Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001911.1 Hibiscus syriacus cultivar Beakdansim tig00003869_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: 75855
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1630 original size:27 final size:27
Alignment explanation
Indices: 1600--1656 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
1590 GGCAGCTCTT
* *
1600 TCCTGGTATGAGTTAGGTAGAGGCAGC
1 TCCTAGTATGAGTTAGGCAGAGGCAGC
*
1627 TCCTAGTATGAGTTAGGCAGAGGCATC
1 TCCTAGTATGAGTTAGGCAGAGGCAGC
1654 TCC
1 TCC
1657 ACGCTTTCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (27 bp):
TCCTAGTATGAGTTAGGCAGAGGCAGC
Found at i:3854 original size:3 final size:3
Alignment explanation
Indices: 3846--3871 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3836 ATTATAAACT
3846 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
3872 TACAAAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:17967 original size:5 final size:5
Alignment explanation
Indices: 17949--17997 Score: 59
Period size: 5 Copynumber: 10.2 Consensus size: 5
17939 TATTCCTCTT
*
17949 TTAT- TTAT- TTATA TTATA TTAT- TTATA TTATA TTATA TATATC TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA T-TATA TTATA
17997 T
1 T
17998 CATTATATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
4 12 0.30
5 24 0.60
6 4 0.10
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (5 bp):
TTATA
Found at i:17972 original size:14 final size:15
Alignment explanation
Indices: 17949--18013 Score: 73
Period size: 14 Copynumber: 4.4 Consensus size: 15
17939 TATTCCTCTT
17949 TTAT-TTATT-TATA
1 TTATATTATTATATA
17962 TTATATTATT-TATA
1 TTATATTATTATATA
*
17976 TTATATTATATATATC
1 TTATATTAT-TATATA
*
17992 TTATATCATTATATA
1 TTATATTATTATATA
18007 TATATAT
1 T-TATAT
18014 ATGTATGTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
13 4 0.09
14 18 0.40
15 7 0.16
16 16 0.36
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATATTATTATATA
Found at i:17977 original size:24 final size:23
Alignment explanation
Indices: 17900--17988 Score: 58
Period size: 24 Copynumber: 3.7 Consensus size: 23
17890 TCGTCCCCTA
* *
17900 TATATATATTTTTAATTATATTTT
1 TATATTTATTTAT-ATTATATTTT
*
17924 TTTATTTATTTACTA-TAT-TCCTCTT
1 TATATTTATTTA-TATTATAT--T-TT
17949 T-TATTTATTTATATTATATTATT
1 TATATTTATTTATATTATATT-TT
17972 TATATTATATTATATAT
1 TATATT-TATT-TATAT
17989 ATCTTATATC
Statistics
Matches: 52, Mismatches: 4, Indels: 16
0.72 0.06 0.22
Matches are distributed among these distances:
22 1 0.02
23 9 0.17
24 28 0.54
25 9 0.17
26 5 0.10
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65
Consensus pattern (23 bp):
TATATTTATTTATATTATATTTT
Found at i:21555 original size:11 final size:11
Alignment explanation
Indices: 21535--21593 Score: 50
Period size: 12 Copynumber: 5.0 Consensus size: 11
21525 CAATCAGAAC
21535 AAAA-AGAAAA
1 AAAAGAGAAAA
21545 AAAAGAGAAAAA
1 AAAAGAG-AAAA
21557 AGCAAAGAGAAAATA
1 A--AAAGAG-AAA-A
21572 AAAAGAGAAAA
1 AAAAGAGAAAA
21583 ACAAAG-GAAAA
1 A-AAAGAGAAAA
21594 TTGAAGAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.09
11 9 0.21
12 12 0.28
13 6 0.14
14 10 0.23
15 2 0.05
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.02
Consensus pattern (11 bp):
AAAAGAGAAAA
Found at i:21562 original size:25 final size:27
Alignment explanation
Indices: 21534--21583 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
21524 TCAATCAGAA
21534 CAAAAAG-AAA-AAAAAGAGAAAAAAG
1 CAAAAAGAAAATAAAAAGAGAAAAAAG
*
21559 CAAAGAGAAAATAAAAAGAGAAAAA
1 CAAAAAGAAAATAAAAAGAGAAAAA
21584 CAAAGGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 6 0.27
26 3 0.14
27 13 0.59
ACGTcount: A:0.78, C:0.04, G:0.16, T:0.02
Consensus pattern (27 bp):
CAAAAAGAAAATAAAAAGAGAAAAAAG
Found at i:21565 original size:14 final size:12
Alignment explanation
Indices: 21541--21593 Score: 63
Period size: 12 Copynumber: 4.2 Consensus size: 12
21531 GAACAAAAAG
21541 AAAAAAAAGAGA
1 AAAAAAAAGAGA
21553 AAAAAGCAAAGAGA
1 AAAAA--AAAGAGA
21567 AAATAAAAAGAGA
1 AAA-AAAAAGAGA
*
21580 AAAACAAAG-GA
1 AAAAAAAAGAGA
21591 AAA
1 AAA
21594 TTGAAGAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
11 5 0.14
12 10 0.27
13 10 0.27
14 10 0.27
15 2 0.05
ACGTcount: A:0.77, C:0.04, G:0.17, T:0.02
Consensus pattern (12 bp):
AAAAAAAAGAGA
Found at i:21574 original size:27 final size:24
Alignment explanation
Indices: 21544--21594 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 24
21534 CAAAAAGAAA
21544 AAAAAGAGAAAAAAGCAAAGAGAAAAT
1 AAAAAGAG-AAAAA-CAAAG-GAAAAT
21571 AAAAAGAGAAAAACAAAGGAAAAT
1 AAAAAGAGAAAAACAAAGGAAAAT
21595 TGAAGAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 6 0.25
25 5 0.21
26 5 0.21
27 8 0.33
ACGTcount: A:0.75, C:0.04, G:0.18, T:0.04
Consensus pattern (24 bp):
AAAAAGAGAAAAACAAAGGAAAAT
Found at i:21587 original size:25 final size:26
Alignment explanation
Indices: 21532--21594 Score: 80
Period size: 25 Copynumber: 2.5 Consensus size: 26
21522 ATTCAATCAG
*
21532 AACAAAAAG-AAA-AAAAAGAGAAAA
1 AACAAAGAGAAAATAAAAAGAGAAAA
21556 AAGCAAAGAGAAAATAAAAAGAG-AAA
1 AA-CAAAGAGAAAATAAAAAGAGAAAA
21582 AACAAAG-GAAAAT
1 AACAAAGAGAAAAT
21595 TGAAGAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
24 8 0.23
25 11 0.31
26 8 0.23
27 8 0.23
ACGTcount: A:0.76, C:0.05, G:0.16, T:0.03
Consensus pattern (26 bp):
AACAAAGAGAAAATAAAAAGAGAAAA
Found at i:21756 original size:69 final size:69
Alignment explanation
Indices: 21666--21796 Score: 217
Period size: 69 Copynumber: 1.9 Consensus size: 69
21656 GATTCAAACT
*
21666 ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTTCACTCAAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTCCACTCAAAGATCATAGAGCA
21731 TCAA
66 TCAA
* * * *
21735 ATGATATTGATCAAGCACAATCATTTCTGAATCACTGAATCACTCCACTCGAAGATCATAGA
1 ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTCCACTCAAAGATCATAGA
21797 AAATCAAGAG
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 57 1.00
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (69 bp):
ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTCCACTCAAAGATCATAGAGCA
TCAA
Found at i:22343 original size:12 final size:12
Alignment explanation
Indices: 22326--22354 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
22316 AACAAAAATG
22326 CCAAACCTTTGA
1 CCAAACCTTTGA
22338 CCAAACCTTTGA
1 CCAAACCTTTGA
22350 CCAAA
1 CCAAA
22355 TACAATAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.38, C:0.34, G:0.07, T:0.21
Consensus pattern (12 bp):
CCAAACCTTTGA
Found at i:22730 original size:32 final size:32
Alignment explanation
Indices: 22640--22731 Score: 130
Period size: 32 Copynumber: 2.8 Consensus size: 32
22630 TGAGGGCATC
* *
22640 TTTGAAGATTCAACATCAAATGTTGGAGCATTT
1 TTTG-AGATTCAACATCAAATATTGGGGCATTT
* *
22673 TTTTAGATTTAACATCAAATATTGGGGCATTT
1 TTTGAGATTCAACATCAAATATTGGGGCATTT
*
22705 TTTGAGATTCAACATCGAATATTGGGG
1 TTTGAGATTCAACATCAAATATTGGGG
22732 TATCTTTGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
32 49 0.94
33 3 0.06
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.38
Consensus pattern (32 bp):
TTTGAGATTCAACATCAAATATTGGGGCATTT
Found at i:22747 original size:32 final size:32
Alignment explanation
Indices: 22645--22752 Score: 110
Period size: 32 Copynumber: 3.4 Consensus size: 32
22635 GCATCTTTGA
* * ***
22645 AGATTCAACATCAAATGTTGGAGCATTTTTTT
1 AGATTCAACATCAAATATTGGGGCATTTTGGG
* **
22677 AGATTTAACATCAAATATTGGGGCATTTTTTG
1 AGATTCAACATCAAATATTGGGGCATTTTGGG
* *
22709 AGATTCAACATCGAATATTGGGGTATCTTTGGG
1 AGATTCAACATCAAATATTGGGGCAT-TTTGGG
22742 A-ATTCAACATC
1 AGATTCAACATC
22753 CTGATGCAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
32 61 0.92
33 5 0.08
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (32 bp):
AGATTCAACATCAAATATTGGGGCATTTTGGG
Found at i:23543 original size:105 final size:106
Alignment explanation
Indices: 23330--23649 Score: 444
Period size: 106 Copynumber: 3.0 Consensus size: 106
23320 ATATCGTGCC
* * *
23330 ACTCGAGACAACACAAGTTCAACTCCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCC
*
23395 AATTTCATAGCCAATTTCAACTTCACAGTGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGG
23436 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAA-AAATAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCC
*
23500 AATTTCGGAGCCAATTTCAACTTCACAGTGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGG
* * * * * * * ***
23541 ACTCAAGACAGCACAAGCTCAACTTCATAGCGAAGGGGCGGCTGGCTGTCAACAAATAATTTATT
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCC
* * * * * *
23606 AGTTCCAGAGCCAATTTTAACTTCACGGCGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGG
23647 ACT
1 ACT
23650 TGGAACAATA
Statistics
Matches: 191, Mismatches: 22, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
105 95 0.50
106 96 0.50
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (106 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGG
Found at i:23999 original size:87 final size:87
Alignment explanation
Indices: 23908--24073 Score: 278
Period size: 87 Copynumber: 1.9 Consensus size: 87
23898 GACAGTTTCT
* *
23908 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTATCTCGATTGAGATAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATATCGATTGAGATAGTTTCC
*
23973 CTTGAAATAAAATTTTTTCTCC
66 CTTGAAACAAAATTTTTTCTCC
* * *
23995 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATATCGCTTGGGGTAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATATCGATTGAGATAGTTTCC
24060 CTTGAAACAAAATT
66 CTTGAAACAAAATT
24074 GTCTCCCTTA
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 73 1.00
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (87 bp):
CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATATCGATTGAGATAGTTTCC
CTTGAAACAAAATTTTTTCTCC
Found at i:24112 original size:100 final size:101
Alignment explanation
Indices: 23995--24232 Score: 284
Period size: 100 Copynumber: 2.4 Consensus size: 101
23985 TTTTTTCTCC
* * *
23995 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATATCGCTTGGGGTAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATATCGCTTGAGATAGTTTCA
*
24060 CTTGAAACAAAA-TTGTCTCCCTT-ATGACAAATTCT
66 CTTAAAACAAAATTTGTCTCCCTTGA-GACAAATTCT
* * * * * * *
24095 CTTGAAACATGAACATTGAAAACATTTCCTTTGAAATTAATTTTGTCTCTCTTGATATAGTTTCA
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATATCGCTTGAGATAGTTTCA
* ** *
24160 CTTAAAACAAAATTTTGTCTCCCTTGAGATAGTTTTT
66 CTTAAAACAAAA-TTTGTCTCCCTTGAGACAAATTCT
*
24197 CTTGAAACATAAATC-TTGAAAACGTTTCCCTTGAAA
1 CTTGAAACATAAA-CATTGAAAACATTTCCCTTGAAA
24233 CAAAAAATAT
Statistics
Matches: 116, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
100 66 0.57
102 48 0.41
103 2 0.02
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (101 bp):
CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATATCGCTTGAGATAGTTTCA
CTTAAAACAAAATTTGTCTCCCTTGAGACAAATTCT
Found at i:24205 original size:37 final size:38
Alignment explanation
Indices: 24133--24210 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 38
24123 CTTTGAAATT
* *
24133 AATTTTGTCTCTCTTGATATAGTTTCACTTAAAACA-A
1 AATTTTGTCTCCCTTGAGATAGTTTCACTTAAAACATA
** *
24170 AATTTTGTCTCCCTTGAGATAGTTTTTCTTGAAACATA
1 AATTTTGTCTCCCTTGAGATAGTTTCACTTAAAACATA
24208 AAT
1 AAT
24211 CTTGAAAACG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
37 31 0.89
38 4 0.11
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (38 bp):
AATTTTGTCTCCCTTGAGATAGTTTCACTTAAAACATA
Found at i:24320 original size:37 final size:38
Alignment explanation
Indices: 24270--24372 Score: 167
Period size: 36 Copynumber: 2.8 Consensus size: 38
24260 AAAACGAGTT
24270 TTGAGACAGTTTCCCTTGAAACAAAATCTT-GTCTCTC
1 TTGAGACAGTTTCCCTTGAAACAAAATCTTCGTCTCTC
* *
24307 TTGAGATAGTTTCCCTTGAAAC-ATAT-TTCGTCTCTC
1 TTGAGACAGTTTCCCTTGAAACAAAATCTTCGTCTCTC
24343 TTGAGACAGTTTCCCTTGAAACAAAATCTT
1 TTGAGACAGTTTCCCTTGAAACAAAATCTT
24373 TGAATATCTT
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
35 2 0.03
36 31 0.53
37 24 0.41
38 2 0.03
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (38 bp):
TTGAGACAGTTTCCCTTGAAACAAAATCTTCGTCTCTC
Found at i:24485 original size:36 final size:36
Alignment explanation
Indices: 24270--24503 Score: 141
Period size: 36 Copynumber: 6.6 Consensus size: 36
24260 AAAACGAGTT
** * *
24270 TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
1 TTGAGACAGTTTCTTTTGAAAC-AAATTTTGTCCCTC
* ** * * *
24307 TTGAGATAGTTTCCCTTGAAACATATTTCGTCTCTC
1 TTGAGACAGTTTCTTTTGAAACAAATTTTGTCCCTC
** *
24343 TTGAGACAGTTTCCCTTGAAACAAA----AT--CT-
1 TTGAGACAGTTTCTTTTGAAACAAATTTTGTCCCTC
* *
24372 TTGA-ATA-TCTT-TTCCTTGAAACAAATTTCGTCTCC-C
1 TTGAGACAGT-TTCTT--TTGAAACAAATTTTGTC-CCTC
* * *
24408 TTGAGACAGTTTCTTTT-AGAACTAAGTTTTGTCTCTT
1 TTGAGACAGTTTCTTTTGA-AAC-AAATTTTGTCCCTC
*
24445 TTGAGACAATTTCTTTTGAAACAAATTTTGTCCCTC
1 TTGAGACAGTTTCTTTTGAAACAAATTTTGTCCCTC
*
24481 TTGAGACAGTTTCTCTTGAAACA
1 TTGAGACAGTTTCTTTTGAAACA
24504 CAAAAAAAAA
Statistics
Matches: 157, Mismatches: 22, Indels: 37
0.73 0.10 0.17
Matches are distributed among these distances:
27 1 0.01
28 4 0.03
29 14 0.09
30 2 0.01
32 1 0.01
33 1 0.01
35 1 0.01
36 77 0.49
37 52 0.33
38 4 0.03
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (36 bp):
TTGAGACAGTTTCTTTTGAAACAAATTTTGTCCCTC
Found at i:24567 original size:39 final size:36
Alignment explanation
Indices: 24489--24579 Score: 128
Period size: 39 Copynumber: 2.4 Consensus size: 36
24479 TCTTGAGACA
*
24489 GTTTCTCTTGAAACACAAAAAAAAACCCTCGAAATT
1 GTTTCTCTTGAAACACAAAAAAAAACCCTCGAAAAT
* *
24525 GTTTCTCTTGAAACACACACACAAAAAACCTTTGAAAAT
1 GTTTCTCTTGAAACACA-A-A-AAAAAACCCTCGAAAAT
24564 GTTTCTCTTGAAACAC
1 GTTTCTCTTGAAACAC
24580 CAAACCCTCG
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
36 17 0.35
37 1 0.02
38 1 0.02
39 30 0.61
ACGTcount: A:0.41, C:0.23, G:0.09, T:0.27
Consensus pattern (36 bp):
GTTTCTCTTGAAACACAAAAAAAAACCCTCGAAAAT
Found at i:28364 original size:21 final size:22
Alignment explanation
Indices: 28340--28383 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
28330 TTAAGGCCAA
* *
28340 ATTCAGCTTC-AAATTATCTAG
1 ATTCAGCCTCAAAATGATCTAG
*
28361 ATTCATCCTCAAAATGATCTAG
1 ATTCAGCCTCAAAATGATCTAG
28383 A
1 A
28384 ATATTCAGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.34
Consensus pattern (22 bp):
ATTCAGCCTCAAAATGATCTAG
Found at i:33666 original size:85 final size:85
Alignment explanation
Indices: 33565--33733 Score: 214
Period size: 85 Copynumber: 2.0 Consensus size: 85
33555 GTCCGCCATG
** * * * **
33565 AATTTATGACGTGCATTTATGACGCT-CATTGAGTGTCATTGAAGCCCCCATCATAAGTGAAGAC
1 AATTTATGACACGCATTTATGAC-CTACATTGAGTGTCATTGAAGCACACACCATAAGAAAAGAC
*
33629 GACACACATTTGTGTGTCATA
65 GACACACATTCGTGTGTCATA
* * * *
33650 AATTTATGACACGCATTTATGACTTACATTGCGTGTCATTGAAGCACACACCATTAGAAAAGATG
1 AATTTATGACACGCATTTATGACCTACATTGAGTGTCATTGAAGCACACACCATAAGAAAAGACG
33715 ACACACATTCGTGTGTCAT
66 ACACACATTCGTGTGTCAT
33734 GATTGTATGT
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
84 1 0.01
85 70 0.99
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Consensus pattern (85 bp):
AATTTATGACACGCATTTATGACCTACATTGAGTGTCATTGAAGCACACACCATAAGAAAAGACG
ACACACATTCGTGTGTCATA
Found at i:33758 original size:2 final size:2
Alignment explanation
Indices: 33751--33791 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
33741 TGTCGTAAAT
33751 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
33792 TGTAGATTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:42368 original size:94 final size:95
Alignment explanation
Indices: 42226--42408 Score: 271
Period size: 94 Copynumber: 1.9 Consensus size: 95
42216 ATACCAAAAT
* *
42226 GGAAAGTATTGATACCATGGATTCCAGAATGCCAAAATGGTATTGATACTGAAAGAGAGTATCAA
1 GGAAAGTATCGATACCATGGATTCCAGAATGCCAAAATGGTATCGATACTGAAAGAGAGTATCAA
* *
42291 TACTATAATATAGAAGTATCAATACTAGAA
66 TACCACAATATAGAAGTATCAATACTAGAA
* * *
42321 GGAAAGTATCGATACCATGGA-TCCAGAATG-TAGAAATGGTATCGATACTGAAAGGGAGTATCG
1 GGAAAGTATCGATACCATGGATTCCAGAATGCCA-AAATGGTATCGATACTGAAAGAGAGTATCA
*
42384 GTACCACAATATAGAAGTATCAATA
65 ATACCACAATATAGAAGTATCAATA
42409 GCATGGTAGG
Statistics
Matches: 79, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
93 1 0.01
94 58 0.73
95 20 0.25
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.25
Consensus pattern (95 bp):
GGAAAGTATCGATACCATGGATTCCAGAATGCCAAAATGGTATCGATACTGAAAGAGAGTATCAA
TACCACAATATAGAAGTATCAATACTAGAA
Found at i:42892 original size:23 final size:23
Alignment explanation
Indices: 42862--42906 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
42852 GTCAATTATT
42862 CCAGTTAGATGAAAGGTTAAATG
1 CCAGTTAGATGAAAGGTTAAATG
*
42885 CCAGTTAGATGAAATGTTAAAT
1 CCAGTTAGATGAAAGGTTAAAT
42907 ACCTTTGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (23 bp):
CCAGTTAGATGAAAGGTTAAATG
Found at i:43318 original size:242 final size:242
Alignment explanation
Indices: 42886--43407 Score: 767
Period size: 242 Copynumber: 2.2 Consensus size: 242
42876 GGTTAAATGC
*
42886 CAGTTAGATGAAATGTTAAATACCTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTTGACATA
1 CAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTTGACATA
* * * * **
42951 AATGTGTTAATTATGTCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAATGATTAATTGTCTAG
66 AAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATTACCTAG
* * * *
43016 CTTTGTATTTGACAGAAAGGTGTCAATTATGTCAGTTAGATGAAAAGTTAAATACCTTTGAGTAA
131 CTTTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAAGATAAATACCTTTGAATAA
* * * * * * *
43081 AATATTAATTTCCTAGCTTTGCATTTGACAGAAGGGTGTCAATTATG
196 AAGATTAAATGCCTAGATGTGCATTTGACAGAAAGGTGTCAATCATG
* *
43128 CAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAGGATTAATTGCCTAGTTGTGCATTTGACATA
1 CAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTTGACATA
43193 AAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATTACCTAG
66 AAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATTACCTAG
* * *
43258 -TTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGATAAATGCCTTTGAATT
131 CTT-TGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAAGATAAATACCTTTGAATA
* *
43322 AAAGATTAAATGCCTAGATGTGTATTTGGCAGAAAGGTGTCAATCATG
195 AAAGATTAAATGCCTAGATGTGCATTTGACAGAAAGGTGTCAATCATG
* * *
43370 CAAGTTAGATGAAAGGCTAAATGCCTTTGGGTAAAAGA
1 C-AGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGA
43408 CTAAATGCTT
Statistics
Matches: 249, Mismatches: 29, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
241 2 0.01
242 215 0.86
243 32 0.13
ACGTcount: A:0.35, C:0.10, G:0.21, T:0.33
Consensus pattern (242 bp):
CAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTTGACATA
AAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATTACCTAG
CTTTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAAGATAAATACCTTTGAATAA
AAGATTAAATGCCTAGATGTGCATTTGACAGAAAGGTGTCAATCATG
Found at i:43415 original size:81 final size:80
Alignment explanation
Indices: 42886--43407 Score: 729
Period size: 81 Copynumber: 6.5 Consensus size: 80
42876 GGTTAAATGC
* *
42886 CAGTTAGATGAAATGTTAAATACCTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTTGACATA
1 CAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGA
* *
42951 AATGTGTTAATTATG
66 AAGGTGTCAATTATG
* * * *
42966 TCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAATGATTAATTGTCTAGCTTTGTATTTGACAG
1 -CAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAG
43031 AAAGGTGTCAATTATG
65 AAAGGTGTCAATTATG
* * * *
43047 TCAGTTAGATGAAAAGTTAAATACCTTTGAGTAAAATATTAATTTCCTAGCTTTGCATTTGACAG
1 -CAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAG
*
43112 AAGGGTGTCAATTATG
65 AAAGGTGTCAATTATG
* * *
43128 CAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAGGATTAATTGCCTAGTTGTGCATTTGACATA
1 CAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGA
43193 AAGGTGTCAATTATG
66 AAGGTGTCAATTATG
* *
43208 CCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATTACCTAGTTGTGCATTTGACAG
1 -CAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAG
43273 AAAGGTGTCAATTATG
65 AAAGGTGTCAATTATG
* * * * * * * *
43289 CCAGTTAGATGAAAGGATAAATGCCTTTGAATTAAAGATTAAATGCCTAGATGTGTATTTGGCAG
1 -CAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAG
*
43354 AAAGGTGTCAATCATG
65 AAAGGTGTCAATTATG
* * *
43370 CAAGTTAGATGAAAGGCTAAATGCCTTTGGGTAAAAGA
1 C-AGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGA
43408 CTAAATGCTT
Statistics
Matches: 399, Mismatches: 40, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
80 73 0.18
81 326 0.82
ACGTcount: A:0.35, C:0.10, G:0.21, T:0.33
Consensus pattern (80 bp):
CAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGA
AAGGTGTCAATTATG
Found at i:51935 original size:23 final size:23
Alignment explanation
Indices: 51905--51968 Score: 110
Period size: 23 Copynumber: 2.8 Consensus size: 23
51895 TAGTGCAGGA
51905 GGAACCGATTCCCCCTTTGAATG
1 GGAACCGATTCCCCCTTTGAATG
*
51928 GGAACCGATTTCCCCTTTGAATG
1 GGAACCGATTCCCCCTTTGAATG
*
51951 GGAACCGATTCCCTCTTT
1 GGAACCGATTCCCCCTTT
51969 AGGGAATCGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (23 bp):
GGAACCGATTCCCCCTTTGAATG
Found at i:56897 original size:14 final size:14
Alignment explanation
Indices: 56875--56905 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
56865 AAGTTAATGG
56875 GTTGACTCAGACGA
1 GTTGACTCAGACGA
*
56889 GTTGGCTCAGACGA
1 GTTGACTCAGACGA
56903 GTT
1 GTT
56906 AACTTGGATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (14 bp):
GTTGACTCAGACGA
Found at i:64896 original size:3 final size:3
Alignment explanation
Indices: 64888--64975 Score: 83
Period size: 3 Copynumber: 29.7 Consensus size: 3
64878 TGTAATATGC
* * *
64888 AAT AAT AAT ATTT ATT AAT AAT AAT AAA AAT -AT AAT AAT AAT AAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
64933 AA- AAT AAT AAT AAT AGT GAT AAAT AA- AAT AAT AAT AAC AAT AA
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AA
64976 AAAAATGGAT
Statistics
Matches: 70, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
2 6 0.09
3 60 0.86
4 4 0.06
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:64924 original size:14 final size:14
Alignment explanation
Indices: 64905--64974 Score: 63
Period size: 14 Copynumber: 5.1 Consensus size: 14
64895 ATATTTATTA
64905 ATAATAATAAAAAT
1 ATAATAATAAAAAT
*
64919 ATAATAATAATAAT
1 ATAATAATAAAAAT
* *
64933 AAAATAATAATAAT
1 ATAATAATAAAAAT
* *
64947 AGTGATAA-ATAAA-
1 A-TAATAATAAAAAT
*
64960 ATAATAATAACAAT
1 ATAATAATAAAAAT
64974 A
1 A
64975 AAAAAATGGA
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
12 5 0.11
13 4 0.09
14 31 0.70
15 4 0.09
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (14 bp):
ATAATAATAAAAAT
Found at i:64925 original size:17 final size:17
Alignment explanation
Indices: 64903--64975 Score: 87
Period size: 17 Copynumber: 4.2 Consensus size: 17
64893 TAATATTTAT
64903 TAATAATAATAA-AAATA
1 TAATAATAATAATAAA-A
64920 TAATAATAATAATAAAA
1 TAATAATAATAATAAAA
*
64937 TAATAATAATAGTGATAAA
1 TAATAATAATAAT-A-AAA
64956 TAA-AATAATAATAACAA
1 TAATAATAATAATAA-AA
64973 TAA
1 TAA
64976 AAAAATGGAT
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
16 1 0.02
17 31 0.62
18 12 0.24
19 6 0.12
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (17 bp):
TAATAATAATAATAAAA
Found at i:65661 original size:112 final size:114
Alignment explanation
Indices: 65345--65664 Score: 387
Period size: 122 Copynumber: 2.8 Consensus size: 114
65335 GAATTAAGGT
* * * *
65345 AAGGTTGAACAAATTCTTCTCATTATGAATTTATTCTCCTTCTTTAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTAT
* * ***
65410 GAATTCTTCTGGAAATATTGATGTTGATCTATCTCCTTCTGTGATAGCGTCGAGCAA
66 GAACTCTTCTGG--A-A---ATGTTGATCCA-CTCCGAATGTGATA-CGTCGAGCAA
*
65467 AAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTAT
* * * *
65532 GAACTCTTTTGGCAATGTTGATCCA-T-CGAATGATGA-A-TTTGAGCAA
66 GAACTCTTCTGGAAATGTTGATCCACTCCGAATG-TGATACGTCGAGCAA
*
65578 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTA
65643 TGAACTCTTCTGGAAATGTTGA
65 TGAACTCTTCTGGAAATGTTGA
65665 AAACATTCTG
Statistics
Matches: 178, Mismatches: 18, Indels: 14
0.85 0.09 0.07
Matches are distributed among these distances:
111 41 0.23
112 48 0.27
113 4 0.02
114 4 0.02
116 10 0.06
119 1 0.01
122 70 0.39
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (114 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTAT
GAACTCTTCTGGAAATGTTGATCCACTCCGAATGTGATACGTCGAGCAA
Found at i:66925 original size:54 final size:54
Alignment explanation
Indices: 66840--66995 Score: 176
Period size: 54 Copynumber: 2.9 Consensus size: 54
66830 TTACTGGTTC
** *
66840 GTAAAACATTTGAAAACACATTCATCATTTCCTGTGGTTTCTGC-CTAGATGTTT
1 GTAAAACATTTGAAAACACATTCATCATTTCCTGTGGCCTCTGCAC-AGATGTAT
* * *
66894 GTAAAACATTTGATAACATATTCATCTTTTCCTGTGGCCTCTGCACAGATGTAT
1 GTAAAACATTTGAAAACACATTCATCATTTCCTGTGGCCTCTGCACAGATGTAT
* * * *
66948 GTAAAATATTTGACAATACATTCATCCA--T-CTGTGGCTTCTGCACAGAT
1 GTAAAACATTTGAAAACACATTCAT-CATTTCCTGTGGCCTCTGCACAGAT
66996 TTCTAGTCAA
Statistics
Matches: 88, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
52 18 0.20
53 1 0.01
54 67 0.76
55 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37
Consensus pattern (54 bp):
GTAAAACATTTGAAAACACATTCATCATTTCCTGTGGCCTCTGCACAGATGTAT
Found at i:67998 original size:75 final size:75
Alignment explanation
Indices: 67865--68024 Score: 205
Period size: 75 Copynumber: 2.1 Consensus size: 75
67855 GATATGGATC
* * * * *
67865 TTCATCATGCCCCATCATTTGCTAATACAAACATTCAAAATACATCAACATTCTTGATTCTGATT
1 TTCAGCATGCCCCAACATTGGCTAATACAAACATTCAAAATACATCAACATTCCTGATTATGATT
67930 GAAAGGGGCT
66 GAAAGGGGCT
** ** *
67940 TTCAGCATGCCCCAACATTGGCTAATACAAATGTTCAAAA-AGTGTCAATATTCCTGATTATGAT
1 TTCAGCATGCCCCAACATTGGCTAATACAAACATTCAAAATA-CATCAACATTCCTGATTATGAT
*
68004 TGAAATGGGCT
65 TGAAAGGGGCT
68015 TTCAGCATGC
1 TTCAGCATGC
68025 TCTATCATTT
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
74 1 0.01
75 72 0.99
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (75 bp):
TTCAGCATGCCCCAACATTGGCTAATACAAACATTCAAAATACATCAACATTCCTGATTATGATT
GAAAGGGGCT
Done.