Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000359.1 Hibiscus syriacus cultivar Beakdansim tig00000655_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: 52991
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:5614 original size:18 final size:18
Alignment explanation
Indices: 5591--5634 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
5581 AAATTATTGA
5591 TGTTTTGGATACATTTAG
1 TGTTTTGGATACATTTAG
5609 TGTTTTGGATACATTTAG
1 TGTTTTGGATACATTTAG
*
5627 TGTCTTGG
1 TGTTTTGG
5635 TAGAGCTTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.18, C:0.07, G:0.25, T:0.50
Consensus pattern (18 bp):
TGTTTTGGATACATTTAG
Found at i:14056 original size:69 final size:66
Alignment explanation
Indices: 13917--14046 Score: 206
Period size: 69 Copynumber: 1.9 Consensus size: 66
13907 CTCTAGGTCC
* * *
13917 TCTTTCTCTTCACTTCCATTTCCAGCTTCTTCTTCTTGCTCCTCTTGTTCATCTTGTTGTTCTTT
1 TCTTTCTCATCACTTCCATTTCCAGCTTCTTCTTCTTGCTCCTCTTGTTCATCTTCTTGTTCTGT
13982 A
66 A
13983 TCTTTCTCATCACTTCCATTTCCAGCTTCTTCTTCTTCTTGCTCCTCTTGTTCATCTTCTTGTT
1 TCTTTCTCATCACTTCCATTTCCAG---CTTCTTCTTCTTGCTCCTCTTGTTCATCTTCTTGTT
14047 GGTGTTCTTT
Statistics
Matches: 59, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
66 24 0.41
69 35 0.59
ACGTcount: A:0.08, C:0.32, G:0.07, T:0.54
Consensus pattern (66 bp):
TCTTTCTCATCACTTCCATTTCCAGCTTCTTCTTCTTGCTCCTCTTGTTCATCTTCTTGTTCTGT
A
Found at i:15810 original size:60 final size:60
Alignment explanation
Indices: 15684--15818 Score: 186
Period size: 60 Copynumber: 2.2 Consensus size: 60
15674 AGGATGATAT
* * *
15684 TCATAGTTTGGGGATGAAATTGGAATATTTAAAAGTTTAAGGACTAATTTAGAATGAGAG
1 TCATAGTTTGGGGATGAAATTGAAATACTTAAAAGTTTAAGGACTAATTTAGAATCAGAG
*
15744 -CTATAGTTTTGGGATGAAATTGAAATACTTAAAAGTTTAAGGACTAATTT-GAAATCA-ATG
1 TC-ATAGTTTGGGGATGAAATTGAAATACTTAAAAGTTTAAGGACTAATTTAG-AATCAGA-G
15804 TCATAGTTTGGGGAT
1 TCATAGTTTGGGGAT
15819 ATATAATGTA
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
59 3 0.05
60 62 0.94
61 1 0.02
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.35
Consensus pattern (60 bp):
TCATAGTTTGGGGATGAAATTGAAATACTTAAAAGTTTAAGGACTAATTTAGAATCAGAG
Found at i:16944 original size:30 final size:30
Alignment explanation
Indices: 16872--16982 Score: 147
Period size: 30 Copynumber: 3.8 Consensus size: 30
16862 AATTGAATAC
* * *
16872 TTTAGGTACCTATTTTGAC-CAAA-AT-AC
1 TTTAGGTACTTATTTTGACAAAAATATAAA
*
16899 TTTAGGTACCTATTTTGACAAAAATATAAA
1 TTTAGGTACTTATTTTGACAAAAATATAAA
* *
16929 TTTATGTATTTATTTTGACAAAAATATAAA
1 TTTAGGTACTTATTTTGACAAAAATATAAA
16959 TTTAGGTACTTATTTTGACAAAAA
1 TTTAGGTACTTATTTTGACAAAAA
16983 ATAGATACTT
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
27 19 0.26
28 3 0.04
29 2 0.03
30 50 0.68
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.41
Consensus pattern (30 bp):
TTTAGGTACTTATTTTGACAAAAATATAAA
Found at i:22481 original size:29 final size:29
Alignment explanation
Indices: 22449--22508 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
22439 TGGTAATAAT
* * *
22449 AAATTAAAGGGCTAAAACAGAAAAATAGA
1 AAATTAAAAGACTAAAACAGAAAAACAGA
* *
22478 AAATTAAAAGACTAAAATAGCAAAACAGA
1 AAATTAAAAGACTAAAACAGAAAAACAGA
22507 AA
1 AA
22509 CGTAGGGACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.65, C:0.08, G:0.13, T:0.13
Consensus pattern (29 bp):
AAATTAAAAGACTAAAACAGAAAAACAGA
Found at i:24706 original size:25 final size:25
Alignment explanation
Indices: 24675--24774 Score: 200
Period size: 25 Copynumber: 4.0 Consensus size: 25
24665 ATTTAGGGGA
24675 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
24700 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
24725 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
24750 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
24775 GGGTTGATTG
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 75 1.00
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:29421 original size:25 final size:25
Alignment explanation
Indices: 29390--29489 Score: 200
Period size: 25 Copynumber: 4.0 Consensus size: 25
29380 ATTTAGGGGA
29390 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
29415 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
29440 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
29465 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
29490 GGGTTGATTG
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 75 1.00
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:29565 original size:3 final size:3
Alignment explanation
Indices: 29557--29596 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
29547 ATTAATAAAC
29557 ATA ATA ATA ATAA ATA ATA ATA ATA ATA ATA ATA A-A ATA A
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
29597 CGATAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:29582 original size:22 final size:22
Alignment explanation
Indices: 29549--29592 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
29539 AATATGTAAT
29549 TAATAAACATAATAATAATAAA
1 TAATAAACATAATAATAATAAA
29571 TAATAATA-ATAATAATAATAAA
1 TAATAA-ACATAATAATAATAAA
29593 ATAACGATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (22 bp):
TAATAAACATAATAATAATAAA
Found at i:29852 original size:40 final size:40
Alignment explanation
Indices: 29808--30036 Score: 185
Period size: 40 Copynumber: 5.5 Consensus size: 40
29798 ACATGGTTCC
*
29808 TACGTGATGAGGACATCTGGTCGGGGAATGACACGGCTCA
1 TACGTGATGAGGAGATCTGGTCGGGGAATGACACGGCTCA
* * * * * *
29848 TACGTGATGAAGAGTTCTGGCCATCTAAAGGTG-ATAACACGGTTCC
1 TACGTGATGAGGAGATCTGG---TC----GGGGAATGACACGGCTCA
* ** * * *
29894 TACGTGATGAGGACG-GCTGGTTATCTATGG-TTGACATGGCTCC
1 TACGTGATGAGGA-GATCTGG---TC-GGGGAATGACACGGCTCA
29937 TACGTGATGAGGAGATCTGGTCGGGGAATGACACGGCTCA
1 TACGTGATGAGGAGATCTGGTCGGGGAATGACACGGCTCA
*
29977 TACGTGATGAAGAGATCTGGTCGGGGAATGACACGGCTCA
1 TACGTGATGAGGAGATCTGGTCGGGGAATGACACGGCTCA
* *
30017 TACGTGATGAAGAGTTCTGG
1 TACGTGATGAGGAGATCTGG
30037 CCATCTAAAG
Statistics
Matches: 152, Mismatches: 27, Indels: 20
0.76 0.14 0.10
Matches are distributed among these distances:
39 2 0.01
40 87 0.57
42 1 0.01
43 29 0.19
46 29 0.19
47 4 0.03
ACGTcount: A:0.25, C:0.18, G:0.33, T:0.24
Consensus pattern (40 bp):
TACGTGATGAGGAGATCTGGTCGGGGAATGACACGGCTCA
Found at i:29898 original size:46 final size:42
Alignment explanation
Indices: 29754--30069 Score: 149
Period size: 40 Copynumber: 7.4 Consensus size: 42
29744 TGTTGGGGAC
* *
29754 GACACTGCTCATACGTGATGAAGAGTTCTTGTCG-TCTAAGG-G-T
1 GACACGGCTCATACGTGATGAAGAGATC-TG--GATCT-AGGTGAT
* * * * * *
29797 GACATGGTTCCTACGTGATGAGGACATCTGG-TC--GGGGAAT
1 GACACGGCTCATACGTGATGAAGAGATCTGGATCTAGGTG-AT
*
29837 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGAT
1 GACACGGCTCATACGTGATGAAGAGATCTGG--ATCT--AGGTGAT
* * * * *
29883 AACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGT--T
1 GACACGGCTCATACGTGATGAAGA-GATCTGG--ATCTA-GGTGAT
* * * *
29926 GACATGGCTCCTACGTGATGAGGAGATCTGG-TC--GGGGAAT
1 GACACGGCTCATACGTGATGAAGAGATCTGGATCTAGGTG-AT
*
29966 GACACGGCTCATACGTGATGAAGAGATCTGG-TC--GGGGAAT
1 GACACGGCTCATACGTGATGAAGAGATCTGGATCTAGGTG-AT
*
30006 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGAT
1 GACACGGCTCATACGTGATGAAGAGATCTGG--ATCT--AGGTGAT
* * *
30052 AACACGGTTCCTACGTGA
1 GACACGGCTCATACGTGA
30070 CGAGGACGGC
Statistics
Matches: 216, Mismatches: 34, Indels: 43
0.74 0.12 0.15
Matches are distributed among these distances:
37 4 0.02
38 1 0.00
40 99 0.46
42 3 0.01
43 51 0.24
44 1 0.00
45 3 0.01
46 47 0.22
47 7 0.03
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (42 bp):
GACACGGCTCATACGTGATGAAGAGATCTGGATCTAGGTGAT
Found at i:30642 original size:14 final size:14
Alignment explanation
Indices: 30619--30661 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
30609 AAGATGATCT
*
30619 TGTTTTAAGAGAAA
1 TGTTTCAAGAGAAA
30633 TGTTTCAAGAGAAAA
1 TGTTTCAAGAG-AAA
*
30648 TGTTTCAAGTGAAA
1 TGTTTCAAGAGAAA
30662 CGACTCAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 13 0.50
15 13 0.50
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.33
Consensus pattern (14 bp):
TGTTTCAAGAGAAA
Found at i:30650 original size:15 final size:15
Alignment explanation
Indices: 30619--30661 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
30609 AAGATGATCT
*
30619 TGTTTTAAGAG-AAA
1 TGTTTCAAGAGAAAA
30633 TGTTTCAAGAGAAAA
1 TGTTTCAAGAGAAAA
*
30648 TGTTTCAAGTGAAA
1 TGTTTCAAGAGAAA
30662 CGACTCAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.33
Consensus pattern (15 bp):
TGTTTCAAGAGAAAA
Found at i:31203 original size:66 final size:67
Alignment explanation
Indices: 31115--31312 Score: 229
Period size: 67 Copynumber: 3.0 Consensus size: 67
31105 AAAGATTTAC
* ** * * * * *
31115 TTCAAGAGAAACGGTCTCAAGAGATACAAAATTCAATTT-AAGAGAAACAGATTCAAAGATTTTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAAAATTCAATTTCAAAAGAAACAAACTCAAAGATTTTT
31179 GT
66 GT
* ***
31181 TTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAAAATTCAATTTCAAAAGAAACAAACTCAAAGATTTTT
31246 GT
66 GT
*** *
31248 TTCAAAAGAAACTATCTTAAGAGAGA-AAGAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAA-AATTCAATTTCAAAAGAAACAAACTCAAAGATTTT
31312 T
65 T
31313 TTCGCAAAAT
Statistics
Matches: 116, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
66 32 0.28
67 84 0.72
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (67 bp):
TTCAAAAGAAACTATCTTAAGAGAGACAAAATTCAATTTCAAAAGAAACAAACTCAAAGATTTTT
GT
Found at i:31216 original size:37 final size:36
Alignment explanation
Indices: 31175--31296 Score: 130
Period size: 37 Copynumber: 3.5 Consensus size: 36
31165 ATTCAAAGAT
*
31175 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
1 TTTTGTTTCAAAAGAAACTATCTTAAGAGAGA-AAAA
* * * *
31212 TTTTGTTTCAAAAGAAACAAAC-TCA-A-AG---AT
1 TTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAA
31242 TTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAGAA
1 TTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAA-AA
*
31279 TTTTGTTTCCAAAGAAAC
1 TTTTGTTTCAAAAGAAAC
31297 AAACTCAAAG
Statistics
Matches: 68, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
30 21 0.31
31 2 0.03
32 1 0.01
33 2 0.03
34 2 0.03
35 1 0.01
36 2 0.03
37 37 0.54
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (36 bp):
TTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAA
Found at i:31321 original size:67 final size:67
Alignment explanation
Indices: 31157--31312 Score: 260
Period size: 67 Copynumber: 2.3 Consensus size: 67
31147 TCAATTTAAG
* * *
31157 AGAAACAGATTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCA
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCA
31222 AA
66 AA
31224 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGA-AAGAATTTTGTTTC
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGACAA-AATTTTGTTTC
*
31288 CAA
65 AAA
31291 AGAAACAAACTCAAAGATTTTT
1 AGAAACAAACTCAAAGATTTTT
31313 TTCGCAAAAT
Statistics
Matches: 84, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
66 2 0.02
67 82 0.98
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.31
Consensus pattern (67 bp):
AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCA
AA
Found at i:31379 original size:52 final size:53
Alignment explanation
Indices: 31299--31403 Score: 167
Period size: 52 Copynumber: 2.0 Consensus size: 53
31289 AAAGAAACAA
* *
31299 ACTCAAAGATTTTTTTCGCAAAATTGTCTCAAGAGATACAAAACTTTGTTTCAG
1 ACTCAAAGA-TTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAG
*
31353 ACTCAAAGA-TTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
1 ACTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
31404 AAATAAATAG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
52 39 0.81
54 9 0.19
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.33
Consensus pattern (53 bp):
ACTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAG
Found at i:31543 original size:141 final size:140
Alignment explanation
Indices: 31284--31598 Score: 549
Period size: 141 Copynumber: 2.2 Consensus size: 140
31274 AAGAATTTTG
* * *
31284 TTTCCAAAGAAACAAACTCAAAGATTTTTTTCGCAAAATTGTCTCAAGAGATACAAAACTTTGTT
1 TTTCAAAAGAAAC-AACTCAAAGATTTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTT
31349 TCAGACTCAAAGATTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAG
65 TCAGACTCAAAGATTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAG
*
31414 ACTCAAAGTTT
130 ACTCAAAGATT
31425 TTTCAAAAGAAACAATCTCAAAGATTTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTT
1 TTTCAAAAGAAACAA-CTCAAAGATTTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTT
*
31490 TCAGACTCAAAGCTTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAG
65 TCAGACTCAAAGATTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAG
31555 ACTCAAAGATT
130 ACTCAAAGATT
*
31566 TTTCAAAAGAAACAACTCAAAGATATTTATTCA
1 TTTCAAAAGAAACAACTCAAAGAT-TTTTTTCA
31599 AAAGGAACAA
Statistics
Matches: 166, Mismatches: 6, Indels: 4
0.94 0.03 0.02
Matches are distributed among these distances:
140 11 0.07
141 155 0.93
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (140 bp):
TTTCAAAAGAAACAACTCAAAGATTTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTT
CAGACTCAAAGATTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAGA
CTCAAAGATT
Found at i:31569 original size:26 final size:25
Alignment explanation
Indices: 31540--31663 Score: 88
Period size: 29 Copynumber: 4.5 Consensus size: 25
31530 CAAAACTTTG
* *
31540 TTTCAAAATAAATAGACTCAAAGATT
1 TTTCAAAAGAAACA-ACTCAAAGATT
31566 TTTCAAAAGAAACAACTCAAAGATATT
1 TTTCAAAAGAAACAACTCAAAG--ATT
* *
31593 TATTCAAAAGGAACAAACTCCAAGATTTT
1 T-TTCAAAAGAAAC-AACTCAAAGA--TT
31622 TATTCAAAATG-AACAAACTCAAAGATATT
1 T-TTCAAAA-GAAAC-AACTCAAAG--ATT
*
31651 TTTCAAGAGAAAC
1 TTTCAAAAGAAAC
31664 TGTCTCAAGA
Statistics
Matches: 82, Mismatches: 6, Indels: 18
0.77 0.06 0.17
Matches are distributed among these distances:
25 8 0.10
26 12 0.15
27 6 0.07
28 20 0.24
29 34 0.41
30 1 0.01
31 1 0.01
ACGTcount: A:0.49, C:0.15, G:0.09, T:0.27
Consensus pattern (25 bp):
TTTCAAAAGAAACAACTCAAAGATT
Found at i:31623 original size:29 final size:29
Alignment explanation
Indices: 31555--31656 Score: 133
Period size: 29 Copynumber: 3.7 Consensus size: 29
31545 AAATAAATAG
*
31555 ACTCAAAG--ATTT-TTCAAAAGAAAC-A
1 ACTCAAAGATATTTATTCAAAAGGAACAA
31580 ACTCAAAGATATTTATTCAAAAGGAACAA
1 ACTCAAAGATATTTATTCAAAAGGAACAA
* * *
31609 ACTCCAAGATTTTTATTCAAAATGAACAA
1 ACTCAAAGATATTTATTCAAAAGGAACAA
31638 ACTCAAAGATATTT-TTCAA
1 ACTCAAAGATATTTATTCAA
31657 GAGAAACTGT
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
25 8 0.12
27 4 0.06
28 16 0.24
29 39 0.58
ACGTcount: A:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (29 bp):
ACTCAAAGATATTTATTCAAAAGGAACAA
Found at i:31979 original size:36 final size:35
Alignment explanation
Indices: 31895--31998 Score: 129
Period size: 36 Copynumber: 3.0 Consensus size: 35
31885 GAGAAAATGA
* * *
31895 TGTCTCAAGCGAGACGAAATTTGCTTTT-AGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTGAGAAAT
* **
31929 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTT-GAGAAAT
*
31965 TGTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTGAGAAA
31999 CGATCTCAAG
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
34 23 0.40
35 6 0.10
36 29 0.50
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.34
Consensus pattern (35 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTGAGAAAT
Found at i:32006 original size:35 final size:32
Alignment explanation
Indices: 31896--32025 Score: 109
Period size: 35 Copynumber: 3.8 Consensus size: 32
31886 AGAAAATGAT
*
31896 GTCTCAAGCGAGACGAAATTTGCTTTT-AGATATA
1 GTCTCAAGCGAGAC-AAATTTGTTTTTGAGA-A-A
**
31930 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAA
1 GTCTCAAGCGAGAC-AAATTTGTTTTT-GAGAAA
31964 TTGTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAA
1 --GTCTCAAGCGAGACAAA-TTTGTTTTTGAGAAA
* *
31999 CGATCTCAAGTGAGATCAACTTTGTTT
1 -G-TCTCAAGCGAGA-CAAATTTGTTT
32026 AATGTGAAAC
Statistics
Matches: 80, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
34 25 0.31
35 28 0.35
36 27 0.34
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (32 bp):
GTCTCAAGCGAGACAAATTTGTTTTTGAGAAA
Found at i:32152 original size:105 final size:100
Alignment explanation
Indices: 31966--32197 Score: 261
Period size: 105 Copynumber: 2.3 Consensus size: 100
31956 TAGAGAAATT
* *
31966 GTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAACGATCTCAAGTGAGATCAACTTTGTTTAATGT
1 GTCTCAAGCGAGACAAAATTTG-TTTTGAGAAACAATCTCAAGTGAGATCAACTTTGTTTAATGT
* *
32031 GAAACAAATCCGAAATTTGGATCTCAAAGGGAAAAG
65 GAAACAAATCCAAAATTTGGATCTCAAAGGAAAAAG
* *
32067 GTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAACAA-CAATCTAAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGACAAAATTTGTTTTG--AGAAACAATC--TC-AA-GTGAGATCAACTTTGTTT
* * * * *
32131 -TTAGTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
60 AAT-GTGAAACAAATCCAAAATTTGGATCTCAAAGGAAAAAG
* *
32172 GTCTCAAGCGAAACACAATTTGTTTT
1 GTCTCAAGCGAGACAAAATTTGTTTT
32198 AAAATTCTCA
Statistics
Matches: 111, Mismatches: 13, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
100 5 0.05
101 22 0.20
102 7 0.06
103 2 0.02
104 3 0.03
105 72 0.65
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.31
Consensus pattern (100 bp):
GTCTCAAGCGAGACAAAATTTGTTTTGAGAAACAATCTCAAGTGAGATCAACTTTGTTTAATGTG
AAACAAATCCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:32670 original size:4 final size:4
Alignment explanation
Indices: 32661--32700 Score: 66
Period size: 4 Copynumber: 10.5 Consensus size: 4
32651 TGTATCATGG
32661 ATGT ATGT ATGT ATGT ATGT ATGT ATG- -TGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
32701 ATACTTTTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
4 32 0.94
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:33893 original size:21 final size:22
Alignment explanation
Indices: 33849--33899 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
33839 TTTGTATGTG
33849 CTCTTTGTCCACTTTCTCTTCTTT
1 CTCTTT-T-CACTTTCTCTTCTTT
* *
33873 TTCTTTTCACTTTGT-TTCTTT
1 CTCTTTTCACTTTCTCTTCTTT
33894 CTCTTT
1 CTCTTT
33900 GCTTTTCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 11 0.46
22 7 0.29
23 1 0.04
24 5 0.21
ACGTcount: A:0.04, C:0.27, G:0.04, T:0.65
Consensus pattern (22 bp):
CTCTTTTCACTTTCTCTTCTTT
Found at i:34629 original size:46 final size:45
Alignment explanation
Indices: 34537--34630 Score: 134
Period size: 46 Copynumber: 2.1 Consensus size: 45
34527 ATAAATACAG
* * *
34537 TGTTTCAAGGTGGAAAGAATGTTTCAAGGTCTCAAAGAGAGGGAA
1 TGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
* *
34582 TGTTTCAAGGTTGAAAAGAATATTTCAAGGTCTTAAAGAGATAGAA
1 TGTTTCAAGG-TGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
34628 TGT
1 TGT
34631 CAAAAATTGG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 10 0.23
46 33 0.77
ACGTcount: A:0.37, C:0.07, G:0.27, T:0.29
Consensus pattern (45 bp):
TGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
Found at i:36898 original size:31 final size:31
Alignment explanation
Indices: 36842--36934 Score: 177
Period size: 31 Copynumber: 3.0 Consensus size: 31
36832 TGACAAAATG
36842 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAA-AAATAAGTTAGTAT
36874 ACACAAACAAAAGAGAAAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAAAATAAGTTAGTAT
36905 ACACAAACAAAAGAGAAAAATAAGTTAGTA
1 ACACAAACAAAAGAGAAAAATAAGTTAGTA
36935 CATGTAAAAT
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
31 44 0.72
32 17 0.28
ACGTcount: A:0.61, C:0.10, G:0.14, T:0.15
Consensus pattern (31 bp):
ACACAAACAAAAGAGAAAAATAAGTTAGTAT
Found at i:38861 original size:29 final size:29
Alignment explanation
Indices: 38829--38888 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
38819 TGGTAATAAT
* * *
38829 AAATTAAAGGGCTAAAACAGAAAAATAGA
1 AAATTAAAAGACTAAAACAGAAAAACAGA
* *
38858 AAATTAAAAGACTAAAATAGCAAAACAGA
1 AAATTAAAAGACTAAAACAGAAAAACAGA
38887 AA
1 AA
38889 CGTAGGGACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.65, C:0.08, G:0.13, T:0.13
Consensus pattern (29 bp):
AAATTAAAAGACTAAAACAGAAAAACAGA
Found at i:41078 original size:25 final size:25
Alignment explanation
Indices: 41047--41146 Score: 200
Period size: 25 Copynumber: 4.0 Consensus size: 25
41037 ATTTAGGGGA
41047 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
41072 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
41097 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
41122 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
41147 GGGTTGATTG
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 75 1.00
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:41222 original size:3 final size:3
Alignment explanation
Indices: 41214--41253 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
41204 ATTAATAAAC
41214 ATA ATA ATA ATAA ATA ATA ATA ATA ATA ATA ATA A-A ATA A
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
41254 CGATAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:41239 original size:22 final size:22
Alignment explanation
Indices: 41206--41249 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
41196 AATATGTAAT
41206 TAATAAACATAATAATAATAAA
1 TAATAAACATAATAATAATAAA
41228 TAATAATA-ATAATAATAATAAA
1 TAATAA-ACATAATAATAATAAA
41250 ATAACGATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (22 bp):
TAATAAACATAATAATAATAAA
Found at i:49524 original size:34 final size:36
Alignment explanation
Indices: 49481--49555 Score: 100
Period size: 34 Copynumber: 2.1 Consensus size: 36
49471 GGTGCGTAGT
* *
49481 TATTGTTGCTTCAGGGTTGTGTT-TTT-CATTCTTC
1 TATTGTTGCTACAGGGTTATGTTCTTTCCATTCTTC
* *
49515 TATTGTTGCTACAGGTTTATGTTCTTTCCATTCTTT
1 TATTGTTGCTACAGGGTTATGTTCTTTCCATTCTTC
49551 TATTG
1 TATTG
49556 GTTGTTCTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 20 0.57
35 3 0.09
36 12 0.34
ACGTcount: A:0.12, C:0.15, G:0.17, T:0.56
Consensus pattern (36 bp):
TATTGTTGCTACAGGGTTATGTTCTTTCCATTCTTC
Found at i:49613 original size:41 final size:41
Alignment explanation
Indices: 49568--49649 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
49558 TGTTCTTGGC
* *
49568 GTTAGTTTTGTTTGCTTCTTGTGAGTTTAGGGTATGTGTTT
1 GTTAGTTTTGTTTGCTACTTGTGAGTTTAGGGCATGTGTTT
49609 GTTAGTTTTGTTTGCTACTTGTGAGTTTAGGGCATGTGTTT
1 GTTAGTTTTGTTTGCTACTTGTGAGTTTAGGGCATGTGTTT
49650 TTCTATTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.11, C:0.06, G:0.29, T:0.54
Consensus pattern (41 bp):
GTTAGTTTTGTTTGCTACTTGTGAGTTTAGGGCATGTGTTT
Found at i:49635 original size:20 final size:20
Alignment explanation
Indices: 49571--49636 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
49561 TCTTGGCGTT
*
49571 AGTTTTGTTTGCTTCTTGTG
1 AGTTTTGTTTGCTACTTGTG
* * ** *
49591 AGTTTAGGGTATG-TGTTTGTT
1 AGTTT--TGTTTGCTACTTGTG
49612 AGTTTTGTTTGCTACTTGTG
1 AGTTTTGTTTGCTACTTGTG
49632 AGTTT
1 AGTTT
49637 AGGGCATGTG
Statistics
Matches: 33, Mismatches: 10, Indels: 6
0.67 0.20 0.12
Matches are distributed among these distances:
19 4 0.12
20 15 0.45
21 10 0.30
22 4 0.12
ACGTcount: A:0.11, C:0.06, G:0.27, T:0.56
Consensus pattern (20 bp):
AGTTTTGTTTGCTACTTGTG
Done.