Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009170.1 Hibiscus syriacus cultivar Beakdansim tig00112718_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: 105926
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1431 original size:30 final size:30
Alignment explanation
Indices: 1388--1445 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
1378 GGACCTGTCA
* *
1388 AGAGGTTACAAAGAACCCCGGTAACTATCC
1 AGAGGTCACAAAGAACCCCGGCAACTATCC
* * *
1418 AGAGGTCATAAAGATCCTCGGCAACTAT
1 AGAGGTCACAAAGAACCCCGGCAACTAT
1446 TCATATGTTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (30 bp):
AGAGGTCACAAAGAACCCCGGCAACTATCC
Found at i:9905 original size:21 final size:21
Alignment explanation
Indices: 9879--9928 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
9869 TTTAAAAATA
9879 TTAAAAAATATTATTATATTT
1 TTAAAAAATATTATTATATTT
9900 TTAAAAAATATTATTATATTT
1 TTAAAAAATATTATTATATTT
*
9921 ATAAAAAA
1 TTAAAAAA
9929 CTCTAATTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TTAAAAAATATTATTATATTT
Found at i:24437 original size:29 final size:29
Alignment explanation
Indices: 24403--24465 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
24393 AAAAACCTCA
24403 AATAAATTAAATTATTCTAAAATTATAAG
1 AATAAATTAAATTATTCTAAAATTATAAG
24432 AATAAATTAAATTATTCTAAAATTATAAG
1 AATAAATTAAATTATTCTAAAATTATAAG
24461 -ATAAA
1 AATAAA
24466 AGTCGAAGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 5 0.15
29 29 0.85
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (29 bp):
AATAAATTAAATTATTCTAAAATTATAAG
Found at i:26040 original size:22 final size:21
Alignment explanation
Indices: 26012--26071 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 21
26002 ATAAGACCAC
26012 TATGTCCCGAAGGACCACTGT
1 TATGTCCCGAAGGACCACTGT
26033 ATATGTCCCGAAGGACCA---T
1 -TATGTCCCGAAGGACCACTGT
26052 TATGTCCCGAAGGACCACTG
1 TATGTCCCGAAGGACCACTG
26072 ATAATCCCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 17 0.49
19 1 0.03
22 17 0.49
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.22
Consensus pattern (21 bp):
TATGTCCCGAAGGACCACTGT
Found at i:30111 original size:18 final size:18
Alignment explanation
Indices: 30088--30178 Score: 110
Period size: 18 Copynumber: 4.8 Consensus size: 18
30078 GCGTAGAATT
*
30088 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
30106 TGTCCCGAAAGACCACTGTATA
1 TGTCCCGAAGGACCAC----TA
30128 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
30146 TGTCCCGAAAGACCACTA
1 TGTCCCGAAGGACCACTA
*
30164 TATCCCGAAGGACCA
1 TGTCCCGAAGGACCA
30179 ATGATAATCC
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
18 46 0.73
22 17 0.27
ACGTcount: A:0.30, C:0.32, G:0.20, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:32218 original size:16 final size:16
Alignment explanation
Indices: 32199--32298 Score: 68
Period size: 16 Copynumber: 6.3 Consensus size: 16
32189 TTTTATAAAA
*
32199 TATATATTTTAATTAC
1 TATATATTTTAATTAT
*
32215 TATAT-TTAT-A-TAT
1 TATATATTTTAATTAT
*
32228 TGTTATATTTTAATTAT
1 T-ATATATTTTAATTAT
*
32245 T-TATTATATTTAATAAT
1 TATA-TAT-TTTAATTAT
32262 TA-ATATTATTAATTAT
1 TATATATT-TTAATTAT
*
32278 TAT-TATATTTATTTAT
1 TATATAT-TTTAATTAT
32294 TATAT
1 TATAT
32299 TCATTTAATT
Statistics
Matches: 66, Mismatches: 7, Indels: 21
0.70 0.07 0.22
Matches are distributed among these distances:
13 3 0.05
14 4 0.06
15 9 0.14
16 34 0.52
17 16 0.24
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (16 bp):
TATATATTTTAATTAT
Found at i:32296 original size:13 final size:13
Alignment explanation
Indices: 32230--32305 Score: 54
Period size: 13 Copynumber: 6.0 Consensus size: 13
32220 TTATATATTG
*
32230 TTATATTTTAATTA
1 TTATA-TTTATTTA
32244 TT-TATTATATTTA
1 TTATATT-TATTTA
* *
32257 ATA-ATTAATATTA
1 TTATATTTAT-TTA
32270 TTA-A-TTA-TTA
1 TTATATTTATTTA
32280 TTATATTTATTTA
1 TTATATTTATTTA
*
32293 TTATATTCATTTA
1 TTATATTTATTTA
32306 ATTCATACGT
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
10 6 0.12
11 1 0.02
12 9 0.18
13 32 0.64
14 2 0.04
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (13 bp):
TTATATTTATTTA
Found at i:36323 original size:2 final size:2
Alignment explanation
Indices: 36316--36341 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
36306 TTCATAATTG
36316 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
36342 GCATGTTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41037 original size:12 final size:12
Alignment explanation
Indices: 41020--41046 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
41010 GGGAAGTTTC
41020 ACTTAATATATA
1 ACTTAATATATA
41032 ACTTAATATATA
1 ACTTAATATATA
41044 ACT
1 ACT
41047 AAGAAAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (12 bp):
ACTTAATATATA
Found at i:41497 original size:11 final size:11
Alignment explanation
Indices: 41473--41517 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
41463 CTCCTGTTAA
41473 AATTTATATATTT
1 AATTTA-AT-TTT
*
41486 AATATAATTTT
1 AATTTAATTTT
*
41497 AATTTAATATT
1 AATTTAATTTT
41508 AATTTAATTT
1 AATTTAATTT
41518 AGTTTAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 21 0.75
12 2 0.07
13 5 0.18
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
AATTTAATTTT
Found at i:41502 original size:5 final size:5
Alignment explanation
Indices: 41482--41524 Score: 50
Period size: 5 Copynumber: 8.2 Consensus size: 5
41472 AAATTTATAT
* *
41482 ATTTA ATATA ATTTTA ATTTA ATATTA ATTTA ATTTA GTTTA A
1 ATTTA ATTTA A-TTTA ATTTA AT-TTA ATTTA ATTTA ATTTA A
41525 AATATTTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
5 23 0.72
6 9 0.28
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (5 bp):
ATTTA
Found at i:41503 original size:16 final size:16
Alignment explanation
Indices: 41482--41518 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
41472 AAATTTATAT
41482 ATTTAATA-TAATTTTA
1 ATTTAATATTAA-TTTA
41498 ATTTAATATTAATTTA
1 ATTTAATATTAATTTA
41514 ATTTA
1 ATTTA
41519 GTTTAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 17 0.85
17 3 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTTAATATTAATTTA
Found at i:43570 original size:14 final size:13
Alignment explanation
Indices: 43530--43568 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
43520 TATTGAAAGC
43530 TAAATA-TTAAAA
1 TAAATATTTAAAA
*
43542 TAATTCATTTAAAA
1 TAAAT-ATTTAAAA
43556 TAAATATTTAAAA
1 TAAATATTTAAAA
43569 ATTTAATTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 4 0.17
13 9 0.39
14 10 0.43
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAATATTTAAAA
Found at i:43687 original size:18 final size:19
Alignment explanation
Indices: 43664--43701 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
43654 ATATATTTTA
43664 AAAACA-ATAAAATAAATG
1 AAAACATATAAAATAAATG
43682 AAAACATATAAAATAAATG
1 AAAACATATAAAATAAATG
43701 A
1 A
43702 CTAAATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.71, C:0.05, G:0.05, T:0.18
Consensus pattern (19 bp):
AAAACATATAAAATAAATG
Found at i:44979 original size:3 final size:3
Alignment explanation
Indices: 44971--45061 Score: 83
Period size: 3 Copynumber: 29.7 Consensus size: 3
44961 GGCCCGTTTG
* * * * *
44971 TAA TAA TAA TTAA TAA TAC TAT TAG TAA TAAA TAA TAA TAT TAG TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
* * * *
45018 TTA TAA TTA TAA TAA TAA TAA TTA TAA TAA TAA TTA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
45062 TTTAAATGAA
Statistics
Matches: 71, Mismatches: 15, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
3 65 0.92
4 6 0.08
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:45004 original size:19 final size:19
Alignment explanation
Indices: 44977--45059 Score: 71
Period size: 19 Copynumber: 4.3 Consensus size: 19
44967 TTTGTAATAA
* *
44977 TAATTAATAATACTATTAG
1 TAATAAATAATAATATTAG
44996 TAATAAATAATAATATTAG
1 TAATAAATAATAATATTAG
* * *
45015 TAATTATAATTATAATAATAA
1 TAA-TA-AATAATAATATTAG
*
45036 TAAT-TATAATAATAATTA-
1 TAATAAATAATAAT-ATTAG
45054 TAATAA
1 TAATAA
45060 TATTTAAATG
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
18 11 0.22
19 23 0.45
20 3 0.06
21 14 0.27
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.41
Consensus pattern (19 bp):
TAATAAATAATAATATTAG
Found at i:45421 original size:116 final size:116
Alignment explanation
Indices: 45284--46202 Score: 1514
Period size: 116 Copynumber: 8.0 Consensus size: 116
45274 TAGAGTCATT
* ** **
45284 CAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTCTTCTTTTTTCTTCAGATGACGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
45349 TCATTATGAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTTAAA
66 TCATTATGAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTTAAA
*
45400 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGACGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
45465 TCATTATGAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTTAAA
66 TCATTATGAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTTAAA
*
45516 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGACGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
45581 TCATTATGAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTTAAA
66 TCATTATGAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTTAAA
*
45632 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGACGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
45697 TCATTATGAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTTAAA
66 TCATTATGAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTTAAA
45748 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
45813 TCATTATGAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTTAAA
66 TCATTATGAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTTAAA
45864 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
* * * * * *
45926 TCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGAATTTAAA
66 TCATTATGAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTTAAA
45977 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
* * * * * *
46039 TCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGAATTTAAA
66 TCATTATGAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTTAAA
*
46090 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTATTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
*** * * ** *
46152 TCATTATGAACTCGAACTGGTACTGTTGATCCATTGAATGATGGATTTAAA
66 TCATTATGAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTTAAA
46203 TCTTTGCTAA
Statistics
Matches: 777, Mismatches: 26, Indels: 3
0.96 0.03 0.00
Matches are distributed among these distances:
113 267 0.34
116 510 0.66
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.38
Consensus pattern (116 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
TCATTATGAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTTAAA
Found at i:46627 original size:22 final size:22
Alignment explanation
Indices: 46602--46656 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
46592 CATAAAGTTT
* *
46602 TCATCTTTGAAAATAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
*
46624 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
46646 TCATCTTTGAA
1 TCATCTTTGAA
46657 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:47152 original size:54 final size:54
Alignment explanation
Indices: 47028--47336 Score: 362
Period size: 54 Copynumber: 5.8 Consensus size: 54
47018 CACTGGTTCA
* * *
47028 TAAAACATTTGACAATACATTCAT-CTTTTCCTGTGGTTTCTG-TC-GA-G-ATG
1 TAAAACATTTGACAACACATTCATCCTTTT-CTGTGGCTTCTGCTCAGACGTTTG
* *
47078 TAAAACACTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGATGTTTG
1 TAAAACATTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGACGTTTG
* * **
47132 TAAAACATTTGACAACACATTCATCC-TTTCTTGTGGTTTTTGCTCAGACGTTCA
1 TAAAACATTTGACAACACATTCATCCTTTTC-TGTGGCTTCTGCTCAGACGTTTG
* * * *
47186 TAAAGCGTTTGACAACACATTCATCATTTTCTGTGGCTTCTGCTCAGATGTTTG
1 TAAAACATTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGACGTTTG
* * **
47240 TAAAACATTTGACAACACATTCATCC-TTTCTTGTGGTTTTTGCTCAGACGTTCA
1 TAAAACATTTGACAACACATTCATCCTTTTC-TGTGGCTTCTGCTCAGACGTTTG
* * *
47294 TAAAGCGTTTGACAACACATTCATCATTTTCTGTGGCTTCTGC
1 TAAAACATTTGACAACACATTCATCCTTTTCTGTGGCTTCTGC
47337 CAAGATTTAT
Statistics
Matches: 219, Mismatches: 31, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
50 33 0.15
51 7 0.03
52 2 0.01
53 9 0.04
54 160 0.73
55 8 0.04
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.39
Consensus pattern (54 bp):
TAAAACATTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGACGTTTG
Found at i:47226 original size:108 final size:108
Alignment explanation
Indices: 47028--47336 Score: 502
Period size: 108 Copynumber: 2.9 Consensus size: 108
47018 CACTGGTTCA
* * * * * **
47028 TAAAACATTTGACAATACATTCATCTTTTCCTGTGGTTTCTG-TCGAGATG-T-A-AAA-CACTT
1 TAAAACATTTGACAACACATTCATCCTTTCTTGTGGTTTTTGCTC-AGACGTTCATAAAGCGTTT
*
47088 GACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGATGTTTG
65 GACAACACATTCATCATTTTCTGTGGCTTCTGCTCAGATGTTTG
47132 TAAAACATTTGACAACACATTCATCCTTTCTTGTGGTTTTTGCTCAGACGTTCATAAAGCGTTTG
1 TAAAACATTTGACAACACATTCATCCTTTCTTGTGGTTTTTGCTCAGACGTTCATAAAGCGTTTG
47197 ACAACACATTCATCATTTTCTGTGGCTTCTGCTCAGATGTTTG
66 ACAACACATTCATCATTTTCTGTGGCTTCTGCTCAGATGTTTG
47240 TAAAACATTTGACAACACATTCATCCTTTCTTGTGGTTTTTGCTCAGACGTTCATAAAGCGTTTG
1 TAAAACATTTGACAACACATTCATCCTTTCTTGTGGTTTTTGCTCAGACGTTCATAAAGCGTTTG
47305 ACAACACATTCATCATTTTCTGTGGCTTCTGC
66 ACAACACATTCATCATTTTCTGTGGCTTCTGC
47337 CAAGATTTAT
Statistics
Matches: 192, Mismatches: 8, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
104 42 0.22
105 3 0.02
106 1 0.01
107 3 0.02
108 143 0.74
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.39
Consensus pattern (108 bp):
TAAAACATTTGACAACACATTCATCCTTTCTTGTGGTTTTTGCTCAGACGTTCATAAAGCGTTTG
ACAACACATTCATCATTTTCTGTGGCTTCTGCTCAGATGTTTG
Found at i:47307 original size:162 final size:158
Alignment explanation
Indices: 47023--47318 Score: 407
Period size: 162 Copynumber: 1.8 Consensus size: 158
47013 ATAATCACTG
* *
47023 GTTCATAAAACATTTGACAATACATTCATCTTTTCCTGTGGTTTCTGTCGAGATGTAAAACACTT
1 GTTCATAAAACATTTGACAACACATTCATCTTTTCCTGTGGCTTCTGTCGAGATGTAAAACACTT
* **
47088 GACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGATGTTTGTAAAACATTTGACAACACATT
66 GACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGACGTTCATAAAACATTTGACAACACATT
47153 CATCCTTTCTTGTGGTTTTTGCTCAGAC
131 CATCCTTTCTTGTGGTTTTTGCTCAGAC
* * *
47181 GTTCATAAAGCGTTTGACAACACATTCATCATTTT-CTGTGGCTTCTGCTCAGATGTTTGTAAAA
1 GTTCATAAAACATTTGACAACACATTCATC-TTTTCCTGTGGCTTCTG-TC-GA-G-ATGTAAAA
* * * * *
47245 CATTTGACAACACATTCATCC-TTTCTTGTGGTTTTTGCTCAGACGTTCATAAAGCGTTTGACAA
61 CACTTGACAACACATTCATCCTTTTC-TGTGGCTTCTGCTCAGACGTTCATAAAACATTTGACAA
47309 CACATTCATC
125 CACATTCATC
47319 ATTTTCTGTG
Statistics
Matches: 119, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
158 38 0.32
159 6 0.05
160 2 0.02
161 5 0.04
162 68 0.57
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.38
Consensus pattern (158 bp):
GTTCATAAAACATTTGACAACACATTCATCTTTTCCTGTGGCTTCTGTCGAGATGTAAAACACTT
GACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGACGTTCATAAAACATTTGACAACACATT
CATCCTTTCTTGTGGTTTTTGCTCAGAC
Found at i:49553 original size:114 final size:114
Alignment explanation
Indices: 49353--49578 Score: 344
Period size: 114 Copynumber: 2.0 Consensus size: 114
49343 GATCATGCAG
* * * * *
49353 TTCATCTTTCAATTCCAATGATCGGTTCTGGGGTTCCTATCGAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATCGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* *
49418 ACACTTTCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
* * *
49467 TTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATCGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* *
49532 ATACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCA
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCA
49579 CATGGAACTT
Statistics
Matches: 100, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
114 100 1.00
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATCGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
Found at i:51638 original size:14 final size:14
Alignment explanation
Indices: 51615--51663 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
51605 CTTGATTCAA
*
51615 TTTTCCTTTTTTCT
1 TTTTCTTTTTTTCT
51629 TTTTCTTTTTTTC-
1 TTTTCTTTTTTTCT
*
51642 CTTT-TTTTTTTCT
1 TTTTCTTTTTTTCT
51655 TCTTTCTTT
1 T-TTTCTTT
51664 GCTGGATGAG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 8 0.28
13 3 0.10
14 15 0.52
15 3 0.10
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTCTTTTTTTCT
Found at i:51640 original size:22 final size:23
Alignment explanation
Indices: 51615--51659 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
51605 CTTGATTCAA
51615 TTTTCCTTTTTTCTTT-TTCTTT
1 TTTTCCTTTTTTCTTTCTTCTTT
*
51637 TTTTCCTTTTTTTTTTCTTCTTT
1 TTTTCCTTTTTTCTTTCTTCTTT
51660 CTTTGCTGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (23 bp):
TTTTCCTTTTTTCTTTCTTCTTT
Found at i:56897 original size:14 final size:13
Alignment explanation
Indices: 56857--56895 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
56847 TATTGAAAGC
56857 TAAATA-TTAAAA
1 TAAATATTTAAAA
*
56869 TAATTCATTTAAAA
1 TAAAT-ATTTAAAA
56883 TAAATATTTAAAA
1 TAAATATTTAAAA
56896 ATTTAATTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 4 0.17
13 9 0.39
14 10 0.43
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAATATTTAAAA
Found at i:57014 original size:18 final size:19
Alignment explanation
Indices: 56991--57028 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
56981 ATATATTTTA
56991 AAAACA-ATAAAATAAATG
1 AAAACATATAAAATAAATG
57009 AAAACATATAAAATAAATG
1 AAAACATATAAAATAAATG
57028 A
1 A
57029 CTAAATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.71, C:0.05, G:0.05, T:0.18
Consensus pattern (19 bp):
AAAACATATAAAATAAATG
Found at i:58296 original size:3 final size:3
Alignment explanation
Indices: 58288--58378 Score: 92
Period size: 3 Copynumber: 29.7 Consensus size: 3
58278 GGCCCGTTTG
* * * *
58288 TAA TAA TAA TTAA TAA TAA TAT TAG TAA TAAA TAA TAA TAT TAG TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
* * * *
58335 TTA TAA TTA TAA TAA TAA TAA TTA TAA TAA TAA TTA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
58379 TTTAAATGAA
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
3 66 0.92
4 6 0.08
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:69649 original size:2 final size:2
Alignment explanation
Indices: 69642--69682 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
69632 CAAATGTTCT
69642 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
69683 GCATACTCTC
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:73225 original size:29 final size:31
Alignment explanation
Indices: 73157--73222 Score: 89
Period size: 33 Copynumber: 2.1 Consensus size: 31
73147 TATTCAAAGT
* *
73157 TTGGACACCAACCAAGATGAAATTTCCAATAAG
1 TTGGCCACCAACCAAGATGAAATTTCC-A-AAC
73190 TTGGCCACCAACCAAGATGAAATTTCC-AAC
1 TTGGCCACCAACCAAGATGAAATTTCCAAAC
73220 TTG
1 TTG
73223 CCAACTTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 5 0.16
33 26 0.84
ACGTcount: A:0.38, C:0.24, G:0.15, T:0.23
Consensus pattern (31 bp):
TTGGCCACCAACCAAGATGAAATTTCCAAAC
Found at i:82434 original size:115 final size:115
Alignment explanation
Indices: 82290--82518 Score: 458
Period size: 115 Copynumber: 2.0 Consensus size: 115
82280 GTCTTGCTAT
82290 CATGTTCAGAGATAGATAGAGGAAGGTGGTAGGGATGTGGTAGCATCTTATAAAATTTCAAATCC
1 CATGTTCAGAGATAGATAGAGGAAGGTGGTAGGGATGTGGTAGCATCTTATAAAATTTCAAATCC
82355 TTGTATAATTTCATTTTCTAAACTTTTGGATTTATAATATAACCTTTTAC
66 TTGTATAATTTCATTTTCTAAACTTTTGGATTTATAATATAACCTTTTAC
82405 CATGTTCAGAGATAGATAGAGGAAGGTGGTAGGGATGTGGTAGCATCTTATAAAATTTCAAATCC
1 CATGTTCAGAGATAGATAGAGGAAGGTGGTAGGGATGTGGTAGCATCTTATAAAATTTCAAATCC
82470 TTGTATAATTTCATTTTCTAAACTTTTGGATTTATAATATAACCTTTTA
66 TTGTATAATTTCATTTTCTAAACTTTTGGATTTATAATATAACCTTTTA
82519 TGTTCATATC
Statistics
Matches: 114, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
115 114 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.38
Consensus pattern (115 bp):
CATGTTCAGAGATAGATAGAGGAAGGTGGTAGGGATGTGGTAGCATCTTATAAAATTTCAAATCC
TTGTATAATTTCATTTTCTAAACTTTTGGATTTATAATATAACCTTTTAC
Found at i:83713 original size:32 final size:32
Alignment explanation
Indices: 83677--83769 Score: 186
Period size: 32 Copynumber: 2.9 Consensus size: 32
83667 ATCCTATAAG
83677 TAAATTACCTGAGGTGTATTTTACCCTCTGAT
1 TAAATTACCTGAGGTGTATTTTACCCTCTGAT
83709 TAAATTACCTGAGGTGTATTTTACCCTCTGAT
1 TAAATTACCTGAGGTGTATTTTACCCTCTGAT
83741 TAAATTACCTGAGGTGTATTTTACCCTCT
1 TAAATTACCTGAGGTGTATTTTACCCTCT
83770 ACTTTATCAC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 61 1.00
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.41
Consensus pattern (32 bp):
TAAATTACCTGAGGTGTATTTTACCCTCTGAT
Found at i:90411 original size:13 final size:15
Alignment explanation
Indices: 90382--90411 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
90372 TAAAGTATAC
90382 ATAATATATACATAT
1 ATAATATATACATAT
*
90397 ATAATATATAAATAT
1 ATAATATATACATAT
90412 TAGAGGAAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAATATATACATAT
Found at i:90860 original size:11 final size:10
Alignment explanation
Indices: 90829--90903 Score: 51
Period size: 11 Copynumber: 6.8 Consensus size: 10
90819 CATATATATG
90829 TATAATAAAA
1 TATAATAAAA
*
90839 TAAAATAAAAA
1 TATAAT-AAAA
90850 TATACATAAAA
1 TATA-ATAAAA
*
90861 TATATATATATA
1 TATA-ATA-AAA
90873 TATATATAAATA
1 TATA-ATAAA-A
* *
90885 AAGGAATAAAA
1 TA-TAATAAAA
90896 TATAATAA
1 TATAATAA
90904 TGAAAATATG
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
10 10 0.20
11 21 0.41
12 19 0.37
13 1 0.02
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (10 bp):
TATAATAAAA
Found at i:92594 original size:105 final size:105
Alignment explanation
Indices: 92451--93064 Score: 1104
Period size: 105 Copynumber: 5.8 Consensus size: 105
92441 GAAGTTGACG
** *** *
92451 GTTGACAGTCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTACTGTCTTGAGTCCAATATCCTTC
1 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
*
92516 GTTGTGAAGCTGAAATTGGCTCTGAAATTGAGAAATGTTT
66 GTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTT
92556 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
1 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
* *
92621 GTTGTGAAGTTGAAATTGGCTCTGACATTGAGAAATATTT
66 GTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTT
92661 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
1 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
92726 GTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTT
66 GTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTT
92766 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
1 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
92831 GTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTT
66 GTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTT
*
92871 GGTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
1 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
*
92936 GCTGTGAAGTTGAAATTGGCTCT-AAATTTGAGAAATGTTT
66 GTTGTGAAGTTGAAATTGGCTCTGAAA-TTGAGAAATGTTT
*
92976 GGTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
1 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
93041 GTTGTGAAGTTGAAATTGGCTCTG
66 GTTGTGAAGTTGAAATTGGCTCTG
93065 GGTAAAACCT
Statistics
Matches: 493, Mismatches: 14, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
104 3 0.01
105 490 0.99
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (105 bp):
GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
GTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTT
Found at i:100477 original size:21 final size:22
Alignment explanation
Indices: 100452--100500 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
100442 TCTTTATTTG
*
100452 ATCTTCTAATATTTTTATCTTT
1 ATCTTCTAATATTTTTAGCTTT
* *
100474 -TCTTC-CATCTTTTTAGCTTT
1 ATCTTCTAATATTTTTAGCTTT
100494 ATCTTCT
1 ATCTTCT
100501 TCATCAAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.16, C:0.20, G:0.02, T:0.61
Consensus pattern (22 bp):
ATCTTCTAATATTTTTAGCTTT
Found at i:100625 original size:39 final size:39
Alignment explanation
Indices: 100577--100654 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
100567 TTCGCAGCAG
* *
100577 GTGCAACTTTCGCTTTGGTAAC-GAGTGAGTCCCCGGGTA
1 GTGCAACTTTCCCTTTAGTAACAGA-TGAGTCCCCGGGTA
* * *
100616 GTGCTACTTTCCCTTTAGTAGCAGATGCGTCCCCGGGTA
1 GTGCAACTTTCCCTTTAGTAACAGATGAGTCCCCGGGTA
100655 ATATTCCGGG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
39 31 0.94
40 2 0.06
ACGTcount: A:0.17, C:0.26, G:0.28, T:0.29
Consensus pattern (39 bp):
GTGCAACTTTCCCTTTAGTAACAGATGAGTCCCCGGGTA
Found at i:104585 original size:4 final size:4
Alignment explanation
Indices: 104560--104630 Score: 58
Period size: 4 Copynumber: 17.2 Consensus size: 4
104550 AAATGGGGAA
* *
104560 AAAT AAA- AAGAT ATAT ATAAT AAAT AAAT AAACT AAA- AAA- AACT AAAT
1 AAAT AAAT AA-AT AAAT A-AAT AAAT AAAT AAA-T AAAT AAAT AAAT AAAT
104608 AAAT AAAT AAAT ATAAT CAAAT A
1 AAAT AAAT AAAT A-AAT -AAAT A
104631 TGTACGTATA
Statistics
Matches: 56, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
3 7 0.12
4 34 0.61
5 14 0.25
6 1 0.02
ACGTcount: A:0.70, C:0.04, G:0.01, T:0.24
Consensus pattern (4 bp):
AAAT
Done.