Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009241.1 Hibiscus syriacus cultivar Beakdansim tig00112871_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: 57761
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Found at i:6736 original size:277 final size:277
Alignment explanation
Indices: 6242--6796 Score: 1110
Period size: 277 Copynumber: 2.0 Consensus size: 277
6232 GCTTAAAACT
6242 AGCCTCTTTAGATTCATTTTATGGTATCATTGTACCATTAGTAATCTTGCTTTCTATTATTTAAC
1 AGCCTCTTTAGATTCATTTTATGGTATCATTGTACCATTAGTAATCTTGCTTTCTATTATTTAAC
6307 AATTGTAGTTCATGGTTTTGCAGTTGTCAACTTAACATTAATAGATCTGCCTGGTTTAACGAAGG
66 AATTGTAGTTCATGGTTTTGCAGTTGTCAACTTAACATTAATAGATCTGCCTGGTTTAACGAAGG
6372 TTGCTGTAGGTATACCCCCCGCTCTCCTAAAGAATTTCTCTTTCTGTTCGTCTGTCAGATTGTAA
131 TTGCTGTAGGTATACCCCCCGCTCTCCTAAAGAATTTCTCTTTCTGTTCGTCTGTCAGATTGTAA
6437 ATAGAGGTATTTGTTTTTGGTAGAGGGACAGCCAGAGAGTATCGTTCAAGACATAGAAAGCATGG
196 ATAGAGGTATTTGTTTTTGGTAGAGGGACAGCCAGAGAGTATCGTTCAAGACATAGAAAGCATGG
6502 TTCGCTCATATGTTGAG
261 TTCGCTCATATGTTGAG
6519 AGCCTCTTTAGATTCATTTTATGGTATCATTGTACCATTAGTAATCTTGCTTTCTATTATTTAAC
1 AGCCTCTTTAGATTCATTTTATGGTATCATTGTACCATTAGTAATCTTGCTTTCTATTATTTAAC
6584 AATTGTAGTTCATGGTTTTGCAGTTGTCAACTTAACATTAATAGATCTGCCTGGTTTAACGAAGG
66 AATTGTAGTTCATGGTTTTGCAGTTGTCAACTTAACATTAATAGATCTGCCTGGTTTAACGAAGG
6649 TTGCTGTAGGTATACCCCCCGCTCTCCTAAAGAATTTCTCTTTCTGTTCGTCTGTCAGATTGTAA
131 TTGCTGTAGGTATACCCCCCGCTCTCCTAAAGAATTTCTCTTTCTGTTCGTCTGTCAGATTGTAA
6714 ATAGAGGTATTTGTTTTTGGTAGAGGGACAGCCAGAGAGTATCGTTCAAGACATAGAAAGCATGG
196 ATAGAGGTATTTGTTTTTGGTAGAGGGACAGCCAGAGAGTATCGTTCAAGACATAGAAAGCATGG
6779 TTCGCTCATATGTTGAG
261 TTCGCTCATATGTTGAG
6796 A
1 A
6797 AGGTAACAGT
Statistics
Matches: 278, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
277 278 1.00
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.37
Consensus pattern (277 bp):
AGCCTCTTTAGATTCATTTTATGGTATCATTGTACCATTAGTAATCTTGCTTTCTATTATTTAAC
AATTGTAGTTCATGGTTTTGCAGTTGTCAACTTAACATTAATAGATCTGCCTGGTTTAACGAAGG
TTGCTGTAGGTATACCCCCCGCTCTCCTAAAGAATTTCTCTTTCTGTTCGTCTGTCAGATTGTAA
ATAGAGGTATTTGTTTTTGGTAGAGGGACAGCCAGAGAGTATCGTTCAAGACATAGAAAGCATGG
TTCGCTCATATGTTGAG
Found at i:17749 original size:19 final size:19
Alignment explanation
Indices: 17702--17752 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
17692 TCACAATATG
17702 ATAATTTTAAAAAAATTAT
1 ATAATTTTAAAAAAATTAT
**
17721 ATAAAATTAAAAAAATTAT
1 ATAATTTTAAAAAAATTAT
* *
17740 CTATTTTTAAAAA
1 ATAATTTTAAAAA
17753 GAAAAACATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (19 bp):
ATAATTTTAAAAAAATTAT
Found at i:25479 original size:2 final size:2
Alignment explanation
Indices: 25472--25503 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
25462 GATCCTTTCC
25472 AT AT AT 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 AT AT AT
25504 GAATGAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27053 original size:83 final size:83
Alignment explanation
Indices: 26911--27076 Score: 260
Period size: 83 Copynumber: 2.0 Consensus size: 83
26901 AAATGAACCC
* * * *
26911 CAACTATAGAACATTGTTTTGTTGAGTCCATCGATTATTGAAAGTTACAAAATACTCCTCTGACT
1 CAACTATAGAACACTGCTTTGTTGAGTCCATCGACTATTAAAAGTTACAAAATACTCCTCTGACT
26976 ATAACACATTGCTTTGAT
66 ATAACACATTGCTTTGAT
* *
26994 CAACTATAGGACACTGCTTTGTTGAGTCCATCGACTATTAAAAGTTACAAAATATTCCTCTGACT
1 CAACTATAGAACACTGCTTTGTTGAGTCCATCGACTATTAAAAGTTACAAAATACTCCTCTGACT
* *
27059 ATAACACGTTGTTTTGAT
66 ATAACACATTGCTTTGAT
27077 GAGTCTCTCA
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
83 75 1.00
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (83 bp):
CAACTATAGAACACTGCTTTGTTGAGTCCATCGACTATTAAAAGTTACAAAATACTCCTCTGACT
ATAACACATTGCTTTGAT
Found at i:32695 original size:16 final size:16
Alignment explanation
Indices: 32674--32711 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
32664 AAAAATAATT
32674 TAATAAAGTAAAATAA
1 TAATAAAGTAAAATAA
* *
32690 TAATAATGTAATATAA
1 TAATAAAGTAAAATAA
32706 T-ATAAA
1 TAATAAA
32712 TACATGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (16 bp):
TAATAAAGTAAAATAA
Found at i:33446 original size:36 final size:37
Alignment explanation
Indices: 33400--33475 Score: 111
Period size: 36 Copynumber: 2.1 Consensus size: 37
33390 GTTTAAAACA
33400 TAGCAAAATTCTATCATATTTTT-AGGAG-TTGAATCC
1 TAGCAAAATTCTATCATATTTTTGA-GAGTTTGAATCC
* *
33436 TAGCAGAATTCTATCTTATTTTTGAGAGTTTGAATCC
1 TAGCAAAATTCTATCATATTTTTGAGAGTTTGAATCC
33473 TAG
1 TAG
33476 TAGGACGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
36 24 0.67
37 12 0.33
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.41
Consensus pattern (37 bp):
TAGCAAAATTCTATCATATTTTTGAGAGTTTGAATCC
Found at i:34246 original size:106 final size:108
Alignment explanation
Indices: 33942--34565 Score: 562
Period size: 109 Copynumber: 5.9 Consensus size: 108
33932 GTTCCGAGTC
* * ** * * **
33942 CAATATCCTCCGCTGTGAAGTTGAAATTGGTTCTGGAACCGGGAAATTGTTTGATGACAGTCAGC
1 CAATATCCTCCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATGTTTGTTGACAACCAGC
* * *
34007 C-TCCCATTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGT-C-
66 CGTCCC-TTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCA
* * ** * * * *
34048 TAATATCTTTAGCTGTGAAGTTGAAATTGACTCTG-AA---CG-AAAT-CTTGTTGACAATCAGC
1 CAATATCCTCCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATGTTTGTTGACAACCAGC
34107 CGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-C-
66 CGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCA
* * *
34148 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTTGAAAAATGTTTGTTGACAACCAGC
1 CAATATCCTCCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATGTTTGTTGACAACCAGC
* *
34213 TGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTCGAGTGGCA
66 CGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-GCA
* * * * ** * * *
34257 CGATATCCTCCGTTGTGGAGTTGAAA-TCGCGGATGAAACT-GAAAAAT-TATTCATTGACAACC
1 CAATATCCTCCGCTGTGAAGTTGAAATTGGC-TCTGAAATTGGGAAAATGT-TT-GTTGACAACC
* * *
34319 AGCCGTCCCTTCGTTGTGAAGTTGGACTTGTGTTTTCTCGGGTAGCA
63 AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-GCA
* * * * * ** *
34366 CGATATCCTCCG-TCGTGGAGTTGAAATCGGTTCTGGAATTGGGAAGTTGTTCGTTGACAACCAG
1 CAATATCCTCCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATGTTTGTTGACAACCAG
* *
34430 CCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGGGTAGCA
65 CCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-GCA
* * * * * * *
34475 CGATATCCTCCG-TCGTGGAGTTGAAATCGGTTCCGAAATTGGGAAATTG-TTGTTGGCAACCAG
1 CAATATCCTCCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATGTTTGTTGACAACCAG
*
34538 ACGTCCCTTCGTTGTGAAGTTGAACTTG
65 CCGTCCCTTCGTTGTGAAGTTGAACTTG
34566 ACTCTAGCTA
Statistics
Matches: 441, Mismatches: 60, Indels: 32
0.83 0.11 0.06
Matches are distributed among these distances:
100 77 0.17
101 9 0.02
102 1 0.00
105 6 0.01
106 81 0.18
107 1 0.00
108 53 0.12
109 206 0.47
110 6 0.01
111 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.33
Consensus pattern (108 bp):
CAATATCCTCCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATGTTTGTTGACAACCAGC
CGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCA
Found at i:34327 original size:109 final size:108
Alignment explanation
Indices: 34092--34565 Score: 564
Period size: 109 Copynumber: 4.4 Consensus size: 108
34082 GAACGAAATC
* *
34092 TTGTTGACAATCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT--C-CAATAT
1 TTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTAGCACGATAT
* * * *
34154 CCTTCG-CTGTGAAGTTGAAATTGGCTCTGAAATTTGAAAAA-TG
66 CCTCCGTC-GTGGAGTTGAAATCGGCGCTGAAA-TTGAAAAATTG
* * *
34197 TTTGTTGACAACCAGCTGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTCGAGTGGCACGATA
1 -TTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTAGCACGATA
* * * *
34262 TCCTCCGTTGTGGAGTTGAAATC-GCGGATGAAACTGAAAAATTA
65 TCCTCCGTCGTGGAGTTGAAATCGGC-GCTGAAATTGAAAAATTG
* * * *
34306 TTCATTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGGACTTGTGTTTTCTCGGGTAGCACGATA
1 TT-GTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTAGCACGATA
** * ** *
34371 TCCTCCGTCGTGGAGTTGAAATCGGTTCTGGAATTGGGAAGTTG
65 TCCTCCGTCGTGGAGTTGAAATCGGCGCTGAAATTGAAAAATTG
* *
34415 TTCGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGGGTAGCACGATA
1 TT-GTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTAGCACGATA
** * **
34480 TCCTCCGTCGTGGAGTTGAAATCGGTTCCGAAATTGGGAAATTG
65 TCCTCCGTCGTGGAGTTGAAATCGGCGCTGAAATTGAAAAATTG
* *
34524 TTGTTGGCAACCAGACGTCCCTTCGTTGTGAAGTTGAACTTG
1 TTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTG
34566 ACTCTAGCTA
Statistics
Matches: 322, Mismatches: 38, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
106 52 0.16
108 50 0.16
109 219 0.68
110 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (108 bp):
TTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTAGCACGATAT
CCTCCGTCGTGGAGTTGAAATCGGCGCTGAAATTGAAAAATTG
Found at i:35234 original size:36 final size:36
Alignment explanation
Indices: 35179--35263 Score: 89
Period size: 36 Copynumber: 2.4 Consensus size: 36
35169 AGATTTTGTG
* * * * * **
35179 TTTCAAGAGAAACTGTCTCATGGGAGACAAAATTTG
1 TTTCAAGGGAAATTATCTCAAGAGAGACAAAATTCA
* *
35215 TTTCGAGGGAAATTATCTCAAGAGAGACGAAATTCA
1 TTTCAAGGGAAATTATCTCAAGAGAGACAAAATTCA
35251 TTTCAAGGGAAAT
1 TTTCAAGGGAAAT
35264 GTTTTCAATG
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (36 bp):
TTTCAAGGGAAATTATCTCAAGAGAGACAAAATTCA
Found at i:35339 original size:103 final size:103
Alignment explanation
Indices: 35177--35552 Score: 623
Period size: 103 Copynumber: 3.7 Consensus size: 103
35167 AAAGATTTTG
* * *
35177 TGTTTCAAGAGAAACTGTCTCATGGGAGAC-AAAA-TTTGTTTCGAGGGAAATTATCTCAAGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGA
*
35240 GACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
66 GACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* *
35278 TGTTTCAGGAGAAACTGTCTCAAGGGAGACAAAATTTTTGTTTCAAGGGAAACTATCTCAAGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGA
*
35343 GACAAAATTCATTTCAAGGGAAATGTTTCCAATGTTTA
66 GACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
35381 TGTTTCAAGAGAAACTGTCTCAAGGGAGA-AAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGA
*
35445 GACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTA
66 GACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* * * *
35483 TGTTTCAAGAGAAAATGTCTCAATGGAGAAAAAAATTTTGTTTCAAGGGAAACTGTCTCAAGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGA
35548 GACAA
66 GACAA
35553 TGGTGAGCAC
Statistics
Matches: 258, Mismatches: 14, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
101 28 0.11
102 100 0.39
103 130 0.50
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (103 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGA
GACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
Found at i:35528 original size:205 final size:204
Alignment explanation
Indices: 35177--35552 Score: 635
Period size: 205 Copynumber: 1.8 Consensus size: 204
35167 AAAGATTTTG
* * * *
35177 TGTTTCAAGAGAAACTGTCTCATGGGAGACAAAATTTGTTTCGAGGGAAATTATCTCAAGAGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGA
* * * *
35242 CGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAGGAGAAACTGTCTCAAGGGAGA
66 CAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAAATGTCTCAAGGGAGA
* *
35307 CAAAATTTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTC
131 AAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTC
35372 CAATGTTTA
196 CAATGTTTA
35381 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAA-TTTGTTTCAAGGGAAACTATCTCAAGAGAG
*
35446 ACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAAATGTCTCAATGGAG
65 ACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAAATGTCTCAAGGGAG
*
35511 AAAAAAATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
130 AAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAA
35553 TGGTGAGCAC
Statistics
Matches: 159, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
204 32 0.20
205 127 0.80
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (204 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGA
CAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAAATGTCTCAAGGGAGA
AAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTC
CAATGTTTA
Found at i:37072 original size:17 final size:18
Alignment explanation
Indices: 37039--37072 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
37029 TTGCATGTGC
*
37039 TTTTTGTTCCTTTTTTTA
1 TTTTTGTTCCTTGTTTTA
37057 TTTTTGTT-CTTGTTTT
1 TTTTTGTTCCTTGTTTT
37073 TTCCTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.03, C:0.09, G:0.09, T:0.79
Consensus pattern (18 bp):
TTTTTGTTCCTTGTTTTA
Found at i:37082 original size:22 final size:23
Alignment explanation
Indices: 37057--37104 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
37047 CCTTTTTTTA
37057 TTTTTG-TTCTTGT-TTTTTCCT
1 TTTTTGCTTCTTGTCTTTTTCCT
* *
37078 TTTTTGCTTCTTTTCTTTTTTCT
1 TTTTTGCTTCTTGTCTTTTTCCT
37101 TTTT
1 TTTT
37105 GCCCTTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 6 0.26
22 6 0.26
23 11 0.48
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (23 bp):
TTTTTGCTTCTTGTCTTTTTCCT
Found at i:37105 original size:22 final size:21
Alignment explanation
Indices: 37049--37106 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
37039 TTTTTGTTCC
*
37049 TTTTTTTATTTTTG-TTCTTG
1 TTTTTTTCTTTTTGCTTCTTG
* *
37069 TTTTTTCCTTTTTTGCTTCTTT
1 TTTTTTTC-TTTTTGCTTCTTG
37091 TCTTTTTTCTTTTTGC
1 T-TTTTTTCTTTTTGC
37107 CCTTTTTGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 6 0.19
21 6 0.19
22 13 0.42
23 6 0.19
ACGTcount: A:0.02, C:0.14, G:0.07, T:0.78
Consensus pattern (21 bp):
TTTTTTTCTTTTTGCTTCTTG
Found at i:40450 original size:16 final size:16
Alignment explanation
Indices: 40429--40462 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
40419 AATAATAATT
40429 TAATAAAGTAAAATAA
1 TAATAAAGTAAAATAA
* *
40445 TAATAATGTAATATAA
1 TAATAAAGTAAAATAA
40461 TA
1 TA
40463 TAATATAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (16 bp):
TAATAAAGTAAAATAA
Found at i:40576 original size:13 final size:15
Alignment explanation
Indices: 40557--40589 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
40547 AAAAGTAAAA
*
40557 ATAAAAAAAATACA-
1 ATAAAAAATATACAT
40571 ATAAAAAATATACAT
1 ATAAAAAATATACAT
40586 ATAA
1 ATAA
40590 TGATAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (15 bp):
ATAAAAAATATACAT
Found at i:41205 original size:36 final size:38
Alignment explanation
Indices: 41126--41227 Score: 129
Period size: 36 Copynumber: 2.7 Consensus size: 38
41116 GTGCTTGTGG
* * * *
41126 ATCCTATCTTTAGGAGTTTAAAACATAGCAAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAATTCT
*
41164 ATCCTATTTTTAGGAG-TTGAATCCTAGC-AGAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAATTCT
41200 ATCCTATTTTT-GAGAGTTTGAATCCTAG
1 ATCCTATTTTTAG-GAGTTTGAATCCTAG
41228 TAGGACGAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
35 1 0.02
36 21 0.37
37 20 0.35
38 15 0.26
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (38 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAATTCT
Found at i:48446 original size:20 final size:20
Alignment explanation
Indices: 48421--48533 Score: 181
Period size: 20 Copynumber: 5.7 Consensus size: 20
48411 TTTTCCAAAT
48421 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
48441 TCGCAATGAGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
48461 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
48481 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
48501 ACGCAATGCAAATACATAAA
1 TCGCAATGCGAATACGTAAA
*
48521 TCGCAACGCGAAT
1 TCGCAATGCGAAT
48534 CTGACTATCG
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 85 1.00
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:48543 original size:20 final size:20
Alignment explanation
Indices: 48520--48586 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
48510 AAATACATAA
* *
48520 ATCGCAACGCGAATCTGACT
1 ATCGCAACGAGATTCTGACT
48540 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
48560 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
48580 ATCGCAA
1 ATCGCAA
48587 TACTGAATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAACGAGATTCTGACT
Done.