Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002351.1 Hibiscus syriacus cultivar Beakdansim tig00004796_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: 71320
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1047 original size:11 final size:11
Alignment explanation
Indices: 1029--1114 Score: 68
Period size: 11 Copynumber: 7.8 Consensus size: 11
1019 CATATAAACT
1029 AACACTAAATG
1 AACACTAAATG
* *
1040 AACTCTAAA-C
1 AACACTAAATG
1050 AAGCACTAAATG
1 AA-CACTAAATG
* *
1062 AACTCTAAACG
1 AACACTAAATG
*
1073 AACACTAAA-C
1 AACACTAAATG
*
1083 AAGCACTAAACG
1 AA-CACTAAATG
*
1095 AACACTGAATG
1 AACACTAAATG
*
1106 AACGCTAAA
1 AACACTAAA
1115 AGAATATGTT
Statistics
Matches: 58, Mismatches: 13, Indels: 8
0.73 0.16 0.10
Matches are distributed among these distances:
10 4 0.07
11 50 0.86
12 4 0.07
ACGTcount: A:0.51, C:0.23, G:0.10, T:0.15
Consensus pattern (11 bp):
AACACTAAATG
Found at i:1049 original size:22 final size:22
Alignment explanation
Indices: 1023--1114 Score: 107
Period size: 22 Copynumber: 4.2 Consensus size: 22
1013 ACTGAACATA
*
1023 TAAACTAACACTAAATGAACTC
1 TAAACGAACACTAAATGAACTC
1045 TAAAC-AAGCACTAAATGAACTC
1 TAAACGAA-CACTAAATGAACTC
* *
1067 TAAACGAACACTAAA-CAAGCAC
1 TAAACGAACACTAAATGAA-CTC
* *
1089 TAAACGAACACTGAATGAACGC
1 TAAACGAACACTAAATGAACTC
1111 TAAA
1 TAAA
1115 AGAATATGTT
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
21 4 0.07
22 53 0.87
23 4 0.07
ACGTcount: A:0.51, C:0.23, G:0.10, T:0.16
Consensus pattern (22 bp):
TAAACGAACACTAAATGAACTC
Found at i:1114 original size:33 final size:33
Alignment explanation
Indices: 1023--1114 Score: 121
Period size: 33 Copynumber: 2.8 Consensus size: 33
1013 ACTGAACATA
* *
1023 TAAACTAACACTAAATGAACTCTAAACAAGCAC
1 TAAACGAACACTAAATGAACACTAAACAAGCAC
* * *
1056 TAAATGAACTCTAAACGAACACTAAACAAGCAC
1 TAAACGAACACTAAATGAACACTAAACAAGCAC
* *
1089 TAAACGAACACTGAATGAACGCTAAA
1 TAAACGAACACTAAATGAACACTAAA
1115 AGAATATGTT
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.51, C:0.23, G:0.10, T:0.16
Consensus pattern (33 bp):
TAAACGAACACTAAATGAACACTAAACAAGCAC
Found at i:5894 original size:2 final size:2
Alignment explanation
Indices: 5889--5917 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5879 CAATGAGCGG
5889 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 T
5918 TGCAGTTATC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14532 original size:16 final size:16
Alignment explanation
Indices: 14492--14558 Score: 55
Period size: 18 Copynumber: 3.9 Consensus size: 16
14482 AGTTAAAAAG
*
14492 ATATATTAAAATAAATA
1 ATATAATAAAAT-AATA
14509 A-ATAAATAAAATAATA
1 ATAT-AATAAAATAATA
*
14525 ATATAATAATAAATAGTA
1 ATATAAT-A-AAATAATA
14543 ATAGTAATAAATATAA
1 ATA-TAATAAA-ATAA
14559 AGGGGATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
16 10 0.24
17 13 0.32
18 14 0.34
19 4 0.10
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
ATATAATAAAATAATA
Found at i:14607 original size:16 final size:16
Alignment explanation
Indices: 14582--14617 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
14572 AAGTTGTGGT
*
14582 TAAAATAAAAAATAAA
1 TAAAAGAAAAAATAAA
*
14598 TAAAAGAAAAAATAAT
1 TAAAAGAAAAAATAAA
14614 TAAA
1 TAAA
14618 TAAACAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (16 bp):
TAAAAGAAAAAATAAA
Found at i:14626 original size:16 final size:15
Alignment explanation
Indices: 14584--14626 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
14574 GTTGTGGTTA
14584 AAATAAAAAATAAAT
1 AAATAAAAAATAAAT
* *
14599 AAAAGAAAAAATAATT
1 -AAATAAAAAATAAAT
14615 AAATAAACAAAT
1 AAATAAA-AAAT
14627 TAAAGAGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (15 bp):
AAATAAAAAATAAAT
Found at i:15389 original size:68 final size:66
Alignment explanation
Indices: 15214--15396 Score: 227
Period size: 61 Copynumber: 2.8 Consensus size: 66
15204 TAAAACATCT
* * * *
15214 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATAC----CTAAAA-AATAATATAT
1 TAAAACCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACAAAGATAAAATAAAAATATAT
*
15273 TC
65 CC
*
15275 TAAATCCTAATTAAAATACTAAAACCTATTTAAACT-AAATACAAAGATAAAATAAAAATAATAT
1 TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAATAAAAAT-ATAT
15339 CC
65 CC
*
15341 TAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATA
1 TAAAACCTAATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATAAAATA
15397 TAATGTTTAA
Statistics
Matches: 107, Mismatches: 6, Indels: 11
0.86 0.05 0.09
Matches are distributed among these distances:
60 11 0.10
61 29 0.27
64 5 0.05
65 5 0.05
66 23 0.21
67 16 0.15
68 18 0.17
ACGTcount: A:0.57, C:0.13, G:0.01, T:0.28
Consensus pattern (66 bp):
TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAATAAAAATATATC
C
Found at i:17271 original size:19 final size:20
Alignment explanation
Indices: 17247--17284 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
17237 AAGTTCGCTA
17247 AAAAAAT-AAAACAAAAATT
1 AAAAAATAAAAACAAAAATT
17266 AAAAAATAAAAACAAAAAT
1 AAAAAATAAAAACAAAAAT
17285 ATAACGAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.82, C:0.05, G:0.00, T:0.13
Consensus pattern (20 bp):
AAAAAATAAAAACAAAAATT
Found at i:22886 original size:16 final size:16
Alignment explanation
Indices: 22862--22898 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
22852 AAAAAAAGAA
22862 AAATA-TAATAATAAT
1 AAATATTAATAATAAT
*
22877 AAATATTAATAGTAAT
1 AAATATTAATAATAAT
22893 AAATAT
1 AAATAT
22899 AAAAGGGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
AAATATTAATAATAAT
Found at i:22967 original size:21 final size:22
Alignment explanation
Indices: 22934--22974 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
22924 GGTTAAAATA
22934 AAAAATAAGAATTAAATAAAAG
1 AAAAATAAGAATTAAATAAAAG
*
22956 AAAAA-AATAATTAAATAAA
1 AAAAATAAGAATTAAATAAA
22975 CAAATTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (22 bp):
AAAAATAAGAATTAAATAAAAG
Found at i:23558 original size:21 final size:20
Alignment explanation
Indices: 23534--23579 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
23524 TTCAAAATCC
23534 TAAAAACAAACTAAAACATCT
1 TAAAAACAAACTAAAACA-CT
** *
23555 TAAATCCTAACTAAAACACT
1 TAAAAACAAACTAAAACACT
23575 TAAAA
1 TAAAA
23580 CTATTTAAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.59, C:0.20, G:0.00, T:0.22
Consensus pattern (20 bp):
TAAAAACAAACTAAAACACT
Found at i:23680 original size:64 final size:64
Alignment explanation
Indices: 23527--23661 Score: 168
Period size: 64 Copynumber: 2.1 Consensus size: 64
23517 TATAGCCTTC
*
23527 AAAAT-CCTAAAAACA-AACTAAAACATCTTAAATCCTAACTAAAACACTTAAAACTATTTAAAC
1 AAAATACCTAAAAA-AGAA-TAAAATATCTTAAATCCTAACTAAAACACTTAAAACTATTTAAAC
23590 T
64 T
* * * * *
23591 AAAATACCTAAAAAATAATATAATATTTTAAATCCTAATTAAAATAC-TAAAACCTATTTAAACT
1 AAAATACCTAAAAAAGAATAAAATATCTTAAATCCTAACTAAAACACTTAAAA-CTATTTAAACT
23655 AAAATAC
1 AAAATAC
23662 AAAGATAGAG
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
63 5 0.08
64 48 0.76
65 10 0.16
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (64 bp):
AAAATACCTAAAAAAGAATAAAATATCTTAAATCCTAACTAAAACACTTAAAACTATTTAAACT
Found at i:27913 original size:8 final size:8
Alignment explanation
Indices: 27900--27940 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
27890 CTCATTTTCA
27900 GAGAATTT
1 GAGAATTT
27908 GAGAATTT
1 GAGAATTT
*
27916 -AGAGTTT
1 GAGAATTT
*
27923 GGGAATTT
1 GAGAATTT
27931 GAGAATTT
1 GAGAATTT
27939 GA
1 GA
27941 AAGCTTGTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:28249 original size:128 final size:128
Alignment explanation
Indices: 28021--28627 Score: 1124
Period size: 128 Copynumber: 4.7 Consensus size: 128
28011 ACTATTTACA
* *
28021 TGAAGGCGCGTTCCCGGGGGTGCGCCTTCCATTATTTTGTCAAAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
28086 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
*
28149 TGAAGGCGCATTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
28214 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGAACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
* * *
28277 TGAAGGCGCGTTTCCGGGGGCGCGTCTTTCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
28342 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
*
28405 TGAAGGCGTGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
28470 TTATGTCACTCATGTCCCTCAGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
*
28533 TGAAGGCGCGTTCCCAGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
28598 TTATGTCACTCATGTCCCTCGGGGACACTA
66 TTATGTCACTCATGTCCCTCGGGGACACTA
28628 GATGGATTGT
Statistics
Matches: 462, Mismatches: 17, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
128 462 1.00
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.33
Consensus pattern (128 bp):
TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
Found at i:29062 original size:34 final size:34
Alignment explanation
Indices: 29023--29129 Score: 160
Period size: 34 Copynumber: 3.1 Consensus size: 34
29013 TAAGTTGAAA
* *
29023 TTTAATGTTAAATTTCGAATACTATAATTTATAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
* *
29057 TTTAATTTTAAATTTCGAATAATATTATTTTTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
* *
29091 TTTTATTTTAAATTTCGAATAATATAATTTGTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
29125 TTTAA
1 TTTAA
29130 AAACATTTAT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 65 1.00
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.55
Consensus pattern (34 bp):
TTTAATTTTAAATTTCGAATAATATAATTTATAT
Found at i:29682 original size:21 final size:20
Alignment explanation
Indices: 29653--29721 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 20
29643 GGTATAAAAC
* *
29653 CCTGTGGGCTAGGCATGTAA
1 CCTGCGGGCTAGGAATGTAA
29673 CCTGGCGGGCTAGGAATGTAA
1 CCT-GCGGGCTAGGAATGTAA
*
29694 CCCTGCGGGCTCGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
29715 CCCTGCG
1 -CCTGCG
29722 AAGATGGCAT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
20 3 0.07
21 38 0.86
22 3 0.07
ACGTcount: A:0.19, C:0.26, G:0.35, T:0.20
Consensus pattern (20 bp):
CCTGCGGGCTAGGAATGTAA
Found at i:29752 original size:21 final size:21
Alignment explanation
Indices: 29726--29773 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
29716 CCTGCGAAGA
*
29726 TGGCATATGAACTGGTGGGCT
1 TGGCATATGAACTGGAGGGCT
*
29747 TGGCATATGAAGTGGAGGGCT
1 TGGCATATGAACTGGAGGGCT
*
29768 GGGCAT
1 TGGCAT
29774 GTACCCCTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.12, G:0.42, T:0.25
Consensus pattern (21 bp):
TGGCATATGAACTGGAGGGCT
Found at i:31543 original size:35 final size:32
Alignment explanation
Indices: 31502--31586 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 32
31492 AATTCTAAAT
31502 AAATAATAATTATATAAATATTATTTTAATAAAAA
1 AAATAATAATTATATAAATA-TA--TTAATAAAAA
* * *
31537 AAATAATATTTACATAAATATATTAATATAAA
1 AAATAATAATTATATAAATATATTAATAAAAA
* * *
31569 ATATAATAACTATTTAAA
1 AAATAATAATTATATAAA
31587 AAAATACTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
32 22 0.52
34 2 0.05
35 18 0.43
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (32 bp):
AAATAATAATTATATAAATATATTAATAAAAA
Found at i:31563 original size:32 final size:34
Alignment explanation
Indices: 31502--31577 Score: 93
Period size: 35 Copynumber: 2.3 Consensus size: 34
31492 AATTCTAAAT
*
31502 AAATAATAATTATATAAATATTATTTTAATAAAAA
1 AAATAATAATTACATAAATATTA-TTTAATAAAAA
* *
31537 AAATAATATTTACATAAATA-TA-TTAATATAAA
1 AAATAATAATTACATAAATATTATTTAATAAAAA
*
31569 ATATAATAA
1 AAATAATAA
31578 CTATTTAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
32 16 0.44
34 2 0.06
35 18 0.50
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (34 bp):
AAATAATAATTACATAAATATTATTTAATAAAAA
Found at i:31602 original size:34 final size:34
Alignment explanation
Indices: 31530--31607 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 34
31520 TATTATTTTA
* * * *
31530 ATAAAAAAAATAATATTTACATAAATATATTAAT
1 ATAAAAATAATAATATTTACATAAAAATACTAAC
31564 ATAAAATATAATAACTATTTA-A-AAAAATACTAAC
1 ATAAAA-ATAATAA-TATTTACATAAAAATACTAAC
31598 ATAAAAATAA
1 ATAAAAATAA
31608 ATTTCTTACC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
33 4 0.11
34 21 0.55
35 7 0.18
36 6 0.16
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (34 bp):
ATAAAAATAATAATATTTACATAAAAATACTAAC
Found at i:34007 original size:28 final size:28
Alignment explanation
Indices: 33966--34021 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
33956 CCTCTTAACC
*
33966 TGCTAAGTGAATTATAGTATGCAGGTCT
1 TGCTAAGCGAATTATAGTATGCAGGTCT
* *
33994 TGCTAAGCGGATTATAGTCTGCAGGTCT
1 TGCTAAGCGAATTATAGTATGCAGGTCT
34022 GCTTTTGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.25, C:0.14, G:0.27, T:0.34
Consensus pattern (28 bp):
TGCTAAGCGAATTATAGTATGCAGGTCT
Found at i:38150 original size:26 final size:26
Alignment explanation
Indices: 38121--38190 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 26
38111 AAAGGTTAGT
38121 AAAAAAATAAATAATAATAAT-AAACA
1 AAAAAAATAAATAA-AATAATAAAACA
* * *
38147 AAAATAATACAAGAAAATAATAAAAGA
1 AAAAAAATA-AATAAAATAATAAAACA
*
38174 AAATAAAATGAATAAAA
1 AAA-AAAATAAATAAAA
38191 CAAAAAGTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
26 14 0.40
27 17 0.49
28 4 0.11
ACGTcount: A:0.76, C:0.03, G:0.04, T:0.17
Consensus pattern (26 bp):
AAAAAAATAAATAAAATAATAAAACA
Found at i:38173 original size:13 final size:13
Alignment explanation
Indices: 38136--38179 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
38126 AATAAATAAT
38136 AATAATAAACA-AA
1 AATAATAAA-AGAA
*
38149 AATAATACAAGAA
1 AATAATAAAAGAA
38162 AATAATAAAAGAA
1 AATAATAAAAGAA
38175 AATAA
1 AATAA
38180 AATGAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 1 0.04
13 27 0.96
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.16
Consensus pattern (13 bp):
AATAATAAAAGAA
Found at i:38189 original size:19 final size:18
Alignment explanation
Indices: 38160--38195 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
38150 ATAATACAAG
*
38160 AAAATAATAAAAGAAAAT
1 AAAATAATAAAACAAAAT
38178 AAAATGAATAAAACAAAA
1 AAAAT-AATAAAACAAAA
38196 AGTAAAGGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.78, C:0.03, G:0.06, T:0.14
Consensus pattern (18 bp):
AAAATAATAAAACAAAAT
Found at i:38912 original size:16 final size:17
Alignment explanation
Indices: 38879--38912 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
38869 TGTTGATGGT
*
38879 TCGTGTTTTGCTTGTGA
1 TCGTGTTTGGCTTGTGA
38896 TCGTGTTTGGCTT-TGA
1 TCGTGTTTGGCTTGTGA
38912 T
1 T
38913 GATGTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.06, C:0.12, G:0.29, T:0.53
Consensus pattern (17 bp):
TCGTGTTTGGCTTGTGA
Found at i:39390 original size:30 final size:31
Alignment explanation
Indices: 39354--39422 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 31
39344 AAAATTATAT
*
39354 ATTATATACTTTTTAAAAAATG-TTTT-CAAA
1 ATTATATACTTTTT-AAAAATGTTTTTAAAAA
*
39384 ATTATATAGTTTTTAAAAATGTTTTTAAAAA
1 ATTATATACTTTTTAAAAATGTTTTTAAAAA
39415 ATTATATA
1 ATTATATA
39423 TTATATATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
29 7 0.20
30 17 0.49
31 11 0.31
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (31 bp):
ATTATATACTTTTTAAAAATGTTTTTAAAAA
Found at i:39436 original size:29 final size:29
Alignment explanation
Indices: 39404--39471 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
39394 TTTTAAAAAT
39404 GTTTTTAAAAAA--TTATATATTATATATAA
1 GTTTTTAAAAAATGTTATATA-TA-ATATAA
* * *
39433 GTTTTCAAAAAATGTTTTATATAATATAT
1 GTTTTTAAAAAATGTTATATATAATATAA
39462 GTTTTTAAAA
1 GTTTTTAAAA
39472 TGTTTTAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 25 0.76
30 2 0.06
31 6 0.18
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.49
Consensus pattern (29 bp):
GTTTTTAAAAAATGTTATATATAATATAA
Found at i:39497 original size:36 final size:36
Alignment explanation
Indices: 39450--39710 Score: 218
Period size: 36 Copynumber: 7.3 Consensus size: 36
39440 AAAAATGTTT
* *
39450 TATATAATATATGTTTTTAAAATGTTTTAAAAACTA
1 TATATTATATATGTTTTCAAAATGTTTTAAAAACTA
** *
39486 TATATTATATATACTTTCAATATGTTTTAAAAACTA
1 TATATTATATATGTTTTCAAAATGTTTTAAAAACTA
*
39522 TATAATATATAAATGTTTTCAAAAATGTTTT----A-TA
1 TAT-AT-TATATATGTTTTC-AAAATGTTTTAAAAACTA
*
39556 TA-A-TATATAT-TTTT-AAAATGTTTTCAAAACTA
1 TATATTATATATGTTTTCAAAATGTTTTAAAAACTA
** *
39588 TATATTATATATACTTTCAAAATGTTTTAAAAACCA
1 TATATTATATATGTTTTCAAAATGTTTTAAAAACTA
* * * *
39624 TATAATATATAAATGTTTTCAAAATATTTTTCAAAACCA
1 TAT-AT-TATATATGTTTTCAAAAT-GTTTTAAAAACTA
* * *
39663 TATACTATATA-GATTTTAAAAACGTTTTCAAAAACTA
1 TATATTATATATG-TTTTCAAAATGTTTT-AAAAACTA
*
39700 TATAATATATA
1 TATATTATATA
39711 CTTATTTTCG
Statistics
Matches: 182, Mismatches: 26, Indels: 33
0.76 0.11 0.14
Matches are distributed among these distances:
27 10 0.05
29 4 0.02
30 6 0.03
31 1 0.01
32 5 0.03
33 1 0.01
34 11 0.06
35 4 0.02
36 58 0.32
37 33 0.18
38 26 0.14
39 23 0.13
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (36 bp):
TATATTATATATGTTTTCAAAATGTTTTAAAAACTA
Found at i:39497 original size:69 final size:72
Alignment explanation
Indices: 39347--39498 Score: 183
Period size: 71 Copynumber: 2.1 Consensus size: 72
39337 TTATTTTAAA
*
39347 ATTATATATTATATACTTTTTAAAAAATGTTTTCAAAATTATATAGTTTTTAAAAATGTTTTTAA
1 ATTATATA-TATATACTTTTCAAAAAATGTTTTCAAAATTATATAGTTTTTAAAAATGTTTTTAA
39412 AAAATTAT
65 AAAATTAT
*
39420 A-TAT-TATATATAAGTTTTCAAAAAATGTTTT-ATATAA-TATAT-GTTTTT-AAAATG-TTTT
1 ATTATATATATAT-ACTTTTCAAAAAATGTTTTCA-A-AATTATATAGTTTTTAAAAATGTTTTT
*
39478 AAAAACTATAT
63 AAAAAAT-TAT
39489 ATTATATATA
1 ATTATATATA
39499 CTTTCAATAT
Statistics
Matches: 70, Mismatches: 3, Indels: 14
0.80 0.03 0.16
Matches are distributed among these distances:
68 10 0.14
69 10 0.14
70 15 0.21
71 29 0.41
72 5 0.07
73 1 0.01
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (72 bp):
ATTATATATATATACTTTTCAAAAAATGTTTTCAAAATTATATAGTTTTTAAAAATGTTTTTAAA
AAATTAT
Found at i:39556 original size:27 final size:27
Alignment explanation
Indices: 39526--39579 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
39516 AAACTATATA
*
39526 ATAT-ATAAATGTTTTCAAAAATGTTTT
1 ATATAATAAATATTTT-AAAAATGTTTT
* *
39553 ATATAATATATATTTTTAAAATGTTTT
1 ATATAATAAATATTTTAAAAATGTTTT
39580 CAAAACTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.52
Consensus pattern (27 bp):
ATATAATAAATATTTTAAAAATGTTTT
Found at i:39563 original size:39 final size:39
Alignment explanation
Indices: 39450--39584 Score: 120
Period size: 39 Copynumber: 3.5 Consensus size: 39
39440 AAAAATGTTT
*
39450 TATATAATATATGTTTT-TAAAATGTTTTAAAAACTATATA
1 TATATAA-A-ATGTTTTCAAAAATGTTTTAAAAACTATATA
* ** *
39490 T-TAT-ATATACTTTC-AATATGTTTTAAAAACTATATA
1 TATATAAAATGTTTTCAAAAATGTTTTAAAAACTATATA
*
39526 -ATATATAAATGTTTTCAAAAATGTTTTATATAA-TATATA
1 TATATA-AAATGTTTTCAAAAATGTTTTA-AAAACTATATA
* *
39565 TTTTTAAAATGTTTTCAAAA
1 TATATAAAATGTTTTCAAAA
39585 CTATATATTA
Statistics
Matches: 77, Mismatches: 11, Indels: 15
0.75 0.11 0.15
Matches are distributed among these distances:
36 29 0.38
38 8 0.10
39 33 0.43
40 7 0.09
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (39 bp):
TATATAAAATGTTTTCAAAAATGTTTTAAAAACTATATA
Found at i:39570 original size:102 final size:102
Alignment explanation
Indices: 39399--39647 Score: 401
Period size: 102 Copynumber: 2.4 Consensus size: 102
39389 ATAGTTTTTA
* * *
39399 AAAATGTTTTTAAAAAATTATATATTATATATAA-GTTTTCAAAAAATGTTTTATATAATATATG
1 AAAATG-TTTT-AAAAACTATATAATATATA-AATGTTTTC-AAAAATGTTTTATATAATATATA
39463 TTTTTAAAATGTTTTAAAAACTATATATTATATATACTTTC
62 TTTTTAAAATGTTTTAAAAACTATATATTATATATACTTTC
*
39504 AATATGTTTTAAAAACTATATAATATATAAATGTTTTCAAAAATGTTTTATATAATATATATTTT
1 AAAATGTTTTAAAAACTATATAATATATAAATGTTTTCAAAAATGTTTTATATAATATATATTTT
*
39569 TAAAATGTTTTCAAAACTATATATTATATATACTTTC
66 TAAAATGTTTTAAAAACTATATATTATATATACTTTC
*
39606 AAAATGTTTTAAAAACCATATAATATATAAATGTTTTCAAAA
1 AAAATGTTTTAAAAACTATATAATATATAAATGTTTTCAAAA
39648 TATTTTTCAA
Statistics
Matches: 136, Mismatches: 7, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
102 104 0.76
103 23 0.17
104 4 0.03
105 5 0.04
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.45
Consensus pattern (102 bp):
AAAATGTTTTAAAAACTATATAATATATAAATGTTTTCAAAAATGTTTTATATAATATATATTTT
TAAAATGTTTTAAAAACTATATATTATATATACTTTC
Found at i:39798 original size:2 final size:2
Alignment explanation
Indices: 39791--39817 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
39781 TACTATATGC
39791 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 A
39818 ATTACTCCGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43046 original size:20 final size:16
Alignment explanation
Indices: 42997--43036 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
42987 ATAACGACGA
42997 AACCAGAGAAATCCAC
1 AACCAGAGAAATCCAC
43013 AACCAGAGAAATCCAC
1 AACCAGAGAAATCCAC
43029 AACCAGAG
1 AACCAGAG
43037 TCTAAAATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.50, C:0.30, G:0.15, T:0.05
Consensus pattern (16 bp):
AACCAGAGAAATCCAC
Found at i:56074 original size:18 final size:19
Alignment explanation
Indices: 56053--56090 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
56043 AAAATGAGTG
*
56053 AAAATGAAAAAAT-AAAAA
1 AAAATAAAAAAATGAAAAA
56071 AAAATAAAAAAATGAAAAA
1 AAAATAAAAAAATGAAAAA
56090 A
1 A
56091 TGGAAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.11
Consensus pattern (19 bp):
AAAATAAAAAAATGAAAAA
Found at i:57073 original size:55 final size:55
Alignment explanation
Indices: 57004--57763 Score: 854
Period size: 55 Copynumber: 13.9 Consensus size: 55
56994 AGGTTTCCCA
*
57004 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * *
57059 ACGATGGTTGAAGATTGTTCGAGTCTCATACTCTCTTAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * *
57114 ACGATTGATGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATGGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* *
57169 ACGATTGTTGAAGATTGTTTGAGTCTTATACTCTCTGCAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * * *
57224 ACGATTGATGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATGGGGAGCATAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * * *
57279 ACGATTGATGAAAATTGTTCGAGTCTTATACTCTCTGCATAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * *
57334 ACGACTGTTGAAGATTGTTGGAGTCTTATACTCTCTGCAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * *
57389 ACGATTGATGAAGATTGTTCAAGTCTTATACTCTCTGAAGGAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * * * * *
57444 ACGATTGATGAAGATTCTTCAAGT-TCCATACTCCCT-AGAGAAAGAGGGAGC-GA-
1 ACGATTGTTGAAGATTGTTCGAGTCT-TATACTCTCTGA-AGAAATAGGGAGCAGAC
* * * * * *
57497 ACCCA--GTTGAAGA-TGTTCGAGT-TCCATACTC-CTTAAAGAAAGAAGAAGC-GAAC
1 A-CGATTGTTGAAGATTGTTCGAGTCT-TATACTCTC-TGAAGAAATAGGGAGCAG-AC
* * * * *
57550 CCG--T-TTGAAGAGATGTTCGAGT-TCCATACTCCCT-AGAGAAATAGGGAAC-GA-
1 ACGATTGTTGAAGA-TTGTTCGAGTCT-TATACTCTCTGA-AGAAATAGGGAGCAGAC
* *
57601 ACCCATTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGAC
1 A-CGA-TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * * *
57658 GCGATCGTTGAAGATTGTTCGAGTCCTATACTCTCTGAAGAAATAGGGGGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* *
57713 AAGTTTGTTGAAGA-TGATTCGAGTCTTATACTCTCTGAAGAAATAGGGAGC
1 ACGATTGTTGAAGATTG-TTCGAGTCTTATACTCTCTGAAGAAATAGGGAGC
57764 GAACCCATTT
Statistics
Matches: 613, Mismatches: 70, Indels: 44
0.84 0.10 0.06
Matches are distributed among these distances:
50 1 0.00
51 36 0.06
52 13 0.02
53 30 0.05
54 9 0.01
55 511 0.83
56 13 0.02
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (55 bp):
ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
Found at i:57528 original size:51 final size:51
Alignment explanation
Indices: 57465--57626 Score: 200
Period size: 53 Copynumber: 3.1 Consensus size: 51
57455 AGATTCTTCA
57465 AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCAGTTGAAGATGTTCG
1 AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCAGTTGAAGATGTTCG
* * * *
57516 AGTTCCATACTCCTTAAAGAAAGAAGAAGCGAACCC-GTTTGAAGAGATGTTCG
1 AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCAG-TTG-A-AGATGTTCG
* *
57569 AGTTCCATACTCCCTAGAGAAATAGGGAACGAACCCATTTGTTGAAGATTGTTCG
1 AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCA---GTTGAAGA-TGTTCG
57624 AGT
1 AGT
57627 CTTATACTCT
Statistics
Matches: 93, Mismatches: 10, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
50 1 0.01
51 35 0.38
52 1 0.01
53 39 0.42
54 3 0.03
55 10 0.11
56 3 0.03
57 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (51 bp):
AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCAGTTGAAGATGTTCG
Found at i:57807 original size:56 final size:54
Alignment explanation
Indices: 57452--57896 Score: 181
Period size: 55 Copynumber: 8.2 Consensus size: 54
57442 ACACGATTGA
* * *
57452 TGAAGATTCTTC-AAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCA--GT-
1 TGAAGATT-TTCGAA-TTCTATACTCCCTGA-AGAAATAGGGAGCGAACCCATTTTC
* * * * * * * * * **
57504 TGAAGATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGAAGCGAACCCGTTTGA
1 TGAAGATTTTCGAATTCTATACTCCCTGAAGAAATAGGGAGCGAACCCATTTTC
* * * * *
57558 AG-AGATGTTCGAGTTCCATACTCCCT-AGAGAAATAGGGAACGAACCCATTTGT-
1 TGAAGATTTTCGAATTCTATACTCCCTGA-AGAAATAGGGAGCGAACCCATTT-TC
* * * * **
57611 TGAAGATTGTTCG-AGTCTTATACTCTCTGAAGAAATAGGGGGC-AGACGCGATCGT-
1 TGAAGATT-TTCGAATTC-TATACTCCCTGAAGAAATAGGGAGCGA-AC-CCATTTTC
* * * * *
57666 TGAAGATTGTTCGAGTCCTATACTCTCTGAAGAAATAGGGGGC-AGA-CAAGTTTGT-
1 TGAAGATT-TTCGAATTCTATACTCCCTGAAGAAATAGGGAGCGA-ACCCA-TTT-TC
* * *
57721 TGAAGATGATTCG-AGTCTTATACTCTCTGAAGAAATAGGGAGCGAACCCATTTTTC
1 TGAAGAT-TTTCGAATTC-TATACTCCCTGAAGAAATAGGGAGCGAACCCA-TTTTC
* * *
57777 TGAAGATTTATTGAATTCTATACTCCCTGAA-AAGGACTAGAGAGCTG-ACGCGATTTT-
1 TGAAGATTT-TCGAATTCTATACTCCCTGAAGAA--A-TAGGGAGC-GAAC-CCATTTTC
* * * * *
57834 TGAAGATGTTCGAGTTCTATTCT-CCTGGAGAAAGAGGGAGCGAACCCATTTTC
1 TGAAGATTTTCGAATTCTATACTCCCTGAAGAAATAGGGAGCGAACCCATTTTC
*
57887 AGAAGATTTT
1 TGAAGATTTT
57897 TTTTTTTTTT
Statistics
Matches: 306, Mismatches: 56, Indels: 61
0.72 0.13 0.14
Matches are distributed among these distances:
51 32 0.10
52 17 0.06
53 60 0.20
54 11 0.04
55 113 0.37
56 45 0.15
57 12 0.04
58 13 0.04
59 3 0.01
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (54 bp):
TGAAGATTTTCGAATTCTATACTCCCTGAAGAAATAGGGAGCGAACCCATTTTC
Found at i:58901 original size:20 final size:16
Alignment explanation
Indices: 58852--58891 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
58842 ATAACGACGA
58852 AACCAGAGAAATCCAC
1 AACCAGAGAAATCCAC
58868 AACCAGAGAAATCCAC
1 AACCAGAGAAATCCAC
58884 AACCAGAG
1 AACCAGAG
58892 TCTAAAATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.50, C:0.30, G:0.15, T:0.05
Consensus pattern (16 bp):
AACCAGAGAAATCCAC
Found at i:65363 original size:69 final size:69
Alignment explanation
Indices: 65247--65382 Score: 200
Period size: 69 Copynumber: 2.0 Consensus size: 69
65237 GCCTGGATTG
* * * *
65247 AGGATTATCCGGCATCGTTATTGCTTCGTCGAGGTCGAATTGATGAGTGATATAGGGGATGATTA
1 AGGATTATCCGGCATCGTAATTGCATCGTCGAGGTCGAATTGATGAGTGAGATAAGGGATGATTA
65312 CAGA
66 CAGA
* * * *
65316 AGGATTTTCCGGCATCGTAATTGCATCGTCGAGGTCGAATTGCTGAGTGGGATAAGGGATTATTA
1 AGGATTATCCGGCATCGTAATTGCATCGTCGAGGTCGAATTGATGAGTGAGATAAGGGATGATTA
65381 CA
66 CA
65383 AAGTTATTGT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 59 1.00
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.30
Consensus pattern (69 bp):
AGGATTATCCGGCATCGTAATTGCATCGTCGAGGTCGAATTGATGAGTGAGATAAGGGATGATTA
CAGA
Found at i:65447 original size:2 final size:2
Alignment explanation
Indices: 65440--65474 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
65430 TCGCCGGAGT
*
65440 GA GA GA GA GA GA GA GA GA GA GA GA GA GG GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
65475 GAGTTTAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (2 bp):
GA
Found at i:66355 original size:22 final size:22
Alignment explanation
Indices: 66329--66372 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
66319 ACCAATGACC
66329 GAAAACATACCATAAAGACAGA
1 GAAAACATACCATAAAGACAGA
* *
66351 GAAAACCTATCATAAAGACAGA
1 GAAAACATACCATAAAGACAGA
66373 ATAATGCGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.57, C:0.18, G:0.14, T:0.11
Consensus pattern (22 bp):
GAAAACATACCATAAAGACAGA
Found at i:66390 original size:22 final size:23
Alignment explanation
Indices: 66361--66415 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
66351 GAAAACCTAT
*
66361 CATAAAGACAGAATAATGCGTGC
1 CATAAAGACAGAAGAATGCGTGC
* *
66384 TAT-AAGACAGAAGAATGTGTGC
1 CATAAAGACAGAAGAATGCGTGC
66406 CATAAAGACA
1 CATAAAGACA
66416 TAATTATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 19 0.70
23 8 0.30
ACGTcount: A:0.45, C:0.15, G:0.22, T:0.18
Consensus pattern (23 bp):
CATAAAGACAGAAGAATGCGTGC
Done.