Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005080.1 Hibiscus syriacus cultivar Beakdansim tig00011409_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: 86723
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:2609 original size:56 final size:55
Alignment explanation
Indices: 2456--2698 Score: 228
Period size: 56 Copynumber: 4.3 Consensus size: 55
2446 ACCGACCCAA
** *
2456 TGACATTCTGGGAATTTTTATGAAAAAGGTGATTTTAGGAATTGTTGTG-AAAAGG
1 TGACATTCTGGGAATTTTT-TGAAAAAGGTGACATTAGGAATTTTTGTGAAAAAGG
* *
2511 TGACATTCTGGGAATTTTGTGAAAAAGGTGACATTCTGGGAATTTTTGTGAAAAAGG
1 TGACATTCTGGGAATTTTTTGAAAAAGGTGACA-T-TAGGAATTTTTGTGAAAAAGG
* * * **
2568 TTACATTCTAGGAATTATTTTGAAAAAATGTGACATT-GGAATTATTT-TGAAAAAAA
1 TGACATTCTGGGAATT-TTTTG-AAAAAGGTGACATTAGGAATT-TTTGTGAAAAAGG
* * *
2624 TGACATTTTGGGAATTATTTTGAAAAA--TGAGATTATGGGAATTATTT-TGAAAAATG
1 TGACATTCTGGGAATT-TTTTGAAAAAGGTGACATTA--GGAATT-TTTGTGAAAAAGG
*
2680 TGACATTTTGGGAATTTTT
1 TGACATTCTGGGAATTTTT
2699 GAATGTGAAC
Statistics
Matches: 162, Mismatches: 17, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
53 6 0.04
54 12 0.07
55 27 0.17
56 77 0.48
57 24 0.15
58 5 0.03
59 11 0.07
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.38
Consensus pattern (55 bp):
TGACATTCTGGGAATTTTTTGAAAAAGGTGACATTAGGAATTTTTGTGAAAAAGG
Found at i:2701 original size:27 final size:28
Alignment explanation
Indices: 2456--2698 Score: 232
Period size: 29 Copynumber: 8.7 Consensus size: 28
2446 ACCGACCCAA
2456 TGACATTCTGGGAATTTTTATGAAAAAGG
1 TGACATTCTGGGAATTTTT-TGAAAAAGG
* * *
2485 TG--ATTTTAGGAATTGTTGTG-AAAAGG
1 TGACATTCTGGGAATT-TTTTGAAAAAGG
*
2511 TGACATTCTGGGAATTTTGTGAAAAAGG
1 TGACATTCTGGGAATTTTTTGAAAAAGG
2539 TGACATTCTGGGAATTTTTGTGAAAAAGG
1 TGACATTCTGGGAATTTTT-TGAAAAAGG
* * *
2568 TTACATTCTAGGAATTATTTTGAAAAAATG
1 TGACATTCTGGGAATT-TTTTG-AAAAAGG
**
2598 TGACA-T-T-GGAATTATTTTGAAAAAAA
1 TGACATTCTGGGAATT-TTTTGAAAAAGG
*
2624 TGACATTTTGGGAATTATTTTGAAAAA--
1 TGACATTCTGGGAATT-TTTTGAAAAAGG
* * *
2651 TGAGATTATGGGAATTATTTTGAAAAATG
1 TGACATTCTGGGAATT-TTTTGAAAAAGG
*
2680 TGACATTTTGGGAATTTTT
1 TGACATTCTGGGAATTTTT
2699 GAATGTGAAC
Statistics
Matches: 186, Mismatches: 16, Indels: 25
0.82 0.07 0.11
Matches are distributed among these distances:
26 18 0.10
27 55 0.30
28 41 0.22
29 59 0.32
30 13 0.07
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.38
Consensus pattern (28 bp):
TGACATTCTGGGAATTTTTTGAAAAAGG
Found at i:3670 original size:8 final size:8
Alignment explanation
Indices: 3657--3684 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
3647 TAGGGTAAGC
3657 CTTACGGA
1 CTTACGGA
3665 CTTACGGA
1 CTTACGGA
3673 CTTACGGA
1 CTTACGGA
3681 CTTA
1 CTTA
3685 AGGATACAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (8 bp):
CTTACGGA
Found at i:10200 original size:28 final size:28
Alignment explanation
Indices: 10031--10219 Score: 170
Period size: 29 Copynumber: 6.6 Consensus size: 28
10021 CCCGACCCAG
* *
10031 TGACATTCTGGGAATTTTTTATGAAAAAGG
1 TGACATTCTGGGAATTATTT-TGAAAAA-A
* *
10061 TGACATTCT-GGAA-AATTTGTGAAAAATG
1 TGACATTCTGGGAATTATTT-TGAAAAA-A
10089 TGACATTCTGGGAATT-TTTGTGAAAAAA
1 TGACATTCTGGGAATTATTT-TGAAAAAA
10117 CTGACATTCTGGGAATTATTTTTGAAAAAA
1 -TGACATTCTGGGAATTA-TTTTGAAAAAA
* *
10147 TGACAATT-TAGGAATTATTTTTAAAAAA
1 TGAC-ATTCTGGGAATTATTTTGAAAAAA
* * *
10175 TGACATTCTAGGAATTATTTAGAAAAATG
1 TGACATTCTGGGAATTATTTTGAAAAA-A
* *
10204 TGAAATTTTGGGAATT
1 TGACATTCTGGGAATT
10220 TTTGAATATG
Statistics
Matches: 137, Mismatches: 14, Indels: 17
0.82 0.08 0.10
Matches are distributed among these distances:
27 3 0.02
28 51 0.37
29 60 0.44
30 20 0.15
31 3 0.02
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.37
Consensus pattern (28 bp):
TGACATTCTGGGAATTATTTTGAAAAAA
Found at i:18615 original size:23 final size:23
Alignment explanation
Indices: 18588--18662 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
18578 ATTCGGAATA
18588 ATTAAATAAATTTTTAAATAAAC
1 ATTAAATAAATTTTTAAATAAAC
* * *
18611 ATTAAAT--A-TTATAATTCAGAATA
1 ATTAAATAAATTTTTAAAT-A-AA-C
*
18634 ATTAAATAAGTTTTTAAATAAAC
1 ATTAAATAAATTTTTAAATAAAC
18657 ATTAAA
1 ATTAAA
18663 GATTATAATT
Statistics
Matches: 39, Mismatches: 7, Indels: 12
0.67 0.12 0.21
Matches are distributed among these distances:
20 6 0.15
21 2 0.05
22 2 0.05
23 20 0.51
24 2 0.05
25 1 0.03
26 6 0.15
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.39
Consensus pattern (23 bp):
ATTAAATAAATTTTTAAATAAAC
Found at i:18624 original size:46 final size:46
Alignment explanation
Indices: 18574--18674 Score: 175
Period size: 46 Copynumber: 2.2 Consensus size: 46
18564 AATTGGTATA
* *
18574 TATAATTCGGAATAATTAAATAAATTTTTAAATAAACATTAAATAT
1 TATAATTCAGAATAATTAAATAAATTTTTAAATAAACATTAAAGAT
*
18620 TATAATTCAGAATAATTAAATAAGTTTTTAAATAAACATTAAAGAT
1 TATAATTCAGAATAATTAAATAAATTTTTAAATAAACATTAAAGAT
18666 TATAATTCA
1 TATAATTCA
18675 AATTATAAGT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 52 1.00
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (46 bp):
TATAATTCAGAATAATTAAATAAATTTTTAAATAAACATTAAAGAT
Found at i:19345 original size:24 final size:24
Alignment explanation
Indices: 19311--19400 Score: 108
Period size: 24 Copynumber: 3.8 Consensus size: 24
19301 GAGATATCAT
*
19311 AAATCAAAACAAAATTCAGATAAG
1 AAATCAAAACAGAATTCAGATAAG
* * * *
19335 ATATCAGAACAGAATCCAGATCAG
1 AAATCAAAACAGAATTCAGATAAG
* *
19359 AAATCAAAATAGAATTCAGATAAA
1 AAATCAAAACAGAATTCAGATAAG
*
19383 AAATCATAACAGAATTCA
1 AAATCAAAACAGAATTCA
19401 AATCGAAAAT
Statistics
Matches: 53, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.57, C:0.14, G:0.10, T:0.19
Consensus pattern (24 bp):
AAATCAAAACAGAATTCAGATAAG
Found at i:19394 original size:48 final size:48
Alignment explanation
Indices: 19306--19397 Score: 130
Period size: 48 Copynumber: 1.9 Consensus size: 48
19296 AAACGGAGAT
* * *
19306 ATCATAAATCAAAACAAAATTCAGATAAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAAAATTCAGATAAAAAATCAGAACAGAATCCAG
* * *
19354 ATCAGAAATCAAAATAGAATTCAGATAAAAAATCATAACAGAAT
1 ATCAGAAATCAAAACAAAATTCAGATAAAAAATCAGAACAGAAT
19398 TCAAATCGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 38 1.00
ACGTcount: A:0.57, C:0.14, G:0.10, T:0.20
Consensus pattern (48 bp):
ATCAGAAATCAAAACAAAATTCAGATAAAAAATCAGAACAGAATCCAG
Found at i:19409 original size:24 final size:23
Alignment explanation
Indices: 19306--19412 Score: 90
Period size: 24 Copynumber: 4.4 Consensus size: 23
19296 AAACGGAGAT
*
19306 ATCATAAATCAAAACAAAATTCAG
1 ATCA-AAATCAAAACAGAATTCAG
* *
19330 AT-AAGATATCAGAACAGAATCCAG
1 ATCAA-A-ATCAAAACAGAATTCAG
*
19354 ATCAGAAATCAAAATAGAATTCAG
1 ATCA-AAATCAAAACAGAATTCAG
* * *
19378 ATAAAAAATCATAACAGAATTCAA
1 AT-CAAAATCAAAACAGAATTCAG
19402 ATCGAAAATCA
1 ATC-AAAATCA
19413 GATAAAACTT
Statistics
Matches: 66, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
22 1 0.02
23 2 0.03
24 59 0.89
25 3 0.05
26 1 0.02
ACGTcount: A:0.56, C:0.15, G:0.09, T:0.20
Consensus pattern (23 bp):
ATCAAAATCAAAACAGAATTCAG
Found at i:19412 original size:48 final size:48
Alignment explanation
Indices: 19306--19408 Score: 127
Period size: 48 Copynumber: 2.2 Consensus size: 48
19296 AAACGGAGAT
* * * *
19306 ATCATAAATCAAAACAAAATTCAGATAAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAAAATTCAGATAAAAAATCAGAACAGAATCCAA
* * * *
19354 ATCAGAAATCAAAATAGAATTCAGATAAAAAATCATAACAGAATTCAA
1 ATCAGAAATCAAAACAAAATTCAGATAAAAAATCAGAACAGAATCCAA
19402 ATC-GAAA
1 ATCAGAAA
19409 ATCAGATAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
47 4 0.09
48 43 0.91
ACGTcount: A:0.56, C:0.15, G:0.10, T:0.19
Consensus pattern (48 bp):
ATCAGAAATCAAAACAAAATTCAGATAAAAAATCAGAACAGAATCCAA
Found at i:23476 original size:44 final size:44
Alignment explanation
Indices: 23416--23587 Score: 148
Period size: 44 Copynumber: 3.9 Consensus size: 44
23406 ACTTATCATG
* * * *
23416 TGCACAAAGGAGAGGAGCATGCAGAAACGGTAAGGTTTTACCCT
1 TGCACATAGCAGAGGAGCTTGCAGAAACGGTAAGGTCTTACCCT
* * * *
23460 TACACATAGCAGAGGAGCTTG-GGAAATGGTAAGGTCTTATCCT
1 TGCACATAGCAGAGGAGCTTGCAGAAACGGTAAGGTCTTACCCT
* * * * * * * * *
23503 TGCACACAACAAAGGAGCTTGGAGAGACGGAAATGACTCACCCT
1 TGCACATAGCAGAGGAGCTTGCAGAAACGGTAAGGTCTTACCCT
* * * *
23547 TGTACATAGCAGAGGAGCCTGCAGTAATGGTAAGGTCTTAC
1 TGCACATAGCAGAGGAGCTTGCAGAAACGGTAAGGTCTTAC
23588 AAGTCAAAGA
Statistics
Matches: 94, Mismatches: 33, Indels: 2
0.73 0.26 0.02
Matches are distributed among these distances:
43 35 0.37
44 59 0.63
ACGTcount: A:0.33, C:0.19, G:0.28, T:0.20
Consensus pattern (44 bp):
TGCACATAGCAGAGGAGCTTGCAGAAACGGTAAGGTCTTACCCT
Found at i:23494 original size:43 final size:43
Alignment explanation
Indices: 23439--23524 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
23429 GGAGCATGCA
* * * *
23439 GAAACGGTAAGGTTTTACCCTTACACATAGCAGAGGAGCTTGG
1 GAAACGGTAAGGTCTTACCCTTACACACAACAAAGGAGCTTGG
* * *
23482 GAAATGGTAAGGTCTTATCCTTGCACACAACAAAGGAGCTTGG
1 GAAACGGTAAGGTCTTACCCTTACACACAACAAAGGAGCTTGG
23525 AGAGACGGAA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (43 bp):
GAAACGGTAAGGTCTTACCCTTACACACAACAAAGGAGCTTGG
Found at i:23729 original size:12 final size:12
Alignment explanation
Indices: 23669--23755 Score: 63
Period size: 12 Copynumber: 7.3 Consensus size: 12
23659 GAGATATCAT
*
23669 AAATCAAAACAG
1 AAATCAGAACAG
*
23681 AATTCAGATA-AG
1 AAATCAGA-ACAG
* *
23693 ATATCATAACA-
1 AAATCAGAACAG
*
23704 AAATCCAGATCAG
1 AAAT-CAGAACAG
23717 AAATCAGAACAG
1 AAATCAGAACAG
* *
23729 AATTCAGATCAG
1 AAATCAGAACAG
*
23741 AAATCATAACA-
1 AAATCAGAACAG
23752 AAAT
1 AAAT
23756 TCAAATCGAA
Statistics
Matches: 57, Mismatches: 14, Indels: 9
0.71 0.17 0.11
Matches are distributed among these distances:
11 8 0.14
12 44 0.77
13 5 0.09
ACGTcount: A:0.55, C:0.16, G:0.10, T:0.18
Consensus pattern (12 bp):
AAATCAGAACAG
Found at i:23747 original size:48 final size:48
Alignment explanation
Indices: 23664--23772 Score: 148
Period size: 48 Copynumber: 2.3 Consensus size: 48
23654 AAACGGAGAT
* * * *
23664 ATCATAAATCAAAACAGAATTCAGATAAGATATCATAACAAAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATAAGAAATCATAACAAAATCCAA
* *
23712 ATCAGAAATCAGAACAGAATTCAGATCAGAAATCATAACAAAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATAAGAAATCATAACAAAATCCAA
23760 ATC-GAAAATCAGA
1 ATCAG-AAATCAGA
23773 TAAAACTTTC
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
47 1 0.02
48 53 0.98
ACGTcount: A:0.54, C:0.17, G:0.10, T:0.19
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATAAGAAATCATAACAAAATCCAA
Found at i:23770 original size:24 final size:24
Alignment explanation
Indices: 23664--23766 Score: 118
Period size: 24 Copynumber: 4.3 Consensus size: 24
23654 AAACGGAGAT
* * *
23664 ATCATAAATCAAAACAGAATTCAG
1 ATCAGAAATCATAACAAAATTCAG
* * *
23688 ATAAGATATCATAACAAAATCCAG
1 ATCAGAAATCATAACAAAATTCAG
* *
23712 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCATAACAAAATTCAG
*
23736 ATCAGAAATCATAACAAAATTCAA
1 ATCAGAAATCATAACAAAATTCAG
23760 ATC-GAAA
1 ATCAGAAA
23767 ATCAGATAAA
Statistics
Matches: 65, Mismatches: 14, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
23 4 0.06
24 61 0.94
ACGTcount: A:0.54, C:0.17, G:0.10, T:0.19
Consensus pattern (24 bp):
ATCAGAAATCATAACAAAATTCAG
Found at i:28002 original size:43 final size:44
Alignment explanation
Indices: 27920--28089 Score: 177
Period size: 44 Copynumber: 3.9 Consensus size: 44
27910 ACTTATTATG
* * *
27920 TGCACAAAGCAGAGGAGCTTGTAGAAACGGTAAGGTCTTACCCT
1 TGCACAAAGCAAAGGAGCCTGCAGAAACGGTAAGGTCTTACCCT
* * * * *
27964 TGCACATAGCACAGGAGCCTGGA-AAATGGTAAGGTCTTATCCT
1 TGCACAAAGCAAAGGAGCCTGCAGAAACGGTAAGGTCTTACCCT
* *
28007 TGCACACAA-CAAAGGAGCCTACAGAAACGGTAAGGACTTACCCT
1 TGCACA-AAGCAAAGGAGCCTGCAGAAACGGTAAGGTCTTACCCT
* * * *
28051 TGCAC--AGCATAGGAGCTTGCGGTAACGGTAAGGTCTTAC
1 TGCACAAAGCAAAGGAGCCTGCAGAAACGGTAAGGTCTTAC
28090 AAGTCAAAGA
Statistics
Matches: 104, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
41 1 0.01
42 26 0.25
43 35 0.34
44 42 0.40
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.20
Consensus pattern (44 bp):
TGCACAAAGCAAAGGAGCCTGCAGAAACGGTAAGGTCTTACCCT
Found at i:28239 original size:24 final size:24
Alignment explanation
Indices: 28181--28274 Score: 75
Period size: 24 Copynumber: 3.9 Consensus size: 24
28171 AAATTAAAAT
* **
28181 AGAATTTAGATCAGTTATCAGAAC
1 AGAATTCAGATCAGAAATCAGAAC
* * *
28205 A-AAATCTAGATCAGAAATTAGAAT
1 AGAATTC-AGATCAGAAATCAGAAC
* *
28229 AGAATTCAGATCATAAATCATAAC
1 AGAATTCAGATCAGAAATCAGAAC
*
28253 AGAATTCAAATACA-AAATCAGA
1 AGAATTCAGAT-CAGAAATCAGA
28275 TAAAACATTC
Statistics
Matches: 54, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
23 3 0.06
24 45 0.83
25 6 0.11
ACGTcount: A:0.51, C:0.13, G:0.12, T:0.24
Consensus pattern (24 bp):
AGAATTCAGATCAGAAATCAGAAC
Found at i:28447 original size:17 final size:16
Alignment explanation
Indices: 28425--28475 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
28415 TATTAGCTGA
28425 CAGAATCATATGTTATT
1 CAGAATCATAT-TTATT
*
28442 CAGAAT-GTGATTTA-T
1 CAGAATCAT-ATTTATT
28457 CAGAATCATATCTTATT
1 CAGAATCATAT-TTATT
28474 CA
1 CA
28476 TACATTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 9 0.32
16 8 0.29
17 11 0.39
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (16 bp):
CAGAATCATATTTATT
Found at i:30419 original size:13 final size:13
Alignment explanation
Indices: 30401--30445 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
30391 TCAGTCGGAT
*
30401 TGGCTCGACTCGG
1 TGGCTCGGCTCGG
*
30414 TGGCTCGGCTTGG
1 TGGCTCGGCTCGG
* *
30427 CGGCTCGGCTCAG
1 TGGCTCGGCTCGG
30440 TGGCTC
1 TGGCTC
30446 ATCAAGCTGC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.04, C:0.31, G:0.40, T:0.24
Consensus pattern (13 bp):
TGGCTCGGCTCGG
Found at i:33868 original size:112 final size:112
Alignment explanation
Indices: 33670--33894 Score: 432
Period size: 112 Copynumber: 2.0 Consensus size: 112
33660 AATAACAAAG
*
33670 ATTTATTTACTTGATTAGATTTTTCATCATAATTTCAACAAAATGTTTGCTACTTTTTCAAACAT
1 ATTTATTTACTTAATTAGATTTTTCATCATAATTTCAACAAAATGTTTGCTACTTTTTCAAACAT
*
33735 TTTATAATGGAAATTTTAATCATAGTTATGTAGGGTTGAAATTTTAT
66 TTTATAATGGAAATTTCAATCATAGTTATGTAGGGTTGAAATTTTAT
33782 ATTTATTTACTTAATTAGATTTTTCATCATAATTTCAACAAAATGTTTGCTACTTTTTCAAACAT
1 ATTTATTTACTTAATTAGATTTTTCATCATAATTTCAACAAAATGTTTGCTACTTTTTCAAACAT
33847 TTTATAATGGAAATTTCAATCATAGTTATGTAGGGTTGAAATTTTAT
66 TTTATAATGGAAATTTCAATCATAGTTATGTAGGGTTGAAATTTTAT
33894 A
1 A
33895 CAATAATAAG
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
112 111 1.00
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.47
Consensus pattern (112 bp):
ATTTATTTACTTAATTAGATTTTTCATCATAATTTCAACAAAATGTTTGCTACTTTTTCAAACAT
TTTATAATGGAAATTTCAATCATAGTTATGTAGGGTTGAAATTTTAT
Found at i:33938 original size:112 final size:111
Alignment explanation
Indices: 33694--33917 Score: 294
Period size: 112 Copynumber: 2.0 Consensus size: 111
33684 TTAGATTTTT
* * *
33694 CATCATAATTTCAACAAAATGTTTGCTACTTTTTCAAACATTTTATAATGGAAATTTTAATCATA
1 CATCATAATGTAAACAAAATGTTTGCTACTTTTTCAAACATTTTATAATGGAAATTTCAATCATA
* * * * * *
33759 GTTATGTAGGGTTGAAATTTTATATTTATTTACTTAATTAGATTTTT
66 GTTATGTAGGGTTGAAATTTTATA-TCATATACATAATGAGATTATA
* *
33806 CATCATAATTTCAACAAAATGTTTGCTACTTTTTCAAACATTTTATAATGGAAATTTCAATCATA
1 CATCATAATGTAAACAAAATGTTTGCTACTTTTTCAAACATTTTATAATGGAAATTTCAATCATA
33871 GTTATGTAGGGTTGAAATTTTATA-CA-ATA-ATAAGTGAG-TTCATA
66 GTTATGTAGGGTTGAAATTTTATATCATATACATAA-TGAGATT-ATA
33915 CAT
1 CAT
33918 TCTACATGTA
Statistics
Matches: 103, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
108 5 0.05
109 9 0.09
110 1 0.01
112 88 0.85
ACGTcount: A:0.36, C:0.10, G:0.11, T:0.43
Consensus pattern (111 bp):
CATCATAATGTAAACAAAATGTTTGCTACTTTTTCAAACATTTTATAATGGAAATTTCAATCATA
GTTATGTAGGGTTGAAATTTTATATCATATACATAATGAGATTATA
Found at i:41444 original size:18 final size:18
Alignment explanation
Indices: 41423--41476 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 18
41413 TGCCTTCATT
* *
41423 TATTTAATCTCTTTTTAC
1 TATTAAATCTCATTTTAC
41441 TATTAAATCTCATTTTAC
1 TATTAAATCTCATTTTAC
41459 TATTAAATCTCATTTTAC
1 TATTAAATCTCATTTTAC
41477 CAAAATTCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.30, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TATTAAATCTCATTTTAC
Found at i:47462 original size:18 final size:19
Alignment explanation
Indices: 47439--47477 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
47429 GTGAACAGAT
47439 AAGCCAAGCC-ACTGAGTC
1 AAGCCAAGCCGACTGAGTC
47457 AAGCCAAGCCGACTGAGTC
1 AAGCCAAGCCGACTGAGTC
47476 AA
1 AA
47478 CCTACATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.36, C:0.31, G:0.23, T:0.10
Consensus pattern (19 bp):
AAGCCAAGCCGACTGAGTC
Found at i:50459 original size:87 final size:86
Alignment explanation
Indices: 50325--50609 Score: 390
Period size: 87 Copynumber: 3.2 Consensus size: 86
50315 CTTACAGACT
* * * * * * *
50325 TAAGAATATCCTTGGGTAGGTATATTGACCCCAGGCATATCCTTAGGTTGGTTTCCTTTGGTGTG
1 TAAGGATACCCTTGGGTAGGCA-ATAGGCCCAAGGCATATCCTTAGGTTGG-TTCCTTTGCTGTG
*
50390 TACTTAAGGTAACCCTACGGATC
64 TGCTTAAGGTAACCCTACGGATC
50413 TAAGGATACCCTTGGGTAGGCAATAGGCCCAAGGCATATCCTTAGGTTGGCTTCCTTTGCTGTGT
1 TAAGGATACCCTTGGGTAGGCAATAGGCCCAAGGCATATCCTTAGGTTGG-TTCCTTTGCTGTGT
*
50478 GCTTAAGGTAACTCTACGGATC
65 GCTTAAGGTAACCCTACGGATC
* * * *
50500 TAAGGATACCCTTGAGTAGGCCCATAGGCCCCAAGGCATATCCTTAGGTTGGTTCTCTTTGTTTT
1 TAAGGATACCCTTGGGTAGG-CAATAGG-CCCAAGGCATATCCTTAGGTTGGTTC-CTTTGCTGT
50565 GTGCTTAAGGTAACCCTACGGATC
63 GTGCTTAAGGTAACCCTACGGATC
*
50589 TAAGGATATCCTTGGGTAGGC
1 TAAGGATACCCTTGGGTAGGC
50610 CCGGTAGGCC
Statistics
Matches: 177, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
87 77 0.44
88 29 0.16
89 71 0.40
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (86 bp):
TAAGGATACCCTTGGGTAGGCAATAGGCCCAAGGCATATCCTTAGGTTGGTTCCTTTGCTGTGTG
CTTAAGGTAACCCTACGGATC
Found at i:50560 original size:89 final size:89
Alignment explanation
Indices: 50353--50611 Score: 393
Period size: 89 Copynumber: 2.9 Consensus size: 89
50343 GGTATATTGA
* *
50353 CCCC-AGGCATATCCTTAGGTTGGTT-TCCTTTGGTGTGTACTTAAGGTAACCCTACGGATCTAA
1 CCCCAAGGCATATCCTTAGGTTGGTTCT-CTTTGCTGTGTGCTTAAGGTAACCCTACGGATCTAA
*
50416 GGATACCCTTGGGTAGG-CAATAGG
65 GGATACCCTTGGGTAGGCCCATAGG
*
50440 -CCCAAGGCATATCCTTAGGTTGGCTTC-CTTTGCTGTGTGCTTAAGGTAACTCTACGGATCTAA
1 CCCCAAGGCATATCCTTAGGTTGG-TTCTCTTTGCTGTGTGCTTAAGGTAACCCTACGGATCTAA
*
50503 GGATACCCTTGAGTAGGCCCATAGG
65 GGATACCCTTGGGTAGGCCCATAGG
* *
50528 CCCCAAGGCATATCCTTAGGTTGGTTCTCTTTGTTTTGTGCTTAAGGTAACCCTACGGATCTAAG
1 CCCCAAGGCATATCCTTAGGTTGGTTCTCTTTGCTGTGTGCTTAAGGTAACCCTACGGATCTAAG
*
50593 GATATCCTTGGGTAGGCCC
66 GATACCCTTGGGTAGGCCC
50612 GGTAGGCCTA
Statistics
Matches: 156, Mismatches: 10, Indels: 10
0.89 0.06 0.06
Matches are distributed among these distances:
86 3 0.02
87 68 0.44
88 11 0.07
89 74 0.47
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.31
Consensus pattern (89 bp):
CCCCAAGGCATATCCTTAGGTTGGTTCTCTTTGCTGTGTGCTTAAGGTAACCCTACGGATCTAAG
GATACCCTTGGGTAGGCCCATAGG
Found at i:60280 original size:31 final size:31
Alignment explanation
Indices: 60245--60345 Score: 87
Period size: 31 Copynumber: 3.2 Consensus size: 31
60235 GTAGGTGTTG
*
60245 AACCTATAAAAGGAATTATCAGCAGCGACTA
1 AACCTATAAAAGGAATTACCAGCAGCGACTA
* * *
60276 AACCTACAGAGATAGGAATTACCAGTCAG-TACAA
1 AACCTATA-A-A-AGGAATTACCAG-CAGCGACTA
* * * *
60310 AACGTATATAAGGAATTACCAGCAACGACTG
1 AACCTATAAAAGGAATTACCAGCAGCGACTA
60341 AACCT
1 AACCT
60346 GCTAGAGTCT
Statistics
Matches: 53, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
30 2 0.04
31 25 0.47
32 2 0.04
33 1 0.02
34 20 0.38
35 3 0.06
ACGTcount: A:0.44, C:0.21, G:0.17, T:0.19
Consensus pattern (31 bp):
AACCTATAAAAGGAATTACCAGCAGCGACTA
Found at i:62266 original size:13 final size:14
Alignment explanation
Indices: 62248--62283 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
62238 AAGTCAACGG
62248 GTTGACTCAG-TGA
1 GTTGACTCAGCTGA
*
62261 GTTGACTTAGCTGA
1 GTTGACTCAGCTGA
62275 GTTGACTCA
1 GTTGACTCA
62284 ATGGATCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (14 bp):
GTTGACTCAGCTGA
Found at i:64368 original size:31 final size:32
Alignment explanation
Indices: 64300--64374 Score: 98
Period size: 32 Copynumber: 2.4 Consensus size: 32
64290 GAGGCCTGAG
** *
64300 AGCCTACCCAAGAAAGTTATCGGGGCCACGAA
1 AGCCTACCCAAGAAAAATATCGGGGCCACAAA
* *
64332 AGCCTACCCAAGAAAAATCTTGGGGCCA-AAA
1 AGCCTACCCAAGAAAAATATCGGGGCCACAAA
64363 AGCCTACCCAAG
1 AGCCTACCCAAG
64375 GGTCAGCTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
31 14 0.37
32 24 0.63
ACGTcount: A:0.37, C:0.29, G:0.21, T:0.12
Consensus pattern (32 bp):
AGCCTACCCAAGAAAAATATCGGGGCCACAAA
Found at i:74912 original size:14 final size:14
Alignment explanation
Indices: 74901--74956 Score: 58
Period size: 15 Copynumber: 3.9 Consensus size: 14
74891 GATGACTCGG
74901 ATGAGTTGACTCAA
1 ATGAGTTGACTCAA
*
74915 ATGGGTTGACTCAGA
1 ATGAGTTGACTCA-A
* * *
74930 ACGAGTTGAGTTAA
1 ATGAGTTGACTCAA
74944 ACTGAGTTGACTC
1 A-TGAGTTGACTC
74957 GGTGACTGGA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
14 14 0.44
15 18 0.56
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (14 bp):
ATGAGTTGACTCAA
Found at i:76470 original size:11 final size:11
Alignment explanation
Indices: 76456--76507 Score: 63
Period size: 10 Copynumber: 4.9 Consensus size: 11
76446 ATAATGTGAA
*
76456 ATTTAAGAAAT
1 ATTTTAGAAAT
*
76467 ATTTTATAAA-
1 ATTTTAGAAAT
76477 ATTTTAGAAAT
1 ATTTTAGAAAT
*
76488 ATTTTATAAA-
1 ATTTTAGAAAT
76498 ATTTTAGAAA
1 ATTTTAGAAA
76508 GATTAAAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
10 18 0.51
11 17 0.49
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (11 bp):
ATTTTAGAAAT
Found at i:76479 original size:21 final size:21
Alignment explanation
Indices: 76454--76507 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
76444 AAATAATGTG
*
76454 AAATTTAAGAAATATTTTATA
1 AAATTTTAGAAATATTTTATA
76475 AAATTTTAGAAATATTTTATA
1 AAATTTTAGAAATATTTTATA
76496 AAATTTTAGAAA
1 AAATTTTAGAAA
76508 GATTAAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.43
Consensus pattern (21 bp):
AAATTTTAGAAATATTTTATA
Found at i:79825 original size:627 final size:623
Alignment explanation
Indices: 78982--80241 Score: 1920
Period size: 626 Copynumber: 2.0 Consensus size: 623
78972 ATATAAAAGT
*
78982 TTTAAATATGGTCATTTATTAATAGATTTATAGTGCATGAATGATGGTTCAAATTCAAAACTTTT
1 TTTAAATATGGTCATTTATTAATAGATTTATAGTGCATGAACGATGGTTCAAATTCAAAACTTTT
*
79047 TCTATAATTCGTTATATTTACATTTAGGAATAATTCAACTTGTATTATGATATTTTATGAAGAAT
66 TCTATAATTCGTTATATTTACATTTAGGAATAATTCAACTTGTATTATAATATTTTATGAAGAAT
* * * *
79112 CTTATATATAGTATAAGAACTATTGACATGATTAAAAACTCTATAAAATAATGTCAAACTTAAAA
131 CTTATATATAGCATAAAAACTATTGACATGATTAAAAAATCTATAAAATAATGTCAAACTGAAAA
* *
79177 CAATAATATAAAATGATATGGATGTAAATATATTGTATTCTAAACAATTAAACCACCTAAAATAT
196 CAATAATATAAAATGATATGGATGTAAATATATTGTATTATAAACAATTAAACCAACTAAAATAT
* *
79242 AATAAATTTATATAAATAT-AAAATCATTTATATCGGATTTTGAAATAAATATGTGAATTCTTAA
261 AATAAATTTATATAAATATAAAAATCATTTATATCGAATTTTGAAATAAATATGTGAATTATTAA
* * *
79306 CTTTTAGTTAAATGTAACCGATTAAAATTCTTTCGATGTAAAAGGGTTAT-TATTAAAATCCAAC
326 CTTTAAGTTAAATGTAACAGATTAAAATTCTTTCAATGTAAAAGGGTTATCT-TTAAAATCCAAC
*
79370 CACATTGTATCTGTTTGAACAAACTTTGAATGTTTAGGAAAAAATAGAAATATCACTATGTTATC
390 CACATTGTATCTGTTTGAACAAACTTTGAATGTTTA--AAAAAATAGAAATATCACTATGATATC
* * * * *
79435 CAAGTTTATAAATATATCCATCAACCCATTGAAAGAACAAAT-TAAAACTTTGTTTCAACATTTA
453 AAAGTTTATAAATATATCCATCAACCCATGGAAAGAAC-AATGTAAAACCTTATTTCAACATTCA
* *
79499 AATGGCTAGTTTGAAAGTTTTATTTTTGTTTTCCCTATATGTTATGTTCGTGGTTTTGATATCTA
517 AATGGCTAGTTTCAAAGTTTTATTTTTGTTTTCCCTATATGTTATGTTCGTGGTTTTAATATC-A
*
79564 -CAGTACGTTCACTTCATCCATTTTCAATATCTCATCAAATGA
581 GCAATACGTTCACTTCATCCATTTTCAATATCTCATCAAATGA
* *
79606 TTTAAATATGGTCATTTATTGATAGATTTATAGTGCATTAACGATGGTTCAAATTCAAAAC-TTT
1 TTTAAATATGGTCATTTATTAATAGATTTATAGTGCATGAACGATGGTTCAAATTCAAAACTTTT
* * *
79670 TCTATACTTGGTTATATTTACATTTAGGAATAATTTAACTTGTATTATAATATTTTATGAAGAAT
66 TCTATAATTCGTTATATTTACATTTAGGAATAATTCAACTTGTATTATAATATTTTATGAAGAAT
* *
79735 CTTATATATATATAGCATAAAAACTATTGACGTGATTAAAAAATCTATAAAATATTGTCAAACTG
131 C---T-TATATATAGCATAAAAACTATTGACATGATTAAAAAATCTATAAAATAATGTCAAACTG
* * *
79800 AAAACAATAATATAAAATGATATGGATGTAAATATGTTGTATTATAAACAATTAAACCAACTGAC
192 AAAACAATAATATAAAATGATATGGATGTAAATATATTGTATTATAAACAATTAAACCAACTAAA
79865 ATATAATAAATTTATATAAATATAAAAATCATTTATATCGAATTTTGAAATAAATATGTGAATTA
257 ATATAATAAATTTATATAAATATAAAAATCATTTATATCGAATTTTGAAATAAATATGTGAATTA
* * *
79930 TTAAGTTTAAGTTGATTGTAACAGATTAAAATTCTTTCAATGTAAAAGGGTTATCTTTAAAATCC
322 TTAACTTTAAGTTAAATGTAACAGATTAAAATTCTTTCAATGTAAAAGGGTTATCTTTAAAATCC
* * * * **
79995 AACCATATTGTATCTTTTTTAACAAACTTTGAATGTTTATAAAAATAGAAATATCGGTATGATAT
387 AACCACATTGTATCTGTTTGAACAAACTTTGAATGTTTAAAAAAATAGAAATATCACTATGATAT
* * * *
80060 CAAAGTTTATAAATATATCCATCAACCCATGGAAAGGACATTGTGAAACCTTATTTCAATATTCA
452 CAAAGTTTATAAATATATCCATCAACCCATGGAAAGAACAATGTAAAACCTTATTTCAACATTCA
* * **
80125 AATGGCTAGTTTCAATGTTTTCTTTTTGTTTTTTCTATATGTTATGTTCGTGGTTTTAATATCAG
517 AATGGCTAGTTTCAAAGTTTTATTTTTGTTTTCCCTATATGTTATGTTCGTGGTTTTAATATCAG
* * *
80190 CAATATGTTCACTTTATCCATTTTCAATATCTCATCAAGTGA
582 CAATACGTTCACTTCATCCATTTTCAATATCTCATCAAATGA
*
80232 TTGAAA-ATGG
1 TTTAAATATGG
80242 AGCGAAAGTA
Statistics
Matches: 575, Mismatches: 53, Indels: 15
0.89 0.08 0.02
Matches are distributed among these distances:
623 65 0.11
624 58 0.10
625 7 0.01
626 176 0.31
627 136 0.24
628 132 0.23
629 1 0.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (623 bp):
TTTAAATATGGTCATTTATTAATAGATTTATAGTGCATGAACGATGGTTCAAATTCAAAACTTTT
TCTATAATTCGTTATATTTACATTTAGGAATAATTCAACTTGTATTATAATATTTTATGAAGAAT
CTTATATATAGCATAAAAACTATTGACATGATTAAAAAATCTATAAAATAATGTCAAACTGAAAA
CAATAATATAAAATGATATGGATGTAAATATATTGTATTATAAACAATTAAACCAACTAAAATAT
AATAAATTTATATAAATATAAAAATCATTTATATCGAATTTTGAAATAAATATGTGAATTATTAA
CTTTAAGTTAAATGTAACAGATTAAAATTCTTTCAATGTAAAAGGGTTATCTTTAAAATCCAACC
ACATTGTATCTGTTTGAACAAACTTTGAATGTTTAAAAAAATAGAAATATCACTATGATATCAAA
GTTTATAAATATATCCATCAACCCATGGAAAGAACAATGTAAAACCTTATTTCAACATTCAAATG
GCTAGTTTCAAAGTTTTATTTTTGTTTTCCCTATATGTTATGTTCGTGGTTTTAATATCAGCAAT
ACGTTCACTTCATCCATTTTCAATATCTCATCAAATGA
Done.