Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000160.1 Hibiscus syriacus cultivar Beakdansim tig00000282_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: 192322
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:1418 original size:20 final size:21
Alignment explanation
Indices: 1385--1423 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1375 TTTAAATAAT
1385 TTGATTGACAAAATTAAAAGA
1 TTGATTGACAAAATTAAAAGA
*
1406 TTGA-TGACCAAATTAAAA
1 TTGATTGACAAAATTAAAA
1424 TCTCTCTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.51, C:0.08, G:0.13, T:0.28
Consensus pattern (21 bp):
TTGATTGACAAAATTAAAAGA
Found at i:2239 original size:37 final size:37
Alignment explanation
Indices: 2192--2270 Score: 140
Period size: 37 Copynumber: 2.1 Consensus size: 37
2182 AGAATGTGAC
*
2192 ACATATCATTTAATGGAAAAATTTAAGGACAGTTACG
1 ACATGTCATTTAATGGAAAAATTTAAGGACAGTTACG
*
2229 ACATGTCATTTAATGGAAAAATTTAATGACAGTTACG
1 ACATGTCATTTAATGGAAAAATTTAAGGACAGTTACG
2266 ACATG
1 ACATG
2271 GACACCTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.30
Consensus pattern (37 bp):
ACATGTCATTTAATGGAAAAATTTAAGGACAGTTACG
Found at i:3073 original size:61 final size:61
Alignment explanation
Indices: 2984--3133 Score: 178
Period size: 61 Copynumber: 2.5 Consensus size: 61
2974 ATTTTACAAT
* * *
2984 TTCGCAACTCGATTTTTAAA-TTCGCAACACGAATTTCCTTTTCGCAACAAGATTTTTTC-AA
1 TTCGCAACACGA-ATTTAAATTTCGCAACACGAATTTCCTTTTCGCAACAAGA-TTCTTCGAA
* ** * * **
3045 TTCGCAACGCGGGTTTAAATTTGGCAACACGAATTTCGTTTTCGCAACTCGATTCTTCGAA
1 TTCGCAACACGAATTTAAATTTCGCAACACGAATTTCCTTTTCGCAACAAGATTCTTCGAA
3106 TTCGCAACACGAATTTAAATTTCGCAAC
1 TTCGCAACACGAATTTAAATTTCGCAAC
3134 TCAGCTTTTA
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
60 11 0.15
61 64 0.85
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (61 bp):
TTCGCAACACGAATTTAAATTTCGCAACACGAATTTCCTTTTCGCAACAAGATTCTTCGAA
Found at i:3131 original size:20 final size:20
Alignment explanation
Indices: 2942--3133 Score: 88
Period size: 20 Copynumber: 9.4 Consensus size: 20
2932 ATAAATCGAA
*
2942 TTCGCAACTCGAATTTTACAAT
1 TTCGCAACACGAA-TTTA-AAT
*
2964 TT--CAACTCGAATTTTACAAT
1 TTCGCAACACGAA-TTTA-AAT
* *
2984 TTCGCAACTCGATTTTTAAA-
1 TTCGCAACACGA-ATTTAAAT
***
3004 TTCGCAACACGAATTTCCTT
1 TTCGCAACACGAATTTAAAT
* * *
3024 TTCGCAACAAGATTTTTTCAA-
1 TTCGCAACACGA--ATTTAAAT
* **
3045 TTCGCAACGCGGGTTTAAAT
1 TTCGCAACACGAATTTAAAT
* ***
3065 TTGGCAACACGAATTTCGTT
1 TTCGCAACACGAATTTAAAT
* * *
3085 TTCGCAACTCGATTCTTCGAA-
1 TTCGCAACACGAAT-TT-AAAT
3106 TTCGCAACACGAATTTAAAT
1 TTCGCAACACGAATTTAAAT
3126 TTCGCAAC
1 TTCGCAAC
3134 TCAGCTTTTA
Statistics
Matches: 129, Mismatches: 31, Indels: 22
0.71 0.17 0.12
Matches are distributed among these distances:
19 10 0.08
20 76 0.59
21 25 0.19
22 18 0.14
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (20 bp):
TTCGCAACACGAATTTAAAT
Found at i:3939 original size:12 final size:12
Alignment explanation
Indices: 3918--3951 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3908 ACCACATTTC
*
3918 CAATACCAAACA
1 CAATATCAAACA
3930 CAATATCAAACA
1 CAATATCAAACA
*
3942 CAATCTCAAA
1 CAATATCAAA
3952 ATCCATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:6372 original size:12 final size:12
Alignment explanation
Indices: 6355--6401 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
6345 AGTAAAGGGA
6355 AATCAAAATCGC
1 AATCAAAATCGC
**
6367 AATCAAAATCAA
1 AATCAAAATCGC
*
6379 AATCAAAATCCC
1 AATCAAAATCGC
*
6391 AATCACAATCG
1 AATCAAAATCG
6402 TCTTCACCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.53, C:0.26, G:0.04, T:0.17
Consensus pattern (12 bp):
AATCAAAATCGC
Found at i:6376 original size:6 final size:6
Alignment explanation
Indices: 6354--6388 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
6344 AAGTAAAGGG
* *
6354 AAATCA AAATCG CAATCA AAATCA AAATCA AAATC
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATC
6389 CCAATCACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.60, C:0.20, G:0.03, T:0.17
Consensus pattern (6 bp):
AAATCA
Found at i:6711 original size:20 final size:20
Alignment explanation
Indices: 6686--6795 Score: 79
Period size: 20 Copynumber: 5.8 Consensus size: 20
6676 ATAATGAATC
*
6686 AAATTCGCAACTCAAAAATA
1 AAATTCGCAACTCGAAAATA
* *
6706 AAATTCGTAACTCGAAAATC
1 AAATTCGCAACTCGAAAATA
* * * * *
6726 GAGTTCGCAATTCGAAACTT
1 AAATTCGCAACTCGAAAATA
*
6746 AAATTCGCAACACG-----A
1 AAATTCGCAACTCGAAAATA
* *
6761 AAA-TCGTAACTCGAAAATG
1 AAATTCGCAACTCGAAAATA
6780 AAATTCGCAACTCGAA
1 AAATTCGCAACTCGAA
6796 TTTCATTTTC
Statistics
Matches: 66, Mismatches: 18, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
14 8 0.12
15 3 0.05
19 3 0.05
20 52 0.79
ACGTcount: A:0.45, C:0.21, G:0.13, T:0.22
Consensus pattern (20 bp):
AAATTCGCAACTCGAAAATA
Found at i:7893 original size:12 final size:12
Alignment explanation
Indices: 7876--7932 Score: 55
Period size: 12 Copynumber: 4.9 Consensus size: 12
7866 TTATATGGTA
7876 TGAACAGTACCG
1 TGAACAGTACCG
* *
7888 TGAACATTA--A
1 TGAACAGTACCG
*
7898 TTAACAGTACCG
1 TGAACAGTACCG
*
7910 TGAACAGTACCC
1 TGAACAGTACCG
*
7922 TAAACAGTACC
1 TGAACAGTACC
7933 CTGCTACAGT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
10 7 0.20
12 28 0.80
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.21
Consensus pattern (12 bp):
TGAACAGTACCG
Found at i:7932 original size:24 final size:23
Alignment explanation
Indices: 7878--7949 Score: 74
Period size: 22 Copynumber: 3.1 Consensus size: 23
7868 ATATGGTATG
* * *
7878 AACAGTACCGTGAACATTA-ATT
1 AACAGTACCGTGAACAGTACCTA
7900 AACAGTACCGTGAACAGTACCCTA
1 AACAGTACCGTGAACAGTA-CCTA
* *
7924 AACAGTACCCTGCTACAGTACCTA
1 AACAGTACCGTG-AACAGTACCTA
7948 AA
1 AA
7950 TGCTAAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
22 18 0.43
24 18 0.43
25 6 0.14
ACGTcount: A:0.39, C:0.26, G:0.14, T:0.21
Consensus pattern (23 bp):
AACAGTACCGTGAACAGTACCTA
Found at i:9171 original size:3 final size:3
Alignment explanation
Indices: 9163--9229 Score: 73
Period size: 3 Copynumber: 21.3 Consensus size: 3
9153 CACGTTTGGG
* *
9163 AGA AGA AGA AGA TGA ATGG AGA AGA AGA AG- AGA AGGA AGA AGA AGA
1 AGA AGA AGA AGA AGA A-GA AGA AGA AGA AGA AGA A-GA AGA AGA AGA
9209 AGA AGAA AGA ATGA AGA AGA A
1 AGA AG-A AGA A-GA AGA AGA A
9230 ATGAGAGAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
2 2 0.04
3 42 0.76
4 11 0.20
ACGTcount: A:0.61, C:0.00, G:0.34, T:0.04
Consensus pattern (3 bp):
AGA
Found at i:9239 original size:23 final size:23
Alignment explanation
Indices: 9182--9229 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
9172 AGATGAATGG
9182 AGAAGAAGAAGAGAAGGAAGAAGA
1 AGAAGAAGAA-AGAAGGAAGAAGA
*
9206 AGAAGAAGAAAGAATGAAGAAGA
1 AGAAGAAGAAAGAAGGAAGAAGA
9229 A
1 A
9230 ATGAGAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (23 bp):
AGAAGAAGAAAGAAGGAAGAAGA
Found at i:19008 original size:21 final size:21
Alignment explanation
Indices: 18984--19188 Score: 218
Period size: 21 Copynumber: 9.8 Consensus size: 21
18974 TGAAATAATC
**
18984 TCACGTAGGGCACCTACCTCA
1 TCACGTAAAGCACCTACCTCA
**
19005 TCACGTAAAGCACC-ATTTTCA
1 TCACGTAAAGCACCTA-CCTCA
19026 TCACGTAAAGCACCTACCTCA
1 TCACGTAAAGCACCTACCTCA
* **
19047 TCACGTAAAACACC-ATTGTCA
1 TCACGTAAAGCACCTA-CCTCA
* *
19068 TCACGTAAAACACCTATCTCA
1 TCACGTAAAGCACCTACCTCA
*
19089 CCACGTAAAGCACCTACCTCA
1 TCACGTAAAGCACCTACCTCA
**
19110 TCACGTAAAGCACC-ATTGTCA
1 TCACGTAAAGCACCTA-CCTCA
* * * *
19131 TTACGTAAAACACCGACCTCG
1 TCACGTAAAGCACCTACCTCA
19152 TCACGTAAAGCACCTACCTCA
1 TCACGTAAAGCACCTACCTCA
19173 TCACGTAAAGCACCTA
1 TCACGTAAAGCACCTA
19189 ACTGATCCCG
Statistics
Matches: 153, Mismatches: 25, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
20 3 0.02
21 147 0.96
22 3 0.02
ACGTcount: A:0.34, C:0.34, G:0.11, T:0.21
Consensus pattern (21 bp):
TCACGTAAAGCACCTACCTCA
Found at i:19094 original size:63 final size:62
Alignment explanation
Indices: 19002--19186 Score: 280
Period size: 63 Copynumber: 2.9 Consensus size: 62
18992 GGCACCTACC
* * *
19002 TCATCACGTAAAGCACCATTTTCATCACGTAAAGCACCTACCTCATCACGTAAAACACCATTG
1 TCATCACGTAAAACACCA-TCTCATCACGTAAAGCACCTACCTCATCACGTAAAGCACCATTG
*
19065 TCATCACGTAAAACACCTATCTCACCACGTAAAGCACCTACCTCATCACGTAAAGCACCATTG
1 TCATCACGTAAAACACC-ATCTCATCACGTAAAGCACCTACCTCATCACGTAAAGCACCATTG
* * *
19128 TCATTACGTAAAACACCGACCTCGTCACGTAAAGCACCTACCTCATCACGTAAAGCACC
1 TCATCACGTAAAACACC-ATCTCATCACGTAAAGCACCTACCTCATCACGTAAAGCACC
19187 TAACTGATCC
Statistics
Matches: 112, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
63 111 0.99
64 1 0.01
ACGTcount: A:0.35, C:0.34, G:0.10, T:0.21
Consensus pattern (62 bp):
TCATCACGTAAAACACCATCTCATCACGTAAAGCACCTACCTCATCACGTAAAGCACCATTG
Found at i:19342 original size:42 final size:41
Alignment explanation
Indices: 19287--19495 Score: 271
Period size: 42 Copynumber: 5.0 Consensus size: 41
19277 GAGTCGACTG
* * *
19287 GAGGTGATGGATCTCAGTGTCGAGGTGTAGAATCGGCTCGAT
1 GAGGTGATGGATCTC-GTGTCGAAGTGGAGAATCGACTCGAT
* *
19329 GAGGTGATGGATCTCGATGCCGACGTGGAGAATCGACTCGAT
1 GAGGTGATGGATCTCG-TGTCGAAGTGGAGAATCGACTCGAT
*
19371 GAGGTGATGGATCTCGGTATCGAAGTGGAGAATCGACTCGAT
1 GAGGTGATGGATCTC-GTGTCGAAGTGGAGAATCGACTCGAT
*
19413 GA-G-G-TGGATCTCGATGTCGAAGTGGAGAATCGGCTCGAT
1 GAGGTGATGGATCTCG-TGTCGAAGTGGAGAATCGACTCGAT
* *
19452 GAGGTGATGGATCTCGGTGTCGAGGTGAAGAATCGACTCGAT
1 GAGGTGATGGATCTC-GTGTCGAAGTGGAGAATCGACTCGAT
19494 GA
1 GA
19496 AAAAGTGGGG
Statistics
Matches: 148, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
38 1 0.01
39 33 0.22
40 2 0.01
41 3 0.02
42 107 0.72
43 2 0.01
ACGTcount: A:0.24, C:0.15, G:0.37, T:0.23
Consensus pattern (41 bp):
GAGGTGATGGATCTCGTGTCGAAGTGGAGAATCGACTCGAT
Found at i:19444 original size:81 final size:84
Alignment explanation
Indices: 19287--19495 Score: 316
Period size: 81 Copynumber: 2.5 Consensus size: 84
19277 GAGTCGACTG
* * *
19287 GAGGTGATGGATCTCAGTGTCGAGGTGTAGAATCGGCTCGATGAGGTGATGGATCTCGATGCCGA
1 GAGGTGATGGATCTCGGTGTCGAGGTGAAGAATCGACTCGATGAGGTGATGGATCTCGATGCCGA
*
19352 CGTGGAGAATCGACTCGAT
66 AGTGGAGAATCGACTCGAT
* * * *
19371 GAGGTGATGGATCTCGGTATCGAAGTGGAGAATCGACTCGATGA-G-G-TGGATCTCGATGTCGA
1 GAGGTGATGGATCTCGGTGTCGAGGTGAAGAATCGACTCGATGAGGTGATGGATCTCGATGCCGA
*
19433 AGTGGAGAATCGGCTCGAT
66 AGTGGAGAATCGACTCGAT
19452 GAGGTGATGGATCTCGGTGTCGAGGTGAAGAATCGACTCGATGA
1 GAGGTGATGGATCTCGGTGTCGAGGTGAAGAATCGACTCGATGA
19496 AAAAGTGGGG
Statistics
Matches: 114, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
81 73 0.64
82 1 0.01
83 1 0.01
84 39 0.34
ACGTcount: A:0.24, C:0.15, G:0.37, T:0.23
Consensus pattern (84 bp):
GAGGTGATGGATCTCGGTGTCGAGGTGAAGAATCGACTCGATGAGGTGATGGATCTCGATGCCGA
AGTGGAGAATCGACTCGAT
Found at i:19671 original size:2 final size:2
Alignment explanation
Indices: 19664--19694 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
19654 ATAAATTGTT
19664 TA 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 T
19695 GTGTGTGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19699 original size:2 final size:2
Alignment explanation
Indices: 19694--19722 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19684 TATATATATA
19694 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
19723 ATGTACACCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:21008 original size:13 final size:14
Alignment explanation
Indices: 20995--21064 Score: 54
Period size: 14 Copynumber: 5.1 Consensus size: 14
20985 AAGAAAATCG
20995 AATTCGAAACTCGA
1 AATTCGAAACTCGA
* * *
21009 AAATCG-AATTCGC
1 AATTCGAAACTCGA
*
21022 AATTCGAAACT-TA
1 AATTCGAAACTCGA
* *
21035 AATTCGCAACACGA
1 AATTCGAAACTCGA
* *
21049 AAATCGCAACTCGA
1 AATTCGAAACTCGA
21063 AA
1 AA
21065 AATGAAAATC
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
13 19 0.45
14 23 0.55
ACGTcount: A:0.44, C:0.23, G:0.13, T:0.20
Consensus pattern (14 bp):
AATTCGAAACTCGA
Found at i:21012 original size:20 final size:20
Alignment explanation
Indices: 20987--21064 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 20
20977 TTTATTTCAA
20987 GAAAATCGAATTCGAAACTC
1 GAAAATCGAATTCGAAACTC
* *
21007 GAAAATCGAATTCGCAATTC
1 GAAAATCGAATTCGAAACTC
* ** * *
21027 GAAACTTAAATTCGCAACAC
1 GAAAATCGAATTCGAAACTC
*
21047 GAAAATCGCAACTCGAAA
1 GAAAATCG-AATTCGAAA
21065 AATGAAAATC
Statistics
Matches: 45, Mismatches: 12, Indels: 1
0.78 0.21 0.02
Matches are distributed among these distances:
20 38 0.84
21 7 0.16
ACGTcount: A:0.45, C:0.22, G:0.14, T:0.19
Consensus pattern (20 bp):
GAAAATCGAATTCGAAACTC
Found at i:21087 original size:20 final size:21
Alignment explanation
Indices: 21047--21104 Score: 100
Period size: 20 Copynumber: 2.8 Consensus size: 21
21037 TTCGCAACAC
21047 GAAAATCGCAACTCGAAAAAT
1 GAAAATCGCAACTCGAAAAAT
21068 GAAAATCGCAACTC-AAAAAT
1 GAAAATCGCAACTCGAAAAAT
*
21088 GAAATTCGCAACTCGAA
1 GAAAATCGCAACTCGAA
21105 TTTCATTTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
20 19 0.54
21 16 0.46
ACGTcount: A:0.50, C:0.21, G:0.14, T:0.16
Consensus pattern (21 bp):
GAAAATCGCAACTCGAAAAAT
Found at i:21128 original size:20 final size:20
Alignment explanation
Indices: 21105--21168 Score: 92
Period size: 20 Copynumber: 3.2 Consensus size: 20
21095 GCAACTCGAA
21105 TTTCATTTTCGAGTTGCGAT
1 TTTCATTTTCGAGTTGCGAT
* ** *
21125 TTTCGTTTTCGAGTTATGAA
1 TTTCATTTTCGAGTTGCGAT
21145 TTTCATTTTCGAGTTGCGAT
1 TTTCATTTTCGAGTTGCGAT
21165 TTTC
1 TTTC
21169 GTATTGCGAA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.16, C:0.14, G:0.19, T:0.52
Consensus pattern (20 bp):
TTTCATTTTCGAGTTGCGAT
Found at i:21836 original size:20 final size:20
Alignment explanation
Indices: 21753--21841 Score: 72
Period size: 20 Copynumber: 4.5 Consensus size: 20
21743 AAACATTTAT
21753 GTTGCGAAATTAAAAGAT-GA
1 GTTGCGAAATTAAAA-ATCGA
* * *
21773 GTTGCGAAATTTAAATTCGC
1 GTTGCGAAATTAAAAATCGA
* ** * *
21793 GTTGCAAAAGCAAAACTCGT
1 GTTGCGAAATTAAAAATCGA
*
21813 GTTGCGAATTTAAAAATCGA
1 GTTGCGAAATTAAAAATCGA
*
21833 GTTGTGAAA
1 GTTGCGAAA
21842 CAGAAATTTA
Statistics
Matches: 51, Mismatches: 17, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
19 1 0.02
20 50 0.98
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.28
Consensus pattern (20 bp):
GTTGCGAAATTAAAAATCGA
Found at i:21919 original size:20 final size:19
Alignment explanation
Indices: 21865--21924 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
21855 TGCGAAAATG
21865 TCAAATTCGAGTTGCGAAT
1 TCAAATTCGAGTTGCGAAT
* *
21884 TCTACTTCTGTA-TTGCGAAT
1 TCAAATTC-G-AGTTGCGAAT
21904 TCCAAATTCGAGTTGCGAAT
1 T-CAAATTCGAGTTGCGAAT
21924 T
1 T
21925 TAGAAATTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
19 7 0.21
20 20 0.61
21 6 0.18
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (19 bp):
TCAAATTCGAGTTGCGAAT
Found at i:21936 original size:40 final size:40
Alignment explanation
Indices: 21866--21942 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
21856 GCGAAAATGT
**
21866 CAAATTCGAGTTGCGAATTCTACTTCTGTATTGCGAATTC
1 CAAATTCGAGTTGCGAATTCTAAATCTGTATTGCGAATTC
21906 CAAATTCGAGTTGCGAATT-TAGAAAT-TGTATTGCGAA
1 CAAATTCGAGTTGCGAATTCT--AAATCTGTATTGCGAA
21943 ATTGGCTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 1 0.03
40 30 0.91
41 2 0.06
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (40 bp):
CAAATTCGAGTTGCGAATTCTAAATCTGTATTGCGAATTC
Found at i:34325 original size:18 final size:18
Alignment explanation
Indices: 34302--34358 Score: 87
Period size: 18 Copynumber: 3.2 Consensus size: 18
34292 TTAAGACATT
34302 AATATGATTCATATGCTA
1 AATATGATTCATATGCTA
* * *
34320 AATATGATTTATATGATT
1 AATATGATTCATATGCTA
34338 AATATGATTCATATGCTA
1 AATATGATTCATATGCTA
34356 AAT
1 AAT
34359 TTTTAATTTG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.42
Consensus pattern (18 bp):
AATATGATTCATATGCTA
Found at i:34333 original size:9 final size:9
Alignment explanation
Indices: 34299--34352 Score: 63
Period size: 9 Copynumber: 6.0 Consensus size: 9
34289 TTATTAAGAC
34299 ATTAATATG
1 ATTAATATG
*
34308 ATTCATATG
1 ATTAATATG
* *
34317 CTAAATATG
1 ATTAATATG
*
34326 ATTTATATG
1 ATTAATATG
34335 ATTAATATG
1 ATTAATATG
*
34344 ATTCATATG
1 ATTAATATG
34353 CTAAATTTTT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.44
Consensus pattern (9 bp):
ATTAATATG
Found at i:35907 original size:9 final size:9
Alignment explanation
Indices: 35873--35907 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
35863 GAACTCGGTT
*
35873 AATTAACTG
1 AATTAACCG
*
35882 AATTAATCG
1 AATTAACCG
35891 AATTAACCG
1 AATTAACCG
35900 AATTAACC
1 AATTAACC
35908 TTTAAATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.29
Consensus pattern (9 bp):
AATTAACCG
Found at i:37058 original size:14 final size:14
Alignment explanation
Indices: 37041--37068 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
37031 ATTCACATCC
37041 TTGCATCTATATGT
1 TTGCATCTATATGT
37055 TTGCATCTATATGT
1 TTGCATCTATATGT
37069 AATTACATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.50
Consensus pattern (14 bp):
TTGCATCTATATGT
Found at i:40008 original size:13 final size:13
Alignment explanation
Indices: 39990--40019 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
39980 CTCATGAACG
39990 CATTTATGACGCA
1 CATTTATGACGCA
*
40003 CATTTATGACGCT
1 CATTTATGACGCA
40016 CATT
1 CATT
40020 GCGCGTCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (13 bp):
CATTTATGACGCA
Found at i:40183 original size:2 final size:2
Alignment explanation
Indices: 40176--40251 Score: 145
Period size: 2 Copynumber: 38.5 Consensus size: 2
40166 TGTCGTAAAT
40176 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- 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
40217 TA TA TA 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 T
40252 TGTAGATTGA
Statistics
Matches: 73, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 72 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:46352 original size:28 final size:28
Alignment explanation
Indices: 46312--46366 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
46302 TGGATCTCAA
46312 AAAAAAATGTACCCCGTACTTTTGCTGT
1 AAAAAAATGTACCCCGTACTTTTGCTGT
*
46340 AAAAAAATTTACCCCGTACTTTTGCTG
1 AAAAAAATGTACCCCGTACTTTTGCTG
46367 AAGTCACTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.33
Consensus pattern (28 bp):
AAAAAAATGTACCCCGTACTTTTGCTGT
Found at i:46448 original size:2 final size:2
Alignment explanation
Indices: 46443--46501 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
46433 AAAAGTGAAA
46443 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46485 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
46502 AAAAGTCAGA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:50773 original size:32 final size:32
Alignment explanation
Indices: 50733--50850 Score: 130
Period size: 32 Copynumber: 3.7 Consensus size: 32
50723 ACATGGCAGT
50733 GTCAGTGTTGCATTCAGATAATGCACAACAGA
1 GTCAGTGTTGCATTCAGATAATGCACAACAGA
* * * * *
50765 GTCGGTGTTGCATTTAGGTAATGCATAGCAGA
1 GTCAGTGTTGCATTCAGATAATGCACAACAGA
* * *
50797 GTCAGTGTTGCATTCAAAAAAATGTACAACATGA
1 GTCAGTGTTGCATTC-AGATAATGCACAACA-GA
*
50831 -TCAATGTTGCATTCAGATAA
1 GTCAGTGTTGCATTCAGATAA
50851 AGTATAGAAG
Statistics
Matches: 68, Mismatches: 16, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
32 44 0.65
33 22 0.32
34 2 0.03
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (32 bp):
GTCAGTGTTGCATTCAGATAATGCACAACAGA
Found at i:52016 original size:21 final size:21
Alignment explanation
Indices: 51989--52037 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
51979 ACAATTGTCA
*
51989 AATAATATTAGTAGTAATAAT
1 AATAATATTAATAGTAATAAT
*
52010 ATTAATATTAATAGTAATAAT
1 AATAATATTAATAGTAATAAT
52031 AATAATA
1 AATAATA
52038 GTAGGAGGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (21 bp):
AATAATATTAATAGTAATAAT
Found at i:52021 original size:12 final size:12
Alignment explanation
Indices: 51989--52034 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
51979 ACAATTGTCA
*
51989 AATAATATTAGT
1 AATAATAATAGT
* *
52001 AGTAATAATATT
1 AATAATAATAGT
*
52013 AATATTAATAGT
1 AATAATAATAGT
52025 AATAATAATA
1 AATAATAATA
52035 ATAGTAGGAG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (12 bp):
AATAATAATAGT
Found at i:52021 original size:15 final size:15
Alignment explanation
Indices: 51989--52037 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
51979 ACAATTGTCA
* *
51989 AATAATATTAGTAGT
1 AATAATATTAATAAT
*
52004 AATAATATTAATATT
1 AATAATATTAATAAT
* *
52019 AATAGTAATAATAAT
1 AATAATATTAATAAT
52034 AATA
1 AATA
52038 GTAGGAGGAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (15 bp):
AATAATATTAATAAT
Found at i:56088 original size:16 final size:15
Alignment explanation
Indices: 56064--56146 Score: 53
Period size: 16 Copynumber: 5.3 Consensus size: 15
56054 AAATAAATAT
*
56064 AATAATAATAATTAA
1 AATATTAATAATTAA
**
56079 TAATATTAATTGTTAA
1 -AATATTAATAATTAA
*
56095 AATAATGAATTAATTAA
1 AAT-ATTAA-TAATTAA
*
56112 AATA-TAATAATATATC
1 AATATTAATAAT-TA-A
*
56128 AATA-TAGTAATTAA
1 AATATTAATAATTAA
56142 AATAT
1 AATAT
56147 ATATTTTATA
Statistics
Matches: 52, Mismatches: 10, Indels: 11
0.71 0.14 0.15
Matches are distributed among these distances:
14 8 0.15
15 9 0.17
16 27 0.52
17 8 0.15
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.39
Consensus pattern (15 bp):
AATATTAATAATTAA
Found at i:59420 original size:2 final size:2
Alignment explanation
Indices: 59413--59460 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
59403 CGTTGAGATA
59413 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59455 AT AT AT
1 AT AT AT
59461 CGAGTATAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59882 original size:3 final size:3
Alignment explanation
Indices: 59874--59900 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
59864 ACTATTTTTC
59874 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
59901 GAAGAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:61560 original size:29 final size:24
Alignment explanation
Indices: 61499--61544 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
61489 AATTGAAATG
61499 ATTTTTATTTTATATTAATAATAT
1 ATTTTTATTTTATATTAATAATAT
61523 ATTTTTATTTTATATTAATAAT
1 ATTTTTATTTTATATTAATAAT
61545 TTTATAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
ATTTTTATTTTATATTAATAATAT
Found at i:62522 original size:15 final size:15
Alignment explanation
Indices: 62498--62527 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
62488 ATAGGTGATT
62498 AAATTAAATTAATTA
1 AAATTAAATTAATTA
*
62513 AAATTGAATTAATTA
1 AAATTAAATTAATTA
62528 TTTTTTTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (15 bp):
AAATTAAATTAATTA
Found at i:62990 original size:2 final size:2
Alignment explanation
Indices: 62983--63013 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
62973 TACTAAAACC
62983 TA 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 T
63014 TGGAATTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:63439 original size:7 final size:7
Alignment explanation
Indices: 63427--63562 Score: 67
Period size: 7 Copynumber: 19.4 Consensus size: 7
63417 TAGATTATAA
63427 CCTAAAC
1 CCTAAAC
63434 CCTAAAC
1 CCTAAAC
63441 CCTAAAC
1 CCTAAAC
**
63448 TTTAAAC
1 CCTAAAC
** *
63455 TATAAAT
1 CCTAAAC
63462 CCTAAAC
1 CCTAAAC
**
63469 ATTAAAC
1 CCTAAAC
*
63476 CCTAAGC
1 CCTAAAC
* *
63483 CTTAATC
1 CCTAAAC
63490 CCTAAGA-
1 CCTAA-AC
** *
63497 TATAAAT
1 CCTAAAC
63504 CCTAAAC
1 CCTAAAC
*
63511 CCTAATC
1 CCTAAAC
* *
63518 CTTAAGC
1 CCTAAAC
*
63525 CATAAAC
1 CCTAAAC
*
63532 CCTAAAT
1 CCTAAAC
* *
63539 CATAAAT
1 CCTAAAC
*
63546 CATAAAC
1 CCTAAAC
63553 CCTAAAC
1 CCTAAAC
63560 CCT
1 CCT
63563 TATTTCGATT
Statistics
Matches: 96, Mismatches: 31, Indels: 4
0.73 0.24 0.03
Matches are distributed among these distances:
6 1 0.01
7 95 0.99
ACGTcount: A:0.43, C:0.30, G:0.02, T:0.24
Consensus pattern (7 bp):
CCTAAAC
Found at i:63446 original size:14 final size:14
Alignment explanation
Indices: 63425--63562 Score: 75
Period size: 14 Copynumber: 9.9 Consensus size: 14
63415 GTTAGATTAT
63425 AACC-TAAACCCTA
1 AACCATAAACCCTA
* **
63438 AACCCTAAACTTTA
1 AACCATAAACCCTA
* *
63452 AACTATAAATCCTA
1 AACCATAAACCCTA
63466 AA-CATTAAACCCTA
1 AACCA-TAAACCCTA
* * *
63480 AGCCTTAATCCCTA
1 AACCATAAACCCTA
* *
63494 AGA-TATAAATCCTA
1 A-ACCATAAACCCTA
* * *
63508 AACCCTAATCCTTA
1 AACCATAAACCCTA
*
63522 AGCCATAAACCCTA
1 AACCATAAACCCTA
* * *
63536 AATCATAAATCATA
1 AACCATAAACCCTA
*
63550 AACCCTAAACCCT
1 AACCATAAACCCT
63563 TATTTCGATT
Statistics
Matches: 86, Mismatches: 34, Indels: 9
0.67 0.26 0.07
Matches are distributed among these distances:
13 6 0.07
14 79 0.92
15 1 0.01
ACGTcount: A:0.44, C:0.30, G:0.02, T:0.24
Consensus pattern (14 bp):
AACCATAAACCCTA
Found at i:63501 original size:42 final size:41
Alignment explanation
Indices: 63427--63562 Score: 146
Period size: 42 Copynumber: 3.2 Consensus size: 41
63417 TAGATTATAA
* * **
63427 CCTAAACCCTAAACCCTAAACTTTAAACTATAAATCCTAAAC
1 CCTAAACCCTAAGCCATAAACCCTAAA-TATAAATCCTAAAC
** * *
63469 ATTAAACCCTAAGCCTTAATCCCTAAGATATAAATCCTAAAC
1 CCTAAACCCTAAGCCATAAACCCTAA-ATATAAATCCTAAAC
* * *
63511 CCTAATCCTTAAGCCATAAACCCTAAATCATAAATCATAAAC
1 CCTAAACCCTAAGCCATAAACCCTAAAT-ATAAATCCTAAAC
63553 CCTAAACCCT
1 CCTAAACCCT
63563 TATTTCGATT
Statistics
Matches: 76, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
41 2 0.03
42 73 0.96
43 1 0.01
ACGTcount: A:0.43, C:0.30, G:0.02, T:0.24
Consensus pattern (41 bp):
CCTAAACCCTAAGCCATAAACCCTAAATATAAATCCTAAAC
Found at i:63538 original size:35 final size:34
Alignment explanation
Indices: 63425--63560 Score: 94
Period size: 35 Copynumber: 3.9 Consensus size: 34
63415 GTTAGATTAT
* * *
63425 AACCTAAACCCTAAACCCTAAACTTTAAACTATA
1 AACCTAAATCCTAAACCCTAAACCTTAAACCATA
* * * *
63459 AATCCTAAA-CATTAAACCCTAAGCCTTAATCCCTA
1 AA-CCTAAATC-CTAAACCCTAAACCTTAAACCATA
** * *
63494 AGATATAAATCCTAAACCCTAATCCTTAAGCCATA
1 A-ACCTAAATCCTAAACCCTAAACCTTAAACCATA
* * * *
63529 AACCCTAAATCATAAATCATAAACCCTAAACC
1 AA-CCTAAATCCTAAACCCTAAACCTTAAACC
63561 CTTATTTCGA
Statistics
Matches: 77, Mismatches: 20, Indels: 9
0.73 0.19 0.08
Matches are distributed among these distances:
34 4 0.05
35 71 0.92
36 2 0.03
ACGTcount: A:0.45, C:0.29, G:0.02, T:0.24
Consensus pattern (34 bp):
AACCTAAATCCTAAACCCTAAACCTTAAACCATA
Found at i:65432 original size:11 final size:11
Alignment explanation
Indices: 65418--65494 Score: 82
Period size: 11 Copynumber: 6.8 Consensus size: 11
65408 TCGAGCATGT
65418 ATCGAGCTTAA
1 ATCGAGCTTAA
65429 ATCGAGCTTAAA
1 ATCGAGCTT-AA
* *
65441 ATCGAGTTTGA
1 ATCGAGCTTAA
*
65452 ATCGAACTTAAA
1 ATCGAGCTT-AA
*
65464 ATCGAGCTTGA
1 ATCGAGCTTAA
* *
65475 ATCGAGTTTCA
1 ATCGAGCTTAA
65486 ATCGAGCTT
1 ATCGAGCTT
65495 GAGTCTTGAG
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
11 35 0.65
12 19 0.35
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (11 bp):
ATCGAGCTTAA
Found at i:65446 original size:23 final size:23
Alignment explanation
Indices: 65418--65496 Score: 106
Period size: 23 Copynumber: 3.5 Consensus size: 23
65408 TCGAGCATGT
*
65418 ATCGAGCTTAAATCGAGCTTAAA
1 ATCGAGCTTGAATCGAGCTTAAA
* *
65441 ATCGAGTTTGAATCGAACTTAAA
1 ATCGAGCTTGAATCGAGCTTAAA
**
65464 ATCGAGCTTGAATCGAG-TTTCA
1 ATCGAGCTTGAATCGAGCTTAAA
65486 ATCGAGCTTGA
1 ATCGAGCTTGA
65497 GTCTTGAGTT
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 14 0.29
23 35 0.71
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.29
Consensus pattern (23 bp):
ATCGAGCTTGAATCGAGCTTAAA
Found at i:65456 original size:34 final size:34
Alignment explanation
Indices: 65418--65494 Score: 111
Period size: 34 Copynumber: 2.3 Consensus size: 34
65408 TCGAGCATGT
*
65418 ATCGAGCTT-AAATCGAGCTTAAAATCGAGTTTGA
1 ATCGAGCTTAAAATCGAGCTT-AAATCGAGTTTCA
* *
65452 ATCGAACTTAAAATCGAGCTTGAATCGAGTTTCA
1 ATCGAGCTTAAAATCGAGCTTAAATCGAGTTTCA
65486 ATCGAGCTT
1 ATCGAGCTT
65495 GAGTCTTGAG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
34 27 0.71
35 11 0.29
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (34 bp):
ATCGAGCTTAAAATCGAGCTTAAATCGAGTTTCA
Found at i:65514 original size:24 final size:22
Alignment explanation
Indices: 65418--65515 Score: 79
Period size: 23 Copynumber: 4.3 Consensus size: 22
65408 TCGAGCATGT
* **
65418 ATCGAGCTTAAATCGAGCTTAAA
1 ATCGAGCTTGAATCGAG-TTTCA
* * **
65441 ATCGAGTTTGAATCGAACTTAAA
1 ATCGAGCTTGAATCG-AGTTTCA
65464 ATCGAGCTTGAATCGAGTTTCA
1 ATCGAGCTTGAATCGAGTTTCA
*
65486 ATCGAGCTTGAGTCTTGAGTTTCA
1 ATCGAGCTTGAATC--GAGTTTCA
*
65510 GTCGAG
1 ATCGAG
65516 TTTTTGAATT
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
22 17 0.27
23 32 0.51
24 14 0.22
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (22 bp):
ATCGAGCTTGAATCGAGTTTCA
Found at i:65551 original size:16 final size:16
Alignment explanation
Indices: 65527--65557 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
65517 TTTTGAATTT
*
65527 TTTTTGAGTTCGAGTC
1 TTTTCGAGTTCGAGTC
65543 TTTTCGAGTTCGAGT
1 TTTTCGAGTTCGAGT
65558 TGAGTTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.13, G:0.26, T:0.48
Consensus pattern (16 bp):
TTTTCGAGTTCGAGTC
Found at i:66027 original size:12 final size:13
Alignment explanation
Indices: 66010--66038 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
66000 TTTAATTACG
66010 AAAATTAAAA-TT
1 AAAATTAAAATTT
66022 AAAATTAAAATTT
1 AAAATTAAAATTT
66035 AAAA
1 AAAA
66039 ATTCGATTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:66180 original size:17 final size:17
Alignment explanation
Indices: 66158--66198 Score: 68
Period size: 15 Copynumber: 2.5 Consensus size: 17
66148 GGAGAGAACA
66158 AAATAAAAAAAATATAT
1 AAATAAAAAAAATATAT
66175 AAAT--AAAAAATATAT
1 AAATAAAAAAAATATAT
66190 AAATAAAAA
1 AAATAAAAA
66199 GACTATTAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 15 0.68
17 7 0.32
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (17 bp):
AAATAAAAAAAATATAT
Found at i:66184 original size:15 final size:15
Alignment explanation
Indices: 66164--66198 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
66154 AACAAAATAA
66164 AAAAAATATATAAAT
1 AAAAAATATATAAAT
66179 AAAAAATATATAAAT
1 AAAAAATATATAAAT
66194 AAAAA
1 AAAAA
66199 GACTATTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAAAATATATAAAT
Found at i:66268 original size:19 final size:17
Alignment explanation
Indices: 66241--66284 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
66231 TCGAAGGGGT
66241 AAAAAAATAAATAATATA
1 AAAAAAATAAA-AATATA
*
66259 AAATAAAATAAAAATATC
1 AAA-AAAATAAAAATATA
66277 AAAAAAAT
1 AAAAAAAT
66285 GTTAAATGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 5 0.21
18 11 0.46
19 8 0.33
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.20
Consensus pattern (17 bp):
AAAAAAATAAAAATATA
Found at i:67641 original size:3 final size:3
Alignment explanation
Indices: 67626--67660 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
67616 TAAATAAATA
*
67626 AAT AAT GAT AAT AAT AAT AAT AAT AAAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT A
67661 TATCCTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:67685 original size:9 final size:10
Alignment explanation
Indices: 67610--67683 Score: 54
Period size: 9 Copynumber: 8.1 Consensus size: 10
67600 AAACGGAAAA
67610 AATAA-ATA-
1 AATAATATAT
67618 AATAA-ATA-
1 AATAATATAT
*
67626 AATAAT-GAT
1 AATAATATAT
67635 AATAATA-AT
1 AATAATATAT
*
67644 AATAATAAAT
1 AATAATATAT
67654 AATAATATAT
1 AATAATATAT
** *
67664 CCTAAAATAT
1 AATAATATAT
67674 -ATAATATAT
1 AATAATATAT
67683 A
1 A
67684 TATTTCAAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
8 14 0.26
9 22 0.41
10 18 0.33
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (10 bp):
AATAATATAT
Found at i:67778 original size:31 final size:34
Alignment explanation
Indices: 67740--67918 Score: 111
Period size: 38 Copynumber: 5.0 Consensus size: 34
67730 CCAAAACTAT
67740 ATATTATAT-AGTTTTC-AAAAAT-TATTTTAAA
1 ATATTATATAAGTTTTCAAAAAATGTATTTTAAA
*
67771 ATATTATATAAGTTTTCAAAAAATGTTTTTTAAAATTA
1 ATATTATATAAGTTTTCAAAAAATGTATTTT--AA--A
*
67809 TATATTATATAATTTTTC-AAAAATGT-TTTTAAAATTA
1 -ATATTATATAAGTTTTCAAAAAATGTATTTT--AA--A
* * *
67846 TATATTTATATAATTTTTCCAAAAATGTTTTTTTAAAAAA
1 -ATA-TTATATAAGTTTTCAAAAAATG-TATTTT---AAA
*
67886 TATATTATATAA-TTTTTAAAAAATGT-TTTTAAA
1 -ATATTATATAAGTTTTCAAAAAATGTATTTTAAA
67919 GCTATATATT
Statistics
Matches: 131, Mismatches: 4, Indels: 24
0.82 0.03 0.15
Matches are distributed among these distances:
31 9 0.07
32 7 0.05
33 9 0.07
34 5 0.04
36 6 0.05
37 16 0.12
38 34 0.26
39 31 0.24
40 6 0.05
41 4 0.03
42 4 0.03
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (34 bp):
ATATTATATAAGTTTTCAAAAAATGTATTTTAAA
Found at i:67847 original size:37 final size:37
Alignment explanation
Indices: 67732--68045 Score: 324
Period size: 37 Copynumber: 8.5 Consensus size: 37
67722 AAAAATTTCC
* *
67732 AAAACTATATATTATAT-AGTTTTCAAAAAT-TATTTT
1 AAAATTATATATTATATAATTTTTCAAAAATGT-TTTT
*
67768 --AA--A-ATATTATATAAGTTTTCAAAAAATGTTTTTT
1 AAAATTATATATTATATAATTTTTC-AAAAATG-TTTTT
67802 AAAATTATATATTATATAATTTTTCAAAAATGTTTTT
1 AAAATTATATATTATATAATTTTTCAAAAATGTTTTT
67839 AAAATTATATATTTATATAATTTTTCCAAAAATGTTTTTTT
1 AAAATTATATA-TTATATAATTTTT-CAAAAATG--TTTTT
* *
67880 AAAA-AATATATTATATAATTTTTAAAAAATGTTTTT
1 AAAATTATATATTATATAATTTTTCAAAAATGTTTTT
** * *
67916 AAAGCTATATATTATATAATTTTTCAACAAA-ATTTTA
1 AAAATTATATATTATATAATTTTTCAA-AAATGTTTTT
* * *
67953 AAAATTATATACTATATAAGTTTTC-AAAATGTTTTA
1 AAAATTATATATTATATAATTTTTCAAAAATGTTTTT
* * *
67989 AAAACTATATAATATATAAATTTTCAAAAATCGTTTTCT
1 AAAATTATATATTATATAATTTTTCAAAAAT-GTTTT-T
68028 GAAAATTATATATTATAT
1 -AAAATTATATATTATAT
68046 TTTGCCAAAA
Statistics
Matches: 239, Mismatches: 19, Indels: 36
0.81 0.06 0.12
Matches are distributed among these distances:
31 9 0.04
32 8 0.03
33 6 0.03
34 6 0.03
35 4 0.02
36 38 0.16
37 66 0.28
38 36 0.15
39 37 0.15
40 20 0.08
41 9 0.04
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.47
Consensus pattern (37 bp):
AAAATTATATATTATATAATTTTTCAAAAATGTTTTT
Found at i:68112 original size:14 final size:14
Alignment explanation
Indices: 68080--68113 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
68070 TATATTACTA
* *
68080 TATACATATATATG
1 TATATATATACATG
68094 TATATATATACATG
1 TATATATATACATG
68108 TATATA
1 TATATA
68114 AACAAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (14 bp):
TATATATATACATG
Found at i:68775 original size:80 final size:80
Alignment explanation
Indices: 68673--69533 Score: 729
Period size: 84 Copynumber: 10.4 Consensus size: 80
68663 ATTTTATTGA
* * ** * *
68673 CAGATAACCCTTCTTGCCTTGGGCTATGCTATAAATAATGTACCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
68738 CTCGAAGGTCTTTGG
66 CTCGAAGGTCTTTGG
* * * * *
68753 CATATAACCCTTCTAGTCTTGGGCTATGCTGTAAATGATGTGTCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
*
68818 CTCGAAGGTTTTTGG
66 CTCGAAGGTCTTTGG
** * * * * *
68833 CAGATAGTCCTTCTAGCCTTGAGCTATAC--CATATATGATGTGTCATT-GAGTTGAGTGTAATC
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCA-A-ATGATGTG-CCTTGGAGCTGAGCGTAGTC
* *
68895 GAACTCAAATGTCTTTGTTGG
63 GAACTCGAAGGTC--T-TTGG
* * * * * * *
68916 CATATAACCCTTGTAGCCTTGAGTTATCCTGCAAATGATGTGCCCTCGAAGCTGAGCGTGGTCGA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGA
68981 ACTCGAAGGTCTTTGG
65 ACTCGAAGGTCTTTGG
* * * * * * * * * *
68997 CATATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGACGTGTCTTAGAGTTGAGCGTAGTTGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
69062 CTCGAAGGTCATTTGGTG
66 CTCGAAGGTC-TTT-G-G
* * * * * * * *
69080 ACAGATAACCCTTCTAGCCCTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATTG
1 -CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCG
*
69145 AACTCGAGGGTCTTTGG
64 AACTCGAAGGTCTTTGG
* * * *
69162 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* *
69227 CTTGAAAGTCTTTGGTTGG
66 CTCGAAGGTC--T--TTGG
* * * * * * * *
69246 CAAATAACCCTTCTCGACTTAAGTTATGTTACAAATGATATGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
69311 CTCGAAGGTCTTTTGATG
66 CTCGAAGGTC-TTTG--G
* * * * *
69329 ACAGATAACCCTTCTAGCTTTGAGTTATGTTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGA
1 -CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
*
69394 ACTCGAAGGTTTGTGTATGG
65 ACTCGAAGG--TCT-T-TGG
* * * ** * * * * * *
69414 CATATAACCTTTCTCGATTTAAGCTATGCTGCAAGTGTTGTGACTTTGAGCTGAACGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
69479 CTCGAAGGTCTTTTATTGG
66 CTCGAAGGTC---T-TTGG
* *
69498 CAGACAACCCTTCTAGCCTTGAGTTATGCTGCAAAT
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAAT
69534 AGTTTCTTTA
Statistics
Matches: 626, Mismatches: 127, Indels: 52
0.78 0.16 0.06
Matches are distributed among these distances:
78 1 0.00
79 1 0.00
80 176 0.28
81 81 0.13
82 6 0.01
83 42 0.07
84 284 0.45
85 31 0.05
86 2 0.00
87 2 0.00
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.32
Consensus pattern (80 bp):
CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
CTCGAAGGTCTTTGG
Found at i:69135 original size:165 final size:162
Alignment explanation
Indices: 68724--69491 Score: 724
Period size: 165 Copynumber: 4.7 Consensus size: 162
68714 ACCTTGGAGC
* * * *
68724 TGAGCGTAGTCGAACTCGAAGGTC-TT--TGGCATATAACCCTTCTAGTCTTGGGCTATGCTGTA
1 TGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCATATAACCCTTCTAGCCTTGAGTTATGCTGCA
* * * * * * *
68786 AATGATGTGTCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTTTTTGGCAGATAGTCCTTCTAGCC
66 AATGATGTGCCTCGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGAC
* *
68851 TTGAGCTATAC--CATATATGATGTGTCATTGAGT
131 TTAAGCTATGCTGCA-A-ATGATGTGTC-TTGAGT
* * * * * * *
68884 TGAGTGTAATCGAACTCAAATGTCTTTGTTGGCATATAACCCTTGTAGCCTTGAGTTATCCTGCA
1 TGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCATATAACCCTTCTAGCCTTGAGTTATGCTGCA
* *
68949 AATGATGTGCCCTCGAAGCTGAGCGTGGTCGAACTCGAAGGTCTTTGGCATATAGCCCTTCTCGA
66 AATGATGTG-CCTCGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGA
*
69014 CTTAAGCTATGCTGCAAATGACGTGTCTTAGAGT
130 CTTAAGCTATGCTGCAAATGATGTGTCTT-GAGT
* * * * *
69048 TGAGCGTAGTTGAACTCGAAGGTCATTTGGTGACAGATAACCCTTCTAGCCCTGAGTTATGCTGT
1 TGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGGCATATAACCCTTCTAGCCTTGAGTTATGCTGC
* * * *
69113 AAATGATGTGCCCTCGAAGCTGAGTGTAATTGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCG
65 AAATGATGTG-CCTCGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCG
* *
69178 ACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGC
129 ACTTAAGCTATGCTGCAAATGATGTGTCTT-GAGT
* * * * * * * *
69213 TGAGCGTAGTCGAACTTGAAAGTCTTTGGTTGGCAAATAACCCTTCTCGACTTAAGTTATGTTAC
1 TGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGGCATATAACCCTTCTAGCCTTGAGTTATGCTGC
* * * *
69278 AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGATGACAGATAACCCTTC
65 AAATGATGTGCCTCGAAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTG--G-CAGATAGCCCTTC
* * * * * * * *
69343 TAG-CTTTGAGTTATGTTGTAAATGATATGCCTTGGAGC
126 TCGAC-TTAAGCTATGCTGCAAATGATGTGTCTT-GAGT
* * * ** * *
69381 TGAGCGTAGTCGAACTCGAAGGT-TTGTGTATGGCATATAACCTTTCTCGATTTAAGCTATGCTG
1 TGAGCGTAGTCGAACTCGAAGGTCTT-TG-GTGGCATATAACCCTTCTAGCCTTGAGTTATGCTG
* * * * *
69445 CAAGTGTTGTGACTTTG-AGCTGAACGTAGTCGAACTCGAAGGTCTTT
64 CAAATGATGTG-CCTCGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTT
69492 TATTGGCAGA
Statistics
Matches: 507, Mismatches: 84, Indels: 27
0.82 0.14 0.04
Matches are distributed among these distances:
160 20 0.04
161 2 0.00
163 41 0.08
164 120 0.24
165 184 0.36
166 2 0.00
167 7 0.01
168 127 0.25
169 4 0.01
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (162 bp):
TGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCATATAACCCTTCTAGCCTTGAGTTATGCTGCA
AATGATGTGCCTCGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGAC
TTAAGCTATGCTGCAAATGATGTGTCTTGAGT
Found at i:70453 original size:83 final size:85
Alignment explanation
Indices: 70348--70571 Score: 238
Period size: 95 Copynumber: 2.5 Consensus size: 85
70338 GGCTAGCTGA
*
70348 ATCCATAAAGTCGGGGCATTTAACCAATTACTCTAGAGGGACAACTTA-AT-ATATAAACACCTT
1 ATCCATAAAGTCGGGGCGTTTAACCAATTACTCTAGAGGGACAACTTATATAATATAAACACCTT
* * *
70411 TATCAGGTTAGTTGAATCTT
66 TATCAGGCTAGCTGAATATT
*
70431 ATCCATAAAGTTGGGGCGTTTAACCAATTAC-CTTAGAGGGACAAATTAAGCTTTATTGTATAAT
1 ATCCATAAAGTCGGGGCGTTTAACCAATTACTC-TAGAGGGAC-----AA-C-TTA---TATAAT
**
70495 ATAATTACCTTTATCAGGCTAGCTGAATATT
55 ATAAACACCTTTATCAGGCTAGCTGAATATT
* * *
70526 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGATAACT
1 ATCCATAAAGTCGGGGCGTTTAACCAATTACTCTAGAGGGACAACT
70572 CAATCTTTAT
Statistics
Matches: 116, Mismatches: 11, Indels: 23
0.77 0.07 0.15
Matches are distributed among these distances:
82 1 0.01
83 38 0.33
88 3 0.03
89 2 0.02
90 5 0.04
94 2 0.02
95 64 0.55
96 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Consensus pattern (85 bp):
ATCCATAAAGTCGGGGCGTTTAACCAATTACTCTAGAGGGACAACTTATATAATATAAACACCTT
TATCAGGCTAGCTGAATATT
Found at i:70563 original size:95 final size:96
Alignment explanation
Indices: 70396--70595 Score: 269
Period size: 95 Copynumber: 2.1 Consensus size: 96
70386 GGACAACTTA
** * * * **
70396 ATATATAAACACCTTTATCAGGTTAGTTGAATCTTATCCATAAAGTTGGGGCGTTTAACCAATTA
1 ATATATAATTACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTA
*
70461 CCTTAGAGGGACAAATTAAGCTTTATTGTAT
66 CCTTAGAGGGACAAATCAAGCTTTATTGTAT
70492 A-ATATAATTACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATT-
1 ATATATAATTACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTA
* * * *
70555 GCTCTAGAGGGATAACTCAATCTTTATTGTAT
66 CCT-TAGAGGGACAAATCAAGCTTTATTGTAT
70587 ATATATAAT
1 ATATATAAT
70596 ATTATAATCT
Statistics
Matches: 90, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
94 2 0.02
95 80 0.89
96 8 0.09
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (96 bp):
ATATATAATTACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTA
CCTTAGAGGGACAAATCAAGCTTTATTGTAT
Found at i:74059 original size:13 final size:14
Alignment explanation
Indices: 74039--74072 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
74029 AGAACAAAAT
74039 TAAAAAAATATAAA
1 TAAAAAAATATAAA
74053 TAAAAAAATATAAA
1 TAAAAAAATATAAA
74067 TAAAAA
1 TAAAAA
74073 GAGTATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
TAAAAAAATATAAA
Found at i:74181 original size:17 final size:17
Alignment explanation
Indices: 74161--74207 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
74151 AAAATGTTAA
*
74161 ATGAAAAAAAAAATAAT
1 ATGAAAAAAAAAATAAG
*
74178 ATGAAAAAAAAGATAAG
1 ATGAAAAAAAAAATAAG
*
74195 AT-AAAAATAAAAT
1 ATGAAAAAAAAAAT
74208 TCAGAGGGCT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
16 9 0.35
17 17 0.65
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (17 bp):
ATGAAAAAAAAAATAAG
Found at i:75540 original size:16 final size:16
Alignment explanation
Indices: 75520--75571 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
75510 AAAAACAAAA
*
75520 AATAAAAATAAATAAT
1 AATAATAATAAATAAT
*
75536 GATAATAAT-AATAAAT
1 AATAATAATAAAT-AAT
75552 AATAATAATAAATAAT
1 AATAATAATAAATAAT
75568 AATA
1 AATA
75572 TATCCTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
15 3 0.10
16 25 0.81
17 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (16 bp):
AATAATAATAAATAAT
Found at i:75542 original size:13 final size:13
Alignment explanation
Indices: 75520--75571 Score: 72
Period size: 13 Copynumber: 4.1 Consensus size: 13
75510 AAAAACAAAA
75520 AATAAA-AATAAAT
1 AATAAATAAT-AAT
*
75533 AAT-GATAATAAT
1 AATAAATAATAAT
75545 AATAAATAATAAT
1 AATAAATAATAAT
75558 AATAAATAATAAT
1 AATAAATAATAAT
75571 A
1 A
75572 TATCCTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
12 7 0.20
13 28 0.80
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (13 bp):
AATAAATAATAAT
Found at i:75545 original size:3 final size:3
Alignment explanation
Indices: 75520--75571 Score: 59
Period size: 3 Copynumber: 16.3 Consensus size: 3
75510 AAAAACAAAA
* *
75520 AAT AAA AAT AAAT AAT GAT AAT AAT AAT AAAT AAT AAT AAT AAAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT -AAT AAT
75568 AAT A
1 AAT A
75572 TATCCTAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
3 33 0.79
4 9 0.21
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:75571 original size:10 final size:10
Alignment explanation
Indices: 75519--75569 Score: 61
Period size: 10 Copynumber: 5.2 Consensus size: 10
75509 AAAAAACAAA
*
75519 AAATAAAAAT
1 AAATAATAAT
*
75529 AAATAATGAT
1 AAATAATAAT
75539 -AATAATAAT
1 AAATAATAAT
75548 AAATAATAAT
1 AAATAATAAT
75558 -AATAAATAAT
1 AAAT-AATAAT
75568 AA
1 AA
75570 TATATCCTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
9 11 0.31
10 23 0.66
11 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (10 bp):
AAATAATAAT
Found at i:75689 original size:36 final size:37
Alignment explanation
Indices: 75647--75951 Score: 135
Period size: 37 Copynumber: 8.2 Consensus size: 37
75637 ATTCCAAAAC
75647 TATATATTATATAGTTTTCAAAAATTATTTT-AAA-A
1 TATATATTATATAGTTTTCAAAAATTATTTTAAAATA
*
75682 TAT-TA-TATA-AGTTTTCAAAAAAAATGTTTTTTAAAAT-
1 TATATATTATATAGTTTTC---AAAAAT-TATTTTAAAATA
*
75719 TATATATTATATAATTTTTCAAAAATGT-TTTTAAAATTTAAAA
1 TATATATTATAT-AGTTTTCAAAAAT-TATTTTAAAA--T---A
* * * *
75762 TGATATATTATATAATTTTC--CAATTTTTTTAAAACA
1 T-ATATATTATATAGTTTTCAAAAATTATTTTAAAATA
* * * * **
75798 -ATAAATTATATAATTTTTCAAAAAATATTTTTAAAGC
1 TATATATTATAT-AGTTTTCAAAAATTATTTTAAAATA
*
75835 TATATATTATATAATTGTTC-AAAA-TATTTTTAAAAT-
1 TATATATTATATAGTT-TTCAAAAATTA-TTTTAAAATA
* *
75871 TATATACTATATAAGTTTTC-AAAA-TGTTTTAAAAT-
1 TATATATTATAT-AGTTTTCAAAAATTATTTTAAAATA
* *
75906 TATACAATATATAAATGTTTTC-AAAA-TATTTTCAAAAT-
1 TATA-TAT-TATATA-GTTTTCAAAAATTATTTT-AAAATA
*
75944 TATGTATT
1 TATATATT
75952 TTAAAAATAT
Statistics
Matches: 215, Mismatches: 26, Indels: 57
0.72 0.09 0.19
Matches are distributed among these distances:
32 7 0.03
33 4 0.02
34 12 0.06
35 28 0.13
36 30 0.14
37 62 0.29
38 31 0.14
39 5 0.02
40 1 0.00
41 17 0.08
43 7 0.03
44 11 0.05
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.47
Consensus pattern (37 bp):
TATATATTATATAGTTTTCAAAAATTATTTTAAAATA
Found at i:75774 original size:116 final size:113
Alignment explanation
Indices: 75648--75871 Score: 274
Period size: 116 Copynumber: 1.9 Consensus size: 113
75638 TTCCAAAACT
* *
75648 ATATATTATATAGTTTTCAAAAATTATTTT-AA-AAT-ATTATATAAGTTTTCAAAAAAAATGTT
1 ATATATTATATAATTTTC--AAATTATTTTAAACAATAATTATATAAGTTTTC--AAAAAAT-AT
* * *
75710 TTTTAAAATTATATATTATATAATTTTTCAAAAATGTTTTTAAAATTTAAAATG
61 TTTTAAAACTATATATTATATAATTGTTC-AAAATATTTTTAAAATTTAAAATG
* * *
75764 ATATATTATATAATTTTCCAATTTTTTTAAAACAATAAATTATATAATTTTTCAAAAAATATTTT
1 ATATATTATATAATTTTCAAATTATTTT-AAACAAT-AATTATATAAGTTTTCAAAAAATATTTT
*
75829 TAAAGCTATATATTATATAATTGTTCAAAATATTTTTAAAATT
64 TAAAACTATATATTATATAATTGTTCAAAATATTTTTAAAATT
75872 ATATACTATA
Statistics
Matches: 94, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
114 8 0.09
115 16 0.17
116 46 0.49
117 10 0.11
119 14 0.15
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (113 bp):
ATATATTATATAATTTTCAAATTATTTTAAACAATAATTATATAAGTTTTCAAAAAATATTTTTA
AAACTATATATTATATAATTGTTCAAAATATTTTTAAAATTTAAAATG
Found at i:75895 original size:72 final size:71
Alignment explanation
Indices: 75755--75946 Score: 183
Period size: 74 Copynumber: 2.6 Consensus size: 71
75745 GTTTTTAAAA
* * ** * *
75755 TTTAAAA-TGATATATTATATAATTTTC-CAATTTTTTTAAAACAATAAATTATATAATTTTTCA
1 TTTAAAACT-ATATATTATATAATTTTCAAAATATTTTTAAAATTATAAACTATATAAGTTTTC-
*
75818 AAAAATATT
64 AAAAAT-GT
* *
75827 TTTAAAGCTATATATTATATAATTGTTCAAAATATTTTTAAAATTATATACTATATAAGTTTTC-
1 TTTAAAACTATATATTATATAATT-TTCAAAATATTTTTAAAATTATAAACTATATAAGTTTTCA
75891 AAAATGT
65 AAAATGT
* * * *
75898 TTTAAAATTATACAATATATAAATGTTTTCAAAATATTTTCAAAATTAT
1 TTTAAAACTATATATTATAT-AA--TTTTCAAAATATTTTTAAAATTAT
75947 GTATTTTAAA
Statistics
Matches: 100, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
71 17 0.17
72 28 0.28
73 25 0.25
74 30 0.30
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (71 bp):
TTTAAAACTATATATTATATAATTTTCAAAATATTTTTAAAATTATAAACTATATAAGTTTTCAA
AAATGT
Found at i:76016 original size:40 final size:38
Alignment explanation
Indices: 75950--76061 Score: 113
Period size: 38 Copynumber: 2.9 Consensus size: 38
75940 AAATTATGTA
75950 TTTTAAAAATATTTTTAAAAACTATATAATATATAAAT
1 TTTTAAAAATATTTTTAAAAACTATATAATATATAAAT
* * *
75988 TTTTAAAAATCGTTTTCTAAAAATTATAT-AT-TAT-ATT
1 TTTTAAAAAT-ATTTT-TAAAAACTATATAATATATAAAT
* * *
76025 TTTTCAAAAACATTTTCATAAACTATATATATATATA
1 TTTT-AAAAATATTTTTAAAAACTATATA-ATATATA
76062 TATATAATAA
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
36 9 0.15
37 10 0.17
38 20 0.34
39 9 0.15
40 11 0.19
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.46
Consensus pattern (38 bp):
TTTTAAAAATATTTTTAAAAACTATATAATATATAAAT
Found at i:76041 original size:37 final size:37
Alignment explanation
Indices: 75950--76060 Score: 120
Period size: 37 Copynumber: 3.0 Consensus size: 37
75940 AAATTATGTA
* *
75950 TTTTAAAAATATTTT-TAAAAACTATATAATATATAAAT
1 TTTTAAAAACATTTTCTAAAAACTATAT-ATATAT-ATT
* *
75988 TTTTAAAAATCGTTTTCTAAAAATTATATAT-TATATT
1 TTTTAAAAA-CATTTTCTAAAAACTATATATATATATT
*
76025 TTTTCAAAAACATTTTC-ATAAACTATATATATATAT
1 TTTT-AAAAACATTTTCTAAAAACTATATATATATAT
76061 ATATATAATA
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
36 11 0.18
37 17 0.27
38 17 0.27
39 6 0.10
40 11 0.18
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.47
Consensus pattern (37 bp):
TTTTAAAAACATTTTCTAAAAACTATATATATATATT
Found at i:81218 original size:106 final size:106
Alignment explanation
Indices: 81033--81235 Score: 282
Period size: 106 Copynumber: 1.9 Consensus size: 106
81023 AATGTAACAG
* * * *
81033 TGAAATGAAGTGATATATCACTGAAAAGTTTCTGTAATGAAGTGACTGAACACTGAAAAATTGTT
1 TGAAATGAAGTGATATATCAATGAAAAGTGTCTGTAATGAAGTAACTGAACACTGAAAAATTATT
* *
81098 GTCATTGTGTATTAATTGGTGTATGAGAAAATGACGTTTTT
66 GTCATTGTGTATTAAATGGTATATGAGAAAATGACGTTTTT
* * * * *
81139 TGAAATGAAGTGATATATCAATGAAAAGTGTCTG-ATGTGAAGTAATTGACCATTGAAAAGTTAT
1 TGAAATGAAGTGATATATCAATGAAAAGTGTCTGTA-ATGAAGTAACTGAACACTGAAAAATTAT
*
81203 TGTCTTTGTGTATTAAATGGTATATGAGAAAAT
65 TGTCATTGTGTATTAAATGGTATATGAGAAAAT
81236 AACATATTAA
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
105 1 0.01
106 83 0.99
ACGTcount: A:0.36, C:0.06, G:0.22, T:0.35
Consensus pattern (106 bp):
TGAAATGAAGTGATATATCAATGAAAAGTGTCTGTAATGAAGTAACTGAACACTGAAAAATTATT
GTCATTGTGTATTAAATGGTATATGAGAAAATGACGTTTTT
Found at i:81333 original size:22 final size:20
Alignment explanation
Indices: 81292--81330 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
81282 TCTAAAATGA
*
81292 AATGATATATGACTAAAAAT
1 AATGATATATCACTAAAAAT
81312 AATGATATATCACTAAAAA
1 AATGATATATCACTAAAAA
81331 AATTATGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (20 bp):
AATGATATATCACTAAAAAT
Found at i:92399 original size:53 final size:53
Alignment explanation
Indices: 92311--92415 Score: 165
Period size: 53 Copynumber: 2.0 Consensus size: 53
92301 TTTCTGGTTG
* *
92311 TCATGTTTTACAGATCAGAGGACTCATATCACCTTCTCATACAATTTATATGA
1 TCATGTTTTACAGATCAGAGGACTCATATCACCTTCTCAGACAATCTATATGA
** *
92364 TCATGTTTTACAGATCAGAGGACTTGTATCTCCTTCTCAGACAATCTATATG
1 TCATGTTTTACAGATCAGAGGACTCATATCACCTTCTCAGACAATCTATATG
92416 CCATCATCTA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (53 bp):
TCATGTTTTACAGATCAGAGGACTCATATCACCTTCTCAGACAATCTATATGA
Found at i:98805 original size:19 final size:19
Alignment explanation
Indices: 98781--98819 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
98771 TCGAATGCAT
98781 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
98800 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
98819 T
1 T
98820 GAATATTTTC
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:98836 original size:65 final size:64
Alignment explanation
Indices: 98718--98926 Score: 203
Period size: 65 Copynumber: 3.2 Consensus size: 64
98708 TATTCAAAGG
* *
98718 CATGCACCGATGCA-TCAGTCCATGCATCGATGCA-TCGATGAAT-TAATT-GAACATCGAATGC
1 CATGCACCGATGCACTC--TCCATGCATCGATGCACTC--TGAATAT-TTTCAAACATCGAATGC
*
98779 ATTC
61 ATTT
98783 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTC-AAACATCGAATGCATTT
* * *** * * **
98848 GATGCATCGATGCACAAGCCATACATCGATGCAC-CAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATA-TTTTCAAACATCGAATGCATTT
*
98912 CATGCATCGATGCAC
1 CATGCACCGATGCAC
98927 ACTTGGTGCA
Statistics
Matches: 125, Mismatches: 13, Indels: 13
0.83 0.09 0.09
Matches are distributed among these distances:
63 7 0.06
64 52 0.42
65 64 0.51
66 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (64 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTT
Found at i:98944 original size:64 final size:65
Alignment explanation
Indices: 98767--98929 Score: 213
Period size: 65 Copynumber: 2.5 Consensus size: 65
98757 GAATTAATTG
* * * *
98767 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
* ** * **
98832 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATACATCGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATA-TTTTCA
98895 A
65 A
98896 AACATCGAATGCATTTCATGCATCGATGCACACT
1 AACATCGAATGCATTTCATGCATCGATGCACACT
98930 TGGTGCACCG
Statistics
Matches: 84, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
64 36 0.43
65 48 0.57
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:100427 original size:117 final size:118
Alignment explanation
Indices: 100276--100489 Score: 274
Period size: 117 Copynumber: 1.8 Consensus size: 118
100266 ATCTTATTTT
*
100276 GAAAGCTAAAAAGGACTTGGAAAATAAAAATGAAATGTT-GAAAAAGGAGTTAGAGCTTTCAAAA
1 GAAAGCTAAAAAGGACTTGGAAAATAAAAATGAAAT-TTCGAAAAAGAAGTTAGAGCTTTCAAAA
*
100340 ATAAAATCGGAAAACT-TTGAAAAAGAAATTTTCAAATTAAACAAACTTCTTCTA
65 ATAAAATCGG-AAACTATGGAAAAAGAAATTTTCAAATTAAACAAACTTCTTCTA
* * * * * *
100394 GAAA-CTAAAATGGATTTTGAAAA-ACAAAATGAAATTTCGAAGAAGAATTTAGAGCTTTCAAAG
1 GAAAGCTAAAAAGGACTTGGAAAATA-AAAATGAAATTTCGAAAAAGAAGTTAGAGCTTTCAAAA
** *
100457 ATAAAATTTGAAAGTATGGAAAAAGAAATTTTC
65 ATAAAATCGGAAACTATGGAAAAAGAAATTTTC
100490 GATTTAGAAG
Statistics
Matches: 82, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
116 7 0.09
117 71 0.87
118 4 0.05
ACGTcount: A:0.50, C:0.08, G:0.16, T:0.26
Consensus pattern (118 bp):
GAAAGCTAAAAAGGACTTGGAAAATAAAAATGAAATTTCGAAAAAGAAGTTAGAGCTTTCAAAAA
TAAAATCGGAAACTATGGAAAAAGAAATTTTCAAATTAAACAAACTTCTTCTA
Found at i:101059 original size:20 final size:21
Alignment explanation
Indices: 101026--101065 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
101016 TTTTAACGTA
101026 ATTGATATTCATTTT-AAACC
1 ATTGATATTCATTTTCAAACC
101046 ATTGATA-TCAATTTTCAAAC
1 ATTGATATTC-ATTTTCAAAC
101066 AATTTGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 12 0.67
21 4 0.22
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (21 bp):
ATTGATATTCATTTTCAAACC
Found at i:101073 original size:22 final size:20
Alignment explanation
Indices: 101025--101069 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
101015 ATTTTAACGT
101025 AATTGATATTCATTTTAAAC
1 AATTGATATTCATTTTAAAC
*
101045 CATTGATA-TCAATTTTCAAAC
1 AATTGATATTC-ATTTT-AAAC
101066 AATT
1 AATT
101070 TGATTTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 2 0.10
20 12 0.57
21 7 0.33
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.42
Consensus pattern (20 bp):
AATTGATATTCATTTTAAAC
Found at i:106013 original size:21 final size:21
Alignment explanation
Indices: 105971--106014 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
105961 ACCCCGGGAG
*
105971 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
105992 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
106013 CT
1 CT
106015 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:107034 original size:19 final size:19
Alignment explanation
Indices: 107010--107048 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
107000 TCGAATGCAT
107010 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
107029 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
107048 T
1 T
107049 GAATATTTTC
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:107065 original size:65 final size:64
Alignment explanation
Indices: 106947--107155 Score: 198
Period size: 65 Copynumber: 3.2 Consensus size: 64
106937 TATTCAAAGG
* *
106947 CATGCACCGATGCA-TCAGTCCATGCATCGATGCA-TCGATGAAT-TAATT-GAACATCGAATGC
1 CATGCACCGATGCACTC--TCCATGCATCGATGCACTC--TGAATAT-TTTCAAACATCGAATGC
*
107008 ATTC
61 ATTT
107012 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTC-AAACATCGAATGCATTT
* * *** *
107077 GATGCATCGATGCACAAGCCATACATCGATGCAC-C--AAGCTATTTTTCAAACATCGAATGCAT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAA--TA-TTTTCAAACATCGAATGCAT
107139 TT
63 TT
*
107141 CATGCATCGATGCAC
1 CATGCACCGATGCAC
107156 ACTTGGTGCA
Statistics
Matches: 126, Mismatches: 10, Indels: 17
0.82 0.07 0.11
Matches are distributed among these distances:
62 2 0.02
63 7 0.06
64 51 0.40
65 64 0.51
66 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (64 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTT
Found at i:107173 original size:64 final size:63
Alignment explanation
Indices: 106996--107158 Score: 204
Period size: 65 Copynumber: 2.5 Consensus size: 63
106986 GAATTAATTG
* * *
106996 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAA-TATTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCAC-C--AAGTATTTTCA
107060 A
63 A
* ** *
107061 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATACATCGATGCACCAAGCTATTTTTC-A
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACCAAG-TA-TTTTCAA
107125 AACATCGAATGCATTTCATGCATCGATGCACACT
1 AACATCGAATGCATTTCATGCATCGATGCACACT
107159 TGGTGCACCG
Statistics
Matches: 85, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
62 2 0.02
64 35 0.41
65 48 0.56
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (63 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACCAAGTATTTTCAA
Found at i:107931 original size:7 final size:7
Alignment explanation
Indices: 107919--107943 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
107909 AAGAAATAGA
107919 AACCAAG
1 AACCAAG
107926 AACCAAG
1 AACCAAG
107933 AACCAAG
1 AACCAAG
107940 AACC
1 AACC
107944 TAGAGTCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.32, G:0.12, T:0.00
Consensus pattern (7 bp):
AACCAAG
Found at i:111900 original size:3 final size:3
Alignment explanation
Indices: 111894--111923 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
111884 AAACTCATCA
111894 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
111924 CGTCGTTTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:112905 original size:13 final size:14
Alignment explanation
Indices: 112875--112906 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
112865 CTTAATTGCG
112875 AAAATTAAAAAGTT
1 AAAATTAAAAAGTT
112889 -AAATTAAAAA-TT
1 AAAATTAAAAAGTT
112901 AAAATT
1 AAAATT
112907 CATTCCGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 2 0.12
13 15 0.88
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (14 bp):
AAAATTAAAAAGTT
Found at i:114159 original size:10 final size:9
Alignment explanation
Indices: 114142--114178 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
114132 TTCTTGGACC
114142 TGAAAAAAA
1 TGAAAAAAA
114151 TGAAAAAAA
1 TGAAAAAAA
114160 TGAAAAAAA
1 TGAAAAAAA
114169 T-AAATAAAA
1 TGAAA-AAAA
114178 T
1 T
114179 ATTATAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 3 0.11
9 24 0.89
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (9 bp):
TGAAAAAAA
Found at i:114196 original size:17 final size:18
Alignment explanation
Indices: 114176--114221 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 18
114166 AAATAAATAA
114176 AATATTATAATATA-AAT-
1 AATA-TATAATATATAATG
114193 AATA-ATAATATATAATG
1 AATATATAATATATAATG
114210 AATATAATAATA
1 AATAT-ATAATA
114222 AAAACTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 8 0.32
16 3 0.12
17 8 0.32
19 6 0.24
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (18 bp):
AATATATAATATATAATG
Found at i:114206 original size:22 final size:21
Alignment explanation
Indices: 114166--114235 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 21
114156 AAAATGAAAA
114166 AAATAAATAAAATATTATAATAT
1 AAAT-AATAAAATA-TATAATAT
114189 AAATAATAATAATATATAATGAAT
1 AAATAATAA-AATATATAAT--AT
114213 ATAATAATAAAAACTATATAATA
1 A-AATAAT-AAAA-TATATAATA
114236 CTATATTTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
22 11 0.27
23 8 0.20
24 4 0.10
25 8 0.20
26 10 0.24
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (21 bp):
AAATAATAAAATATATAATAT
Found at i:114346 original size:36 final size:36
Alignment explanation
Indices: 114306--114457 Score: 143
Period size: 36 Copynumber: 4.2 Consensus size: 36
114296 TTAAACTATG
114306 TTTTCAAAACTATATAATATATGTTTTTAAAAAATA
1 TTTTCAAAACTATATAATATATGTTTTTAAAAAATA
* *
114342 TTTTCAAAA-T-TATAATATAT-ATTTTCAAAAATCGA
1 TTTTCAAAACTATATAATATATGTTTTTAAAAAAT--A
* * * * **
114377 TTTTTAAAACTATGTATTATATGTTTTCAAAACGT-
1 TTTTCAAAACTATATAATATATGTTTTTAAAAAATA
* *
114412 TTTCTAAAAACTATATATTATATG-TTTTAAAAATATA
1 TTT-TCAAAACTATATAATATATGTTTTTAAAAA-ATA
114449 TTTTCAAAA
1 TTTTCAAAA
114458 ACTACATTAT
Statistics
Matches: 92, Mismatches: 16, Indels: 16
0.74 0.13 0.13
Matches are distributed among these distances:
33 10 0.11
34 10 0.11
35 20 0.22
36 34 0.37
37 11 0.12
38 7 0.08
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.45
Consensus pattern (36 bp):
TTTTCAAAACTATATAATATATGTTTTTAAAAAATA
Found at i:114372 original size:86 final size:88
Alignment explanation
Indices: 114222--114391 Score: 238
Period size: 86 Copynumber: 2.0 Consensus size: 88
114212 TATAATAATA
* *
114222 AAAACTATATAATACTATATTTTCAAAAATATGTTTTCAAACATTATATTATACATTTTCAAAAA
1 AAAACTATATAATACTATATTTTCAAAAATATATTTTCAAACATTATAATATACATTTTCAAAAA
* * *
114287 TTGTTTTTTTTAAACTATGTTTTC
66 TCG-ATTTTTAAAACTATGTTTTC
* * *
114311 AAAACTATATAATA-TATGTTTTTAAAAA-ATATTTTCAAA-ATTATAATATATATTTTCAAAAA
1 AAAACTATATAATACTATATTTTCAAAAATATATTTTCAAACATTATAATATACATTTTCAAAAA
114373 TCGATTTTTAAAACTATGT
66 TCGATTTTTAAAACTATGT
114392 ATTATATGTT
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
85 14 0.19
86 23 0.32
87 10 0.14
88 12 0.16
89 14 0.19
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (88 bp):
AAAACTATATAATACTATATTTTCAAAAATATATTTTCAAACATTATAATATACATTTTCAAAAA
TCGATTTTTAAAACTATGTTTTC
Found at i:114434 original size:71 final size:72
Alignment explanation
Indices: 114306--114457 Score: 166
Period size: 71 Copynumber: 2.1 Consensus size: 72
114296 TTAAACTATG
* * *
114306 TTTTCAAAACTATATAATATATGTTTTTAAAAAATATTTTCAAAATTATAATATATAT-TTTCAA
1 TTTTCAAAACTATATAATATATGTTTTCAAAAAATATTTTAAAAACTATAATATATATGTTTCAA
114370 AAATCGA
66 AAATCGA
* * * ** *
114377 TTTTTAAAACTATGTATTATATGTTTTCAAAACGT-TTTCTAAAAACTAT-ATATTATATGTTTT
1 TTTTCAAAACTATATAATATATGTTTTCAAAAAATATTT-TAAAAACTATAATA-TATATGTTTC
**
114440 AAAAATATA
64 AAAAATCGA
114449 TTTTCAAAA
1 TTTTCAAAA
114458 ACTACATTAT
Statistics
Matches: 66, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
70 6 0.09
71 42 0.64
72 18 0.27
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.45
Consensus pattern (72 bp):
TTTTCAAAACTATATAATATATGTTTTCAAAAAATATTTTAAAAACTATAATATATATGTTTCAA
AAATCGA
Found at i:122033 original size:33 final size:32
Alignment explanation
Indices: 121989--122051 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 32
121979 TTGAAAAAAT
*
121989 AATATAAATATATA-TTATTATAATTATCTCTA
1 AATATAAATATATATTTATAAT-ATTATCTCTA
122021 AATATATAATATATATTTATAATATTATCTC
1 AATATA-AATATATATTTATAATATTATCTC
122052 GGATCTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 6 0.21
33 16 0.57
34 6 0.21
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (32 bp):
AATATAAATATATATTTATAATATTATCTCTA
Found at i:122747 original size:23 final size:23
Alignment explanation
Indices: 122698--122744 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
122688 AAACTCCATT
*
122698 AGAAGAAGAGAGGAAGAAGAAGA
1 AGAAGAAGAGAGAAAGAAGAAGA
* *
122721 AGAAGATGAGAGAAAAGAGGAAGA
1 AGAAGAAGAGAG-AAAGAAGAAGA
122745 GAAACTTCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.60, C:0.00, G:0.38, T:0.02
Consensus pattern (23 bp):
AGAAGAAGAGAGAAAGAAGAAGA
Found at i:124367 original size:22 final size:21
Alignment explanation
Indices: 124333--124373 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
124323 ATAATTATTT
124333 AAAAAATTAAATAAAAATACC
1 AAAAAATTAAATAAAAATACC
*
124354 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
124374 ATTTTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACC
Found at i:129669 original size:20 final size:20
Alignment explanation
Indices: 129646--129684 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
129636 CTCATCGCAA
129646 CATCACCCTCTTTGTAGCAG
1 CATCACCCTCTTTGTAGCAG
129666 CATCACCCTCTTTGTAGCA
1 CATCACCCTCTTTGTAGCA
129685 CAACCCCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.36, G:0.13, T:0.31
Consensus pattern (20 bp):
CATCACCCTCTTTGTAGCAG
Found at i:134551 original size:23 final size:23
Alignment explanation
Indices: 134523--134581 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
134513 TTTCATAATC
*
134523 AAAAACCCTGTTTACAAGAACCA
1 AAAAACTCTGTTTACAAGAACCA
* * *
134546 AAAAACTATGTTTACCAGAACCG
1 AAAAACTCTGTTTACAAGAACCA
134569 AAAAACTCTGTTT
1 AAAAACTCTGTTT
134582 CTACATTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.44, C:0.22, G:0.10, T:0.24
Consensus pattern (23 bp):
AAAAACTCTGTTTACAAGAACCA
Found at i:143483 original size:18 final size:18
Alignment explanation
Indices: 143460--143495 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
143450 GTGTTTAGGA
143460 TGGTAAGGAAAGCTTTGT
1 TGGTAAGGAAAGCTTTGT
143478 TGGTAAGGAAAGCTTTGT
1 TGGTAAGGAAAGCTTTGT
143496 GACTAAGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.06, G:0.33, T:0.33
Consensus pattern (18 bp):
TGGTAAGGAAAGCTTTGT
Found at i:156587 original size:10 final size:10
Alignment explanation
Indices: 156572--156605 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
156562 TTCATTTACC
156572 ATTTATTTCT
1 ATTTATTTCT
*
156582 ATTTATTTTT
1 ATTTATTTCT
*
156592 ATCTATTTCT
1 ATTTATTTCT
156602 ATTT
1 ATTT
156606 TACTAACCTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.71
Consensus pattern (10 bp):
ATTTATTTCT
Found at i:166044 original size:13 final size:13
Alignment explanation
Indices: 166026--166062 Score: 67
Period size: 12 Copynumber: 2.9 Consensus size: 13
166016 TAAGTTGGAA
166026 AAAAAAAACAAAG
1 AAAAAAAACAAAG
166039 -AAAAAAACAAAG
1 AAAAAAAACAAAG
166051 AAAAAAAACAAA
1 AAAAAAAACAAA
166063 ACAAAAAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.86, C:0.08, G:0.05, T:0.00
Consensus pattern (13 bp):
AAAAAAAACAAAG
Found at i:166068 original size:13 final size:12
Alignment explanation
Indices: 166024--166069 Score: 65
Period size: 13 Copynumber: 3.7 Consensus size: 12
166014 CCTAAGTTGG
166024 AAAAAAAAAACA
1 AAAAAAAAAACA
*
166036 AAGAAAAAAACA
1 AAAAAAAAAACA
166048 AAGAAAAAAAACA
1 AA-AAAAAAAACA
166061 AAACAAAAA
1 AAA-AAAAA
166070 GAGAAGAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
12 14 0.47
13 16 0.53
ACGTcount: A:0.87, C:0.09, G:0.04, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAACA
Found at i:167080 original size:105 final size:105
Alignment explanation
Indices: 166897--167567 Score: 1137
Period size: 105 Copynumber: 6.4 Consensus size: 105
166887 CAGGTTTGAC
166897 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
1 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
* * *
166962 GACGAAGGGACCGCTGGTTGTCCACAAAAATCTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
* *
167002 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCAC
1 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
167067 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
*
167107 CCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
1 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
167172 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
*
167212 CCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
1 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
167277 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
*
167317 CCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGAC-ACGCAAGTTCAACTTCAC
1 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
167381 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
* * ****
167421 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTATAAGTTCAACTTCAC
1 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
** **
167486 GACGAAGGGACCGCTGACTGTCAACCGACGATTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATT
* * *
167527 TCAGAGCCAATTTCAACTTCACAGCGGAGGATATTGGACTC
1 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
167568 GGAACAATAT
Statistics
Matches: 543, Mismatches: 21, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
104 101 0.19
105 392 0.72
106 50 0.09
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (105 bp):
CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
Found at i:169361 original size:22 final size:20
Alignment explanation
Indices: 169319--169376 Score: 70
Period size: 18 Copynumber: 3.1 Consensus size: 20
169309 ATTTCTTTAC
*
169319 TTCT-TTATTATTATATTTA
1 TTCTATTATTATTATATTTT
*
169338 TT-TA-CATTATT-TATTTT
1 TTCTATTATTATTATATTTT
169355 TTCTATTATTATTATATTTT
1 TTCTATTATTATTATATTTT
169375 TT
1 TT
169377 TCCTCCCTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
17 7 0.22
18 9 0.28
19 8 0.25
20 8 0.25
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (20 bp):
TTCTATTATTATTATATTTT
Found at i:169530 original size:14 final size:15
Alignment explanation
Indices: 169511--169551 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 15
169501 TATATATATA
169511 TATTTTTTTTTTC-T
1 TATTTTTTTTTTCAT
*
169525 TA-TTTTATTTTCAT
1 TATTTTTTTTTTCAT
169539 TATTTTTTATTTT
1 TATTTTTT-TTTT
169552 ATATGTACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 9 0.41
14 5 0.23
15 4 0.18
16 4 0.18
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.80
Consensus pattern (15 bp):
TATTTTTTTTTTCAT
Found at i:178203 original size:12 final size:12
Alignment explanation
Indices: 178188--178230 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
178178 GTTATTTAAA
*
178188 CGGGTATTGGGT
1 CGGGTATTGGGC
178200 CGGGTATTGGGC
1 CGGGTATTGGGC
* *
178212 CGGGAATCGGGC
1 CGGGTATTGGGC
178224 CGGGTAT
1 CGGGTAT
178231 ATATATATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.12, C:0.16, G:0.49, T:0.23
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:178235 original size:2 final size:2
Alignment explanation
Indices: 178228--178328 Score: 79
Period size: 2 Copynumber: 53.5 Consensus size: 2
178218 TCGGGCCGGG
* * *
178228 TA TA TA TA TA TA TA TA TA TA TA AA T- TA AA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
178269 TA T- TT TT TA TT TA AA T- TA AA TT TA T- TA -A TA T- 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
178306 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
178329 TATTTTTAAT
Statistics
Matches: 78, Mismatches: 15, Indels: 12
0.74 0.14 0.11
Matches are distributed among these distances:
1 6 0.08
2 72 0.92
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:178373 original size:13 final size:13
Alignment explanation
Indices: 178355--178391 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
178345 CGGGTCAAGT
*
178355 ATCGGGTCGGGTA
1 ATCGGGGCGGGTA
178368 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
178381 ATCGGGGCGGG
1 ATCGGGGCGGG
178392 GATTACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.14, C:0.16, G:0.54, T:0.16
Consensus pattern (13 bp):
ATCGGGGCGGGTA
Found at i:178447 original size:6 final size:6
Alignment explanation
Indices: 178436--178460 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
178426 AAATGGATTT
178436 TCCCCG TCCCCG TCCCCG TCCCCG T
1 TCCCCG TCCCCG TCCCCG TCCCCG T
178461 TTATCATCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.64, G:0.16, T:0.20
Consensus pattern (6 bp):
TCCCCG
Found at i:185477 original size:44 final size:44
Alignment explanation
Indices: 185411--185505 Score: 181
Period size: 44 Copynumber: 2.2 Consensus size: 44
185401 AGGGCTTCAA
185411 CAATTTTATTTCCGCTTCGCATTACATGTTAAACTCTAACGTAT
1 CAATTTTATTTCCGCTTCGCATTACATGTTAAACTCTAACGTAT
*
185455 CAATTTTATTTCCGCTTTGCATTACATGTTAAACTCTAACGTAT
1 CAATTTTATTTCCGCTTCGCATTACATGTTAAACTCTAACGTAT
185499 CAATTTT
1 CAATTTT
185506 TCCCTCTTAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.27, C:0.21, G:0.08, T:0.43
Consensus pattern (44 bp):
CAATTTTATTTCCGCTTCGCATTACATGTTAAACTCTAACGTAT
Done.