Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001409.1 Hibiscus syriacus cultivar Beakdansim tig00002746_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: 124107
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:37 original size:30 final size:30
Alignment explanation
Indices: 1--354 Score: 589
Period size: 30 Copynumber: 12.0 Consensus size: 30
1 TTACCGA-GATCTTTATGACCTCTGGATAG
1 TTACCGAGGATCTTTATGACCTCTGGATAG
*
30 TTTACCGAGGATC-TT-TGACCTCTGGACAG
1 -TTACCGAGGATCTTTATGACCTCTGGATAG
59 TTACCGAGGATCTTTATGACCTCTGGATAG
1 TTACCGAGGATCTTTATGACCTCTGGATAG
*
89 TTACCCGAGGATCTTTATGACCTCTGGACAG
1 TTA-CCGAGGATCTTTATGACCTCTGGATAG
120 TTACCGAGGATCTTTATGACCTCTGGATAG
1 TTACCGAGGATCTTTATGACCTCTGGATAG
*
150 TTACCGA-GATC-TT-TGACCTCT-GACAG
1 TTACCGAGGATCTTTATGACCTCTGGATAG
*
176 TTACCGAGGATCTTTATGACCTCTGGACAG
1 TTACCGAGGATCTTTATGACCTCTGGATAG
206 TTACCGAGGATCTTTATGACCTCTGGATAG
1 TTACCGAGGATCTTTATGACCTCTGGATAG
*
236 TTACCGAGGATCTTTATGACCTCTGGACAG
1 TTACCGAGGATCTTTATGACCTCTGGATAG
266 TTACCGAGGATCTTTATGACCTCTGGATAG
1 TTACCGAGGATCTTTATGACCTCTGGATAG
296 TTACCGAGGATCTTTATGA-CTCTGGATAG
1 TTACCGAGGATCTTTATGACCTCTGGATAG
325 TTACCGAGGATCTTTATGACCTCTGGATAG
1 TTACCGAGGATCTTTATGACCTCTGGATAG
355 GTCATTCGGA
Statistics
Matches: 307, Mismatches: 8, Indels: 18
0.92 0.02 0.05
Matches are distributed among these distances:
26 11 0.04
27 12 0.04
28 16 0.05
29 56 0.18
30 179 0.58
31 33 0.11
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (30 bp):
TTACCGAGGATCTTTATGACCTCTGGATAG
Found at i:5426 original size:4 final size:4
Alignment explanation
Indices: 5417--5442 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
5407 ACTAATTGAC
5417 AGTT AGTT AGTT AGTT AGTT AGTT AG
1 AGTT AGTT AGTT AGTT AGTT AGTT AG
5443 ATTGAAATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (4 bp):
AGTT
Found at i:14202 original size:22 final size:24
Alignment explanation
Indices: 14160--14204 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
14150 GTAATAAAGT
14160 AATAATATATATTTTTAATTTTTG
1 AATAATATATATTTTTAATTTTTG
*
14184 AATAATTTA-ATTTTT-ATTTTT
1 AATAATATATATTTTTAATTTTT
14205 CGTATTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 6 0.30
24 8 0.40
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
AATAATATATATTTTTAATTTTTG
Found at i:14219 original size:23 final size:23
Alignment explanation
Indices: 14160--14250 Score: 64
Period size: 23 Copynumber: 3.9 Consensus size: 23
14150 GTAATAAAGT
14160 AATAATATATATTTTTAATTTTTG
1 AATAAT-TATATTTTTAATTTTTG
14184 AATAATT-TAATTTTT-ATTTTTCG
1 AATAATTAT-ATTTTTAATTTTT-G
* *
14207 TATTATTATA--TTTAAGTTTTTG
1 AATAATTATATTTTTAA-TTTTTG
* *
14229 AATATTTTTATATTTTGAATTT
1 AATA--ATTATATTTTTAATTT
14251 AATTTTTTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 17
0.69 0.08 0.23
Matches are distributed among these distances:
21 3 0.06
22 11 0.21
23 19 0.37
24 12 0.23
25 3 0.06
26 4 0.08
ACGTcount: A:0.32, C:0.01, G:0.05, T:0.62
Consensus pattern (23 bp):
AATAATTATATTTTTAATTTTTG
Found at i:22103 original size:15 final size:15
Alignment explanation
Indices: 22083--22114 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
22073 TGTAACATAT
22083 ATCAAATTATCTCAA
1 ATCAAATTATCTCAA
22098 ATCAAATTATCTCAA
1 ATCAAATTATCTCAA
22113 AT
1 AT
22115 TGGTCTCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.34
Consensus pattern (15 bp):
ATCAAATTATCTCAA
Found at i:23959 original size:27 final size:29
Alignment explanation
Indices: 23917--23997 Score: 103
Period size: 27 Copynumber: 2.9 Consensus size: 29
23907 ACTCAGATGC
* *
23917 TAATATAAATAAACTTGTCTACCACAATT
1 TAATATGAAGAAACTTGTCTACCACAATT
* *
23946 TAATGTG-A-AAACTTGTCTACCACAGTT
1 TAATATGAAGAAACTTGTCTACCACAATT
*
23973 TAATATGAAGAAACGTGTCTACCAC
1 TAATATGAAGAAACTTGTCTACCAC
23998 TTTGAGTTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
27 24 0.53
28 2 0.04
29 19 0.42
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.31
Consensus pattern (29 bp):
TAATATGAAGAAACTTGTCTACCACAATT
Found at i:27584 original size:29 final size:29
Alignment explanation
Indices: 27547--27629 Score: 130
Period size: 29 Copynumber: 2.9 Consensus size: 29
27537 CTCAAGATGC
*
27547 TAATATGAATAAACTTGTCTACCACAATT
1 TAATATGAAGAAACTTGTCTACCACAATT
*
27576 TAATGTGAAGAAACTTGTCTACCACAATT
1 TAATATGAAGAAACTTGTCTACCACAATT
* *
27605 TAATATGAAGAAACGTGTCAACCAC
1 TAATATGAAGAAACTTGTCTACCAC
27630 TTTGAGTTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (29 bp):
TAATATGAAGAAACTTGTCTACCACAATT
Found at i:29231 original size:157 final size:158
Alignment explanation
Indices: 28887--29288 Score: 571
Period size: 158 Copynumber: 2.5 Consensus size: 158
28877 AGTTACATAA
* * * **
28887 GTATTCTATTATGGTAT-GTGAGTATGTGGTTTAAATTTGGTACAAAAAATAAACTTAAAATAAA
1 GTATTCTACTATGGTTTAG-GAGTATGTGGTTCAAATTTGGT--AAAAAATGGACTTAAAATAAA
* *
28951 TGACAAATTGAATG-AATAAGGAGATTATGGAAAATTGAAGGACCAAATTGAAAAATAAATAATT
63 TGACGAATTGAA-GAAATAAGGAGATTATGAAAAATTGAAGGACCAAATTGAAAAATAAATAATT
29015 TGTAATCAAAAAGAGGAATTGAAAGTACACAT
127 TGTAATCAAAAAGAGGAATTGAAAGTACACAT
* * *
29047 GTATTCTACTATGGTTTAGGAGCATGTGGCTCAAATTTGGTAAAAAAGGGACTTAAAATAAATGA
1 GTATTCTACTATGGTTTAGGAGTATGTGGTTCAAATTTGGTAAAAAATGGACTTAAAATAAATGA
* *
29112 CGAATTGAAGAAATAAGGAGATTATGAAAAATTGAAGGACTAAATTGAAAAATAAA-AATTTGTT
66 CGAATTGAAGAAATAAGGAGATTATGAAAAATTGAAGGACCAAATTGAAAAATAAATAATTTGTA
29176 ATCAAAAAGAGGAATTGAAAGTA-AGCAT
131 ATCAAAAAGAGGAATTGAAAGTACA-CAT
* *
29204 GTATTCTACTATGGTTTAGGAGTATGTGGTTCAAATTTGGTAAAAATATGGACTTAAAATGAAGG
1 GTATTCTACTATGGTTTAGGAGTATGTGGTTCAAATTTGGTAAAAA-ATGGACTTAAAATAAATG
*
29269 A-GAAATTGAATAAATAAGGA
65 ACG-AATTGAAGAAATAAGGA
29289 AATCAGAGAC
Statistics
Matches: 219, Mismatches: 18, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
156 1 0.00
157 79 0.36
158 104 0.47
160 34 0.16
161 1 0.00
ACGTcount: A:0.45, C:0.06, G:0.20, T:0.29
Consensus pattern (158 bp):
GTATTCTACTATGGTTTAGGAGTATGTGGTTCAAATTTGGTAAAAAATGGACTTAAAATAAATGA
CGAATTGAAGAAATAAGGAGATTATGAAAAATTGAAGGACCAAATTGAAAAATAAATAATTTGTA
ATCAAAAAGAGGAATTGAAAGTACACAT
Found at i:29586 original size:60 final size:60
Alignment explanation
Indices: 29482--29606 Score: 162
Period size: 60 Copynumber: 2.1 Consensus size: 60
29472 TAAAGAAAGC
* * *
29482 AAATGATCCTCTGACTATAGGGTACTACTTTATTAAGTCTCTCGATTATTAAAAGTTACA
1 AAATGATCCTCTGACTATAGGGTACTACTTTATTAAGTCCCTCGACTATAAAAAGTTACA
** * * *
29542 AAATGATCCT-TCGACTATAGGGTGTTGCTTTTTTGAGTCCCTCGACTATAAAAAGTTACA
1 AAATGATCCTCT-GACTATAGGGTACTACTTTATTAAGTCCCTCGACTATAAAAAGTTACA
29602 AAATG
1 AAATG
29607 GTCACCTGAC
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 1 0.02
60 55 0.98
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (60 bp):
AAATGATCCTCTGACTATAGGGTACTACTTTATTAAGTCCCTCGACTATAAAAAGTTACA
Found at i:30479 original size:31 final size:31
Alignment explanation
Indices: 30444--30512 Score: 138
Period size: 31 Copynumber: 2.2 Consensus size: 31
30434 GGTAGTATCA
30444 ATACTATAGTTTAAGGATTTAATAAAACATT
1 ATACTATAGTTTAAGGATTTAATAAAACATT
30475 ATACTATAGTTTAAGGATTTAATAAAACATT
1 ATACTATAGTTTAAGGATTTAATAAAACATT
30506 ATACTAT
1 ATACTAT
30513 TGTCGGGGGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (31 bp):
ATACTATAGTTTAAGGATTTAATAAAACATT
Found at i:32385 original size:20 final size:20
Alignment explanation
Indices: 32334--32389 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 20
32324 AAATGACCAA
*
32334 CAAA-TTCGCAACGCGATCT
1 CAAATTTCGCAACGCGAACT
32353 CAAATTT-GCAACGCGAACT
1 CAAATTTCGCAACGCGAACT
*
32372 CCAATTTCGCAACGCGAA
1 CAAATTTCGCAACGCGAA
32390 TTTAGAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 21 0.64
20 12 0.36
ACGTcount: A:0.34, C:0.30, G:0.16, T:0.20
Consensus pattern (20 bp):
CAAATTTCGCAACGCGAACT
Found at i:32511 original size:19 final size:19
Alignment explanation
Indices: 32434--32505 Score: 99
Period size: 19 Copynumber: 3.7 Consensus size: 19
32424 ACACGTTTGC
*
32434 CAAATTCGCAACACTGAATTT
1 CAAATTCGC-A-ACTAAATTT
32455 CAAATTCGCAACTAAATTT
1 CAAATTCGCAACTAAATTT
*
32474 CAAATTTGCAACTAAATTT
1 CAAATTCGCAACTAAATTT
*
32493 CAAATTCGTAACT
1 CAAATTCGCAACT
32506 CGATTTTTGA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
19 37 0.79
20 1 0.02
21 9 0.19
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.32
Consensus pattern (19 bp):
CAAATTCGCAACTAAATTT
Found at i:32735 original size:16 final size:15
Alignment explanation
Indices: 32700--32738 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
32690 TCCCCATCTC
*
32700 TAATTTTTTTTTACA
1 TAATTTTTTTCTACA
*
32715 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
32731 TAATTTTT
1 TAATTTTT
32739 CAATGATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:33531 original size:24 final size:24
Alignment explanation
Indices: 33480--33533 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
33470 GTATTCGAAA
*
33480 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
33504 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
33528 TTTGAT
1 TTTGAT
33534 GATGTTTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:36071 original size:34 final size:34
Alignment explanation
Indices: 36018--36082 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
36008 TTGATGTGAA
** * *
36018 AGTCAAATTCGCATTGCGATTTTTGCGTTGCGAT
1 AGTCAAATTCGCAACGCGATTATAGCGTTGCGAT
*
36052 AGTCAAATTTGCAACGCGATTATAGCGTTGC
1 AGTCAAATTCGCAACGCGATTATAGCGTTGC
36083 AATTGTTGCG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (34 bp):
AGTCAAATTCGCAACGCGATTATAGCGTTGCGAT
Found at i:37688 original size:21 final size:21
Alignment explanation
Indices: 37664--37781 Score: 107
Period size: 21 Copynumber: 5.6 Consensus size: 21
37654 GTGAATCGGA
*
37664 CTCTTGAACGGTGGAAGGGAC
1 CTCTTGAACGATGGAAGGGAC
*
37685 CTCTTGAACGAT-GACAGGGGC
1 CTCTTGAACGATGGA-AGGGAC
* * *
37706 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGATGGAAGGGAC
*
37727 CTCTTGAACGAT-AACAGAGG-C
1 CTCTTGAACGATGGA-AG-GGAC
* *
37748 CTCTTGAACGATGGGAGGCAC
1 CTCTTGAACGATGGAAGGGAC
*
37769 CTCTTGAATGATG
1 CTCTTGAACGATG
37782 ACAGGTGCAT
Statistics
Matches: 80, Mismatches: 11, Indels: 12
0.78 0.11 0.12
Matches are distributed among these distances:
20 3 0.04
21 74 0.93
22 3 0.04
ACGTcount: A:0.24, C:0.21, G:0.34, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGATGGAAGGGAC
Found at i:37730 original size:42 final size:42
Alignment explanation
Indices: 37664--37786 Score: 183
Period size: 42 Copynumber: 2.9 Consensus size: 42
37654 GTGAATCGGA
*
37664 CTCTTGAACGGTGGAAGGGACCTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGGGC
* * *
37706 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATAACAGAGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGGGC
* * *
37748 CTCTTGAACGATGGGAGGCACCTCTTGAATGATGACAGG
1 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGG
37787 TGCATCGGGC
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.24, C:0.21, G:0.34, T:0.20
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGGGC
Found at i:37942 original size:4 final size:4
Alignment explanation
Indices: 37926--37967 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
37916 GGGCTGCTGA
* * *
37926 AAAT AAAT TAAT AAAT AAAT CAGT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
37968 TTCTGAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:38089 original size:21 final size:21
Alignment explanation
Indices: 38065--38114 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
38055 TGAAACAATC
*
38065 TCACGTAGAG-CGACTACCTCA
1 TCACGTAGAGTAGA-TACCTCA
*
38086 TCACGTAAAGTAGATACCTCA
1 TCACGTAGAGTAGATACCTCA
*
38107 CCACGTAG
1 TCACGTAG
38115 CACACCATTG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.20
Consensus pattern (21 bp):
TCACGTAGAGTAGATACCTCA
Found at i:38147 original size:63 final size:62
Alignment explanation
Indices: 38080--38199 Score: 152
Period size: 63 Copynumber: 1.9 Consensus size: 62
38070 TAGAGCGACT
* *
38080 ACCTCATCACGTAAAGTA-GATACCTCACCACGTAGCACACCATTGTCATCGCGTAAAACATCC
1 ACCTCACCACGTAAAG-ACG-TACCTCACCACGTAGCACACCATTGTCATCACGTAAAACATCC
* * * *
38143 ACCTCACCATGTAAAGACCGTACCTCATCATGTAGCACACCATTGTCTTCACGTAAA
1 ACCTCACCACGTAAAGA-CGTACCTCACCACGTAGCACACCATTGTCATCACGTAAA
38200 GTACCGACCT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
62 1 0.02
63 47 0.96
64 1 0.02
ACGTcount: A:0.33, C:0.33, G:0.12, T:0.23
Consensus pattern (62 bp):
ACCTCACCACGTAAAGACGTACCTCACCACGTAGCACACCATTGTCATCACGTAAAACATCC
Found at i:38231 original size:63 final size:63
Alignment explanation
Indices: 38100--38239 Score: 158
Period size: 63 Copynumber: 2.2 Consensus size: 63
38090 GTAAAGTAGA
* * * *
38100 TACCTCACCACGTAGCACACCATTGTCATCGCGTAAAACATCCACCTCACCATGTAAAGACCG
1 TACCTCATCACGTAGCACACCATTGTCATCACGTAAAACATCCACCTCACCACGCAAAGACCG
* * ** **
38163 TACCTCATCATGTAGCACACCATTGTCTTCACGTAAAGTA-CCGACCTCATGACGCAAAGCACCG
1 TACCTCATCACGTAGCACACCATTGTCATCACGTAAAACATCC-ACCTCACCACGCAAAG-ACCG
38227 -ACCTCATCACGTA
1 TACCTCATCACGTA
38240 ACTCCCCTAA
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
62 2 0.03
63 58 0.91
64 4 0.06
ACGTcount: A:0.31, C:0.35, G:0.14, T:0.21
Consensus pattern (63 bp):
TACCTCATCACGTAGCACACCATTGTCATCACGTAAAACATCCACCTCACCACGCAAAGACCG
Found at i:39961 original size:20 final size:20
Alignment explanation
Indices: 39932--40082 Score: 172
Period size: 20 Copynumber: 7.8 Consensus size: 20
39922 TCTGAAACTT
*
39932 AAATCTGCAATGCGAAAATGA
1 AAATC-GCAACGCGAAAATGA
* *
39953 AAATCGCAATGAGAAAATGA
1 AAATCGCAACGCGAAAATGA
39973 AAATCGCAACGCGAAAATGA
1 AAATCGCAACGCGAAAATGA
* *
39993 AAATCGCAACGTGAACATGA
1 AAATCGCAACGCGAAAATGA
*
40013 AAATCGCAACGCAAAAATGA
1 AAATCGCAACGCGAAAATGA
40033 AAATCGCAACGAC-AAAAT--
1 AAATCGCAACG-CGAAAATGA
40051 ---T-GCAACGCGAAAATGA
1 AAATCGCAACGCGAAAATGA
*
40067 AAATCACAACGCGAAA
1 AAATCGCAACGCGAAA
40083 CTAAATTCGC
Statistics
Matches: 113, Mismatches: 9, Indels: 17
0.81 0.06 0.12
Matches are distributed among these distances:
13 1 0.01
14 11 0.10
15 1 0.01
19 1 0.01
20 93 0.82
21 6 0.05
ACGTcount: A:0.51, C:0.19, G:0.18, T:0.13
Consensus pattern (20 bp):
AAATCGCAACGCGAAAATGA
Found at i:40486 original size:22 final size:23
Alignment explanation
Indices: 40461--40524 Score: 87
Period size: 22 Copynumber: 2.8 Consensus size: 23
40451 GATGGAGATA
40461 GACGGATTTCGTCGA-AGATGGG
1 GACGGATTTCGTCGAGAGATGGG
*
40483 GACGGATTACGTC-AGAGATGGG
1 GACGGATTTCGTCGAGAGATGGG
*
40505 GACGGATGTCGTCGTAGAGA
1 GACGGATTTCGTCG-AGAGA
40525 GTGAGAGATG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
21 1 0.03
22 30 0.83
24 5 0.14
ACGTcount: A:0.25, C:0.14, G:0.41, T:0.20
Consensus pattern (23 bp):
GACGGATTTCGTCGAGAGATGGG
Found at i:40956 original size:15 final size:15
Alignment explanation
Indices: 40936--40970 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
40926 AAGTAACGAG
40936 AGCATCATATTGACT
1 AGCATCATATTGACT
40951 AGCATCATATTGACT
1 AGCATCATATTGACT
40966 AGCAT
1 AGCAT
40971 AAAAGCTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (15 bp):
AGCATCATATTGACT
Found at i:43092 original size:15 final size:15
Alignment explanation
Indices: 43072--43105 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
43062 CGCCGCCTAG
43072 GCACCGAGGACGTAA
1 GCACCGAGGACGTAA
43087 GCACCGAGGACGTAA
1 GCACCGAGGACGTAA
43102 GCAC
1 GCAC
43106 ATTGCCGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.32, C:0.29, G:0.32, T:0.06
Consensus pattern (15 bp):
GCACCGAGGACGTAA
Found at i:58584 original size:64 final size:64
Alignment explanation
Indices: 58508--58635 Score: 215
Period size: 64 Copynumber: 2.0 Consensus size: 64
58498 ACATCTACCA
*
58508 GGGGAATGGAATGTTATTCTCCCG-TTTGGATTGCAAACATTTC-CAACCTCCGGTAATAAGTTA
1 GGGGAATGGAATGTCATTCTCCCGATTT-GATTGCAAACA-TTCACAACCTCCGGTAATAAGTTA
58571 T
64 T
58572 GGGGAATGGAATGTCATTCTCCCGATTTGATTGCAAACATTCACAACCTCCGGTAATAAGTTAT
1 GGGGAATGGAATGTCATTCTCCCGATTTGATTGCAAACATTCACAACCTCCGGTAATAAGTTAT
58636 TCCCAACAGT
Statistics
Matches: 61, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
63 3 0.05
64 55 0.90
65 3 0.05
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (64 bp):
GGGGAATGGAATGTCATTCTCCCGATTTGATTGCAAACATTCACAACCTCCGGTAATAAGTTAT
Found at i:58994 original size:11 final size:11
Alignment explanation
Indices: 58980--59006 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
58970 ATATATAAAT
58980 TAATTATAGTA
1 TAATTATAGTA
58991 TAATTATAGTA
1 TAATTATAGTA
59002 TAATT
1 TAATT
59007 CAACTTGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (11 bp):
TAATTATAGTA
Found at i:60396 original size:60 final size:60
Alignment explanation
Indices: 60277--60409 Score: 137
Period size: 60 Copynumber: 2.2 Consensus size: 60
60267 ATGTTCCAAC
** *
60277 TTCATCCCTAAAACTATGACTATCATTCTAAATTAATCCTTAAACTTTTGAACATTTCAA-T
1 TTCATCCC--AAACTATGACTATCATTCTAAATTAATCCCCAAACTTTTAAACATTTCAAGT
* * * *
60338 TTCGTACCCAAACTATGACCT-TCATTTTAAATTAGTCCCCAGACATTTTAAACA-TTCAAGT
1 TTCAT-CCCAAACTATGA-CTATCATTCTAAATTAATCCCCAAAC-TTTTAAACATTTCAAGT
60399 TTCATCCCAAA
1 TTCATCCCAAA
60410 ATTATACATA
Statistics
Matches: 60, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
60 38 0.63
61 19 0.32
62 3 0.05
ACGTcount: A:0.35, C:0.24, G:0.05, T:0.36
Consensus pattern (60 bp):
TTCATCCCAAACTATGACTATCATTCTAAATTAATCCCCAAACTTTTAAACATTTCAAGT
Found at i:61324 original size:21 final size:22
Alignment explanation
Indices: 61300--61344 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
61290 CTCCTTAAAA
*
61300 TATAATATAATATT-CTTATTT
1 TATAATATAATATTCCATATTT
*
61321 TATATTATAATATTCCATATTT
1 TATAATATAATATTCCATATTT
61343 TA
1 TA
61345 ATATTATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.56
Consensus pattern (22 bp):
TATAATATAATATTCCATATTT
Found at i:64405 original size:33 final size:33
Alignment explanation
Indices: 64321--64416 Score: 96
Period size: 34 Copynumber: 3.0 Consensus size: 33
64311 TCGGGCTGGG
* *
64321 TATATATATATTTA-AATTAAATATA-TAATAT
1 TATATATATATATATAATTAAATTTATTAATAT
* *
64352 TATATAT-TTTAATTTAAATTAAATTTATTAATAT
1 TATATATATAT-ATAT-AATTAAATTTATTAATAT
64386 TATATATATATATATAATT--ATTT-TTAATAT
1 TATATATATATATATAATTAAATTTATTAATAT
64416 T
1 T
64417 TATCGTGACG
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
30 10 0.19
31 12 0.22
33 14 0.26
34 16 0.30
35 2 0.04
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (33 bp):
TATATATATATATATAATTAAATTTATTAATAT
Found at i:64530 original size:29 final size:30
Alignment explanation
Indices: 64465--64535 Score: 135
Period size: 30 Copynumber: 2.4 Consensus size: 30
64455 TCCCCGTCCT
64465 CGTCCCCGTTTAGCATAAACGGTTTTTTCC
1 CGTCCCCGTTTAGCATAAACGGTTTTTTCC
64495 CGTCCCCGTTTAGCATAAACGG-TTTTTCC
1 CGTCCCCGTTTAGCATAAACGGTTTTTTCC
64524 CGTCCCCGTTTA
1 CGTCCCCGTTTA
64536 ATTCGGTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 19 0.46
30 22 0.54
ACGTcount: A:0.15, C:0.32, G:0.17, T:0.35
Consensus pattern (30 bp):
CGTCCCCGTTTAGCATAAACGGTTTTTTCC
Found at i:65110 original size:18 final size:18
Alignment explanation
Indices: 65087--65122 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
65077 TGCCTAATTT
65087 ATTATTGTTTTCAACAGC
1 ATTATTGTTTTCAACAGC
65105 ATTATTGTTTTCAACAGC
1 ATTATTGTTTTCAACAGC
65123 CCCTGTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (18 bp):
ATTATTGTTTTCAACAGC
Found at i:70523 original size:141 final size:145
Alignment explanation
Indices: 70210--70687 Score: 498
Period size: 141 Copynumber: 3.2 Consensus size: 145
70200 AGAGGAAAAC
* * * *
70210 TTCTTTATTGAATCACAGAACCATTATTGTTACAAACATACATATATACATACATACAAACAAAC
1 TTCTTTATTGAATCACAGCACCATTATTGTTAC--ACACACATACATACATACATACATAC--AC
* * *
70275 AAATTTGGAAGCAAACCCTGATCTTAAATTTGGTTTCAGGCACATCAGTGCATTCAGGCCGGACC
62 AAATTTAGAAACAAACCCTGATCTTAAATTTGATTTCAGG-ACATCAGTGCATTCAGGCCGGACC
*
70340 TCATAATAAGAATCAGCAGG
126 TCATAATAAGAATCAACAGG
* *
70360 TTCTTTATTGAACCACAACACCATTATTGTTACACACACATACATACATACATACATACAC-AA-
1 TTCTTTATTGAATCACAGCACCATTATTGTTACACACACATACATACATACATACATACACAAAT
* * ** *
70423 TTAGAAACAAACCTTGATTTTATGTTTGATTTCAGG-CA-CAGTGCATTCAGGTCGGACCTCATA
66 TTAGAAACAAACCCTGATCTTAAATTTGATTTCAGGACATCAGTGCATTCAGGCCGGACCTCATA
70486 ATAAGAATCAACAGG
131 ATAAGAATCAACAGG
* *
70501 TTCTTTATAGAATCACGGCACCATTATTGTTACATACACATGCATGCATGCATACATACATACAT
1 TTCTTTATTGAATCACAGCACCATTATTGTTAC--ACACA--CAT--A--CATACATACATAC--
* * * * *
70566 AATATATACAAATTTGGAAACAAACCCTGATCTTAAATTTG-GTTCAAGGCACATCTGTGGATTC
56 ---ATACACAAATTTAGAAACAAACCCTGATCTTAAATTTGATTTC-AGG-ACATCAGTGCATTC
* *
70630 AGGCCGGACCTCATACTAAAGAATCAGCAGG
116 AGGCCGGACCTCATAAT-AAGAATCAACAGG
* *
70661 TTCTTTATTAAATCACAGCATCATTAT
1 TTCTTTATTGAATCACAGCACCATTAT
70688 CAGGGATGGA
Statistics
Matches: 273, Mismatches: 35, Indels: 30
0.81 0.10 0.09
Matches are distributed among these distances:
141 67 0.25
142 2 0.01
143 5 0.02
144 29 0.11
145 5 0.02
146 2 0.01
147 1 0.00
148 23 0.08
149 13 0.05
150 30 0.11
154 5 0.02
155 5 0.02
156 26 0.10
158 2 0.01
159 23 0.08
160 35 0.13
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.29
Consensus pattern (145 bp):
TTCTTTATTGAATCACAGCACCATTATTGTTACACACACATACATACATACATACATACACAAAT
TTAGAAACAAACCCTGATCTTAAATTTGATTTCAGGACATCAGTGCATTCAGGCCGGACCTCATA
ATAAGAATCAACAGG
Found at i:70586 original size:156 final size:159
Alignment explanation
Indices: 70397--70687 Score: 378
Period size: 156 Copynumber: 1.8 Consensus size: 159
70387 TGTTACACAC
* * ** *
70397 ACATACATACATACATACATACACAATTAGAAACAAACCTTGATTTTATGTTTGATTTC-AGGCA
1 ACATACATACATACATACATACACAATTAGAAACAAACCCTGATCTTAAATTTG-GTTCAAGGCA
* *
70461 CA-GTGCATTCAGGTCGGACCTCATAAT-AAGAATCAACAGGTTCTTTA-TAGAATCACGGCACC
65 CATGTGCATTCAGGCCGGACCTCATAATAAAGAATCAACAGGTTCTTTATTA-AATCACAGCACC
70523 ATTATTGTTACATACACATGCATGCATGCAT
129 ATTATTGTTACATACACATGCATGCATGCAT
* *
70554 ACATACATACATA-ATATATACA-AATTTGGAAACAAACCCTGATCTTAAATTTGGTTCAAGGCA
1 ACATACATACATACATACATACACAA-TTAGAAACAAACCCTGATCTTAAATTTGGTTCAAGGCA
* * * *
70617 CATCTGTGGATTCAGGCCGGACCTCATACTAAAGAATCAGCAGGTTCTTTATTAAATCACAGCAT
65 CA--TGTGCATTCAGGCCGGACCTCATAATAAAGAATCAACAGGTTCTTTATTAAATCACAGCAC
70682 CATTAT
128 CATTAT
70688 CAGGGATGGA
Statistics
Matches: 114, Mismatches: 13, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
155 5 0.04
156 38 0.33
157 13 0.11
159 22 0.19
160 34 0.30
161 2 0.02
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (159 bp):
ACATACATACATACATACATACACAATTAGAAACAAACCCTGATCTTAAATTTGGTTCAAGGCAC
ATGTGCATTCAGGCCGGACCTCATAATAAAGAATCAACAGGTTCTTTATTAAATCACAGCACCAT
TATTGTTACATACACATGCATGCATGCAT
Found at i:71276 original size:20 final size:20
Alignment explanation
Indices: 71247--71288 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
71237 TATCATTACA
*
71247 CATGCATACATACATATATG
1 CATGCATACATACATACATG
*
71267 CATGCGTACATACATACATG
1 CATGCATACATACATACATG
71287 CA
1 CA
71289 AATTTGGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (20 bp):
CATGCATACATACATACATG
Found at i:72302 original size:64 final size:64
Alignment explanation
Indices: 72200--72326 Score: 209
Period size: 64 Copynumber: 2.0 Consensus size: 64
72190 TTTCTATTAT
* * * * *
72200 TTTGGATACATGACTTACCACATCAATCATAAGTGTTAACTATTAGTCAAGTAATTGTTTTTAC
1 TTTGGATACATGACTCACCACATCAACCATAAGCGTTAACCATTAGTCAAGTAATCGTTTTTAC
72264 TTTGGATACATGACTCACCACATCAACCATAAGCGTTAACCATTAGTCAAGTAATCGTTTTTA
1 TTTGGATACATGACTCACCACATCAACCATAAGCGTTAACCATTAGTCAAGTAATCGTTTTTA
72327 TCTAGCCAGA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 58 1.00
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (64 bp):
TTTGGATACATGACTCACCACATCAACCATAAGCGTTAACCATTAGTCAAGTAATCGTTTTTAC
Found at i:75082 original size:97 final size:96
Alignment explanation
Indices: 74909--75209 Score: 341
Period size: 97 Copynumber: 3.0 Consensus size: 96
74899 CCGGTTTTGT
* * * *
74909 TCCACCATTCAACTGATCAAATTATCAGTTCTCGATTCAATCAGTCGGTTCAGTTCGAGTCTAAC
1 TCCACGATTCAACTGATCAAATTATCAGTTCCCGATTCAA-CAGTCGGTTCAGTTCGACTCGAAC
* *
74974 AACCATGCTGTCAAGAAAATAGAATATATTTC
65 AATCATGCTGTCAAGAAAACAGAATATATTTC
* * * * *
75006 TCCGCGGTTCAACAGATCAAATTATCAGTTCCCGCTTCAACCAGTCGGTTCAGTTCAACTCGAAC
1 TCCACGATTCAACTGATCAAATTATCAGTTCCCGATTCAA-CAGTCGGTTCAGTTCGACTCGAAC
*
75071 AATCAAGCTGTCAAGAAAACAGAATATATTTCCGATATTAC
65 AATCATGCTGTCAAGAAAACAG-A-ATA--T---AT-TT-C
* * *
75112 TCCACGATTCAACTGATCAAATTATGAGTTGCCGATTCTAATAGTCGGTTCAGTTCGACTCGAAC
1 TCCACGATTCAACTGATCAAATTATCAGTTCCCGATTC-AACAGTCGGTTCAGTTCGACTCGAAC
* *
75177 AATCATGTTGTCAAGAAAACAGAATATGTTTC
65 AATCATGCTGTCAAGAAAACAGAATATATTTC
75209 T
1 T
75210 TCCTATAATG
Statistics
Matches: 170, Mismatches: 24, Indels: 20
0.79 0.11 0.09
Matches are distributed among these distances:
97 76 0.45
98 3 0.02
99 4 0.02
101 1 0.01
102 1 0.01
104 5 0.03
105 3 0.02
106 75 0.44
107 2 0.01
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.30
Consensus pattern (96 bp):
TCCACGATTCAACTGATCAAATTATCAGTTCCCGATTCAACAGTCGGTTCAGTTCGACTCGAACA
ATCATGCTGTCAAGAAAACAGAATATATTTC
Found at i:75163 original size:106 final size:106
Alignment explanation
Indices: 74999--75208 Score: 296
Period size: 106 Copynumber: 2.0 Consensus size: 106
74989 AAAATAGAAT
* * * *
74999 ATATTTCTCCGCGGTTCAACAGATCAAATTATCAGTTCCCGCTTCAACCAGTCGGTTCAGTTCAA
1 ATATTACTCCACGATTCAACAGATCAAATTATCAGTTCCCGATTCAACCAGTCGGTTCAGTTCAA
75064 CTCGAACAATCAAGCTGTCAAGAAAACAGAATATATTTCCG
66 CTCGAACAATCAAGCTGTCAAGAAAACAGAATATATTTCCG
* * * * *
75105 ATATTACTCCACGATTCAACTGATCAAATTATGAGTTGCCGATTCTAA-TAGTCGGTTCAGTTCG
1 ATATTACTCCACGATTCAACAGATCAAATTATCAGTTCCCGATTC-AACCAGTCGGTTCAGTTCA
* * *
75169 ACTCGAACAATCATGTTGTCAAGAAAACAGAATATGTTTC
65 ACTCGAACAATCAAGCTGTCAAGAAAACAGAATATATTTC
75209 TTCCTATAAT
Statistics
Matches: 91, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
106 89 0.98
107 2 0.02
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (106 bp):
ATATTACTCCACGATTCAACAGATCAAATTATCAGTTCCCGATTCAACCAGTCGGTTCAGTTCAA
CTCGAACAATCAAGCTGTCAAGAAAACAGAATATATTTCCG
Found at i:75607 original size:30 final size:30
Alignment explanation
Indices: 75573--75652 Score: 117
Period size: 30 Copynumber: 2.7 Consensus size: 30
75563 GCCCGACGGA
* ** *
75573 TTCAAACATGTATATATGATGATATTATCC
1 TTCAAACATGTATATACGACAATAGTATCC
75603 TTCAAACATGTATATACGACAATAGTATCC
1 TTCAAACATGTATATACGACAATAGTATCC
75633 TTCAAACATGTATATA-GACA
1 TTCAAACATGTATATACGACA
75653 TGTCGGTCAT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 4 0.09
30 42 0.91
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (30 bp):
TTCAAACATGTATATACGACAATAGTATCC
Found at i:77837 original size:60 final size:60
Alignment explanation
Indices: 77744--77885 Score: 149
Period size: 60 Copynumber: 2.4 Consensus size: 60
77734 TCATATCTCC
* * * * * * * **
77744 AAATTATGATTCTCGTTTTAAATTAATCCTTAAAATTTTAAATATTTTAATTTTATTTCA
1 AAATTATGAATCTCATTCTAAACTAATCCTTAAAATTTTAAACATTTCAATTTCATCCCA
* * * *
77804 AAATTATGAATCTCATTCTAAACTAGTCTTTAAATTTTTAAACATTTCAATTTCATCCCT
1 AAATTATGAATCTCATTCTAAACTAATCCTTAAAATTTTAAACATTTCAATTTCATCCCA
* *
77864 AAATTATGAATATCATGCTAAA
1 AAATTATGAATCTCATTCTAAA
77886 TTGGTCCCAA
Statistics
Matches: 67, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 67 1.00
ACGTcount: A:0.38, C:0.13, G:0.04, T:0.45
Consensus pattern (60 bp):
AAATTATGAATCTCATTCTAAACTAATCCTTAAAATTTTAAACATTTCAATTTCATCCCA
Found at i:78902 original size:26 final size:28
Alignment explanation
Indices: 78846--78902 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 28
78836 AAATTAATAT
* **
78846 ATTTTTTATAAATATAATAATTTTTTTA
1 ATTTTTTATAAATATAATAAATTTTAAA
78874 ATTTTTT-TAAATA-AATAAATTTTAAA
1 ATTTTTTATAAATATAATAAATTTTAAA
78900 ATT
1 ATT
78903 ACTAGAATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 13 0.50
27 6 0.23
28 7 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
ATTTTTTATAAATATAATAAATTTTAAA
Found at i:89829 original size:35 final size:35
Alignment explanation
Indices: 89755--89822 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
89745 TTCATGTTCA
*
89755 AAATTTCAAAACACTTCAATTACATTTTAAACCAC
1 AAATTTCAAAACACTTCAATTACATTCTAAACCAC
* * *
89790 AAATTTCAAAATATTTCAATTATATTCTAAACC
1 AAATTTCAAAACACTTCAATTACATTCTAAACC
89823 CTAAATTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (35 bp):
AAATTTCAAAACACTTCAATTACATTCTAAACCAC
Found at i:90453 original size:35 final size:35
Alignment explanation
Indices: 90414--90488 Score: 98
Period size: 35 Copynumber: 2.1 Consensus size: 35
90404 TTCATGTTTA
*
90414 AAATTCCAAAACACTTC-AATTACGTTCTAAACCTT
1 AAATTCCAAAACA-TTCTAATTACATTCTAAACCTT
* * *
90449 AAATTTCAAAATATTCTAATTATATTCTAAACCTT
1 AAATTCCAAAACATTCTAATTACATTCTAAACCTT
90484 AAATT
1 AAATT
90489 AAAGTATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 3 0.09
35 32 0.91
ACGTcount: A:0.43, C:0.19, G:0.01, T:0.37
Consensus pattern (35 bp):
AAATTCCAAAACATTCTAATTACATTCTAAACCTT
Found at i:90539 original size:35 final size:35
Alignment explanation
Indices: 90484--90560 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
90474 TCTAAACCTT
* *
90484 AAATTAAAGTATTTTAGAATTTGGGGTTTAAAATG
1 AAATTGAATTATTTTAGAATTTGGGGTTTAAAATG
* *
90519 TAATTGAATTATTTTAGAATTTGGGGTTTACAATG
1 AAATTGAATTATTTTAGAATTTGGGGTTTAAAATG
90554 AAATTGA
1 AAATTGA
90561 GGATTGTGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.38, C:0.01, G:0.19, T:0.42
Consensus pattern (35 bp):
AAATTGAATTATTTTAGAATTTGGGGTTTAAAATG
Found at i:90766 original size:659 final size:658
Alignment explanation
Indices: 89510--90939 Score: 2401
Period size: 659 Copynumber: 2.2 Consensus size: 658
89500 TAAGATGTGA
*
89510 TATTTTTTCTACTTAATTTTATGATGACATTATCAAAATTATTCACTTTATCTATCTCAATCACT
1 TATTTTTTCTACTTAATTTTATGATGAC-TTATCACAATTATTCACTTTATCTATCTCAATCACT
89575 ATAATGTTTGATGTGAAATCAAACATTAAAATATCACTTTCATATA--TTTTTTACTGCTAACGG
65 ATAATGTTTGATGTGAAATCAAACATTAAAATATCACTTTCATATATTTTTTTTACTGCTAACGG
* * * * *
89638 AGGAAGATGAAGTGGAACTCATTTGAAGCTTCAAAGAATGCAACAATTTAAAGTTGGATGTAATC
130 AGGAAAATGAAGCGGAACTCATTTGAAGCTTCAAAGAATGCAACAATTCAAAGTGGGATCTAATC
* * * *
89703 ACTGTCAAATTTATATGGGAGTAAACACTGTTAAATAGCAAATTCATGTTCAAAATTTCAAAACA
195 ACTATCAAATTTATATGGAAGTAAACACTGTCAAATAGCAAATTCATGTTCAAAATTCCAAAACA
*
89768 CTTCAATTACATTTTAAACCACAAATTTCAAAATATTTCAATTATATTCTAAACCCTAAATTAAA
260 CTTCAATTACATTCTAAACCACAAATTTCAAAATATTTCAATTATATTCTAAACCCTAAATTAAA
* *
89833 GTATTTAGAATTTGGGGTTTAAAATGTAATTGAATTATTTTGGAATTTGGGGTTTAGAATGAAAT
325 GTATTTAGAATTTGGGGTTTAAAATGTAATTGAATTATTTTAGAATTTGGGGTTTACAATGAAAT
* *
89898 TGAGGATTGTGTTGCAAGTTTTAAAAGTTGGGAGACCTAAATGCAAGCGCCTGAAAAGTTCAGTG
390 TGAGGATTGTGTTGCAAGTTTTAAAAGTTGGGAGACCTAAATGCAAGCACCTGAAAAGTTCAGTA
* *
89963 ACTATATTACAAACGTACTAAATGTTGGAGGACTGCCACATCATCTTCTTCTAAGGGCAGTGTAA
455 ACCATATTACAAACGTACTAAATGTTAGAGGACTGCCACATCATCTTCTTCTAAGGGCAGTGTAA
90028 CGACATCAAACGGTCGGGTACGTCGGGGACCATATTGCAAACGGACTAAATGTCAGAGGATTATA
520 CGACATCAAACGGTCGGGTACGTCGGGGACCATATTGCAAACGGACTAAATGTCAGAGGATTATA
* * *
90093 TTGCAAGTTTTAAAAGTTAGGGGACCTAAATGCATGTTTCAGAAAAGTTCAGTGATCATTACTAT
585 TTGCAAGTTTTAAAAGTTAGGGGACCTAAATGCAAGTTTCAGAAAAATTCAGTGACCATTACTAT
*
90158 ATTTTACCC
650 ACTTTACCC
*
90167 TATTTTTTCTAATTAATTTTATGATGACGTTATCACAATTATTCACTTTATCTATCTCAATCACT
1 TATTTTTTCTACTTAATTTTATGATGAC-TTATCACAATTATTCACTTTATCTATCTCAATCACT
90232 ATAATGTTTGATGTGAAATCAAACATTAAAATATCACTTTCATATATTTTTTTTACTGCTAACGG
65 ATAATGTTTGATGTGAAATCAAACATTAAAATATCACTTTCATATATTTTTTTTACTGCTAACGG
*
90297 AGGAAAATGAAGCGGAACTCATTTGAAGCTTCAAAGAATGCAACAATTCAAAGTGGGCTCTAATC
130 AGGAAAATGAAGCGGAACTCATTTGAAGCTTCAAAGAATGCAACAATTCAAAGTGGGATCTAATC
* * *
90362 ACTATCAAATTTATATTGAAGTAAACATTGTCAAATAGCAAATTCATGTTTAAAATTCCAAAACA
195 ACTATCAAATTTATATGGAAGTAAACACTGTCAAATAGCAAATTCATGTTCAAAATTCCAAAACA
* ** *
90427 CTTCAATTACGTTCTAAACCTTAAATTTCAAAATA-TTCTAATTATATTCTAAACCTTAAATTAA
260 CTTCAATTACATTCTAAACCACAAATTTCAAAATATTTC-AATTATATTCTAAACCCTAAATTAA
90491 AGTATTTTAGAATTTGGGGTTTAAAATGTAATTGAATTATTTTAGAATTTGGGGTTTACAATGAA
324 AGTA-TTTAGAATTTGGGGTTTAAAATGTAATTGAATTATTTTAGAATTTGGGGTTTACAATGAA
*
90556 ATTGAGGATTGTGTTGCAAGTTTTAAAAGTTAGGG-GACCTAAATGCAAGCACCTGAAAAGTTTA
388 ATTGAGGATTGTGTTGCAAGTTTTAAAAGTT-GGGAGACCTAAATGCAAGCACCTGAAAAGTTCA
* *
90620 GTAACCATATTGCAAA-GTACTAAATGTTAGAGGACTGCCACGTCATCTTCTTCTAAGGGCAGTG
452 GTAACCATATTACAAACGTACTAAATGTTAGAGGACTGCCACATCATCTTCTTCTAAGGGCAGTG
* *
90684 TAACGACATCAAACGGTCGGTTACGTCGGGGACCATATTGCAAACGGACTAAATGTTAGAGGATT
517 TAACGACATCAAACGGTCGGGTACGTCGGGGACCATATTGCAAACGGACTAAATGTCAGAGGATT
90749 ATATTGCAAGTTTTAAAAGTTAGGGGACCTAAATGCAAGTTTCAGAAAAATTCAGTGACCATTAC
582 ATATTGCAAGTTTTAAAAGTTAGGGGACCTAAATGCAAGTTTCAGAAAAATTCAGTGACCATTAC
90814 TATACTTTACCC
647 TATACTTTACCC
90826 TATTTTTTTCTACTTAATTTTATG-T-ACTTCATCACAATTATTCACTTTATCTATCTCAATCAC
1 TA-TTTTTTCTACTTAATTTTATGATGACTT-ATCACAATTATTCACTTTATCTATCTCAATCAC
* *
90889 TATAATGTTTAATGTGAAATCGAACATTAAAAT-TCACTTTCATAT-TTTTTT
64 TATAATGTTTGATGTGAAATCAAACATTAAAATATCACTTTCATATATTTTTT
90940 GGGTAATCTA
Statistics
Matches: 727, Mismatches: 39, Indels: 15
0.93 0.05 0.02
Matches are distributed among these distances:
656 6 0.01
657 122 0.17
658 69 0.09
659 378 0.52
660 149 0.20
661 3 0.00
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35
Consensus pattern (658 bp):
TATTTTTTCTACTTAATTTTATGATGACTTATCACAATTATTCACTTTATCTATCTCAATCACTA
TAATGTTTGATGTGAAATCAAACATTAAAATATCACTTTCATATATTTTTTTTACTGCTAACGGA
GGAAAATGAAGCGGAACTCATTTGAAGCTTCAAAGAATGCAACAATTCAAAGTGGGATCTAATCA
CTATCAAATTTATATGGAAGTAAACACTGTCAAATAGCAAATTCATGTTCAAAATTCCAAAACAC
TTCAATTACATTCTAAACCACAAATTTCAAAATATTTCAATTATATTCTAAACCCTAAATTAAAG
TATTTAGAATTTGGGGTTTAAAATGTAATTGAATTATTTTAGAATTTGGGGTTTACAATGAAATT
GAGGATTGTGTTGCAAGTTTTAAAAGTTGGGAGACCTAAATGCAAGCACCTGAAAAGTTCAGTAA
CCATATTACAAACGTACTAAATGTTAGAGGACTGCCACATCATCTTCTTCTAAGGGCAGTGTAAC
GACATCAAACGGTCGGGTACGTCGGGGACCATATTGCAAACGGACTAAATGTCAGAGGATTATAT
TGCAAGTTTTAAAAGTTAGGGGACCTAAATGCAAGTTTCAGAAAAATTCAGTGACCATTACTATA
CTTTACCC
Found at i:92973 original size:29 final size:29
Alignment explanation
Indices: 92931--92992 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
92921 TTAACGGCGG
92931 AGTGCTTAAATTGATAAAATTGAAACATC
1 AGTGCTTAAATTGATAAAATTGAAACATC
*
92960 AGTGCTTAAATTGATAAAATTGAAACGTC
1 AGTGCTTAAATTGATAAAATTGAAACATC
92989 AGTG
1 AGTG
92993 ACATTTTCGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.42, C:0.10, G:0.18, T:0.31
Consensus pattern (29 bp):
AGTGCTTAAATTGATAAAATTGAAACATC
Found at i:104250 original size:18 final size:18
Alignment explanation
Indices: 104227--104265 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
104217 CTATCTAAAA
104227 TTTAAAATTATCATATAT
1 TTTAAAATTATCATATAT
* * *
104245 TTTAAATTTTTTATATAT
1 TTTAAAATTATCATATAT
104263 TTT
1 TTT
104266 GAACACCCCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTAAAATTATCATATAT
Found at i:107427 original size:14 final size:15
Alignment explanation
Indices: 107398--107430 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
107388 CCATTTTTAC
*
107398 TATTTACTTTATTTT
1 TATTTACTTCATTTT
107413 TATTTA-TTCATTTT
1 TATTTACTTCATTTT
107427 TATT
1 TATT
107431 GTTTATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (15 bp):
TATTTACTTCATTTT
Found at i:108090 original size:18 final size:18
Alignment explanation
Indices: 108067--108106 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
108057 TGAGCCTTTG
108067 CCATTTTCTTTGTTTTTA
1 CCATTTTCTTTGTTTTTA
108085 CCATTTTCTTTGTTTTTA
1 CCATTTTCTTTGTTTTTA
108103 CCAT
1 CCAT
108107 ATTATAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.12, C:0.20, G:0.05, T:0.62
Consensus pattern (18 bp):
CCATTTTCTTTGTTTTTA
Found at i:116498 original size:23 final size:23
Alignment explanation
Indices: 116465--116510 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
116455 ACAAGGGCGG
*
116465 AGGCAGTGGACAATAGTAGGTGC
1 AGGCAGAGGACAATAGTAGGTGC
* *
116488 AGGCAGAGGACAATTGTTGGTGC
1 AGGCAGAGGACAATAGTAGGTGC
116511 GGAAACGGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.28, C:0.13, G:0.39, T:0.20
Consensus pattern (23 bp):
AGGCAGAGGACAATAGTAGGTGC
Found at i:121014 original size:29 final size:31
Alignment explanation
Indices: 120973--121040 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 31
120963 GATAAAACAT
120973 TTTA-TATTATATTAAA-ATTATT-TAATAA
1 TTTATTATTATATTAAATATTATTGTAATAA
* * *
121001 TTTATTATTTTATTAAATTTTATTGTACTAA
1 TTTATTATTATATTAAATATTATTGTAATAA
121032 TTT-TTATTA
1 TTTATTATTA
121041 CTTTTTACGG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 4 0.12
29 11 0.33
30 10 0.30
31 8 0.24
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (31 bp):
TTTATTATTATATTAAATATTATTGTAATAA
Found at i:122743 original size:21 final size:21
Alignment explanation
Indices: 122717--122788 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
122707 GGTGTATATT
*
122717 CCGCAGCCGTTTCAGATGGCA
1 CCGCAGCCGTTTCAGATGCCA
122738 CCGCAGCCGTATT-AGATGCCA
1 CCGCAGCCGT-TTCAGATGCCA
** **
122759 CTACAGCTATTTCAGATGCCA
1 CCGCAGCCGTTTCAGATGCCA
122780 CCGCAGCCG
1 CCGCAGCCG
122789 AGTCAAATGA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
20 2 0.05
21 36 0.90
22 2 0.05
ACGTcount: A:0.22, C:0.35, G:0.24, T:0.19
Consensus pattern (21 bp):
CCGCAGCCGTTTCAGATGCCA
Found at i:122803 original size:42 final size:42
Alignment explanation
Indices: 122720--122828 Score: 112
Period size: 42 Copynumber: 2.6 Consensus size: 42
122710 GTATATTCCG
* * * * *
122720 CAGCCGTTTCAGATGGCACCGCAGCCGTATTAGATGCCACTA
1 CAGCCATTTCAGATGCCACCGCAGCCGTATCAAATGACACTA
*
122762 CAGCTATTTCAGATGCCACCGCAGCCG-AGTCAAATGACACTA
1 CAGCCATTTCAGATGCCACCGCAGCCGTA-TCAAATGACACTA
** * *
122804 CCTCCATATCAGATGCCATCGCAGC
1 CAGCCATTTCAGATGCCACCGCAGC
122829 TAGGTTAGAT
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 1 0.02
42 54 0.98
ACGTcount: A:0.27, C:0.33, G:0.20, T:0.20
Consensus pattern (42 bp):
CAGCCATTTCAGATGCCACCGCAGCCGTATCAAATGACACTA
Found at i:123290 original size:13 final size:13
Alignment explanation
Indices: 123274--123315 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
123264 AAAATAAAAA
123274 TAAAAATATTATT
1 TAAAAATATTATT
123287 TAAAAATATTATT
1 TAAAAATATTATT
123300 TAAAAATATT-TT
1 TAAAAATATTATT
123312 TAAA
1 TAAA
123316 TTATTAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 6 0.21
13 23 0.79
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TAAAAATATTATT
Found at i:124013 original size:24 final size:23
Alignment explanation
Indices: 123959--124013 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
123949 CAAAATTATT
* *
123959 AAAAACTAAAAAACTAAATAAGA
1 AAAAAATAAAAAACTAAAGAAGA
* * *
123982 ATATAATATAAAAATTAAAGAAGA
1 AAAAAATA-AAAAACTAAAGAAGA
124006 AAAAAATA
1 AAAAAATA
124014 CTTACTGTGA
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.73, C:0.04, G:0.05, T:0.18
Consensus pattern (23 bp):
AAAAAATAAAAAACTAAAGAAGA
Done.