTTTGAA
11579 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 4 0.14
22 25 0.86
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAACCTA
Found at i:14433 original size:183 final size:184
Alignment explanation
Indices: 14120--14674 Score: 952
Period size: 183 Copynumber: 3.0 Consensus size: 184
14110 CTTATTTCTA
* ** * * * * * *
14120 CTATGAGCAAATTCATCTTTTAAATTCAATGATTGGTTTTGGGGTTCATACCAAATCATATCAGA
1 CTATGAGCAAATTCCTCTTCCAAATTCAATAACTGGTTCTGTGGTTCATACCAAACCAGATCAGA
* * * *
14185 TAATTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT-GTCTTCCAAATTCAATGATTGGTT
66 TAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAATTCAATAACTGGTT
14249 CTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
131 CTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
*
14303 CTATGAGCACATTCCTCTTCCAAATTCAATAACTGGTTCTGTGGTTCATACC-AACCAGATCAGA
1 CTATGAGCAAATTCCTCTTCCAAATTCAATAACTGGTTCTGTGGTTCATACCAAACCAGATCAGA
14367 TAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAATTCAATAACTGGTT
66 TAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAATTCAATAACTGGTT
*
14432 CTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATA
131 CTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
*
14486 CTATGAGCATATTCCTCTTCCAAATTCAATAACTGGTTCTGTGGTTCATACCAAACCAGATCAGA
1 CTATGAGCAAATTCCTCTTCCAAATTCAATAACTGGTTCTGTGGTTCATACCAAACCAGATCAGA
14551 TAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAATTCAATAACTGGTT
66 TAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAATTCAATAACTGGTT
14616 CTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
131 CTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
14670 CTATG
1 CTATG
14675 GGTCTCCTTA
Statistics
Matches: 353, Mismatches: 17, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
182 49 0.14
183 169 0.48
184 135 0.38
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.28
Consensus pattern (184 bp):
CTATGAGCAAATTCCTCTTCCAAATTCAATAACTGGTTCTGTGGTTCATACCAAACCAGATCAGA
TAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAATTCAATAACTGGTT
CTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
Found at i:14512 original size:92 final size:92
Alignment explanation
Indices: 14120--14674 Score: 952
Period size: 92 Copynumber: 6.1 Consensus size: 92
14110 CTTATTTCTA
* * ** * * * * * *
14120 CTATGAGCAAATTCATCTTTTAAATTCAATGATTGGTTTTGGGGTTCATACCAAATCATATCAGA
1 CTATGAGCACATTCCTCTTCCAAATTCAATAACTGGTTCTGTGGTTCATACCAAACCAGATCAGA
*
14185 TAATTCAAAGAACACTTCCAGAAGATG
66 TAACTCAAAGAACACTTCCAGAAGATG
* * *
14212 CTATGAGCACATT-GTCTTCCAAATTCAATGATTGGTTCTGTGGTTCATACCAAACCAGATCAGA
1 CTATGAGCACATTCCTCTTCCAAATTCAATAACTGGTTCTGTGGTTCATACCAAACCAGATCAGA
14276 TAACTCAAAGAACACTTCCAGAAGATG
66 TAACTCAAAGAACACTTCCAGAAGATG
14303 CTATGAGCACATTCCTCTTCCAAATTCAATAACTGGTTCTGTGGTTCATACC-AACCAGATCAGA
1 CTATGAGCACATTCCTCTTCCAAATTCAATAACTGGTTCTGTGGTTCATACCAAACCAGATCAGA
14367 TAACTCAAAGAACACTTCCAGAAGATG
66 TAACTCAAAGAACACTTCCAGAAGATG
14394 CTATGAGCACATTCCTCTTCCAAATTCAATAACTGGTTCTGTGGTTCATACCAAACCAGATCAGA
1 CTATGAGCACATTCCTCTTCCAAATTCAATAACTGGTTCTGTGGTTCATACCAAACCAGATCAGA
*
14459 TAACTCAAAGAACACTTCCAGAAGATA
66 TAACTCAAAGAACACTTCCAGAAGATG
*
14486 CTATGAGCATATTCCTCTTCCAAATTCAATAACTGGTTCTGTGGTTCATACCAAACCAGATCAGA
1 CTATGAGCACATTCCTCTTCCAAATTCAATAACTGGTTCTGTGGTTCATACCAAACCAGATCAGA
14551 TAACTCAAAGAACACTTCCAGAAGATG
66 TAACTCAAAGAACACTTCCAGAAGATG
14578 CTATGAGCACATTCCTCTTCCAAATTCAATAACTGGTTCTGTGGTTCATACCAAACCAGATCAGA
1 CTATGAGCACATTCCTCTTCCAAATTCAATAACTGGTTCTGTGGTTCATACCAAACCAGATCAGA
14643 TAACTCAAAGAACACTTCCAGAAGATG
66 TAACTCAAAGAACACTTCCAGAAGATG
14670 CTATG
1 CTATG
14675 GGTCTCCTTA
Statistics
Matches: 445, Mismatches: 16, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
91 174 0.39
92 271 0.61
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.28
Consensus pattern (92 bp):
CTATGAGCACATTCCTCTTCCAAATTCAATAACTGGTTCTGTGGTTCATACCAAACCAGATCAGA
TAACTCAAAGAACACTTCCAGAAGATG
Found at i:17244 original size:2 final size:2
Alignment explanation
Indices: 17237--17287 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
17227 ACAACAAAGG
17237 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
17279 AT AT AT AT A
1 AT AT AT AT A
17288 AAGGATAAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:23723 original size:3 final size:3
Alignment explanation
Indices: 23715--23823 Score: 130
Period size: 3 Copynumber: 35.7 Consensus size: 3
23705 TTATTTATTA
* * *
23715 AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT TAT AAT AAT TAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
23761 AAT AAT AAT ACT AAT AAT AAT ATTT AAT AAT AAT AAT AAT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
*
23806 ATTT AAT AAT AAT AAT AA
1 A-AT AAT AAT AAT AAT AA
23824 ATTTAAATGA
Statistics
Matches: 90, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
2 1 0.01
3 83 0.92
4 6 0.07
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:25333 original size:22 final size:22
Alignment explanation
Indices: 25291--25339 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 22
25281 GATTTATTCC
25291 CAAAATTTTAGTATTTACTTTT
1 CAAAATTTTAGTATTTACTTTT
*
25313 -AAAATTTT-TTATTTAATCTTTT
1 CAAAATTTTAGTATTT-A-CTTTT
25335 CAAAA
1 CAAAA
25340 GAAATTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 5 0.22
21 9 0.39
22 5 0.22
23 4 0.17
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (22 bp):
CAAAATTTTAGTATTTACTTTT
Found at i:34981 original size:15 final size:15
Alignment explanation
Indices: 34961--35013 Score: 97
Period size: 15 Copynumber: 3.5 Consensus size: 15
34951 ATTTACTTCA
34961 GAATGATTAAGCGCT
1 GAATGATTAAGCGCT
*
34976 GAATGATTAAGCGTT
1 GAATGATTAAGCGCT
34991 GAATGATTAAGCGCT
1 GAATGATTAAGCGCT
35006 GAATGATT
1 GAATGATT
35014 TAGAGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.34, C:0.09, G:0.26, T:0.30
Consensus pattern (15 bp):
GAATGATTAAGCGCT
Found at i:35738 original size:3 final size:3
Alignment explanation
Indices: 35730--35797 Score: 129
Period size: 3 Copynumber: 23.0 Consensus size: 3
35720 TCTCTCTCCC
35730 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
35777 TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
35798 GAGAAAATAA
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 62 0.97
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:35969 original size:21 final size:21
Alignment explanation
Indices: 35943--35996 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
35933 GTTTCCAGAT
*
35943 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
35964 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
35985 TCGCAATGCGAA
1 TCGCAATGCGAA
35997 TATGTAAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.20
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:36035 original size:21 final size:19
Alignment explanation
Indices: 36011--36066 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 19
36001 TAAATCGCAA
*
36011 TGCGATAGTCCAAGTTCGCGT
1 TGCGATAGTCCAAATT--CGT
*
36032 TGCGATTTATTCCAAATTCGT
1 TGCGA--TAGTCCAAATTCGT
36053 TGCGATAGTCCAAA
1 TGCGATAGTCCAAA
36067 ATCGCTACGA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 8 0.27
21 13 0.43
23 9 0.30
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.32
Consensus pattern (19 bp):
TGCGATAGTCCAAATTCGT
Found at i:36827 original size:21 final size:21
Alignment explanation
Indices: 36801--36872 Score: 85
Period size: 21 Copynumber: 3.4 Consensus size: 21
36791 ATTGAAATAA
36801 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
* * *
36822 ATCGCAA--CGAATTTAGAAT
1 ATCGCAACGCGAACTTGGACT
36841 AAATCGCAACGCGAACTTGGACT
1 --ATCGCAACGCGAACTTGGACT
36864 ATCGCAACG
1 ATCGCAACG
36873 AACAGTCAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
19 9 0.22
21 23 0.56
23 9 0.22
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Found at i:36828 original size:37 final size:38
Alignment explanation
Indices: 36778--36870 Score: 134
Period size: 42 Copynumber: 2.4 Consensus size: 38
36768 CGTTGTGATT
36778 TTGGACTATCGCAATTGA-AATAAATCGCAACGCGAAC
1 TTGGACTATCGCAATTGAGAATAAATCGCAACGCGAAC
*
36815 TTGGACTATCGCAACGAATTTAGAATAAATCGCAACGCGAAC
1 TTGGACTATCG---C-AATTGAGAATAAATCGCAACGCGAAC
36857 TTGGACTATCGCAA
1 TTGGACTATCGCAA
36871 CGAACAGTCA
Statistics
Matches: 50, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
37 11 0.22
38 2 0.04
39 1 0.02
40 1 0.02
41 5 0.10
42 30 0.60
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.23
Consensus pattern (38 bp):
TTGGACTATCGCAATTGAGAATAAATCGCAACGCGAAC
Found at i:37228 original size:58 final size:57
Alignment explanation
Indices: 37166--37318 Score: 152
Period size: 58 Copynumber: 2.6 Consensus size: 57
37156 TGATGTATTT
*
37166 TAAATTAGTCATTGAACTTTTGAATATTTCAATTTCAC-CCTCAAACTATGACTC-ATTC
1 TAAATTAGTC-TTGAACTTTTGAATATTTCAATTTCACATC-CAAACTATGACTCGA-TC
* * *
37224 TAAATTAATCCTTGAACTTTTGAATATCAT-AATTTCATATCCAAACTATGACTCGATC
1 TAAATTAGT-CTTGAACTTTTGAATAT-TTCAATTTCACATCCAAACTATGACTCGATC
* * *
37282 TAAATTGGTCTCTAAACTTTTGAGTA-TTCTAATTTCA
1 TAAATTAGTCT-TGAACTTTTGAATATTTC-AATTTCA
37319 TTCTCAAATT
Statistics
Matches: 79, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
56 1 0.01
57 2 0.03
58 72 0.91
59 4 0.05
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (57 bp):
TAAATTAGTCTTGAACTTTTGAATATTTCAATTTCACATCCAAACTATGACTCGATC
Found at i:52827 original size:53 final size:53
Alignment explanation
Indices: 52759--52881 Score: 146
Period size: 50 Copynumber: 2.4 Consensus size: 53
52749 TTAACAGTAA
* * *
52759 AACGCG-CCCCTGCACCGCGTTATTATACGATGGTGTGGCGTCACGTG-GGTAT
1 AACGCGCCCCCTGCACCGCG-TATTATACGATGATGTGGCGCCACGTGAGATAT
*
52811 AACGCGCCCCCTGCA-C-CGTGTTATACGATGATGTGGCGCCACGTGAGATAT
1 AACGCGCCCCCTGCACCGCGTATTATACGATGATGTGGCGCCACGTGAGATAT
* * *
52862 AGCACACCCCCTGCACCGCG
1 AACGCGCCCCCTGCACCGCG
52882 CTATACGGTG
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
50 24 0.40
51 18 0.30
52 8 0.13
53 10 0.17
ACGTcount: A:0.20, C:0.33, G:0.28, T:0.20
Consensus pattern (53 bp):
AACGCGCCCCCTGCACCGCGTATTATACGATGATGTGGCGCCACGTGAGATAT
Found at i:53394 original size:23 final size:21
Alignment explanation
Indices: 53354--53399 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
53344 ATAATAAAGG
*
53354 TATTATTTTTTTTCATTTATT
1 TATTATTTTTTTTAATTTATT
*
53375 TATTATCTTTATTTTAATTTTTT
1 TATTAT-TTT-TTTTAATTTATT
53398 TA
1 TA
53400 CTGTGACTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 3 0.14
23 12 0.57
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (21 bp):
TATTATTTTTTTTAATTTATT
Found at i:56893 original size:10 final size:10
Alignment explanation
Indices: 56878--56931 Score: 60
Period size: 10 Copynumber: 5.6 Consensus size: 10
56868 ACAGAAGGTG
56878 TAAAAAATCA
1 TAAAAAATCA
56888 TAAAAAAT-A
1 TAAAAAATCA
56897 TAAAAAATACA
1 TAAAAAAT-CA
56908 -AAAAAAT-A
1 TAAAAAATCA
*
56916 CAAAAAATCA
1 TAAAAAATCA
*
56926 GAAAAA
1 TAAAAA
56932 TTACAAAACA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
8 1 0.03
9 16 0.41
10 21 0.54
11 1 0.03
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.15
Consensus pattern (10 bp):
TAAAAAATCA
Found at i:56930 original size:9 final size:9
Alignment explanation
Indices: 56879--56939 Score: 61
Period size: 9 Copynumber: 6.4 Consensus size: 9
56869 CAGAAGGTGT
*
56879 AAAAAATCAT
1 AAAAAAT-AC
*
56889 AAAAAATAT
1 AAAAAATAC
56898 AAAAAATAC
1 AAAAAATAC
56907 AAAAAAATAC
1 -AAAAAATAC
56917 AAAAAAT-C
1 AAAAAATAC
56925 AGAAAAATTAC
1 A-AAAAA-TAC
56936 AAAA
1 AAAA
56940 CAATTAGTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
8 2 0.04
9 22 0.48
10 20 0.43
11 2 0.04
ACGTcount: A:0.75, C:0.08, G:0.02, T:0.15
Consensus pattern (9 bp):
AAAAAATAC
Found at i:56936 original size:19 final size:18
Alignment explanation
Indices: 56879--56939 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 18
56869 CAGAAGGTGT
*
56879 AAAAAATCATAAAAAATAT
1 AAAAAATCA-AAAAAATAC
56898 AAAAAATACAAAAAAATAC
1 AAAAAAT-CAAAAAAATAC
*
56917 AAAAAATCAGAAAAATTAC
1 AAAAAATCA-AAAAAATAC
56936 AAAA
1 AAAA
56940 CAATTAGTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
18 2 0.05
19 34 0.89
20 2 0.05
ACGTcount: A:0.75, C:0.08, G:0.02, T:0.15
Consensus pattern (18 bp):
AAAAAATCAAAAAAATAC
Found at i:60992 original size:54 final size:54
Alignment explanation
Indices: 60928--61037 Score: 211
Period size: 54 Copynumber: 2.0 Consensus size: 54
60918 GATGACGAGT
60928 CGTTTGATCATTACTCTCCACTACACAGTTGCTTTTCTCGTAGTTCGTGGCCGC
1 CGTTTGATCATTACTCTCCACTACACAGTTGCTTTTCTCGTAGTTCGTGGCCGC
*
60982 CGTTTGATCATTACTCTCCACTACACGGTTGCTTTTCTCGTAGTTCGTGGCCGC
1 CGTTTGATCATTACTCTCCACTACACAGTTGCTTTTCTCGTAGTTCGTGGCCGC
61036 CG
1 CG
61038 CTATAGCTTT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.14, C:0.30, G:0.20, T:0.36
Consensus pattern (54 bp):
CGTTTGATCATTACTCTCCACTACACAGTTGCTTTTCTCGTAGTTCGTGGCCGC
Found at i:61933 original size:42 final size:41
Alignment explanation
Indices: 61887--61998 Score: 131
Period size: 41 Copynumber: 2.7 Consensus size: 41
61877 GGTTAAACAA
61887 TAGCGGCGTTTATAGTAAAAACGCCGCAATATAGCAG-ACATG
1 TAGCGGCGTTTATAGTAAAAACGCCGCAATATAG-AGTA-ATG
* *
61929 TAGCGGCGTTT-TAGCT-AAAACGCCGCAATATAGTGTTAATT
1 TAGCGGCGTTTATAG-TAAAAACGCCGCAATATAGAG-TAATG
**
61970 TAGCGGCGTTTATACCAAAAACGCCGCAA
1 TAGCGGCGTTTATAGTAAAAACGCCGCAA
61999 CAGAGTGGTA
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
40 1 0.02
41 33 0.54
42 27 0.44
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (41 bp):
TAGCGGCGTTTATAGTAAAAACGCCGCAATATAGAGTAATG
Found at i:62015 original size:42 final size:42
Alignment explanation
Indices: 61887--62022 Score: 159
Period size: 42 Copynumber: 3.3 Consensus size: 42
61877 GGTTAAACAA
* ** *
61887 TAGCGGCGTTTATAGTAAAAACGCCGCAATATAGCAG-ACAT
1 TAGCGGCGTTTATAGCAAAAACGCCGCAATATAGTGGTAAAT
* * *
61928 GTAGCGGCGTTT-TAGCTAAAACGCCGCAATATAGTGTTAATT
1 -TAGCGGCGTTTATAGCAAAAACGCCGCAATATAGTGGTAAAT
* * *
61970 TAGCGGCGTTTATACCAAAAACGCCGCAACAGAGTGGTAAAT
1 TAGCGGCGTTTATAGCAAAAACGCCGCAATATAGTGGTAAAT
62012 TAGCGGCGTTT
1 TAGCGGCGTTT
62023 TTTGTATAAA
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
41 31 0.39
42 48 0.61
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (42 bp):
TAGCGGCGTTTATAGCAAAAACGCCGCAATATAGTGGTAAAT
Found at i:65485 original size:21 final size:21
Alignment explanation
Indices: 65459--65511 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
65449 CGTTATATAT
* *
65459 GCAGAGAGAGCAGCAGTGGAA
1 GCAGAGAGAGAAGCAGCGGAA
* *
65480 GCAGAGAAAGAAGCAGCGGCA
1 GCAGAGAGAGAAGCAGCGGAA
*
65501 GCACAGAGAGA
1 GCAGAGAGAGA
65512 GTATCAGCAG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.17, G:0.40, T:0.02
Consensus pattern (21 bp):
GCAGAGAGAGAAGCAGCGGAA
Found at i:65881 original size:44 final size:44
Alignment explanation
Indices: 65831--65928 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 44
65821 ATCTTGTGTT
* *
65831 ATTTAGCGGCGTTTGCAAACTAGAAATGCCGCAATATACCAAAC
1 ATTTAGCGGCGTTTGCAAACTACAAACGCCGCAATATACCAAAC
* * * * **
65875 ATTTAGCGACGTTTGTATACTACAAACGCCGCAATATACTATGC
1 ATTTAGCGGCGTTTGCAAACTACAAACGCCGCAATATACCAAAC
65919 ATTTAGCGGC
1 ATTTAGCGGC
65929 ATTTTTTGCA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (44 bp):
ATTTAGCGGCGTTTGCAAACTACAAACGCCGCAATATACCAAAC
Found at i:66059 original size:43 final size:43
Alignment explanation
Indices: 65984--66256 Score: 194
Period size: 43 Copynumber: 6.3 Consensus size: 43
65974 TGTTTTCGAT
* * * * * * *
65984 AAAAACACCGCTAAAAAACATAACTTACTGCGGCGTTTTTGGG
1 AAAAACGCCGCTAAATATCAAAACCTATTGCGGCGTTTTTAGG
* * * *
66027 AAAAACGTCGCAAAATATCAAAACCTATTGCGGCGGTTTTAAG
1 AAAAACGCCGCTAAATATCAAAACCTATTGCGGCGTTTTTAGG
* * * *
66070 TAAAACGCCGCTACATCTCAAAA-CTATTTGCGGCGTTTTTAGA
1 AAAAACGCCGCTAAATATCAAAACCTA-TTGCGGCGTTTTTAGG
* * ** **
66113 AAAAACGCCGTTAAACATCAACGCCTATTGCGGCGTTTTTCTG
1 AAAAACGCCGCTAAATATCAAAACCTATTGCGGCGTTTTTAGG
* * *
66156 ACAAACGCCGCTAAATAACAAATCCTATTGCGGCGTTTGTTCA-G
1 AAAAACGCCGCTAAATATCAAAACCTATTGCGGCGTTT-TT-AGG
* * *** * *
66200 -AAAACGCCGCTATATGTTGTAACCTATTGCGGTGTTTTTTTA-C
1 AAAAACGCCGCTAAATATCAAAACCTATTGCGGCG--TTTTTAGG
66243 AAAAACGCCGCTAA
1 AAAAACGCCGCTAA
66257 CTTTAGCGGC
Statistics
Matches: 176, Mismatches: 47, Indels: 13
0.75 0.20 0.06
Matches are distributed among these distances:
42 3 0.02
43 150 0.85
44 20 0.11
45 3 0.02
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (43 bp):
AAAAACGCCGCTAAATATCAAAACCTATTGCGGCGTTTTTAGG
Found at i:66101 original size:129 final size:129
Alignment explanation
Indices: 65943--66211 Score: 269
Period size: 129 Copynumber: 2.1 Consensus size: 129
65933 TTTGCACTAG
** ** *
65943 AAACGCCGCTAATTCTCAACCCTTATTGCGTTG-TTTTCGATAAAAACACCGCTAAAAAACATA-
1 AAACGCCGCTAATTCTCAAAACTTATTGCGGCGTTTTTAGA-AAAAACACCGCTAAAAAACA-AC
* * * *
66006 ACTTACTGCGGCGTTTTTGGGAAAAACGTCGCAAAATATCAAAACCTATTGCGGCGGTT-TTAAG
64 ACCTACTGCGGCGTTTTTCGGAAAAACGCCGCAAAATAACAAAACCTATTGCGGCGGTTGTTAAG
66070 TA
129 -A
* * * *
66072 AAACGCCGCTACA-TCTCAAAAC-TATTTGCGGCGTTTTTAGAAAAAACGCCGTTAAACATCAAC
1 AAACGCCGCTA-ATTCTCAAAACTTA-TTGCGGCGTTTTTAGAAAAAACACCGCTAAAAAACAAC
* * * * * * * *
66135 GCCTATTGCGGCGTTTTTCTGACAAACGCCGCTAAATAACAAATCCTATTGCGGCGTTTGTTCAG
64 ACCTACTGCGGCGTTTTTCGGAAAAACGCCGCAAAATAACAAAACCTATTGCGGCGGTTGTTAAG
66200 A
129 A
66201 AAACGCCGCTA
1 AAACGCCGCTA
66212 TATGTTGTAA
Statistics
Matches: 114, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
128 3 0.03
129 100 0.88
130 11 0.10
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (129 bp):
AAACGCCGCTAATTCTCAAAACTTATTGCGGCGTTTTTAGAAAAAACACCGCTAAAAAACAACAC
CTACTGCGGCGTTTTTCGGAAAAACGCCGCAAAATAACAAAACCTATTGCGGCGGTTGTTAAGA
Found at i:66294 original size:12 final size:14
Alignment explanation
Indices: 66258--66294 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
66248 CGCCGCTAAC
66258 TTTAGCGGCGCTAT
1 TTTAGCGGCGCTAT
66272 TTTCAGCGGCGCT-T
1 TTT-AGCGGCGCTAT
66286 TTT-GCGGCG
1 TTTAGCGGCG
66295 TTTGTCATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.27
14 7 0.32
15 9 0.41
ACGTcount: A:0.08, C:0.24, G:0.32, T:0.35
Consensus pattern (14 bp):
TTTAGCGGCGCTAT
Found at i:66975 original size:25 final size:25
Alignment explanation
Indices: 66947--67002 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
66937 AACACCCAAA
66947 AAATTTTGAGAAAAAAATTCTTTAT
1 AAATTTTGAGAAAAAAATTCTTTAT
66972 AAATTTTGAGAAAAAAATTCTTTAT
1 AAATTTTGAGAAAAAAATTCTTTAT
66997 AAATTT
1 AAATTT
67003 AATATAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (25 bp):
AAATTTTGAGAAAAAAATTCTTTAT
Found at i:70863 original size:20 final size:20
Alignment explanation
Indices: 70837--70905 Score: 93
Period size: 20 Copynumber: 3.4 Consensus size: 20
70827 GAATTGGGAA
*
70837 AATCGCAATGCGATACTGAC
1 AATCGCAATGCGATACTCAC
*
70857 TATCGCAATGCGATACTCAC
1 AATCGCAATGCGATACTCAC
* *
70877 AATCGCAATGCGATAATACAA
1 AATCGCAATGCGATACT-CAC
70898 AATCGCAA
1 AATCGCAA
70906 CGAGATACTG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 33 0.77
21 10 0.23
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.20
Consensus pattern (20 bp):
AATCGCAATGCGATACTCAC
Found at i:71472 original size:20 final size:21
Alignment explanation
Indices: 71436--71497 Score: 69
Period size: 19 Copynumber: 3.1 Consensus size: 21
71426 AGAATAGTTT
*
71436 CGAG-AATGAAAATCGCAACG
1 CGAGAAATAAAAATCGCAACG
**
71456 CG-GAAATAACTATCGCAA-G
1 CGAGAAATAAAAATCGCAACG
71475 -GAGAAATAAAAATCGCAACG
1 CGAGAAATAAAAATCGCAACG
71495 CGA
1 CGA
71498 AACCAAAATC
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
18 1 0.03
19 16 0.48
20 14 0.42
21 2 0.06
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.11
Consensus pattern (21 bp):
CGAGAAATAAAAATCGCAACG
Found at i:71489 original size:19 final size:20
Alignment explanation
Indices: 71444--71510 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 20
71434 TTCGAGAATG
71444 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGCGGAAATA
**
71464 ACTATCGCAA-G-GAGAAATA
1 AAAATCGCAACGCG-GAAATA
**
71483 AAAATCGCAACGC-GAAACC
1 AAAATCGCAACGCGGAAATA
71502 AAAATCGCA
1 AAAATCGCA
71511 TTGCGATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
18 1 0.03
19 28 0.74
20 9 0.24
ACGTcount: A:0.49, C:0.22, G:0.18, T:0.10
Consensus pattern (20 bp):
AAAATCGCAACGCGGAAATA
Found at i:71557 original size:33 final size:33
Alignment explanation
Indices: 71520--71607 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
71510 ATTGCGATTT
71520 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
* *
71553 TCATTTCGCGTTGTGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
71586 TCATTTCCGCATTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
71608 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 37 0.74
34 13 0.26
ACGTcount: A:0.12, C:0.26, G:0.22, T:0.40
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:71609 original size:20 final size:19
Alignment explanation
Indices: 71572--71632 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 19
71562 GTTGTGATTC
**
71572 TCTCGTTGCGATAGTCATT
1 TCTCGTTGCGATTCTCATT
71591 TC-CGCATTGCGATTCTCATT
1 TCTCG--TTGCGATTCTCATT
*
71611 ATCTCGTTGCGATTTTCATT
1 -TCTCGTTGCGATTCTCATT
71631 TC
1 TC
71633 AACCAAAAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
18 2 0.06
19 4 0.11
20 25 0.71
21 2 0.06
22 2 0.06
ACGTcount: A:0.15, C:0.25, G:0.16, T:0.44
Consensus pattern (19 bp):
TCTCGTTGCGATTCTCATT
Found at i:73799 original size:42 final size:42
Alignment explanation
Indices: 73723--73811 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
73713 GACTCGCCTG
* *
73723 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCTACCGTTCAAGAGGCCCCTA
* * * * *
73765 TCATTCCTCGAGAGTCCCCTCCTACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCTACCGTTCAAGAGGCCCCTA
73807 TCATC
1 TCATC
73812 GTTGAAGAGG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.21, C:0.37, G:0.17, T:0.25
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCTACCGTTCAAGAGGCCCCTA
Found at i:75210 original size:14 final size:14
Alignment explanation
Indices: 75191--75226 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
75181 ATTGTTTAAT
75191 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
75205 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
75219 TGATTTGT
1 TGATTTGT
75227 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:75357 original size:19 final size:19
Alignment explanation
Indices: 75333--75409 Score: 74
Period size: 19 Copynumber: 4.3 Consensus size: 19
75323 AAAAAGTACT
*
75333 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
**
75352 ATCGCAA--CG--A-GGGA
1 ATCGCAACGCGAAATGAAA
75366 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
75385 ATCGCAACGCGAAATTAAA
1 ATCGCAACGCGAAATGAAA
*
75404 TTCGCA
1 ATCGCA
75410 TTGCGATTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
14 9 0.19
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 32 0.68
ACGTcount: A:0.43, C:0.21, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:75415 original size:19 final size:19
Alignment explanation
Indices: 75374--75434 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 19
75364 GAATCGCAAC
* * **
75374 GCGAAATGAAAATCGCAAC
1 GCGAAATTAAATTCGCATT
75393 GCGAAATTAAATTCGCATT
1 GCGAAATTAAATTCGCATT
** * *
75412 GCGATTTTCATTTCGCATT
1 GCGAAATTAAATTCGCATT
75431 GCGA
1 GCGA
75435 TTCCCTCGTT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (19 bp):
GCGAAATTAAATTCGCATT
Found at i:75435 original size:19 final size:19
Alignment explanation
Indices: 75404--75501 Score: 99
Period size: 19 Copynumber: 5.7 Consensus size: 19
75394 CGAAATTAAA
75404 TTCGCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
75423 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
75439 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
75456 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
75472 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
75489 TTCGCATTGCGAT
1 TTCGCATTGCGAT
75502 AGTAATTTCC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 12 0.19
16 13 0.21
17 13 0.21
19 25 0.40
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:75452 original size:33 final size:33
Alignment explanation
Indices: 75410--75501 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
75400 TAAATTCGCA
75410 TTGCGATTTTCATTTCGCATTGCGATTCCCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCCCTCG
*
75443 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCCCTCG
75476 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
75502 AGTAATTTCC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCCCTCG
Found at i:77657 original size:12 final size:12
Alignment explanation
Indices: 77640--77664 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
77630 TCTTCGGGGA
77640 CTTTTTCTTCTT
1 CTTTTTCTTCTT
77652 CTTTTTCTTCTT
1 CTTTTTCTTCTT
77664 C
1 C
77665 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:77873 original size:24 final size:24
Alignment explanation
Indices: 77839--77892 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
77829 CTGAAACATC
*
77839 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
77863 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
77887 ATCAAA
1 ATCAAA
77893 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:78720 original size:20 final size:20
Alignment explanation
Indices: 78634--78728 Score: 102
Period size: 20 Copynumber: 4.7 Consensus size: 20
78624 GATTCTGTAT
* *
78634 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
78654 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
78674 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
78695 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
78715 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
78729 TTTACCAATT
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 44 0.70
21 14 0.22
22 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:78742 original size:41 final size:41
Alignment explanation
Indices: 78655--78749 Score: 129
Period size: 41 Copynumber: 2.3 Consensus size: 41
78645 GAAAGTCAGA
* * ** *
78655 ATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAT
78696 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTACCAAT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTT-CCAAT
78738 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
78750 TTACTTATTC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 46 0.96
42 2 0.04
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:78759 original size:20 final size:21
Alignment explanation
Indices: 78717--78764 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
78707 ATAGTCAGTA
78717 TCGCATTGCGATTTTACCAAT
1 TCGCATTGCGATTTTACCAAT
* **
78738 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACCAAT
78758 TCGCATT
1 TCGCATT
78765 ACGAATTGGG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.42
Consensus pattern (21 bp):
TCGCATTGCGATTTTACCAAT
Found at i:85570 original size:7 final size:7
Alignment explanation
Indices: 85558--85585 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
85548 TTGTTAAGTC
85558 AAAATTT
1 AAAATTT
85565 AAAATTT
1 AAAATTT
85572 AAAATTT
1 AAAATTT
85579 AAAATTT
1 AAAATTT
85586 GAAGATTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
AAAATTT
Found at i:86352 original size:20 final size:20
Alignment explanation
Indices: 86323--86364 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
86313 TCAATTCAAG
86323 ATTTTATTTATA-AATGAAA
1 ATTTTATTTATACAATGAAA
86342 ATTTATATTTATACAATGAAA
1 ATTT-TATTTATACAATGAAA
86363 AT
1 AT
86365 ATCATACAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 4 0.19
20 8 0.38
21 9 0.43
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (20 bp):
ATTTTATTTATACAATGAAA
Found at i:87680 original size:2 final size:2
Alignment explanation
Indices: 87673--87726 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
87663 AAATGAGAAT
87673 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
87715 TA TA TA TA TA TA
1 TA TA TA TA TA TA
87727 CACTCATGTC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:89572 original size:19 final size:19
Alignment explanation
Indices: 89548--89598 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
89538 ACCAATTAAA
*
89548 TCGCAATACGATCGATAAT
1 TCGCAATGCGATCGATAAT
89567 TCGCAATGCGATCGATAAT
1 TCGCAATGCGATCGATAAT
89586 TCGCAATGCGATC
1 TCGCAATGCGATC
89599 TCCGGTATCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (19 bp):
TCGCAATGCGATCGATAAT
Found at i:89652 original size:21 final size:21
Alignment explanation
Indices: 89626--89668 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
89616 ATTTCCAGAT
89626 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
*
89647 TCGCAATGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
89668 T
1 T
89669 TGGAAACACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGACTA
Found at i:90093 original size:21 final size:21
Alignment explanation
Indices: 89988--90099 Score: 124
Period size: 21 Copynumber: 5.4 Consensus size: 21
89978 CCAAGTTCGT
89988 AAGTTCGCATTGCGATAGTCG
1 AAGTTCGCATTGCGATAGTCG
* * *
90009 -ACTATCGCATTGCAAT-TTAC-
1 AAGT-TCGCATTGCGATAGT-CG
*
90029 ATA-TTCGCATTGCGATAGTCC
1 A-AGTTCGCATTGCGATAGTCG
*
90050 AAGTTCGTATTGCGATAGTCG
1 AAGTTCGCATTGCGATAGTCG
90071 AAGTTCGCATTGCGATAGTCG
1 AAGTTCGCATTGCGATAGTCG
90092 AAGTTCGC
1 AAGTTCGC
90100 TGCGAATCTG
Statistics
Matches: 76, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
20 16 0.21
21 59 0.78
22 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (21 bp):
AAGTTCGCATTGCGATAGTCG
Found at i:94539 original size:110 final size:112
Alignment explanation
Indices: 94378--94588 Score: 354
Period size: 110 Copynumber: 1.9 Consensus size: 112
94368 AATGAAATGG
*
94378 AAAAAATGAGAAATGCGGGAAAAAATTAAGTGGCTTCCACATCAGC-AAAAAAAAGGTCATGTCA
1 AAAAAAAGAGAAATGCGGGAAAAAATTAAGTGGCTTCCACATCAGCAAAAAAAAAGGTCATGTCA
*
94442 CCA-TGTTTCTAATTTAACGCTTGAGTGACAAAAATGAAATGGAAAA
66 CCATTGTTTCTAATTTAACGCCTGAGTGACAAAAATGAAATGGAAAA
* *
94488 AAAAAAAGAGAAATGCGGGAAAAAATTAAGTGGCTTCCACATCATCCAAAAAAAAGGTCATGTCA
1 AAAAAAAGAGAAATGCGGGAAAAAATTAAGTGGCTTCCACATCAGCAAAAAAAAAGGTCATGTCA
94553 CCATGTTGTTTCTAATTTAACGCCTGAGTGACAAAA
66 CCA--TTGTTTCTAATTTAACGCCTGAGTGACAAAA
94589 GATGGAGCAC
Statistics
Matches: 94, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
110 44 0.47
111 21 0.22
114 29 0.31
ACGTcount: A:0.44, C:0.15, G:0.18, T:0.22
Consensus pattern (112 bp):
AAAAAAAGAGAAATGCGGGAAAAAATTAAGTGGCTTCCACATCAGCAAAAAAAAAGGTCATGTCA
CCATTGTTTCTAATTTAACGCCTGAGTGACAAAAATGAAATGGAAAA
Found at i:106223 original size:20 final size:20
Alignment explanation
Indices: 106187--106241 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
106177 GATTGCCTTA
106187 TACA-TTTTT-AAAT-TA-T
1 TACATTTTTTAAAATATATT
106203 TACATTTATTTAAAATATATT
1 TACATTT-TTTAAAATATATT
**
106224 TTTATTTTTTAAAATATA
1 TACATTTTTTAAAATATA
106242 ACTCTCATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 4 0.12
17 2 0.06
18 3 0.09
19 4 0.12
20 13 0.41
21 6 0.19
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (20 bp):
TACATTTTTTAAAATATATT
Found at i:108522 original size:31 final size:31
Alignment explanation
Indices: 108419--108522 Score: 77
Period size: 31 Copynumber: 3.4 Consensus size: 31
108409 AATTGTTTGG
* * * *
108419 ATTACTAAA-TTTTCAAA-AGTTATAAAGTT
1 ATTATTAAATTTTTCAAACTGTTATAAAATA
* * * *
108448 ATTATTAAATTTATCAAATTGCTATAAAACA
1 ATTATTAAATTTTTCAAACTGTTATAAAATA
** * **
108479 ACCATTACATTTTTTTAACTGTTATAAAATA
1 ATTATTAAATTTTTCAAACTGTTATAAAATA
108510 ATTATTAAATTTT
1 ATTATTAAATTTT
108523 AGCAAACCCT
Statistics
Matches: 54, Mismatches: 19, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
29 8 0.15
30 7 0.13
31 39 0.72
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (31 bp):
ATTATTAAATTTTTCAAACTGTTATAAAATA
Found at i:108928 original size:22 final size:22
Alignment explanation
Indices: 108885--108930 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
108875 CGGATCTAAC
*
108885 AAATTTTTAAATACTTTCTATA
1 AAATTTTTAAATACTTTATATA
*
108907 AAATTTTTATAA-ATTTTATATA
1 AAATTTTTA-AATACTTTATATA
108929 AA
1 AA
108931 TTTACTCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (22 bp):
AAATTTTTAAATACTTTATATA
Found at i:109656 original size:21 final size:21
Alignment explanation
Indices: 109632--109671 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
109622 CAACATCCTC
109632 AAGACACCGGAAATCCCAAAT
1 AAGACACCGGAAATCCCAAAT
* * *
109653 AAGACGCTGGAGATCCCAA
1 AAGACACCGGAAATCCCAA
109672 GCAAGACCCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.28, G:0.20, T:0.10
Consensus pattern (21 bp):
AAGACACCGGAAATCCCAAAT
Found at i:113515 original size:16 final size:17
Alignment explanation
Indices: 113496--113529 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
113486 TTTAAAGTAG
113496 TATT-TTTTTACTTTTA
1 TATTGTTTTTACTTTTA
*
113512 TATTGTTTTTTCTTTTA
1 TATTGTTTTTACTTTTA
113529 T
1 T
113530 CATTAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.15, C:0.06, G:0.03, T:0.76
Consensus pattern (17 bp):
TATTGTTTTTACTTTTA
Found at i:120243 original size:12 final size:12
Alignment explanation
Indices: 120226--120250 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
120216 ACCCGGTTAG
120226 TTTTTATTTTTT
1 TTTTTATTTTTT
120238 TTTTTATTTTTT
1 TTTTTATTTTTT
120250 T
1 T
120251 ATATATAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTTTATTTTTT
Found at i:120989 original size:25 final size:27
Alignment explanation
Indices: 120961--121015 Score: 78
Period size: 25 Copynumber: 2.1 Consensus size: 27
120951 TACAGTAAAA
* *
120961 AATTACAGAAATATCA-T-TTTTTTAC
1 AATTACAAAAATATCACTATTTTTAAC
120986 AATTACAAAAATATCACTATTTTTAAC
1 AATTACAAAAATATCACTATTTTTAAC
121013 AAT
1 AAT
121016 AATTACTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 15 0.58
26 1 0.04
27 10 0.38
ACGTcount: A:0.45, C:0.13, G:0.02, T:0.40
Consensus pattern (27 bp):
AATTACAAAAATATCACTATTTTTAAC
Found at i:121232 original size:29 final size:29
Alignment explanation
Indices: 120986--121236 Score: 256
Period size: 29 Copynumber: 8.6 Consensus size: 29
120976 ATTTTTTTAC
* **
120986 AATTACAAAAATATCACTATTTTTAACAAT
1 AATTACCAAAATATCAC-CGTTTTAACAAT
*
121016 AATTA-CTAAATATCACCGTTTTAACAAT
1 AATTACCAAAATATCACCGTTTTAACAAT
* * *
121044 AATTACCAAAATAGCATCATTTTAACAAT
1 AATTACCAAAATATCACCGTTTTAACAAT
* *
121073 AATTACCAACATAGCACCGTTTTAACAAT
1 AATTACCAAAATATCACCGTTTTAACAAT
*
121102 AATTACCAAAATATCACTGTTTTAACAAT
1 AATTACCAAAATATCACCGTTTTAACAAT
*
121131 AATTACCAAAATATTACCGTTTTAA-AATT
1 AATTACCAAAATATCACCGTTTTAACAA-T
* * * *
121160 AATTACAAAAATAACACCCTTTTTAAAAAT
1 AATTACCAAAATATCA-CCGTTTTAACAAT
* * * *
121190 AAATACAAAAATAACACAC-TTTTAAAAAT
1 AATTACCAAAATATCAC-CGTTTTAACAAT
* *
121219 AATTACGAAAATAACACC
1 AATTACCAAAATATCACC
121237 ATAACCGAAA
Statistics
Matches: 193, Mismatches: 23, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
28 18 0.09
29 143 0.74
30 30 0.16
31 2 0.01
ACGTcount: A:0.49, C:0.17, G:0.03, T:0.31
Consensus pattern (29 bp):
AATTACCAAAATATCACCGTTTTAACAAT
Found at i:121796 original size:21 final size:21
Alignment explanation
Indices: 121752--121836 Score: 104
Period size: 21 Copynumber: 4.1 Consensus size: 21
121742 CCACTTCATT
*
121752 TTATTTTATTCT-TAATGC-TA
1 TTATTTTATT-TATAGTGCTTA
**
121772 TTATAATATTTATAGTGCTTA
1 TTATTTTATTTATAGTGCTTA
121793 TTATTTTATTTATAGTGCTTA
1 TTATTTTATTTATAGTGCTTA
*
121814 TTATTTTATCTATAGTGC-TA
1 TTATTTTATTTATAGTGCTTA
121834 TTA
1 TTA
121837 GATATATATA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
19 1 0.02
20 18 0.32
21 38 0.67
ACGTcount: A:0.27, C:0.07, G:0.08, T:0.58
Consensus pattern (21 bp):
TTATTTTATTTATAGTGCTTA
Found at i:121828 original size:42 final size:40
Alignment explanation
Indices: 121752--121836 Score: 100
Period size: 41 Copynumber: 2.1 Consensus size: 40
121742 CCACTTCATT
*
121752 TTATTTTATTCTTAATGCTATTATAATATTTATAGTGCTTA
1 TTATTTTATTCTTAATGCTATTATAATATCTATAGTGC-TA
* **
121793 TTATTTTATT-TATAGTGCTTATTATTTTATCTATAGTGCTA
1 TTATTTTATTCT-TAATGC-TATTATAATATCTATAGTGCTA
121834 TTA
1 TTA
121837 GATATATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
40 1 0.03
41 20 0.53
42 17 0.45
ACGTcount: A:0.27, C:0.07, G:0.08, T:0.58
Consensus pattern (40 bp):
TTATTTTATTCTTAATGCTATTATAATATCTATAGTGCTA
Found at i:128453 original size:31 final size:30
Alignment explanation
Indices: 128413--128517 Score: 99
Period size: 31 Copynumber: 3.4 Consensus size: 30
128403 ACGTATGTTA
*
128413 CATATACATTAATGATGATATAATATATAT
1 CATATACATTAATGATGATATAATGTATAT
**
128443 CATAGTACATTGGTAATGACTTGACGT-ATGT-TA-
1 CATA-TACA-T--TAATGA--TGATATAATGTATAT
128476 CATATACATTAATGATGATATAATGTATAT
1 CATATACATTAATGATGATATAATGTATAT
128506 CATAGTACATTA
1 CATA-TACATTA
128518 GTAATGACGT
Statistics
Matches: 60, Mismatches: 5, Indels: 19
0.71 0.06 0.23
Matches are distributed among these distances:
27 4 0.07
28 4 0.07
29 8 0.13
30 8 0.13
31 12 0.20
32 5 0.08
33 4 0.07
34 8 0.13
35 3 0.05
36 4 0.07
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (30 bp):
CATATACATTAATGATGATATAATGTATAT
Found at i:128471 original size:63 final size:63
Alignment explanation
Indices: 128398--128566 Score: 275
Period size: 63 Copynumber: 2.7 Consensus size: 63
128388 ATCAATGATA
*
128398 ACTTGACGTATGTTACATATACATTAATGATGATATAATATATATCATAGTACATTGGTAATG
1 ACTTGACGTATGTTACATATACATTAATGATGATATAATATATATCATAGTACATTAGTAATG
*
128461 ACTTGACGTATGTTACATATACATTAATGATGATATAATGTATATCATAGTACATTAGTAATG
1 ACTTGACGTATGTTACATATACATTAATGATGATATAATATATATCATAGTACATTAGTAATG
* * * * *
128524 ACGTGACGTATGTTACATGTACATTAGTGATGACATAACATAT
1 ACTTGACGTATGTTACATATACATTAATGATGATATAATATAT
128567 GTTATATATG
Statistics
Matches: 98, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 98 1.00
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (63 bp):
ACTTGACGTATGTTACATATACATTAATGATGATATAATATATATCATAGTACATTAGTAATG
Found at i:128551 original size:32 final size:32
Alignment explanation
Indices: 128447--128570 Score: 108
Period size: 32 Copynumber: 3.9 Consensus size: 32
128437 ATATATCATA
* *
128447 GTACATTGGTAATGACTTGACGTATGTTACAT
1 GTACATTAGTAATGACATGACGTATGTTACAT
* * * * * * *
128479 ATACATTAATGATGATATAATGTAT-AT-CAT
1 GTACATTAGTAATGACATGACGTATGTTACAT
*
128509 AGTACATTAGTAATGACGTGACGTATGTTACAT
1 -GTACATTAGTAATGACATGACGTATGTTACAT
* * *
128542 GTACATTAGTGATGACATAACATATGTTA
1 GTACATTAGTAATGACATGACGTATGTTA
128571 TATATGGTAC
Statistics
Matches: 68, Mismatches: 21, Indels: 6
0.72 0.22 0.06
Matches are distributed among these distances:
30 3 0.04
31 19 0.28
32 43 0.63
33 3 0.04
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.36
Consensus pattern (32 bp):
GTACATTAGTAATGACATGACGTATGTTACAT
Found at i:136578 original size:29 final size:31
Alignment explanation
Indices: 136510--136585 Score: 77
Period size: 31 Copynumber: 2.5 Consensus size: 31
136500 AACTACATCA
*
136510 GATATCACTAAACTTTAAATATTGTATTATT
1 GATAACACTAAACTTTAAATATTGTATTATT
* * *
136541 GATACCACTAAATTTTCAAT-TT-TATTAATT
1 GATAACACTAAACTTTAAATATTGTATT-ATT
*
136571 -ATAACACTGAACTTT
1 GATAACACTAAACTTT
136586 TATTTCCATT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
29 16 0.42
30 5 0.13
31 17 0.45
ACGTcount: A:0.38, C:0.13, G:0.05, T:0.43
Consensus pattern (31 bp):
GATAACACTAAACTTTAAATATTGTATTATT
Found at i:146920 original size:31 final size:30
Alignment explanation
Indices: 146879--146942 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
146869 ATTTTAAAAG
146879 TTACAAATAACCATTA-AAT-TTATCAAATAA
1 TTACAAATAACCATTATAATATTAT--AATAA
*
146909 TTACAAAATAACTATTATAATATTATAATAA
1 TTAC-AAATAACCATTATAATATTATAATAA
146940 TTA
1 TTA
146943 TGGTAATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 4 0.13
31 19 0.63
32 3 0.10
33 4 0.13
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (30 bp):
TTACAAATAACCATTATAATATTATAATAA
Found at i:147043 original size:31 final size:31
Alignment explanation
Indices: 146968--147057 Score: 117
Period size: 32 Copynumber: 2.8 Consensus size: 31
146958 ATTAATTATA
* * *
146968 TGATAAAGTTTAATAATCGTTTTATAATCATT
1 TGATAAA-TTTAATGATCATTTTATAATAATT
**
147000 CAATAAAATTTAATGATCATTTTATAATAATT
1 TGAT-AAATTTAATGATCATTTTATAATAATT
147032 TGATAAATTTAATGATCATTTTATAA
1 TGATAAATTTAATGATCATTTTATAA
147058 CTTTTTTTAT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
31 22 0.44
32 25 0.50
33 3 0.06
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.46
Consensus pattern (31 bp):
TGATAAATTTAATGATCATTTTATAATAATT
Found at i:153960 original size:2 final size:2
Alignment explanation
Indices: 153953--154004 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
153943 TAACATGATC
153953 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
153995 AT AT AT AT AT
1 AT AT AT AT AT
154005 GGATACATGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:154356 original size:18 final size:18
Alignment explanation
Indices: 154335--154382 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
154325 TTTTGATTAT
154335 ATATAATAATTAATCTAA
1 ATATAATAATTAATCTAA
*
154353 ATATAATATTTAATCTAA
1 ATATAATAATTAATCTAA
154371 AT-TAATTAATTA
1 ATATAA-TAATTA
154383 TATCAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 3 0.11
18 24 0.89
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATAATAATTAATCTAA
Found at i:168899 original size:31 final size:31
Alignment explanation
Indices: 168864--168923 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
168854 TGAAATGACT
*
168864 TTTTTGTTAATATATAATAATGATATATATC
1 TTTTTATTAATATATAATAATGATATATATC
* *
168895 TTTTTATTAATATTTAATTATGATATATA
1 TTTTTATTAATATATAATAATGATATATA
168924 ATATTTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (31 bp):
TTTTTATTAATATATAATAATGATATATATC
Found at i:168931 original size:31 final size:31
Alignment explanation
Indices: 168865--168931 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
168855 GAAATGACTT
* *
168865 TTTTGTTAATATATAATAATGATATATATCT
1 TTTTATTAATATATAATAATGATATATATCA
* *
168896 TTTTATTAATATTTAATTATGATATATAAT-A
1 TTTTATTAATATATAATAATGATATAT-ATCA
168927 TTTTA
1 TTTTA
168932 AATAAAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 29 0.94
32 2 0.06
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.55
Consensus pattern (31 bp):
TTTTATTAATATATAATAATGATATATATCA
Found at i:169029 original size:16 final size:16
Alignment explanation
Indices: 169008--169045 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
168998 CTCAACTTCT
*
169008 ACCGTCTCACCTTCCC
1 ACCGTCTCACCCTCCC
169024 ACCGTCTCACCCTCCC
1 ACCGTCTCACCCTCCC
169040 ACCGTC
1 ACCGTC
169046 ATTGTTTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.13, C:0.58, G:0.08, T:0.21
Consensus pattern (16 bp):
ACCGTCTCACCCTCCC
Found at i:175962 original size:15 final size:15
Alignment explanation
Indices: 175942--175973 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
175932 TGTTAGTCAA
175942 AAGACAAACAATTTT
1 AAGACAAACAATTTT
*
175957 AAGACAAACACTTTT
1 AAGACAAACAATTTT
175972 AA
1 AA
175974 TAATTTGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.16, G:0.06, T:0.25
Consensus pattern (15 bp):
AAGACAAACAATTTT
Found at i:182735 original size:9 final size:9
Alignment explanation
Indices: 182711--182755 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
182701 TCTAGGAGGA
*
182711 CCACCAGAG
1 CCACCAAAG
*
182720 CCTCCAAAG
1 CCACCAAAG
* *
182729 CCCCCAAAA
1 CCACCAAAG
182738 CCACCAAAG
1 CCACCAAAG
182747 CCACCAAAG
1 CCACCAAAG
182756 GGGTCGCCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.40, C:0.47, G:0.11, T:0.02
Consensus pattern (9 bp):
CCACCAAAG
Found at i:187952 original size:19 final size:18
Alignment explanation
Indices: 187930--187972 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
187920 TTTAACATTG
187930 AAAATTA-ATTTTGGAAAAT
1 AAAATTAGA-TTT-GAAAAT
*
187949 AAAATTAGATTTGAGAAT
1 AAAATTAGATTTGAAAAT
187967 AAAATT
1 AAAATT
187973 TGGAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 11 0.50
19 10 0.45
20 1 0.05
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (18 bp):
AAAATTAGATTTGAAAAT
Found at i:188864 original size:3 final size:3
Alignment explanation
Indices: 188856--188882 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
188846 TAAAAAATAA
188856 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
188883 TGATTGCAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:189929 original size:162 final size:163
Alignment explanation
Indices: 189721--190013 Score: 543
Period size: 162 Copynumber: 1.8 Consensus size: 163
189711 TTCTGAATTC
*
189721 TAATATATTAATATTTAATTATTATATTATATATAGGATATGAATCTATTTATTTTATTGTAAAG
1 TAATATATTAATATTTAATTATTATATTACATATAGGATATGAATCTATTTATTTTATTGTAAAG
* * *
189786 TTGAATGAATTTTATATGTTATTGTAGGATTAATATTTTAATAATATAATTATGTTATATATAAA
66 TTGAATGAATTTTAAAAGTTATTGTAGGATTAATATTTTAATAATATAATTATATTATATATAAA
189851 ATTTTAAGTTGATAGATAACGATTCAAAAAAAT
131 ATTTTAAGTTGATAGATAACGATTCAAAAAAAT
189884 TAATATATTAATATTTAATTA-TATATTACATATAGGATATGAATCTATTTATTTTATTGTAAAG
1 TAATATATTAATATTTAATTATTATATTACATATAGGATATGAATCTATTTATTTTATTGTAAAG
189948 TTGAATGAATTTTAAAAGTTATTGTAGGATTAATATTTTAATAATATAATTATATTATATATAAA
66 TTGAATGAATTTTAAAAGTTATTGTAGGATTAATATTTTAATAATATAATTATATTATATATAAA
190013 A
131 A
190014 AAAGATTTAT
Statistics
Matches: 126, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
162 105 0.83
163 21 0.17
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (163 bp):
TAATATATTAATATTTAATTATTATATTACATATAGGATATGAATCTATTTATTTTATTGTAAAG
TTGAATGAATTTTAAAAGTTATTGTAGGATTAATATTTTAATAATATAATTATATTATATATAAA
ATTTTAAGTTGATAGATAACGATTCAAAAAAAT
Found at i:195316 original size:20 final size:20
Alignment explanation
Indices: 195291--195459 Score: 110
Period size: 20 Copynumber: 8.4 Consensus size: 20
195281 GATTTTCCAT
*
195291 AATCGCAACGGGAATATGAA
1 AATCGCAACGCGAATATGAA
*
195311 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGCGAATATGA-A
* * *
195331 AATCGCAACGCGATTCTGAC
1 AATCGCAACGCGAATATGAA
*
195351 TATCGCAA--CGAATATCCGTAA
1 AATCGCAACGCGAATAT--G-AA
* ** *
195372 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATATGAA
* * *
195392 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATATGAA
* * *
195412 AATCGCAACGCGTATCTGTA
1 AATCGCAACGCGAATATGAA
* * *
195432 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATATGAA
195452 AATCGCAA
1 AATCGCAA
195460 TGCGTATCCG
Statistics
Matches: 116, Mismatches: 26, Indels: 14
0.74 0.17 0.09
Matches are distributed among these distances:
18 5 0.04
19 1 0.01
20 96 0.83
21 10 0.09
23 4 0.03
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGAATATGAA
Found at i:195396 original size:81 final size:80
Alignment explanation
Indices: 195310--195507 Score: 215
Period size: 81 Copynumber: 2.5 Consensus size: 80
195300 GGGAATATGA
* *
195310 AAATCGCAACGCGAACATATAAATCGCAACGCGATTCTG-ACTATCGCAACGA-ATATCCGTAAA
1 AAATCGCAACGCGAACATATAAATCGCAACGCGATTCTGTA-AATCGCAACGAGA-ATACGT-AA
195373 ATCGCAACGCGTATCCGT
63 ATCGCAACGCGTATCCGT
* * **
195391 AAATCGCAACGAGAATACGTAAATCGCAACGCG-TATCTGTAAATCGCAACGAGAATACGTAAAT
1 AAATCGCAACGCGAACATATAAATCGCAACGCGAT-TCTGTAAATCGCAACGAGAATACGTAAAT
*
195455 CGCAATGCGTATCCGT
65 CGCAACGCGTATCCGT
* * * *
195471 AAATTGCATCGACAATACGTA-AAATCGCAACGCGATT
1 AAATCGCAACG-CGA-ACATATAAATCGCAACGCGATT
195508 TTTAAAGCGC
Statistics
Matches: 96, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
80 29 0.30
81 63 0.66
82 4 0.04
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.20
Consensus pattern (80 bp):
AAATCGCAACGCGAACATATAAATCGCAACGCGATTCTGTAAATCGCAACGAGAATACGTAAATC
GCAACGCGTATCCGT
Found at i:195426 original size:40 final size:41
Alignment explanation
Indices: 195352--195504 Score: 222
Period size: 40 Copynumber: 3.8 Consensus size: 41
195342 GATTCTGACT
*
195352 ATCGCAACGA-ATATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGA-ATACGTAAAATCGCAACGCGTATCCGTAA
*
195393 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
195433 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* * *
195473 ATTGCATCGACAATACGTAAAATCGCAACGCG
1 ATCGCAACGAGAATACGTAAAATCGCAACGCG
195505 ATTTTTAAAG
Statistics
Matches: 102, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
40 74 0.73
41 27 0.26
42 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:195471 original size:20 final size:20
Alignment explanation
Indices: 195352--195474 Score: 147
Period size: 20 Copynumber: 6.1 Consensus size: 20
195342 GATTCTGACT
**
195352 ATCGCAACGAATATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
195373 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
195393 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
195413 ATCGCAACGCGTATCTGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
195433 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
195453 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
195473 AT
1 AT
195475 TGCATCGACA
Statistics
Matches: 85, Mismatches: 17, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
20 69 0.81
21 16 0.19
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:195472 original size:60 final size:61
Alignment explanation
Indices: 195352--195502 Score: 162
Period size: 60 Copynumber: 2.5 Consensus size: 61
195342 GATTCTGACT
* * *
195352 ATCGCAACGAATATCCGTAAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAA
1 ATCGCAACGAATATCCGTAAAATCGCAACGAGAATACGTAAATCGCAACGAGAATACGTAA
** * * * * *
195413 ATCGCAACGCGTATCTGT-AAATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAATATCCGTAAAATCGCAACGAGAATACGTAAATCGCAACGAGAATACGTAA
* * *
195473 ATTGCATCGACA-ATACGTAAAATCGCAACG
1 ATCGCAACGA-ATATCCGTAAAATCGCAACG
195503 CGATTTTTAA
Statistics
Matches: 72, Mismatches: 16, Indels: 4
0.78 0.17 0.04
Matches are distributed among these distances:
60 46 0.64
61 26 0.36
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.20
Consensus pattern (61 bp):
ATCGCAACGAATATCCGTAAAATCGCAACGAGAATACGTAAATCGCAACGAGAATACGTAA
Found at i:196125 original size:21 final size:20
Alignment explanation
Indices: 196064--196139 Score: 93
Period size: 20 Copynumber: 3.8 Consensus size: 20
196054 TTCTAAACTT
196064 AAAATCGCAAC-ATGAAAATG
1 AAAATCGCAACGA-GAAAATG
196084 AAAATCGCAAC-ACGAAAATG
1 AAAATCGCAACGA-GAAAATG
**
196104 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGA-AAATG
196125 AAAATCGCAACGAGA
1 AAAATCGCAACGAGA
196140 TAGTCATTTC
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
20 30 0.61
21 19 0.39
ACGTcount: A:0.51, C:0.18, G:0.18, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACGAGAAAATG
Found at i:196191 original size:19 final size:19
Alignment explanation
Indices: 196143--196246 Score: 66
Period size: 19 Copynumber: 5.9 Consensus size: 19
196133 AACGAGATAG
196143 TCATTTCGCATTGCGA--T
1 TCATTTCGCATTGCGATTT
*
196160 TC-TCTCG--TTGCGATTT
1 TCATTTCGCATTGCGATTT
**
196176 TCATTTCGCATTGCGATAG
1 TCATTTCGCATTGCGATTT
* *
196195 TCATTTCCGCGTTGTGATTT
1 TCATTT-CGCATTGCGATTT
*
196215 TCA---CG--TTGCAATTT
1 TCATTTCGCATTGCGATTT
*
196229 TCATTTCACATTGCGATT
1 TCATTTCGCATTGCGATT
196247 CTCTCGTTGC
Statistics
Matches: 64, Mismatches: 12, Indels: 20
0.67 0.12 0.21
Matches are distributed among these distances:
14 16 0.25
16 9 0.14
17 7 0.11
19 20 0.31
20 12 0.19
ACGTcount: A:0.16, C:0.22, G:0.17, T:0.44
Consensus pattern (19 bp):
TCATTTCGCATTGCGATTT
Found at i:196235 original size:53 final size:52
Alignment explanation
Indices: 196138--196245 Score: 153
Period size: 53 Copynumber: 2.1 Consensus size: 52
196128 ATCGCAACGA
* * *
196138 GATAGTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 GATAGTCATTTCGCATTGCGATTCTCACGTTGCAATTTTCATTTCACATTGC
* * *
196190 GATAGTCATTTCCGCGTTGTGATTTTCACGTTGCAATTTTCATTTCACATTGC
1 GATAGTCATTT-CGCATTGCGATTCTCACGTTGCAATTTTCATTTCACATTGC
196243 GAT
1 GAT
196246 TCTCTCGTTG
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
52 11 0.22
53 38 0.78
ACGTcount: A:0.18, C:0.21, G:0.19, T:0.43
Consensus pattern (52 bp):
GATAGTCATTTCGCATTGCGATTCTCACGTTGCAATTTTCATTTCACATTGC
Found at i:198834 original size:24 final size:24
Alignment explanation
Indices: 198800--198853 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
198790 CTGAAAAATC
198800 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
198824 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
198848 ATCAAA
1 ATCAAA
198854 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:198867 original size:24 final size:24
Alignment explanation
Indices: 198800--198867 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
198790 CTGAAAAATC
* * *
198800 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
198824 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
198848 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
198868 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:199728 original size:20 final size:19
Alignment explanation
Indices: 199707--199919 Score: 93
Period size: 20 Copynumber: 10.9 Consensus size: 19
199697 GCGATAGTCA
199707 GAATCTCGTTGCGATTTAC
1 GAATCTCGTTGCGATTTAC
* * *
199726 AGATTCGCATTGCGATTTAC
1 -GAATCTCGTTGCGATTTAC
*
199746 GTAT-TCGCATTGCGATTTAC
1 GAATCTCG--TTGCGATTTAC
*
199766 GTAT-TCGAATTGCGATTTAC
1 GAATCTCG--TTGCGATTTAC
* *
199786 TG-ATACGCATTGCGATTTAC
1 -GAAT-CTCGTTGCGATTTAC
*
199806 GTATTCTCGTTGCGATTT-C
1 G-AATCTCGTTGCGATTTAC
*
199825 ----CGCGTTGCGATTTAC
1 GAATCTCGTTGCGATTTAC
*
199840 GTATTCTCGTTGCGATTTAC
1 G-AATCTCGTTGCGATTTAC
* *
199860 GGATACGCGTTGCGATTTTAC
1 GAAT-CTCGTTGCGA-TTTAC
* * *
199881 GGATACTTGTTGCGATAGT-C
1 GAAT-CTCGTTGCGAT-TTAC
*
199901 AGAATCGCGTTGCGATTTA
1 -GAATCTCGTTGCGATTTA
199920 TATTTTCGCG
Statistics
Matches: 150, Mismatches: 25, Indels: 36
0.71 0.12 0.17
Matches are distributed among these distances:
14 12 0.08
15 1 0.01
18 1 0.01
19 6 0.04
20 105 0.70
21 24 0.16
22 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (19 bp):
GAATCTCGTTGCGATTTAC
Found at i:199759 original size:40 final size:40
Alignment explanation
Indices: 199715--199877 Score: 171
Period size: 40 Copynumber: 4.2 Consensus size: 40
199705 CAGAATCTCG
*
199715 TTGCGATTTACAG-ATTCGCATTGCGATTTAC-GTATTCGCA
1 TTGCGATTTAC-GTATTCGCATTGCGATTTACTG-ATACGCA
*
199755 TTGCGATTTACGTATTCGAATTGCGATTTACTGATACGCA
1 TTGCGATTTACGTATTCGCATTGCGATTTACTGATACGCA
* * *
199795 TTGCGATTTACGTATTCTCGTTGCGATTT-C-----CGCG
1 TTGCGATTTACGTATTCGCATTGCGATTTACTGATACGCA
* * * *
199829 TTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCG
1 TTGCGATTTACGTATTCGCATTGCGATTTACTGATACGCA
199869 TTGCGATTT
1 TTGCGATTT
199878 TACGGATACT
Statistics
Matches: 109, Mismatches: 6, Indels: 16
0.83 0.05 0.12
Matches are distributed among these distances:
34 32 0.29
35 1 0.01
39 2 0.02
40 73 0.67
41 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (40 bp):
TTGCGATTTACGTATTCGCATTGCGATTTACTGATACGCA
Found at i:199859 original size:74 final size:75
Alignment explanation
Indices: 199755--199896 Score: 205
Period size: 74 Copynumber: 1.9 Consensus size: 75
199745 CGTATTCGCA
* * *
199755 TTGCGATTTACGTATTCGAATTGCGATTTACTGATACGCATTGCGA-TTTACGTATTCTCGTTGC
1 TTGCGATTTACGTATTCGAATTGCGATTTACGGATACGCATTGCGATTTTACGGATACTCGTTGC
199819 GATTTCCGCG
66 GATTTCCGCG
*** * *
199829 TTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTTGTTGC
1 TTGCGATTTACGTATTCGAATTGCGATTTACGGATACGCATTGCGATTTTACGGATACTCGTTGC
199894 GAT
66 GAT
199897 AGTCAGAATC
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
74 41 0.69
75 18 0.31
ACGTcount: A:0.18, C:0.19, G:0.23, T:0.39
Consensus pattern (75 bp):
TTGCGATTTACGTATTCGAATTGCGATTTACGGATACGCATTGCGATTTTACGGATACTCGTTGC
GATTTCCGCG
Found at i:199881 original size:21 final size:20
Alignment explanation
Indices: 199713--199896 Score: 137
Period size: 20 Copynumber: 9.4 Consensus size: 20
199703 GTCAGAATCT
* *
199713 CGTTGCGATTTACAGATTCG
1 CGTTGCGATTTACGGATACG
* * *
199733 CATTGCGATTTACGTATTCG
1 CGTTGCGATTTACGGATACG
* * *
199753 CATTGCGATTTACGTATTCG
1 CGTTGCGATTTACGGATACG
** *
199773 AATTGCGATTTACTGATACG
1 CGTTGCGATTTACGGATACG
* * * *
199793 CATTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACG
199813 CGTTGCGATTT-C-----CG
1 CGTTGCGATTTACGGATACG
* * *
199827 CGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACG
199847 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
*
199867 CGTTGCGATTTTACGGATACT
1 CGTTGCGA-TTTACGGATACG
*
199888 TGTTGCGAT
1 CGTTGCGAT
199897 AGTCAGAATC
Statistics
Matches: 137, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.09
15 1 0.01
19 1 0.01
20 105 0.77
21 18 0.13
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTACGGATACG
Found at i:199928 original size:20 final size:18
Alignment explanation
Indices: 199905--199998 Score: 89
Period size: 20 Copynumber: 4.8 Consensus size: 18
199895 ATAGTCAGAA
199905 TCGCGTTGCGATTTATATTT
1 TCGCGTTGCGATTT-TA-TT
199925 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTT-AT-T
* **
199945 TCGCGTTGCGATTCTGGAGA
1 TCGCGTTGCGATT-T-TATT
199965 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGA-TTTTATT
*
199984 TCGCATTGCGATTTT
1 TCGCGTTGCGATTTT
199999 GTTGGTCATT
Statistics
Matches: 62, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
18 4 0.06
19 13 0.21
20 41 0.66
21 4 0.06
ACGTcount: A:0.14, C:0.18, G:0.23, T:0.45
Consensus pattern (18 bp):
TCGCGTTGCGATTTTATT
Found at i:199949 original size:40 final size:38
Alignment explanation
Indices: 199905--199997 Score: 105
Period size: 40 Copynumber: 2.4 Consensus size: 38
199895 ATAGTCAGAA
* **
199905 TCGCGTTGCGATTTATATTTTCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTAGA-GATCGCGTTGCGATTTTCAT-T
* *
199945 TCGCGTTGCGATTCTGGAGATCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATT-TAGAGATCGCGTTGCGATTTTCATT
*
199984 TCGCATTGCGATTT
1 TCGCGTTGCGATTT
199998 TGTTGGTCAT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
38 1 0.02
39 13 0.28
40 30 0.65
41 2 0.04
ACGTcount: A:0.14, C:0.18, G:0.24, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTAGAGATCGCGTTGCGATTTTCATT
Found at i:203304 original size:2 final size:2
Alignment explanation
Indices: 203293--203344 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
203283 TTTTAAAAAA
*
203293 AT AT AA 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
203335 AT AT AT AT AT
1 AT AT AT AT AT
203345 TTGATAAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:218766 original size:37 final size:36
Alignment explanation
Indices: 218657--218767 Score: 123
Period size: 37 Copynumber: 3.0 Consensus size: 36
218647 TTTTAATTTA
* * * *
218657 AATATTAATTTTATCAACACTTTAAAGTAAATTAAAA
1 AATATTAATATTATGAACAATTTAAAGTAAATT-AAT
* ** * *
218694 AATATTAATGTTATGATTAGTTTAAATTAAATTAAT
1 AATATTAATATTATGAACAATTTAAAGTAAATTAAT
218730 AATCATTAATATTATGAACAATTTAAAGTAAATTAAT
1 AAT-ATTAATATTATGAACAATTTAAAGTAAATTAAT
218767 A
1 A
218768 TGAATGGGTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
36 5 0.08
37 56 0.92
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.41
Consensus pattern (36 bp):
AATATTAATATTATGAACAATTTAAAGTAAATTAAT
Found at i:226631 original size:24 final size:24
Alignment explanation
Indices: 226586--226631 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
226576 GGGACTAAAT
**
226586 AAAAAATAGAATATATTTTTACTA
1 AAAAAATAGAATATATAGTTACTA
226610 AAAAAATAAGAAT-TATAGTTAC
1 AAAAAAT-AGAATATATAGTTAC
226632 ATAGGTATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.33
Consensus pattern (24 bp):
AAAAAATAGAATATATAGTTACTA
Found at i:227614 original size:19 final size:20
Alignment explanation
Indices: 227570--227621 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
227560 TTATCATTAA
*
227570 TTTTAAAAAATTATAACTTC
1 TTTTAAAAGATTATAACTTC
*
227590 TATTAAAAGATTATATA-TT-
1 TTTTAAAAGATTATA-ACTTC
227609 TTTTAAAAGATTA
1 TTTTAAAAGATTA
227622 GCGAATCTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 12 0.43
20 15 0.54
21 1 0.04
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (20 bp):
TTTTAAAAGATTATAACTTC
Done.