Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009405.1 Hibiscus syriacus cultivar Beakdansim tig00113337_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: 1310060
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 6
Found at i:660223 original size:23 final size:23
Alignment explanation
Indices: 660191--660240 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
660181 GGATTTTGCA
*
660191 GATACCCATAATTCGGGTAATTG
1 GATACCCATAATTCGGGTAATCG
*
660214 GATACTCATAATTCGGGTAATCG
1 GATACCCATAATTCGGGTAATCG
660237 GATA
1 GATA
660241 TTCGGTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (23 bp):
GATACCCATAATTCGGGTAATCG
Found at i:662845 original size:15 final size:15
Alignment explanation
Indices: 662827--662960 Score: 106
Period size: 15 Copynumber: 8.5 Consensus size: 15
662817 CTTCTCTTCC
*
662827 TCTTTCTTGGGTTCT
1 TCTTTCTTTGGTTCT
*
662842 TCTTTCTTTGGCTCT
1 TCTTTCTTTGGTTCT
* * *
662857 TCCTTCTTAGGCTCT
1 TCTTTCTTTGGTTCT
662872 TCTTTCTTTGGTTCCT
1 TCTTTCTTTGGTT-CT
* *
662888 CTCCCTTCTTGGGTTCT
1 -T-CTTTCTTTGGTTCT
662905 TCTTTCTTTGGTTCCT
1 TCTTTCTTTGGTT-CT
* *
662921 CCTGTTTCTTGGGTTCT
1 --TCTTTCTTTGGTTCT
* * *
662938 TCCTTCTTTGGCTCC
1 TCTTTCTTTGGTTCT
662953 TCTTTCTT
1 TCTTTCTT
662961 CTCTGGTTCC
Statistics
Matches: 94, Mismatches: 19, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
15 63 0.67
16 5 0.05
17 5 0.05
18 21 0.22
ACGTcount: A:0.01, C:0.28, G:0.15, T:0.56
Consensus pattern (15 bp):
TCTTTCTTTGGTTCT
Found at i:662889 original size:18 final size:18
Alignment explanation
Indices: 662868--662971 Score: 69
Period size: 18 Copynumber: 6.1 Consensus size: 18
662858 CCTTCTTAGG
662868 CTCTTCTTTCTTTGGTTC
1 CTCTTCTTTCTTTGGTTC
* * *
662886 CTCTCCCTTC-TTGGGT-
1 CTCTTCTTTCTTTGGTTC
662902 -TCTTCTTTCTTTGGTTC
1 CTCTTCTTTCTTTGGTTC
* * *
662919 CTCCTGTTTC-TTGGGT-
1 CTCTTCTTTCTTTGGTTC
* *
662935 -TCTTCCTTCTTTGGCTC
1 CTCTTCTTTCTTTGGTTC
*
662952 CTCTT-TCTTCTCTGGTTC
1 CTCTTCT-TTCTTTGGTTC
662970 CT
1 CT
662972 TTGCTGGTCC
Statistics
Matches: 63, Mismatches: 16, Indels: 14
0.68 0.17 0.15
Matches are distributed among these distances:
15 13 0.21
16 10 0.16
17 10 0.16
18 30 0.48
ACGTcount: A:0.00, C:0.31, G:0.14, T:0.55
Consensus pattern (18 bp):
CTCTTCTTTCTTTGGTTC
Found at i:662969 original size:33 final size:33
Alignment explanation
Indices: 662830--662962 Score: 164
Period size: 33 Copynumber: 4.1 Consensus size: 33
662820 CTCTTCCTCT
662830 TTCTTGGGTTCTTCTTTCTTTGG---CTCTTCC
1 TTCTTGGGTTCTTCTTTCTTTGGTTCCTCTTCC
* * *
662860 TTCTTAGGCTCTTCTTTCTTTGGTTCCTCTCCC
1 TTCTTGGGTTCTTCTTTCTTTGGTTCCTCTTCC
* **
662893 TTCTTGGGTTCTTCTTTCTTTGGTTCCTCCTGT
1 TTCTTGGGTTCTTCTTTCTTTGGTTCCTCTTCC
* * *
662926 TTCTTGGGTTCTTCCTTCTTTGGCTCCTCTTTC
1 TTCTTGGGTTCTTCTTTCTTTGGTTCCTCTTCC
662959 TTCT
1 TTCT
662963 CTGGTTCCTT
Statistics
Matches: 86, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
30 21 0.24
33 65 0.76
ACGTcount: A:0.01, C:0.29, G:0.15, T:0.56
Consensus pattern (33 bp):
TTCTTGGGTTCTTCTTTCTTTGGTTCCTCTTCC
Found at i:665191 original size:152 final size:153
Alignment explanation
Indices: 664909--665222 Score: 513
Period size: 152 Copynumber: 2.1 Consensus size: 153
664899 ACATCATGCT
*
664909 CACATAATTTCTAATTGAAATTAGGTTTAGGTGAGAGTTATGACCCCCACTAATTTAGGGTATAA
1 CACA-AATTTCTAATTGAAATTAGGTTTAGGTGAGAGTTATGACCCCAACTAATTTAGGGTATAA
* *
664974 TAAAAATAAATTAATTAAATGCAACTGCACTATTTTGGACAACAATTTCAATTAGAAATTATGTA
65 TAAAAATAAATTAATTAAATGCAACTACACTATTTTGAACAACAATTTCAATTAGAAATTATGTA
* *
665039 AGTACGATGTTGGTCTCTTTAGTA
130 AGCACAATGTTGGTCTCTTTAGTA
*
665063 CACAAATTTCTAATTGAAATTAGGTTTAGGTGGGAGTTATGA-CCCAACTAATTTAGGGTATAAT
1 CACAAATTTCTAATTGAAATTAGGTTTAGGTGAGAGTTATGACCCCAACTAATTTAGGGTATAAT
* *
665127 AAAAATAAATTAATTAAATGCAACTACACTGTTTTGAACAATAATTTCAATTAGAAATTATGTAA
66 AAAAATAAATTAATTAAATGCAACTACACTATTTTGAACAACAATTTCAATTAGAAATTATGTAA
* *
665192 GCATAATGTTGGTTTCTTTAGTA
131 GCACAATGTTGGTCTCTTTAGTA
*
665215 AACAAATT
1 CACAAATT
665223 CAATGTTTGG
Statistics
Matches: 149, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
152 108 0.72
153 37 0.25
154 4 0.03
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (153 bp):
CACAAATTTCTAATTGAAATTAGGTTTAGGTGAGAGTTATGACCCCAACTAATTTAGGGTATAAT
AAAAATAAATTAATTAAATGCAACTACACTATTTTGAACAACAATTTCAATTAGAAATTATGTAA
GCACAATGTTGGTCTCTTTAGTA
Found at i:665434 original size:14 final size:14
Alignment explanation
Indices: 665415--665443 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
665405 ATATGACAGA
665415 CGCCCATATTTTTT
1 CGCCCATATTTTTT
665429 CGCCCATATTTTTT
1 CGCCCATATTTTTT
665443 C
1 C
665444 ACTTGTACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.31, G:0.07, T:0.48
Consensus pattern (14 bp):
CGCCCATATTTTTT
Found at i:671058 original size:18 final size:18
Alignment explanation
Indices: 671012--671058 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
671002 TTCTCTTTCG
*
671012 TTTTACTTTACGTTTTTA
1 TTTTACTTTATGTTTTTA
671030 TTTTACTTTATGTTTTTA
1 TTTTACTTTATGTTTTTA
671048 TTTTACTTTAT
1 TTTTACTTTAT
671059 TTAAAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.17, C:0.09, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTTACTTTATGTTTTTA
Found at i:672063 original size:85 final size:85
Alignment explanation
Indices: 671959--672146 Score: 331
Period size: 85 Copynumber: 2.2 Consensus size: 85
671949 AAATAGTATG
* *
671959 CATATCTTTAAAACACATAGCATGTTACCTCATTAAAAGTCTTAACAAGAAAATTCGATGAAACA
1 CATATCTTTAATACACATAGCATGTTACCTCATTAAAAGTCTTAACAAGAAAATTCAATGAAACA
672024 TAATCTCAATTAAGAGTACA
66 TAATCTCAATTAAGAGTACA
672044 CATATCTTTAATACACATAGCATGTTACCTCATTAAAAGTCTTAACAAGAAAATTCAATGAAACA
1 CATATCTTTAATACACATAGCATGTTACCTCATTAAAAGTCTTAACAAGAAAATTCAATGAAACA
* *
672109 TAATCTCGATTATGAGTACA
66 TAATCTCAATTAAGAGTACA
*
672129 CATATTTTTAATACACAT
1 CATATCTTTAATACACAT
672147 CATCACGTAA
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 98 1.00
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.31
Consensus pattern (85 bp):
CATATCTTTAATACACATAGCATGTTACCTCATTAAAAGTCTTAACAAGAAAATTCAATGAAACA
TAATCTCAATTAAGAGTACA
Found at i:672932 original size:28 final size:28
Alignment explanation
Indices: 672901--672966 Score: 132
Period size: 28 Copynumber: 2.4 Consensus size: 28
672891 TATTAATAAC
672901 ATAAAATTTTCTAATAGAATAAAAACAA
1 ATAAAATTTTCTAATAGAATAAAAACAA
672929 ATAAAATTTTCTAATAGAATAAAAACAA
1 ATAAAATTTTCTAATAGAATAAAAACAA
672957 ATAAAATTTT
1 ATAAAATTTT
672967 AAAGTGGATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.32
Consensus pattern (28 bp):
ATAAAATTTTCTAATAGAATAAAAACAA
Found at i:678041 original size:3 final size:3
Alignment explanation
Indices: 678033--678058 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
678023 GTGTGTTTCT
678033 CTG CTG CTG CTG CTG CTG CTG CTG CT
1 CTG CTG CTG CTG CTG CTG CTG CTG CT
678059 ACTACAGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.31, T:0.35
Consensus pattern (3 bp):
CTG
Found at i:679324 original size:16 final size:18
Alignment explanation
Indices: 679292--679325 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
679282 TATTAATGTA
679292 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
679310 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
679326 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:680482 original size:35 final size:35
Alignment explanation
Indices: 680432--680507 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
680422 AATTGAATTT
* * *
680432 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAAAATGA
*
680467 AATTGAATTACTTTGGAAATTGGGGTTTAAAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAAAATGA
680502 AATTGA
1 AATTGA
680508 GGATTGTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.37, C:0.01, G:0.22, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAAAATGA
Found at i:684955 original size:184 final size:184
Alignment explanation
Indices: 684646--685005 Score: 720
Period size: 184 Copynumber: 2.0 Consensus size: 184
684636 AATCTTCCAC
684646 CTTTACTTGGGTAAGATTCTCTTGTCTCTTCGCTTCATCAAATGGATTCTCCTCATCCTCTCCTC
1 CTTTACTTGGGTAAGATTCTCTTGTCTCTTCGCTTCATCAAATGGATTCTCCTCATCCTCTCCTC
684711 AAATGTCCGCCCAATCCCATTTATCTCTTCTCTATCACACCAACTTAGGCCTCGGCTACTCCATC
66 AAATGTCCGCCCAATCCCATTTATCTCTTCTCTATCACACCAACTTAGGCCTCGGCTACTCCATC
684776 GCCGTCGCTCTTGGTTTCCTCCTCCTCCTCTCTATTATCCTCCTTGTCTCTTCG
131 GCCGTCGCTCTTGGTTTCCTCCTCCTCCTCTCTATTATCCTCCTTGTCTCTTCG
684830 CTTTACTTGGGTAAGATTCTCTTGTCTCTTCGCTTCATCAAATGGATTCTCCTCATCCTCTCCTC
1 CTTTACTTGGGTAAGATTCTCTTGTCTCTTCGCTTCATCAAATGGATTCTCCTCATCCTCTCCTC
684895 AAATGTCCGCCCAATCCCATTTATCTCTTCTCTATCACACCAACTTAGGCCTCGGCTACTCCATC
66 AAATGTCCGCCCAATCCCATTTATCTCTTCTCTATCACACCAACTTAGGCCTCGGCTACTCCATC
684960 GCCGTCGCTCTTGGTTTCCTCCTCCTCCTCTCTATTATCCTCCTTG
131 GCCGTCGCTCTTGGTTTCCTCCTCCTCCTCTCTATTATCCTCCTTG
685006 CTTCCTACAT
Statistics
Matches: 176, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
184 176 1.00
ACGTcount: A:0.15, C:0.36, G:0.11, T:0.37
Consensus pattern (184 bp):
CTTTACTTGGGTAAGATTCTCTTGTCTCTTCGCTTCATCAAATGGATTCTCCTCATCCTCTCCTC
AAATGTCCGCCCAATCCCATTTATCTCTTCTCTATCACACCAACTTAGGCCTCGGCTACTCCATC
GCCGTCGCTCTTGGTTTCCTCCTCCTCCTCTCTATTATCCTCCTTGTCTCTTCG
Found at i:694615 original size:47 final size:47
Alignment explanation
Indices: 694561--694652 Score: 148
Period size: 47 Copynumber: 2.0 Consensus size: 47
694551 ATATATAGAG
* *
694561 ATAGTCTTTTAATTGAGGGAAGATTATTGAACCATTAAACTATTAAT
1 ATAGTCTTTTAATTGAGGAAAGATAATTGAACCATTAAACTATTAAT
* *
694608 ATAGTCTTTTAATTGAGGAAAGATAATTGAATCATTAAATTATTA
1 ATAGTCTTTTAATTGAGGAAAGATAATTGAACCATTAAACTATTA
694653 CTAAAAGTGG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.39
Consensus pattern (47 bp):
ATAGTCTTTTAATTGAGGAAAGATAATTGAACCATTAAACTATTAAT
Found at i:695474 original size:2 final size:2
Alignment explanation
Indices: 695467--695507 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
695457 TTTAAAACTA
695467 AT AT AT 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 AT AT AT A
695508 AAACACAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:696755 original size:21 final size:21
Alignment explanation
Indices: 696726--696782 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
696716 TAATCGATAT
* * **
696726 AATACTAACATAACAGTTTAC
1 AATATTAACATAACAATCCAC
* *
696747 AATATTAACGTGACAATCCAC
1 AATATTAACATAACAATCCAC
*
696768 GATATTAACATAACA
1 AATATTAACATAACA
696783 CTATATAATG
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.47, C:0.19, G:0.07, T:0.26
Consensus pattern (21 bp):
AATATTAACATAACAATCCAC
Found at i:697513 original size:23 final size:23
Alignment explanation
Indices: 697487--697546 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
697477 AGGCAGAGAA
697487 AAACATGTCATAAAGACAAAGAT
1 AAACATGTCATAAAGACAAAGAT
* *
697510 AAACGTGTCACAAAGACAAAGAT
1 AAACATGTCATAAAGACAAAGAT
*
697533 AAACATATCATAAA
1 AAACATGTCATAAA
697547 AATATAGAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.57, C:0.15, G:0.12, T:0.17
Consensus pattern (23 bp):
AAACATGTCATAAAGACAAAGAT
Found at i:698071 original size:2 final size:2
Alignment explanation
Indices: 698064--698106 Score: 61
Period size: 2 Copynumber: 21.5 Consensus size: 2
698054 ACGTAACATG
*
698064 TA TA TA TA T- TA TG TA TGA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
698106 T
1 T
698107 TTGAAAATAC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 1 0.03
2 34 0.92
3 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:698250 original size:15 final size:16
Alignment explanation
Indices: 698232--698270 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
698222 TATATTCAAT
*
698232 TTTTTAGTATT-TTTA
1 TTTTTAATATTGTTTA
698247 TTTTTAATATTGTTTA
1 TTTTTAATATTGTTTA
*
698263 TATTTAAT
1 TTTTTAAT
698271 TTTTTTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (16 bp):
TTTTTAATATTGTTTA
Found at i:698262 original size:16 final size:15
Alignment explanation
Indices: 698232--698277 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
698222 TATATTCAAT
*
698232 TTTTTAGTATTTTTA
1 TTTTTAATATTTTTA
698247 TTTTTAATATTGTTTA
1 TTTTTAATATT-TTTA
* *
698263 TATTTAATTTTTTTA
1 TTTTTAATATTTTTA
698278 ATACATGAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 14 0.52
16 13 0.48
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (15 bp):
TTTTTAATATTTTTA
Found at i:699919 original size:32 final size:31
Alignment explanation
Indices: 699883--699959 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
699873 CGGGGCCGTG
*
699883 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
699915 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
699946 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
699960 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:699942 original size:63 final size:63
Alignment explanation
Indices: 699836--699959 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
699826 CCCTAAGGGA
* * ** *
699836 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
699899 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
699960 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:700845 original size:5 final size:5
Alignment explanation
Indices: 700835--700875 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
700825 GAAAGTCAAC
*
700835 GGTCG GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTC
700876 AACCCGGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 28 0.88
7 4 0.12
ACGTcount: A:0.05, C:0.22, G:0.54, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:700867 original size:17 final size:17
Alignment explanation
Indices: 700845--700878 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
700835 GGTCGGGTCG
700845 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
700862 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
700879 CCGGTCAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.24, G:0.47, T:0.18
Consensus pattern (17 bp):
GGTCGGGTCGGGTCAAC
Found at i:700911 original size:9 final size:9
Alignment explanation
Indices: 700872--700960 Score: 79
Period size: 9 Copynumber: 9.3 Consensus size: 9
700862 GGTCGGGTCG
*
700872 GGTCAACCC
1 GGTCAAACC
700881 GGTCAAACC
1 GGTCAAACC
* *
700890 GATTCAGACC
1 G-GTCAAACC
700900 GGTCAAACC
1 GGTCAAACC
*
700909 GGTTGAAACC
1 GG-TCAAACC
700919 GGTCAAACC
1 GGTCAAACC
*
700928 GGTTAGAACC
1 GGTCA-AACC
*
700938 GGTTGAAAACC
1 GG-T-CAAACC
700949 GGTCAAACC
1 GGTCAAACC
700958 GGT
1 GGT
700961 TTCCAGCAGC
Statistics
Matches: 65, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
9 35 0.54
10 22 0.34
11 7 0.11
12 1 0.02
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:700929 original size:19 final size:18
Alignment explanation
Indices: 700879--700960 Score: 83
Period size: 19 Copynumber: 4.3 Consensus size: 18
700869 TCGGGTCAAC
* *
700879 CCGGTCAAACCGATTCAGA
1 CCGGTCAAACCGGTT-AAA
700898 CCGGTCAAACCGGTTGAAA
1 CCGGTCAAACCGGTT-AAA
700917 CCGGTCAAACCGGTTAGAA
1 CCGGTCAAACCGGTTA-AA
* *
700936 CCGGTTGAAAACCGGTCAAA
1 CCGG-T-CAAACCGGTTAAA
700956 CCGGT
1 CCGGT
700961 TTCCAGCAGC
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
18 1 0.02
19 38 0.69
20 7 0.13
21 9 0.16
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (18 bp):
CCGGTCAAACCGGTTAAA
Found at i:700961 original size:20 final size:21
Alignment explanation
Indices: 700923--700961 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
700913 GAAACCGGTC
*
700923 AAACCGGTTAGAACCGGTTGA
1 AAACCGGTCAGAACCGGTTGA
700944 AAACCGGTCA-AACCGGTT
1 AAACCGGTCAGAACCGGTT
700962 TCCAGCAGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (21 bp):
AAACCGGTCAGAACCGGTTGA
Found at i:707214 original size:32 final size:31
Alignment explanation
Indices: 707178--707254 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
707168 CGGGGCCGTG
*
707178 GGGCCTACCTAAGAACACATCTTAAGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAAGGCCGCA
** ** *
707210 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAAGGCCGCA
*
707241 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
707255 GTCACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAAGGCCGCA
Found at i:707237 original size:63 final size:63
Alignment explanation
Indices: 707131--707254 Score: 144
Period size: 63 Copynumber: 2.0 Consensus size: 63
707121 CCCTAAGGGA
* * * ** *
707131 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAAGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
707194 ACATCTTAAGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAAGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
707255 GTCACATTAG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAAGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:708152 original size:22 final size:22
Alignment explanation
Indices: 708127--708169 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
708117 GAAAGTCAAC
708127 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
708149 GGTCAACGGTCGGGTCTGGTC
1 GGTCAACGGTCGGGTCGGGTC
708170 AGCCCGGCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.09, C:0.23, G:0.47, T:0.21
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:708223 original size:20 final size:20
Alignment explanation
Indices: 708198--708256 Score: 84
Period size: 20 Copynumber: 2.9 Consensus size: 20
708188 CAGACCGGTC
708198 AAACCGGTTCGAACCGGTTG-
1 AAACCGG-TCGAACCGGTTGA
708218 AAACCGGTCAGAACCGGTTGA
1 AAACCGGTC-GAACCGGTTGA
*
708239 AAACCGGTCAAACCGGTT
1 AAACCGGTCGAACCGGTT
708257 TCCAGCAGCC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
19 2 0.06
20 25 0.69
21 9 0.25
ACGTcount: A:0.31, C:0.25, G:0.27, T:0.17
Consensus pattern (20 bp):
AAACCGGTCGAACCGGTTGA
Found at i:710309 original size:20 final size:18
Alignment explanation
Indices: 710270--710310 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
710260 CATTATTTTA
*
710270 TTTCTAATAAATTAATGT
1 TTTCTAATAAATGAATGT
710288 TTTCTAATAAGATGACATGT
1 TTTCTAATAA-ATGA-ATGT
710308 TTT
1 TTT
710311 ATCATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 10 0.50
19 3 0.15
20 7 0.35
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.49
Consensus pattern (18 bp):
TTTCTAATAAATGAATGT
Found at i:720457 original size:15 final size:15
Alignment explanation
Indices: 720424--720457 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
720414 ACCCTCCCGC
**
720424 ACAATATCCACCTGG
1 ACAATATCCACCTCA
720439 ACAATATCCACCTCA
1 ACAATATCCACCTCA
720454 ACAA
1 ACAA
720458 GGACAGTGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.35, G:0.06, T:0.18
Consensus pattern (15 bp):
ACAATATCCACCTCA
Found at i:731264 original size:25 final size:25
Alignment explanation
Indices: 731235--731282 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
731225 ACTTATTTTA
*
731235 TAGGCTTTCTTCCAACTAAAGTTAC
1 TAGGCTTTCTTCCAAATAAAGTTAC
*
731260 TAGGCTTTCTTGCAAATAAAGTT
1 TAGGCTTTCTTCCAAATAAAGTT
731283 TTTCATTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (25 bp):
TAGGCTTTCTTCCAAATAAAGTTAC
Found at i:741846 original size:15 final size:15
Alignment explanation
Indices: 741813--741846 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
741803 ACCCTCCCGC
**
741813 ACAATATCCACCTGG
1 ACAATATCCACCTCA
741828 ACAATATCCACCTCA
1 ACAATATCCACCTCA
741843 ACAA
1 ACAA
741847 GGACAGTGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.35, G:0.06, T:0.18
Consensus pattern (15 bp):
ACAATATCCACCTCA
Found at i:752632 original size:25 final size:25
Alignment explanation
Indices: 752603--752650 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
752593 ACTTATTTTA
*
752603 TAGGCTTTCTTCCAACTAAAGTTAC
1 TAGGCTTTCTTCCAAATAAAGTTAC
*
752628 TAGGCTTTCTTGCAAATAAAGTT
1 TAGGCTTTCTTCCAAATAAAGTT
752651 TTTCATTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (25 bp):
TAGGCTTTCTTCCAAATAAAGTTAC
Found at i:761471 original size:18 final size:18
Alignment explanation
Indices: 761443--761496 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 18
761433 GAGGGTCTAC
*
761443 GTGGACCTACGGGACATA
1 GTGGTCCTACGGGACATA
*
761461 GTGGTCTTACGGGACATA
1 GTGGTCCTACGGGACATA
761479 GTGGTCCTACGGGACATA
1 GTGGTCCTACGGGACATA
761497 TGTGTTCTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.24, C:0.20, G:0.33, T:0.22
Consensus pattern (18 bp):
GTGGTCCTACGGGACATA
Found at i:761506 original size:18 final size:17
Alignment explanation
Indices: 761449--761507 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 17
761439 CTACGTGGAC
*
761449 CTACGGGACATAGTGGT
1 CTACGGGACATAGTGTT
*
761466 CTTACGGGACATAGTGGTC
1 C-TACGGGACATAGT-GTT
761485 CTACGGGACATATGTGTT
1 CTACGGGACATA-GTGTT
761503 CTACG
1 CTACG
761508 TGGTCCTACG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.03
18 31 0.86
19 4 0.11
ACGTcount: A:0.22, C:0.20, G:0.31, T:0.27
Consensus pattern (17 bp):
CTACGGGACATAGTGTT
Found at i:761535 original size:28 final size:28
Alignment explanation
Indices: 761479--761535 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
761469 ACGGGACATA
*
761479 GTGGTCCTACGGGACATATGTGTTCTAC
1 GTGGTCCTACGGGACATATGTGGTCTAC
761507 GTGGTCCTACGGGACATA-GTGGTCGTAC
1 GTGGTCCTACGGGACATATGTGGTC-TAC
761535 G
1 G
761536 GGACAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.18, C:0.21, G:0.33, T:0.28
Consensus pattern (28 bp):
GTGGTCCTACGGGACATATGTGGTCTAC
Found at i:764034 original size:34 final size:34
Alignment explanation
Indices: 763996--764065 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
763986 AAATGAAATA
763996 AACAGTAAGTCAATCAAGCTAGAAACTTTAACCG
1 AACAGTAAGTCAATCAAGCTAGAAACTTTAACCG
764030 AACAGTAAGTCAATCAAGCTAGAAACTTTAACCG
1 AACAGTAAGTCAATCAAGCTAGAAACTTTAACCG
764064 AA
1 AA
764066 AAAAGGTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.46, C:0.20, G:0.14, T:0.20
Consensus pattern (34 bp):
AACAGTAAGTCAATCAAGCTAGAAACTTTAACCG
Found at i:785638 original size:33 final size:33
Alignment explanation
Indices: 785596--785662 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
785586 GACATGCTGG
785596 ATTTTATCGAAGATTTATCAAGGACTTCTCCAC
1 ATTTTATCGAAGATTTATCAAGGACTTCTCCAC
785629 ATTTTATCGAAGATTTATCAAGGACTTCTCCAC
1 ATTTTATCGAAGATTTATCAAGGACTTCTCCAC
785662 A
1 A
785663 ATATCCAAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (33 bp):
ATTTTATCGAAGATTTATCAAGGACTTCTCCAC
Found at i:788544 original size:102 final size:102
Alignment explanation
Indices: 788363--788548 Score: 309
Period size: 102 Copynumber: 1.8 Consensus size: 102
788353 ATGGAATGAC
* *
788363 TCTACCTGACTAGCTTGGGGGTGGAAGGTATGCTCCCTTTCACCTAGAGTATGGGATGGTAGGTG
1 TCTACCTGACTAGCTTGGGGATGGAAGGTATGCTCCCTTTCACCTAGAGTATGGGATGGTAGGTA
788428 TGATGGGCTGACTCCCTTCATAGCAGAATAAAAAAAA
66 TGATGGGCTGACTCCCTTCATAGCAGAATAAAAAAAA
* * * *
788465 TCTATCTGACTAGCTTGGGGATGGAAGGTATGCTCCCTTTCATCTAGAGTGTGGGATGGTATGTA
1 TCTACCTGACTAGCTTGGGGATGGAAGGTATGCTCCCTTTCACCTAGAGTATGGGATGGTAGGTA
*
788530 TGATGGTCTGACTCCCTTC
66 TGATGGGCTGACTCCCTTC
788549 GTAAAAAAAT
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
102 77 1.00
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (102 bp):
TCTACCTGACTAGCTTGGGGATGGAAGGTATGCTCCCTTTCACCTAGAGTATGGGATGGTAGGTA
TGATGGGCTGACTCCCTTCATAGCAGAATAAAAAAAA
Found at i:791279 original size:74 final size:76
Alignment explanation
Indices: 791151--791301 Score: 288
Period size: 74 Copynumber: 2.0 Consensus size: 76
791141 TCCTCACAAT
791151 CAGAAGGTTGAGGTTGAAAGATAGATCACTACAATGCTTTCTTCTTCTATCATTCAACCTAGCAG
1 CAGAAGGTTGAGGTTGAAAGATAGATCACTACAATGCTTTCTTCTTCTATCATTCAACCTAGCAG
791216 AAGCCCCTTTG
66 AAGCCCCTTTG
791227 CAGAA-GTTGAGGTT-AAAGATAGATCACTACAATGCTTTCTTCTTCTATCATTCAACCTAGCAG
1 CAGAAGGTTGAGGTTGAAAGATAGATCACTACAATGCTTTCTTCTTCTATCATTCAACCTAGCAG
791290 AAGCCCCTTTG
66 AAGCCCCTTTG
791301 C
1 C
791302 CTCTCCTTGC
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
74 61 0.81
75 9 0.12
76 5 0.07
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.30
Consensus pattern (76 bp):
CAGAAGGTTGAGGTTGAAAGATAGATCACTACAATGCTTTCTTCTTCTATCATTCAACCTAGCAG
AAGCCCCTTTG
Found at i:794842 original size:2 final size:2
Alignment explanation
Indices: 794837--794888 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
794827 AAAATAAATT
794837 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
794878 TA TA TA TA TA T
1 TA TA TA TA TA T
794889 GATTCATTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:800344 original size:21 final size:20
Alignment explanation
Indices: 800318--800379 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 20
800308 CGCAAATCAG
800318 TTTCCAGATTCGCAATGCGAT
1 TTTCCA-ATTCGCAATGCGAT
**
800339 TTTCCAATTTCGCGTTGCGAT
1 TTTCCAA-TTCGCAATGCGAT
800360 TTTCCCAATTCGCAATGCGA
1 TTT-CCAATTCGCAATGCGA
800380 ATAAGTAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 1 0.03
21 30 0.86
22 4 0.11
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.35
Consensus pattern (20 bp):
TTTCCAATTCGCAATGCGAT
Found at i:800394 original size:20 final size:21
Alignment explanation
Indices: 800369--800420 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
800359 TTTTCCCAAT
*
800369 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
800389 TCGCAATACGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
800410 TCGCAATGCGA
1 TCGCAATGCGA
800421 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:800434 original size:20 final size:20
Alignment explanation
Indices: 800409--800503 Score: 84
Period size: 20 Copynumber: 4.7 Consensus size: 20
800399 AATTTGGAAA
*
800409 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
800429 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
800450 ATCGCAACACGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
800470 TTCGCAACGAGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
800490 ATCGCAACGGGATA
1 ATCGCAACGCGATA
800504 ATACAGAATC
Statistics
Matches: 59, Mismatches: 13, Indels: 6
0.76 0.17 0.08
Matches are distributed among these distances:
19 2 0.03
20 42 0.71
21 13 0.22
22 2 0.03
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:801264 original size:24 final size:24
Alignment explanation
Indices: 801237--801286 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
801227 TCGAAATTTC
801237 ATATTGGTCAATACCCGGACTTTG
1 ATATTGGTCAATACCCGGACTTTG
* *
801261 ATATTGGTCAATACTCGGATTTTG
1 ATATTGGTCAATACCCGGACTTTG
801285 AT
1 AT
801287 GATGTTTCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.38
Consensus pattern (24 bp):
ATATTGGTCAATACCCGGACTTTG
Found at i:803804 original size:20 final size:20
Alignment explanation
Indices: 803776--803851 Score: 82
Period size: 20 Copynumber: 3.9 Consensus size: 20
803766 CAACGGGGAA
803776 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
* *
803796 ATCGTAACGCGGAAATGGCT
1 ATCGCAACGCGAAAATGGCT
* ***
803816 ATCGCAATGCG-AAATGAAA
1 ATCGCAACGCGAAAATGGCT
*
803835 ATCGCAATGCGAAAATG
1 ATCGCAACGCGAAAATG
803852 AAAATCGCAT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 16 0.33
20 32 0.67
ACGTcount: A:0.38, C:0.20, G:0.25, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:803852 original size:20 final size:20
Alignment explanation
Indices: 803816--803866 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
803806 GGAAATGGCT
803816 ATCGCAATGCG-AAATGAAA
1 ATCGCAATGCGAAAATGAAA
803835 ATCGCAATGCGAAAATGAAA
1 ATCGCAATGCGAAAATGAAA
*
803855 ATCGCATTGCGA
1 ATCGCAATGCGA
803867 TTTTCTCGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 11 0.37
20 19 0.63
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.18
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGAAA
Found at i:805544 original size:41 final size:42
Alignment explanation
Indices: 805489--805580 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
805479 CCTCTTCAAC
* * *
805489 GATGACAGTGGCCTCTTGAACG-GTGGGGGGGACTCTCGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTATCGAGG
* * *
805530 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTATTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTATCGAGG
805572 GATGACAGG
1 GATGACAGG
805581 TGAGTCAGGC
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 20 0.47
42 23 0.53
ACGTcount: A:0.22, C:0.15, G:0.42, T:0.21
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTATCGAGG
Found at i:805966 original size:20 final size:20
Alignment explanation
Indices: 805943--806030 Score: 106
Period size: 20 Copynumber: 4.5 Consensus size: 20
805933 GAAACTTAAA
*
805943 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGGAAATGACT
*
805963 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGGAAATGACT
* *
805983 ATCGTAACGCGGAAATGGCT
1 ATCGCAACGCGGAAATGACT
* **
806003 ATCGCAATGC-GAAATGAAA
1 ATCGCAACGCGGAAATGACT
806022 ATCGCAACG
1 ATCGCAACG
806031 ACAAAATCGC
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
19 14 0.24
20 45 0.76
ACGTcount: A:0.36, C:0.23, G:0.25, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:806025 original size:19 final size:19
Alignment explanation
Indices: 806003--806061 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
805993 GGAAATGGCT
806003 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
806022 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
806036 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
806055 ATCGCAA
1 ATCGCAA
806062 CGACAAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.47, C:0.20, G:0.19, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:806038 original size:14 final size:14
Alignment explanation
Indices: 806019--806077 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
806009 ATGCGAAATG
806019 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
806033 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
806052 AAAATCGCAACGAC
1 AAAATCGCAACGAC
806066 AAAATCGCAACG
1 AAAATCGCAACG
806078 CGAAGCACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.49, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:806045 original size:33 final size:33
Alignment explanation
Indices: 806003--806081 Score: 149
Period size: 33 Copynumber: 2.4 Consensus size: 33
805993 GGAAATGGCT
806003 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
806036 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
806069 ATCGCAACGCGAA
1 ATCGCAATGCGAA
806082 GCACAAATCG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:806132 original size:19 final size:20
Alignment explanation
Indices: 806108--806156 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
806098 GATTTTGTCG
806108 TTGCGATTTTCATTT-CGCA
1 TTGCGATTTTCATTTCCGCA
*** *
806127 TTGCGATAGCCATTTCCGCG
1 TTGCGATTTTCATTTCCGCA
806147 TTGCGATTTT
1 TTGCGATTTT
806157 AAGTTTCGTG
Statistics
Matches: 22, Mismatches: 7, Indels: 1
0.73 0.23 0.03
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.43
Consensus pattern (20 bp):
TTGCGATTTTCATTTCCGCA
Found at i:808095 original size:20 final size:20
Alignment explanation
Indices: 808072--808127 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
808062 TCTGAAACTT
808072 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
808092 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
808112 ACTATCGCAACGCGAA
1 AAAATCGCAACACGAA
808128 TTTGACTATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.50, C:0.23, G:0.16, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:808133 original size:20 final size:20
Alignment explanation
Indices: 808075--808143 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 20
808065 GAAACTTAAA
* **
808075 ATCGCAACACGAAAATGAAA
1 ATCGCAACGCGAAAATGACT
*
808095 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
808115 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
808135 ATCGCAACG
1 ATCGCAACG
808144 AGAGAATCGC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.42, C:0.25, G:0.17, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:808475 original size:22 final size:22
Alignment explanation
Indices: 808420--808477 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
808410 GATGGAGATA
*
808420 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
*
808442 GAAGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
*
808464 GACGGATGTCGTCG
1 GACGGATTTCGTCG
808478 TAGAGAGTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.19, C:0.16, G:0.45, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:810849 original size:28 final size:28
Alignment explanation
Indices: 810815--810971 Score: 289
Period size: 28 Copynumber: 5.6 Consensus size: 28
810805 AATTTTAATG
*
810815 AGCTTAACGAGCAACGAGTTGATTAACA
1 AGCTTAACGAGCAACGAGCTGATTAACA
810843 AGCTTAACGAGCAACGAGCTGATTAACA
1 AGCTTAACGAGCAACGAGCTGATTAACA
810871 AGCTTAACGAGCAACGAGCTGATTAACA
1 AGCTTAACGAGCAACGAGCTGATTAACA
810899 AGCTTAACGAGCAACGAGCTGATTAACA
1 AGCTTAACGAGCAACGAGCTGATTAACA
810927 AGCTTAACGAGCAACGAGCTGATTAACA
1 AGCTTAACGAGCAACGAGCTGATTAACA
*
810955 GGCTTAACGAGC-ACGAG
1 AGCTTAACGAGCAACGAG
810972 TCGAGCAACA
Statistics
Matches: 127, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
27 5 0.04
28 122 0.96
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.18
Consensus pattern (28 bp):
AGCTTAACGAGCAACGAGCTGATTAACA
Found at i:810996 original size:31 final size:29
Alignment explanation
Indices: 810958--811016 Score: 91
Period size: 31 Copynumber: 2.0 Consensus size: 29
810948 ATTAACAGGC
810958 TTAACGAGCACGAGTCGAGCAACAAGTTTTT
1 TTAACGAGCACGAGTCGAGC-ACAA-TTTTT
*
810989 TTAACGAGCATGAGTCGAGCACAATTTT
1 TTAACGAGCACGAGTCGAGCACAATTTT
811017 AACGAGCTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 4 0.15
30 4 0.15
31 19 0.70
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (29 bp):
TTAACGAGCACGAGTCGAGCACAATTTTT
Found at i:811017 original size:26 final size:28
Alignment explanation
Indices: 810958--811023 Score: 82
Period size: 31 Copynumber: 2.3 Consensus size: 28
810948 ATTAACAGGC
810958 TTAACGAGCACGAGTCGAGCAACAAGTTTTT
1 TTAACGAGCACGAGTCGAGCAACAA---TTT
*
810989 TTAACGAGCATGAGTCGAGC-ACAA-TT
1 TTAACGAGCACGAGTCGAGCAACAATTT
811015 TTAACGAGC
1 TTAACGAGC
811024 TTAACAAGCA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
26 11 0.32
30 4 0.12
31 19 0.56
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (28 bp):
TTAACGAGCACGAGTCGAGCAACAATTT
Found at i:815844 original size:29 final size:29
Alignment explanation
Indices: 815812--815949 Score: 134
Period size: 29 Copynumber: 4.6 Consensus size: 29
815802 ATCATTTTTT
*
815812 TAATATTTTCGATTATTTTTAGCGCCTAA
1 TAATATTTTCGATTATTTTTAGTGCCTAA
* * **
815841 TAATATTTTCGGTCATTTTTTAGTGTTTAA
1 TAATATTTTCGATTA-TTTTTAGTGCCTAA
* * * *
815871 TAATATTTTTGGTTATTTTTAGGGTCTAA
1 TAATATTTTCGATTATTTTTAGTGCCTAA
*
815900 TAATGA-TTTCGATCATTTTTTTTAGTGCCTAA
1 TAAT-ATTTTCG---ATTATTTTTAGTGCCTAA
815932 TAATATTTTCGATTATTT
1 TAATATTTTCGATTATTT
815950 GTTATCGGTT
Statistics
Matches: 88, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
29 39 0.44
30 25 0.28
31 1 0.01
32 23 0.26
ACGTcount: A:0.25, C:0.09, G:0.12, T:0.54
Consensus pattern (29 bp):
TAATATTTTCGATTATTTTTAGTGCCTAA
Found at i:815877 original size:59 final size:60
Alignment explanation
Indices: 815812--815949 Score: 181
Period size: 59 Copynumber: 2.3 Consensus size: 60
815802 ATCATTTTTT
* **
815812 TAATATTTTCGATTATTTTTAGCGCCTAATAAT-ATTTTCGGTCA-TTTTTTAGTGTTTAA
1 TAATATTTTCGATTATTTTTAGCGCCTAATAATGA-TTTCGATCATTTTTTTAGTGCCTAA
* * * *
815871 TAATATTTTTGGTTATTTTTAGGGTCTAATAATGATTTCGATCATTTTTTTTAGTGCCTAA
1 TAATATTTTCGATTATTTTTAGCGCCTAATAATGATTTCGATCA-TTTTTTTAGTGCCTAA
815932 TAATATTTTCGATTATTT
1 TAATATTTTCGATTATTT
815950 GTTATCGGTT
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
59 37 0.55
60 1 0.01
61 29 0.43
ACGTcount: A:0.25, C:0.09, G:0.12, T:0.54
Consensus pattern (60 bp):
TAATATTTTCGATTATTTTTAGCGCCTAATAATGATTTCGATCATTTTTTTAGTGCCTAA
Found at i:815932 original size:32 final size:32
Alignment explanation
Indices: 815812--815949 Score: 96
Period size: 32 Copynumber: 4.6 Consensus size: 32
815802 ATCATTTTTT
* *
815812 TAATATTTTCG---ATTATTTTTAGCGCCTAA
1 TAATATTTTCGATCATTTTTTTTAGGGCCTAA
* * **
815841 TAATATTTTCGGTCA--TTTTTTAGTGTTTAA
1 TAATATTTTCGATCATTTTTTTTAGGGCCTAA
** * *
815871 TAATATTTT---TGGTTATTTTTAGGGTCTAA
1 TAATATTTTCGATCATTTTTTTTAGGGCCTAA
*
815900 TAATGA-TTTCGATCATTTTTTTTAGTGCCTAA
1 TAAT-ATTTTCGATCATTTTTTTTAGGGCCTAA
*
815932 TAATATTTTCGATTATTT
1 TAATATTTTCGATCATTT
815950 GTTATCGGTT
Statistics
Matches: 84, Mismatches: 15, Indels: 17
0.72 0.13 0.15
Matches are distributed among these distances:
27 1 0.01
29 30 0.36
30 21 0.25
31 1 0.01
32 31 0.37
ACGTcount: A:0.25, C:0.09, G:0.12, T:0.54
Consensus pattern (32 bp):
TAATATTTTCGATCATTTTTTTTAGGGCCTAA
Found at i:816775 original size:7 final size:7
Alignment explanation
Indices: 816765--816790 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
816755 AAAAAAATCC
816765 AAAAGGT
1 AAAAGGT
816772 AAAAGGT
1 AAAAGGT
816779 AAAAGGT
1 AAAAGGT
816786 AAAAG
1 AAAAG
816791 AGATAGTGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.27, T:0.12
Consensus pattern (7 bp):
AAAAGGT
Found at i:817535 original size:17 final size:18
Alignment explanation
Indices: 817496--817542 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
817486 TATTTATGAG
817496 GGAATTGAAATCTGTGAA
1 GGAATTGAAATCTGTGAA
*
817514 GGAATTGAAATCTGT-CA
1 GGAATTGAAATCTGTGAA
*
817531 GGAATTGGAATC
1 GGAATTGAAATC
817543 CAATTCCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.36, C:0.09, G:0.28, T:0.28
Consensus pattern (18 bp):
GGAATTGAAATCTGTGAA
Found at i:827754 original size:4 final size:4
Alignment explanation
Indices: 827745--827779 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
827735 TTCAACTATG
827745 TATT TATT TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TATT TAT
827780 ACATGCATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:828288 original size:2 final size:2
Alignment explanation
Indices: 828279--828307 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
828269 TTTTTAATTA
828279 AT AT -T 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
828308 CTAAAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:828503 original size:39 final size:39
Alignment explanation
Indices: 828453--828555 Score: 113
Period size: 39 Copynumber: 2.6 Consensus size: 39
828443 TTTAAAAAAT
*
828453 AATTTAGAATGTTA-ATGTGAAATAATTTAATAAATTA-A
1 AATTTAGAATGTTATA-GTGAAATAATTTAAGAAATTAGA
* * * *
828491 AATTTTATAATGTTATGGTAGCAA-AATTTAAGAAATTAGG
1 AA-TTTAGAATGTTATAGT-GAAATAATTTAAGAAATTAGA
828531 AATTTAGAATGTTATAGTGAAATAA
1 AATTTAGAATGTTATAGTGAAATAA
828556 CTTGAAATTA
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
38 5 0.10
39 42 0.81
40 5 0.10
ACGTcount: A:0.47, C:0.01, G:0.15, T:0.38
Consensus pattern (39 bp):
AATTTAGAATGTTATAGTGAAATAATTTAAGAAATTAGA
Found at i:829141 original size:23 final size:23
Alignment explanation
Indices: 829112--829157 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
829102 CAAAAAATTA
*
829112 GTCATTTTAGTTATACAAATACT
1 GTCATTTTAGTCATACAAATACT
829135 GTCATTTTAGTCATACAAATACT
1 GTCATTTTAGTCATACAAATACT
829158 ATACAAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (23 bp):
GTCATTTTAGTCATACAAATACT
Found at i:829641 original size:197 final size:198
Alignment explanation
Indices: 829300--829695 Score: 661
Period size: 197 Copynumber: 2.0 Consensus size: 198
829290 AAAATCGAGC
*
829300 GTCATGAGAAAACTATCTCTAAATACAAACCGCGTATACAAATATAATTTGATGGTTCAAAGCAA
1 GTCATGAGAAAACTATCTCTAAATACAAACCGCGTATACAAATATAATTTGATGGTCCAAAGCAA
* *
829365 ATAAGATCAACATGAATGTATAATTTTAATTCTTATGATTAGGTCCTAAATGCATAATTGGTTGT
66 AGAAGATCAACATGAATGTATAATTTTAATTCTTATGATTAGGTCATAAATGCATAATTGGTTGT
*
829430 AATTAGGTTATATAGTTCTGATTCTACTCAATTAGGTCATGAATTTATAA-TTTTAGTTAGTAAT
131 AATTAGGCTATATAGTTCTGATTCTACTCAATTAGGTCATGAATTTATAATTTTTAGTTAGTAAT
829494 TAG
196 TAG
* * *
829497 GTCATGAGAAAACTATCTCTGAATACAAA-CGTTGTATTCAAATATAATTTGATGGTCCAAAGCA
1 GTCATGAGAAAACTATCTCTAAATACAAACCG-CGTATACAAATATAATTTGATGGTCCAAAGCA
* *
829561 GAGAATATCAACATGAATGTATAATTTTAATTCTTATGATTAGGTCATAAATGCATAATTGGTTG
65 AAGAAGATCAACATGAATGTATAATTTTAATTCTTATGATTAGGTCATAAATGCATAATTGGTTG
* * *
829626 TAATTAGGCTATATAGTTCTTATTCTACTTAATTAGGTCATGAATTTATAATTTTTATTTAGTAA
130 TAATTAGGCTATATAGTTCTGATTCTACTCAATTAGGTCATGAATTTATAATTTTTAGTTAGTAA
829691 TTAG
195 TTAG
829695 G
1 G
829696 CTAATTATTT
Statistics
Matches: 185, Mismatches: 12, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
196 2 0.01
197 166 0.90
198 17 0.09
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (198 bp):
GTCATGAGAAAACTATCTCTAAATACAAACCGCGTATACAAATATAATTTGATGGTCCAAAGCAA
AGAAGATCAACATGAATGTATAATTTTAATTCTTATGATTAGGTCATAAATGCATAATTGGTTGT
AATTAGGCTATATAGTTCTGATTCTACTCAATTAGGTCATGAATTTATAATTTTTAGTTAGTAAT
TAG
Found at i:830587 original size:61 final size:60
Alignment explanation
Indices: 830502--830680 Score: 200
Period size: 61 Copynumber: 3.0 Consensus size: 60
830492 TTCGTGCTTA
* * * *
830502 ATTCTTCTTAAATAAGTCCTAAATGCATAATTTTGATTAGTAATTAGGCCTTATAATTTCG
1 ATTCTTCTTAATTAGGTCCCAAATGCATAATTTTG-TTAGTAATTAAGCCTTATAATTTCG
* * * * * *
830563 TTTCTTCTTAATTAGGTCCCAAATGAATAA-TTAGTAAGTAATTAAACCTTATAATTTTG
1 ATTCTTCTTAATTAGGTCCCAAATGCATAATTTTGTTAGTAATTAAGCCTTATAATTTCG
* * *
830622 ATTCCTCTCAATTAGGTCCTC-AATGCATAATTTTGGTTAGTAATTATGCCTTATAATTT
1 ATTCTTCTTAATTAGGTCC-CAAATGCATAATTTT-GTTAGTAATTAAGCCTTATAATTT
830681 TTATTCTTTT
Statistics
Matches: 97, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
59 45 0.46
60 6 0.06
61 46 0.47
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (60 bp):
ATTCTTCTTAATTAGGTCCCAAATGCATAATTTTGTTAGTAATTAAGCCTTATAATTTCG
Found at i:830681 original size:61 final size:61
Alignment explanation
Indices: 830517--830686 Score: 193
Period size: 59 Copynumber: 2.8 Consensus size: 61
830507 TCTTAAATAA
* * * * * * *
830517 GTCCTAAATGCATAATTTTGATTAGTAATTAGGCCTTATAATTTCGTTTCTTCTTAATTAG
1 GTCCTCAATGCATAATTTTGGTTAGTAATTAAGCCTTATAATTTTGATTCCTCTCAATTAG
* * * *
830578 GTCC-CAAATGAATAA--TTAGTAAGTAATTAAACCTTATAATTTTGATTCCTCTCAATTAG
1 GTCCTC-AATGCATAATTTTGGTTAGTAATTAAGCCTTATAATTTTGATTCCTCTCAATTAG
* *
830637 GTCCTCAATGCATAATTTTGGTTAGTAATTATGCCTTATAATTTTTATTC
1 GTCCTCAATGCATAATTTTGGTTAGTAATTAAGCCTTATAATTTTGATTC
830687 TTTTTTATTT
Statistics
Matches: 88, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
59 47 0.53
60 1 0.01
61 40 0.45
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.44
Consensus pattern (61 bp):
GTCCTCAATGCATAATTTTGGTTAGTAATTAAGCCTTATAATTTTGATTCCTCTCAATTAG
Found at i:830791 original size:41 final size:41
Alignment explanation
Indices: 830746--830828 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
830736 AACTTTTAAT
830746 TAAATATGTTTTGGGCAATAAATCAAGATTATTAATTTAGC
1 TAAATATGTTTTGGGCAATAAATCAAGATTATTAATTTAGC
830787 TAAATATGTTTTGGGCAATAAATCAAGATTATTAATTTAGC
1 TAAATATGTTTTGGGCAATAAATCAAGATTATTAATTTAGC
830828 T
1 T
830829 TAATTTAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.40
Consensus pattern (41 bp):
TAAATATGTTTTGGGCAATAAATCAAGATTATTAATTTAGC
Found at i:831961 original size:39 final size:39
Alignment explanation
Indices: 831900--832024 Score: 171
Period size: 39 Copynumber: 3.2 Consensus size: 39
831890 ACAAACAGAC
* *
831900 ATCAAAAGGAATTAAACATTTAATTTTAGCAACTCAATA
1 ATCAAAAGGAATTAATCCTTTAATTTTAGCAACTCAATA
* * *
831939 ATCGAAAGGAACTAATCCTTTAATTTTTA-CAATTCAATA
1 ATCAAAAGGAATTAATCCTTTAA-TTTTAGCAACTCAATA
* *
831978 ATCAAAAGAAATTTATCCTTTAATTTTAGCAACTCAATA
1 ATCAAAAGGAATTAATCCTTTAATTTTAGCAACTCAATA
832017 ATCAAAAG
1 ATCAAAAG
832025 TCTTTGACTA
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
38 5 0.07
39 64 0.86
40 5 0.07
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.33
Consensus pattern (39 bp):
ATCAAAAGGAATTAATCCTTTAATTTTAGCAACTCAATA
Found at i:833252 original size:12 final size:12
Alignment explanation
Indices: 833235--833262 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
833225 AAATATAATA
833235 AATTATAAATTT
1 AATTATAAATTT
833247 AATTATAAATTT
1 AATTATAAATTT
833259 AATT
1 AATT
833263 TATTAACGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
AATTATAAATTT
Found at i:834752 original size:564 final size:553
Alignment explanation
Indices: 833773--834821 Score: 1364
Period size: 565 Copynumber: 1.9 Consensus size: 553
833763 TATTATAATC
* ** * * *
833773 GAGTTAAGGCCGGCAGCTATGCAGTTTCCTTAAGACGGATTTTCGGCTACTCATATAGTGTTTAA
1 GAGTTAAGGCCGGCAGCTACGCAGTTTCCTTAAGACAAATTTTCGGCCACTCATATAATGCTTAA
833838 GATCATTGGTCATCTATCTCTCAAGATACAACAATTAAATGATGAGCTACAGTTGTAGTGCTACA
66 GATCATTGGTCATCTATCTCTCAAGATACAACAATTAAATGATGAGCTACAGTTGTAGTGCTACA
* **
833903 GAGATCACGAGTTATTTATTATATTTGTCTATCACAGAAAAATTAGAGAAAAAAAACTTTTGAAT
131 GAGATCACAAACTATTTATTATATTTGTCTATCACAGAAAAATTAGAG--AAAAAACTTTTGAAT
** *
833968 TGGTTTTGAGTTATTTGAATTGTATTTACATTGTATTTATAGAGTTTCTCATGGGAGAAGAATTG
194 TAATTTTGAGTTATTTGAATTGTATTTACATTGTATTTATAGAGTTTCTCATAGGAGAAGAATTG
* * **
834033 AAAAAATCTATTATGAAAAGTAAGGTCATTAATGAGTATCTGAATAAATTTGGAAGTAATCAATG
259 AAAAAATATATTATGAAAAATAAGGTCATTAATGAGTATCCAAATAAATTTGGAAGTAATCAATG
* * * **
834098 AGTATCGCATTTAATAGAATATATTTGTGAACAACAAGATATATTATATTAATATTTGAATTAAA
324 AGTATCACATTTAATAGAATATATTCGTGAACAACAAGATATATCATATTAATATTAAAATTAAA
* *
834163 AGAAATCATATAATATCATTTTTAATTCATAATATT-AAAAAAT-GTCACATTTAATAAAAATAT
389 AGAAATCATATAATATCATTTTTAATTCAGAATATTAAAAAAATAGTCACATTTAAGAAAAATAT
* * *
834226 TTAATTTATATAAACTATTTGACAAGCCCTCGAAGGGCTCGATCAGTTCGAACATTCATGTCGCT
454 TTAATTTATATAAAATATCTAACAAGCCCTCGAAGGGCTCGATCAGTTCGAACATTCATGTCGCT
834291 TGAAAATAATATAGAAAAAATACACGATTGGGAAT
519 TGAAAATAATATAGAAAAAATACACGATTGGGAAT
* * * * *
834326 GAGTTAAGGTCTGTAGCTACGCAGTTTCCTTGAGACAAATATTT-GGCCACTCCTATAATGCTT-
1 GAGTTAAGGCCGGCAGCTACGCAGTTTCCTTAAGACAAAT-TTTCGGCCACTCATATAATGCTTA
* * * * *
834389 AGATCATTGGTCGTTTGTCTC-CTAGGATACAACAATTAGATGATGAGCTACAGTTGTGCAGTGC
65 AGATCATTGGTCATCTATCTCTC-AAGATACAACAATTAAATGATGAGCTACAGTTGT--AGTGC
* * * *
834453 TACAGAGATCACAAACTATTTATTGTCTTTGTTTATCACCA-AAAAATTAGAG-AAAAATTTTTG
127 TACAGAGATCACAAACTATTTATTATATTTGTCTATCA-CAGAAAAATTAGAGAAAAAACTTTTG
*
834516 AATTAATTTTGAGTTATTTGAATTGTGTTTAACCTAGTAGGTTTACACGGTATTTATAGAGTTTC
191 AATTAATTTTGAGTTATTTGAATTGTATTT-A-C----A---TT-----GTATTTATAGAGTTTC
* * *
834581 TCATATGAGAAGAATTGGAAAAATATATTCTGAAAAATAAGGTCATTAATGAGTATCCAAATAAA
242 TCATAGGAGAAGAATTGAAAAAATATATTATGAAAAATAAGGTCATTAATGAGTATCCAAATAAA
* * * *
834646 TTT-GAATTAATCAATTAGTA-CAACATTTAATAGAATATGTTCGTGAACTACAAGATATATCAT
307 TTTGGAAGTAATCAATGAGTATC-ACATTTAATAGAATATATTCGTGAACAACAAGATATATCAT
834709 ATTAATA-TAAAATTAAAAGAAATCATATAGCA-ATCATTTTTAATTCAGAATATTAAAAAAATA
371 ATTAATATTAAAATTAAAAGAAATCATATA--ATATCATTTTTAATTCAGAATATTAAAAAAATA
834772 CGTCACATTTAAGAAAAATATTTAATTTATATAAAATATCTAACAAGCCC
434 -GTCACATTTAAGAAAAATATTTAATTTATATAAAATATCTAACAAGCCC
834822 CTAAAAAGGG
Statistics
Matches: 423, Mismatches: 48, Indels: 36
0.83 0.09 0.07
Matches are distributed among these distances:
551 38 0.09
552 51 0.12
553 49 0.12
554 51 0.12
555 2 0.00
557 1 0.00
560 2 0.00
563 21 0.05
564 79 0.19
565 84 0.20
567 45 0.11
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.35
Consensus pattern (553 bp):
GAGTTAAGGCCGGCAGCTACGCAGTTTCCTTAAGACAAATTTTCGGCCACTCATATAATGCTTAA
GATCATTGGTCATCTATCTCTCAAGATACAACAATTAAATGATGAGCTACAGTTGTAGTGCTACA
GAGATCACAAACTATTTATTATATTTGTCTATCACAGAAAAATTAGAGAAAAAACTTTTGAATTA
ATTTTGAGTTATTTGAATTGTATTTACATTGTATTTATAGAGTTTCTCATAGGAGAAGAATTGAA
AAAATATATTATGAAAAATAAGGTCATTAATGAGTATCCAAATAAATTTGGAAGTAATCAATGAG
TATCACATTTAATAGAATATATTCGTGAACAACAAGATATATCATATTAATATTAAAATTAAAAG
AAATCATATAATATCATTTTTAATTCAGAATATTAAAAAAATAGTCACATTTAAGAAAAATATTT
AATTTATATAAAATATCTAACAAGCCCTCGAAGGGCTCGATCAGTTCGAACATTCATGTCGCTTG
AAAATAATATAGAAAAAATACACGATTGGGAAT
Found at i:858645 original size:22 final size:24
Alignment explanation
Indices: 858620--858666 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
858610 GTTCATCATC
**
858620 TTGCCAA-G-TTCCTCTTTTTCTT
1 TTGCCAATGCTTCCTCAATTTCTT
858642 TTGCCAATGCTTCCTCAATTTCTT
1 TTGCCAATGCTTCCTCAATTTCTT
858666 T
1 T
858667 CCTTTGCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.33
23 1 0.05
24 13 0.62
ACGTcount: A:0.13, C:0.28, G:0.09, T:0.51
Consensus pattern (24 bp):
TTGCCAATGCTTCCTCAATTTCTT
Found at i:860562 original size:22 final size:22
Alignment explanation
Indices: 860534--860635 Score: 121
Period size: 22 Copynumber: 5.0 Consensus size: 22
860524 ACTGAATATT
860534 TGTCCCGAAGGACCACTGTATA
1 TGTCCCGAAGGACCACTGTATA
860556 TGTCCCGAAGGACCAC----TA
1 TGTCCCGAAGGACCACTGTATA
860574 TGTCCCGAAGGACCACTGTATA
1 TGTCCCGAAGGACCACTGTATA
* *
860596 TGTCTCGAAGGACAAC----TA
1 TGTCCCGAAGGACCACTGTATA
*
860614 TGTCCCGAAGAACCACTGTATA
1 TGTCCCGAAGGACCACTGTATA
860636 ACCCTCGACT
Statistics
Matches: 67, Mismatches: 5, Indels: 16
0.76 0.06 0.18
Matches are distributed among these distances:
18 33 0.49
22 34 0.51
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (22 bp):
TGTCCCGAAGGACCACTGTATA
Found at i:860577 original size:18 final size:18
Alignment explanation
Indices: 860534--860630 Score: 95
Period size: 18 Copynumber: 4.9 Consensus size: 18
860524 ACTGAATATT
860534 TGTCCCGAAGGACCACTGTATA
1 TGTCCCGAAGGACCAC----TA
860556 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
860574 TGTCCCGAAGGACCACTGTATA
1 TGTCCCGAAGGACCAC----TA
* *
860596 TGTCTCGAAGGACAACTA
1 TGTCCCGAAGGACCACTA
*
860614 TGTCCCGAAGAACCACT
1 TGTCCCGAAGGACCACT
860631 GTATAACCCT
Statistics
Matches: 66, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
18 34 0.52
22 32 0.48
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:860578 original size:40 final size:40
Alignment explanation
Indices: 860534--860635 Score: 177
Period size: 40 Copynumber: 2.5 Consensus size: 40
860524 ACTGAATATT
*
860534 TGTCCCGAAGGACCACTGTATATGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTGTATATGTCCCGAAGGACAACTA
*
860574 TGTCCCGAAGGACCACTGTATATGTCTCGAAGGACAACTA
1 TGTCCCGAAGGACCACTGTATATGTCCCGAAGGACAACTA
*
860614 TGTCCCGAAGAACCACTGTATA
1 TGTCCCGAAGGACCACTGTATA
860636 ACCCTCGACT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 59 1.00
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (40 bp):
TGTCCCGAAGGACCACTGTATATGTCCCGAAGGACAACTA
Found at i:865170 original size:21 final size:21
Alignment explanation
Indices: 865128--865172 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
865118 TTGTAAAAAA
* *
865128 TTACCTAAAATATCATTATTT
1 TTACCTAAAACACCATTATTT
865149 TTACCTAAAACACCAATT-TTT
1 TTACCTAAAACACC-ATTATTT
865170 TTA
1 TTA
865173 ATATTTCCGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.38, C:0.18, G:0.00, T:0.44
Consensus pattern (21 bp):
TTACCTAAAACACCATTATTT
Found at i:866964 original size:3 final size:3
Alignment explanation
Indices: 866956--866980 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
866946 AATCAAATAA
866956 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
866981 GGGTGAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:874779 original size:24 final size:24
Alignment explanation
Indices: 874751--874807 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
874741 GCCTGAACCA
*
874751 CTGCTG-TTGCTGTTGTTGAAAATG
1 CTGCTGATTG-TGATGTTGAAAATG
*
874775 CTGCTGATTGTGATGTTGAAATTG
1 CTGCTGATTGTGATGTTGAAAATG
874799 CTGCTGATT
1 CTGCTGATT
874808 CTGAACCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 27 0.90
25 3 0.10
ACGTcount: A:0.18, C:0.12, G:0.28, T:0.42
Consensus pattern (24 bp):
CTGCTGATTGTGATGTTGAAAATG
Found at i:876156 original size:42 final size:42
Alignment explanation
Indices: 876097--876176 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
876087 GCTTTACCTT
* *
876097 TTTTTTTAATTTGGAAAAAACTGAACTCCTATCATTTTACCC
1 TTTTTTTAATTTCGAAAAAACTAAACTCCTATCATTTTACCC
* *
876139 TTTTTTTAATTTCGAAAAAACTAAAGTCCTATCGTTTT
1 TTTTTTTAATTTCGAAAAAACTAAACTCCTATCATTTT
876177 TGCTTCTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.31, C:0.16, G:0.07, T:0.45
Consensus pattern (42 bp):
TTTTTTTAATTTCGAAAAAACTAAACTCCTATCATTTTACCC
Found at i:890302 original size:12 final size:12
Alignment explanation
Indices: 890285--890317 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
890275 AGGAAGCATC
890285 AAGACCAACTCT
1 AAGACCAACTCT
890297 AAGACCAACTCT
1 AAGACCAACTCT
*
890309 AAGCCCAAC
1 AAGACCAAC
890318 ATTCTTAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.42, C:0.36, G:0.09, T:0.12
Consensus pattern (12 bp):
AAGACCAACTCT
Found at i:892039 original size:22 final size:22
Alignment explanation
Indices: 891972--892053 Score: 96
Period size: 23 Copynumber: 3.8 Consensus size: 22
891962 ATAGAACCCC
*
891972 AGGGGGTATCGATTCCCC-T-A
1 AGGGGGAATCGATTCCCCTTCA
* *
891992 TGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGATTCCCCTTC-A
*
892015 AGGGGGAATCGGTTCCCCTTCA
1 AGGGGGAATCGATTCCCCTTCA
*
892037 AGGGGGTATCGATTCCC
1 AGGGGGAATCGATTCCC
892054 TCTGCCCTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
20 15 0.28
21 1 0.02
22 16 0.30
23 21 0.40
ACGTcount: A:0.18, C:0.26, G:0.32, T:0.24
Consensus pattern (22 bp):
AGGGGGAATCGATTCCCCTTCA
Found at i:898617 original size:100 final size:100
Alignment explanation
Indices: 898444--898649 Score: 385
Period size: 100 Copynumber: 2.1 Consensus size: 100
898434 GCTTCAGATG
898444 AAGCTGGTTCTCGGTTAGCATTGTTATAAACTAGCTTTTCAATGCAGTGCTCACCAAGCAAAGGC
1 AAGCTGGTTCTCGGTTAGCATTGTTATAAACTAGCTTTTCAATGCAGTGCTCACCAAGCAAAGGC
898509 TAATCCTTTTGATAAATTACCGGGTCAAATGTAAT
66 TAATCCTTTTGATAAATTACCGGGTCAAATGTAAT
* * *
898544 AAGCTGGTTCTCGGTTAGCATTGTTATAAACTAGCTTTTCAATTCAGTGCTCACCAAGCAAGGGT
1 AAGCTGGTTCTCGGTTAGCATTGTTATAAACTAGCTTTTCAATGCAGTGCTCACCAAGCAAAGGC
898609 TAATCCTTTTGATAAATTACCGGGTCAAATGTAAT
66 TAATCCTTTTGATAAATTACCGGGTCAAATGTAAT
898644 AAGCTG
1 AAGCTG
898650 AATTTCGGCA
Statistics
Matches: 103, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
100 103 1.00
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (100 bp):
AAGCTGGTTCTCGGTTAGCATTGTTATAAACTAGCTTTTCAATGCAGTGCTCACCAAGCAAAGGC
TAATCCTTTTGATAAATTACCGGGTCAAATGTAAT
Found at i:902513 original size:120 final size:120
Alignment explanation
Indices: 902300--902544 Score: 490
Period size: 120 Copynumber: 2.0 Consensus size: 120
902290 CGAAATCCGG
902300 TAGAATTCGAATAAAGATACATCCTTTTATATACGAGACATCTTTGCACCAACTTGAGGAGTGTT
1 TAGAATTCGAATAAAGATACATCCTTTTATATACGAGACATCTTTGCACCAACTTGAGGAGTGTT
902365 AACTAACATATTCAACGTCTTTTTAGGTTTTTTGTTTATTTAATTAGCTTACTAT
66 AACTAACATATTCAACGTCTTTTTAGGTTTTTTGTTTATTTAATTAGCTTACTAT
902420 TAGAATTCGAATAAAGATACATCCTTTTATATACGAGACATCTTTGCACCAACTTGAGGAGTGTT
1 TAGAATTCGAATAAAGATACATCCTTTTATATACGAGACATCTTTGCACCAACTTGAGGAGTGTT
902485 AACTAACATATTCAACGTCTTTTTAGGTTTTTTGTTTATTTAATTAGCTTACTAT
66 AACTAACATATTCAACGTCTTTTTAGGTTTTTTGTTTATTTAATTAGCTTACTAT
902540 TAGAA
1 TAGAA
902545 ATTACATTTA
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 125 1.00
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.40
Consensus pattern (120 bp):
TAGAATTCGAATAAAGATACATCCTTTTATATACGAGACATCTTTGCACCAACTTGAGGAGTGTT
AACTAACATATTCAACGTCTTTTTAGGTTTTTTGTTTATTTAATTAGCTTACTAT
Found at i:905062 original size:3 final size:3
Alignment explanation
Indices: 905054--905081 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
905044 TAACTCCCCT
905054 TCC TCC TCC TCC TCC TCC TCC TCC TCC T
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC T
905082 TCTTCTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (3 bp):
TCC
Found at i:905086 original size:3 final size:3
Alignment explanation
Indices: 905080--905119 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
905070 CCTCCTCCTC
905080 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
905120 CCTGTTAACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:905185 original size:15 final size:16
Alignment explanation
Indices: 905160--905190 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
905150 AAACCCTAAC
905160 CCCAGAAAATCAAAAG
1 CCCAGAAAATCAAAAG
905176 CCCA-AAAATCAAAAG
1 CCCAGAAAATCAAAAG
905191 GGAACTCGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.58, C:0.26, G:0.10, T:0.06
Consensus pattern (16 bp):
CCCAGAAAATCAAAAG
Found at i:913092 original size:3 final size:3
Alignment explanation
Indices: 913084--913160 Score: 127
Period size: 3 Copynumber: 25.7 Consensus size: 3
913074 CATCAACATC
* *
913084 CTT CTT CTT CTT CTT CTT CTT CTT TTT CTT CTT CTT TTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
*
913132 CTT CTT TTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
913161 GTGAAAATGC
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
CTT
Found at i:914089 original size:28 final size:29
Alignment explanation
Indices: 914029--914108 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 29
914019 TAGAGAGTGA
* * **
914029 AAGAAGAAAAAGATGAATAAGAAGAAGTTAG
1 AAGAAGAAAAAGAT--ACAAGAAGAGGAAAG
914060 AAGAAGAAAAAGATA-AAGAAGAGGAAAG
1 AAGAAGAAAAAGATACAAGAAGAGGAAAG
914088 AAG-A-AAAAAGA-ACAAGAAGAG
1 AAGAAGAAAAAGATACAAGAAGAG
914109 TTGACGTGGG
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
25 1 0.02
26 15 0.33
27 1 0.02
28 13 0.29
29 1 0.02
31 14 0.31
ACGTcount: A:0.66, C:0.01, G:0.26, T:0.06
Consensus pattern (29 bp):
AAGAAGAAAAAGATACAAGAAGAGGAAAG
Found at i:914672 original size:14 final size:15
Alignment explanation
Indices: 914647--914677 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
914637 CCTTTATTCC
914647 ATCTAAATTATTATT
1 ATCTAAATTATTATT
914662 ATCTAAA-TATTATT
1 ATCTAAATTATTATT
914676 AT
1 AT
914678 AATAATAACG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (15 bp):
ATCTAAATTATTATT
Found at i:914944 original size:21 final size:20
Alignment explanation
Indices: 914915--914965 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
914905 CCTTAACTTA
*
914915 ATAAAAAATAT-TTAATTGAT
1 ATAAAAAATATGATAATT-AT
914935 ATATAAAAAT-TGATAATTAT
1 ATA-AAAAATATGATAATTAT
914955 ATAAAAAATAT
1 ATAAAAAATAT
914966 AATATGGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 6 0.22
20 10 0.37
21 11 0.41
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (20 bp):
ATAAAAAATATGATAATTAT
Found at i:928848 original size:21 final size:21
Alignment explanation
Indices: 928830--928878 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
928820 CTTCTGAAGC
928830 AGAACCATCACATGATGAACA
1 AGAACCATCACATGATGAACA
928851 AGAACCATCACATGATGAACA
1 AGAACCATCACATGATGAACA
928872 AGAACCA
1 AGAACCA
928879 GAGAGTTCTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.49, C:0.24, G:0.14, T:0.12
Consensus pattern (21 bp):
AGAACCATCACATGATGAACA
Found at i:933940 original size:21 final size:21
Alignment explanation
Indices: 933914--933953 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
933904 ATAAATGTTA
*
933914 AAAAATATTAATATTTTAAGT
1 AAAAATAATAATATTTTAAGT
933935 AAAAATAATAATATTTTAA
1 AAAAATAATAATATTTTAA
933954 TTAATTTTTT
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:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (21 bp):
AAAAATAATAATATTTTAAGT
Found at i:935893 original size:40 final size:41
Alignment explanation
Indices: 935849--935939 Score: 123
Period size: 40 Copynumber: 2.2 Consensus size: 41
935839 CCCTAAACTA
* * *
935849 TTAATATT-ATTCTAAATTTGTCTTTAAACTT-TTGAACATT
1 TTAAT-TTCATTCTAAATTGGTCTCTAAACTTCTTAAACATT
935889 TTAATTTCATTCTAAATTGGTCTCTAAACTTCTTAAACATT
1 TTAATTTCATTCTAAATTGGTCTCTAAACTTCTTAAACATT
*
935930 TCAATTTCAT
1 TTAATTTCAT
935940 CCCAAATTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
39 2 0.04
40 26 0.58
41 17 0.38
ACGTcount: A:0.32, C:0.14, G:0.04, T:0.49
Consensus pattern (41 bp):
TTAATTTCATTCTAAATTGGTCTCTAAACTTCTTAAACATT
Found at i:935947 original size:41 final size:40
Alignment explanation
Indices: 935862--935947 Score: 109
Period size: 41 Copynumber: 2.1 Consensus size: 40
935852 ATATTATTCT
* * * * * *
935862 AAATTTGTCTTTAAACTTTTGAACATTTTAATTTCATTCT
1 AAATTGGTCTCTAAACTTTTAAACATTTCAATTTCATCCC
935902 AAATTGGTCTCTAAACTTCTTAAACATTTCAATTTCATCCC
1 AAATTGGTCTCTAAACTT-TTAAACATTTCAATTTCATCCC
935943 AAATT
1 AAATT
935948 ATATGTATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 16 0.41
41 23 0.59
ACGTcount: A:0.33, C:0.17, G:0.05, T:0.45
Consensus pattern (40 bp):
AAATTGGTCTCTAAACTTTTAAACATTTCAATTTCATCCC
Found at i:939145 original size:22 final size:23
Alignment explanation
Indices: 939091--939137 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
939081 TATAAGAGGA
*
939091 AAAAAGTAAATTTATAAAATCTT
1 AAAAAGTAAATTAATAAAATCTT
*
939114 AAAAATTAAATTAATAAAAT-TT
1 AAAAAGTAAATTAATAAAATCTT
939136 AA
1 AA
939138 GTAGTAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (23 bp):
AAAAAGTAAATTAATAAAATCTT
Found at i:952128 original size:15 final size:15
Alignment explanation
Indices: 952108--952141 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
952098 CAGTTGTGAC
* *
952108 TTCATTATCATATTT
1 TTCATTACCACATTT
952123 TTCATTACCACATTT
1 TTCATTACCACATTT
952138 TTCA
1 TTCA
952142 GCAATAAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.26, C:0.21, G:0.00, T:0.53
Consensus pattern (15 bp):
TTCATTACCACATTT
Found at i:952740 original size:715 final size:713
Alignment explanation
Indices: 951360--952790 Score: 2469
Period size: 715 Copynumber: 2.0 Consensus size: 713
951350 TTAATCTAAA
*
951360 ATATTTATTTTAATATCATTTGGAAGTTGTGACTTCATTATCATATTTTTCATTACCACCTTTTT
1 ATATTTATTTTAATATCATTTGGAAGTTGTGACTTCATTATCATATTTTTCATTACCACATTTTT
*
951425 CAGCAATAAAACAATTTTTATTTATAGTGGCGGACCCTAAAAATGAGTGAATCCGCCACTGTTTG
66 CAGCAATAAAACAATTTTTATTTATAGTGGCGCACCCTAAAAATGAGTGAATCCGCCACTGTTTG
* * **** *
951490 ACTGTGATAACTTTGATGTCTGAACTTTTAAGGCATCCATTAGCAAAGTCTTCTACCTTTCATGA
131 ACTGTGATAACTTTGATGTCTGAACTTTGAAGGCATCCATGAGCAAAAAAGTCCACCTTTCATGA
*
951555 ATTAGGATAAACTCCAAATATTTAATTTGTTGTGTGGACGGTGTACATGTAAATTAAATTAGACT
196 ATTAGGATAAACTCCAAATATTTAATTTGTTGTGTGGACGGTGCACATGTAAATTAAATTAGACT
*
951620 ATATATCAAAAAAATATTTTTAATAACTTGAAAAAATATATGATACATTAATAAATTATGTAAGG
261 ATATATCAAAAAAATATTTTTAATAACTTGAAAAAAGATATGATACATTAATAAATTATGTAAGG
951685 TCACCTCATATATATATATATATATATATATTGATGTGTGGATGTTGCACATTTGAATTAAATCA
326 TCACCTCA-ATATATATATATATATATATATTGATGTGTGGATGTTGCACATTTGAATTAAATCA
* *
951750 TAGTGAAAACTACACCGATACCACCAAGCTCTAAGCGTTGTATCATTTATATCATTTAACTTTTA
390 TAGTGAAAACTACACCAATACCACCAAGCTCTAAGCGTTGTATCATTTATACCATTTAACTTTTA
*
951815 ATTTTATCAATCATAGCATTGAACTTTGATTTTTGTTTCAATGATACCACTGGGTCGTTAAATCA
455 ATTTTATCAATCATAGCATTAAACTTTGATTTTTGTTTCAATGATACCACTGGGTCGTTAAATCA
951880 TTAACAATTGGATCAACACGACGTCGTTTTGGTGAAGTGTCTATATCAACAGCCGTCAGCCACAT
520 TTAACAATTGGATCAACACGACGTCGTTTTGGTGAAGTGTCTATATCAACAGCCGTCAGCCACAT
*
951945 CATCTTGTCGTTAACGATTTAAATCCCATTGGTATGATTGAAATGAAAATTAGAGTTTAATGTTA
585 CATCTTGTCGTTAACGATTTAAATCCCATTGGTATGATTGAAATGAAAATTAGAGTTCAATGTTA
* *
952010 TAATTGATAAAATTGAAAGTTTAATGGTATAAACTATACAATACCTAAAGTTCGATGGCATCTG
650 TAATTGATAAAATTGAAAGTTTAATGGTATAAACAATACAATACCTAAAGTTCGATGACATCTG
*
952074 ATATTTATATTTAATATCATTTGGCAGTTGTGACTTCATTATCATATTTTTCATTACCACATTTT
1 ATATTTAT-TTTAATATCATTTGGAAGTTGTGACTTCATTATCATATTTTTCATTACCACATTTT
952139 TCAGCAATAAAACAATTTTTATTTATAGTGGCGCACCCTAAACAATGAGTGAATCCGCCACTGTT
65 TCAGCAATAAAACAATTTTTATTTATAGTGGCGCACCCTAAA-AATGAGTGAATCCGCCACTGTT
**
952204 TGACTGTGATGTCTTTGATGTCTGAACTTTGAAGGCATCCCATGAGCAAAAAAGTCCACCTTTCA
129 TGACTGTGATAACTTTGATGTCTGAACTTTGAAGGCAT-CCATGAGCAAAAAAGTCCACCTTTCA
952269 TGAATTAGGATAAACTCCAAATATTTAATTTGTTGTGTGGACGGTGCACATGTAAATTAAATTAG
193 TGAATTAGGATAAACTCCAAATATTTAATTTGTTGTGTGGACGGTGCACATGTAAATTAAATTAG
952334 ACTATATAATCAAAAAAATA-TTTTAATAACTTGAAAAAAAAGATATGATACATTAATAAATTAT
258 ACTATAT-ATCAAAAAAATATTTTTAATAACTTG--AAAAAAGATATGATACATTAATAAATTAT
952398 GTAAGGTCACCTC-ATATATATATATATATATAT-TTGATGTGTGGATGTTGCACATTTGAATTA
320 GTAAGGTCACCTCAATATATATATATATATATATATTGATGTGTGGATGTTGCACATTTGAATTA
* *
952461 AATTATAGTGAAAACTACACCAATACCACCGAA-CTCTAAGCGTTGTATCGTTTATACCATTTAA
385 AATCATAGTGAAAACTACACCAATACCACC-AAGCTCTAAGCGTTGTATCATTTATACCATTTAA
*
952525 CTTTTAATTTTATCAAT-ATAGCATTAAACTTTGATTTTTGTTTCAATGATACCATTGGGTCGTT
449 CTTTTAATTTTATCAATCATAGCATTAAACTTTGATTTTTGTTTCAATGATACCACTGGGTCGTT
* * *
952589 AAATCATTAACAATTGGATCAACACGACGTCGTTTTGGTGATGTGTTTATATCAGCAGCCGTCAG
514 AAATCATTAACAATTGGATCAACACGACGTCGTTTTGGTGAAGTGTCTATATCAACAGCCGTCAG
* *
952654 CCACCTCATCTTGTCGTTAACGATTTAAATCCCATTGGTATGATTGAAATGAAAATTAGAGTTCG
579 CCACATCATCTTGTCGTTAACGATTTAAATCCCATTGGTATGATTGAAATGAAAATTAGAGTTCA
* *
952719 GTGTTATAATTGA-ACAAATTGAAAGTTTAATTGTATAAACAATACAATACCTAAAGTTCGATGA
644 ATGTTATAATTGATA-AAATTGAAAGTTTAATGGTATAAACAATACAATACCTAAAGTTCGATGA
952783 CATCTG
708 CATCTG
952789 AT
1 AT
952791 CTAATTTACC
Statistics
Matches: 679, Mismatches: 30, Indels: 15
0.94 0.04 0.02
Matches are distributed among these distances:
714 9 0.01
715 330 0.49
716 161 0.24
717 126 0.19
718 12 0.02
719 41 0.06
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.36
Consensus pattern (713 bp):
ATATTTATTTTAATATCATTTGGAAGTTGTGACTTCATTATCATATTTTTCATTACCACATTTTT
CAGCAATAAAACAATTTTTATTTATAGTGGCGCACCCTAAAAATGAGTGAATCCGCCACTGTTTG
ACTGTGATAACTTTGATGTCTGAACTTTGAAGGCATCCATGAGCAAAAAAGTCCACCTTTCATGA
ATTAGGATAAACTCCAAATATTTAATTTGTTGTGTGGACGGTGCACATGTAAATTAAATTAGACT
ATATATCAAAAAAATATTTTTAATAACTTGAAAAAAGATATGATACATTAATAAATTATGTAAGG
TCACCTCAATATATATATATATATATATATTGATGTGTGGATGTTGCACATTTGAATTAAATCAT
AGTGAAAACTACACCAATACCACCAAGCTCTAAGCGTTGTATCATTTATACCATTTAACTTTTAA
TTTTATCAATCATAGCATTAAACTTTGATTTTTGTTTCAATGATACCACTGGGTCGTTAAATCAT
TAACAATTGGATCAACACGACGTCGTTTTGGTGAAGTGTCTATATCAACAGCCGTCAGCCACATC
ATCTTGTCGTTAACGATTTAAATCCCATTGGTATGATTGAAATGAAAATTAGAGTTCAATGTTAT
AATTGATAAAATTGAAAGTTTAATGGTATAAACAATACAATACCTAAAGTTCGATGACATCTG
Found at i:953416 original size:60 final size:58
Alignment explanation
Indices: 953279--953465 Score: 153
Period size: 60 Copynumber: 3.1 Consensus size: 58
953269 GTATATACGT
* * * * * *
953279 ATAGTTTGGGATAAAAATGGAATGCTCAAAGAGTTTGGGGGCAATTTAGAATGAAGGTC
1 ATAGTTTGGGATAAAATTGAAATGTTCAAA-AGTTTGAGGACAATTTAGAATGAAGATC
* *
953338 ATTGTTTGGGGATGAAATTGAAATGTTCAAAAGTTTGAGGACTAATTTAGAATGATA-ATC
1 ATAGTTT-GGGATAAAATTGAAATGTTCAAAAGTTTGAGGAC-AATTTAGAATGA-AGATC
* * * * * * *
953398 ATAGTTTATGGATAAAATTAAAATATTTAAAAGTTT-AGGGACCAATTTAAAATAAAGGTC
1 ATAGTTT-GGGATAAAATTGAAATGTTCAAAAGTTTGA-GGA-CAATTTAGAATGAAGATC
*
953458 ATACTTTG
1 ATAGTTTG
953466 AGGACATATG
Statistics
Matches: 102, Mismatches: 20, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
59 17 0.17
60 83 0.81
61 2 0.02
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.33
Consensus pattern (58 bp):
ATAGTTTGGGATAAAATTGAAATGTTCAAAAGTTTGAGGACAATTTAGAATGAAGATC
Found at i:955247 original size:28 final size:28
Alignment explanation
Indices: 955216--955271 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
955206 AATAACTTTT
955216 ATAAATCTAAAGAAAGAAAGAAACAAGA
1 ATAAATCTAAAGAAAGAAAGAAACAAGA
955244 ATAAATCTAAAGAAAGAAAGAAACAAGA
1 ATAAATCTAAAGAAAGAAAGAAACAAGA
955272 GAGTTTGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.68, C:0.07, G:0.14, T:0.11
Consensus pattern (28 bp):
ATAAATCTAAAGAAAGAAAGAAACAAGA
Found at i:955524 original size:23 final size:23
Alignment explanation
Indices: 955493--955551 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
955483 TGGTGCCACA
* *
955493 TCACCTGCCATGTTATCACCATG
1 TCACCTGCCACGTTATAACCATG
*
955516 TCATCTGCCACGTTATAACCATG
1 TCACCTGCCACGTTATAACCATG
955539 TCACCTGCCACGT
1 TCACCTGCCACGT
955552 CATCTGCCAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.22, C:0.36, G:0.14, T:0.29
Consensus pattern (23 bp):
TCACCTGCCACGTTATAACCATG
Found at i:955554 original size:35 final size:35
Alignment explanation
Indices: 955515--955598 Score: 141
Period size: 35 Copynumber: 2.4 Consensus size: 35
955505 TTATCACCAT
*
955515 GTCATCTGCCACGTTATAACCATGTCACCTGCCAC
1 GTCATCTGCCACATTATAACCATGTCACCTGCCAC
*
955550 GTCATCTGCCACATTATCACCATGTCACCTGCCAC
1 GTCATCTGCCACATTATAACCATGTCACCTGCCAC
*
955585 GTCATCTACCACAT
1 GTCATCTGCCACAT
955599 CAGTCGCTGA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.24, C:0.38, G:0.12, T:0.26
Consensus pattern (35 bp):
GTCATCTGCCACATTATAACCATGTCACCTGCCAC
Found at i:955558 original size:12 final size:12
Alignment explanation
Indices: 955515--955596 Score: 51
Period size: 12 Copynumber: 7.0 Consensus size: 12
955505 TTATCACCAT
955515 GTCATCTGCCAC
1 GTCATCTGCCAC
* ** *
955527 GTTAT-AACCAT
1 GTCATCTGCCAC
*
955538 GTCACCTGCCAC
1 GTCATCTGCCAC
955550 GTCATCTGCCAC
1 GTCATCTGCCAC
* * * *
955562 ATTATC-ACCAT
1 GTCATCTGCCAC
*
955573 GTCACCTGCCAC
1 GTCATCTGCCAC
*
955585 GTCATCTACCAC
1 GTCATCTGCCAC
955597 ATCAGTCGCT
Statistics
Matches: 47, Mismatches: 21, Indels: 4
0.65 0.29 0.06
Matches are distributed among these distances:
11 12 0.26
12 35 0.74
ACGTcount: A:0.23, C:0.39, G:0.12, T:0.26
Consensus pattern (12 bp):
GTCATCTGCCAC
Found at i:959122 original size:48 final size:48
Alignment explanation
Indices: 959070--959166 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
959060 ACATGAACCT
*
959070 AGAATCGATCCCTTACAAATAATGCAAGTTTAAAATATATAAGCCTTA
1 AGAATCGACCCCTTACAAATAATGCAAGTTTAAAATATATAAGCCTTA
959118 AGAATCGACCCCTTACAAATAATGCAAGTTTAAAATATATAAGCCTTA
1 AGAATCGACCCCTTACAAATAATGCAAGTTTAAAATATATAAGCCTTA
959166 A
1 A
959167 TAACAAGGCC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28
Consensus pattern (48 bp):
AGAATCGACCCCTTACAAATAATGCAAGTTTAAAATATATAAGCCTTA
Found at i:962505 original size:28 final size:28
Alignment explanation
Indices: 962481--962536 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
962471 TTAACATCTG
962481 AGTTGAATAATAGTAAATATGACATAAT
1 AGTTGAATAATAGTAAATATGACATAAT
962509 AGTTGAATAATAGTAAATATGACATAAT
1 AGTTGAATAATAGTAAATATGACATAAT
962537 TTAAGGGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.50, C:0.04, G:0.14, T:0.32
Consensus pattern (28 bp):
AGTTGAATAATAGTAAATATGACATAAT
Found at i:962509 original size:17 final size:17
Alignment explanation
Indices: 962487--962536 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
962477 TCTGAGTTGA
962487 ATAATAGTAAATATGAC
1 ATAATAGTAAATATGAC
962504 ATAATAG----T-TGA-
1 ATAATAGTAAATATGAC
962515 ATAATAGTAAATATGAC
1 ATAATAGTAAATATGAC
962532 ATAAT
1 ATAAT
962537 TTAAGGGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 12
0.69 0.00 0.31
Matches are distributed among these distances:
11 7 0.26
12 3 0.11
13 1 0.04
15 1 0.04
16 3 0.11
17 12 0.44
ACGTcount: A:0.52, C:0.04, G:0.12, T:0.32
Consensus pattern (17 bp):
ATAATAGTAAATATGAC
Found at i:969725 original size:25 final size:25
Alignment explanation
Indices: 969692--969744 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
969682 TAAGCCTAGT
969692 CGAGTTTATGAAATTCGCGTCTAAC
1 CGAGTTTATGAAATTCGCGTCTAAC
969717 CGAGTTTATGAAATTCGCGTCTAAC
1 CGAGTTTATGAAATTCGCGTCTAAC
969742 CGA
1 CGA
969745 ATTGAGTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (25 bp):
CGAGTTTATGAAATTCGCGTCTAAC
Found at i:972424 original size:18 final size:18
Alignment explanation
Indices: 972403--972444 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
972393 TATAAAATAA
* *
972403 TTATTAAATTTATCACTG
1 TTATTAAAATAATCACTG
972421 TTA-TAAAATAATCACTG
1 TTATTAAAATAATCACTG
972438 TATATTA
1 T-TATTA
972445 TAAAATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 13 0.65
18 5 0.25
19 2 0.10
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (18 bp):
TTATTAAAATAATCACTG
Found at i:987589 original size:24 final size:24
Alignment explanation
Indices: 987556--987602 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
987546 GTATTCGTGT
987556 GCCTGATTCTGGTACTGCTGCTGG
1 GCCTGATTCTGGTACTGCTGCTGG
* *
987580 GCCTGGTTCTGGTATTGCTGCTG
1 GCCTGATTCTGGTACTGCTGCTG
987603 CTGCTCGGCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.06, C:0.23, G:0.34, T:0.36
Consensus pattern (24 bp):
GCCTGATTCTGGTACTGCTGCTGG
Found at i:997031 original size:174 final size:171
Alignment explanation
Indices: 996741--997086 Score: 494
Period size: 174 Copynumber: 2.0 Consensus size: 171
996731 GCACTCCTTC
* * * * * *
996741 GCATTACTAGGTACCTGTGAATTGCTCTCATTAGTAGCCACAATACCCTCATTAGCATCCAATAA
1 GCATTACTAGGTACCAGGGAACTGCTCTCATTAGCAGCCACAATACCCCCATTAGCACCCAATAA
* * * * *
996806 CGCCGAAACATCAGCATCTTCTACACCCTTTTGAGCTTCTGTACCAATATCAACATCCTTTTCAC
66 CGCCGAAACATCAGCATCTTCTACACACTTTTCAGCTTCTGCACCAATATCAACATCCATTCCAC
* *
996871 CGGACTCAACCCCAGAAGGCCTCGTTTCACTAATAATCAAATTA
131 CAGACTCAACCCC---AGGACTCGTTTCACTAATAATCAAATTA
*
996915 GCATTACTAGGTACCAGGGAACTGCTCTCATTAGCAGCCACATTACCCCCATTAGCACCCAATAA
1 GCATTACTAGGTACCAGGGAACTGCTCTCATTAGCAGCCACAATACCCCCATTAGCACCCAATAA
* * * *
996980 TGCCGAAATATCGGCATCTTCTACACACTTTTCATCTTCTGCACCAATATCAACATCCATTCCAC
66 CGCCGAAACATCAGCATCTTCTACACACTTTTCAGCTTCTGCACCAATATCAACATCCATTCCAC
*
997045 CAGACTCAACCCCAGGACTCGTTTTACTAATAATCAAATTA
131 CAGACTCAACCCCAGGACTCGTTTCACTAATAATCAAATTA
997086 G
1 G
997087 AAAAAGCTTT
Statistics
Matches: 153, Mismatches: 19, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
171 27 0.18
174 126 0.82
ACGTcount: A:0.30, C:0.31, G:0.12, T:0.27
Consensus pattern (171 bp):
GCATTACTAGGTACCAGGGAACTGCTCTCATTAGCAGCCACAATACCCCCATTAGCACCCAATAA
CGCCGAAACATCAGCATCTTCTACACACTTTTCAGCTTCTGCACCAATATCAACATCCATTCCAC
CAGACTCAACCCCAGGACTCGTTTCACTAATAATCAAATTA
Found at i:1001103 original size:21 final size:21
Alignment explanation
Indices: 1001077--1001123 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
1001067 AGTAGATTTG
1001077 ACTGCTATTTCCAATCTTTTT
1 ACTGCTATTTCCAATCTTTTT
*
1001098 ACTGCTATTTCCAATTTTTTT
1 ACTGCTATTTCCAATCTTTTT
1001119 ACTGC
1 ACTGC
1001124 GTGACTTGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.19, C:0.23, G:0.06, T:0.51
Consensus pattern (21 bp):
ACTGCTATTTCCAATCTTTTT
Found at i:1001296 original size:45 final size:45
Alignment explanation
Indices: 1001227--1001340 Score: 149
Period size: 45 Copynumber: 2.5 Consensus size: 45
1001217 AAGTACTACT
* * *
1001227 TAAAATATTATTTTTCTACCGAAAAT-ATTAATATTAGGTGCTATC
1 TAAAATATTATTTTTCTACTGAAAATGA-TAATATTAGATGATATC
*
1001272 TAAAACATTATTTTTCTACTGAAAATGATAATATTAGATGATATC
1 TAAAATATTATTTTTCTACTGAAAATGATAATATTAGATGATATC
*
1001317 TAAAATGTTATTTTTTTCTACTGA
1 TAAAATATTA--TTTTTCTACTGA
1001341 TTTTTAAATA
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
45 47 0.78
46 1 0.02
47 12 0.20
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.44
Consensus pattern (45 bp):
TAAAATATTATTTTTCTACTGAAAATGATAATATTAGATGATATC
Found at i:1002023 original size:34 final size:33
Alignment explanation
Indices: 1001937--1002026 Score: 89
Period size: 34 Copynumber: 2.7 Consensus size: 33
1001927 AAATAATACA
1001937 TATTTAA-GTTTGAATATTAAAATGAGTTTTATC
1 TATTTAATG-TTGAATATTAAAATGAGTTTTATC
* *
1001970 T-TTTAAATATTTCAA-ATTAAAA-GATGTTGTTATC
1 TATTT-AAT-GTTGAATATTAAAATGA-GTT-TTATC
1002004 TATTTAATGTTGAATATTAAAAT
1 TATTTAATGTTGAATATTAAAAT
1002027 ATATTTATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
32 5 0.11
33 17 0.38
34 20 0.44
35 3 0.07
ACGTcount: A:0.39, C:0.03, G:0.10, T:0.48
Consensus pattern (33 bp):
TATTTAATGTTGAATATTAAAATGAGTTTTATC
Found at i:1005703 original size:68 final size:68
Alignment explanation
Indices: 1005618--1006015 Score: 612
Period size: 68 Copynumber: 5.9 Consensus size: 68
1005608 AGGGTTTTTA
*
1005618 AGGGTAAACTACCTATTTGGTTACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTATTA
1 AGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTATTA
1005683 TTT
66 TTT
* *
1005686 AGGGTAAACTACCTATTTGGTAACTTACATATTATCTAATTTATGTTTTGGTCACTCGATTATTA
1 AGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTATTA
1005751 TTT
66 TTT
1005754 AGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTATTA
1 AGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTATTA
1005819 TTT
66 TTT
* * *
1005822 AGGGTAAACTACCTATTTGGTAACTTACATATTATCAAATTTATGTTTTGGTCACTCGATTATTA
1 AGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTATTA
1005887 TTT
66 TTT
* * * ** * *
1005890 AGGCTAAACTACATATTTGGTCACTTATATATTATCTAATATAAT-TCAT-AT-A-T--ATTTTT
1 AGGGTAAACTACCTATTTGGTCACTTATATATTATCTAAT-TTATGTTTTGGTCACTCGATTATT
1005949 ATTT
65 ATTT
*
1005953 AGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTTTGTTTT-GTCACTCGATTATT
1 AGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTATT
1006016 TTTTCTCAAA
Statistics
Matches: 299, Mismatches: 25, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
62 2 0.01
63 50 0.17
64 1 0.00
65 2 0.01
66 1 0.00
67 6 0.02
68 234 0.78
69 3 0.01
ACGTcount: A:0.28, C:0.13, G:0.12, T:0.47
Consensus pattern (68 bp):
AGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTATTA
TTT
Done.