Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004097.1 Hibiscus syriacus cultivar Beakdansim tig00008959_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: 83924
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:8159 original size:2 final size:2
Alignment explanation
Indices: 8152--8176 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8142 ATCACTAATA
8152 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
8177 ACTTACAGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9492 original size:21 final size:21
Alignment explanation
Indices: 9467--9506 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
9457 CGGAATGTTA
*
9467 AAAAATATTAATATTTTAGGT
1 AAAAATAATAATATTTTAGGT
9488 AAAAATAATAATATTTTAG
1 AAAAATAATAATATTTTAG
9507 ATATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (21 bp):
AAAAATAATAATATTTTAGGT
Found at i:10503 original size:3 final size:3
Alignment explanation
Indices: 10497--10535 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
10487 TTGGATTTAC
10497 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
10536 GATTAAAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:10733 original size:43 final size:43
Alignment explanation
Indices: 10685--10771 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
10675 CTTTTATGCC
10685 TTGTCTTAGGAAACCAAAGCTTTCTTTCAACATATCAAATCAT
1 TTGTCTTAGGAAACCAAAGCTTTCTTTCAACATATCAAATCAT
*
10728 TTGTCTTAGGAAACCAAAGCTTTCTTTTAACATATCAAATCAT
1 TTGTCTTAGGAAACCAAAGCTTTCTTTCAACATATCAAATCAT
10771 T
1 T
10772 ATTCATTAGC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.37
Consensus pattern (43 bp):
TTGTCTTAGGAAACCAAAGCTTTCTTTCAACATATCAAATCAT
Found at i:10766 original size:21 final size:21
Alignment explanation
Indices: 10699--10766 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
10689 CTTAGGAAAC
*
10699 CAAAGCTTTCTTTCAACATAT
1 CAAAGCTTTCTTTTAACATAT
* * * ** * *
10720 CAAATCATTTGTCTTAGGAAAC
1 CAAAGC-TTTCTTTTAACATAT
10742 CAAAGCTTTCTTTTAACATAT
1 CAAAGCTTTCTTTTAACATAT
10763 CAAA
1 CAAA
10767 TCATTATTCA
Statistics
Matches: 31, Mismatches: 15, Indels: 2
0.65 0.31 0.04
Matches are distributed among these distances:
21 18 0.58
22 13 0.42
ACGTcount: A:0.37, C:0.21, G:0.07, T:0.35
Consensus pattern (21 bp):
CAAAGCTTTCTTTTAACATAT
Found at i:13408 original size:24 final size:25
Alignment explanation
Indices: 13356--13422 Score: 100
Period size: 24 Copynumber: 2.7 Consensus size: 25
13346 ATGTGAAATT
* *
13356 TGTCCCAAATGACCTCTGTATACTA
1 TGTCCCAAAGGACCTGTGTATACTA
*
13381 TGTCCCGAAGGACCTGTGT-TACTA
1 TGTCCCAAAGGACCTGTGTATACTA
13405 TGTCCCAAAGGACCTGTG
1 TGTCCCAAAGGACCTGTG
13423 AAACCCTCGA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
24 22 0.58
25 16 0.42
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (25 bp):
TGTCCCAAAGGACCTGTGTATACTA
Found at i:22706 original size:24 final size:22
Alignment explanation
Indices: 22678--22750 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 22
22668 AAATAATAAA
22678 TTTAATATTTCTTTTATTTTAATT
1 TTTAATATTT-TTTTATTTT-ATT
*
22702 TTTAATTTTTATTCTTATTTTATT
1 TTTAATATTT-TT-TTATTTTATT
* *
22726 TTGTAGATAATTTTTTATTTGATT
1 TT-TA-ATATTTTTTTATTTTATT
22750 T
1 T
22751 GTAGGGACCA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
24 26 0.63
25 11 0.27
26 4 0.10
ACGTcount: A:0.23, C:0.03, G:0.04, T:0.70
Consensus pattern (22 bp):
TTTAATATTTTTTTATTTTATT
Found at i:25082 original size:18 final size:18
Alignment explanation
Indices: 25059--25107 Score: 98
Period size: 18 Copynumber: 2.7 Consensus size: 18
25049 ATGAAAGTAG
25059 TCATGGGATGACTTTCAT
1 TCATGGGATGACTTTCAT
25077 TCATGGGATGACTTTCAT
1 TCATGGGATGACTTTCAT
25095 TCATGGGATGACT
1 TCATGGGATGACT
25108 CTACTTAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.37
Consensus pattern (18 bp):
TCATGGGATGACTTTCAT
Found at i:28101 original size:23 final size:23
Alignment explanation
Indices: 28069--28136 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 23
28059 CACTTAATTC
*
28069 CTAATTAATAGTAAATTAAAAGTA
1 CTAA-TAATAGTAAATTAAAAATA
* *
28093 CTAATAATA-AATAATTAAAAATC
1 CTAATAATAGTA-AATTAAAAATA
*
28116 CTAAATAATAGTAAACTAAAA
1 CT-AATAATAGTAAATTAAAA
28137 TTCCATGCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
22 1 0.03
23 16 0.44
24 18 0.50
25 1 0.03
ACGTcount: A:0.59, C:0.07, G:0.04, T:0.29
Consensus pattern (23 bp):
CTAATAATAGTAAATTAAAAATA
Found at i:28137 original size:23 final size:23
Alignment explanation
Indices: 28067--28137 Score: 65
Period size: 23 Copynumber: 3.0 Consensus size: 23
28057 AACACTTAAT
*
28067 TCCTAATTAATAGTAAATTAAAA
1 TCCTAAATAATAGTAAATTAAAA
* *
28090 GTACT-AATAATA-AATAATTAAAAA
1 -TCCTAAATAATAGTA-AATT-AAAA
*
28114 TCCTAAATAATAGTAAACTAAAA
1 TCCTAAATAATAGTAAATTAAAA
28137 T
1 T
28138 TCCATGCAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
22 1 0.03
23 18 0.49
24 17 0.46
25 1 0.03
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.31
Consensus pattern (23 bp):
TCCTAAATAATAGTAAATTAAAA
Found at i:35062 original size:13 final size:13
Alignment explanation
Indices: 35044--35068 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35034 CGACTATCAT
35044 CATATTATGATAC
1 CATATTATGATAC
35057 CATATTATGATA
1 CATATTATGATA
35069 GTGAAAGAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (13 bp):
CATATTATGATAC
Found at i:43521 original size:20 final size:21
Alignment explanation
Indices: 43476--43529 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
43466 GTTGTTTGCT
*
43476 TTTTCTTTCGTTTCCCTCTGTT
1 TTTTCTTTC-TTTCCCTCTGTA
43498 TTTTCTTT-TTTCCCT-TGGTA
1 TTTTCTTTCTTTCCCTCT-GTA
*
43518 TTTTCCTTCTTT
1 TTTTCTTTCTTT
43530 TTTTTTCTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 1 0.04
20 16 0.57
21 3 0.11
22 8 0.29
ACGTcount: A:0.02, C:0.24, G:0.07, T:0.67
Consensus pattern (21 bp):
TTTTCTTTCTTTCCCTCTGTA
Found at i:44064 original size:14 final size:13
Alignment explanation
Indices: 44031--44076 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
44021 ATGTAATATT
44031 AATAATATT-AT-
1 AATAATATTAATA
*
44042 AATACTATTAATGA
1 AATAATATTAAT-A
44056 AATAATATTAATA
1 AATAATATTAATA
44069 TAATAATA
1 -AATAATA
44077 ATTATAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
11 8 0.28
12 2 0.07
13 1 0.03
14 18 0.62
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (13 bp):
AATAATATTAATA
Found at i:44078 original size:25 final size:25
Alignment explanation
Indices: 44031--44078 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
44021 ATGTAATATT
* *
44031 AATAATATTATAATACTATTAATGA
1 AATAATATTATAATAATAATAATGA
44056 AATAATATTA-ATATAATAATAAT
1 AATAATATTATA-ATAATAATAAT
44079 TATAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 19 0.95
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (25 bp):
AATAATATTATAATAATAATAATGA
Found at i:44373 original size:40 final size:41
Alignment explanation
Indices: 44229--44804 Score: 298
Period size: 40 Copynumber: 13.7 Consensus size: 41
44219 TTTTGTTGGT
* * ** *
44229 GGGGACGACACTGCTCATACGCAATGAAGAGGTCTGGTCATCTA
1 GGGGATGACACGGCTCATACGTGATGAAGAGATCTGG--ATC-A
* * *
44273 AGGG-TGACACGGCTCCTACGTGAT-AAG-GACGGCTGGTTATCTA
1 GGGGATGACACGGCTCATACGTGATGAAGAGA--TCTGG--ATC-A
* *
44316 -GGG-TGACACGGCCCATACGTGATGAAGAGGTCTGG-TC-
1 GGGGATGACACGGCTCATACGTGATGAAGAGATCTGGATCA
*
44353 GGGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAA
1 GGGG-ATGACACGGCTCATACGTGATGAAGAGATCTGG--ATC---A
* * * * * * *
44400 GGTGATAACACGGTTCCTACGTGTTGAGGACG-GCTGGTTATCTA
1 GGGGATGACACGGCTCATACGTGATGAAGA-GATCTGG--ATC-A
44444 -GGG-TGACACGGCTCATACGTGATGAAGAGATCTGG-TC-
1 GGGGATGACACGGCTCATACGTGATGAAGAGATCTGGATCA
*
44481 GGGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAA
1 GGGG-ATGACACGGCTCATACGTGATGAAGAGATCTGG--ATC---A
* * * * * * *
44528 GGTGATAACACAGTTCCTACGTGATGAGGACG-GCTGGTTATCTA
1 GGGGATGACACGGCTCATACGTGATGAAGA-GATCTGG--ATC-A
44572 -GGG-TGACACGGCTCATACGTGATGAAGAGATCTGG-TC-
1 GGGGATGACACGGCTCATACGTGATGAAGAGATCTGGATCA
*
44609 GGGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAA
1 GGGG-ATGACACGGCTCATACGTGATGAAGAGATCTGG--ATC---A
* * * * * *
44656 GGTGATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTA
1 GGGGATGACACGGCTCATACGTGATGAAGA-GATCTGG--ATC-A
*
44700 -GGG-TGACACGGCTCATACGTGATTAAGAGATCTGG-TC-
1 GGGGATGACACGGCTCATACGTGATGAAGAGATCTGGATCA
44737 GGGGAATGACACGGCTCATACGTGATGAAGAGATCTGG-TCA
1 GGGG-ATGACACGGCTCATACGTGATGAAGAGATCTGGATCA
* * * *
44778 GAGGATGACACGGTTCCTATGTGATGA
1 GGGGATGACACGGCTCATACGTGATGA
44805 GGACTACTGG
Statistics
Matches: 416, Mismatches: 72, Indels: 92
0.72 0.12 0.16
Matches are distributed among these distances:
38 12 0.03
39 8 0.02
40 145 0.35
41 7 0.02
42 100 0.24
43 40 0.10
44 7 0.02
46 85 0.20
47 12 0.03
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.23
Consensus pattern (41 bp):
GGGGATGACACGGCTCATACGTGATGAAGAGATCTGGATCA
Found at i:44461 original size:128 final size:128
Alignment explanation
Indices: 44235--44774 Score: 933
Period size: 128 Copynumber: 4.2 Consensus size: 128
44225 TGGTGGGGAC
* ** * * * *
44235 GACACTGCTCATACGCAATGAAGAGGTCTGGTCATCT-AAGG-G-TGACACGGCTCCTACGTGAT
1 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGAT
* * *
44297 AAGGACGGCTGGTTATCTAGGGTGACACGGCCCATACGTGATGAAGAGGTCTGGTCGGGGAAT
66 GAGGACGGCTGGTTATCTAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAAT
*
44360 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGTT
1 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGAT
44425 GAGGACGGCTGGTTATCTAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAAT
66 GAGGACGGCTGGTTATCTAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAAT
*
44488 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACAGTTCCTACGTGAT
1 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGAT
44553 GAGGACGGCTGGTTATCTAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAAT
66 GAGGACGGCTGGTTATCTAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAAT
44616 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGAT
1 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGAT
*
44681 GAGGACGGCTGGTTATCTAGGGTGACACGGCTCATACGTGATTAAGAGATCTGGTCGGGGAAT
66 GAGGACGGCTGGTTATCTAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAAT
*
44744 GACACGGCTCATACGTGATGAAGAGATCTGG
1 GACACGGCTCATACGTGATGAAGAGTTCTGG
44775 TCAGAGGATG
Statistics
Matches: 396, Mismatches: 16, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
125 32 0.08
126 4 0.01
127 1 0.00
128 359 0.91
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.23
Consensus pattern (128 bp):
GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGAT
GAGGACGGCTGGTTATCTAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAAT
Found at i:44463 original size:88 final size:87
Alignment explanation
Indices: 44236--44775 Score: 316
Period size: 82 Copynumber: 6.4 Consensus size: 87
44226 GGTGGGGACG
* ** * *
44236 ACACTGCTCATACGCAATGAAGAG-GTCTGGTCATCTAAGGG-TGACACGGCTCCTACGTGAT-A
1 ACACGGCTCATACGTGATGAAGAGAG-CTGGTTATCT-AGGGATGACACGGCTCATACGTGATGA
* ** *
44298 AG-GACGGCTGGTTATCTAGG-G-TG
64 AGAGA--TCTGGCCATCTAGGTGATA
* *
44321 ACACGGCCCATACGTGATGAAGAG-GTCTGG---TC-GGGGAATGACACGGCTCATACGTGATGA
1 ACACGGCTCATACGTGATGAAGAGAG-CTGGTTATCTAGGG-ATGACACGGCTCATACGTGATGA
*
44381 AGAGTTCTGGCCATCTAAAGGTGATA
64 AGAGATCTGGCCATCT--AGGTGATA
* * * *
44407 ACACGGTTCCTACGTGTTGAGGACG-GCTGGTTATCTAGGG-TGACACGGCTCATACGTGATGAA
1 ACACGGCTCATACGTGATGAAGA-GAGCTGGTTATCTAGGGATGACACGGCTCATACGTGATGAA
* *
44470 GAGATCTGG---TC--GGGGAATG
65 GAGATCTGGCCATCTAGGTG-ATA
** ** * * * *
44489 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACAGTTCCTACGTGATG
1 ACACGGCTCATACGTGATGAAGAGAGCTGGTTATCT--AGG-GATGACACGGCTCATACGTGATG
* * ** *
44554 AGGACG-GCTGGTTATCTAGG-G-TG
63 AAGA-GATCTGGCCATCTAGGTGATA
* *
44577 ACACGGCTCATACGTGATGAAGAGATCTGG---TC-GGGGAATGACACGGCTCATACGTGATGAA
1 ACACGGCTCATACGTGATGAAGAGAGCTGGTTATCTAGGG-ATGACACGGCTCATACGTGATGAA
*
44638 GAGTTCTGGCCATCTAAAGGTGATA
65 GAGATCTGGCCATCT--AGGTGATA
* * * *
44663 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTAGGG-TGACACGGCTCATACGTGATTAA
1 ACACGGCTCATACGTGATGAAGA-GAGCTGGTTATCTAGGGATGACACGGCTCATACGTGATGAA
* *
44726 GAGATCTGG---TC--GGGGAATG
65 GAGATCTGGCCATCTAGGTG-ATA
*
44745 ACACGGCTCATACGTGATGAAGAGATCTGGT
1 ACACGGCTCATACGTGATGAAGAGAGCTGGT
44776 CAGAGGATGA
Statistics
Matches: 360, Mismatches: 57, Indels: 79
0.73 0.11 0.16
Matches are distributed among these distances:
80 3 0.01
81 10 0.03
82 116 0.32
83 3 0.01
84 10 0.03
85 35 0.10
86 72 0.20
87 4 0.01
88 92 0.26
89 6 0.02
90 7 0.02
91 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.23
Consensus pattern (87 bp):
ACACGGCTCATACGTGATGAAGAGAGCTGGTTATCTAGGGATGACACGGCTCATACGTGATGAAG
AGATCTGGCCATCTAGGTGATA
Found at i:45199 original size:35 final size:36
Alignment explanation
Indices: 45158--45253 Score: 108
Period size: 36 Copynumber: 2.7 Consensus size: 36
45148 ACAAAATTCA
**
45158 TTTCAAGAGAAACGATCTCAAAGAT-GTTTATTTTG
1 TTTCAAGAGAAACGATCTCAAAGATGGTAAATTTTG
*
45193 TTTCAAGGGAAACAGAT-TCAAAGATGGTAAATTTTG
1 TTTCAAGAGAAAC-GATCTCAAAGATGGTAAATTTTG
* *
45229 TTTCCAA-AGAAACAAACTCAAAGAT
1 TTT-CAAGAGAAACGATCTCAAAGAT
45254 TTTTCTCAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
35 21 0.41
36 27 0.53
37 3 0.06
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (36 bp):
TTTCAAGAGAAACGATCTCAAAGATGGTAAATTTTG
Found at i:45517 original size:15 final size:15
Alignment explanation
Indices: 45497--45534 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
45487 ATCTTGTTTT
45497 AAGAGAAAATGCTTC
1 AAGAGAAAATGCTTC
*
45512 AAGAGAAAATGTTTC
1 AAGAGAAAATGCTTC
*
45527 AAGTGAAA
1 AAGAGAAA
45535 CGACTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.50, C:0.08, G:0.21, T:0.21
Consensus pattern (15 bp):
AAGAGAAAATGCTTC
Found at i:45587 original size:31 final size:30
Alignment explanation
Indices: 45523--45597 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 30
45513 AGAGAAAATG
*
45523 TTTCAAGTGAAACGACTCAAAAATGGTTTTA
1 TTTCAAGTGAAACAACTCAAAAAT-GTTTTA
*
45554 TTTCAAGTGAAACAAACTCAAAGAT-TTTGTA
1 TTTCAAGTGAAAC-AACTCAAAAATGTTT-TA
* *
45585 TTTCTAGAGAAAC
1 TTTCAAGTGAAAC
45598 TGCCTCAAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 3 0.08
31 26 0.68
32 9 0.24
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (30 bp):
TTTCAAGTGAAACAACTCAAAAATGTTTTA
Found at i:45700 original size:40 final size:40
Alignment explanation
Indices: 45630--45709 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
45620 GTTTTAATAA
45630 AAACAATCTCAAAGGTAGGTAGTTTTAAAAGAAATTGTCT
1 AAACAATCTCAAAGGTAGGTAGTTTTAAAAGAAATTGTCT
* * *
45670 AAACGATCTCAAAGGTGGGTA-TTTTCAAAAGAAGTTGTCT
1 AAACAATCTCAAAGGTAGGTAGTTTT-AAAAGAAATTGTCT
45710 CGAGAGACAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 4 0.11
40 32 0.89
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (40 bp):
AAACAATCTCAAAGGTAGGTAGTTTTAAAAGAAATTGTCT
Found at i:45802 original size:63 final size:62
Alignment explanation
Indices: 45691--45814 Score: 167
Period size: 63 Copynumber: 2.0 Consensus size: 62
45681 AAGGTGGGTA
* * * *
45691 TTTTCAAAAGAAGTTGTCTCGAGAGACAAAGTTTTGTTTCAAAGGAAACAAACTCAAAGATT
1 TTTTCAAAAGAAATTGTCTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATT
* * **
45753 TTTTCAAAAGAAATTGTCTTTAAGAGATAAAATTTTGTTTCAAAAGAAACGGACTCAAAGAT
1 TTTTCAAAAGAAATTGTC-TCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGAT
45815 GGATCACATC
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
62 17 0.32
63 36 0.68
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (62 bp):
TTTTCAAAAGAAATTGTCTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATT
Found at i:46080 original size:64 final size:64
Alignment explanation
Indices: 45982--46191 Score: 237
Period size: 67 Copynumber: 3.2 Consensus size: 64
45972 ATGAACATAT
** * * * * * *
45982 TCAAAGATTTACTTCAAGAGAAACTGTCTCAAGAGATACAAAATTCAT-TTT-AAGAGAAACAGA
1 TCAAAGATTTTTTTCAAAAGAAATTATCTTAAGAGATACAAAATT-TTGTTTCAA-AGAAACAAA
*
46045 T
64 C
*
46046 TCAAAGATTTTTTTCAAAAGAAATTATTTTAAGAG-TGACAAAATTTTGTTTCCAAAGAAACAAA
1 TCAAAGATTTTTTTCAAAAGAAATTATCTTAAGAGAT-ACAAAATTTTGTTT-CAAAGAAACAAA
46110 C
64 C
*
46111 TCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAA
1 TCAAAGA-TTTT-TTTCAAAAGAAATTATCTTAAGAGATACAAAATTTTGTTT-CAAAGAAACAA
46176 AC
63 AC
46178 TCAAAGATTTTTTT
1 TCAAAGATTTTTTT
46192 TTTTCAAAAG
Statistics
Matches: 127, Mismatches: 12, Indels: 13
0.84 0.08 0.09
Matches are distributed among these distances:
63 2 0.02
64 39 0.31
65 18 0.14
66 10 0.08
67 58 0.46
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (64 bp):
TCAAAGATTTTTTTCAAAAGAAATTATCTTAAGAGATACAAAATTTTGTTTCAAAGAAACAAAC
Found at i:46103 original size:37 final size:37
Alignment explanation
Indices: 46047--46172 Score: 103
Period size: 37 Copynumber: 3.6 Consensus size: 37
46037 GAAACAGATT
46047 CAAAGATTTT-TTTCAAAAGAAATTATTTTAAGAGTGA
1 CAAAGATTTTGTTTCAAAAGAAATTA-TTTAAGAGTGA
* * *
46084 CAAA-ATTTTGTTTCCAAAG-AA--A--CAA-ACT--
1 CAAAGATTTTGTTTCAAAAGAAATTATTTAAGAGTGA
*
46112 CAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGA
1 CAAAGA-TTTTGTTTCAAAAGAAATTAT-TTAAGAGTGA
*
46151 CAAA-ATTTTGTTTCCAAAGAAA
1 CAAAGATTTTGTTTCAAAAGAAA
46173 CAAACTCAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 24
0.68 0.08 0.24
Matches are distributed among these distances:
28 4 0.06
29 1 0.01
30 15 0.22
31 4 0.06
33 1 0.01
34 1 0.01
36 9 0.13
37 29 0.42
38 1 0.01
39 4 0.06
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.33
Consensus pattern (37 bp):
CAAAGATTTTGTTTCAAAAGAAATTATTTAAGAGTGA
Found at i:46145 original size:67 final size:66
Alignment explanation
Indices: 46036--46192 Score: 262
Period size: 67 Copynumber: 2.4 Consensus size: 66
46026 TCATTTTAAG
* * * *
46036 AGAAACAGATTCAAAGA-TTTTTTTCAAAAGAAATTATTTTAAGAGTGACAAAATTTTGTTTCCA
1 AGAAACAAACTCAAAGATTTTTTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCA
46100 A
66 A
46101 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAAACTCAAAGATTTTT-TTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
46166 AA
65 AA
46168 AGAAACAAACTCAAAGATTTTTTTT
1 AGAAACAAACTCAAAGATTTTTTTT
46193 TTTCAAAAGA
Statistics
Matches: 86, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
65 15 0.17
66 7 0.08
67 64 0.74
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (66 bp):
AGAAACAAACTCAAAGATTTTTTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCA
A
Found at i:46202 original size:32 final size:32
Alignment explanation
Indices: 46089--46223 Score: 112
Period size: 32 Copynumber: 4.1 Consensus size: 32
46079 AGTGACAAAA
*
46089 TTTTGTTTCCAAAGAAACAAACTCAAAGA--T
1 TTTTGTTTCAAAAGAAACAAACTCAAAGATTT
** * * ***
46119 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
1 TTTTGTTTCAAAAGAAACAAAC-TCA-A-AG--ATTT
*
46156 TTTTGTTTCCAAAGAAACAAACTCAAAGATTT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGATTT
* *
46188 TTTTTTTTCAAAAGAAACAATCTCAAAGATTT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGATTT
46220 TTTT
1 TTTT
46224 CACAAAATTG
Statistics
Matches: 81, Mismatches: 17, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
30 18 0.22
31 2 0.02
32 35 0.43
33 2 0.02
34 2 0.02
35 2 0.02
36 2 0.02
37 18 0.22
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (32 bp):
TTTTGTTTCAAAAGAAACAAACTCAAAGATTT
Found at i:46290 original size:52 final size:53
Alignment explanation
Indices: 46209--46312 Score: 174
Period size: 52 Copynumber: 2.0 Consensus size: 53
46199 AAGAAACAAT
*
46209 CTCAAAGATTTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
1 CTCAAAGA-TTTTCTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
*
46263 CTCAAAGA-TTTCTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
1 CTCAAAGATTTTCTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
46313 AAATAAATAG
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
52 40 0.83
54 8 0.17
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (53 bp):
CTCAAAGATTTTCTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
Found at i:46357 original size:27 final size:28
Alignment explanation
Indices: 46308--46431 Score: 144
Period size: 29 Copynumber: 4.4 Consensus size: 28
46298 CAAAACTTTG
* * *
46308 TTTCAAAATAAATAGACTCAAAGATTTT
1 TTTCAAAAGAAACAAACTCAAAGATTTT
*
46336 TTTCAAACGAAAC-AACTCAAAGATTTT
1 TTTCAAAAGAAACAAACTCAAAGATTTT
* *
46363 TATTCAAAAGGAACAAACTCCAAGATTTCT
1 T-TTCAAAAGAAACAAACTCAAAGATTT-T
* *
46393 ATTCAAAAGGAACAAACTCAAAGA-TTT
1 TTTCAAAAGAAACAAACTCAAAGATTTT
46420 TTTCAAAAGAAA
1 TTTCAAAAGAAA
46432 TTGTCTTTAA
Statistics
Matches: 82, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
27 25 0.30
28 22 0.27
29 34 0.41
30 1 0.01
ACGTcount: A:0.48, C:0.15, G:0.09, T:0.28
Consensus pattern (28 bp):
TTTCAAAAGAAACAAACTCAAAGATTTT
Found at i:46420 original size:58 final size:54
Alignment explanation
Indices: 46323--46428 Score: 140
Period size: 56 Copynumber: 1.9 Consensus size: 54
46313 AAATAAATAG
* *
46323 ACTCAAAGATTTTTTTCAAACGAAACAACTCAAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTATTCAAAAGAAACAACTCAAAGA-TTTT-TTCAAAAGGAACAA
* *
46379 ACTCCAAGATTTCTATTCAAAAGGAACAAACTCAAAGATTTTTTCAAAAG
1 ACTCAAAGATTT-TATTCAAAAGAAAC-AACTCAAAGATTTTTTCAAAAG
46429 AAATTGTCTT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
56 19 0.43
57 15 0.34
58 10 0.23
ACGTcount: A:0.45, C:0.17, G:0.09, T:0.28
Consensus pattern (54 bp):
ACTCAAAGATTTTATTCAAAAGAAACAACTCAAAGATTTTTTCAAAAGGAACAA
Found at i:46754 original size:36 final size:35
Alignment explanation
Indices: 46670--46767 Score: 117
Period size: 36 Copynumber: 2.8 Consensus size: 35
46660 GAGAAAATGA
* * *
46670 TGTCTCAAGCGAGACGAAATTTG-CTTTAAGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAAAT
* **
46704 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTA-AGAAAT
*
46740 TGTCTCAAGCGAGACAAAGTTTGTTTTT
1 TGTCTCAAGCGAGACAAAATTTGTTTTT
46768 GAGGAAACGA
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
34 19 0.37
35 4 0.08
36 29 0.56
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (35 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAAAT
Found at i:46782 original size:36 final size:36
Alignment explanation
Indices: 46671--46789 Score: 111
Period size: 36 Copynumber: 3.4 Consensus size: 36
46661 AGAAAATGAT
* * * *
46671 GTCTCAAGCGAGACGAAATTTG-CTTTA-AGATATA
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAATC
** *
46705 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAATC
*
46741 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGGAAA-C
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGA-GAAATC
*
46776 GATCTCAAGTGAGA
1 G-TCTCAAGCGAGA
46790 TCAACTTTGT
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
34 19 0.27
35 7 0.10
36 44 0.63
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (36 bp):
GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAATC
Found at i:46929 original size:105 final size:105
Alignment explanation
Indices: 46784--46973 Score: 283
Period size: 105 Copynumber: 1.8 Consensus size: 105
46774 ACGATCTCAA
* *
46784 GTGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAGGTCTCA
1 GTGAGATCAACTTTGTTTAATGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAGGTCTCA
46849 AGCGAGACGAAATTTGTTTTGAAAGAAACAACAATCTAAG
66 AGCGAGACGAAATTTGTTTTGAAAGAAACAACAATCTAAG
* * * * * *
46889 GTGAGATTAATTTTGTTTTAA-GTTAATCAAATTCAAAATTTGTATCTCAAAGGAAAAATGTCTC
1 GTGAGATCAACTTTG-TTTAATGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAGGTCTC
*
46953 AAGCGAGACGAAGTTTGTTTT
65 AAGCGAGACGAAATTTGTTTT
46974 AAGAGAATTT
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
105 70 0.93
106 5 0.07
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (105 bp):
GTGAGATCAACTTTGTTTAATGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAGGTCTCA
AGCGAGACGAAATTTGTTTTGAAAGAAACAACAATCTAAG
Found at i:46987 original size:36 final size:36
Alignment explanation
Indices: 46947--47083 Score: 143
Period size: 36 Copynumber: 3.8 Consensus size: 36
46937 AAAGGAAAAA
* * *
46947 TGTCTCAAGCGAGACGAAGTTTGTTTTAAGAGAATT
1 TGTCTCAAGCGAGACAAAATTTGTTTTAAGAGAAAT
** * **
46983 TGTCTCAAATGAGACAAAATTTGTTTTTAGA-AAGC
1 TGTCTCAAGCGAGACAAAATTTGTTTTAAGAGAAAT
* * *
47018 TGTTTCAAGCGAGACAAAATTTACTTTGAA-AGAAAT
1 TGTCTCAAGCGAGACAAAATTT-GTTTTAAGAGAAAT
47054 TGTCTCAAGCGAGACAAAAATTTGTTTTAA
1 TGTCTCAAGCGAGAC-AAAATTTGTTTTAA
47084 AATTCTCAAA
Statistics
Matches: 80, Mismatches: 18, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
35 22 0.28
36 51 0.64
37 7 0.09
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTAAGAGAAAT
Found at i:47447 original size:18 final size:19
Alignment explanation
Indices: 47426--47482 Score: 73
Period size: 18 Copynumber: 3.1 Consensus size: 19
47416 ATGCAAATTT
47426 TATGTATTATGTAT-TATG
1 TATGTATTATGTATATATG
*
47444 TATGTA-TGTGTATATATG
1 TATGTATTATGTATATATG
*
47462 TATGTATGTATGTATGTATG
1 TATGTAT-TATGTATATATG
47482 T
1 T
47483 TTTCTCGATC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 6 0.18
18 16 0.48
20 11 0.33
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.53
Consensus pattern (19 bp):
TATGTATTATGTATATATG
Found at i:47449 original size:4 final size:4
Alignment explanation
Indices: 47426--47482 Score: 77
Period size: 4 Copynumber: 15.2 Consensus size: 4
47416 ATGCAAATTT
*
47426 TATG TAT- TATG TAT- TATG TATG TATG --TG TATA TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
47470 TATG TATG TATG T
1 TATG TATG TATG T
47483 TTTCTCGATC
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
2 2 0.04
3 6 0.13
4 39 0.83
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.53
Consensus pattern (4 bp):
TATG
Found at i:47811 original size:23 final size:24
Alignment explanation
Indices: 47767--47811 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
47757 GTCTGAAAAT
*
47767 ATCAATAGTTTTGAAAAATATTTA
1 ATCAAAAGTTTTGAAAAATATTTA
47791 ATCAAAAGTTTTG-AAAATATT
1 ATCAAAAGTTTTGAAAAATATT
47812 GCTCCTTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (24 bp):
ATCAAAAGTTTTGAAAAATATTTA
Found at i:49329 original size:26 final size:24
Alignment explanation
Indices: 49299--49369 Score: 78
Period size: 20 Copynumber: 3.0 Consensus size: 24
49289 CAAGGTGGAA
49299 AGAATATTTCAAGGTCTCAAAGAG
1 AGAATATTTCAAGGTCTCAAAGAG
* *
49323 AGGGAATGTTTCAAGG--TCGAA-A-
1 A--GAATATTTCAAGGTCTCAAAGAG
49345 AGAATATTTCAAGGTCTCAAAGAG
1 AGAATATTTCAAGGTCTCAAAGAG
49369 A
1 A
49370 TAGAATGTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
20 12 0.32
22 5 0.14
23 2 0.05
24 6 0.16
26 12 0.32
ACGTcount: A:0.41, C:0.11, G:0.24, T:0.24
Consensus pattern (24 bp):
AGAATATTTCAAGGTCTCAAAGAG
Found at i:49354 original size:20 final size:20
Alignment explanation
Indices: 49286--49360 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 20
49276 AAATACAGTG
*
49286 TTTCAAGGT-GGAAAGAATA
1 TTTCAAGGTCGAAAAGAATA
* *
49305 TTTCAAGGTCTCAAAGAGAGGGAATG
1 TTTCAAGG--TCGAA-A-A--GAATA
49331 TTTCAAGGTCGAAAAGAATA
1 TTTCAAGGTCGAAAAGAATA
49351 TTTCAAGGTC
1 TTTCAAGGTC
49361 TCAAAGAGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
19 8 0.18
20 14 0.32
21 1 0.02
22 2 0.05
23 2 0.05
24 5 0.11
26 12 0.27
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.27
Consensus pattern (20 bp):
TTTCAAGGTCGAAAAGAATA
Found at i:49374 original size:26 final size:26
Alignment explanation
Indices: 49296--49375 Score: 82
Period size: 26 Copynumber: 3.3 Consensus size: 26
49286 TTTCAAGGTG
49296 GAAAGAATATTTCAAGGTCTCAAAGA
1 GAAAGAATATTTCAAGGTCTCAAAGA
** *
49322 GAGGGAATGTTTCAAGG--TC---GA
1 GAAAGAATATTTCAAGGTCTCAAAGA
49343 -AAAGAATATTTCAAGGTCTCAAAGA
1 GAAAGAATATTTCAAGGTCTCAAAGA
*
49368 GATAGAAT
1 GAAAGAAT
49376 GTCAAAATTT
Statistics
Matches: 41, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
20 13 0.32
21 2 0.05
22 2 0.05
24 2 0.05
25 2 0.05
26 20 0.49
ACGTcount: A:0.42, C:0.10, G:0.24, T:0.24
Consensus pattern (26 bp):
GAAAGAATATTTCAAGGTCTCAAAGA
Found at i:49376 original size:46 final size:45
Alignment explanation
Indices: 49284--49377 Score: 152
Period size: 46 Copynumber: 2.1 Consensus size: 45
49274 ATAAATACAG
* *
49284 TGTTTCAAGGTGGAAAGAATATTTCAAGGTCTCAAAGAGAGGGAA
1 TGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
*
49329 TGTTTCAAGGTCGAAAAGAATATTTCAAGGTCTCAAAGAGATAGAA
1 TGTTTCAAGGT-GAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
49375 TGT
1 TGT
49378 CAAAATTTGG
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
45 11 0.24
46 34 0.76
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.27
Consensus pattern (45 bp):
TGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
Found at i:50623 original size:31 final size:32
Alignment explanation
Indices: 50567--50628 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
50557 TGACAAAATG
50567 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
50599 ACACAAACAAAAGAGAA-AAATAAGTTAGTA
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTA
50629 CATGTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:52180 original size:22 final size:22
Alignment explanation
Indices: 52137--52180 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
52127 AAATTTACAT
*
52137 TCACATAAAATAAAATAAATTG
1 TCACATAAAATAAAACAAATTG
* * *
52159 TCACTTAAAATAACACACATTG
1 TCACATAAAATAAAACAAATTG
52181 CATCGTTTGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.27
Consensus pattern (22 bp):
TCACATAAAATAAAACAAATTG
Found at i:53886 original size:20 final size:21
Alignment explanation
Indices: 53841--53894 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
53831 GTTGTTTGCT
*
53841 TTTTCTTTCGTTTCCCTCTGTT
1 TTTTCTTTC-TTTCCCTCTGTA
53863 TTTTCTTT-TTTCCCT-TGGTA
1 TTTTCTTTCTTTCCCTCT-GTA
*
53883 TTTTCCTTCTTT
1 TTTTCTTTCTTT
53895 TTTTTTCTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 1 0.04
20 16 0.57
21 3 0.11
22 8 0.29
ACGTcount: A:0.02, C:0.24, G:0.07, T:0.67
Consensus pattern (21 bp):
TTTTCTTTCTTTCCCTCTGTA
Found at i:54429 original size:14 final size:13
Alignment explanation
Indices: 54396--54441 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
54386 ATGTAATATT
54396 AATAATATT-AT-
1 AATAATATTAATA
*
54407 AATACTATTAATGA
1 AATAATATTAAT-A
54421 AATAATATTAATA
1 AATAATATTAATA
54434 TAATAATA
1 -AATAATA
54442 ATTATAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
11 8 0.28
12 2 0.07
13 1 0.03
14 18 0.62
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (13 bp):
AATAATATTAATA
Found at i:54443 original size:25 final size:25
Alignment explanation
Indices: 54396--54443 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
54386 ATGTAATATT
* *
54396 AATAATATTATAATACTATTAATGA
1 AATAATATTATAATAATAATAATGA
54421 AATAATATTA-ATATAATAATAAT
1 AATAATATTATA-ATAATAATAAT
54444 TATAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 19 0.95
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (25 bp):
AATAATATTATAATAATAATAATGA
Found at i:58245 original size:21 final size:21
Alignment explanation
Indices: 58219--58281 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
58209 AACATTGATC
*
58219 CAAAGCTTCCAATCAACAGGA
1 CAAAGCTTCCAATCAACAAGA
*
58240 CAAAGCTTCCAATTAACAAGA
1 CAAAGCTTCCAATCAACAAGA
*
58261 CAAAGCTTCCCATCAA-AAGA
1 CAAAGCTTCCAATCAACAAGA
58281 C
1 C
58282 CAACAATTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
20 5 0.13
21 33 0.87
ACGTcount: A:0.44, C:0.29, G:0.11, T:0.16
Consensus pattern (21 bp):
CAAAGCTTCCAATCAACAAGA
Found at i:58596 original size:37 final size:40
Alignment explanation
Indices: 58554--58665 Score: 158
Period size: 41 Copynumber: 2.9 Consensus size: 40
58544 CATTACAAGA
* * *
58554 AACATTAAAAGAAACAAATTTCCTTCCACAACAACT-A-C
1 AACATTACAAGAAATAAATTTCCTTCAACAACAACTAACC
*
58592 -ACATTACAAGAAATAAATTTCCTTCAACAAAAACTACACC
1 AACATTACAAGAAATAAATTTCCTTCAACAACAACTA-ACC
58632 AACATTACAAGAAATAAATTTCCTTCAACAACAA
1 AACATTACAAGAAATAAATTTCCTTCAACAACAA
58666 TTGTCTTACC
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
37 31 0.48
39 1 0.02
40 1 0.02
41 32 0.49
ACGTcount: A:0.51, C:0.24, G:0.03, T:0.22
Consensus pattern (40 bp):
AACATTACAAGAAATAAATTTCCTTCAACAACAACTAACC
Found at i:58649 original size:41 final size:38
Alignment explanation
Indices: 58554--58662 Score: 148
Period size: 37 Copynumber: 2.8 Consensus size: 38
58544 CATTACAAGA
* * * *
58554 AACATTAAAAGAAACAAATTTCCTTCCACAACAACTAC
1 AACATTACAAGAAATAAATTTCCTTCAACAAAAACTAC
58592 -ACATTACAAGAAATAAATTTCCTTCAACAAAAACTACACC
1 AACATTACAAGAAATAAATTTCCTTCAACAAAAACT--A-C
58632 AACATTACAAGAAATAAATTTCCTTCAACAA
1 AACATTACAAGAAATAAATTTCCTTCAACAA
58663 CAATTGTCTT
Statistics
Matches: 63, Mismatches: 4, Indels: 5
0.88 0.06 0.07
Matches are distributed among these distances:
37 31 0.49
39 1 0.02
40 1 0.02
41 30 0.48
ACGTcount: A:0.50, C:0.24, G:0.03, T:0.23
Consensus pattern (38 bp):
AACATTACAAGAAATAAATTTCCTTCAACAAAAACTAC
Found at i:68362 original size:2 final size:2
Alignment explanation
Indices: 68357--68391 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
68347 AAGTGTGTAC
68357 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
68392 GTTCTCTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:71551 original size:23 final size:23
Alignment explanation
Indices: 71508--71567 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
71498 TAACAAATAT
71508 GTGTCACAAAGAC--AGATAAAC
1 GTGTCACAAAGACAAAGATAAAC
*
71529 GTGTCATAAAGACAAAGATAAAC
1 GTGTCACAAAGACAAAGATAAAC
* *
71552 ATATCACAAAGACAAA
1 GTGTCACAAAGACAAA
71568 ATTATTCTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.36
23 21 0.64
ACGTcount: A:0.53, C:0.17, G:0.15, T:0.15
Consensus pattern (23 bp):
GTGTCACAAAGACAAAGATAAAC
Found at i:71827 original size:2 final size:2
Alignment explanation
Indices: 71820--71893 Score: 134
Period size: 2 Copynumber: 38.0 Consensus size: 2
71810 AAAATCAAAC
71820 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
71862 AT AT AT AT AT AT AT AT AT AT -T AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
71894 TAAATTATCA
Statistics
Matches: 70, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.03
2 68 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:74109 original size:10 final size:10
Alignment explanation
Indices: 74096--74148 Score: 52
Period size: 10 Copynumber: 5.0 Consensus size: 10
74086 TAAAAATAAT
74096 TATATGTATA
1 TATATGTATA
74106 TATATGTATA
1 TATATGTATA
*
74116 TATATAATAATA
1 TATAT-GT-ATA
* *
74128 CTCTATATATA
1 -TATATGTATA
74139 TATATGTATA
1 TATATGTATA
74149 ATTAAATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
10 23 0.64
11 4 0.11
12 5 0.14
13 4 0.11
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (10 bp):
TATATGTATA
Found at i:75322 original size:15 final size:15
Alignment explanation
Indices: 75304--75358 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 15
75294 TGAAATGTAA
75304 ATAAATATATATATT
1 ATAAATATATATATT
*
75319 ATAACT-TATAATATT
1 ATAAATATAT-ATATT
*
75334 ATATA-ATA-ATATT
1 ATAAATATATATATT
*
75347 ATATATATATAT
1 ATAAATATATAT
75359 TTAAGCGGTC
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
13 10 0.30
14 6 0.18
15 17 0.52
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
ATAAATATATATATT
Found at i:75358 original size:13 final size:14
Alignment explanation
Indices: 75308--75359 Score: 58
Period size: 13 Copynumber: 3.9 Consensus size: 14
75298 ATGTAAATAA
75308 ATATAT-ATATTAT
1 ATATATAATATTAT
75321 A-ACTTATAATATTAT
1 ATA--TATAATATTAT
75336 ATA-ATAATATTAT
1 ATATATAATATTAT
75349 ATATAT-ATATT
1 ATATATAATATT
75360 TAAGCGGTCG
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
12 1 0.03
13 19 0.56
14 5 0.15
15 8 0.24
16 1 0.03
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (14 bp):
ATATATAATATTAT
Found at i:76306 original size:124 final size:120
Alignment explanation
Indices: 75990--76343 Score: 462
Period size: 124 Copynumber: 2.9 Consensus size: 120
75980 TCCAATGCTA
*
75990 CTTGT-GAGCACGATATCCTTCATCATGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTT
1 CTTGTGGA-CACGATATCCTTCGTCATGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTT
* * *
76054 GAGCCTTGAATTGGATATCTTTCGTCGTGAAGTTGAAATCCAA-GTATTGTATATTG
65 GAGCCTTGAATTGGATATCTTT-GTCGTGAAGTTGAAATCCAATCTAATGAATATTG
* ** * * *
76110 CTTGTGGGCATAATATCCTTCGTAATGAAGTTGAAATCGTGGATGACCCCTTTGTTGTGAAGTTG
1 CTTGTGGACACGATATCCTTCGTCATGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTG
* *
76175 AGCCTTGAATTGGATATCATTTGTCGTGAAGTTAAAATCCAATCTAAAGATGAATGTTG
66 AGCCTTGAATTGGATATC-TTTGTCGTGAAGTTGAAATCCAATCT--A-ATGAATATTG
* * * *
76234 -TTGGTGGACACGATATCCTTCGTCGTGAAGTTGAAATCATGGATGGCTCCTTCATTGTGAAGTT
1 CTT-GTGGACACGATATCCTTCGTCATGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTT
*
76298 GAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCT
65 GAGCCTTGAATTGGATAT-CTTTGTCGTGAAGTTGAAATCCAATCT
76344 TTGTTTCACC
Statistics
Matches: 202, Mismatches: 24, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
120 93 0.46
121 5 0.02
123 3 0.01
124 100 0.50
125 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.34
Consensus pattern (120 bp):
CTTGTGGACACGATATCCTTCGTCATGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTG
AGCCTTGAATTGGATATCTTTGTCGTGAAGTTGAAATCCAATCTAATGAATATTG
Done.