Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005169.1 Hibiscus syriacus cultivar Beakdansim tig00011664_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: 50609
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:1186 original size:204 final size:195
Alignment explanation
Indices: 494--1224 Score: 714
Period size: 198 Copynumber: 3.7 Consensus size: 195
484 ACAATAACTA
* * * * *
494 CATAAAATGTCGATACATTTTATACAAGTATTGA-CCCAAAAAACATCAAAACCAAT-AT-ATAA
1 CATAAAGTGTCGATACA-TTTA-AAAAGTATCGATCCC-AAAAACATC-GAACCGATAATAATAA
* * * * * *
556 TGTAATAGGTAAATTAACAATGTAATCGGTATAAATATA-CGG-TTAATTAGAAAACATGTCAAC
62 TGTAATAGGTAAATTTACAATGTAACCGGTATAAATATATCGGTTTTATGAGAAAATAGGTCAA-
* * *
619 ATAATGTATCGACACTTGTGTAATTTGTGTCGATACTTATTGTCCA-GGATGAATGCACAAACGA
126 ATAATGTATCGACACTTAT-TAATTTGTGTCGATACTT-TTGTCCATGAATGAATGCCCAAACG-
*
683 GGTGCACG
188 GGTGCAAG
* * *
691 CATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATTGAAACGATAATTATAATG
1 CATAAAGTGTCGATACATTTA--AAAAGTATCGATCCCAAAAACATCGAACCGATAATAATAATG
* * * * *
756 TATTAGGTAAATTTACAATGTAACCGATATAAATATATCGGTTTTATGATAAAATTGGTCAGCAT
64 TAATAGGTAAATTTACAATGTAACCGGTATAAATATATCGGTTTTATGAGAAAATAGGTCA-AAT
* * * * * *
821 CAA-GTATCGACACTTGCTAAATTTGTGTCGACACTTTTGGTCCAT-AATGAATACCAAAAAGGG
128 -AATGTATCGACACTT-ATTAATTTGTGTCGATACTTTT-GTCCATGAATGAATGCCCAAACGGG
*
884 TGCAAC
190 TGCAAG
*
890 CATAAAGTGTCGATACATTATAAAAAGTATCGATCCCAGAAACATCGAAACC-ATAAGT-ATAAT
1 CATAAAGTGTCGATACATT-TAAAAAGTATCGATCCCAAAAACATCG-AACCGATAA-TAATAAT
* * *
953 GTAATAGGTAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTAAA
63 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATATCGGTTTTATGAGAAAATAGGTC-AAA
* *
1018 TAATGTATCGACACGTTATTAGTTTGTGTCGATACTTTTTTCCAAAATGAAATATGAATGCCCAA
127 TAATGTATCGACAC-TTATTAATTTGTGTCGATACTTTTGTCC---ATG--A-ATGAATGCCCAA
*
1083 CCGGGTGCAAG
185 ACGGGTGCAAG
**
1094 CATAAAGTGTCGATACATTTAAAATTA-TATCGATCTAAAAAACATCGTAACCGATAATAATAAT
1 CATAAAGTGTCGATACATTTAAAA--AGTATCGATCCCAAAAACATCG-AACCGATAATAATAAT
* * **
1158 GTAATAGGTAAA-TTGCAATGTTACCGGTATAAATATATCGG-TTTACTTCGAAAATAGGTCAAT
63 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATATCGGTTTTA-TGAGAAAATAGGTCAA-
1221 ATAA
126 ATAA
1225 GCACTACCTA
Statistics
Matches: 445, Mismatches: 59, Indels: 53
0.80 0.11 0.10
Matches are distributed among these distances:
196 9 0.02
197 41 0.09
198 158 0.36
199 37 0.08
200 63 0.14
201 3 0.01
203 12 0.03
204 100 0.22
205 22 0.05
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (195 bp):
CATAAAGTGTCGATACATTTAAAAAGTATCGATCCCAAAAACATCGAACCGATAATAATAATGTA
ATAGGTAAATTTACAATGTAACCGGTATAAATATATCGGTTTTATGAGAAAATAGGTCAAATAAT
GTATCGACACTTATTAATTTGTGTCGATACTTTTGTCCATGAATGAATGCCCAAACGGGTGCAAG
Found at i:1326 original size:87 final size:85
Alignment explanation
Indices: 1219--1379 Score: 268
Period size: 87 Copynumber: 1.9 Consensus size: 85
1209 AAATAGGTCA
1219 ATATAAGCACTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCACTACCTATTACATTATATAAGAGCTA-CTAATATGTTATTGTACTTGATAATA-TT
*
1284 CCGGTTAAATGCCTATTTTATT
64 CAGGTTAAATGCCTATTTTATT
* * *
1306 ATATAAGCGCTATCTATTACATTATATAAGCGCTACTAATATGTTATTGTACTTGATAATATTCA
1 ATATAAGCACTACCTATTACATTATATAAGAGCTACTAATATGTTATTGTACTTGATAATATTCA
1371 GGTTAAATG
66 GGTTAAATG
1380 ATATAACATT
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
85 12 0.17
86 26 0.37
87 32 0.46
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (85 bp):
ATATAAGCACTACCTATTACATTATATAAGAGCTACTAATATGTTATTGTACTTGATAATATTCA
GGTTAAATGCCTATTTTATT
Found at i:2658 original size:21 final size:21
Alignment explanation
Indices: 2592--2658 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
2582 TCAGTTAAAT
*
2592 AAATGAGTTATGATCTACCAG
1 AAATGAGTTATGATCTACAAG
* * * *
2613 AAAT-ATGTTAAG-TAATATAAT
1 AAATGA-GTTATGAT-CTACAAG
2634 AAATGAGTTATGATCTACAAG
1 AAATGAGTTATGATCTACAAG
2655 AAAT
1 AAAT
2659 ATATTAATTT
Statistics
Matches: 33, Mismatches: 9, Indels: 8
0.66 0.18 0.16
Matches are distributed among these distances:
20 2 0.06
21 29 0.88
22 2 0.06
ACGTcount: A:0.46, C:0.07, G:0.15, T:0.31
Consensus pattern (21 bp):
AAATGAGTTATGATCTACAAG
Found at i:5415 original size:14 final size:15
Alignment explanation
Indices: 5390--5419 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
5380 TGACTTGCCC
5390 TTCTCTTCATCTCCA
1 TTCTCTTCATCTCCA
5405 TTCTC-TCATCTCCA
1 TTCTCTTCATCTCCA
5419 T
1 T
5420 ACTTTTTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.13, C:0.40, G:0.00, T:0.47
Consensus pattern (15 bp):
TTCTCTTCATCTCCA
Found at i:5865 original size:14 final size:14
Alignment explanation
Indices: 5848--5875 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5838 TATATATAGT
5848 TGTGTATATGTGTA
1 TGTGTATATGTGTA
5862 TGTGTATATGTGTA
1 TGTGTATATGTGTA
5876 AATAATAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (14 bp):
TGTGTATATGTGTA
Found at i:8485 original size:11 final size:12
Alignment explanation
Indices: 8460--8485 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
8450 GTAGAAATTA
8460 TTTTAATGACTT
1 TTTTAATGACTT
8472 TTTTAATGACTT
1 TTTTAATGACTT
8484 TT
1 TT
8486 AACAACTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (12 bp):
TTTTAATGACTT
Found at i:9472 original size:21 final size:21
Alignment explanation
Indices: 9448--9490 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
9438 TCCTCCCTAC
*
9448 TCATGCCCATGCCCATCCCCA
1 TCATCCCCATGCCCATCCCCA
*
9469 TCATCCCCATGCCCATTCCCA
1 TCATCCCCATGCCCATCCCCA
9490 T
1 T
9491 ACTCATGCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.51, G:0.07, T:0.23
Consensus pattern (21 bp):
TCATCCCCATGCCCATCCCCA
Found at i:10991 original size:20 final size:20
Alignment explanation
Indices: 10968--11007 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
10958 ACTTTTATCT
10968 TTTAAAA-ATATTATTTAATA
1 TTTAAAACATATT-TTTAATA
10988 TTTAAAACATATTTTTAATA
1 TTTAAAACATATTTTTAATA
11008 ATGTTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTAAAACATATTTTTAATA
Found at i:12982 original size:21 final size:23
Alignment explanation
Indices: 12945--12989 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
12935 AGCATTTAAA
12945 TTTTAATTTTTTAATTTAACTAC
1 TTTTAATTTTTTAATTTAACTAC
*
12968 TTTT-ATTTTTT-ATTTAGCTAC
1 TTTTAATTTTTTAATTTAACTAC
12989 T
1 T
12990 AACTTCTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.48
22 7 0.33
23 4 0.19
ACGTcount: A:0.24, C:0.09, G:0.02, T:0.64
Consensus pattern (23 bp):
TTTTAATTTTTTAATTTAACTAC
Found at i:16899 original size:21 final size:21
Alignment explanation
Indices: 16873--16925 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
16863 TACGTCAGAA
16873 GTTTTGAAACCTTAGTGGGAG
1 GTTTTGAAACCTTAGTGGGAG
16894 GTTTTGAAACCTTAGTGGGAG
1 GTTTTGAAACCTTAGTGGGAG
*
16915 GTTTCGAAACC
1 GTTTTGAAACC
16926 ATGCTCCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.13, G:0.30, T:0.32
Consensus pattern (21 bp):
GTTTTGAAACCTTAGTGGGAG
Found at i:21734 original size:42 final size:41
Alignment explanation
Indices: 21653--21753 Score: 121
Period size: 42 Copynumber: 2.4 Consensus size: 41
21643 AGGTTTTATG
* * * *
21653 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACA
1 GATGGCCCGAAGGACTTAGCATCATGCTCAAAAGACTTACA
* * *
21694 GATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACT
1 GATGGCCCGAAGGACTT-AGCATCATGCTCAAAAGACTTACA
*
21736 GATGGCCCGAAGAACTTA
1 GATGGCCCGAAGGACTTA
21754 TAAATTGTGA
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
41 16 0.33
42 33 0.67
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.24
Consensus pattern (41 bp):
GATGGCCCGAAGGACTTAGCATCATGCTCAAAAGACTTACA
Found at i:21959 original size:41 final size:41
Alignment explanation
Indices: 21868--21967 Score: 103
Period size: 41 Copynumber: 2.4 Consensus size: 41
21858 AGGTTTTATG
* * * * *
21868 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACA
1 GATGGCCCGAAAGACTTAGCATCATGCTCGAAAGACTTACA
* * *
21909 GACGACCCGAAAGA-TTAAGCATCATGCTCGAAAGACTTACT
1 GATGGCCCGAAAGACTT-AGCATCATGCTCGAAAGACTTACA
*
21950 GATGGCCCGAAGGACTTA
1 GATGGCCCGAAAGACTTA
21968 TAAATTGTGA
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
40 2 0.04
41 42 0.91
42 2 0.04
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.22
Consensus pattern (41 bp):
GATGGCCCGAAAGACTTAGCATCATGCTCGAAAGACTTACA
Found at i:22243 original size:215 final size:214
Alignment explanation
Indices: 21484--22605 Score: 1955
Period size: 214 Copynumber: 5.2 Consensus size: 214
21474 CTTAAAAATT
*
21484 ACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTA
1 ACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
* * *
21549 AAATTTTGAAAATCACATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTCATTT
66 AAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTGAAACGTCATTTTTCATTT
21614 TCAAATTC-TTGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTT
131 TCAAATTCATT-TGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTT
*
21678 GCTCTAAAGGCTTACAGATG
195 GCTCTAAAGGCTTACAGACG
* *
21698 ACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGAACTTATAAATTGTG
1 ACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
*
21763 AAATTTTGAAAATCACATTCTTCGTTTTCAAAAATTCCATCTTCTTGAAACGTCATTTTCTCATT
66 AAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTGAAACGTCATTTT-TCATT
21828 TTCAAATTCATTTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTT
130 TTCAAATTCATTTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTT
21893 GCTCTAAAGGCTTACAGACG
195 GCTCTAAAGGCTTACAGACG
*
21913 ACCCGAAAGA-TTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
1 ACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
*
21977 AAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATATTCTTGAAACGTCATTTTCTCATT
66 AAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTGAAACGTCATTTT-TCATT
22042 TTCAAATTCATTTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTT
130 TTCAAATTCATTTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTT
* *
22107 GTTCTAAAGGCTTACACACG
195 GCTCTAAAGGCTTACAGACG
*
22127 ACCTGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
1 ACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
*
22192 AAATTTTGAAAATCGTATTCTTCGTTTTCAAAAATTCCATCTTCTTGAAACGTCA-TTTTCATTT
66 AAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTGAAACGTCATTTTTCATTT
* * *
22256 TCAAATTCATTTGAAAACATCCTACTCGAAGGTTTTATGGATGGCCCGAAGAACTTATCATCTTA
131 TCAAATTCATTTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTTG
22321 CTCTAAAGGCTTACAGACG
196 CTCTAAAGGCTTACAGACG
*
22340 ACCCGAAGGATTTAAGCATTATGCTCGAAAGA-TTACTGATGGCCCGAAGGACTTATAAATTGTG
1 ACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
* * *
22404 AAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTTCATCTTCTTAAAACATCATTTTTTCATT
66 AAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTGAAACGTCA-TTTTTCATT
*
22469 TTCAAATTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTT
130 TTCAAATTCATTTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTT
*
22534 GCTCTAAAGGCTTACAGATG
195 GCTCTAAAGGCTTACAGACG
* *
22554 ACCTGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGACCCGAAGGA
1 ACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGA
22606 TTTAAGCATC
Statistics
Matches: 866, Mismatches: 36, Indels: 11
0.95 0.04 0.01
Matches are distributed among these distances:
212 83 0.10
213 115 0.13
214 446 0.52
215 220 0.25
216 2 0.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (214 bp):
ACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
AAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTGAAACGTCATTTTTCATTT
TCAAATTCATTTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTTG
CTCTAAAGGCTTACAGACG
Found at i:22479 original size:427 final size:430
Alignment explanation
Indices: 21484--22605 Score: 1995
Period size: 427 Copynumber: 2.6 Consensus size: 430
21474 CTTAAAAATT
*
21484 ACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTA
1 ACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
*
21549 AAATTTTGAAAATCACATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCA-TTTTTCATT
66 AAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTTCATT
21613 TTCAAATTC-TTGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCT
131 TTCAAATTCATT-TGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCT
* *
21677 TGCTCTAAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGC
195 TGCTCTAAAGGCTTACAGATGACCTGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGC
*
21742 CCGAAGAACTTATAAATTGTGAAATTTTGAAAATCACATTCTTCGTTTTCAAAAATTCCATCTTC
260 CCGAAGGACTTATAAATTGTGAAATTTTGAAAATCACATTCTTCGTTTTCAAAAATTCCATCTTC
21807 TTGAAACGTCATTTTCTCATTTTCAAATTCATTTGAAAACATCCTACCCGAAGGTTTTATGGATG
325 TTGAAACGTCATTTTCTCATTTTCAAATTCATTTGAAAACATCCTACCCGAAGGTTTTATGGATG
* *
21872 GCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGACG
390 GCCCGAAGAACTTATCATCTTACTCTAAAGGCTTACAGACG
*
21913 ACCCGAAAGA-TTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
1 ACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
* * * *
21977 AAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATATTCTTGAAACGTCATTTTCTCATT
66 AAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTTCATT
22042 TTCAAATTCATTTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTT
131 TTCAAATTCATTTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTT
* * *
22107 GTTCTAAAGGCTTACACACGACCTGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCC
196 GCTCTAAAGGCTTACAGATGACCTGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCC
**
22172 CGAAGGACTTATAAATTGTGAAATTTTGAAAATCGTATTCTTCGTTTTCAAAAATTCCATCTTCT
261 CGAAGGACTTATAAATTGTGAAATTTTGAAAATCACATTCTTCGTTTTCAAAAATTCCATCTTCT
*
22237 TGAAACGTCA-TTT-TCATTTTCAAATTCATTTGAAAACATCCTACTCGAAGGTTTTATGGATGG
326 TGAAACGTCATTTTCTCATTTTCAAATTCATTTGAAAACATCCTACCCGAAGGTTTTATGGATGG
22300 CCCGAAGAACTTATCATCTTACTCTAAAGGCTTACAGACG
391 CCCGAAGAACTTATCATCTTACTCTAAAGGCTTACAGACG
*
22340 ACCCGAAGGATTTAAGCATTATGCTCGAAAGA-TTACTGATGGCCCGAAGGACTTATAAATTGTG
1 ACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
*
22404 AAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTTCATCTTCTTAAAACATCATTTTTTCATT
66 AAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTTCATT
*
22469 TTCAAATTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTT
131 TTCAAATTCATTTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTT
*
22534 GCTCTAAAGGCTTACAGATGACCTGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGACC
196 GCTCTAAAGGCTTACAGATGACCTGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCC
22599 CGAAGGA
261 CGAAGGA
22606 TTTAAGCATC
Statistics
Matches: 660, Mismatches: 30, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
427 320 0.48
428 127 0.19
429 211 0.32
430 2 0.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (430 bp):
ACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTG
AAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTTCATT
TTCAAATTCATTTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTT
GCTCTAAAGGCTTACAGATGACCTGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCC
CGAAGGACTTATAAATTGTGAAATTTTGAAAATCACATTCTTCGTTTTCAAAAATTCCATCTTCT
TGAAACGTCATTTTCTCATTTTCAAATTCATTTGAAAACATCCTACCCGAAGGTTTTATGGATGG
CCCGAAGAACTTATCATCTTACTCTAAAGGCTTACAGACG
Found at i:22590 original size:42 final size:42
Alignment explanation
Indices: 22509--22637 Score: 179
Period size: 42 Copynumber: 3.1 Consensus size: 42
22499 AGGTTTTATG
* * * * * * *
22509 GATGGCCCGAAGGACTT-ATCATCTTGCTCTAAAGGCTTACA
1 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
*
22550 GATGACCTGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
1 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
22592 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
1 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
22634 GATG
1 GATG
22638 GGTTTGCTTT
Statistics
Matches: 78, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
41 14 0.18
42 64 0.82
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (42 bp):
GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
Found at i:22691 original size:34 final size:35
Alignment explanation
Indices: 22641--22816 Score: 119
Period size: 36 Copynumber: 4.9 Consensus size: 35
22631 ACTGATGGGT
* * * *
22641 TTGCTTTACTATTCTTCTATGAAGGCTTAAGGTGG
1 TTGCTTCACTACTCTTCTGTGAAGGCTTAAGATGG
* *
22676 -TGCTTCACTACTCTTCGGTGAAGGTTTAAGATGG
1 TTGCTTCACTACTCTTCTGTGAAGGCTTAAGATGG
* *
22710 TTTGCTTCACTCCTCTT-TGGTGAAGGCTTAAGATTGAT
1 -TTGCTTCACTACTCTTCT-GTGAAGGCTTAAGA-TG-G
* *
22748 TTGCTTCA--AC-CTTATTGGTGAAGGCTTAAGATTGAT
1 TTGCTTCACTACTCTT-CT-GTGAAGGCTTAAGA-TG-G
* * * *
22784 TTGCTTCATTCCTTTTCAGTGAAGGCTTAAGAT
1 TTGCTTCACTACTCTTCTGTGAAGGCTTAAGAT
22817 TGACTTTGCT
Statistics
Matches: 116, Mismatches: 15, Indels: 19
0.77 0.10 0.13
Matches are distributed among these distances:
34 31 0.27
35 1 0.01
36 57 0.49
37 24 0.21
38 1 0.01
39 2 0.02
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.40
Consensus pattern (35 bp):
TTGCTTCACTACTCTTCTGTGAAGGCTTAAGATGG
Found at i:22726 original size:36 final size:36
Alignment explanation
Indices: 22660--22826 Score: 162
Period size: 36 Copynumber: 4.6 Consensus size: 36
22650 TATTCTTCTA
* * *
22660 TGAAGGCTTAAGGTG--GTGCTTCACTACTCTTCGG
1 TGAAGGCTTAAGATGATTTGCTTCACTCCTCTTCGG
* * *
22694 TGAAGGTTTAAGATGGTTTGCTTCACTCCTCTTTGG
1 TGAAGGCTTAAGATGATTTGCTTCACTCCTCTTCGG
* *
22730 TGAAGGCTTAAGATTGATTTGCTTCA-ACCT-TATTGG
1 TGAAGGCTTAAGA-TGATTTGCTTCACTCCTCT-TCGG
* * *
22766 TGAAGGCTTAAGATTGATTTGCTTCATTCCTTTTCAG
1 TGAAGGCTTAAGA-TGATTTGCTTCACTCCTCTTCGG
22803 TGAAGGCTTAAGATTGACTTTGCT
1 TGAAGGCTTAAGA-TGA-TTTGCT
22827 CTAATCTCAT
Statistics
Matches: 115, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
34 13 0.11
35 1 0.01
36 61 0.53
37 33 0.29
38 7 0.06
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.39
Consensus pattern (36 bp):
TGAAGGCTTAAGATGATTTGCTTCACTCCTCTTCGG
Found at i:22815 original size:37 final size:35
Alignment explanation
Indices: 22692--22826 Score: 173
Period size: 36 Copynumber: 3.7 Consensus size: 35
22682 ACTACTCTTC
* *
22692 GGTGAAGGTTTAAGA-TGGTTTGCTTCACTCCTCTTT
1 GGTGAAGGCTTAAGATTGATTTGCTTCA-TCCT-TTT
*
22728 GGTGAAGGCTTAAGATTGATTTGCTTCAACCTTATT
1 GGTGAAGGCTTAAGATTGATTTGCTTCATCCTT-TT
22764 GGTGAAGGCTTAAGATTGATTTGCTTCATTCCTTTT
1 GGTGAAGGCTTAAGATTGATTTGCTTCA-TCCTTTT
*
22800 CAGTGAAGGCTTAAGATTGACTTTGCT
1 -GGTGAAGGCTTAAGATTGA-TTTGCT
22827 CTAATCTCAT
Statistics
Matches: 89, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
35 1 0.01
36 49 0.55
37 33 0.37
38 6 0.07
ACGTcount: A:0.21, C:0.15, G:0.24, T:0.40
Consensus pattern (35 bp):
GGTGAAGGCTTAAGATTGATTTGCTTCATCCTTTT
Found at i:24157 original size:125 final size:123
Alignment explanation
Indices: 23935--24183 Score: 281
Period size: 125 Copynumber: 2.0 Consensus size: 123
23925 TACCACAATG
* * * *
23935 TTATCTCATATTGGTACAGGCCTTCAAAATGCCCCAACATCTCAGATTGTAAGGCTCACTCTCAA
1 TTATCTCATACTGGTACAGGCCTTCAAAATGCCCCAACACCTCAAATCGTAAGGCTCACTCTCAA
*
24000 TGTCTTCTTGGTCCGAATCTTGTCATCCCAACACGATGTGGGTTCAGTCATGTCCCAACA
66 TGTCTTCTTGGTCCGAATCATGTCATCCCAACACGATGT-GGTTCAGTCATG-CCCAACA
* * * **
24060 TTATCTTATACTGGTAC-GAGCCTTCGAAATGCCCCATCACCTCAAATCGTAAGGCTCGTTCTTC
1 TTATCTCATACTGGTACAG-GCCTTCAAAATGCCCCAACACCTCAAATCGTAAGGCTCACTC-TC
* * * * *
24124 -ATGCCTCTT-TT-GTCTGAATCATGTCATCTCAACATGATGTGGTTCCGTCATGCCTAACA
64 AATG--TCTTCTTGGTCCGAATCATGTCATCCCAACACGATGTGGTTCAGTCATGCCCAACA
24183 T
1 T
24184 ATCACAACTT
Statistics
Matches: 105, Mismatches: 15, Indels: 10
0.81 0.12 0.08
Matches are distributed among these distances:
123 7 0.07
124 12 0.11
125 78 0.74
126 4 0.04
127 4 0.04
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.32
Consensus pattern (123 bp):
TTATCTCATACTGGTACAGGCCTTCAAAATGCCCCAACACCTCAAATCGTAAGGCTCACTCTCAA
TGTCTTCTTGGTCCGAATCATGTCATCCCAACACGATGTGGTTCAGTCATGCCCAACA
Found at i:29570 original size:21 final size:21
Alignment explanation
Indices: 29546--29602 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
29536 AATGCGAAGT
*
29546 GGTCTTCATGTCTTTATAAAG
1 GGTCTTCATGTCTTTATAAAC
* *
29567 GGTCTTCATATCTTTATGAAC
1 GGTCTTCATGTCTTTATAAAC
29588 GGTCTTC-TCGTCTTT
1 GGTCTTCAT-GTCTTT
29603 GGTATGACTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 1 0.03
21 30 0.97
ACGTcount: A:0.18, C:0.19, G:0.18, T:0.46
Consensus pattern (21 bp):
GGTCTTCATGTCTTTATAAAC
Found at i:31867 original size:31 final size:26
Alignment explanation
Indices: 31810--31866 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
31800 AAAGCAACAC
*
31810 TAAATAAATCTAACATAACATCAAAA
1 TAAAAAAATCTAACATAACATCAAAA
*
31836 TAAAAAAATCTAACATAACATCAAAC
1 TAAAAAAATCTAACATAACATCAAAA
31862 TAAAA
1 TAAAA
31867 TGAAACTCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.63, C:0.16, G:0.00, T:0.21
Consensus pattern (26 bp):
TAAAAAAATCTAACATAACATCAAAA
Found at i:34728 original size:20 final size:20
Alignment explanation
Indices: 34703--34751 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
34693 ATTATATCAT
34703 AAATCTTAATTTAAAATTTA
1 AAATCTTAATTTAAAATTTA
34723 AAATCTTAATTTAAAATTTA
1 AAATCTTAATTTAAAATTTA
34743 AAATCTTAA
1 AAATCTTAA
34752 ATTGGATATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (20 bp):
AAATCTTAATTTAAAATTTA
Found at i:34753 original size:7 final size:7
Alignment explanation
Indices: 34710--34752 Score: 54
Period size: 7 Copynumber: 6.1 Consensus size: 7
34700 CATAAATCTT
34710 AATTTAA
1 AATTTAA
34717 AATTTAA
1 AATTTAA
34724 AATCTT--
1 AAT-TTAA
34730 AATTTAA
1 AATTTAA
34737 AATTTAA
1 AATTTAA
34744 AATCTTAA
1 AAT-TTAA
34752 A
1 A
34753 TTGGATATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
5 2 0.06
6 3 0.09
7 20 0.62
8 7 0.22
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (7 bp):
AATTTAA
Found at i:35346 original size:33 final size:34
Alignment explanation
Indices: 35296--35379 Score: 125
Period size: 34 Copynumber: 2.5 Consensus size: 34
35286 CAACCCATTG
*
35296 TCTGCGCCGCTTGTCCTCCT-AAAAAAACACTTC
1 TCTGCGCCGCTTCTCCTCCTAAAAAAAACACTTC
* *
35329 TCTGCGCTGCTTCTCCTCCTAAAAAAAACCCTTC
1 TCTGCGCCGCTTCTCCTCCTAAAAAAAACACTTC
*
35363 TCTGTGCCGCTTCTCCT
1 TCTGCGCCGCTTCTCCT
35380 TTCGTTGTTC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 18 0.40
34 27 0.60
ACGTcount: A:0.19, C:0.38, G:0.12, T:0.31
Consensus pattern (34 bp):
TCTGCGCCGCTTCTCCTCCTAAAAAAAACACTTC
Found at i:35776 original size:32 final size:32
Alignment explanation
Indices: 35740--35808 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
35730 ACTAGGCTAT
35740 TATATA-TATATGTTGATT-TATATATATGTATG
1 TATATATTATAT-TTG-TTGTATATATATGTATG
* *
35772 TATATATTGTATTTGTTGTTTATATATGTATG
1 TATATATTATATTTGTTGTATATATATGTATG
35804 TATAT
1 TATAT
35809 TATGAATTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 2 0.06
32 27 0.82
33 4 0.12
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (32 bp):
TATATATTATATTTGTTGTATATATATGTATG
Found at i:35818 original size:32 final size:32
Alignment explanation
Indices: 35752--35824 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
35742 TATATATATG
*
35752 TTGAT-TTATATATATGTATGTATATATTGTAT
1 TTGATGTT-TATATATGTATGTATATATTGAAT
*
35784 TTGTTGTTTATATATGTATGTATAT-TATGAAT
1 TTGATGTTTATATATGTATGTATATAT-TGAAT
35816 TTGATGTTT
1 TTGATGTTT
35825 GTATGTTATG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 1 0.03
32 33 0.92
33 2 0.06
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (32 bp):
TTGATGTTTATATATGTATGTATATATTGAAT
Found at i:35875 original size:21 final size:22
Alignment explanation
Indices: 35797--35887 Score: 139
Period size: 22 Copynumber: 4.2 Consensus size: 22
35787 TTGTTTATAT
* *
35797 ATGTATGTATATTATGAATTTG
1 ATGTTTGTATGTTATGAATTTG
35819 ATGTTTGTATGTTATGAATTTG
1 ATGTTTGTATGTTATGAATTTG
*
35841 TTGTTTGTATGTTATGAATTTG
1 ATGTTTGTATGTTATGAATTTG
*
35863 ATGTTTG-ATGTTATGTATTTG
1 ATGTTTGTATGTTATGAATTTG
35884 ATGT
1 ATGT
35888 GTATGATGAT
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
21 17 0.27
22 47 0.73
ACGTcount: A:0.23, C:0.00, G:0.22, T:0.55
Consensus pattern (22 bp):
ATGTTTGTATGTTATGAATTTG
Found at i:37027 original size:57 final size:57
Alignment explanation
Indices: 36939--37096 Score: 253
Period size: 57 Copynumber: 2.8 Consensus size: 57
36929 TGTAAGAAAT
* *
36939 ATTATATGGTTTATGGTCTATGTTAGAAATATTATATGGTTTGTCAATGTTTAAAAC
1 ATTATATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGTCAATGTTCAAAAC
* * * *
36996 ATTATATGGTTTGTGGTTTATGTTAAAAATATTATATGGTTTTTCGATGTTCAAAAC
1 ATTATATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGTCAATGTTCAAAAC
*
37053 ATTATATGGTTTGTGGTCCATGTTAGAAATATTATATGGTTTGT
1 ATTATATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGT
37097 ATTAAAGTTA
Statistics
Matches: 91, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 91 1.00
ACGTcount: A:0.29, C:0.05, G:0.19, T:0.47
Consensus pattern (57 bp):
ATTATATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGTCAATGTTCAAAAC
Found at i:37095 original size:30 final size:30
Alignment explanation
Indices: 36927--37096 Score: 185
Period size: 30 Copynumber: 5.9 Consensus size: 30
36917 TCTTTTTGAT
* *
36927 TATGTAAGAAATATTATATGGTTTATGGTC
1 TATGTTAGAAATATTATATGGTTTGTGGTC
36957 TATGTTAGAAATATTATATGG-TT-T-GTC
1 TATGTTAGAAATATTATATGGTTTGTGGTC
* * *
36984 AATGTTTA-AAACATTATATGGTTTGTGGTT
1 TATG-TTAGAAATATTATATGGTTTGTGGTC
*
37014 TATGTTAAAAATATTATATGGTTT-T--TC
1 TATGTTAGAAATATTATATGGTTTGTGGTC
* *
37041 GATGTTCA-AAACATTATATGGTTTGTGGTC
1 TATGTT-AGAAATATTATATGGTTTGTGGTC
*
37071 CATGTTAGAAATATTATATGGTTTGT
1 TATGTTAGAAATATTATATGGTTTGT
37097 ATTAAAGTTA
Statistics
Matches: 119, Mismatches: 11, Indels: 20
0.79 0.07 0.13
Matches are distributed among these distances:
27 39 0.33
28 8 0.07
29 8 0.07
30 64 0.54
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.46
Consensus pattern (30 bp):
TATGTTAGAAATATTATATGGTTTGTGGTC
Found at i:38440 original size:31 final size:31
Alignment explanation
Indices: 38403--38461 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
38393 AGTTGTATGG
* *
38403 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATTTCAGAATTGCAAAACTAAA
38434 ATTATTTAAATTTCAGAATTGCAAAACT
1 ATTATTTAAATTTCAGAATTGCAAAACT
38462 CTTTTCAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATTTCAGAATTGCAAAACTAAA
Found at i:38787 original size:22 final size:22
Alignment explanation
Indices: 38761--38809 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
38751 GATTTTTTTA
38761 TTATTAAAAGTTATA-AAATTAT
1 TTATTAAAA-TTATATAAATTAT
* *
38783 TTATT-TAATTATATAAATTTT
1 TTATTAAAATTATATAAATTAT
38804 TTATTA
1 TTATTA
38810 TTAAAAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 5 0.22
21 13 0.57
22 5 0.22
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TTATTAAAATTATATAAATTAT
Found at i:39775 original size:19 final size:19
Alignment explanation
Indices: 39751--39794 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
39741 TATAAATATA
39751 AAAAAATCAGAAAAAATAC
1 AAAAAATCAGAAAAAATAC
* *
39770 AAAAAATCTGAAAAATTAC
1 AAAAAATCAGAAAAAATAC
39789 AAAAAA
1 AAAAAA
39795 ATTAATATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.73, C:0.09, G:0.05, T:0.14
Consensus pattern (19 bp):
AAAAAATCAGAAAAAATAC
Found at i:44196 original size:3 final size:3
Alignment explanation
Indices: 44188--44290 Score: 172
Period size: 3 Copynumber: 34.3 Consensus size: 3
44178 GAATTGTCTG
* *
44188 AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAAT AAT GAT GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT
44233 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
44281 AAT AAT AAT A
1 AAT AAT AAT A
44291 CGGGTAAACT
Statistics
Matches: 96, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
2 2 0.02
3 91 0.95
4 3 0.03
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Done.