Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008960.1 Hibiscus syriacus cultivar Beakdansim tig00112294_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: 362692
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:143462 original size:33 final size:33
Alignment explanation
Indices: 143417--143505 Score: 133
Period size: 33 Copynumber: 2.7 Consensus size: 33
143407 AAAAATGACT
* *
143417 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
143450 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
143483 ATCGCAACGCGAAACTAAAAATC
1 ATCGCAACGCGAAA-TGAAAATC
143506 CCAATGCGAT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 43 0.86
34 7 0.14
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:143473 original size:19 final size:18
Alignment explanation
Indices: 143417--143475 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 18
143407 AAAAATGACT
143417 ATCGCAACGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
143436 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
143450 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
143469 ATCGCAA
1 ATCGCAA
143476 CGACAAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:143534 original size:19 final size:19
Alignment explanation
Indices: 143510--143554 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
143500 AAAATCCCAA
*
143510 TGCGATTATAGTTTCGCGT
1 TGCGATTATAGTTTCACGT
* *
143529 TGCGATTTTCGTTTCACGT
1 TGCGATTATAGTTTCACGT
143548 TGCGATT
1 TGCGATT
143555 TTCATTCTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.13, C:0.18, G:0.24, T:0.44
Consensus pattern (19 bp):
TGCGATTATAGTTTCACGT
Found at i:143570 original size:20 final size:19
Alignment explanation
Indices: 143521--143583 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
143511 GCGATTATAG
* *
143521 TTTCGCGTTGCGATTTTCG
1 TTTCACGTTGCGATTTTCA
143540 TTTCACGTTGCGATTTTCA
1 TTTCACGTTGCGATTTTCA
*
143559 TTCTCTCGTTGCGATTTTCA
1 TT-TCACGTTGCGATTTTCA
143579 TTTCA
1 TTTCA
143584 ACCAAAAGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 21 0.54
20 18 0.46
ACGTcount: A:0.11, C:0.22, G:0.17, T:0.49
Consensus pattern (19 bp):
TTTCACGTTGCGATTTTCA
Found at i:143783 original size:94 final size:93
Alignment explanation
Indices: 143671--143948 Score: 378
Period size: 94 Copynumber: 3.1 Consensus size: 93
143661 ATTGATTGCA
* * *
143671 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAAATTCAGAGTATTAAAGAATACACAGTT
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
143736 TAGCAGAATTGGCAGCAAACGAATAAAT
66 TAGCAGAATTGGCAGCAAACGAATAAAT
143764 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
143829 TTAGCAGAATTGGCAGC-AAC---CAAAT
65 TTAGCAGAATTGGCAGCAAACGAATAAAT
* *
143854 ATACTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCATAGTGTTAATA-AAT----AG
1 TTACTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAA-AGAATACACAG
* *
143914 TTTAGCAGTATTAGCAG-AAACTGAATAAAT
64 TTTAGCAGAATTGGCAGCAAAC-GAATAAAT
143944 TTACT
1 TTACT
143949 AAGCAATCTA
Statistics
Matches: 167, Mismatches: 10, Indels: 19
0.85 0.05 0.10
Matches are distributed among these distances:
86 20 0.12
89 19 0.11
90 46 0.28
91 1 0.01
93 7 0.04
94 74 0.44
ACGTcount: A:0.49, C:0.17, G:0.12, T:0.23
Consensus pattern (93 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAAACGAATAAAT
Found at i:145662 original size:20 final size:20
Alignment explanation
Indices: 145637--145732 Score: 84
Period size: 20 Copynumber: 5.2 Consensus size: 20
145627 TTTTGGTTGA
145637 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
145657 AATGAAAATCGCAACGCG-G
1 AATGAAAATCGCAACGAGAG
**
145676 AAATGACTATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
145695 -A-G--AATCGCAAC-ACGA-
1 AATGAAAATCGCAACGA-GAG
145710 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
145730 AAT
1 AAT
145733 CGCAATGCGA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 8 0.13
16 4 0.06
17 2 0.03
18 1 0.02
19 13 0.21
20 34 0.55
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:145703 original size:14 final size:14
Alignment explanation
Indices: 145684--145737 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
145674 GGAAATGACT
145684 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
145698 ATCGCAACACGAAATGAAA
1 ATCGC-A-ACG--A-GAGA
145717 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
145731 ATCGCAA
1 ATCGCAA
145738 TGCGATTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 15 0.45
15 2 0.06
16 3 0.09
17 3 0.09
18 2 0.06
19 8 0.24
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.09
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:145721 original size:33 final size:34
Alignment explanation
Indices: 145635--145737 Score: 118
Period size: 33 Copynumber: 2.9 Consensus size: 34
145625 TCTTTTGGTT
*
145635 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGCG
1 GAAATGAAAATCGCAAC--GAG-A-G--AATCGCAACACG
**
145675 GAAATGACTATCGCAACGAGAGAATCGCAACAC-
1 GAAATGAAAATCGCAACGAGAGAATCGCAACACG
145708 GAAATGAAAATCGCAACGAGAGAATCGCAA
1 GAAATGAAAATCGCAACGAGAGAATCGCAA
145738 TGCGATTTTG
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
33 28 0.48
34 10 0.17
36 1 0.02
37 1 0.02
38 3 0.05
40 15 0.26
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.11
Consensus pattern (34 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACACG
Found at i:145786 original size:33 final size:33
Alignment explanation
Indices: 145738--145830 Score: 123
Period size: 33 Copynumber: 2.8 Consensus size: 33
145728 AGAATCGCAA
**
145738 TGCGATTTTGGTTTCGCGTTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
*
145771 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
* **
145804 TGTGATAGTCATTTCCGCGTTGCGATT
1 TGCGATTTTCATTT-CGCGTTGCGATT
145831 TTCATTCTCG
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 41 0.77
34 12 0.23
ACGTcount: A:0.11, C:0.20, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
Found at i:146427 original size:21 final size:21
Alignment explanation
Indices: 146381--146495 Score: 164
Period size: 20 Copynumber: 5.6 Consensus size: 21
146371 CGATAGTCAG
* *
146381 ATTCGCATTGCGATTTACGT-
1 ATTCGCATTGCGATTTTCCTA
146401 ATTCGCATTGCGATTTTCCTA
1 ATTCGCATTGCGATTTTCCTA
146422 ATTCGCATTGCGATTTTCCTA
1 ATTCGCATTGCGATTTTCCTA
146443 ATTCGCATTGCGATTTTCCTA
1 ATTCGCATTGCGATTTTCCTA
* * *
146464 A-TCGCGTTGCGATTTACGT-
1 ATTCGCATTGCGATTTTCCTA
146483 ATTCGCATTGCGA
1 ATTCGCATTGCGA
146496 ATTAGGAAAA
Statistics
Matches: 87, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
19 1 0.01
20 43 0.49
21 43 0.49
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.40
Consensus pattern (21 bp):
ATTCGCATTGCGATTTTCCTA
Found at i:146517 original size:21 final size:21
Alignment explanation
Indices: 146493--146532 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
146483 ATTCGCATTG
146493 CGAATTAGGA-AAATCGCAACT
1 CGAATT-GGAGAAATCGCAACT
*
146514 CGAATTTGAGAAATCGCAA
1 CGAATTGGAGAAATCGCAA
146533 TGCGATAGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.20
Consensus pattern (21 bp):
CGAATTGGAGAAATCGCAACT
Found at i:147095 original size:18 final size:19
Alignment explanation
Indices: 147066--147111 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
147056 AATTTATGCA
147066 AGAAAA-ATAAACTATA-T
1 AGAAAATATAAACTATAGT
*
147083 AGAAAATATAAACTGTAGT
1 AGAAAATATAAACTATAGT
147102 A-AAAATATAA
1 AGAAAATATAA
147112 GATTATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 6 0.23
18 18 0.69
19 2 0.08
ACGTcount: A:0.63, C:0.04, G:0.09, T:0.24
Consensus pattern (19 bp):
AGAAAATATAAACTATAGT
Found at i:151531 original size:21 final size:21
Alignment explanation
Indices: 151505--151555 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
151495 CCCCGGGAGC
151505 TAGCTCTTCACGAGCTACTCT
1 TAGCTCTTCACGAGCTACTCT
*
151526 TAGCTCTTCACGAGCTGCTCT
1 TAGCTCTTCACGAGCTACTCT
151547 TAGCTCTTC
1 TAGCTCTTC
151556 TCATGCTCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.16, C:0.33, G:0.16, T:0.35
Consensus pattern (21 bp):
TAGCTCTTCACGAGCTACTCT
Found at i:152781 original size:45 final size:46
Alignment explanation
Indices: 152732--152820 Score: 153
Period size: 46 Copynumber: 2.0 Consensus size: 46
152722 ACATCGAATT
* *
152732 CATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTCAGTG
1 CATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAGTG
152777 CATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
1 CATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
152821 GCTTTTTCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 19 0.46
46 22 0.54
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (46 bp):
CATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAGTG
Found at i:152866 original size:45 final size:45
Alignment explanation
Indices: 152803--152908 Score: 212
Period size: 45 Copynumber: 2.4 Consensus size: 45
152793 GCACAAGACC
152803 ATGCATCGATGCACTCAGGCTTTTTCAAAACATCGAATGCATTTT
1 ATGCATCGATGCACTCAGGCTTTTTCAAAACATCGAATGCATTTT
152848 ATGCATCGATGCACTCAGGCTTTTTCAAAACATCGAATGCATTTT
1 ATGCATCGATGCACTCAGGCTTTTTCAAAACATCGAATGCATTTT
152893 ATGCATCGATGCACTC
1 ATGCATCGATGCACTC
152909 TTAGTGCACC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 61 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (45 bp):
ATGCATCGATGCACTCAGGCTTTTTCAAAACATCGAATGCATTTT
Found at i:157202 original size:13 final size:13
Alignment explanation
Indices: 157180--157220 Score: 73
Period size: 13 Copynumber: 3.2 Consensus size: 13
157170 CCAACTCTAG
*
157180 GACTTGCTTCTTT
1 GACTTACTTCTTT
157193 GACTTACTTCTTT
1 GACTTACTTCTTT
157206 GACTTACTTCTTT
1 GACTTACTTCTTT
157219 GA
1 GA
157221 AACCTTTGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.15, C:0.22, G:0.12, T:0.51
Consensus pattern (13 bp):
GACTTACTTCTTT
Found at i:157347 original size:7 final size:7
Alignment explanation
Indices: 157330--157369 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
157320 CACTTTGTAA
157330 AAAAAAG
1 AAAAAAG
157337 -AAAAAG
1 AAAAAAG
157343 AAAAAAG
1 AAAAAAG
*
157350 GAAAAAG
1 AAAAAAG
157357 AAAAAAG
1 AAAAAAG
157364 AAAAAA
1 AAAAAA
157370 TGAAGTTGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 6 0.20
7 24 0.80
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:158003 original size:20 final size:20
Alignment explanation
Indices: 157974--158012 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
157964 AAAGCTCATA
*
157974 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
157994 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
158013 GTGGTGGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:161243 original size:30 final size:31
Alignment explanation
Indices: 161190--161249 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
161180 AATTTAAAGA
*
161190 AAAAAAACAAAAGATAAAGATAAAATAATAG
1 AAAAAAACAAAAAATAAAGATAAAATAATAG
* *
161221 AAAAAAATAAAAAATAAA-ATAAATTAATA
1 AAAAAAACAAAAAATAAAGATAAAATAATA
161250 AAGAAATGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.17
Consensus pattern (31 bp):
AAAAAAACAAAAAATAAAGATAAAATAATAG
Found at i:161562 original size:16 final size:16
Alignment explanation
Indices: 161516--161573 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
161506 TAACCCGACA
*
161516 TGAAAGCAACTTGAAC
1 TGAAAGTAACTTGAAC
* * *
161532 -AAAAATTACTCTGAAC
1 TGAAAGTAACT-TGAAC
161548 TGAAAGTAACTTGAAC
1 TGAAAGTAACTTGAAC
*
161564 CGAAAGTAAC
1 TGAAAGTAAC
161574 CCAAATCGAA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
15 6 0.19
16 19 0.59
17 7 0.22
ACGTcount: A:0.47, C:0.17, G:0.16, T:0.21
Consensus pattern (16 bp):
TGAAAGTAACTTGAAC
Found at i:170053 original size:61 final size:61
Alignment explanation
Indices: 169948--170073 Score: 146
Period size: 61 Copynumber: 2.1 Consensus size: 61
169938 GGCCTAGTGA
* * ** * * *
169948 TAAGACCTTATAGACCCTATAAAACTCCCATAGTGTTTCCCATTTTCTTTGTGCATTGTGG
1 TAAGACCATATAGACCCTATAAAACTCCCATAGGGTGGCCCATTTGCATTGTGCACTGTGG
* * *
170009 TAAGACCATAT-GAACCCTTTAACACTCCCATAGGGTGGCTCATTTGCATTGTGCACTGTGG
1 TAAGACCATATAG-ACCCTATAAAACTCCCATAGGGTGGCCCATTTGCATTGTGCACTGTGG
170070 TAAG
1 TAAG
170074 TCCTTATGGA
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
60 1 0.02
61 53 0.98
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.33
Consensus pattern (61 bp):
TAAGACCATATAGACCCTATAAAACTCCCATAGGGTGGCCCATTTGCATTGTGCACTGTGG
Found at i:176109 original size:2 final size:2
Alignment explanation
Indices: 176102--176144 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
176092 GTGTCGACAG
* *
176102 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AC 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
176144 A
1 A
176145 ATTTTTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:177764 original size:20 final size:20
Alignment explanation
Indices: 177739--177790 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
177729 CAATGTTGGT
177739 AGTATCGATACTACCTTATG
1 AGTATCGATACTACCTTATG
177759 AGTATCGATACTACCTTATG
1 AGTATCGATACTACCTTATG
177779 AGTATCGATACT
1 AGTATCGATACT
177791 TCCGTACTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (20 bp):
AGTATCGATACTACCTTATG
Found at i:178011 original size:107 final size:106
Alignment explanation
Indices: 177825--178097 Score: 359
Period size: 107 Copynumber: 2.5 Consensus size: 106
177815 CGATACCAAA
* * * * * *
177825 GGTAGTATCGAGACTACCTTTTGAGTATCAATACTTCCATTGCCTTTGGTATTGGTACTTCTTTT
1 GGTAGTATCGATACTACCTTGTGAGTATCAATACTTCCA-TACCTTTGGTATCGATACTTCCTTT
* * *
177890 GGTAACGGTACCATTTTTGCGTTATGGAATTTGAGCAATGTT
65 GGTAACGATACCATTTTTGCATTATAGAATTTGAGCAATGTT
* *
177932 GGTAGTATCGATACTACCTTGTGAGTATCGATACTTCCTATACATTTGGTATCGATA-TTCCTTT
1 GGTAGTATCGATACTACCTTGTGAGTATCAATACTTCC-ATACCTTTGGTATCGATACTTCCTTT
* *
177996 GGATATCGATACCATTTTTGCATTCTAGAATTTGAGCAATGTT
65 GG-TAACGATACCATTTTTGCATTATAGAATTTGAGCAATGTT
* *
178039 GGTAGTATCGATACTACCCCTGTGAGTATCAAAACTTCCGATACCTTTGGTATCGATAC
1 GGTAGTATCGATACTA-CCTTGTGAGTATCAATACTTCC-ATACCTTTGGTATCGATAC
178098 CATATGAACA
Statistics
Matches: 144, Mismatches: 18, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
106 8 0.06
107 99 0.69
108 37 0.26
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.38
Consensus pattern (106 bp):
GGTAGTATCGATACTACCTTGTGAGTATCAATACTTCCATACCTTTGGTATCGATACTTCCTTTG
GTAACGATACCATTTTTGCATTATAGAATTTGAGCAATGTT
Found at i:179442 original size:19 final size:19
Alignment explanation
Indices: 179418--179456 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
179408 TCGAATGCAT
*
179418 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGAACTC
*
179437 TCCATGCATCGATGAACTC
1 TCCATGCACCGATGAACTC
179456 T
1 T
179457 GAATTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.36, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGAACTC
Found at i:179484 original size:67 final size:64
Alignment explanation
Indices: 179404--179566 Score: 191
Period size: 67 Copynumber: 2.5 Consensus size: 64
179394 GAATTAATTG
* * *** * * * *
179404 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGAACTCTGAATTTTTTTTT
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGAA-TCAG-ACTATTTCTT
179469 AA
64 -A
* * *
179471 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTCTTA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGAATCAGACTATTTCTTA
179535 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
179567 CTTGTTGCAT
Statistics
Matches: 83, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
64 32 0.39
65 6 0.07
66 3 0.04
67 42 0.51
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGAATCAGACTATTTCTTA
Found at i:179559 original size:64 final size:63
Alignment explanation
Indices: 179354--179566 Score: 194
Period size: 64 Copynumber: 3.3 Consensus size: 63
179344 TTATTCAAAG
* * * *
179354 TCATGCACCGATGCATC-AGTCCATGCATCGATGCATCGATGAATTAATTGAACATCGAATGCAT
1 TCATGCACCGATGCA-CAAG-CCATGCATCGATGCATC-AGGTATTTATTAAACATCGAATGCAT
179418 T
63 T
* *** * ** * *
179419 CCATGCACCGATGCACTCTCCATGCATCGATGAACTCTGAATTTTTTTTTAAAACATCGAATGCA
1 TCATGCACCGATGCACAAGCCATGCATCGATGCA-TC--AGGTATTTATT-AAACATCGAATGCA
179484 TT
62 TT
* * *
179486 TGATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTCTTAAACATCGAATGCATT
1 TCATGCACCGATGCACAAGCCATGCATCGATGCATCAGG-TATTTATTAAACATCGAATGCATT
*
179550 TCATGCATCGATGCACA
1 TCATGCACCGATGCACA
179567 CTTGTTGCAT
Statistics
Matches: 120, Mismatches: 23, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
64 48 0.40
65 22 0.18
66 8 0.07
67 42 0.35
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (63 bp):
TCATGCACCGATGCACAAGCCATGCATCGATGCATCAGGTATTTATTAAACATCGAATGCATT
Found at i:187930 original size:19 final size:19
Alignment explanation
Indices: 187906--187944 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
187896 TCGAATGCAT
187906 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
187925 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
187944 T
1 T
187945 GAATTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:187980 original size:67 final size:64
Alignment explanation
Indices: 187843--188054 Score: 187
Period size: 64 Copynumber: 3.2 Consensus size: 64
187833 TATTCAAAGG
* * ** **
187843 CATGCACCGATGCATC-AGTCCATGCATCGATGCATCGATG-AATTAATTGAACATCGAATGCAT
1 CATGCATCGATGCA-CAAG-CCATGCATCGATGCATC-ATGCTATTTCTAAAACATCGAATGCAT
*
187906 TC
63 TT
* *** * * *
187908 CATGCACCGATGCACTCTCCATGCATCGATGCACTC-TGAATTTTTTTTTAAAACATCGAATGCA
1 CATGCATCGATGCACAAGCCATGCATCGATGCA-TCATG---CTATTTCTAAAACATCGAATGCA
187972 TTT
62 TTT
* * *
187975 GATGCATCGATGCACAAGCCTTGCATCGATGCATCATGCTATTTCTCAAACATCGAATGCATTT
1 CATGCATCGATGCACAAGCCATGCATCGATGCATCATGCTATTTCTAAAACATCGAATGCATTT
188039 CATGCATCGATGCACA
1 CATGCATCGATGCACA
188055 CTTGGTGCAC
Statistics
Matches: 120, Mismatches: 20, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
63 2 0.02
64 53 0.44
65 16 0.13
66 2 0.02
67 47 0.39
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (64 bp):
CATGCATCGATGCACAAGCCATGCATCGATGCATCATGCTATTTCTAAAACATCGAATGCATTT
Found at i:191496 original size:36 final size:36
Alignment explanation
Indices: 191445--191515 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
191435 AACCAAAGAG
* * * *
191445 ATATATTCAAGGATTTCAACCTATTGATTAATTCAT
1 ATATACTCAACGATTTCAACCTATCGATAAATTCAT
191481 ATATACTCAACGATTTCAACCTATCGATAAATTCA
1 ATATACTCAACGATTTCAACCTATCGATAAATTCA
191516 GGTACGTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.37
Consensus pattern (36 bp):
ATATACTCAACGATTTCAACCTATCGATAAATTCAT
Found at i:192160 original size:2 final size:2
Alignment explanation
Indices: 192153--192178 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
192143 TACACTTATG
192153 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
192179 TCAATGAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:193156 original size:57 final size:57
Alignment explanation
Indices: 193083--193269 Score: 302
Period size: 57 Copynumber: 3.3 Consensus size: 57
193073 CGATTTGCGA
* * *
193083 AATTTGCGTTACGAAAACGAAATTTGTGTTGCGATAGTTGTGTTTACCTATATCAGT
1 AATTAGCGTTGCGAAAACGAAATTTGTGTTGCGATAGTTGTGTTTACCTATATCGGT
*
193140 AATTAGCGTTGCGAAAACGAAATTCGTGTTGCGATAGTTGTGTTTACCTATATCGGT
1 AATTAGCGTTGCGAAAACGAAATTTGTGTTGCGATAGTTGTGTTTACCTATATCGGT
* *
193197 AATTAGCGTTGCGAAAACGAAATTTGCGTTGTGATAGTTGTGTTTACCTATATCGGT
1 AATTAGCGTTGCGAAAACGAAATTTGTGTTGCGATAGTTGTGTTTACCTATATCGGT
**
193254 AATTAATGTTGCGAAA
1 AATTAGCGTTGCGAAA
193270 TTCGCGTTGT
Statistics
Matches: 121, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 121 1.00
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.36
Consensus pattern (57 bp):
AATTAGCGTTGCGAAAACGAAATTTGTGTTGCGATAGTTGTGTTTACCTATATCGGT
Found at i:193291 original size:20 final size:20
Alignment explanation
Indices: 193266--193305 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
193256 TTAATGTTGC
* *
193266 GAAATTCGCGTTGTGAAAAT
1 GAAATTCGCATTGCGAAAAT
*
193286 GAAATTTGCATTGCGAAAAT
1 GAAATTCGCATTGCGAAAAT
193306 TTCCATGTTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.30
Consensus pattern (20 bp):
GAAATTCGCATTGCGAAAAT
Found at i:193750 original size:2 final size:2
Alignment explanation
Indices: 193701--193737 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
193691 TATTATAGAT
*
193701 TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
193738 GACATTGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:195365 original size:36 final size:36
Alignment explanation
Indices: 195320--195388 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
195310 AACCAAAGAG
*
195320 ATATACTCAAAGACTTTAAAATATCGATTAATTCAT
1 ATATACTCAAAGACTTTAAAATATCAATTAATTCAT
* * **
195356 ATATACTCAAGGATTTTAACCTATCAATTAATT
1 ATATACTCAAAGACTTTAAAATATCAATTAATT
195389 TAGGTACGCT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.42, C:0.14, G:0.06, T:0.38
Consensus pattern (36 bp):
ATATACTCAAAGACTTTAAAATATCAATTAATTCAT
Found at i:203223 original size:24 final size:24
Alignment explanation
Indices: 203191--203248 Score: 116
Period size: 24 Copynumber: 2.4 Consensus size: 24
203181 TGAGGAGAAT
203191 AAGAAGAAGATGAAAATGGAAGAG
1 AAGAAGAAGATGAAAATGGAAGAG
203215 AAGAAGAAGATGAAAATGGAAGAG
1 AAGAAGAAGATGAAAATGGAAGAG
203239 AAGAAGAAGA
1 AAGAAGAAGA
203249 AGAATAGGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.60, C:0.00, G:0.33, T:0.07
Consensus pattern (24 bp):
AAGAAGAAGATGAAAATGGAAGAG
Found at i:204777 original size:2 final size:2
Alignment explanation
Indices: 204770--204811 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
204760 ATGTAAATTT
204770 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
204812 GCATCCTTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:205381 original size:46 final size:46
Alignment explanation
Indices: 205312--205862 Score: 673
Period size: 46 Copynumber: 11.8 Consensus size: 46
205302 TTTCATTTTA
* * *
205312 TTCATGCATTAATGCACCCTTTCATGCATTTTATTTATGGCATCAT
1 TTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATGGCATCCT
* *
205358 TTCATGCCTTAATGCATCATTTCATGCATTTTATTTATGGCATCTT
1 TTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATGGCATCCT
* * * *
205404 TTCATGCATTTTATTTTTGGCATCCTTTCATGC--CTTA---AT-GCATCAT
1 TTCATGC--CTTA---AT-GCATCCTTTCATGCATTTTATTTATGGCATCCT
* * * *
205450 TTCATTCATTTTATTTACGGCATCCTTTCATGCATTTTATTTGTGGCATCCT
1 TTCATGC--CTTA---A-TGCATCCTTTCATGCATTTTATTTATGGCATCCT
* * *
205502 GTCACGCCTTAATGCATCCTTTCATGCATTTGATTTATGGCATCCT
1 TTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATGGCATCCT
* *
205548 TTCATGCCTTAATGCATCCTTTCTTGCATTTTATTTATGGCACCCT
1 TTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATGGCATCCT
* *
205594 TTCATGCCTTAATGCATTCTTTCATGCATTTTATTTATGACATCCT
1 TTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATGGCATCCT
*
205640 TTCATGTCTTAATGCATCCTTTCATGCATTTTATTTATGGCATCCT
1 TTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATGGCATCCT
* * * *
205686 TTCATGCCTTAAAGCATCCTTTCATTCTTTTTATTTATAGCATCCT
1 TTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATGGCATCCT
* * *
205732 TTCATGCCTTAATGCATACATTCATGTATTTTATTTATGGCATCCT
1 TTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATGGCATCCT
* * *
205778 TTCATTCCTTAATGCATCATTTCATGCATTTTATTTGTGGCATCCT
1 TTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATGGCATCCT
205824 TTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATG
1 TTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATG
205863 TATCCCGTTA
Statistics
Matches: 437, Mismatches: 55, Indels: 26
0.84 0.11 0.05
Matches are distributed among these distances:
46 397 0.91
47 3 0.01
48 6 0.01
50 6 0.01
51 2 0.00
52 23 0.05
ACGTcount: A:0.21, C:0.22, G:0.11, T:0.47
Consensus pattern (46 bp):
TTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATGGCATCCT
Found at i:205412 original size:72 final size:72
Alignment explanation
Indices: 205329--205830 Score: 458
Period size: 72 Copynumber: 7.1 Consensus size: 72
205319 ATTAATGCAC
* *
205329 CCTTTCATGCATTTTATTTATGGCATCATTTCATGCCTTAATGCATCATTTCATGCATTTTATTT
1 CCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTATTT
205394 ATGGCAT
66 ATGGCAT
* * * *
205401 CTTTTCATGCATTTTATTTTTGGCATCCTTTCATGCCTTAATGCATCATTTCATTCATTTTATTT
1 CCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTATTT
*
205466 ACGGCAT
66 ATGGCAT
* * * *
205473 CCTTTCATGCATTTTATTTGTGGCATCCTGTCACGCCTTAATGCATCCTTTCATGCATTTGATTT
1 CCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTATTT
205538 ATGGCAT
66 ATGGCAT
* * * * *
205545 CCTTTCATGC--CTTA---AT-GCATCCTTTCTTGCATTTTATTTATGGCACCCTTTCATGC--C
1 CCTTTCATGCATTTTATTTATGGCATCCTTTCATGC--CTTA---AT-GCATCCTTTCATGCATT
205602 TTA---AT-GCAT
60 TTATTTATGGCAT
* * *
205611 TCTTTCATGCATTTTATTTATGACATCCTTTCATGTCTTAATGCATCCTTTCATGCATTTTATTT
1 CCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTATTT
205676 ATGGCAT
66 ATGGCAT
* * * * *
205683 CCTTTCATGC--CTTA---A-AGCATCCTTTCATTCTTTTTATTTATAGCATCCTTTCATGC--C
1 CCTTTCATGCATTTTATTTATGGCATCCTTTCATGC--CTTA---AT-GCATCCTTTCATGCATT
205740 TTA---AT-GCAT
60 TTATTTATGGCAT
* * * * *
205749 ACATTCATGTATTTTATTTATGGCATCCTTTCATTCCTTAATGCATCATTTCATGCATTTTATTT
1 CCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTATTT
*
205814 GTGGCAT
66 ATGGCAT
205821 CCTTTCATGC
1 CCTTTCATGC
205831 CTTAATGCAT
Statistics
Matches: 344, Mismatches: 50, Indels: 72
0.74 0.11 0.15
Matches are distributed among these distances:
66 72 0.21
67 10 0.03
68 18 0.05
70 17 0.05
71 10 0.03
72 217 0.63
ACGTcount: A:0.20, C:0.22, G:0.11, T:0.47
Consensus pattern (72 bp):
CCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTATTT
ATGGCAT
Found at i:208515 original size:2 final size:2
Alignment explanation
Indices: 208508--208550 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
208498 CCATAAAAGC
208508 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
208550 T
1 T
208551 TTCTGATATC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:210819 original size:46 final size:46
Alignment explanation
Indices: 210750--211398 Score: 935
Period size: 46 Copynumber: 14.2 Consensus size: 46
210740 TTTCATTTTA
* * *
210750 TTCATGCATTAATGCATCCTTTCATGCATTTTATTTATGTCATCCT
1 TTCATGCCTTAATGCATCATTTCATGCATTTTATTTATGGCATCCT
* * *
210796 TTTATGCCTTAATGCATCATTTCATGGATTTTATTTATGTCATCCT
1 TTCATGCCTTAATGCATCATTTCATGCATTTTATTTATGGCATCCT
*
210842 TTCATGCCTTAATGCATCATTTCATGCATTTTATTTGTGGCATCCT
1 TTCATGCCTTAATGCATCATTTCATGCATTTTATTTATGGCATCCT
* * *
210888 TTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATAGAATCCT
1 TTCATGCCTTAATGCATCATTTCATGCATTTTATTTATGGCATCCT
* * * *
210934 TTTATGACTTAATGCATCCTTTCATGCATTTTACTTATGGCATCCT
1 TTCATGCCTTAATGCATCATTTCATGCATTTTATTTATGGCATCCT
** * *
210980 TTCATGCCTTAATTTATCCTTTCATGCACTTTATTTATGGCATCCT
1 TTCATGCCTTAATGCATCATTTCATGCATTTTATTTATGGCATCCT
* * * *
211026 TTTATGCCTAAATGCATTC-TTTCATACATTTTAATTATGGCATCCT
1 TTCATGCCTTAATGCA-TCATTTCATGCATTTTATTTATGGCATCCT
** * * * *
211072 TTCATGTATTAATGCATCCTTTTATGCATTTGATTTATGGAATCCT
1 TTCATGCCTTAATGCATCATTTCATGCATTTTATTTATGGCATCCT
* *
211118 TTCATGCCTTAATGCATCATGTCATGCATTTTATTTATGGTATCCT
1 TTCATGCCTTAATGCATCATTTCATGCATTTTATTTATGGCATCCT
*
211164 TTCATGCCTTAATGCATCATTTCATGCATTTTATTTATGACATCCT
1 TTCATGCCTTAATGCATCATTTCATGCATTTTATTTATGGCATCCT
*
211210 TTCATGCCTTAATGCATCATTTCATG-ATTTTATTTATGGCATTCT
1 TTCATGCCTTAATGCATCATTTCATGCATTTTATTTATGGCATCCT
*
211255 TTCATGCCTTAATGCATCATTTCATGTATTTTATTTATGGCATCCT
1 TTCATGCCTTAATGCATCATTTCATGCATTTTATTTATGGCATCCT
* *
211301 TTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATGGCATGCT
1 TTCATGCCTTAATGCATCATTTCATGCATTTTATTTATGGCATCCT
* *
211347 TTCATTCCTTAATGTATCATTTCATGCA-TTTATTTATGGCATCCT
1 TTCATGCCTTAATGCATCATTTCATGCATTTTATTTATGGCATCCT
211392 TTCATGC
1 TTCATGC
211399 ATTTTATTTA
Statistics
Matches: 540, Mismatches: 60, Indels: 7
0.89 0.10 0.01
Matches are distributed among these distances:
45 67 0.12
46 471 0.87
47 2 0.00
ACGTcount: A:0.22, C:0.20, G:0.11, T:0.47
Consensus pattern (46 bp):
TTCATGCCTTAATGCATCATTTCATGCATTTTATTTATGGCATCCT
Found at i:211017 original size:21 final size:20
Alignment explanation
Indices: 210975--211017 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
210965 TACTTATGGC
210975 ATCCTTTCATGCCTTAATTT
1 ATCCTTTCATGCCTTAATTT
*
210995 ATCCTTTCATGCACTTTATTT
1 ATCCTTTCATGC-CTTAATTT
211016 AT
1 AT
211018 GGCATCCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (20 bp):
ATCCTTTCATGCCTTAATTT
Found at i:213629 original size:20 final size:21
Alignment explanation
Indices: 213584--213634 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
213574 AGAGGATCAA
213584 TATCGATACTGATTAAAGGAGG
1 TATCGATACTGA-TAAAGGAGG
* *
213606 TATCGATACTGA-AATGGGGG
1 TATCGATACTGATAAAGGAGG
213626 TATCGATAC
1 TATCGATAC
213635 CAAGGGTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 15 0.56
22 12 0.44
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.27
Consensus pattern (21 bp):
TATCGATACTGATAAAGGAGG
Found at i:214327 original size:23 final size:23
Alignment explanation
Indices: 214297--214381 Score: 111
Period size: 23 Copynumber: 3.8 Consensus size: 23
214287 TTTAGTCCTC
*
214297 CGGGACAAAATTATGTGGTCATT
1 CGGGACAAAACTATGTGGTCATT
*
214320 CGGGACAAAACTATGTGGTCCTT
1 CGGGACAAAACTATGTGGTCATT
* *
214343 TGGGACAAACCTATGTGGTCATT
1 CGGGACAAAACTATGTGGTCATT
*
214366 TGGGAC-AAA-TATGTGG
1 CGGGACAAAACTATGTGG
214382 CACTTTGGTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
21 7 0.12
22 2 0.04
23 47 0.84
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.28
Consensus pattern (23 bp):
CGGGACAAAACTATGTGGTCATT
Found at i:214358 original size:46 final size:44
Alignment explanation
Indices: 214298--214389 Score: 123
Period size: 46 Copynumber: 2.0 Consensus size: 44
214288 TTAGTCCTCC
*
214298 GGGACAAAATTATGTGGTCATTCGGGACAAAACTATGTGGTC-CTTT
1 GGGACAAAACTATGTGGTCATTCGGGAC-AAA-TATGTGG-CACTTT
* *
214344 GGGACAAACCTATGTGGTCATTTGGGACAAATATGTGGCACTTT
1 GGGACAAAACTATGTGGTCATTCGGGACAAATATGTGGCACTTT
214388 GG
1 GG
214390 TGCATATTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 1 0.02
44 13 0.31
45 3 0.07
46 25 0.60
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (44 bp):
GGGACAAAACTATGTGGTCATTCGGGACAAATATGTGGCACTTT
Found at i:215944 original size:21 final size:22
Alignment explanation
Indices: 215902--215944 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
215892 ACATTAAGTT
*
215902 CAAAAAATTCAAACCATTCAAA
1 CAAAAAATTCAAACCATCCAAA
* *
215924 CAAAATATTC-AATCATCCAAA
1 CAAAAAATTCAAACCATCCAAA
215945 ACACAAATCC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.56, C:0.23, G:0.00, T:0.21
Consensus pattern (22 bp):
CAAAAAATTCAAACCATCCAAA
Found at i:230680 original size:23 final size:22
Alignment explanation
Indices: 230616--230690 Score: 80
Period size: 23 Copynumber: 3.4 Consensus size: 22
230606 GTCGAGGGTT
*
230616 CTATGTGGTCATTCGGGAAAAAA
1 CTATGTGGTCATTCGGG-ACAAA
* * *
230639 CTATGTGGTCCTCCAGGACAAA
1 CTATGTGGTCATTCGGGACAAA
*
230661 CCTATGTGGTCATTTGGGACAAA
1 -CTATGTGGTCATTCGGGACAAA
230684 -TATGTGG
1 CTATGTGG
230691 CACTTCAGAG
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
21 7 0.16
22 4 0.09
23 32 0.74
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (22 bp):
CTATGTGGTCATTCGGGACAAA
Found at i:233767 original size:82 final size:82
Alignment explanation
Indices: 233624--233931 Score: 366
Period size: 82 Copynumber: 3.8 Consensus size: 82
233614 GTAGACAATC
* * * * *
233624 TACACTATTCATGTCATTTGCTTGTCATTGACATTTCACATTAACTCAGATAAATTGAAATATTT
1 TACAATATTCACGTCCTTTGCTTGTCATTGACATTTCACATCAACTCAGATAAACTGAAATATTT
*
233689 TAGAGAATTAGGGAATA
66 TAGAGAATCAGGGAATA
* * * * *
233706 TACAATATTCTCGTCCTTTGCTTATCATTGACATTTCACATCAAATTAGATAAACTAAAATATTT
1 TACAATATTCACGTCCTTTGCTTGTCATTGACATTTCACATCAACTCAGATAAACTGAAATATTT
*
233771 TAGAGAATCAGGGAATC
66 TAGAGAATCAGGGAATA
* * * *
233788 TACACTATTCACGTCCTTTCCTTGTCGTTAACATTTCACATCAACTCAGATAAACTGAAATATTT
1 TACAATATTCACGTCCTTTGCTTGTCATTGACATTTCACATCAACTCAGATAAACTGAAATATTT
233853 TAGAGAATCAGGGAATA
66 TAGAGAATCAGGGAATA
* * ** * * * * * *
233870 TACACTTTTCATATCATTTTCTCT-TTATTGACATTTCACACCAACTTAAATAAACTGAAATA
1 TACAATATTCACGTCCTTTGCT-TGTCATTGACATTTCACATCAACTCAGATAAACTGAAATA
233932 AATTCTATTG
Statistics
Matches: 192, Mismatches: 33, Indels: 2
0.85 0.15 0.01
Matches are distributed among these distances:
82 191 0.99
83 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.36
Consensus pattern (82 bp):
TACAATATTCACGTCCTTTGCTTGTCATTGACATTTCACATCAACTCAGATAAACTGAAATATTT
TAGAGAATCAGGGAATA
Found at i:233902 original size:164 final size:167
Alignment explanation
Indices: 233620--233973 Score: 441
Period size: 164 Copynumber: 2.1 Consensus size: 167
233610 CCTTGTAGAC
* * * * * *
233620 AATCTACACTATTCATGTCATTTGCTTGTCATTGACATTTCACATTAACTCAGATAAATTGAAAT
1 AATCTACACTATTCACGTCCTTTCCTTGTCATTAACATTTCACATCAACTCAGATAAACTGAAAT
* * * *
233685 ATTTTAGAGAATTAGGGAATATACAATATTCTCGTCCTTTGCTTATCATTGACATTTCACATCAA
66 ATTTTAGAGAATCAGGGAATATACAATATTCTCATCATTTGCTTATCATTGACATTTCACACCAA
* * * *
233750 ATTAGATAAACT-AAA-ATATT-T-TAGAGAATCAGGG
131 ATTAAATAAACTGAAATAAATTCTATAGA-AATAAGAG
*
233784 AATCTACACTATTCACGTCCTTTCCTTGTCGTTAACATTTCACATCAACTCAGATAAACTGAAAT
1 AATCTACACTATTCACGTCCTTTCCTTGTCATTAACATTTCACATCAACTCAGATAAACTGAAAT
* * * *
233849 ATTTTAGAGAATCAGGGAATATACACTTTTCAT-ATCATTTTCTCT-TTATTGACATTTCACACC
66 ATTTTAGAGAATCAGGGAATATACAATATTC-TCATCATTTGCT-TATCATTGACATTTCACACC
* *
233912 AACTTAAATAAACTGAAATAAATTCTATTGAAATAAGAG
129 AAATTAAATAAACTGAAATAAATTCTATAGAAATAAGAG
*
233951 AATTTACACTATTCACGTCCTTT
1 AATCTACACTATTCACGTCCTTT
233974 TCTTTTCAAA
Statistics
Matches: 162, Mismatches: 22, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
164 121 0.75
165 5 0.03
166 4 0.02
167 29 0.18
168 3 0.02
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (167 bp):
AATCTACACTATTCACGTCCTTTCCTTGTCATTAACATTTCACATCAACTCAGATAAACTGAAAT
ATTTTAGAGAATCAGGGAATATACAATATTCTCATCATTTGCTTATCATTGACATTTCACACCAA
ATTAAATAAACTGAAATAAATTCTATAGAAATAAGAG
Found at i:239533 original size:19 final size:20
Alignment explanation
Indices: 239511--239551 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
239501 TGTTATTTGC
*
239511 AAATGAA-GATGTTATGGAA
1 AAATGAAGGACGTTATGGAA
239530 AAATGAATGGACGTTATGGAA
1 AAATGAA-GGACGTTATGGAA
239551 A
1 A
239552 TTGTCTGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
21 12 0.63
ACGTcount: A:0.46, C:0.02, G:0.27, T:0.24
Consensus pattern (20 bp):
AAATGAAGGACGTTATGGAA
Found at i:241365 original size:14 final size:14
Alignment explanation
Indices: 241346--241376 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
241336 TCCCACATTA
241346 TTTTCTTTTCTTTC
1 TTTTCTTTTCTTTC
241360 TTTTCTTTTCTTTC
1 TTTTCTTTTCTTTC
241374 TTT
1 TTT
241377 AATTCTGCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTCTTTTCTTTC
Found at i:243831 original size:20 final size:20
Alignment explanation
Indices: 243802--243840 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
243792 ATTTCACCAT
*
243802 ATACAACTATATGCTCCTAA
1 ATACAACTATATGATCCTAA
*
243822 ATACATCTATATGATCCTA
1 ATACAACTATATGATCCTA
243841 TATAAGATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.33
Consensus pattern (20 bp):
ATACAACTATATGATCCTAA
Found at i:252020 original size:17 final size:19
Alignment explanation
Indices: 251995--252037 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
251985 GTTGAAGCAT
*
251995 AAAAGAAAAAAC-A-AAAA
1 AAAACAAAAAACGAGAAAA
252012 AAAACAAAAAACGAGAAAA
1 AAAACAAAAAACGAGAAAA
*
252031 GAAACAA
1 AAAACAA
252038 CGTTTAGAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 11 0.50
18 1 0.05
19 10 0.45
ACGTcount: A:0.81, C:0.09, G:0.09, T:0.00
Consensus pattern (19 bp):
AAAACAAAAAACGAGAAAA
Found at i:253674 original size:18 final size:18
Alignment explanation
Indices: 253651--253696 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
253641 TACTGAATAT
*
253651 ACGCACACGCACACGTGC
1 ACGCACACGCACACGCGC
253669 ACGCACACGCACACGCGC
1 ACGCACACGCACACGCGC
*
253687 ACGCGCACGC
1 ACGCACACGC
253697 GCCTACGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.26, C:0.48, G:0.24, T:0.02
Consensus pattern (18 bp):
ACGCACACGCACACGCGC
Found at i:253698 original size:6 final size:6
Alignment explanation
Indices: 253651--253696 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
253641 TACTGAATAT
** * *
253651 ACGCAC ACGCAC ACGTGC ACGCAC ACGCAC ACGCGC ACGCGC ACGC
1 ACGCAC ACGCAC ACGCAC ACGCAC ACGCAC ACGCAC ACGCAC ACGC
253697 GCCTACGTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.26, C:0.48, G:0.24, T:0.02
Consensus pattern (6 bp):
ACGCAC
Found at i:253709 original size:6 final size:6
Alignment explanation
Indices: 253700--253907 Score: 236
Period size: 6 Copynumber: 34.7 Consensus size: 6
253690 CGCACGCGCC
* * * *
253700 TACGTA TACGCA TACGCC TACGCA TACGCA TACGCA TATGTA TACGCA
1 TACGCA TACGCA TACGCA TACGCA TACGCA TACGCA TACGCA TACGCA
* * * * * *
253748 TATGCA TACGCC TACGCA TACGCA TACGTA TATGCA TATGCA TACGCC
1 TACGCA TACGCA TACGCA TACGCA TACGCA TACGCA TACGCA TACGCA
* *
253796 TACGCA TACGCA TACACC TACGCA TACGCA TACGCA TACGCA TACGCA
1 TACGCA TACGCA TACGCA TACGCA TACGCA TACGCA TACGCA TACGCA
** * * ** *
253844 TACGCA TATACA TACGCA TATGCA TACGCA TACGCG TACGTG TATGCA
1 TACGCA TACGCA TACGCA TACGCA TACGCA TACGCA TACGCA TACGCA
*
253892 TACGCA TACGTA TACG
1 TACGCA TACGCA TACG
253908 TATGCATATA
Statistics
Matches: 168, Mismatches: 34, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 168 1.00
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (6 bp):
TACGCA
Found at i:253908 original size:6 final size:6
Alignment explanation
Indices: 253891--253935 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
253881 ACGTGTATGC
* * * *
253891 ATACGC ATACGT ATACGT ATGCAT ATACGT ATACAT ATACGT ATA
1 ATACGT ATACGT ATACGT ATACGT ATACGT ATACGT ATACGT ATA
253936 TAATTTTATA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (6 bp):
ATACGT
Found at i:253917 original size:12 final size:12
Alignment explanation
Indices: 253891--253935 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
253881 ACGTGTATGC
* *
253891 ATACGCATACGT
1 ATACGTATACAT
*
253903 ATACGTATGCAT
1 ATACGTATACAT
253915 ATACGTATACAT
1 ATACGTATACAT
253927 ATACGTATA
1 ATACGTATA
253936 TAATTTTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (12 bp):
ATACGTATACAT
Found at i:254270 original size:74 final size:74
Alignment explanation
Indices: 254119--254272 Score: 173
Period size: 74 Copynumber: 2.1 Consensus size: 74
254109 CAGGAGAACG
* * * * **
254119 TCTCACATTGCATAAACCCGTAAAGGGGAGTCATATGAAATATGAAGACCAACTTAAACCGTGAA
1 TCTCACATAGCATAAACCCGTAAAGGGAAGTCATATAAAATATCAAGACCAACTTAAACCACGAA
*
254184 AGAGAATCA
66 AAAGAATCA
* * * * **
254193 TCTCACATAGCTTAAACCTGTGAAGGGAAGTCATCTAAAATATCAAGACTGACTTAAACCACGAA
1 TCTCACATAGCATAAACCCGTAAAGGGAAGTCATATAAAATATCAAGACCAACTTAAACCACGAA
* *
254258 AAAGATTTA
66 AAAGAATCA
254267 TCTCAC
1 TCTCAC
254273 TTGACTTAGA
Statistics
Matches: 65, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
74 65 1.00
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (74 bp):
TCTCACATAGCATAAACCCGTAAAGGGAAGTCATATAAAATATCAAGACCAACTTAAACCACGAA
AAAGAATCA
Found at i:259410 original size:16 final size:17
Alignment explanation
Indices: 259370--259441 Score: 67
Period size: 16 Copynumber: 4.2 Consensus size: 17
259360 TCACTATTTA
259370 TATAATATAAATAATAT
1 TATAATATAAATAATAT
*
259387 TATAATATAAA-AATGT
1 TATAATATAAATAATAT
* *
259403 TATGATATATAT-ATAT
1 TATAATATAAATAATAT
*
259419 ATATATATATATATATATAT
1 -TATA-ATATAAATA-ATAT
259439 TAT
1 TAT
259442 CATTAACTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
16 16 0.36
17 14 0.31
18 8 0.18
19 3 0.07
20 4 0.09
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
TATAATATAAATAATAT
Found at i:259414 original size:2 final size:2
Alignment explanation
Indices: 259407--259438 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
259397 AAATGTTATG
259407 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
259439 TATCATTAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:261872 original size:57 final size:57
Alignment explanation
Indices: 261799--261923 Score: 178
Period size: 57 Copynumber: 2.2 Consensus size: 57
261789 ATCACAAATG
** * *
261799 TGGGCATCAAACTATAAAATTATGAAATTTTGCTTCTTTGTATGAGTATTGGCTTCA
1 TGGGCATCAAACTATAAAACAATGAAATTTTGCTACTTTGTATGAGTATCGGCTTCA
* * *
261856 TGGGCATCAAATTATAAAACAATGAATTTTTGCTACTTTTTATGAGTATCGGCTTCA
1 TGGGCATCAAACTATAAAACAATGAAATTTTGCTACTTTGTATGAGTATCGGCTTCA
*
261913 TAGGCATCAAA
1 TGGGCATCAAA
261924 GTAAGTGATT
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.38
Consensus pattern (57 bp):
TGGGCATCAAACTATAAAACAATGAAATTTTGCTACTTTGTATGAGTATCGGCTTCA
Found at i:262016 original size:12 final size:12
Alignment explanation
Indices: 261999--262031 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
261989 TATGTTATAA
*
261999 AGCTATAAGTAG
1 AGCTATAAGAAG
262011 AGCTATAAGAAG
1 AGCTATAAGAAG
262023 AGCTATAAG
1 AGCTATAAG
262032 CTCATCCATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.45, C:0.09, G:0.24, T:0.21
Consensus pattern (12 bp):
AGCTATAAGAAG
Found at i:271537 original size:22 final size:23
Alignment explanation
Indices: 271484--271533 Score: 61
Period size: 21 Copynumber: 2.2 Consensus size: 23
271474 ATAGAAATTG
271484 AAATAGAAATGTGCCTAAAAATAA
1 AAAT-GAAATGTGCCTAAAAATAA
271508 AAATGAAATGT-CC-AAATAA-AA
1 AAATGAAATGTGCCTAAA-AATAA
271529 AAATG
1 AAATG
271534 GAAAGTTGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 10 0.40
22 4 0.16
23 7 0.28
24 4 0.16
ACGTcount: A:0.60, C:0.08, G:0.12, T:0.20
Consensus pattern (23 bp):
AAATGAAATGTGCCTAAAAATAA
Found at i:275606 original size:23 final size:23
Alignment explanation
Indices: 275509--275611 Score: 134
Period size: 23 Copynumber: 4.5 Consensus size: 23
275499 GCACCAAAGT
* *
275509 ACCACATATAAATGTCCCGAAGG
1 ACCACGTAGAAATGTCCCGAAGG
* * *
275532 ACCACATAGTATTGTCCCGAAGG
1 ACCACGTAGAAATGTCCCGAAGG
*
275555 ACCACGTAGAAATATCCCGAAGG
1 ACCACGTAGAAATGTCCCGAAGG
*
275578 ACCACGTAGAAATGTCCTGAAGG
1 ACCACGTAGAAATGTCCCGAAGG
*
275601 ACCACGAAGAA
1 ACCACGTAGAA
275612 TTGTATCAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.16
Consensus pattern (23 bp):
ACCACGTAGAAATGTCCCGAAGG
Found at i:275917 original size:16 final size:17
Alignment explanation
Indices: 275885--275918 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
275875 TAGGTCAATG
*
275885 CTTTTTAGTTTATATCA
1 CTTTTTAATTTATATCA
275902 CTTTTTAATTTA-ATCA
1 CTTTTTAATTTATATCA
275918 C
1 C
275919 ATAAGTCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.26, C:0.15, G:0.03, T:0.56
Consensus pattern (17 bp):
CTTTTTAATTTATATCA
Found at i:276470 original size:19 final size:20
Alignment explanation
Indices: 276446--276485 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
276436 AGAATTTGTC
*
276446 CTTAAA-AATGGTATCGATA
1 CTTAAACAATGGTATCCATA
*
276465 CTTAAACATTGGTATCCATA
1 CTTAAACAATGGTATCCATA
276485 C
1 C
276486 CCCTGGTATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (20 bp):
CTTAAACAATGGTATCCATA
Found at i:281130 original size:23 final size:23
Alignment explanation
Indices: 281100--281144 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
281090 ATCATGTAGA
*
281100 ATTGTCTCGAAGGACCACATAGT
1 ATTGTCTCAAAGGACCACATAGT
*
281123 ATTGTCTCAAAGGACCGCATAG
1 ATTGTCTCAAAGGACCACATAG
281145 AACCCTCGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.24
Consensus pattern (23 bp):
ATTGTCTCAAAGGACCACATAGT
Found at i:286283 original size:54 final size:55
Alignment explanation
Indices: 286220--286328 Score: 184
Period size: 54 Copynumber: 2.0 Consensus size: 55
286210 CGGCATTAGG
*
286220 AAGTCAAAAAGCATCCAAACTTTAACAACATTAAATG-AATAATAATGTTTATCA
1 AAGTCAAAAAACATCCAAACTTTAACAACATTAAATGCAATAATAATGTTTATCA
* *
286274 AAGTCAAAAAACTTCCAAACTTTAACAACATTCAATGCAATAATAATGTTTATCA
1 AAGTCAAAAAACATCCAAACTTTAACAACATTAAATGCAATAATAATGTTTATCA
286329 CATCTTCTCT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
54 34 0.67
55 17 0.33
ACGTcount: A:0.49, C:0.17, G:0.06, T:0.28
Consensus pattern (55 bp):
AAGTCAAAAAACATCCAAACTTTAACAACATTAAATGCAATAATAATGTTTATCA
Found at i:291188 original size:22 final size:22
Alignment explanation
Indices: 291163--291211 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
291153 CCTTTCTTAT
291163 GTATTAATTTGTCTCTAGATAA
1 GTATTAATTTGTCTCTAGATAA
*
291185 GTATTAATTTGTTTCTAGATAA
1 GTATTAATTTGTCTCTAGATAA
291207 GTATT
1 GTATT
291212 TGAAACACCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.06, G:0.14, T:0.49
Consensus pattern (22 bp):
GTATTAATTTGTCTCTAGATAA
Found at i:320293 original size:30 final size:31
Alignment explanation
Indices: 320238--320316 Score: 108
Period size: 30 Copynumber: 2.6 Consensus size: 31
320228 ACTATTACAA
*
320238 TTATAATTATAA-CTTTATGAAAAGTATTACT
1 TTATAATGATAAGCTTTA-GAAAAGTATTACT
320269 TTATAATGATAAGCTTTA-AAAAGTATTACT
1 TTATAATGATAAGCTTTAGAAAAGTATTACT
* *
320299 TTATAACGATAAGTTTTA
1 TTATAATGATAAGCTTTA
320317 TTATTATAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
30 28 0.64
31 11 0.25
32 5 0.11
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.43
Consensus pattern (31 bp):
TTATAATGATAAGCTTTAGAAAAGTATTACT
Found at i:321446 original size:34 final size:34
Alignment explanation
Indices: 321365--321638 Score: 153
Period size: 33 Copynumber: 7.6 Consensus size: 34
321355 TGCAAATGAT
* *
321365 TTTTGAAAACTTATATAATATATGGATTTTAAAAATA
1 TTTTGAAAA-TTATATAATATA--GATTTAAAAAACA
* * *
321402 TTTTAAAAAATCATATAATATAGATTTAAAAAATA
1 TTTT-GAAAATTATATAATATAGATTTAAAAAACA
* *
321437 TTTTGAAAA-TATATCATATATGATTT-TAAAACA
1 TTTTGAAAATTATATAATATA-GATTTAAAAAACA
* *
321470 ATTTGAAAACGTATATATATATTATATAGTTTTAAAAAAACA
1 TTTTG-AAA---AT-TATATA--ATATAGATTT-AAAAAACA
* * **
321512 TTTT-AAAAATATATAATATATAGTTTTTAAAACA
1 TTTTGAAAATTATATAATATAGA-TTTAAAAAACA
* * *
321546 TTTTGAAAACATATATTATATAG-TTT-TAAAACA
1 TTTTGAAAA-TTATATAATATAGATTTAAAAAACA
* **
321579 TTTTGAAAATATATATAATATATATAGTTTTTAAAACA
1 TTTTGAAAAT-TATAT-A-ATATAGA-TTTAAAAAACA
*
321617 TTTTGAAAAAATATATAATATA
1 TTTTG-AAAATTATATAATATA
321639 TCTATAGTTT
Statistics
Matches: 191, Mismatches: 24, Indels: 45
0.73 0.09 0.17
Matches are distributed among these distances:
33 39 0.20
34 30 0.16
35 28 0.15
36 22 0.12
37 21 0.11
38 21 0.11
39 9 0.05
40 7 0.04
41 5 0.03
42 9 0.05
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (34 bp):
TTTTGAAAATTATATAATATAGATTTAAAAAACA
Found at i:321520 original size:109 final size:106
Alignment explanation
Indices: 321366--321638 Score: 317
Period size: 107 Copynumber: 2.5 Consensus size: 106
321356 GCAAATGATT
** *
321366 TTTGAAAACT-TATATAATATATGGA-TTTTAAAAATATTTTAAAAAATCATATAATATAGA-TT
1 TTTGAAAA-TATATATAATATATATAGTTTTAAAAACATTTTAAAAAAT-ATATAATATAGAGTT
* *
321428 TAAAAAATATTTTG-AAA-ATATATCATATATGATTTTAAAACAA
64 TAAAAAACATTTTGAAAACATATATTATATA-G-TTTTAAAACAA
*
321471 TTTGAAAACGTATATAT-ATATTATATAGTTTTAAAAAAACATTTT-AAAAATATATAATATATA
1 TTTGAAAA--TATATATAATA-TATATAGTTTT--AAAAACATTTTAAAAAATATATAATATAGA
** *
321534 GTTTTTAAAACATTTTGAAAACATATATTATATAGTTTTAAAACAT
61 GTTTAAAAAACATTTTGAAAACATATATTATATAGTTTTAAAACAA
*
321580 TTTGAAAATATATATAATATATATAGTTTTTAAAACATTTTGAAAAAATATATAATATA
1 TTTGAAAATATATATAATATATATAGTTTTAAAAACATTTT-AAAAAATATATAATATA
321639 TCTATAGTTT
Statistics
Matches: 145, Mismatches: 11, Indels: 22
0.81 0.06 0.12
Matches are distributed among these distances:
105 18 0.12
106 4 0.03
107 43 0.30
108 18 0.12
109 37 0.26
110 14 0.10
111 11 0.08
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.41
Consensus pattern (106 bp):
TTTGAAAATATATATAATATATATAGTTTTAAAAACATTTTAAAAAATATATAATATAGAGTTTA
AAAAACATTTTGAAAACATATATTATATAGTTTTAAAACAA
Found at i:321601 original size:40 final size:37
Alignment explanation
Indices: 321365--321693 Score: 255
Period size: 40 Copynumber: 8.9 Consensus size: 37
321355 TGCAAATGAT
* *
321365 TTTTGAAAACT-TATATA-ATATATGGATTTTAAAA-A
1 TTTTGAAAAATATATATATATATATAG-TTTTAAAACA
* * * *
321400 TATTTTAAAAA-AT-CATATA-ATATAGATTTAAAAAATA
1 T-TTTGAAAAATATATATATATATATAG-TTT-TAAAACA
* *
321437 TTTTG-AAAATATAT-CATATAT-GA-TTTTAAAACA
1 TTTTGAAAAATATATATATATATATAGTTTTAAAACA
* *
321470 ATTTGAAAACGTATATATATATTATATAGTTTTAAAAAAACA
1 TTTTGAAAA-ATATATATATA-TATATAGTTTT---AAAACA
321512 TTTT--AAAA-ATATATA-ATATATAGTTTTTAAAACA
1 TTTTGAAAAATATATATATATATATAG-TTTTAAAACA
*
321546 TTTTG--AAA-ACATATAT-TATATAGTTTTAAAACA
1 TTTTGAAAAATATATATATATATATAGTTTTAAAACA
321579 TTTTG-AAAATATATATAATATATATAGTTTTTAAAACA
1 TTTTGAAAAATATATAT-ATATATATAG-TTTTAAAACA
*
321617 TTTTGAAAAAATATATAATATATCTATAGTTTTGAAAACA
1 TTTTG-AAAAATATAT-ATATATATATAGTTTT-AAAACA
*
321657 TTTTGAAAAAGTATATATATATTATATACTTTTAAAA
1 TTTTGAAAAA-TATATATATA-TATATAGTTTTAAAA
321694 AAAAACATTT
Statistics
Matches: 241, Mismatches: 22, Indels: 58
0.75 0.07 0.18
Matches are distributed among these distances:
33 24 0.10
34 35 0.15
35 27 0.11
36 34 0.14
37 19 0.08
38 23 0.10
39 22 0.09
40 46 0.19
41 2 0.01
42 9 0.04
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (37 bp):
TTTTGAAAAATATATATATATATATAGTTTTAAAACA
Found at i:321617 original size:38 final size:36
Alignment explanation
Indices: 321365--321678 Score: 274
Period size: 38 Copynumber: 8.6 Consensus size: 36
321355 TGCAAATGAT
* * *
321365 TTTTGAAAACT-TATATAATATATGGATTTTAAAA-A
1 TTTTGAAAAATATATAT-ATATATAGTTTTTAAAACA
* ** *
321400 TATTTTAAAAA-ATCATATA-ATATAGATTTAAAAAATA
1 T-TTTGAAAAATAT-ATATATATATAG-TTTTTAAAACA
* *
321437 TTTTG-AAAATATAT-CATATAT-GATTTTAAAACA
1 TTTTGAAAAATATATATATATATAGTTTTTAAAACA
* *
321470 ATTTGAAAACGTATATATATATTATATAGTTTTAAAAAAACA
1 TTTTGAAAA---ATATATATA-TATATAGTTTT--TAAAACA
321512 TTTT-AAAAATATATA-ATATATAGTTTTTAAAACA
1 TTTTGAAAAATATATATATATATAGTTTTTAAAACA
*
321546 TTTTG-AAAACATATAT-TATATAG-TTTTAAAACA
1 TTTTGAAAAATATATATATATATAGTTTTTAAAACA
321579 TTTTGAAAATATATATAATATATATAGTTTTTAAAACA
1 TTTTGAAAA-ATATAT-ATATATATAGTTTTTAAAACA
*
321617 TTTTGAAAAAATATATAATATATCTATAGTTTTGAAAACA
1 TTTTG-AAAAATATAT-ATATA--TATAGTTTTTAAAACA
321657 TTTTGAAAAAGTATATATATAT
1 TTTTGAAAAA-TATATATATAT
321679 TATATACTTT
Statistics
Matches: 231, Mismatches: 21, Indels: 52
0.76 0.07 0.17
Matches are distributed among these distances:
33 26 0.11
34 34 0.15
35 21 0.09
36 33 0.14
37 21 0.09
38 35 0.15
39 19 0.08
40 29 0.13
41 4 0.02
42 9 0.04
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (36 bp):
TTTTGAAAAATATATATATATATAGTTTTTAAAACA
Found at i:321621 original size:71 final size:72
Alignment explanation
Indices: 321365--321694 Score: 261
Period size: 75 Copynumber: 4.5 Consensus size: 72
321355 TGCAAATGAT
* ** * * *
321365 TTTTGAAAACTTATATAATATATGGA-TTTTAAAAATATTTT-AAAAA-ATCATATAATATAGAT
1 TTTTGAAAA-ATATATAATATATATAGTTTTTAAAACATTTTGAAAAACAT-ATATTATATAG-T
* *
321427 TTAAAAAATA
63 TTTAAAAACA
* * * *
321437 TTTTG-AAAATATAT--CATATAT-GATTTTAAAACAATTTGAAAACGTATATATATATTATATA
1 TTTTGAAAAATATATAATATATATAGTTTTTAAAACATTTTG-AAA---A-ACATATATTATATA
321498 GTTTTAAAAAAACA
61 GTTTT--AAAAACA
321512 TTTT-AAAAATATAT-A-ATATATAGTTTTTAAAACATTTTG-AAAACATATATTATATAGTTTT
1 TTTTGAAAAATATATAATATATATAGTTTTTAAAACATTTTGAAAAACATATATTATATAGTTTT
321573 -AAAACA
66 AAAAACA
*
321579 TTTTGAAAATATATATAATATATATAGTTTTTAAAACATTTTGAAAAAATATATAATATATCTAT
1 TTTTGAAAA-ATATATAATATATATAGTTTTTAAAACATTTTG-AAAAACATAT-AT-TA--TAT
*
321644 AGTTTTGAAAACA
60 AGTTTTAAAAACA
* *
321657 TTTTGAAAAAGTATATATATATTATATACTTTTAAAAA
1 TTTTGAAAAA-TATATA-ATA-TATATAGTTTTTAAAA
321695 AAAACATTTT
Statistics
Matches: 214, Mismatches: 17, Indels: 46
0.77 0.06 0.17
Matches are distributed among these distances:
67 10 0.05
68 19 0.09
69 6 0.03
70 27 0.13
71 28 0.13
72 5 0.02
73 12 0.06
74 15 0.07
75 29 0.14
76 15 0.07
77 10 0.05
78 21 0.10
79 3 0.01
80 14 0.07
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (72 bp):
TTTTGAAAAATATATAATATATATAGTTTTTAAAACATTTTGAAAAACATATATTATATAGTTTT
AAAAACA
Found at i:321829 original size:15 final size:15
Alignment explanation
Indices: 321807--321856 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 15
321797 TTGTTTTGAA
321807 TTTTCTTTT-TTTAT
1 TTTTCTTTTATTTAT
321821 TTTTCCTTTTATTTAT
1 TTTT-CTTTTATTTAT
* * *
321837 TTAT-TTTAATTTAC
1 TTTTCTTTTATTTAT
321851 TTTTCT
1 TTTTCT
321857 CTCTCTCTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
14 15 0.52
15 6 0.21
16 8 0.28
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTCTTTTATTTAT
Found at i:322956 original size:21 final size:20
Alignment explanation
Indices: 322930--322969 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
322920 ACCTTTTATA
322930 TTTATTTATT-TTTTTGTCTAT
1 TTTATTT-TTATTTTT-TCTAT
322951 TTTATTTTTATTTTTTCTA
1 TTTATTTTTATTTTTTCTA
322970 ATGTTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.78
Consensus pattern (20 bp):
TTTATTTTTATTTTTTCTAT
Found at i:322964 original size:20 final size:21
Alignment explanation
Indices: 322930--322969 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
322920 ACCTTTTATA
*
322930 TTTATTTATTTTTTTGTCTAT
1 TTTATTTATTATTTTGTCTAT
*
322951 TTTATTT-TTATTTTTTCTA
1 TTTATTTATTATTTTGTCTA
322970 ATGTTTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.78
Consensus pattern (21 bp):
TTTATTTATTATTTTGTCTAT
Found at i:323044 original size:18 final size:18
Alignment explanation
Indices: 323018--323055 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
323008 TATTATTCTC
323018 TTTCTTTTTATTTATCTTT
1 TTTCTTTTTATTTAT-TTT
*
323037 TTTC-TTTTCTTTATTTT
1 TTTCTTTTTATTTATTTT
323054 TT
1 TT
323056 ATTTCCTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 9 0.50
19 4 0.22
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTCTTTTTATTTATTTT
Found at i:323107 original size:6 final size:5
Alignment explanation
Indices: 323062--323258 Score: 50
Period size: 5 Copynumber: 37.4 Consensus size: 5
323052 TTTTATTTCC
*
323062 TTTAT ATTTAT TTTAAT TCTCTAT TTATTT TTTAT TTTAT TCTTAT TTT-T
1 TTTAT -TTTAT TTT-AT T-T-TAT TT-TAT TTTAT TTTAT T-TTAT TTTAT
* * * * *
323112 ATTTAT TGTAT ATATAT TATTAT TCATTTT TTTAT TTT-C TTTAT TTT-C
1 -TTTAT TTTAT -TTTAT T-TTAT T--TTAT TTTAT TTTAT TTTAT TTTAT
* * *
323160 TTTAT TCTT-T TTGT-T TTTA- TTTCT TTTAT TTT-C TTTAT CTTCAT
1 TTTAT T-TTAT TT-TAT TTTAT TTTAT TTTAT TTTAT TTTAT -TTTAT
* * * *
323204 TTTAT TTATGAT GTTTAC TTTAT CTTCAT TTTAT TTCAT TTT-C TTTAT
1 TTTAT TT-T-AT -TTTAT TTTAT -TTTAT TTTAT TTTAT TTTAT TTTAT
*
323252 TTCAT TT
1 TTTAT TT
323259 GTTTTGTTTC
Statistics
Matches: 142, Mismatches: 27, Indels: 45
0.66 0.13 0.21
Matches are distributed among these distances:
4 18 0.13
5 70 0.49
6 39 0.27
7 12 0.08
8 3 0.02
ACGTcount: A:0.18, C:0.09, G:0.02, T:0.71
Consensus pattern (5 bp):
TTTAT
Found at i:323118 original size:21 final size:20
Alignment explanation
Indices: 323022--323209 Score: 80
Period size: 21 Copynumber: 8.8 Consensus size: 20
323012 ATTCTCTTTC
*
323022 TTTTTATTTATCTTTTTTCTT
1 TTTTTATTTAT-TTTATTCTT
*
323043 TTCTTTA-TT-TTTTATT-TCC
1 TT-TTTATTTATTTTATTCT-T
*
323062 TTTATATTTATTTTAATTCTCT
1 TTTTTATTTATTTT-ATTCT-T
*
323084 ATTTATTTTTTATTTTATTCTT
1 -TTT-TTATTTATTTTATTCTT
* * *
323106 ATTTTTATTTATTGTATATATA
1 -TTTTTATTTATTTTAT-TCTT
* * * *
323128 TTATTATTCATTTTTTTATT
1 TTTTTATTTATTTTATTCTT
323148 TTCTTTATTT-TCTTTATTCTT
1 TT-TTTATTTAT-TTTATTCTT
* *
323169 TTTGTT-TTTATTTCTTTTATT
1 TTT-TTATTTATTT-TATTCTT
323190 TTCTTTATCTTCATTTTATT
1 TT-TTTAT-TT-ATTTTATT
323210 TATGATGTTT
Statistics
Matches: 127, Mismatches: 22, Indels: 34
0.69 0.12 0.19
Matches are distributed among these distances:
18 4 0.03
19 9 0.07
20 17 0.13
21 56 0.44
22 15 0.12
23 13 0.10
24 13 0.10
ACGTcount: A:0.16, C:0.09, G:0.01, T:0.74
Consensus pattern (20 bp):
TTTTTATTTATTTTATTCTT
Found at i:323156 original size:9 final size:9
Alignment explanation
Indices: 323137--323253 Score: 63
Period size: 9 Copynumber: 13.4 Consensus size: 9
323127 ATTATTATTC
323137 ATTTT-TTT
1 ATTTTCTTT
323145 ATTTTCTTT
1 ATTTTCTTT
323154 ATTTTCTTT
1 ATTTTCTTT
323163 A--TTCTTT
1 ATTTTCTTT
323170 -TTGTT-TTT
1 ATT-TTCTTT
323178 A-TTTCTTTT
1 ATTTTC-TTT
323187 ATTTTCTTT
1 ATTTTCTTT
*
323196 A---TCTTC
1 ATTTTCTTT
*
323202 ATTTTATTT
1 ATTTTCTTT
** *
323211 ATGATGTTT
1 ATTTTCTTT
*
323220 ACTTTATCTTC
1 A-TTT-TCTTT
*
323231 ATTTTATTT
1 ATTTTCTTT
323240 CATTTTCTTT
1 -ATTTTCTTT
323250 ATTT
1 ATTT
323254 CATTTGTTTT
Statistics
Matches: 82, Mismatches: 13, Indels: 27
0.67 0.11 0.22
Matches are distributed among these distances:
6 5 0.06
7 8 0.10
8 9 0.11
9 40 0.49
10 16 0.20
11 4 0.05
ACGTcount: A:0.15, C:0.10, G:0.03, T:0.73
Consensus pattern (9 bp):
ATTTTCTTT
Found at i:323165 original size:33 final size:34
Alignment explanation
Indices: 323128--323212 Score: 106
Period size: 33 Copynumber: 2.6 Consensus size: 34
323118 TGTATATATA
*
323128 TTATTATTCATTTTTTTATTTTC-TTTATTTTCT
1 TTATTCTTCATTTTTTTATTTTCTTTTATTTTCT
*
323161 TTATTCTT-TTTGTTTTTA-TTTCTTTTATTTTCT
1 TTATTCTTCATT-TTTTTATTTTCTTTTATTTTCT
323194 TTA-TCTTCATTTTATTTAT
1 TTATTCTTCATTTT-TTTAT
323213 GATGTTTACT
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
32 12 0.27
33 32 0.73
ACGTcount: A:0.14, C:0.09, G:0.01, T:0.75
Consensus pattern (34 bp):
TTATTCTTCATTTTTTTATTTTCTTTTATTTTCT
Found at i:326924 original size:95 final size:95
Alignment explanation
Indices: 326812--327074 Score: 357
Period size: 95 Copynumber: 2.7 Consensus size: 95
326802 ATATTATAAT
* * * * * * *
326812 ATTATATATATATAATAAAGCTTGAGCTATCCCTCTAAAGTAATTGGTTAAACGCCCTGACTTTA
1 ATTATA-ATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTA
*
326877 TGGATAAGATTCAGCTAGCCTCATAAAGGTG
65 TGGATAAGATTCAGCTAGCCTCATAAAGGCG
326908 ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTAT
1 ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTAT
* *
326973 GGATAATATTCAGCTAGCCTGATAAAGGCG
66 GGATAAGATTCAGCTAGCCTCATAAAGGCG
* * *
327003 ATTATAATAT-CTATACAATGATATGGAGTTGTCCCTCTAGAGCAATTGGTTAAATGCCCCGGCT
1 ATTATAATATACAATA-AA-GCT-T-GAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCT
327067 TTATGGAT
62 TTATGGAT
327075 CCAGCTAGCC
Statistics
Matches: 150, Mismatches: 13, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
94 4 0.03
95 91 0.61
96 8 0.05
97 1 0.01
98 46 0.31
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (95 bp):
ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTAT
GGATAAGATTCAGCTAGCCTCATAAAGGCG
Found at i:328017 original size:84 final size:84
Alignment explanation
Indices: 327870--328412 Score: 669
Period size: 84 Copynumber: 6.5 Consensus size: 84
327860 AAAGCACCTT
* *
327870 CAAC-AAAGACCTTTGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAGCTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAA
* * **
327934 GGCGAGAATGGCTATCACC
66 GGCGAGAAGGGTTATCTGC
* * *
327953 CAACAAAAGACCTTTGAGTTCGATTACACTCAGCTCAAATGCACATCATTTGCAGCATAACTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAA
* * *
328018 GACGAGAAGGGCTATCTGT
66 GGCGAGAAGGGTTATCTGC
* * * *
328037 CAACAATAGACCTTCGAGTTCGATTACACTCAGCTCAAATGCACATCATTTGCAGCATAGCTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAA
* *
328102 GGCAAGAAGGGTTATCTTC
66 GGCGAGAAGGGTTATCTGC
** * * *
328121 CAACAAAAGACCTTCGAGTTCGATTACACTTGGCTCAAAGACACATCATTTGCAGCATAGCTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAA
*
328186 GGCAAGAAGGGTTATCTGC
66 GGCGAGAAGGGTTATCTGC
* *
328205 CAACAAAAGACCTTCGAGTTCGATTCCACTCAGCTCAAAGGCACATCTAATTTACAACATAACTC
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC--ATTTACAGCATAACTC
* * *
328270 AAGGTGAGAAGGGTTATTTGT
64 AAGGCGAGAAGGGTTATCTGC
* * * * *
328291 CAAC-TAAGACCTTCGAGTTCGATTACATTCACCTCAAAGGCATATCCATTTTATAGCATAACTC
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT-CA-TTTACAGCATAACTC
* *
328355 AAGGCGAGAAGGGTTATATGT
64 AAGGCGAGAAGGGTTATCTGC
* * * *
328376 CAA-TAAAGACCTTCGAGTTCAATTATATTCAGCTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAA
328413 GAGCATGCCA
Statistics
Matches: 408, Mismatches: 46, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
83 4 0.01
84 269 0.66
85 100 0.25
86 35 0.09
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.25
Consensus pattern (84 bp):
CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAA
GGCGAGAAGGGTTATCTGC
Found at i:328434 original size:85 final size:85
Alignment explanation
Indices: 327869--328495 Score: 484
Period size: 84 Copynumber: 7.4 Consensus size: 85
327859 AAAAGCACCT
* * * *
327869 TCAAC-AAAGACCTTTGAGTTCGATTACACTCAGCTCAAAG---GCACATCATTTACAGCATAGC
1 TCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGCATGC-CA-AATTTACAGCATAAC
* * **
327930 TCAAGGCGAGAATGGCTATCAC
64 TCAAGGCGAGAAGGGTTATCTG
* * * * *
327952 CCAACAAAAGACCTTTGAGTTCGATTACACTCAGCTC-AA--ATGCACATCATTTGCAGCATAAC
1 TCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGCATGC-CA-AATTTACAGCATAAC
* *
328014 TCAAGACGAGAAGGGCTATCTG
64 TCAAGGCGAGAAGGGTTATCTG
* * * * *
328036 TCAACAATAGACCTTCGAGTTCGATTACACTCAGCTC-AA--ATGCACATCATTTGCAGCATAGC
1 TCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGCATGC-CA-AATTTACAGCATAAC
*
328098 TCAAGGCAAGAAGGGTTATCT-
64 TCAAGGCGAGAAGGGTTATCTG
* * *
328119 TCCAACAAAAGACCTTCGAGTTCGATTACACTT-GGCTCAAAG-A--CACATCATTTGCAGCATA
1 T-CAACAAAAGACCTTCGAGTTCGATTACA-TTCAGCTCAAAGCATGC-CA-AATTTACAGCATA
* *
328180 GCTCAAGGCAAGAAGGGTTATCTG
62 ACTCAAGGCGAGAAGGGTTATCTG
* * * *** * *
328204 CCAACAAAAGACCTTCGAGTTCGATTCCACTCAGCTCAAAGGCACATCTAATTTACAACATAACT
1 TCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTCAAA-GCATGCCAAATTTACAGCATAACT
* *
328269 CAAGGTGAGAAGGGTTATTTG
65 CAAGGCGAGAAGGGTTATCTG
* * * * *
328290 TCAAC-TAAGACCTTCGAGTTCGATTACATTCACCTCAAAGGCATATCC-ATTTTATAGCATAAC
1 TCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTCAAA-GCAT-GCCAAATTTACAGCATAAC
*
328353 TCAAGGCGAGAAGGGTTATATG
64 TCAAGGCGAGAAGGGTTATCTG
* * * *
328375 TCAA-TAAAGACCTTCGAGTTCAATTATATTCAGCTCAAGAGCATGCCAAATTTACAGCATAGCT
1 TCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTCAA-AGCATGCCAAATTTACAGCATAACT
* ** **
328439 TAATTCGAGAA-AATCTATCTG
65 CAAGGCGAGAAGGGT-TATCTG
* * * *
328460 TCAATAAAA-ATCGTCGAGTTCGATTCCATTCAGCTC
1 TCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTC
328496 GATTATGCAT
Statistics
Matches: 462, Mismatches: 63, Indels: 36
0.82 0.11 0.06
Matches are distributed among these distances:
83 8 0.02
84 253 0.55
85 159 0.34
86 41 0.09
87 1 0.00
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (85 bp):
TCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGCATGCCAAATTTACAGCATAACTC
AAGGCGAGAAGGGTTATCTG
Found at i:329306 original size:73 final size:73
Alignment explanation
Indices: 329225--329557 Score: 324
Period size: 73 Copynumber: 4.5 Consensus size: 73
329215 TTGAAAACTT
* * *
329225 ATATAATATATGGTTTTTAAAAAATATTT-AAAAAAT-TATATAATATATAGTTTTAAAAAAAAT
1 ATATAATATATAGTTTTTAAAACAT-TTTGAAAACATATATATAATATATAGTTTT-AAAAAAAT
329288 TTTGAAAAAA
64 TTTGAAAAAA
*
329298 ATATAATATATA-TTTTTAAAACATTTTGAAAACATATATATATTATATAGTTTTAAAAAACATT
1 ATATAATATATAGTTTTTAAAACATTTTGAAAACATATATATAATATATAGTTTTAAAAAA-ATT
*
329362 TT-AAAAAT
65 TTGAAAAAA
* * *
329370 GTATAATATATGGTTTTTAAAACATTTTGAAAAC--ATATAT--TATATAGTTTT-AAAACATTT
1 ATATAATATATAGTTTTTAAAACATTTTGAAAACATATATATAATATATAGTTTTAAAAAAATTT
329430 TGAAATATATATA
66 TG-AA-A-A-A-A
* * * **
329443 ATATATATATATAGTTTTTCAAACATTTTGAATATATATATAATATATATATAGTTTTGGAAAAA
1 ATATA-ATATATAGTTTTTAAAACATTTTGAAAACATATAT-ATA-ATATATAGTTTTAAAAAAA
329508 TTTTGAAAAAA
63 TTTTGAAAAAA
*
329519 TATATATATTATATAGTTTTGAAAAAAACATTTTGAAAA
1 -ATATA-A-TATATAGTTTT---TAAAACATTTTGAAAA
329558 TATTTTTTTA
Statistics
Matches: 218, Mismatches: 19, Indels: 38
0.79 0.07 0.14
Matches are distributed among these distances:
67 5 0.02
68 4 0.02
69 13 0.06
70 1 0.00
71 10 0.05
72 39 0.18
73 58 0.27
74 25 0.11
76 5 0.02
77 10 0.05
78 12 0.06
79 1 0.00
80 13 0.06
81 22 0.10
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.42
Consensus pattern (73 bp):
ATATAATATATAGTTTTTAAAACATTTTGAAAACATATATATAATATATAGTTTTAAAAAAATTT
TGAAAAAA
Found at i:329327 original size:108 final size:108
Alignment explanation
Indices: 329213--329557 Score: 331
Period size: 106 Copynumber: 3.1 Consensus size: 108
329203 TGAAAATGAT
*
329213 TTTTGAAAACT-TATATAATATATGGTTTTTAAAAAATATTTAAAAAATTATATAATATATAGTT
1 TTTTGAAAACTATATATAATATATAGTTTTTAAAAAATATTTAAAAAATTATATAATATATAGTT
329277 TTAAAAAAAATTTTGAAAAAAATATAATATATATTTTTAAAACA
66 TT-AAAAAAATTTTGAAAAAAATATAATATATATTTTTAAAACA
* * * * *
329321 TTTTGAAAACATATATATATTATATAG-TTTTAAAAAACATTTTAAAAA-TGTATAATATATGGT
1 TTTTGAAAAC-TATATATAATATATAGTTTTTAAAAAATATTTAAAAAATTATATAATATATAGT
* * * * *
329384 TTTTAAAACATTTTG-AAAACATATATTATATAGTTTTAAAACA
65 TTTAAAAAAATTTTGAAAAAAATATAATATATATTTTTAAAACA
* * * * *
329427 TTTTGAAATATATATAATATATATATATAGTTTTTCAAACAT-TTTGAATATATATATAATATAT
1 TTTTGAAA-A-CTAT-ATATA-ATATATAGTTTTTAAAAAATATTT-AAAAAAT-TAT-ATA-AT
** *
329491 ATATAGTTTTGGAAAAATTTTGAAAAAATATATATATTATATAGTTTTGAAAAAAACA
58 ATATAGTTTTAAAAAAATTTTGAAAAAA-ATATA-A-TATATA-TTTT---TAAAACA
329549 TTTTGAAAA
1 TTTTGAAAA
329558 TATTTTTTTA
Statistics
Matches: 189, Mismatches: 28, Indels: 27
0.77 0.11 0.11
Matches are distributed among these distances:
106 33 0.17
107 14 0.07
108 31 0.16
109 30 0.16
110 23 0.12
112 2 0.01
113 3 0.02
114 20 0.11
115 4 0.02
116 5 0.03
118 6 0.03
119 3 0.02
121 1 0.01
122 14 0.07
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (108 bp):
TTTTGAAAACTATATATAATATATAGTTTTTAAAAAATATTTAAAAAATTATATAATATATAGTT
TTAAAAAAATTTTGAAAAAAATATAATATATATTTTTAAAACA
Found at i:329458 original size:40 final size:37
Alignment explanation
Indices: 329213--329560 Score: 287
Period size: 40 Copynumber: 9.3 Consensus size: 37
329203 TGAAAATGAT
*
329213 TTTTGAAAACT-TATATA-ATATATGGTTTTTAAAAA-A
1 TTTTGAAAA-TATATATATATATATAG-TTTTAAAAACA
* *
329249 TATTT-AAAAAAT-TATATAATATATAGTTTTAAAAAAAA
1 T-TTTGAAAATATATATAT-ATATATAGTTTT-AAAAACA
* *
329287 TTTTGAAAA-AAATATA-ATATATA-TTTTTAAAACA
1 TTTTGAAAATATATATATATATATAGTTTTAAAAACA
*
329321 TTTTGAAAACATATATATATTATATAGTTTTAAAAAACA
1 TTTTGAAAATATATATATA-TATATAGTTTT-AAAAACA
* * *
329360 TTTT-AAAA-ATGTATA-ATATATGGTTTTTAAAACA
1 TTTTGAAAATATATATATATATATAGTTTTAAAAACA
*
329394 TTTTG-AAA-ACATATAT-TATATAGTTTT-AAAACA
1 TTTTGAAAATATATATATATATATAGTTTTAAAAACA
**
329427 TTTTGAAATATATATAATATATATATATAGTTTTTCAAACA
1 TTTTG-AA-A-ATAT-ATATATATATATAGTTTTAAAAACA
*
329468 TTTTGAATATATATATAATATATATATAGTTTTGGAAAA-A
1 TTTTGAA-A-ATATAT-ATATATATATAGTTTT-AAAAACA
*
329508 TTTTGAAAAAATATATATATTATATAGTTTTGAAAAAAACA
1 TTTTGAAAATATATATATA-TATATAGTTTT---AAAAACA
329549 TTTTGAAAATAT
1 TTTTGAAAATAT
329561 TTTTTTAAAA
Statistics
Matches: 262, Mismatches: 21, Indels: 53
0.78 0.06 0.16
Matches are distributed among these distances:
33 11 0.04
34 42 0.16
35 25 0.10
36 20 0.08
37 37 0.14
38 35 0.13
39 19 0.07
40 48 0.18
41 25 0.10
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (37 bp):
TTTTGAAAATATATATATATATATAGTTTTAAAAACA
Found at i:330723 original size:27 final size:27
Alignment explanation
Indices: 330660--330770 Score: 79
Period size: 27 Copynumber: 4.0 Consensus size: 27
330650 TACATACATA
* *
330660 TATTTTTTTATGTTTTATGTT-T-TA-T
1 TATTTTTTTCTATTTTAT-TTATATATT
330685 TATTTTTATTCT-TTTTACCTTT-TATATT
1 TATTTTT-TTCTATTTTA--TTTATATATT
*
330713 TATTTTTTTCTATTTTATTTATTTATT
1 TATTTTTTTCTATTTTATTTATATATT
* *
330740 TATTTATTTCTAATGTTTTATTTATACATT
1 TATTTTTTTCT-A--TTTTATTTATATATT
330770 T
1 T
330771 TATTATATAT
Statistics
Matches: 71, Mismatches: 5, Indels: 15
0.78 0.05 0.16
Matches are distributed among these distances:
25 12 0.17
26 9 0.13
27 22 0.31
28 14 0.20
30 14 0.20
ACGTcount: A:0.20, C:0.05, G:0.03, T:0.72
Consensus pattern (27 bp):
TATTTTTTTCTATTTTATTTATATATT
Found at i:330781 original size:16 final size:16
Alignment explanation
Indices: 330757--330792 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
330747 TTCTAATGTT
* *
330757 TTATTTATACATTTTA
1 TTATATATACATATTA
330773 TTATATATACATATTA
1 TTATATATACATATTA
330789 TTAT
1 TTAT
330793 TATCTCTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATATATACATATTA
Found at i:330822 original size:16 final size:16
Alignment explanation
Indices: 330792--330843 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 16
330782 CATATTATTA
330792 TTATCTCTTTCTTTTTAT
1 TTATCT-TTT-TTTTTAT
*
330810 TTATCTTTTTTTTTCT
1 TTATCTTTTTTTTTAT
330826 TT-TCTTTATTTTTTAT
1 TTATCTTT-TTTTTTAT
330842 TT
1 TT
330844 CCTTTATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 5 0.16
16 17 0.55
17 3 0.10
18 6 0.19
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.79
Consensus pattern (16 bp):
TTATCTTTTTTTTTAT
Found at i:330828 original size:10 final size:11
Alignment explanation
Indices: 330799--330886 Score: 51
Period size: 12 Copynumber: 8.1 Consensus size: 11
330789 TTATTATCTC
330799 TTTCTTTTTAT
1 TTTCTTTTTAT
330810 TTATCTTTTT-T
1 TT-TCTTTTTAT
330821 TTTCTTTTCT-T
1 TTTCTTTT-TAT
*
330832 TAT-TTTTTAT
1 TTTCTTTTTAT
* *
330842 TTCCTTTATA-
1 TTTCTTTTTAT
*
330852 TTT-ATTTTAT
1 TTTCTTTTTAT
*
330862 TTCTCTATTTAT
1 TT-TCTTTTTAT
*
330874 TTTTTATTTTAT
1 TTTCT-TTTTAT
330886 T
1 T
330887 CTTGTTTTAA
Statistics
Matches: 58, Mismatches: 11, Indels: 15
0.69 0.13 0.18
Matches are distributed among these distances:
9 5 0.09
10 16 0.28
11 17 0.29
12 20 0.34
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTCTTTTTAT
Found at i:330828 original size:21 final size:20
Alignment explanation
Indices: 330799--331057 Score: 86
Period size: 21 Copynumber: 12.2 Consensus size: 20
330789 TTATTATCTC
330799 TTTCTTTTTATTTATCTTTTTT
1 TTTC-TTTTATTTAT-TTTTTT
*
330821 TTTCTTTTCTTTATTTTTTAT
1 TTTCTTTTATTTATTTTTT-T
* *
330842 TTCCTTTATATTTATTTTATT
1 TTTCTTT-TATTTATTTTTTT
*
330863 TCTCTATTTATTT-TTTATTTT
1 TTTCT-TTTATTTATTT-TTTT
* * * *
330884 ATTCTTGTT-TTAATTTAATATA
1 TTTCTT-TTATTTATTT--TTTT
* * *
330906 TATCTATTA-TTATTCTTTTC
1 TTTCTTTTATTTATT-TTTTT
* *
330926 TTTATTTTATTTGTTTTCTTT
1 TTTCTTTTATTTATTTT-TTT
*
330947 ATTCTTTT-TGTT-TTTATTTCT
1 TTTCTTTTAT-TTATTT-TTT-T
330968 TTTC-TTTATCTTCATTTTATTT
1 TTTCTTTTAT-TT-ATTTT-TTT
* * *
330990 ATTCTATTTACTT-TTTTATT
1 TTTCT-TTTATTTATTTTTTT
*
331010 TTTGTTTT-TTTATCTTTTTAT
1 TTTCTTTTATTTAT-TTTTT-T
331031 TTTC-TTTATTTCATTTGTTTT
1 TTTCTTTTATTT-ATTT-TTTT
331052 ATTTCT
1 -TTTCT
331058 AATTTTAGAC
Statistics
Matches: 174, Mismatches: 35, Indels: 55
0.66 0.13 0.21
Matches are distributed among these distances:
18 2 0.01
19 4 0.02
20 42 0.24
21 78 0.45
22 37 0.21
23 7 0.04
24 4 0.02
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (20 bp):
TTTCTTTTATTTATTTTTTT
Found at i:330848 original size:16 final size:17
Alignment explanation
Indices: 330830--330882 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 17
330820 TTTTCTTTTC
330830 TTTATTTTTTATTTCCT
1 TTTATTTTTTATTTCCT
330847 TTATATTTATTTTATTTCTCT
1 TT-TA-TT-TTTTATTTC-CT
330868 ATTTATTTTTTATTT
1 -TTTATTTTTTATTT
330883 TATTCTTGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 2 0.06
18 2 0.06
19 10 0.32
20 11 0.35
21 4 0.13
22 2 0.06
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTATTTTTTATTTCCT
Found at i:330906 original size:126 final size:128
Alignment explanation
Indices: 330769--331011 Score: 291
Period size: 126 Copynumber: 1.9 Consensus size: 128
330759 ATTTATACAT
* * *
330769 TTTATTATATATACATATTATTATT-ATCTCTTTCTTTTTATTTATCTTT-TTTTTTCTTTTCT-
1 TTTAATATATAT-C-TATTATTATTCATCTCTTT-ATTTTATTTAT-TTTCTTTATTCTTTT-TG
*
330831 TTATTT-TTTATTTCCTTTATATTTATTTTATTT-CTCTATTTA-TTTTTTATTTTATTCTTGTT
61 TT-TTTATTTATTTCCTTTATATTCATTTTATTTACTCTATTTACTTTTTTATTTTATTCTTGTT
330893 TTAA
125 TTAA
* * *
330897 TTTAATATATATCTATTATTATTCTTTTCTTTATTTTATTTGTTTTCTTTATTCTTTTTGTTTTT
1 TTTAATATATATCTATTATTATTCATCTCTTTATTTTATTTATTTTCTTTATTCTTTTTGTTTTT
* * * *
330962 ATTTCTTTTCTTTATCTTCATTTTATTTATTCTATTTACTTTTTTATTTT
66 ATTTATTTCCTTTATATTCATTTTATTTACTCTATTTACTTTTTTATTTT
331012 TGTTTTTTTA
Statistics
Matches: 98, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
125 7 0.07
126 54 0.55
127 15 0.15
128 22 0.22
ACGTcount: A:0.18, C:0.09, G:0.01, T:0.72
Consensus pattern (128 bp):
TTTAATATATATCTATTATTATTCATCTCTTTATTTTATTTATTTTCTTTATTCTTTTTGTTTTT
ATTTATTTCCTTTATATTCATTTTATTTACTCTATTTACTTTTTTATTTTATTCTTGTTTTAA
Found at i:330949 original size:13 final size:13
Alignment explanation
Indices: 330922--331057 Score: 56
Period size: 13 Copynumber: 10.4 Consensus size: 13
330912 TTATTATTCT
330922 TTTCTTTAT-TTTA
1 TTTCTTT-TCTTTA
*
330935 TTTGTTTTCTTTA
1 TTTCTTTTCTTTA
* *
330948 TTCTTTTTGTTTTTA
1 TT-TCTTT-TCTTTA
330963 TTTCTTTTCTTTA
1 TTTCTTTTCTTTA
*
330976 TCTTCATTTTATTTA
1 T-TTC-TTTTCTTTA
330991 -TTCTATTTACTTT-
1 TTTCT-TTT-CTTTA
*
331004 TTTATTTT-TGTT-
1 TTTCTTTTCT-TTA
*
331016 TTT-TTATC-TT-
1 TTTCTTTTCTTTA
*
331026 TTTATTTTCTTTA
1 TTTCTTTTCTTTA
331039 TTTCATTTGT-TTTA
1 TTTC-TTT-TCTTTA
331053 TTTCT
1 TTTCT
331058 AATTTTAGAC
Statistics
Matches: 97, Mismatches: 11, Indels: 30
0.70 0.08 0.22
Matches are distributed among these distances:
10 5 0.05
11 8 0.08
12 9 0.09
13 31 0.32
14 28 0.29
15 16 0.16
ACGTcount: A:0.12, C:0.10, G:0.03, T:0.76
Consensus pattern (13 bp):
TTTCTTTTCTTTA
Found at i:331039 original size:52 final size:53
Alignment explanation
Indices: 330921--331046 Score: 123
Period size: 57 Copynumber: 2.3 Consensus size: 53
330911 ATTATTATTC
* * *
330921 TTTTCTTTATTTTATTTGTTTTCTTTATTCTTTTTGTTTTTATTTCTTTTCTTTA
1 TTTTCTTTA-TTTATTTATTTACTTTATTATTTTTGTTTTTATTTC-TTTCTTTA
* *
330976 TCTTCATTTTATTTATTCTATTTACTTTTTTATTTTTGTTTTT-TTATC-TT-TTTA
1 TTTTC--TTTATTTATT-TATTTACTTTATTATTTTTGTTTTTATT-TCTTTCTTTA
331030 TTTTCTTTATTTCATTT
1 TTTTCTTTATTT-ATTT
331047 GTTTTATTTC
Statistics
Matches: 60, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
52 8 0.13
53 3 0.05
54 8 0.13
55 6 0.10
56 8 0.13
57 27 0.45
ACGTcount: A:0.12, C:0.10, G:0.02, T:0.76
Consensus pattern (53 bp):
TTTTCTTTATTTATTTATTTACTTTATTATTTTTGTTTTTATTTCTTTCTTTA
Found at i:331064 original size:57 final size:57
Alignment explanation
Indices: 330951--331064 Score: 126
Period size: 57 Copynumber: 2.0 Consensus size: 57
330941 TTCTTTATTC
* *
330951 TTTTTGTTTTTATTTCTTTTCTTTATCTTCATTTTATTTATTCTATTTACTTTTTTA
1 TTTTTGTTTTTATTTCTTTTCTTTATCTTCATTTCATTTATTCTATTTACTATTTTA
* * * *
331008 TTTTTGTTTTT-TTATCTTTT-TATTTTCTTTATTTCATTTGTTTTATTT-CTAATTTTA
1 TTTTTGTTTTTATT-TCTTTTCT-TTATCTTCATTTCATTTATTCTATTTACT-ATTTTA
331065 GACATTTTCG
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
56 5 0.10
57 43 0.90
ACGTcount: A:0.14, C:0.09, G:0.03, T:0.75
Consensus pattern (57 bp):
TTTTTGTTTTTATTTCTTTTCTTTATCTTCATTTCATTTATTCTATTTACTATTTTA
Found at i:332512 original size:14 final size:14
Alignment explanation
Indices: 332495--332524 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
332485 AGTTAAAATG
332495 AATAAAATAAAGAA
1 AATAAAATAAAGAA
332509 AATAAAATAAAGAA
1 AATAAAATAAAGAA
332523 AA
1 AA
332525 AGAAACAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (14 bp):
AATAAAATAAAGAA
Found at i:332534 original size:14 final size:14
Alignment explanation
Indices: 332495--332536 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
332485 AGTTAAAATG
*
332495 AATAAAATAAAGAA
1 AATAAAACAAAGAA
*
332509 AATAAAATAAAGAA
1 AATAAAACAAAGAA
332523 AA-AGAAACAAAGAA
1 AATA-AAACAAAGAA
332537 TGAAAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 1 0.04
14 25 0.96
ACGTcount: A:0.79, C:0.02, G:0.10, T:0.10
Consensus pattern (14 bp):
AATAAAACAAAGAA
Found at i:332569 original size:20 final size:21
Alignment explanation
Indices: 332539--332577 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
332529 ACAAAGAATG
332539 AAAAATAAAATAAAAAAAGGT
1 AAAAATAAAATAAAAAAAGGT
*
332560 AAAAAT-AAATAAATAAAG
1 AAAAATAAAATAAAAAAAG
332578 ACAATAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (21 bp):
AAAAATAAAATAAAAAAAGGT
Found at i:332626 original size:7 final size:7
Alignment explanation
Indices: 332609--332651 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
332599 ATAATGCAAG
332609 ATAAA-A
1 ATAAATA
332615 ATAAATA
1 ATAAATA
332622 ATAAATA
1 ATAAATA
* *
332629 AAAACAAA
1 ATAA-ATA
332637 ATAAATA
1 ATAAATA
332644 ATAAATA
1 ATAAATA
332651 A
1 A
332652 GTGAATAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
6 5 0.16
7 21 0.68
8 5 0.16
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (7 bp):
ATAAATA
Found at i:332786 original size:3 final size:3
Alignment explanation
Indices: 332707--332766 Score: 77
Period size: 3 Copynumber: 19.3 Consensus size: 3
332697 AAAAGTATAT
*
332707 ATA ATA TATA ATA ATA ATA ATA ATA ATA ATA ATA AAA ATA TATA ATA
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA
332754 ACT- ATA ATA ATA A
1 A-TA ATA ATA ATA A
332767 AGAAGAAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
2 1 0.02
3 43 0.84
4 7 0.14
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:332900 original size:152 final size:154
Alignment explanation
Indices: 332744--333059 Score: 473
Period size: 152 Copynumber: 2.1 Consensus size: 154
332734 AATAATAAAA
* *
332744 ATATATAATAACTATAATAATAA-AGAAGAAAAAAAGAATAAT-AAAAAATAAAACTTACTCTAC
1 ATATATAATAACTATAATAATAATA-AAGAAAAAAA-AATAATAAAAAAACAAAACTTACCCTAC
* * *
332807 TATAATTAATG-AACTAAA-AATGATTAAATTTGGATGGAGACAAAAAAGGGGA-GGGGCCTAGG
64 TATAATTAATGCAACGAAAGAATGATTAAATTTGGATGGACACAAAAAAAGGGAGGGGGCCTAGG
332869 AAGAAAAAAAGGTGAGA-GAAAAATTAT
129 AAG-AAAAAAGGTGAGAGGAAAAA-TAT
*
332896 ATATATAATAACTATAATAATAATAAAGAAGAAAAAATAATAAAAAAACAAAACTTACCCTACTA
1 ATATATAATAACTATAATAATAATAAAGAAAAAAAAATAATAAAAAAACAAAACTTACCCTACTA
** *
332961 TAATTAATGCGCCGAAAGAATGATTAAATTTGGGTGGACACAAAAAAAGGGAGGGGGCCTAGGAA
66 TAATTAATGCAACGAAAGAATGATTAAATTTGGATGGACACAAAAAAAGGGAGGGGGCCTAGGAA
333026 GAAAAAAGGTGAGAGGAAAAATAT
131 GAAAAAAGGTGAGAGGAAAAATAT
333050 ATATATAATA
1 ATATATAATA
333060 TAATATGGAA
Statistics
Matches: 149, Mismatches: 9, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
151 6 0.04
152 62 0.42
153 5 0.03
154 57 0.38
155 19 0.13
ACGTcount: A:0.54, C:0.07, G:0.17, T:0.21
Consensus pattern (154 bp):
ATATATAATAACTATAATAATAATAAAGAAAAAAAAATAATAAAAAAACAAAACTTACCCTACTA
TAATTAATGCAACGAAAGAATGATTAAATTTGGATGGACACAAAAAAAGGGAGGGGGCCTAGGAA
GAAAAAAGGTGAGAGGAAAAATAT
Found at i:333171 original size:15 final size:15
Alignment explanation
Indices: 333151--333181 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
333141 TAAAATAATA
*
333151 AATAAAAATAAAAAT
1 AATAAAAAAAAAAAT
333166 AATAAAAAAAAAAAT
1 AATAAAAAAAAAAAT
333181 A
1 A
333182 GAAAGTAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (15 bp):
AATAAAAAAAAAAAT
Found at i:333179 original size:22 final size:22
Alignment explanation
Indices: 333144--333207 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 22
333134 AATAGAGTAA
* *
333144 AATAATAAATAAAAATAAAAAT
1 AATAAAAAAAAAAAATAAAAAT
*
333166 AAT-AAAAAAAAAAATAGAAAGT
1 AATAAAAAAAAAAAATA-AAAAT
*
333188 AAGAAAAAATAAATAAATAA
1 AATAAAAAA-AAA-AAATAA
333208 CAAAAGATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 11 0.32
22 9 0.26
23 5 0.15
24 4 0.12
25 5 0.15
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (22 bp):
AATAAAAAAAAAAAATAAAAAT
Found at i:336131 original size:252 final size:252
Alignment explanation
Indices: 334818--336127 Score: 1475
Period size: 252 Copynumber: 5.2 Consensus size: 252
334808 TGTGTCAATG
* ** * * * ** *
334818 GAACTCGAAGGTC-TTTGATGATAGATAACCCTTATCGCCTGGAGTTATGCTATAAATTTGATAT
1 GAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAA--TGATGT
* * * * * * * * ** **
334882 GCCTTTGAGCTGAATGTAATCGAACTCTAAGGTC-TTTGATGACATATAGCTTTTCTCACCTTGA
64 GCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGA
* * * * *
334946 GCTATGCTGCAAATTTGATGCGCCTTTGAGCTGAGTC-TAATCGAACGCAAAGGTCTTTTGTTGG
129 GCTATGCTGCAAA--TGATGTGCCTTGGAGCTGAG-CGTAGTCGAACTCGAAGGTCTTTTGTTGG
* * ** * * * *
335010 CATATAACCCTTCTCACCTTGAGCTATGTTGTAAATGATGTGCCTTTGAGTTGAGTGTAATC
191 CAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTC
* * *
335072 GAACTCGAAGGTCTTTTGTTGGCATATAACCCTTCTAGCCTTGAGTTATGCTACAAATGTTGTGC
1 GAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGC
* * * * * * *
335137 CTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGTAGATAACCCTTCTAGCCTTGAGT
66 CTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGC
* * * * *
335202 TATGCTACAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAAATCGAAGGTCTTTTGTTGTCAGAT
131 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAAT
* * * *
335267 AGCCCTTCTCGCCTTGAGCTATGCTT-CAAAT-ATTGTACCTTTGAGCTGAGTGTAATC
196 AGCCCTTCTTGCCTTGAGCTATG-TTGCAAATGA-TGTGCCTTTGAGCTGAGCGTAGTC
* * * * *
335324 GAACTCAAAGGTCTATTATTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGAAAATGATATGC
1 GAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGC
* * ** *
335389 CTTGGAGCTGAGTGTAGTCGAACTCGAAGATATTTTGTTGGCAAATAACCCGCCGTGCCTTGAGC
66 CTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGC
* * * * *
335454 TATGTTGCAAATAATGTGCCTTGGAGCTGAGCATAGTTGAACTCGAAGGTCTTTTGTTAGCAAAT
131 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAAT
* * * *
335519 AGACCTTCTTGTCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTAAGCGTAGTC
196 AGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTC
* *
335576 GAACTCGAAGGTCTTTTGTTGGTAGATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATGTG-
1 GAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGC
* * * *
335640 CTTGGAGCTGAGTGTAGTCGAACTCGAAGGTC-ATTATTGGCATATAACCCTTCTTACCTTGAGC
66 CTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGC
* * * * *
335704 TAAGCTGCAAATGATGTGTCTTGGAGCTGAGAGTAGTCGAACTCGAAGGTCTTTTTTTGGAAAAT
131 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAAT
* * * *
335769 ATCCCTTCTTGCCTTGAGCTATGTTGCAAATAATGTGCCTTAGAGCCGAGCGTAGTC
196 AGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTC
* * * * * * *
335826 AAACTCGAAGGTATTTTGTTGGCAGATAACCTTTCTAGACTTGAGTTATGTTGTAAATGATGTTC
1 GAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGC
** * * *
335891 CTTGGAGCTGAGCATAGTCGAACGCGAAGGTCTTTTTTTGGCAAATAGCCCTTCTTGCCTTGAGC
66 CTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGC
* * * * * * *
335956 TATGTTGCAAATGATGTGCCTTGAAACTAAGTGTAGTCGAACTCGATGGTCTTTTGTTGGAAAAT
131 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAAT
* * * * *
336021 AGCCCTTGTTACCTTGAGCTATGTTGAAAATGATGCT-CCTTTGAGCTGAGCATAGTT
196 AGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATG-TGCCTTTGAGCTGAGCGTAGTC
* *
336078 GAACTCGAAGTTCTTTTGTTGGCAAATAACCCTTCTAGCCTTGAGTTATG
1 GAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATG
336128 TTGTGAATGA
Statistics
Matches: 896, Mismatches: 150, Indels: 22
0.84 0.14 0.02
Matches are distributed among these distances:
250 185 0.21
251 63 0.07
252 529 0.59
253 39 0.04
254 45 0.05
255 35 0.04
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (252 bp):
GAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGC
CTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGC
TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAAT
AGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTC
Found at i:336137 original size:84 final size:84
Alignment explanation
Indices: 334940--336130 Score: 1279
Period size: 84 Copynumber: 14.2 Consensus size: 84
334930 GCTTTTCTCA
* * * * * *
334940 CCTTGAGCTATGCTGCAAATTTGATGCGCCTTTGAGCTGAGTC-TAATCGAACGCAAAGGTCTTT
1 CCTTGAGCTATGTTGCAAA--TGATGTGCCTTGGAGCTGAG-CGTAGTCGAACTCGAAGGTCTTT
*
335004 TGTTGGCATATAACCCTTCTCA-
63 TGTTGGCAAATAACCCTTCT-AG
* * * * *
335026 CCTTGAGCTATGTTGTAAATGATGTGCCTTTGAGTTGAGTGTAATCGAACTCGAAGGTCTTTTGT
1 CCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
*
335091 TGGCATATAACCCTTCTAG
66 TGGCAAATAACCCTTCTAG
* * * * * * * *
335110 CCTTGAGTTATGCTACAAATGTTGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGT
1 CCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
* *
335175 TGGTAGATAACCCTTCTAG
66 TGGCAAATAACCCTTCTAG
* * * * *
335194 CCTTGAGTTATGCTACAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAAATCGAAGGTCTTTTGT
1 CCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
* * * *
335259 TGTCAGATAGCCCTTCTCG
66 TGGCAAATAACCCTTCTAG
* * * * * *
335278 CCTTGAGCTATGCTT-CAAAT-ATTGTACCTTTGAGCTGAGTGTAATCGAACTCAAAGGTCTATT
1 CCTTGAGCTATG-TTGCAAATGA-TGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTT
* *
335341 ATTGGCAGATAACCCTTCTAG
64 GTTGGCAAATAACCCTTCTAG
* * * * * * *
335362 CCTTGAGTTATGCTGAAAATGATATGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGATATTTTGT
1 CCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
**
335427 TGGCAAATAACCCGCCGT-G
66 TGGCAAATAACCCTTC-TAG
* * *
335446 CCTTGAGCTATGTTGCAAATAATGTGCCTTGGAGCTGAGCATAGTTGAACTCGAAGGTCTTTTGT
1 CCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
* *
335511 TAGCAAATAGA-CCTTCTTG
66 TGGCAAATA-ACCCTTCTAG
* *
335530 TCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTAAGCGTAGTCGAACTCGAAGGTCTTTTGT
1 CCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
* *
335595 TGGTAGATAACCCTTCTAG
66 TGGCAAATAACCCTTCTAG
* * * * * *
335614 CCTTGAGTTATGCTACAAATGATGTG-CTTGGAGCTGAGTGTAGTCGAACTCGAAGGTC-ATTAT
1 CCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
*
335677 TGGCATATAACCCTTCTTA-
66 TGGCAAATAACCCTTC-TAG
* * * * *
335696 CCTTGAGCTAAGCTGCAAATGATGTGTCTTGGAGCTGAGAGTAGTCGAACTCGAAGGTCTTTTTT
1 CCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
* * *
335761 TGGAAAATATCCCTTCTTG
66 TGGCAAATAACCCTTCTAG
* * * * *
335780 CCTTGAGCTATGTTGCAAATAATGTGCCTTAGAGCCGAGCGTAGTCAAACTCGAAGGTATTTTGT
1 CCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
* *
335845 TGGCAGATAACCTTTCTAG
66 TGGCAAATAACCCTTCTAG
* * * * * * *
335864 ACTTGAGTTATGTTGTAAATGATGTTCCTTGGAGCTGAGCATAGTCGAACGCGAAGGTCTTTTTT
1 CCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
* *
335929 TGGCAAATAGCCCTTCTTG
66 TGGCAAATAACCCTTCTAG
* * * * *
335948 CCTTGAGCTATGTTGCAAATGATGTGCCTTGAAACTAAGTGTAGTCGAACTCGATGGTCTTTTGT
1 CCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
* * *
336013 TGGAAAATAGCCCTTGTTA-
66 TGGCAAATAACCCTT-CTAG
* * * * *
336032 CCTTGAGCTATGTTGAAAATGATGCT-CCTTTGAGCTGAGCATAGTTGAACTCGAAGTTCTTTTG
1 CCTTGAGCTATGTTGCAAATGATG-TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTG
336096 TTGGCAAATAACCCTTCTAG
65 TTGGCAAATAACCCTTCTAG
*
336116 CCTTGAGTTATGTTG
1 CCTTGAGCTATGTTG
336131 TGAATGAACA
Statistics
Matches: 932, Mismatches: 156, Indels: 36
0.83 0.14 0.03
Matches are distributed among these distances:
82 40 0.04
83 71 0.08
84 798 0.86
85 6 0.01
86 17 0.02
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (84 bp):
CCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
TGGCAAATAACCCTTCTAG
Found at i:336486 original size:121 final size:121
Alignment explanation
Indices: 336142--336780 Score: 725
Period size: 120 Copynumber: 5.3 Consensus size: 121
336132 GAATGAACAC
* * * * * * *
336142 GATATCATTCGTCTTGAAGTTGAAAT-C-ATGGATGACATTGCTTCTTGTGGGCACGAT-TCCCT
1 GATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTG-TATTGCTGCTTGTGAGCACGATAT-CCT
* * * *
336204 TAGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTGTGAAATTGAGCATGGAATTG
64 TCGTCGTGAAGTTGAAATCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTGGAATTG
** * * * *
336262 GATATCCTTCGTCGTGAAGTTGAAATCCAAGTATTATA-TGGTGCTGGTGAACACGATATCCTTC
1 GATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGTATTGCTGCTTGTGAGCACGATATCCTTC
* * **
336326 GTCGTGAAGTTGAAATCGTGGATGGCCCATTCGTCGTGAAGTTGAACCTTAAATTG
66 GTCGTGAAGTTGAAATCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTGGAATTG
* * * *
336382 GATATCCTTCATCGTGAAGTTGAAATGCAAGGGTTGTATTACTGCTTGTGGGCACGATATCCTTC
1 GATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGTATTGCTGCTTGTGAGCACGATATCCTTC
* ** * *
336447 GTCGTGAAGTTAAAATCAG-GGATTACTCTTTCGTTGTGAAGTTGAGCCTGGAATTG
66 GTCGTGAAGTTGAAATC-GTGGATGGCCCATTCGTTGTGAAGTTGAGCCTGGAATTG
* * ** * * * *
336503 GATATCCTTCGTTGTGAAGTTTAAATCCAAGTATTGTA-TGGTGGTTGTGAACACAATATCCATT
1 GATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGTATTGCTGCTTGTGAGCACGATATCC-TT
* * * * * ** *
336567 -GTCGTGAAGTTGAAATCATTGATGGCCCCTTCATCGTGAAGTTGAGCCTTAAATTA
65 CGTCGTGAAGTTGAAATCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTGGAATTG
* *
336623 GATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGAATTGCTGATTGTGAGCACGATATCCTTC
1 GATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGTATTGCTGCTTGTGAGCACGATATCCTTC
* *
336688 GTCATGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTGGAATTG
66 GTCGTGAAGTTGAAATCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTGGAATTG
* *
336744 GATATCATTCGTCGTAAAGTTGAAATCCAAGGGTTGT
1 GATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGT
336781 TTTACCAAAT
Statistics
Matches: 426, Mismatches: 84, Indels: 17
0.81 0.16 0.03
Matches are distributed among these distances:
120 219 0.51
121 204 0.48
122 3 0.01
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.33
Consensus pattern (121 bp):
GATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGTATTGCTGCTTGTGAGCACGATATCCTTC
GTCGTGAAGTTGAAATCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTGGAATTG
Found at i:336608 original size:241 final size:241
Alignment explanation
Indices: 336142--336774 Score: 862
Period size: 241 Copynumber: 2.6 Consensus size: 241
336132 GAATGAACAC
* * * * * * *
336142 GATATCATTCGTCTTGAAGTTGAAAT-C-ATGGATGACATTGCTTCTTGTGGGCACGAT-TCCCT
1 GATATCCTTCATCGTGAAGTTGAAATCCAAGGGTTGA-ATTACTGCTTGTGGGCACGATAT-CCT
* * *
336204 TAGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTGTGAAATTGAGCATGGAATTGGATATCC
64 TCGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTGGAATTGGATATCC
*
336269 TTCGTCGTGAAGTTGAAATCCAAGTATTATATGGTGCTGGTGAACACGATATCCTTCGTCGTGAA
129 TTCGTCGTGAAGTTGAAATCCAAGTATTATATGGTGCTGGTGAACACAATATCCTTCGTCGTGAA
* * *
336334 GTTGAAATCGTGGATGGCCCATTCGTCGTGAAGTTGAACCTTAAATTG
194 GTTGAAATCATGGATGGCCCATTCATCGTGAAGTTGAACCTTAAATTA
* *
336382 GATATCCTTCATCGTGAAGTTGAAATGCAAGGGTTGTATTACTGCTTGTGGGCACGATATCCTTC
1 GATATCCTTCATCGTGAAGTTGAAATCCAAGGGTTGAATTACTGCTTGTGGGCACGATATCCTTC
* * * *
336447 GTCGTGAAGTTAAAATCAG-GGATTACTCTTTCGTTGTGAAGTTGAGCCTGGAATTGGATATCCT
66 GTCGTGAAGTTGAAATC-GTGGATGACCCATTCGTTGTGAAGTTGAGCCTGGAATTGGATATCCT
* * * * *
336511 TCGTTGTGAAGTTTAAATCCAAGTATTGTATGGTGGTTGTGAACACAATATCCATT-GTCGTGAA
130 TCGTCGTGAAGTTGAAATCCAAGTATTATATGGTGCTGGTGAACACAATATCC-TTCGTCGTGAA
* * *
336575 GTTGAAATCATTGATGGCCCCTTCATCGTGAAGTTGAGCCTTAAATTA
194 GTTGAAATCATGGATGGCCCATTCATCGTGAAGTTGAACCTTAAATTA
* * * *
336623 GATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGAATTGCTGATTGTGAGCACGATATCCTTC
1 GATATCCTTCATCGTGAAGTTGAAATCCAAGGGTTGAATTACTGCTTGTGGGCACGATATCCTTC
* * * *
336688 GTCATGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTGGAATTGGATATCATT
66 GTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTGGAATTGGATATCCTT
*
336753 CGTCGTAAAGTTGAAATCCAAG
131 CGTCGTGAAGTTGAAATCCAAG
336775 GGTTGTTTTA
Statistics
Matches: 344, Mismatches: 43, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
240 24 0.07
241 311 0.90
242 9 0.03
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (241 bp):
GATATCCTTCATCGTGAAGTTGAAATCCAAGGGTTGAATTACTGCTTGTGGGCACGATATCCTTC
GTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTGGAATTGGATATCCTT
CGTCGTGAAGTTGAAATCCAAGTATTATATGGTGCTGGTGAACACAATATCCTTCGTCGTGAAGT
TGAAATCATGGATGGCCCATTCATCGTGAAGTTGAACCTTAAATTA
Found at i:336964 original size:64 final size:63
Alignment explanation
Indices: 336863--337063 Score: 276
Period size: 64 Copynumber: 3.1 Consensus size: 63
336853 CTTCGAGTTT
* * *
336863 AATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAATTAGAAAAATGTTTGTTGAGTCC
1 AATATCCTTCGATGTGAAGTTGAAATTGACTCTGAATGAAACT-GAAAATTGTTTGTTGAGTCC
* * * * *
336927 AATATCCTTCGTTGTGAGGTTCAAATTGACTCTGAATGAAACTGAAAAGTTATTTGTTGAGTTC
1 AATATCCTTCGATGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAA-TTGTTTGTTGAGTCC
* * *
336991 AATATCCTTCGATATGAAGTTGAAATTGACTCTGATTGAAACTGGAAAGTTGTTTGTTGAGTCC
1 AATATCCTTCGATGTGAAGTTGAAATTGACTCTGAATGAAACT-GAAAATTGTTTGTTGAGTCC
337055 AATATCCTT
1 AATATCCTT
337064 TTATCCTTTG
Statistics
Matches: 120, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
63 5 0.04
64 111 0.93
65 4 0.03
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (63 bp):
AATATCCTTCGATGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAATTGTTTGTTGAGTCC
Found at i:338192 original size:95 final size:95
Alignment explanation
Indices: 337997--338256 Score: 328
Period size: 95 Copynumber: 2.7 Consensus size: 95
337987 GGCTAGCTAA
* * * * * * *
337997 ATCCATAAAGGCGGGGCGTTTAACCAATTTCTCTATAGGGACAACTTAA-TATCATTGTACAGAT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGTTTTATTGT--ATAT
338061 ATATAATCACCTTTATCAGGCTAGCTGAATAT
64 ATATAATCACCTTTATCAGGCTAGCTGAATAT
*
338093 -TCCATAAAGCCGGGGCATTTAACCAATTGCTCTAGAGGGACAACTCAAGTTTTATTGTATAT-T
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGTTTTATTGTATATAT
338156 ATAATCACCTTTATCAGGCTAGCTGAATATT
66 ATAATCACCTTTATCAGGCTAGCTGAATA-T
*** * * ** *
338187 ATCCATAAAGTTTGGGTGTTTAACCAATTGCTTTAGAGGGACAGTTCAAGCTTTATTGTATATAT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGTTTTATTGTATATAT
338252 ATAAT
66 ATAAT
338257 ATCATAATCT
Statistics
Matches: 143, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
93 30 0.21
94 4 0.03
95 96 0.67
96 13 0.09
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (95 bp):
ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGTTTTATTGTATATAT
ATAATCACCTTTATCAGGCTAGCTGAATAT
Found at i:339869 original size:16 final size:16
Alignment explanation
Indices: 339844--339885 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
339834 AATAAAGTCT
*
339844 TACCCTACATGATATC
1 TACCCCACATGATATC
339860 TACCCCACATGATATC
1 TACCCCACATGATATC
339876 TA-CCCACATG
1 TACCCCACATG
339886 CTAGAATTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 8 0.32
16 17 0.68
ACGTcount: A:0.31, C:0.36, G:0.07, T:0.26
Consensus pattern (16 bp):
TACCCCACATGATATC
Found at i:340723 original size:5 final size:5
Alignment explanation
Indices: 340713--340799 Score: 56
Period size: 5 Copynumber: 17.4 Consensus size: 5
340703 AGTGAAAATG
* * ** *
340713 AATAA AAT-A AAGAA AATAA AAAACA AATAA AATAA AGCAA AAGAA ACA-AA
1 AATAA AATAA AATAA AATAA AATA-A AATAA AATAA AATAA AATAA A-ATAA
*
340763 GAAT-A AA-AA AATAA AATAA AATAA ATAAAA AATAA AA
1 -AATAA AATAA AATAA AATAA AATAA A-ATAA AATAA AA
340800 AAGGGTAAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
4 8 0.12
5 46 0.72
6 10 0.16
ACGTcount: A:0.79, C:0.03, G:0.05, T:0.13
Consensus pattern (5 bp):
AATAA
Found at i:340728 original size:9 final size:9
Alignment explanation
Indices: 340707--340840 Score: 77
Period size: 9 Copynumber: 14.9 Consensus size: 9
340697 GAAAAAAGTG
*
340707 AAAATGAAT
1 AAAATAAAT
*
340716 AAAATAAAG
1 AAAATAAAT
340725 AAAAT-AA-
1 AAAATAAAT
*
340732 AAAACAAAT
1 AAAATAAAT
*
340741 AAAATAAAGC
1 AAAATAAA-T
* *
340751 AAAAGAAACA
1 AAAATAAA-T
340761 AAGAATAAA-
1 AA-AATAAAT
340770 AAAATAAAAT
1 AAAAT-AAAT
340780 AAAATAAAT
1 AAAATAAAT
340789 -AAA-AAAT
1 AAAATAAAT
*
340796 AAAA-AAGGGT
1 AAAATAA--AT
340806 AAAAATAAAT
1 -AAAATAAAT
340816 AATAAT-AAT
1 AA-AATAAAT
340825 -AAATAAAT
1 AAAATAAAT
340833 AAAATAAA
1 AAAATAAA
340841 GACAATAATG
Statistics
Matches: 100, Mismatches: 11, Indels: 28
0.72 0.08 0.20
Matches are distributed among these distances:
7 11 0.11
8 19 0.19
9 40 0.40
10 19 0.19
11 9 0.09
12 2 0.02
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.16
Consensus pattern (9 bp):
AAAATAAAT
Found at i:340735 original size:25 final size:24
Alignment explanation
Indices: 340707--340792 Score: 86
Period size: 25 Copynumber: 3.5 Consensus size: 24
340697 GAAAAAAGTG
*
340707 AAAATGAATAAAATAAAGAAAATA
1 AAAAAGAATAAAATAAAGAAAATA
* *
340731 AAAAACAAATAAAATAAAGCAAAAGA
1 AAAAA-GAATAAAATAAAG-AAAATA
*
340757 AACAAAGAATAAAA-AAATAAAATA
1 AA-AAAGAATAAAATAAAGAAAATA
*
340781 AAATA-AATAAAA
1 AAAAAGAATAAAA
340793 AATAAAAAAG
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
22 7 0.13
23 2 0.04
24 11 0.21
25 15 0.29
26 14 0.27
27 3 0.06
ACGTcount: A:0.78, C:0.03, G:0.06, T:0.13
Consensus pattern (24 bp):
AAAAAGAATAAAATAAAGAAAATA
Found at i:340982 original size:3 final size:3
Alignment explanation
Indices: 340974--341020 Score: 60
Period size: 3 Copynumber: 15.3 Consensus size: 3
340964 GTATAAAGAT
*
340974 ATA ATA ATA ATA ATA ATA AAA ATA TATA ATA ACT- ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA A-TA ATA ATA ATA ATA
341020 A
1 A
341021 AGAAAAAAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 1 0.03
3 34 0.87
4 4 0.10
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:341256 original size:155 final size:152
Alignment explanation
Indices: 340994--341307 Score: 472
Period size: 155 Copynumber: 2.0 Consensus size: 152
340984 TAATAATAAA
* *
340994 AATATATAATAACTATAATAATAATAAAGAAAAAAAGAGTAATAAAAAACAAAACTTACTACTAT
1 AATATATAATAACTATAATAATAATAAAGAAAAAAAAAATAATAAAAAACAAAACTTACTACTAT
** * *
341059 TTTAATGCACTAAAAATGATTAAATTTGGGTGGAGACAAAAAAAGGGGAGGGG-CCTAGGAAGAA
66 AATAATGCACGAAAAATGATTAAATTTGGGTGGAGACAAAAAAAAGGGAGGGGACCTAGGAAG-A
*
341123 AAAAAGGTGAGAGAAAAAT-TAT
130 AAAAAGGTGAGAAAAAAATATAT
*
341145 -ATATATAATAACTATAATAATAATAAAGAAGAAAAAAAATAATAAAAAAATAAAACTTAGCCTA
1 AATATATAATAACTATAATAATAATAAAGAA-AAAAAAAATAAT-AAAAAACAAAACTTA--CTA
*
341209 CTATAATAATGCACGAAAGAATGATTAAATTTGGGTGGAGACAAAAAAAAGGGAGGGGACCTATG
62 CTATAATAATGCACGAAA-AATGATTAAATTTGGGTGGAGACAAAAAAAAGGGAGGGGACCTAGG
341274 AAGAAAAAAGGTGAGAAAAAAATATAT
126 AAGAAAAAAGGTGAGAAAAAAATATAT
341301 AATATAT
1 AATATAT
341308 GGAATAAAAG
Statistics
Matches: 146, Mismatches: 9, Indels: 10
0.88 0.05 0.06
Matches are distributed among these distances:
150 30 0.21
151 10 0.07
152 14 0.10
154 18 0.12
155 57 0.39
156 11 0.08
157 6 0.04
ACGTcount: A:0.55, C:0.06, G:0.17, T:0.22
Consensus pattern (152 bp):
AATATATAATAACTATAATAATAATAAAGAAAAAAAAAATAATAAAAAACAAAACTTACTACTAT
AATAATGCACGAAAAATGATTAAATTTGGGTGGAGACAAAAAAAAGGGAGGGGACCTAGGAAGAA
AAAAGGTGAGAAAAAAATATAT
Done.