Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001797.1 Hibiscus syriacus cultivar Beakdansim tig00003632_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: 157587
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8496 original size:6 final size:6
Alignment explanation
Indices: 8485--8581 Score: 167
Period size: 6 Copynumber: 16.2 Consensus size: 6
8475 TTAAGCATAC
8485 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
* * *
8533 ATACAT ATACAT ATACAT ATACAT ATACAT GTACAT GTACAT GTACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
8581 A
1 A
8582 CACCTATGGG
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 89 1.00
ACGTcount: A:0.47, C:0.16, G:0.03, T:0.33
Consensus pattern (6 bp):
ATACAT
Found at i:12300 original size:12 final size:12
Alignment explanation
Indices: 12283--12307 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12273 ATATTTTTAG
12283 TAAAATATTATT
1 TAAAATATTATT
12295 TAAAATATTATT
1 TAAAATATTATT
12307 T
1 T
12308 TTTATAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAAAATATTATT
Found at i:19414 original size:18 final size:18
Alignment explanation
Indices: 19391--19425 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19381 GATTAGACTC
19391 AAAATAATATATTTATTA
1 AAAATAATATATTTATTA
* *
19409 AAAATATTATTTTTATT
1 AAAATAATATATTTATT
19426 CAATAAAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AAAATAATATATTTATTA
Found at i:22507 original size:22 final size:22
Alignment explanation
Indices: 22482--22538 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
22472 ATATACAAGC
22482 TACAAAGTGAACCTACAGATGA
1 TACAAAGTGAACCTACAGATGA
*
22504 TACAAAGTGAACCTACAGATGG
1 TACAAAGTGAACCTACAGATGA
* *
22526 GACAAAATGAACC
1 TACAAAGTGAACC
22539 CACAAAGTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.46, C:0.19, G:0.19, T:0.16
Consensus pattern (22 bp):
TACAAAGTGAACCTACAGATGA
Found at i:24421 original size:106 final size:106
Alignment explanation
Indices: 24145--24840 Score: 1194
Period size: 106 Copynumber: 6.5 Consensus size: 106
24135 CGAATGAAAT
24145 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
1 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
* * **
24210 TTCGCTGTGAAGTTGAAATTGACTCTGGAATTGGGAAGTTG
66 TTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAAAAGTTG
* *
24251 TTTTTTTTTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAAT
1 ----TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
24316 ATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAAAAGTTG
62 ATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAAAAGTTG
*
24361 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGATTCCAATATCC
1 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
*
24426 TTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG
66 TTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAAAAGTTG
*
24467 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCC
1 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
24532 TTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAAAAGTTG
66 TTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAAAAGTTG
*
24573 TTTGTTGACAACCAGCGGTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
1 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
*
24638 TTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG
66 TTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAAAAGTTG
* * *
24679 TTTGTTGACAACCAGTGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCC
1 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
* *
24744 TTCACTGTGAAGTTAAAATTGGCTCTGAAATTGAAAAGTTG
66 TTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAAAAGTTG
* *
24785 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTCGAGT
1 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
24841 GGCACGATAT
Statistics
Matches: 559, Mismatches: 27, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
106 459 0.82
110 100 0.18
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (106 bp):
TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
TTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAAAAGTTG
Found at i:25384 original size:17 final size:19
Alignment explanation
Indices: 25351--25386 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
25341 TGTTGAATCC
25351 CCAAATAATGCCCCAATAT
1 CCAAATAATGCCCCAATAT
25370 CCAAA-AATG-CCCAATAT
1 CCAAATAATGCCCCAATAT
25387 TTGATATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 4 0.24
19 5 0.29
ACGTcount: A:0.44, C:0.31, G:0.06, T:0.19
Consensus pattern (19 bp):
CCAAATAATGCCCCAATAT
Found at i:26509 original size:8 final size:7
Alignment explanation
Indices: 26497--26567 Score: 61
Period size: 8 Copynumber: 9.1 Consensus size: 7
26487 TGATTTTTGC
26497 TCTTTTT
1 TCTTTTT
26504 TCCTTTTGT
1 T-CTTTT-T
*
26513 TCTTGTT
1 TCTTTTT
26520 TCTCTTTT
1 TCT-TTTT
26528 TCTTTGTT
1 TCTTT-TT
*
26536 TTTTTTT
1 TCTTTTT
26543 TGCTTTTT
1 T-CTTTTT
26551 TGCTTCTTT
1 T-CTT-TTT
26560 TCTTTTT
1 TCTTTTT
26567 T
1 T
26568 GTTCTTGATT
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
7 14 0.26
8 34 0.63
9 6 0.11
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.77
Consensus pattern (7 bp):
TCTTTTT
Found at i:26510 original size:16 final size:17
Alignment explanation
Indices: 26491--26546 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
26481 ACTTTTTGAT
*
26491 TTTTGCTCTTTTTTC-C
1 TTTTGCTCTTGTTTCTC
*
26507 TTTTGTTCTTGTTTCTC
1 TTTTGCTCTTGTTTCTC
* * *
26524 TTTTTCT-TTGTTTTTT
1 TTTTGCTCTTGTTTCTC
26540 TTTTGCT
1 TTTTGCT
26547 TTTTTGCTTC
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
16 26 0.81
17 6 0.19
ACGTcount: A:0.00, C:0.16, G:0.09, T:0.75
Consensus pattern (17 bp):
TTTTGCTCTTGTTTCTC
Found at i:26564 original size:16 final size:16
Alignment explanation
Indices: 26522--26573 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
26512 TTCTTGTTTC
*
26522 TCTTTTTCTTTGTTT-T
1 TCTTTTGCTTT-TTTGT
*
26538 TTTTTTGCTTTTTTGCT
1 TCTTTTGCTTTTTTG-T
26555 TCTTTT-CTTTTTTGT
1 TCTTTTGCTTTTTTGT
26570 TCTT
1 TCTT
26574 GATTGGATCT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 8 0.26
16 17 0.55
17 6 0.19
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (16 bp):
TCTTTTGCTTTTTTGT
Found at i:28460 original size:5 final size:5
Alignment explanation
Indices: 28450--28483 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
28440 GCAAGTGATG
28450 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
28484 GAAAGGTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:29774 original size:22 final size:22
Alignment explanation
Indices: 29749--29805 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
29739 ATATACAAGC
29749 TACAAAGTGAACCTACAGATGA
1 TACAAAGTGAACCTACAGATGA
* *
29771 TACAAAGTGAACCTATAGATGG
1 TACAAAGTGAACCTACAGATGA
*
29793 GACAAAGTGAACC
1 TACAAAGTGAACC
29806 CACAAAGTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.18
Consensus pattern (22 bp):
TACAAAGTGAACCTACAGATGA
Found at i:31823 original size:31 final size:31
Alignment explanation
Indices: 31788--31855 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
31778 TAGTCACTAA
*
31788 TTTTA-AAAACATAAGATATGGTCAGTTTCGT
1 TTTTATAAAAC-TAAGATATGGTCACTTTCGT
** *
31819 TTTTATCTAACTAAGATGTGGTCACTTTCGT
1 TTTTATAAAACTAAGATATGGTCACTTTCGT
31850 TTTTAT
1 TTTTAT
31856 TTAATAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 29 0.91
32 3 0.09
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.46
Consensus pattern (31 bp):
TTTTATAAAACTAAGATATGGTCACTTTCGT
Found at i:31871 original size:31 final size:31
Alignment explanation
Indices: 31806--31874 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
31796 ACATAAGATA
* *
31806 TGGTCAGTTTCGTTTTTATCTAACTAAGATG
1 TGGTCACTTTCGTTTTTATCTAACTAAGACG
*
31837 TGGTCACTTTCGTTTTTATTTAA-TAAAGACG
1 TGGTCACTTTCGTTTTTATCTAACT-AAGACG
31868 TGGTCAC
1 TGGTCAC
31875 CCCGAGTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 1 0.03
31 33 0.97
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.43
Consensus pattern (31 bp):
TGGTCACTTTCGTTTTTATCTAACTAAGACG
Found at i:33061 original size:24 final size:23
Alignment explanation
Indices: 33034--33079 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
33024 TCAAGAGTGA
*
33034 TTATAAGGTAATATATGTTTTTTC
1 TTATAAGGTAATAT-TATTTTTTC
33058 TTATAAGGTAATATTATTTTTT
1 TTATAAGGTAATATTATTTTTT
33080 AGATAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (23 bp):
TTATAAGGTAATATTATTTTTTC
Found at i:33085 original size:22 final size:24
Alignment explanation
Indices: 33036--33085 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
33026 AAGAGTGATT
* **
33036 ATAAGGTAATATATGTTTTTTCTT
1 ATAAGGTAATATATATTTTTTCAG
33060 ATAAGGTAATAT-TATTTTTT-AG
1 ATAAGGTAATATATATTTTTTCAG
33082 ATAA
1 ATAA
33086 ATTACACATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 4 0.17
23 7 0.30
24 12 0.52
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (24 bp):
ATAAGGTAATATATATTTTTTCAG
Found at i:37654 original size:80 final size:80
Alignment explanation
Indices: 37499--37654 Score: 172
Period size: 80 Copynumber: 1.9 Consensus size: 80
37489 TAAAGTGTCT
* * * * *
37499 AATAATAACAAAATCGGTAGAAAAAATAATGTTTTAGATAACGTTTTACCATATATGTTAACAAA
1 AATAATAACAAAATCAGTAGAAAAAATAATATTTTAGATAAAGTTTTACCATATATGATAAAAAA
* *
37564 ACTAATAAAATACCC
66 AATAACAAAATACCC
* * * * *
37579 AATAATAACAAAA-CAAGTAGAAATAATAATATTTTCGATAAATTTTTA-CTTATTTTGATAAAA
1 AATAATAACAAAATC-AGTAGAAAAAATAATATTTTAGATAAAGTTTTACCATA-TATGATAAAA
37642 AAAATAACAAAAT
64 AAAATAACAAAAT
37655 CGATAACGTC
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
79 4 0.06
80 58 0.94
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.31
Consensus pattern (80 bp):
AATAATAACAAAATCAGTAGAAAAAATAATATTTTAGATAAAGTTTTACCATATATGATAAAAAA
AATAACAAAATACCC
Found at i:38048 original size:31 final size:31
Alignment explanation
Indices: 38004--38069 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
37994 ATTATTATTT
38004 TTTATCAAATTATTATAAAATAATCA-TACAA
1 TTTATCAAATTATTATAAAATAATCATTA-AA
* *
38035 TTTATCGAGTTATTATAAAATAATCATTAAA
1 TTTATCAAATTATTATAAAATAATCATTAAA
38066 TTTA
1 TTTA
38070 ATTATCGTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 30 0.94
32 2 0.06
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (31 bp):
TTTATCAAATTATTATAAAATAATCATTAAA
Found at i:42110 original size:8 final size:8
Alignment explanation
Indices: 42097--42137 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
42087 CTCATTTTCA
42097 GAGAATTT
1 GAGAATTT
42105 GAGAATTT
1 GAGAATTT
*
42113 -AGAGTTT
1 GAGAATTT
*
42120 GGGAATTT
1 GAGAATTT
42128 GAGAATTT
1 GAGAATTT
42136 GA
1 GA
42138 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:42436 original size:128 final size:128
Alignment explanation
Indices: 42208--42964 Score: 1399
Period size: 128 Copynumber: 5.9 Consensus size: 128
42198 TAATCGGAGT
*
42208 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATGTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
42273 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
42336 ACTATTCACATGAAGGCGCGTTCCAGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
42401 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTT
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *
42464 ACTATTCACATGAATGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
42529 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
42592 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
42657 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* ***
42720 TC-AGGGGACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
1 ACTA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
42784 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
65 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *
42848 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCATAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
42913 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
42965 AATCAGGTAA
Statistics
Matches: 608, Mismatches: 19, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
127 1 0.00
128 606 1.00
129 1 0.00
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:43426 original size:33 final size:34
Alignment explanation
Indices: 43365--43464 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 34
43355 AAATTTAATG
*
43365 TTAAATTTTGAATATTATAATTTATATTTTAAAT
1 TTAAATTTTGAATAATATAATTTATATTTTAAAT
* * * *
43399 TTAAA-TTTGAATAATATTATTTTTATTTTTATT
1 TTAAATTTTGAATAATATAATTTATATTTTAAAT
*
43432 TTAAATTTTGAATAATATAATTTGTATTTTAAA
1 TTAAATTTTGAATAATATAATTTATATTTTAAA
43465 AACATTTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.50
34 28 0.50
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (34 bp):
TTAAATTTTGAATAATATAATTTATATTTTAAAT
Found at i:44028 original size:21 final size:21
Alignment explanation
Indices: 43975--44047 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
43965 TATGGTATAA
*
43975 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
43996 AA-CCTGGAGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
44017 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
44038 AACCCTGCGG
1 AACCCTGCGG
44048 AGATGGCATA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
20 3 0.07
21 40 0.87
22 3 0.07
ACGTcount: A:0.22, C:0.26, G:0.34, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:44077 original size:21 final size:21
Alignment explanation
Indices: 44051--44098 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
44041 CCTGCGGAGA
*
44051 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
44072 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
44093 GGGCAT
1 TGGCAT
44099 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:45870 original size:35 final size:31
Alignment explanation
Indices: 45825--45913 Score: 88
Period size: 31 Copynumber: 2.7 Consensus size: 31
45815 TTAATAATTC
*
45825 TAAATAAATAATAATTATATAAATATTATTTTTAA
1 TAAAAAAATAATAATTATATAAATA-TA---TTAA
* *
45860 TAAAAAAATAATATTTACATAAATATATTAA
1 TAAAAAAATAATAATTATATAAATATATTAA
* * *
45891 TATAAAAATAATAACTATTTAAA
1 TAAAAAAATAATAATTATATAAA
45914 AAAATACTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
31 22 0.48
34 2 0.04
35 22 0.48
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.39
Consensus pattern (31 bp):
TAAAAAAATAATAATTATATAAATATATTAA
Found at i:45929 original size:33 final size:34
Alignment explanation
Indices: 45859--45934 Score: 95
Period size: 33 Copynumber: 2.3 Consensus size: 34
45849 ATTATTTTTA
* * *
45859 ATAAAAA-AATAATATTTACATAAATATATTAAT
1 ATAAAAATAATAATATTTACATAAAAATACTAAC
45892 ATAAAAATAATAACTATTTA-A-AAAAATACTAAC
1 ATAAAAATAATAA-TATTTACATAAAAATACTAAC
45925 ATAAAAATAA
1 ATAAAAATAA
45935 ATTTCTTACC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 26 0.68
34 6 0.16
35 6 0.16
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.30
Consensus pattern (34 bp):
ATAAAAATAATAATATTTACATAAAAATACTAAC
Found at i:54150 original size:10 final size:11
Alignment explanation
Indices: 54137--54214 Score: 74
Period size: 12 Copynumber: 7.3 Consensus size: 11
54127 ATTAACTAAA
54137 ATTAT-TATAT
1 ATTATATATAT
*
54147 ATTAAATAT-T
1 ATTATATATAT
*
54157 A-TATATACAT
1 ATTATATATAT
54167 A-TATATATAT
1 ATTATATATAT
54177 ATATATATATAT
1 AT-TATATATAT
54189 ATATATATATAT
1 AT-TATATATAT
* *
54201 ATTAAATACAT
1 ATTATATATAT
54212 ATT
1 ATT
54215 TTAAGCTCAA
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
9 5 0.09
10 17 0.29
11 13 0.22
12 23 0.40
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (11 bp):
ATTATATATAT
Found at i:54161 original size:2 final size:2
Alignment explanation
Indices: 54142--54202 Score: 90
Period size: 2 Copynumber: 31.5 Consensus size: 2
54132 CTAAAATTAT
* *
54142 TA TA TA T- TA AA TA T- TA TA TA TA CA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
54182 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
54203 TAAATACATA
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
1 2 0.04
2 51 0.96
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:57334 original size:471 final size:470
Alignment explanation
Indices: 56192--57571 Score: 2041
Period size: 471 Copynumber: 2.9 Consensus size: 470
56182 TGGTAGAACT
* * * * * *
56192 TATACGGTGGGAGACGCCAGCGGTTGGCGTGTCCCGACAGGAAATGATGATTTGTATGATGATTG
1 TATACGGTGGGAGACTCCACCGGTTGGCGAGTCCCTACCGGAAAT-ATGATTTTTATGATGATTG
* **
56257 GAACGACAACAAGGATTTCTTTGTTGGGGATGTTCTATGTGAGTCGCTTAGCTCAAAATCTAA-C
65 GAACGACAACAAGGATTTCTATGTTGGGGATGTTCTATGTGAGTATCTTAGCTCAAAATCTAACC
* * * * * * ** *
56321 -A---TGAATTTGATCATTA-G-AGTACGCATGTATTTACTATTTATTGTCTACTGGTGCGTGTT
130 TATTCTTAATTGGATCATTAGGTAGTA--CATATA-TGA--ATGT-TGGT-T--T--TGTATGTG
*
56380 TTTTGCAGTGTTCAACTTCACCACGGGGCAACATGATGTCCTGGAGGTGACCGAGGCCGATTATG
184 ATTT-CAGTGTTCAACTTCACCACGGGGCAACATGATGTCCTGGAGGTGACCGAGGCCGATTATG
* * * *
56445 ACAACTGCAACGCTGCCAATCCGATATCTAATGTGACCAATGGACCGACGAGGATTACCCTCGAC
248 ACAACTGCAACGCTGCCAATCCGATATCTAATGTGACCAATGGACCGGCGAGAATCACCCTCAAC
* * * * *
56510 AGGACTGGTGATCACTACTTCATTTGCGGTTTCCCCGGTCATTGTGCCGCCGGCCAAAAGCTCAA
313 AGGACCGGTGACCACTACTTCATTTGCGGTTTCCCCGGTCATTGTACCGCCGGCCAAAAGCTGAG
* * * * * * ** * * * *
56575 TGTTGAAGTCAGAAATGGCAACCGCAAC-GGCACTGCT--C-CTACT-CC--TAGACCAAGTCCC
378 TATCGATGT-TGAAACGGCAACCGC-CCTGGCACCACTCCCACAACTCCCGGAACACCAAGCCCC
*
56633 ACCACGCCTGCAACCCCAAGCGGTATGACC
441 ACCACGCCAGCAACCCCAAGCGGTATGACC
56663 TATACGGTGGGAGACTCCACCGGTTGGCGAGTCCCTACCGGAAATATGATTTTTATGATGATTGG
1 TATACGGTGGGAGACTCCACCGGTTGGCGAGTCCCTACCGGAAATATGATTTTTATGATGATTGG
*
56728 AACGACAACAAGGATTTCTATGTTGGGGATGTTCTATGTGAGTATCTTGGCTCAAAATCTAACCT
66 AACGACAACAAGGATTTCTATGTTGGGGATGTTCTATGTGAGTATCTTAGCTCAAAATCTAACCT
*
56793 ATTCTTAATTGGATCATTGGGTAGTACATATATGAATGTTGGTTTTGTATGTGATTTCAGTGTTC
131 ATTCTTAATTGGATCATTAGGTAGTACATATATGAATGTTGGTTTTGTATGTGATTTCAGTGTTC
56858 AACTTCACCACGGGGCAACATGATGTCCTGGAGGTGACCGAGGCCGATTATGACAACTGCAACGC
196 AACTTCACCACGGGGCAACATGATGTCCTGGAGGTGACCGAGGCCGATTATGACAACTGCAACGC
56923 TGCCAATCCGATATCTAATGTGACCAATGGACCGGCGAGAATCACCCTCAACAGGACCGGTGACC
261 TGCCAATCCGATATCTAATGTGACCAATGGACCGGCGAGAATCACCCTCAACAGGACCGGTGACC
*
56988 ACTACTTCATTTGCGGTTTCCCCGGTCATTGTACCGCAGGCCAAAAGCTGAGTATCGATGTTGAA
326 ACTACTTCATTTGCGGTTTCCCCGGTCATTGTACCGCCGGCCAAAAGCTGAGTATCGATGTTGAA
57053 ACGGCAACCGCCCTGGCACCACTCCCACAACTCCCGGAACACCAAGCCCCACCACGCCAGCAACC
391 ACGGCAACCGCCCTGGCACCACTCCCACAACTCCCGGAACACCAAGCCCCACCACGCCAGCAACC
57118 CCAAGCGGTATGACC
456 CCAAGCGGTATGACC
* *
57133 TATACGGTGGGAGACTCCACCGGTTGGCGAGTACCTACCGGAAATAATGATTTTTACGATGATTG
1 TATACGGTGGGAGACTCCACCGGTTGGCGAGTCCCTACCGGAAAT-ATGATTTTTATGATGATTG
* *
57198 GAACGACAACAAGGATTTCTATGTTGGCGATGTTCTCTGTGAGTATCTTAGCTCAAAATCTAACC
65 GAACGACAACAAGGATTTCTATGTTGGGGATGTTCTATGTGAGTATCTTAGCTCAAAATCTAACC
*
57263 TATTCTTAATTGGATCATTAGGTAGTACATATATGAATGTTGGTTTTGTATATGATTTCAGTGTT
130 TATTCTTAATTGGATCATTAGGTAGTACATATATGAATGTTGGTTTTGTATGTGATTTCAGTGTT
57328 CAACTTCACCACGGGGCAACATGATGTCCTGGAGGTGACCGAGGCCGATTATGACAACTGCAACG
195 CAACTTCACCACGGGGCAACATGATGTCCTGGAGGTGACCGAGGCCGATTATGACAACTGCAACG
*
57393 TTGCCAATCCGATATCTAATGTGACCAATGGACCGGCGAGAATCACCCTCAACAGGACCGGTGAC
260 CTGCCAATCCGATATCTAATGTGACCAATGGACCGGCGAGAATCACCCTCAACAGGACCGGTGAC
*
57458 CACTACTTCATTTGCGGTTTCCCGGGTCATTGTACCGCCGGCCAAAAGCTGAGTATCGATGTTGA
325 CACTACTTCATTTGCGGTTTCCCCGGTCATTGTACCGCCGGCCAAAAGCTGAGTATCGATGTTG-
*
57523 AAACGGCAACCGCCCTGGCACCACTCCCACAACACCCGGAACACCAAGC
389 AAACGGCAACCGCCCTGGCACCACTCCCACAACTCCCGGAACACCAAGC
57572 GCCTCCGCAC
Statistics
Matches: 838, Mismatches: 55, Indels: 31
0.91 0.06 0.03
Matches are distributed among these distances:
463 1 0.00
464 20 0.02
465 186 0.22
466 9 0.01
467 4 0.00
468 3 0.00
470 161 0.19
471 378 0.45
472 52 0.06
474 2 0.00
475 17 0.02
476 1 0.00
477 4 0.00
ACGTcount: A:0.26, C:0.25, G:0.24, T:0.26
Consensus pattern (470 bp):
TATACGGTGGGAGACTCCACCGGTTGGCGAGTCCCTACCGGAAATATGATTTTTATGATGATTGG
AACGACAACAAGGATTTCTATGTTGGGGATGTTCTATGTGAGTATCTTAGCTCAAAATCTAACCT
ATTCTTAATTGGATCATTAGGTAGTACATATATGAATGTTGGTTTTGTATGTGATTTCAGTGTTC
AACTTCACCACGGGGCAACATGATGTCCTGGAGGTGACCGAGGCCGATTATGACAACTGCAACGC
TGCCAATCCGATATCTAATGTGACCAATGGACCGGCGAGAATCACCCTCAACAGGACCGGTGACC
ACTACTTCATTTGCGGTTTCCCCGGTCATTGTACCGCCGGCCAAAAGCTGAGTATCGATGTTGAA
ACGGCAACCGCCCTGGCACCACTCCCACAACTCCCGGAACACCAAGCCCCACCACGCCAGCAACC
CCAAGCGGTATGACC
Found at i:58943 original size:42 final size:42
Alignment explanation
Indices: 58896--58975 Score: 160
Period size: 42 Copynumber: 1.9 Consensus size: 42
58886 GATGAATTGT
58896 CACGTTAATACTATGGATAACCATATCAATATCGTGAACTGA
1 CACGTTAATACTATGGATAACCATATCAATATCGTGAACTGA
58938 CACGTTAATACTATGGATAACCATATCAATATCGTGAA
1 CACGTTAATACTATGGATAACCATATCAATATCGTGAA
58976 TTGATACATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.29
Consensus pattern (42 bp):
CACGTTAATACTATGGATAACCATATCAATATCGTGAACTGA
Found at i:61771 original size:18 final size:18
Alignment explanation
Indices: 61748--61782 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
61738 GTGGCATTTT
61748 TTAGGGGTGATACTTGTA
1 TTAGGGGTGATACTTGTA
61766 TTAGGGGTGATACTTGT
1 TTAGGGGTGATACTTGT
61783 GGAGGGGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.20, C:0.06, G:0.34, T:0.40
Consensus pattern (18 bp):
TTAGGGGTGATACTTGTA
Found at i:61790 original size:17 final size:18
Alignment explanation
Indices: 61750--61790 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
61740 GGCATTTTTT
**
61750 AGGGGTGATACTTGTATT
1 AGGGGTGATACTTGTAGG
61768 AGGGGTGATACTTGT-GG
1 AGGGGTGATACTTGTAGG
61785 AGGGGT
1 AGGGGT
61791 TGCCTGGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.20, C:0.05, G:0.44, T:0.32
Consensus pattern (18 bp):
AGGGGTGATACTTGTAGG
Found at i:63937 original size:21 final size:20
Alignment explanation
Indices: 63886--63939 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
63876 TCATCGTTTG
*
63886 CTATTACAGTGCTGAAGTGA
1 CTATTACGGTGCTGAAGTGA
63906 CTATTACGGTGCTGAAGTGA
1 CTATTACGGTGCTGAAGTGA
63926 -TAATTCACGGTGCT
1 CT-ATT-ACGGTGCT
63940 AACGTGGTGG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 1 0.03
20 22 0.71
21 8 0.26
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (20 bp):
CTATTACGGTGCTGAAGTGA
Found at i:68056 original size:7 final size:7
Alignment explanation
Indices: 68041--68078 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
68031 CCACTGTCTG
68041 TCACTGT
1 TCACTGT
*
68048 TCGCTGT
1 TCACTGT
68055 TCACTGT
1 TCACTGT
68062 TCACTGT
1 TCACTGT
*
68069 TCACTAT
1 TCACTGT
68076 TCA
1 TCA
68079 TATCATATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.16, C:0.29, G:0.13, T:0.42
Consensus pattern (7 bp):
TCACTGT
Found at i:71858 original size:26 final size:25
Alignment explanation
Indices: 71827--71883 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
71817 AGACATGTTG
*
71827 TGCATTTTG-TTACTTTTCTTTACAT
1 TGCATTATGATTACTTTT-TTTACAT
* *
71852 TCGCATTATGATTCCTTTTTTTTCAT
1 T-GCATTATGATTACTTTTTTTACAT
71878 TGCATT
1 TGCATT
71884 CACATCAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 6 0.22
26 14 0.52
27 7 0.26
ACGTcount: A:0.16, C:0.18, G:0.09, T:0.58
Consensus pattern (25 bp):
TGCATTATGATTACTTTTTTTACAT
Found at i:73813 original size:106 final size:105
Alignment explanation
Indices: 73628--74920 Score: 2041
Period size: 106 Copynumber: 12.4 Consensus size: 105
73618 ACAGCCTTTT
73628 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
1 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
* *
73693 GAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTCA
66 GAAGGGACCGCTGGTTGTCAACAA-CAACTTCCCAATTTCA
73734 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
1 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
* *
73799 GAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTCA
66 GAAGGGACCGCTGGTTGTCAACAA-CAACTTCCCAATTTCA
73840 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
1 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
* *
73905 GAAGGGACCGCTGGTTGTCAATAATCAACTTCTCAATTTCA
66 GAAGGGACCGCTGGTTGTCAACAA-CAACTTCCCAATTTCA
73946 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
1 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
*
74011 GAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCA
66 GAAGGGACCGCTGGTTGTCAA-CAACAACTTCCCAATTTCA
* *
74052 GAGCCAATTTCAACTTCACAGCGAAGGGTATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
1 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
* *
74117 GAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCA
66 GAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCA
74157 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
1 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
* *
74222 GAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCA
66 GAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCA
**
74257 GAATCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
1 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
*
74322 GAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCA
66 GAAGGGACCGCTGGTTGTCAA-CAACAACTTCCCAATTTCA
* *
74363 GAGCCAATTTCGACTTCACAACGGAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
1 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
*
74428 GAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCA
66 GAAGGGACCGCTGGTTGTCAA-CAACAACTTCCCAATTTCA
* * * * *
74469 GAGCCAATTTCGACTTCACATCGAAGGATATTGGACTCCAGACAACGTATGTTTAACTTCACGAC
1 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
**
74534 GAAGGGACCGCTGGTTGTCAACAA-ATTTTCCCAATTTCA
66 GAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCA
*
74573 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
1 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
* * *
74638 AAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCA
66 GAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCA
74678 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
1 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
* *
74743 GAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCA
66 GAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCA
** * * * *
74778 GAATCAATTTCAACTTCACAACGAAGGATGTTGGACTCGAGACAACACAAGTTCAACTTCACAAC
1 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
* * ** *
74843 GAAGGGACAGCTGGTTGTCAACAAACAATTTCCCGGTTCCA
66 GAAGGGACCGCTGGTTGTCAAC-AACAACTTCCCAATTTCA
* *
74884 GAGCCAATTTCAACTTCACGACGGAGGATATTGGACT
1 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
74921 TGGAACAATG
Statistics
Matches: 1114, Mismatches: 59, Indels: 28
0.93 0.05 0.02
Matches are distributed among these distances:
100 168 0.15
101 6 0.01
102 6 0.01
103 8 0.01
104 101 0.09
105 206 0.18
106 617 0.55
107 2 0.00
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
GAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCA
Found at i:74847 original size:521 final size:523
Alignment explanation
Indices: 73628--74920 Score: 2239
Period size: 521 Copynumber: 2.5 Consensus size: 523
73618 ACAGCCTTTT
73628 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
1 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
* * **
73693 GAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGA
66 GAAGGGACCGCTGCTTGTCAACAA--AA-TT-TC-A-TTCAGAATCAATTTCAACTTCACAACGA
73758 AGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAA
125 AGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAA
* * *
73823 CCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
190 ACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGGAGGATATTGGACTCCAGACAACGC
* *
73888 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAATCAACTTCTCAATTTCAGAGCCAA
255 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAA
73953 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGA
320 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGA
*
74018 CCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGGTAT
385 CCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATAT
*
74083 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTC
450 TGGACTCCAGACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGCTTGTCAACAACAACTTC
74148 CCAATCTCA
515 CCAATCTCA
74157 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
1 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
74222 GAAGGGACCGCTGCTTGTCAACAAAATTTCATTCAGAATCAATTTCAACTTCACAACGAAGGATA
66 GAAGGGACCGCTGCTTGTCAACAAAATTTCATTCAGAATCAATTTCAACTTCACAACGAAGGATA
74287 TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACT
131 TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACT
*
74352 TCCCAATTTCAGAGCCAATTTCGACTTCACAACGGAGGATATTGGACTCCAGACAACGCAAGTTC
196 TCCCAATTTCAGAGCCAATTTCAACTTCACAACGGAGGATATTGGACTCCAGACAACGCAAGTTC
*
74417 AACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCGA
261 AACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAA
* * * *
74482 CTTCACATCGAAGGATATTGGACTCCAGACAACGTATGTTTAACTTCACGACGAAGGGACCGCTG
326 CTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
* **
74547 GTTGTCAA-CAA-ATTTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACT
391 GTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACT
74610 CCAGACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATC
456 CCAGACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATC
74675 TCA
521 TCA
74678 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
1 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
*
74743 GAAGGGACCGCTGCTTGTCAACAAAATTTCATTCAGAATCAATTTCAACTTCACAACGAAGGATG
66 GAAGGGACCGCTGCTTGTCAACAAAATTTCATTCAGAATCAATTTCAACTTCACAACGAAGGATA
* * * * * *
74808 TTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACAGCTGGTTGTCAACAAACAATT
131 TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACT
** * *
74873 TCCCGGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGGACT
196 TCCCAATTTCAGAGCCAATTTCAACTTCACAACGGAGGATATTGGACT
74921 TGGAACAATG
Statistics
Matches: 732, Mismatches: 32, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
521 347 0.47
522 2 0.00
523 289 0.39
524 1 0.00
525 2 0.00
526 2 0.00
527 2 0.00
529 87 0.12
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (523 bp):
GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
GAAGGGACCGCTGCTTGTCAACAAAATTTCATTCAGAATCAATTTCAACTTCACAACGAAGGATA
TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACT
TCCCAATTTCAGAGCCAATTTCAACTTCACAACGGAGGATATTGGACTCCAGACAACGCAAGTTC
AACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAA
CTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
GTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACT
CCAGACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATC
TCA
Found at i:84636 original size:25 final size:25
Alignment explanation
Indices: 84602--84653 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
84592 AAGTCCCTAT
84602 TATCATTAACGGGGACGGAGCTGTA
1 TATCATTAACGGGGACGGAGCTGTA
* *
84627 TATCGTTAACGGGGACGGAGCTTTA
1 TATCATTAACGGGGACGGAGCTGTA
84652 TA
1 TA
84654 GGGGTGCAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.27, C:0.15, G:0.31, T:0.27
Consensus pattern (25 bp):
TATCATTAACGGGGACGGAGCTGTA
Found at i:96149 original size:6 final size:6
Alignment explanation
Indices: 96138--96167 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
96128 CTGGGTTTTC
96138 TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT
1 TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT
96168 GTGTTAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.67
Consensus pattern (6 bp):
TTTCAT
Found at i:99713 original size:29 final size:29
Alignment explanation
Indices: 99621--99713 Score: 75
Period size: 29 Copynumber: 3.2 Consensus size: 29
99611 TTTGGGGAAT
* * *
99621 AGTTTAAGGATGAATTTGGAATGCTCAAA
1 AGTTTATGGATGAATTTAGAATGATCAAA
* *
99650 AGTTTAGTGG-TTAATTTAGAATGA-GAGACA
1 AGTTTA-TGGATGAATTTAGAATGATCA-A-A
* *
99680 A-TTTATGGATGAAATTAGAATGATTAAA
1 AGTTTATGGATGAATTTAGAATGATCAAA
99708 AGTTTA
1 AGTTTA
99714 GGGACCAATT
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
28 6 0.12
29 39 0.78
30 5 0.10
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34
Consensus pattern (29 bp):
AGTTTATGGATGAATTTAGAATGATCAAA
Found at i:104676 original size:12 final size:12
Alignment explanation
Indices: 104661--104692 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
104651 GATTTTGTCC
104661 TTTCATCATTAA
1 TTTCATCATTAA
104673 TTTCATCATTAA
1 TTTCATCATTAA
104685 TTTCATCA
1 TTTCATCA
104693 GATCTGCTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (12 bp):
TTTCATCATTAA
Found at i:117659 original size:17 final size:17
Alignment explanation
Indices: 117639--117683 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 17
117629 GGTAAAACAT
117639 ATTAAATAATAAATATA
1 ATTAAATAATAAATATA
117656 ATT--AT-ATAAATATA
1 ATTAAATAATAAATATA
* *
117670 ATCAAAAAATAAAT
1 ATTAAATAATAAAT
117684 TTGGGGCTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
14 11 0.48
15 2 0.09
16 1 0.04
17 9 0.39
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
ATTAAATAATAAATATA
Found at i:120830 original size:30 final size:30
Alignment explanation
Indices: 120762--120836 Score: 125
Period size: 29 Copynumber: 2.5 Consensus size: 30
120752 CGTCCCTGGG
120762 GGTAGGTCGCCATGCACGCCCAGCGACCTA
1 GGTAGGTCGCCATGCACGCCCAGCGACCTA
**
120792 -CCAGGTCGCCATGCACGCCCAGCGACCTA
1 GGTAGGTCGCCATGCACGCCCAGCGACCTA
120821 GGTAGGTCGCCATGCA
1 GGTAGGTCGCCATGCA
120837 ATCCATGCAG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 27 0.68
30 13 0.32
ACGTcount: A:0.20, C:0.37, G:0.29, T:0.13
Consensus pattern (30 bp):
GGTAGGTCGCCATGCACGCCCAGCGACCTA
Found at i:120908 original size:20 final size:20
Alignment explanation
Indices: 120883--120960 Score: 138
Period size: 20 Copynumber: 3.9 Consensus size: 20
120873 AACACGCTGG
120883 GCATCCGAGGCCATCCGAAA
1 GCATCCGAGGCCATCCGAAA
120903 GCATCCGAGGCCATCCGAAA
1 GCATCCGAGGCCATCCGAAA
*
120923 GCATCCGAGGCCATCCGAGA
1 GCATCCGAGGCCATCCGAAA
*
120943 GCATCCGATGCCATCCGA
1 GCATCCGAGGCCATCCGA
120961 CCGAGGCCAT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.27, C:0.36, G:0.26, T:0.12
Consensus pattern (20 bp):
GCATCCGAGGCCATCCGAAA
Found at i:120974 original size:10 final size:10
Alignment explanation
Indices: 120884--120960 Score: 79
Period size: 10 Copynumber: 7.7 Consensus size: 10
120874 ACACGCTGGG
120884 CATCCGAGGC
1 CATCCGAGGC
*
120894 CATCCGAAAG-
1 CATCCG-AGGC
120904 CATCCGAGGC
1 CATCCGAGGC
*
120914 CATCCGAAAG-
1 CATCCG-AGGC
120924 CATCCGAGGC
1 CATCCGAGGC
120934 CATCCGAGAG-
1 CATCCGAG-GC
*
120944 CATCCGATGC
1 CATCCGAGGC
120954 CATCCGA
1 CATCCGA
120961 CCGAGGCCAT
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
9 5 0.09
10 46 0.82
11 5 0.09
ACGTcount: A:0.27, C:0.36, G:0.25, T:0.12
Consensus pattern (10 bp):
CATCCGAGGC
Found at i:121045 original size:31 final size:32
Alignment explanation
Indices: 121007--121073 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
120997 ACGACCTACC
*
121007 CTCGCTCGGTTG-CTCGGATTCCCTCGCATAG
1 CTCGCTCGGTTGCCTCGGATGCCCTCGCATAG
121038 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGTTG-CCTCGGATGCCCTCGCATAG
121071 CTC
1 CTC
121074 ATTCGGATGG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
31 12 0.36
33 21 0.64
ACGTcount: A:0.09, C:0.39, G:0.25, T:0.27
Consensus pattern (32 bp):
CTCGCTCGGTTGCCTCGGATGCCCTCGCATAG
Found at i:121088 original size:33 final size:33
Alignment explanation
Indices: 121019--121089 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
121009 CGCTCGGTTG
* * *
121019 CTCGGATTCCCTCGCATAGCTCGCTCGGTTGCC
1 CTCGGATGCCCTCGCATAGCTCACTCGGATGCC
* *
121052 CTCGGATGCCCTCGCATAGCTCATTCGGATGGC
1 CTCGGATGCCCTCGCATAGCTCACTCGGATGCC
121085 CTCGG
1 CTCGG
121090 TCGAATGGCC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.11, C:0.37, G:0.27, T:0.25
Consensus pattern (33 bp):
CTCGGATGCCCTCGCATAGCTCACTCGGATGCC
Found at i:121099 original size:14 final size:14
Alignment explanation
Indices: 121080--121112 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
121070 GCTCATTCGG
121080 ATGGCCTCGGTCGA
1 ATGGCCTCGGTCGA
*
121094 ATGGCCTCGGTCGG
1 ATGGCCTCGGTCGA
121108 ATGGC
1 ATGGC
121113 GACCTGGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.12, C:0.27, G:0.39, T:0.21
Consensus pattern (14 bp):
ATGGCCTCGGTCGA
Found at i:125811 original size:23 final size:23
Alignment explanation
Indices: 125784--125838 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
125774 TGAATAATTA
* **
125784 TGTTTTTGTGACATGTTTATCTC
1 TGTTTTTGTGAAACATTTATCTC
125807 TGTTTTTGTGAAACATTTATCTC
1 TGTTTTTGTGAAACATTTATCTC
125830 TGTCTTTTG
1 TGT-TTTTG
125839 GCACTTTTCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 23 0.82
24 5 0.18
ACGTcount: A:0.15, C:0.13, G:0.16, T:0.56
Consensus pattern (23 bp):
TGTTTTTGTGAAACATTTATCTC
Found at i:132071 original size:31 final size:34
Alignment explanation
Indices: 132025--132089 Score: 82
Period size: 31 Copynumber: 2.0 Consensus size: 34
132015 TAAATTTTAA
132025 AAAAGTTAAGAGTTTAAATACTAAA-ATA-GATT
1 AAAAGTTAAGAGTTTAAATACTAAATATATGATT
* **
132057 AAAAG-TAATAGTTTAGGTACTAAATATATGATT
1 AAAAGTTAAGAGTTTAAATACTAAATATATGATT
132090 TATTCGTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 16 0.57
32 8 0.29
33 4 0.14
ACGTcount: A:0.49, C:0.03, G:0.14, T:0.34
Consensus pattern (34 bp):
AAAAGTTAAGAGTTTAAATACTAAATATATGATT
Found at i:134938 original size:13 final size:13
Alignment explanation
Indices: 134915--134963 Score: 62
Period size: 13 Copynumber: 3.5 Consensus size: 13
134905 ATAATAGTCA
134915 ATTATTTAATATTT
1 ATTA-TTAATATTT
134929 ATTATTAATATTT
1 ATTATTAATATTT
*
134942 ATTATTAAATTATTG
1 ATTATT-AA-TATTT
134957 ATTATTA
1 ATTATTA
134964 TCAATTCTGT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 15 0.47
14 7 0.22
15 10 0.31
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (13 bp):
ATTATTAATATTT
Found at i:135564 original size:108 final size:109
Alignment explanation
Indices: 135375--135590 Score: 425
Period size: 108 Copynumber: 2.0 Consensus size: 109
135365 ACCAAATAAC
135375 TTATTTTGATTTGTTAGAACTCGAATCTATTTGAATGGAATATTTATCAAACAATGACCAAATCA
1 TTATTTTGATTTGTTAGAACTCGAATCTATTTGAATGGAATATTTATCAAACAATGACCAAATCA
135440 ATCCTTAAATAGTTTACAATCTATCTCGTCTCA-TTTAAAAAGA
66 ATCCTTAAATAGTTTACAATCTATCTCGTCTCATTTTAAAAAGA
135483 TTATTTTGATTTGTTAGAACTCGAATCTATTTGAATGGAATATTTATCAAACAATGACCAAATCA
1 TTATTTTGATTTGTTAGAACTCGAATCTATTTGAATGGAATATTTATCAAACAATGACCAAATCA
135548 ATCCTTAAATAGTTTACAATCTATCTCGTCTCATTTTAAAAAG
66 ATCCTTAAATAGTTTACAATCTATCTCGTCTCATTTTAAAAAG
135591 CTATAGAGAT
Statistics
Matches: 107, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
108 98 0.92
109 9 0.08
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (109 bp):
TTATTTTGATTTGTTAGAACTCGAATCTATTTGAATGGAATATTTATCAAACAATGACCAAATCA
ATCCTTAAATAGTTTACAATCTATCTCGTCTCATTTTAAAAAGA
Done.