Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000634.1 Hibiscus syriacus cultivar Beakdansim tig00001230_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: 63093
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Found at i:3185 original size:13 final size:13
Alignment explanation
Indices: 3167--3200 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
3157 GGACAATCTT
*
3167 AGACACGACTTTG
1 AGACACAACTTTG
3180 AGACACAACTTTG
1 AGACACAACTTTG
3193 AGACACAA
1 AGACACAA
3201 TTCACAAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.18
Consensus pattern (13 bp):
AGACACAACTTTG
Found at i:3540 original size:3 final size:3
Alignment explanation
Indices: 3532--3567 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
3522 TTCGATTAAT
3532 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3568 CTCGAATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:16598 original size:31 final size:31
Alignment explanation
Indices: 16563--16623 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
16553 TAGGATATTT
16563 CTTTGTTGAGTCTCTCGACTA-TAAGAAGTTG
1 CTTTGTTGAGTCTCTCGACTATTAA-AAGTTG
16594 CTTTGTTGAGTCTCTCGACTATTAAAAGTT
1 CTTTGTTGAGTCTCTCGACTATTAAAAGTT
16624 ACAAAATGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 26 0.90
32 3 0.10
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (31 bp):
CTTTGTTGAGTCTCTCGACTATTAAAAGTTG
Found at i:21131 original size:21 final size:21
Alignment explanation
Indices: 21060--21142 Score: 69
Period size: 21 Copynumber: 3.9 Consensus size: 21
21050 CAGAACCCCA
* **
21060 GGGGGGTATCGATTCCCTTGT
1 GGGGGGAATCGATTCCCTCAT
* * *
21081 GGGGGGAATTGGTTCCCCTTCAA
1 GGGGGGAATCGATT-CCC-TCAT
* *
21104 AGGGGGAATCGGTTCCCTCAT
1 GGGGGGAATCGATTCCCTCAT
21125 GGGGGG-ATCGATTCCCTC
1 GGGGGGAATCGATTCCCTC
21143 TGCACCAAAA
Statistics
Matches: 49, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
20 11 0.22
21 19 0.39
22 6 0.12
23 13 0.27
ACGTcount: A:0.14, C:0.23, G:0.36, T:0.27
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCTCAT
Found at i:21134 original size:20 final size:20
Alignment explanation
Indices: 21105--21142 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
21095 CCCCTTCAAA
*
21105 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
21125 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
21143 TGCACCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.26, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:24970 original size:20 final size:21
Alignment explanation
Indices: 24931--24977 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
24921 GAGTTTGTTT
24931 TCATTTTTCAATTTTGAAAAA
1 TCATTTTTCAATTTTGAAAAA
24952 TCATTTTT-ATATTTT-AAAAA
1 TCATTTTTCA-ATTTTGAAAAA
*
24972 TAATTT
1 TCATTT
24978 CTCATAATCC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAAAA
Found at i:37382 original size:22 final size:20
Alignment explanation
Indices: 37331--37383 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
37321 ATTATTCTAA
*
37331 TATTTTTAAAATAATAATAT
1 TATTTTTATAATAATAATAT
37351 TAAGTTTTTATAATAAATAATAT
1 T-A-TTTTTATAAT-AATAATAT
37374 TATTATTTAT
1 TATT-TTTAT
37384 TATATTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 3 0.11
22 15 0.54
23 9 0.32
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
TATTTTTATAATAATAATAT
Found at i:43677 original size:16 final size:15
Alignment explanation
Indices: 43648--43682 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
43638 ATTTTCATTC
43648 TTTTACTCTGAAATA
1 TTTTACTCTGAAATA
*
43663 TTTTGACTCTTAAATA
1 TTTT-ACTCTGAAATA
43679 TTTT
1 TTTT
43683 CTTGTAAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.29, C:0.11, G:0.06, T:0.54
Consensus pattern (15 bp):
TTTTACTCTGAAATA
Found at i:45947 original size:183 final size:183
Alignment explanation
Indices: 45636--46463 Score: 1041
Period size: 183 Copynumber: 4.5 Consensus size: 183
45626 GATACAAATA
* * ** * * * *
45636 AAAAATGTATCGACACATAACAATATATCATATAAAAATATGA-GAAATCGGGTTCAATATGACA
1 AAAAATGTATCGATACATAACAATATAACAGGTAAAAATATGACAAAAACGGTTTCATTATGACA
* * * * *
45700 AAACCAGTAAAGCGCTACCGGATATGTTGAAAGTATTGATTCCATTGAAATAAGTATTGACACTT
66 AAACCGGTAAAGCGCTACCAGATATGTTGAAAGTATCGATTCCATTTAAATAAGTATCGACACTT
* * *
45765 TTGGAATTTAAAAGAAAAGTAGTACTAGCGCCTAAAAAGTATAGATAATTTAT
131 TTGGAATTCAAAAGAAAAGTAGTAATAGCGCCTAAAAAGTATCGATAATTTAT
* * *
45818 AAAAATATATCGATACACAACAATATAACAGGTAAAAATATGATAAAAACGGTTTCATTATGACA
1 AAAAATGTATCGATACATAACAATATAACAGGTAAAAATATGACAAAAACGGTTTCATTATGACA
*
45883 AAACCGGTAAAGTGCTACCAGATATGTTGAAAGTATCGATTCCATTTAAATAAGTATCGACACTT
66 AAACCGGTAAAGCGCTACCAGATATGTTGAAAGTATCGATTCCATTTAAATAAGTATCGACACTT
* * * * *
45948 TTGAAATTTAAAAGAAAAATAGTACTAGCGCCTAAAAAGTATCGATAAATTAT
131 TTGGAATTCAAAAGAAAAGTAGTAATAGCGCCTAAAAAGTATCGATAATTTAT
* * * *
46001 AAAAATGTATCGATATACAACAATATAACAGGTAAAAATATGATAAAAACGGTTTCATTATGAAA
1 AAAAATGTATCGATACATAACAATATAACAGGTAAAAATATGACAAAAACGGTTTCATTATGACA
* * * *
46066 AAACCAGTAAAGCGCTACCAGATATGTTGAAAGTATCTATTTCATTTAAACAAGTATCGACACTT
66 AAACCGGTAAAGCGCTACCAGATATGTTGAAAGTATCGATTCCATTTAAATAAGTATCGACACTT
** * * * * *
46131 TTATAATTCAAAAGAAAAGCAGTAATAGCGTCTATAAAGTGTCGATACTTTAT
131 TTGGAATTCAAAAGAAAAGTAGTAATAGCGCCTAAAAAGTATCGATAATTTAT
* * *** * **
46184 ATAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAATTAGTTTCACTATGATT
1 AAAAATGTATCGATACATAACAATATAACAGGTAAAAATATGACAAAAACGGTTTCATTATGACA
* * *
46249 AAACCGGTAAAGCGATATC-GAATATGTTGAAAGTATCGATTCCATTAAAATAAGTATCGACACT
66 AAACCGGTAAAGCGCTACCAG-ATATGTTGAAAGTATCGATTCCATTTAAATAAGTATCGACACT
* * * * * *
46313 TTTGGAATTCAAAAGAAAAGAAGTAATAACGCCTATAAAGTGTTGATACTTTAT
130 TTTGGAATTCAAAAGAAAAGTAGTAATAGCGCCTAAAAAGTATCGATAATTTAT
** * *
46367 AAAAAATGCGTCGA-ACCATAACAATATAACAGGTAAAAATATGACAAAACCGATTTCATTATGA
1 -AAAAATGTATCGATA-CATAACAATATAACAGGTAAAAATATGACAAAAACGGTTTCATTATGA
* *
46431 CAAAACCGGTAAAGCGCTATCGGATATGTTGAA
64 CAAAACCGGTAAAGCGCTACCAGATATGTTGAA
46464 TGTGTCGACA
Statistics
Matches: 566, Mismatches: 75, Indels: 8
0.87 0.12 0.01
Matches are distributed among these distances:
182 38 0.07
183 446 0.79
184 81 0.14
185 1 0.00
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (183 bp):
AAAAATGTATCGATACATAACAATATAACAGGTAAAAATATGACAAAAACGGTTTCATTATGACA
AAACCGGTAAAGCGCTACCAGATATGTTGAAAGTATCGATTCCATTTAAATAAGTATCGACACTT
TTGGAATTCAAAAGAAAAGTAGTAATAGCGCCTAAAAAGTATCGATAATTTAT
Found at i:47980 original size:36 final size:36
Alignment explanation
Indices: 47930--48001 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
47920 GCTACTGGGA
** *
47930 AGGGGGCTGTTGTGAGGGGACTATGAGGATGTCATT
1 AGGGGGCTACTGTGAGGGAACTATGAGGATGTCATT
47966 AGGGGGCTACTGTGAGGGAACTATGAGGATGTCATT
1 AGGGGGCTACTGTGAGGGAACTATGAGGATGTCATT
48002 TGTATGAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.22, C:0.10, G:0.42, T:0.26
Consensus pattern (36 bp):
AGGGGGCTACTGTGAGGGAACTATGAGGATGTCATT
Found at i:55241 original size:20 final size:21
Alignment explanation
Indices: 55204--55242 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
55194 CAAACTTGAG
55204 GTATCGATACATTTATAATAA
1 GTATCGATACATTTATAATAA
55225 GTATCGATACA-TTATAAT
1 GTATCGATACATTTATAAT
55243 GTAATAGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.38
Consensus pattern (21 bp):
GTATCGATACATTTATAATAA
Found at i:55848 original size:199 final size:198
Alignment explanation
Indices: 55500--56766 Score: 1736
Period size: 199 Copynumber: 6.4 Consensus size: 198
55490 TGTATCGAAA
* *
55500 ATTTTAAATTGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAATTTAC
1 ATTTAAAATTGTATCGAT-CCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTAC
* * * * * * *
55565 AATGTAACC-GATA-AGAATATATCGGTTTTATGACAGAATAGGTCAACATATTGTGTCGATACT
65 AATGTAACCAG-TAGA-AATATACCGGTTTTATGAGAAAATAGGTCAACATAATGTATCAACACT
* * * * *
55628 TTTTAAAATTATGTTGATACTTTTGGTCCATAATGAATGCCCAACGAGATGCACACATAAAGTGT
128 TTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGATGCACGCATAAAGTGT
55693 CGATAC
193 CGATAC
* * *
55699 ATTTAAAATTGTATCAATCCTGAAAACATCGAAACCGATAATTACAATGTAATAGGTAAATTTAC
1 ATTTAAAATTGTATCGATCC-AAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTAC
* * * *
55764 AATGTAACCAGTAGAAATATACCGGTTTAATTAGAAAATAGGTTAACATAATGTACCAACACTTT
65 AATGTAACCAGTAGAAATATACCGGTTTTATGAGAAAATAGGTCAACATAATGTATCAACACTTT
* * * **
55829 TTAAATTTGTGTCGATACTTTTTGTCCCGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTTA
130 TTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGATGCACGCATAAAGTGTCG
55894 ATAC
195 ATAC
*
55898 ATTTAAAATTGTATCGATCCTAAAAACATCGAAACCTATAATTATAATGTAATAGGTAAATTTAC
1 ATTTAAAATTGTATCGATCC-AAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTAC
* ** * * * * **
55963 AATGTAACCGGTAGAAATATA--TTTTCTTAATTAGAAAATTGGTCCATATAATGTAGAAACACT
65 AATGTAACCAGTAGAAATATACCGGTT-TT-ATGAGAAAATAGGTCAACATAATGTATCAACACT
*
56026 TTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGATGTACGCATAAAGTGT
128 TTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGATGCACGCATAAAGTGT
56091 CGATAC
193 CGATAC
**
56097 ATTTAAAATTGTATCGATCCCAAAAACATCGACCCCGATAATTATAATGTAATAGGTAAATTTAC
1 ATTTAAAATTGTATCGAT-CCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTAC
* *
56162 AATGTAACCAGTATAAATATACCGATTTTATGAGAAAATAGGTCAACATAATGTATCGAA-ACTT
65 AATGTAACCAGTAGAAATATACCGGTTTTATGAGAAAATAGGTCAACATAATGTATC-AACACTT
* * *
56226 TTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGATGCATGCATAAAGTATT
129 TTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGATGCACGCATAAAGTGTC
56291 GATAC
194 GATAC
* *
56296 ATTTAAAATTGTATCGATACCAAAAACATC-AAACTCGGTAATTATAATGTAATAAGTAAATTTA
1 ATTTAAAATTGTATCGAT-CCAAAAACATCGAAAC-CGATAATTATAATGTAATAGGTAAATTTA
* * * * **
56360 CAATATAACCAATAGAAATATACCGGTTTTATGAGAAAATATGTCAACATAATGAATTGACACTT
64 CAATGTAACCAGTAGAAATATACCGGTTTTATGAGAAAATAGGTCAACATAATGTATCAACAC-T
* **
56425 TTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACATATAAAGTGT
128 TTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGATGCACGCATAAAGTGT
56490 CGATAC
193 CGATAC
* * * *
56496 ATTTAAAATTGTATCGATCCCAAAAGCATTGAACCCGATAATTATAATGTAATAGGTAAATTAAC
1 ATTTAAAATTGTATCGAT-CCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTAC
* * ** *
56561 AATGTAACCGGTAGAAATATATCGGTTTTATGAGAAAATAGGTCAACATAATGTATTGATACTTT
65 AATGTAACCAGTAGAAATATACCGGTTTTATGAGAAAATAGGTCAACATAATGTATCAACACTTT
* * * *
56626 TTAAATTTGTGTCGATACTTTTGGTCTAGAATGAATGTCCAACGAGGTGCACGCATAAAGTGTGG
130 TTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGATGCACGCATAAAGTGTCG
56691 ATAC
195 ATAC
* *
56695 ATTTAAAATTGTATCGATCCAAAAAAAATCGAAACCAATAATTATAATGTAATAGGTAAATTTAC
1 ATTTAAAATTGTATCGATCC-AAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTAC
56760 AATGTAA
65 AATGTAA
56767 TAGGTAAATT
Statistics
Matches: 947, Mismatches: 107, Indels: 28
0.88 0.10 0.03
Matches are distributed among these distances:
197 2 0.00
198 8 0.01
199 749 0.79
200 183 0.19
201 5 0.01
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (198 bp):
ATTTAAAATTGTATCGATCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACA
ATGTAACCAGTAGAAATATACCGGTTTTATGAGAAAATAGGTCAACATAATGTATCAACACTTTT
TAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGATGCACGCATAAAGTGTCGA
TAC
Found at i:56765 original size:20 final size:20
Alignment explanation
Indices: 56740--56786 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
56730 CAATAATTAT
56740 AATGTAATAGGTAAATTTAC
1 AATGTAATAGGTAAATTTAC
56760 AATGTAATAGGTAAATTTAC
1 AATGTAATAGGTAAATTTAC
56780 AATGTAA
1 AATGTAA
56787 CCGGTAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.47, C:0.04, G:0.15, T:0.34
Consensus pattern (20 bp):
AATGTAATAGGTAAATTTAC
Found at i:56792 original size:20 final size:20
Alignment explanation
Indices: 56740--56794 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
56730 CAATAATTAT
*
56740 AATGTAATAGGTAAATTTAC
1 AATGTAACAGGTAAATTTAC
*
56760 AATGTAATAGGTAAATTTAC
1 AATGTAACAGGTAAATTTAC
*
56780 AATGTAACCGGTAAA
1 AATGTAACAGGTAAA
56795 AATATACCGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.45, C:0.07, G:0.16, T:0.31
Consensus pattern (20 bp):
AATGTAACAGGTAAATTTAC
Found at i:56871 original size:21 final size:20
Alignment explanation
Indices: 56828--56871 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
56818 ATGTAAACAT
*
56828 ATTGTATCGACACTTTTTAA
1 ATTGTATCGACAATTTTTAA
* *
56848 ATTGTATCGATATATTTTTTA
1 ATTGTATCGACA-ATTTTTAA
56869 ATT
1 ATT
56872 ACGCGTGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (20 bp):
ATTGTATCGACAATTTTTAA
Found at i:57196 original size:18 final size:16
Alignment explanation
Indices: 57152--57210 Score: 66
Period size: 18 Copynumber: 3.5 Consensus size: 16
57142 AACCCTAAAT
57152 CTTCTTCTCAACCAAC
1 CTTCTTCTCAACCAAC
57168 C-TCTTCTCAACGACAAC
1 CTTCTTCTCAAC--CAAC
*
57185 CTTCTCCTCAACCAAGC
1 CTTCTTCTCAACCAA-C
57202 GCTTCTTCT
1 -CTTCTTCT
57211 GAACAAATCA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
15 10 0.28
16 4 0.11
17 6 0.17
18 16 0.44
ACGTcount: A:0.22, C:0.42, G:0.05, T:0.31
Consensus pattern (16 bp):
CTTCTTCTCAACCAAC
Found at i:59749 original size:30 final size:30
Alignment explanation
Indices: 59715--59772 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
59705 TTTCATGTTC
59715 ATTTCATATTT-AATTGGAGTTTGAATTTAA
1 ATTTCA-ATTTGAATTGGAGTTTGAATTTAA
* *
59745 ATTTCAATTTGAGTTTGAGTTTGAATTT
1 ATTTCAATTTGAATTGGAGTTTGAATTT
59773 CAATATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.29, C:0.03, G:0.16, T:0.52
Consensus pattern (30 bp):
ATTTCAATTTGAATTGGAGTTTGAATTTAA
Found at i:59753 original size:24 final size:24
Alignment explanation
Indices: 59722--59776 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
59712 TTCATTTCAT
59722 ATTT-AATTGGAGTTTGAATTTAA
1 ATTTCAATTGGAGTTTGAATTTAA
* * *
59745 ATTTCAATTTGAGTTTGAGTTTGA
1 ATTTCAATTGGAGTTTGAATTTAA
59769 ATTTCAAT
1 ATTTCAAT
59777 ATAAATTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 4 0.14
24 24 0.86
ACGTcount: A:0.31, C:0.04, G:0.16, T:0.49
Consensus pattern (24 bp):
ATTTCAATTGGAGTTTGAATTTAA
Found at i:61721 original size:199 final size:199
Alignment explanation
Indices: 61208--62376 Score: 1656
Period size: 200 Copynumber: 5.9 Consensus size: 199
61198 TTTATTGTAA
** * * *
61208 GTATCGATCCCAAAATTATCGAAACCGATAATTATAAAGTAATAGGTAAATTTACAAAGTAACCG
1 GTATCGATCCCAAAAACATCGAACCCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
* * * * *
61273 GTAAAAATATACCCGTTTTATGACAAAATAGGTCAACATAATGTATCGATACTTTTTAAATTTGT
66 GTAGAAATATACCAGTTTAATTAGAAAATAGGTCAACATAATGTATCGATACTTTTTAAATTTGT
* * * * *
61338 ATCGATACTTTTGGTCTAGAATGAATGTCCAACGAGGTGCACACATAAAGTGTCGATACATTTAT
131 GTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTAA
** *
61403 TGTAA
196 AAT-T
* * * *
61408 GTATTGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATTTAACCA
1 GTATCGATCCCAAAAACATCGAACCCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
* * *
61473 GTAGAAATATACCAATTTAATTAGAAAATAGGTCAACATAATATATCGATAATTTTTAAATTTGT
66 GTAGAAATATACCAGTTTAATTAGAAAATAGGTCAACATAATGTATCGATACTTTTTAAATTTGT
*
61538 GTCGATACTTTTGGTCCAGAATGAATGCCCAATGAGGTGCACGCATAAAGTGTCGATACATTTAA
131 GTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTAA
*
61603 ATTT
196 AATT
* *
61607 TTATCGATCCCAAAAACATCGAACCCGATAATTATAATGTAATAGGTAAATTTATAATGTAACCG
1 GTATCGATCCCAAAAACATCGAACCCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
* *
61672 GTAGAAATATACCAGTTTAATTAGAAAATAGGTCAACATAATGTATCGATACTTTTTTAGATTTA
66 GTAGAAATATACCAGTTTAATTAGAAAATAGGTCAACATAATGTATCGATAC-TTTTTAAATTTG
* *
61737 TGTCGATACCTTTGGTCCAGAATGAATGCCTAACGAGGTGCACGCATAAAGTGTCGATACATTTA
130 TGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTA
61802 AAATT
195 AAATT
* **
61807 GTATCAATCCCAAAAACATCGAACCCGATAATTATAATGTAATAGGTAAATTTACAATGTAATTG
1 GTATCGATCCCAAAAACATCGAACCCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
61872 GTAGAAATATACCAGTTTAATTAGAAAATAGGTCAACATAATGTATCGATACTTTTTTAAAATTT
66 GTAGAAATATACCAGTTTAATTAGAAAATAGGTCAACATAATGTATCGATAC-TTTTT-AAATTT
*
61937 GTGTCGATACTTTTGGTCCAGAATGAATGCCTAACGAGGTGCACGCATAAAGTGTCGATACATTT
129 GTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTT
62002 AAAATT
194 AAAATT
* * *
62008 GTATCAATCCCAAAAACATTGAACCCGATAATTATAATGTAATAGGTAAATTTACAATGTAACTG
1 GTATCGATCCCAAAAACATCGAACCCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
* *
62073 GAAGAAATATACCAGTTTAATTAGAAAATAGGTCAACATAATGTATCGACACTTTTTAAATTTGT
66 GTAGAAATATACCAGTTTAATTAGAAAATAGGTCAACATAATGTATCGATACTTTTTAAATTTGT
* *
62138 TTCGATACTTTTTGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTAA
131 GTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTAA
62203 AATT
196 AATT
*
62207 GTATCGATCCCAAAAACATCTAACCCGATAATTA-AATGTAATAGG------TA-AATGT-A---
1 GTATCGATCCCAAAAACATCGAACCCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
** * * * * * *
62260 --A-AAA-ATACTGGTTTTATGAGAGAATAGGTAAACATATTGTATCGACACTTTTTAAA-TTGT
66 GTAGAAATATACCAGTTTAATTAGAAAATAGGTCAACATAATGTATCGATACTTTTTAAATTTGT
* * * *
62320 ATCGATACTTTTTGTCCAG-ATGAATGCCC-ACAAGGTGCACGCATAAAGTGGCGATAC
131 GTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATAC
62377 CTTATTGTAA
Statistics
Matches: 900, Mismatches: 67, Indels: 24
0.91 0.07 0.02
Matches are distributed among these distances:
180 26 0.03
181 10 0.01
182 22 0.02
183 45 0.05
184 3 0.00
185 1 0.00
190 1 0.00
191 5 0.01
192 2 0.00
198 11 0.01
199 213 0.24
200 374 0.42
201 187 0.21
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (199 bp):
GTATCGATCCCAAAAACATCGAACCCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCG
GTAGAAATATACCAGTTTAATTAGAAAATAGGTCAACATAATGTATCGATACTTTTTAAATTTGT
GTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTAA
AATT
Found at i:62320 original size:20 final size:20
Alignment explanation
Indices: 62295--62332 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
62285 AGGTAAACAT
62295 ATTGTATCGACACTTTTTAA
1 ATTGTATCGACACTTTTTAA
*
62315 ATTGTATCGATACTTTTT
1 ATTGTATCGACACTTTTT
62333 GTCCAGATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.13, G:0.11, T:0.50
Consensus pattern (20 bp):
ATTGTATCGACACTTTTTAA
Done.