Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001773.1 Hibiscus syriacus cultivar Beakdansim tig00003575_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: 77728
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:847 original size:14 final size:13
Alignment explanation
Indices: 825--867 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
815 TTATCGTCAT
825 AATTAAAAATATA
1 AATTAAAAATATA
*
838 AATATAAAAATAATT
1 AAT-TAAAAAT-ATA
*
853 AATTTAAAATATA
1 AATTAAAAATATA
866 AA
1 AA
868 AACTGAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
13 7 0.28
14 13 0.52
15 5 0.20
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AATTAAAAATATA
Found at i:11503 original size:134 final size:137
Alignment explanation
Indices: 11207--11781 Score: 561
Period size: 144 Copynumber: 4.1 Consensus size: 137
11197 ACGTTTGTGA
* ** * *
11207 ACTGAAAAGTTTCTATCATGGTGCATTATTTTGCCTATGAGAAATACACATTTTTTATGATATGA
1 ACTGAAAAGTTTATGCCATGGTGCATTATTTTGCC--T-AGAAAT--GC--TTTTTGTGATATGA
* * *
11272 AGTGATATATCAACACTGAAAAGTTTGCTGAAATGGGTTGATATATCACCGAAAAGTT-ACTGAA
59 AGTGATATATCAACACTGAAAAGTTTGCTTAAATGAGTTGATATATCACTGAAAAGTTGA-TGAA
*
11336 GATAATTTATTGGCC
123 GATAATTAATTGGCC
* *
11351 ACTGAAAAGTTTATGCCATGGTGCATTATTTTGCCT-G-CATG-TTTTTGTGTTATGAAGTGATA
1 ACTGAAAAGTTTATGCCATGGTGCATTATTTTGCCTAGAAATGCTTTTTGTGATATGAAGTGATA
* *
11413 TATCAGCACTGGAAAGTTTGCTTAAATGAGTTGATATATCACTGAAAAGTTGATGAAGATAATTA
66 TATCAACACTGAAAAGTTTGCTTAAATGAGTTGATATATCACTGAAAAGTTGATGAAGATAATTA
*
11478 ATTGACC
131 ATTGGCC
*
11485 ACTTG-AAAGTTTCA-GCCATGGTGTATTATTTTGCCTACGAGAAATGCACTTTTTGTGATATGA
1 AC-TGAAAAGTTT-ATGCCATGGTGCATTATTTTGCCT---AGAAATG--CTTTTTGTGATATGA
* * * * *
11548 AGTGATATATCACCATTGAAAAGTTTG-TTGAGATGAGTTGATATATCATTGAAAAGTTGTTGAA
59 AGTGATATATCAACACTGAAAAGTTTGCTT-AAATGAGTTGATATATCACTGAAAAGTTGATGAA
11612 GATAATTAATTGGCC
123 GATAATTAATTGGCC
* * *
11627 ACTGAAAAGTTTATGTCATGGTGCATTGTTTTGCCTATGAGAAATGCACGTTTTTTGTGATATAA
1 ACTGAAAAGTTTATGCCATGGTGCATTATTTTGCC--T-AGAAATG--C--TTTTTGTGATATGA
* * * * * * * * * * *
11692 AGTAATATATCACCACTGAAAAGTTTGATGAGAGGAGTTGATATATCAATCAAAAGTTGCTAAAT
59 AGTGATATATCAACACTGAAAAGTTTGCTTAAATGAGTTGATATATCACTGAAAAGTTGATGAAG
**
11757 ATAATTAATTATCC
124 ATAATTAATTGGCC
*
11771 ACTAAAAAGTT
1 ACTGAAAAGTT
11782 GACTTTTCTA
Statistics
Matches: 372, Mismatches: 40, Indels: 38
0.83 0.09 0.08
Matches are distributed among these distances:
134 112 0.30
135 4 0.01
138 1 0.00
139 5 0.01
140 1 0.00
141 5 0.01
142 121 0.33
144 122 0.33
145 1 0.00
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (137 bp):
ACTGAAAAGTTTATGCCATGGTGCATTATTTTGCCTAGAAATGCTTTTTGTGATATGAAGTGATA
TATCAACACTGAAAAGTTTGCTTAAATGAGTTGATATATCACTGAAAAGTTGATGAAGATAATTA
ATTGGCC
Found at i:11601 original size:142 final size:143
Alignment explanation
Indices: 11386--11781 Score: 505
Period size: 142 Copynumber: 2.8 Consensus size: 143
11376 TTATTTTGCC
* * * * *
11386 TGCATGTTTTTGTGTTATGAAGTGATATATCAGCACTGGAAAGTTTGCTT-AAATGAGTTGATAT
1 TGCACGTTTTTGTGATATGAAGTGATATATCACCACTGAAAAGTTTG-TTGAGATGAGTTGATAT
* *
11450 ATCACTGAAAAGTTGATGAAGATAATTAATTGACCACTTG-AAAGTTTCA-GCCATGGTGTATTA
65 ATCAATGAAAAGTTGATGAAGATAATTAATTGACCAC-TGAAAAGTTT-ATGCCATGGTGCATTA
11513 TTTTGCCTACGAGAAA
128 TTTTGCCTACGAGAAA
*
11529 TGCAC-TTTTTGTGATATGAAGTGATATATCACCATTGAAAAGTTTGTTGAGATGAGTTGATATA
1 TGCACGTTTTTGTGATATGAAGTGATATATCACCACTGAAAAGTTTGTTGAGATGAGTTGATATA
* * * * *
11593 TCATTGAAAAGTTGTTGAAGATAATTAATTGGCCACTGAAAAGTTTATGTCATGGTGCATTGTTT
66 TCAATGAAAAGTTGATGAAGATAATTAATTGACCACTGAAAAGTTTATGCCATGGTGCATTATTT
*
11658 TGCCTATGAGAAA
131 TGCCTACGAGAAA
* * * *
11671 TGCACGTTTTTTGTGATATAAAGTAATATATCACCACTGAAAAGTTTGATGAGAGGAGTTGATAT
1 TGCACG-TTTTTGTGATATGAAGTGATATATCACCACTGAAAAGTTTGTTGAGATGAGTTGATAT
* * * * *
11736 ATCAATCAAAAGTTGCTAAATATAATTAATT-ATCCACTAAAAAGTT
65 ATCAATGAAAAGTTGATGAAGATAATTAATTGA-CCACTGAAAAGTT
11782 GACTTTTCTA
Statistics
Matches: 222, Mismatches: 25, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
141 5 0.02
142 122 0.55
143 4 0.02
144 91 0.41
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.36
Consensus pattern (143 bp):
TGCACGTTTTTGTGATATGAAGTGATATATCACCACTGAAAAGTTTGTTGAGATGAGTTGATATA
TCAATGAAAAGTTGATGAAGATAATTAATTGACCACTGAAAAGTTTATGCCATGGTGCATTATTT
TGCCTACGAGAAA
Found at i:13661 original size:2 final size:2
Alignment explanation
Indices: 13654--13679 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13644 AAATTAGATT
13654 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
13680 ATAATATTTT
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):
TA
Found at i:16109 original size:25 final size:25
Alignment explanation
Indices: 16080--16141 Score: 115
Period size: 25 Copynumber: 2.5 Consensus size: 25
16070 TTTCAACCAG
16080 GATTGCATGTTCTTTCTGGACAAGA
1 GATTGCATGTTCTTTCTGGACAAGA
*
16105 GATTGCATGTTCTTTCTGGACAAGG
1 GATTGCATGTTCTTTCTGGACAAGA
16130 GATTGCATGTTC
1 GATTGCATGTTC
16142 ATTTAACTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.21, C:0.16, G:0.26, T:0.37
Consensus pattern (25 bp):
GATTGCATGTTCTTTCTGGACAAGA
Found at i:19764 original size:30 final size:30
Alignment explanation
Indices: 19708--19830 Score: 194
Period size: 30 Copynumber: 4.1 Consensus size: 30
19698 GAAGGACCTA
* * *
19708 TCCAGAGGTCACAAAGA-CCCCGGTAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
19737 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
19767 TCCAGAGGTCATAAAGATCCTCAGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
19797 TCCAGAGGTCATAAACATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
19827 TCCA
1 TCCA
19831 TATGTTCCTT
Statistics
Matches: 87, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
29 16 0.18
30 71 0.82
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:19860 original size:31 final size:30
Alignment explanation
Indices: 19819--19916 Score: 117
Period size: 31 Copynumber: 3.2 Consensus size: 30
19809 AAACATCCTC
*
19819 GGTAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATATGTTCCATAGAACATA
* *
19849 GGTATACTGTCCATATGTCTCGAAAG-ACATA
1 GGTA-ACTGTCCATATGT-TCCATAGAACATA
*
19880 GGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGT--AACTGTCCATATGTTCCATAGAACATA
19912 GGTAA
1 GGTAA
19917 ACCCTCGACT
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
30 6 0.11
31 25 0.44
32 25 0.44
33 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (30 bp):
GGTAACTGTCCATATGTTCCATAGAACATA
Found at i:20612 original size:21 final size:21
Alignment explanation
Indices: 20582--20626 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
20572 ATTCTGTCGT
* *
20582 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
20603 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
20624 TTG
1 TTG
20627 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:25079 original size:30 final size:30
Alignment explanation
Indices: 25023--25145 Score: 203
Period size: 30 Copynumber: 4.1 Consensus size: 30
25013 GAAGGACCTA
* * *
25023 TCCAGAGGTCACAAAGA-CCCCGGTAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
25052 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
25082 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
25112 TTCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
25142 TCCA
1 TCCA
25146 TATGTTCCTT
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
29 16 0.18
30 72 0.82
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:25176 original size:31 final size:30
Alignment explanation
Indices: 25134--25231 Score: 117
Period size: 31 Copynumber: 3.2 Consensus size: 30
25124 AAAGATCCTC
*
25134 GGTAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATATGTTCCATAGAACATA
* *
25164 GGTATACTGTCCATATGTCTCGAAAG-ACATA
1 GGTA-ACTGTCCATATGT-TCCATAGAACATA
*
25195 GGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGT--AACTGTCCATATGTTCCATAGAACATA
25227 GGTAA
1 GGTAA
25232 ACCCTCGACT
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
30 6 0.11
31 25 0.44
32 25 0.44
33 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (30 bp):
GGTAACTGTCCATATGTTCCATAGAACATA
Found at i:25929 original size:21 final size:21
Alignment explanation
Indices: 25899--25943 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
25889 ATTCTGTCGT
* *
25899 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
25920 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
25941 TTG
1 TTG
25944 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:26713 original size:17 final size:17
Alignment explanation
Indices: 26691--26755 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
26681 CGTATAAATG
26691 TCCCGAAGGACCTATCA
1 TCCCGAAGGACCTATCA
** *
26708 TCCCGAAGGATGTCATCTGTG
1 TCCCGAAGGACCT-ATC---A
*
26729 TCCCGAAGGACCTGTCA
1 TCCCGAAGGACCTATCA
26746 TCCCGAAGGA
1 TCCCGAAGGA
26756 TGTAATCTGT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
17 21 0.57
18 3 0.08
20 2 0.05
21 11 0.30
ACGTcount: A:0.25, C:0.31, G:0.25, T:0.20
Consensus pattern (17 bp):
TCCCGAAGGACCTATCA
Found at i:26734 original size:21 final size:21
Alignment explanation
Indices: 26708--26771 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
26698 GGACCTATCA
26708 TCCCGAAGGATGTCATCTGTG
1 TCCCGAAGGATGTCATCTGTG
*
26729 TCCCGAAGGA---C--CTGTCA
1 TCCCGAAGGATGTCATCTGT-G
*
26746 TCCCGAAGGATGTAATCTGTG
1 TCCCGAAGGATGTCATCTGTG
26767 TCCCG
1 TCCCG
26772 TAGAACCTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 12
0.69 0.06 0.24
Matches are distributed among these distances:
16 4 0.12
17 10 0.29
18 1 0.03
21 15 0.44
22 4 0.12
ACGTcount: A:0.20, C:0.28, G:0.27, T:0.25
Consensus pattern (21 bp):
TCCCGAAGGATGTCATCTGTG
Found at i:26740 original size:38 final size:38
Alignment explanation
Indices: 26689--26784 Score: 156
Period size: 38 Copynumber: 2.5 Consensus size: 38
26679 CTCGTATAAA
*
26689 TGTCCCGAAGGACCTATCATCCCGAAGGATGTCATCTG
1 TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTG
*
26727 TGTCCCGAAGGACCTGTCATCCCGAAGGATGTAATCTG
1 TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTG
* *
26765 TGTCCCGTAGAACCTATCAT
1 TGTCCCGAAGGACCTATCAT
26785 ATGTCTTATA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 53 1.00
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (38 bp):
TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTG
Found at i:27028 original size:17 final size:17
Alignment explanation
Indices: 26976--27030 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
26966 TTACATATTT
26976 ATATGTCATTTCATATC
1 ATATGTCATTTCATATC
* ** *
26993 ACATGT-ATCACGTATTC
1 ATATGTCATTTCATA-TC
27010 ATATGTCATTTCATATC
1 ATATGTCATTTCATATC
27027 ATAT
1 ATAT
27031 CACATAGCGT
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
16 5 0.18
17 18 0.64
18 5 0.18
ACGTcount: A:0.31, C:0.18, G:0.07, T:0.44
Consensus pattern (17 bp):
ATATGTCATTTCATATC
Found at i:27464 original size:35 final size:36
Alignment explanation
Indices: 27405--27475 Score: 135
Period size: 35 Copynumber: 2.0 Consensus size: 36
27395 TTCATTTAGG
27405 GGGGAATCGATACCCCCCCAGGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCCCAGGGGGAATCTGTTCCC
27441 GGGGAATCGATA-CCCCCCAGGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCCCAGGGGGAATCTGTTCCC
27476 CCTGCACATA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 23 0.66
36 12 0.34
ACGTcount: A:0.20, C:0.32, G:0.31, T:0.17
Consensus pattern (36 bp):
GGGGAATCGATACCCCCCCAGGGGGAATCTGTTCCC
Found at i:27476 original size:20 final size:20
Alignment explanation
Indices: 27418--27477 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
27408 GAATCGATAC
27418 CCCCCCAGGGGGAATCTGTT
1 CCCCCCAGGGGGAATCTGTT
*
27438 ---CCC--GGGGAATC-GATA
1 CCCCCCAGGGGGAATCTG-TT
27453 CCCCCCAGGGGGAATCTGTT
1 CCCCCCAGGGGGAATCTGTT
27473 CCCCC
1 CCCCC
27478 TGCACATACT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 1 0.03
15 9 0.29
17 3 0.10
18 3 0.10
20 14 0.45
21 1 0.03
ACGTcount: A:0.17, C:0.38, G:0.28, T:0.17
Consensus pattern (20 bp):
CCCCCCAGGGGGAATCTGTT
Found at i:33620 original size:17 final size:17
Alignment explanation
Indices: 33595--33660 Score: 51
Period size: 17 Copynumber: 3.6 Consensus size: 17
33585 TCGTATAAAT
*
33595 ATCCTGAAGGACCTATC
1 ATCCCGAAGGACCTATC
* *
33612 ATCCCGAAGGATGTCATATGT
1 ATCCCGAAGGA---CCTAT-C
* *
33633 GTCCCGAAGGACCTGTC
1 ATCCCGAAGGACCTATC
33650 ATCCCGAAGGA
1 ATCCCGAAGGA
33661 TGTAATCTGT
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
17 20 0.54
18 3 0.08
20 4 0.11
21 10 0.27
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.21
Consensus pattern (17 bp):
ATCCCGAAGGACCTATC
Found at i:33652 original size:38 final size:38
Alignment explanation
Indices: 33600--33689 Score: 135
Period size: 38 Copynumber: 2.4 Consensus size: 38
33590 TAAATATCCT
* *
33600 GAAGGACCTATCATCCCGAAGGATGTCATATGTGTCCC
1 GAAGGACCTATCATCCCGAAGGATGTAATATGTGCCCC
* *
33638 GAAGGACCTGTCATCCCGAAGGATGTAATCTGTGCCCC
1 GAAGGACCTATCATCCCGAAGGATGTAATATGTGCCCC
*
33676 GTAGGACCTATCAT
1 GAAGGACCTATCAT
33690 ATGTCTTATA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 46 1.00
ACGTcount: A:0.26, C:0.27, G:0.24, T:0.23
Consensus pattern (38 bp):
GAAGGACCTATCATCCCGAAGGATGTAATATGTGCCCC
Found at i:34211 original size:22 final size:21
Alignment explanation
Indices: 34172--34213 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
34162 ATCAGATTGT
*
34172 CCAGGGGGTACAGATTCCCCC
1 CCAGGGGGAACAGATTCCCCC
*
34193 CCAGGGGGAACAGATTTCCCC
1 CCAGGGGGAACAGATTCCCCC
34214 AGGGGTATCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.36, G:0.29, T:0.14
Consensus pattern (21 bp):
CCAGGGGGAACAGATTCCCCC
Found at i:34215 original size:19 final size:20
Alignment explanation
Indices: 34172--34218 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
34162 ATCAGATTGT
*
34172 CCAGGGGGTACAGATTCCCCC
1 CCAGGGGGAACAGATT-CCCC
*
34193 CCAGGGGGAACAGATT-TCC
1 CCAGGGGGAACAGATTCCCC
34212 CCAGGGG
1 CCAGGGG
34219 TATCGATTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 9 0.38
21 15 0.62
ACGTcount: A:0.21, C:0.32, G:0.34, T:0.13
Consensus pattern (20 bp):
CCAGGGGGAACAGATTCCCC
Found at i:34726 original size:34 final size:32
Alignment explanation
Indices: 34683--34752 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 32
34673 TTTTGTAGAG
*
34683 GGGAAAGGTTCTAGTTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGTTTAGCCCG-G-AAAAACTA
34717 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
34749 GGGA
1 GGGA
34753 GTTTGTAAGG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 11 0.31
33 1 0.03
34 23 0.66
ACGTcount: A:0.31, C:0.14, G:0.31, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
Found at i:37834 original size:220 final size:220
Alignment explanation
Indices: 37448--37884 Score: 847
Period size: 220 Copynumber: 2.0 Consensus size: 220
37438 AATATTTTGA
*
37448 TGTTTCGATATAACAAATTAAGTTAAATGAATTTTAAGATTTTACAAAATATTTTCTAAGTATAT
1 TGTTTCGATATAACAAATTAAGTTAAATGAATTTTAAGATTTTACAAAAGATTTTCTAAGTATAT
37513 TCGATGTAATTATTCGAATATCAAAATATTACTCCAAGTCTTTCAAAGTTCATTTTAATCCTTAC
66 TCGATGTAATTATTCGAATATCAAAATATTACTCCAAGTCTTTCAAAGTTCATTTTAATCCTTAC
* *
37578 TAAAGTGTAAAATTGTGTTTTATACTTAATCTATTTTAAAACAATTTTACAAAGTATTTCGAGCC
131 TAAAGTGTAAAATTATGTTTTATACTTAAACTATTTTAAAACAATTTTACAAAGTATTTCGAGCC
37643 TTAATCGAGCCAAAAATATTTTCTT
196 TTAATCGAGCCAAAAATATTTTCTT
37668 TGTTTCGATATAACAAATTAAGTTAAATGAATTTTAAGATTTTACAAAAGATTTTCTAAGTATAT
1 TGTTTCGATATAACAAATTAAGTTAAATGAATTTTAAGATTTTACAAAAGATTTTCTAAGTATAT
37733 TCGATGTAATTATTCGAATATCAAAATATTACTCCAAGTCTTTCAAAGTTCATTTTAATCCTTAC
66 TCGATGTAATTATTCGAATATCAAAATATTACTCCAAGTCTTTCAAAGTTCATTTTAATCCTTAC
37798 TAAAGTGTAAAATTATGTTTTATACTTAAACTATTTTAAAACAATTTTACAAAGTATTTCGAGCC
131 TAAAGTGTAAAATTATGTTTTATACTTAAACTATTTTAAAACAATTTTACAAAGTATTTCGAGCC
37863 TTAATCGAGCCAAAAATATTTT
196 TTAATCGAGCCAAAAATATTTT
37885 TTTTTATAGG
Statistics
Matches: 214, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
220 214 1.00
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (220 bp):
TGTTTCGATATAACAAATTAAGTTAAATGAATTTTAAGATTTTACAAAAGATTTTCTAAGTATAT
TCGATGTAATTATTCGAATATCAAAATATTACTCCAAGTCTTTCAAAGTTCATTTTAATCCTTAC
TAAAGTGTAAAATTATGTTTTATACTTAAACTATTTTAAAACAATTTTACAAAGTATTTCGAGCC
TTAATCGAGCCAAAAATATTTTCTT
Found at i:37942 original size:20 final size:20
Alignment explanation
Indices: 37917--37976 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
37907 ATCAGATTAT
37917 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
*
37937 CCAGGGGGAACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
*
37957 CTAGGGGGTATC-GATTCCCC
1 CCAGGGGGTA-CAGATTCCCC
37977 GGGAACAGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
20 35 0.97
21 1 0.03
ACGTcount: A:0.20, C:0.33, G:0.30, T:0.17
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:37989 original size:15 final size:15
Alignment explanation
Indices: 37969--38024 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
37959 AGGGGGTATC
37969 GATTCCCCGGGAACA
1 GATTCCCCGGGAACA
*
37984 GATTCCCCCAGGGGTATC-
1 GATT-CCCC--GGG-AACA
*
38002 GATTCCCCGGGTACA
1 GATTCCCCGGGAACA
38017 GATTCCCC
1 GATTCCCC
38025 CTGCATGGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
14 1 0.03
15 15 0.45
16 4 0.12
17 4 0.12
18 7 0.21
19 2 0.06
ACGTcount: A:0.20, C:0.36, G:0.25, T:0.20
Consensus pattern (15 bp):
GATTCCCCGGGAACA
Found at i:38003 original size:33 final size:35
Alignment explanation
Indices: 37942--38026 Score: 147
Period size: 33 Copynumber: 2.5 Consensus size: 35
37932 TCCCCCCAGG
37942 GGGAACAGATTCCCCCTAGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTAGGGGGTATCGATTCCCC
37977 GGGAACAGATTCCCCC-A-GGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTAGGGGGTATCGATTCCCC
*
38010 GGGTACAGATTCCCCCT
1 GGGAACAGATTCCCCCT
38027 GCATGGTTTG
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
33 31 0.65
34 1 0.02
35 16 0.33
ACGTcount: A:0.20, C:0.33, G:0.27, T:0.20
Consensus pattern (35 bp):
GGGAACAGATTCCCCCTAGGGGGTATCGATTCCCC
Found at i:38242 original size:21 final size:21
Alignment explanation
Indices: 38208--38247 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
38198 TTTTTGTAGA
*
38208 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
38230 AAAAT-ATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
38248 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 1 0.06
22 5 0.29
ACGTcount: A:0.38, C:0.35, G:0.10, T:0.17
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:38501 original size:34 final size:32
Alignment explanation
Indices: 38462--38531 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
38452 TTTTGTAAAG
*
38462 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
* *
38496 GGGAAATGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
38528 GGGA
1 GGGA
38532 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:43501 original size:10 final size:10
Alignment explanation
Indices: 43486--43586 Score: 55
Period size: 10 Copynumber: 9.7 Consensus size: 10
43476 TTTGTGTTGG
43486 TCGTTTATGT
1 TCGTTTATGT
43496 TCGTTTATTGTGT
1 TCGTTTA---TGT
*
43509 TCATTTATGT
1 TCGTTTATGT
43519 TCGTTTATTGTGT
1 TCGTTTA---TGT
*
43532 TCATTTATGT
1 TCGTTTATGT
* *
43542 TTG-TT-CGT
1 TCGTTTATGT
*
43550 TTGTGTT-TGT
1 TCGT-TTATGT
*
43560 TCGTTTGTGT
1 TCGTTTATGT
*
43570 TCGTTTACGT
1 TCGTTTATGT
43580 TCGTTTA
1 TCGTTTA
43587 CATTTAAATG
Statistics
Matches: 72, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
8 5 0.07
9 4 0.06
10 45 0.62
13 18 0.25
ACGTcount: A:0.09, C:0.10, G:0.21, T:0.60
Consensus pattern (10 bp):
TCGTTTATGT
Found at i:43501 original size:23 final size:23
Alignment explanation
Indices: 43483--43542 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
43473 GTGTTTGTGT
*
43483 TGGTCGTTTATGTTCGTTTATTG
1 TGGTCATTTATGTTCGTTTATTG
*
43506 TGTTCATTTATGTTCGTTTATTG
1 TGGTCATTTATGTTCGTTTATTG
*
43529 TGTTCATTTATGTT
1 TGGTCATTTATGTT
43543 TGTTCGTTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.12, C:0.08, G:0.20, T:0.60
Consensus pattern (23 bp):
TGGTCATTTATGTTCGTTTATTG
Found at i:43556 original size:14 final size:14
Alignment explanation
Indices: 43516--43570 Score: 67
Period size: 14 Copynumber: 4.0 Consensus size: 14
43506 TGTTCATTTA
*
43516 TGTTCGTTTAT-TG
1 TGTTCGTTTATGTT
*
43529 TGTTCATTTATGTT
1 TGTTCGTTTATGTT
*
43543 TGTTCGTTTGTGTT
1 TGTTCGTTTATGTT
*
43557 TGTTCGTTTGTGTT
1 TGTTCGTTTATGTT
43571 CGTTTACGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
13 10 0.27
14 27 0.73
ACGTcount: A:0.05, C:0.07, G:0.24, T:0.64
Consensus pattern (14 bp):
TGTTCGTTTATGTT
Found at i:53189 original size:22 final size:22
Alignment explanation
Indices: 53161--53212 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
53151 AAGATACTTG
53161 GTCTTCTTATTTTATTCTTTAA
1 GTCTTCTTATTTTATTCTTTAA
53183 GTCTTCTTATTTTATTCTTTAA
1 GTCTTCTTATTTTATTCTTTAA
53205 GTCTTCTT
1 GTCTTCTT
53213 TTAAAGGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.15, C:0.15, G:0.06, T:0.63
Consensus pattern (22 bp):
GTCTTCTTATTTTATTCTTTAA
Found at i:70936 original size:25 final size:25
Alignment explanation
Indices: 70908--70956 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
70898 AAACACAATA
70908 ATTT-GAAAATTAACAATTTTTTTTT
1 ATTTCGAAAATTAA-AATTTTTTTTT
*
70933 ATTTCGAAAATTTAAATTTTTTTT
1 ATTTCGAAAATTAAAATTTTTTTT
70957 GGAAAATTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (25 bp):
ATTTCGAAAATTAAAATTTTTTTTT
Found at i:71362 original size:23 final size:23
Alignment explanation
Indices: 71332--71393 Score: 124
Period size: 23 Copynumber: 2.7 Consensus size: 23
71322 TTCCCCTGTG
71332 GGGGGAATCGGTTCCCATTCAAA
1 GGGGGAATCGGTTCCCATTCAAA
71355 GGGGGAATCGGTTCCCATTCAAA
1 GGGGGAATCGGTTCCCATTCAAA
71378 GGGGGAATCGGTTCCC
1 GGGGGAATCGGTTCCC
71394 TCATGGGGGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.23, C:0.23, G:0.34, T:0.21
Consensus pattern (23 bp):
GGGGGAATCGGTTCCCATTCAAA
Found at i:77366 original size:19 final size:20
Alignment explanation
Indices: 77329--77366 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
77319 TAAAAATGAT
* *
77329 TTTTGAATATTGGAGTAATG
1 TTTTGAATATTCGAATAATG
77349 TTTTG-ATATTCGAATAAT
1 TTTTGAATATTCGAATAAT
77367 TATATCGAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.32, C:0.03, G:0.18, T:0.47
Consensus pattern (20 bp):
TTTTGAATATTCGAATAATG
Done.