Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001023.1 Hibiscus syriacus cultivar Beakdansim tig00002038_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: 140105
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:13853 original size:38 final size:38
Alignment explanation
Indices: 13802--13877 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
13792 CATACCTCTG
* *
13802 GTTTCTTATCACCTTAATTCTATATTGTACGTATATAT
1 GTTTCTTATCACCTTAATTCTAAATTGTACATATATAT
*
13840 GTTTCTTATCACCTTAATTCTAAATTGTATATATATAT
1 GTTTCTTATCACCTTAATTCTAAATTGTACATATATAT
13878 TTATGGAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.29, C:0.14, G:0.07, T:0.50
Consensus pattern (38 bp):
GTTTCTTATCACCTTAATTCTAAATTGTACATATATAT
Found at i:18316 original size:14 final size:14
Alignment explanation
Indices: 18297--18324 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
18287 GAAAAGAAGC
18297 TATGTGATACGTGA
1 TATGTGATACGTGA
18311 TATGTGATACGTGA
1 TATGTGATACGTGA
18325 ATTACAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (14 bp):
TATGTGATACGTGA
Found at i:18616 original size:147 final size:148
Alignment explanation
Indices: 18425--18737 Score: 574
Period size: 147 Copynumber: 2.1 Consensus size: 148
18415 GAGTCGAGGG
* *
18425 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGA-ATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
18490 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
65 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATATGGTCCTTATGGACATTATTA
18555 TATGGCACTACGGTGCAAT
130 TATGGCACTACGGTGCAAT
18574 TCTACGCGGTCCTTCGGG-ATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATA
1 TCTACGCGGTCCTTCGGGAATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATA
18638 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATATGGTCCTTATGGACATTATTAT
66 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATATGGTCCTTATGGACATTATTAT
18703 ATGGCACTACGGTGCAAT
131 ATGGCACTACGGTGCAAT
*
18721 TCTACGCGGTACTTCGG
1 TCTACGCGGTCCTTCGG
18738 TGCAATTATA
Statistics
Matches: 160, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
147 142 0.89
149 18 0.11
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.35
Consensus pattern (148 bp):
TCTACGCGGTCCTTCGGGAATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATA
CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATATGGTCCTTATGGACATTATTAT
ATGGCACTACGGTGCAAT
Found at i:28919 original size:24 final size:24
Alignment explanation
Indices: 28887--28935 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
28877 CCACCATCTG
28887 ACTCCAAGTTATTGTTACTTTGTT
1 ACTCCAAGTTATTGTTACTTTGTT
28911 ACTCCAAGTTATTGTTACTTTGTT
1 ACTCCAAGTTATTGTTACTTTGTT
28935 A
1 A
28936 AGAAGTGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.16, G:0.12, T:0.49
Consensus pattern (24 bp):
ACTCCAAGTTATTGTTACTTTGTT
Found at i:37085 original size:42 final size:42
Alignment explanation
Indices: 37038--37149 Score: 179
Period size: 42 Copynumber: 2.7 Consensus size: 42
37028 AATTTTCGTG
* * *
37038 TTTGTTTCACGTAATTGGTTTTTCGGAAAATATTTTCCCGTA
1 TTTGTTTCACGTAATTCGTTTTCCGGAAAACATTTTCCCGTA
* *
37080 TTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTCCCGTG
1 TTTGTTTCACGTAATTCGTTTTCCGGAAAACATTTTCCCGTA
37122 TTTGTTTCACGTAATTCGTTTTCCGGAA
1 TTTGTTTCACGTAATTCGTTTTCCGGAA
37150 TGTAATTCAT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.19, C:0.18, G:0.18, T:0.46
Consensus pattern (42 bp):
TTTGTTTCACGTAATTCGTTTTCCGGAAAACATTTTCCCGTA
Found at i:37385 original size:22 final size:23
Alignment explanation
Indices: 37338--37398 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 23
37328 TAATTATTAA
* *
37338 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
37359 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* *
37382 -ATATTTTTAATATTATA
1 AATATTTATAATAATATA
37399 TAAAATAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 11 0.32
22 19 0.56
23 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:37474 original size:29 final size:29
Alignment explanation
Indices: 37364--37457 Score: 85
Period size: 29 Copynumber: 3.4 Consensus size: 29
37354 TTATTAATAT
37364 TTATAATAATAT-A-ATATTATATTTTTA
1 TTATAATAATATAAGATATTATATTTTTA
* * * *
37391 --AT-ATTATATAA-A-ATAATCAATTATA
1 TTATAATAATATAAGATATTAT-ATTTTTA
37416 TTATAATAATATAAGATATTATATTTTTA
1 TTATAATAATATAAGATATTATATTTTTA
*
37445 TTTTAATAATATA
1 TTATAATAATATA
37458 TAATAATTTG
Statistics
Matches: 51, Mismatches: 9, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
24 10 0.20
25 9 0.18
27 2 0.04
28 8 0.16
29 18 0.35
30 4 0.08
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (29 bp):
TTATAATAATATAAGATATTATATTTTTA
Found at i:37482 original size:32 final size:30
Alignment explanation
Indices: 37412--37519 Score: 107
Period size: 30 Copynumber: 3.5 Consensus size: 30
37402 AATAATCAAT
37412 TATATTATAATAATATA-AGATATTATATTTT-
1 TATATT-TAATAATATATA-ATATTAT-TTTTA
*
37443 TAT-TTTAATAATATATAATAATTTGTTTTTA
1 TATATTTAATAATATATAAT-A-TTATTTTTA
*
37474 TATATTTAATAATGA-ATAATATTATTTATA
1 TATATTTAATAAT-ATATAATATTATTTTTA
37504 TATATTTCAATAATAT
1 TATATTT-AATAATAT
37520 TTTAGTAAAG
Statistics
Matches: 66, Mismatches: 3, Indels: 16
0.78 0.04 0.19
Matches are distributed among these distances:
29 12 0.18
30 23 0.35
31 16 0.24
32 14 0.21
33 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (30 bp):
TATATTTAATAATATATAATATTATTTTTA
Found at i:37758 original size:14 final size:15
Alignment explanation
Indices: 37737--37777 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
37727 TTACAGAAAT
37737 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
37752 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
37766 GTAATTCATTTT
1 GTAATTCATTTT
37778 TTGGAAAACC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.44
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:37763 original size:20 final size:20
Alignment explanation
Indices: 37685--37754 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
37675 TTTCCAGATG
37685 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
37705 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
37725 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
37745 TTTTCCAGAA
1 TTTTCCAGAA
37755 TTCAAATTCC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:37763 original size:40 final size:40
Alignment explanation
Indices: 37685--37763 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
37675 TTTCCAGATG
* **
37685 TTTTCCAGAAATGTAATTCATTTTCCAGAAATGTAATTCA
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
*
37725 TTTTACAGAAATGTAATTCATTTTCCAGAATTCAAATTC
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTC
37764 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (40 bp):
TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
Found at i:43868 original size:19 final size:19
Alignment explanation
Indices: 43805--43872 Score: 50
Period size: 19 Copynumber: 3.5 Consensus size: 19
43795 TAAATATGGT
*
43805 TTATATATATTATATT-ATA
1 TTATATATTTTA-ATTAATA
* * *
43824 TTATATTAATCTTAAATATTA
1 TTATA-T-ATTTTAATTAATA
*
43845 ATATATATTTTAATTAATA
1 TTATATATTTTAATTAATA
43864 TTATA-ATTT
1 TTATATATTT
43873 ATGTTATAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
18 4 0.11
19 19 0.50
20 4 0.11
21 11 0.29
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (19 bp):
TTATATATTTTAATTAATA
Found at i:44327 original size:11 final size:11
Alignment explanation
Indices: 44311--44364 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
44301 TGAGGCAGAT
44311 AATTATTTCAA
1 AATTATTTCAA
44322 AATTATTTTCAA
1 AATTA-TTTCAA
* *
44334 GA--ATTTGAA
1 AATTATTTCAA
44343 AA-TATTTTCAA
1 AATTA-TTTCAA
44354 AATTATTTCAA
1 AATTATTTCAA
44365 GCATTGGTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
9 6 0.17
10 2 0.06
11 18 0.51
12 9 0.26
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (11 bp):
AATTATTTCAA
Found at i:44338 original size:81 final size:81
Alignment explanation
Indices: 44251--44454 Score: 408
Period size: 81 Copynumber: 2.5 Consensus size: 81
44241 TTTTAGTTAA
44251 AAGAATTTGAAAATATTTTCAAAATTATTTCAAGCATTGGTTAATGAGGATGAGGCAGATAATTA
1 AAGAATTTGAAAATATTTTCAAAATTATTTCAAGCATTGGTTAATGAGGATGAGGCAGATAATTA
44316 TTTCAAAATTATTTTC
66 TTTCAAAATTATTTTC
44332 AAGAATTTGAAAATATTTTCAAAATTATTTCAAGCATTGGTTAATGAGGATGAGGCAGATAATTA
1 AAGAATTTGAAAATATTTTCAAAATTATTTCAAGCATTGGTTAATGAGGATGAGGCAGATAATTA
44397 TTTCAAAATTATTTTC
66 TTTCAAAATTATTTTC
44413 AAGAATTTGAAAATATTTTCAAAATTATTTCAAGCATTGGTT
1 AAGAATTTGAAAATATTTTCAAAATTATTTCAAGCATTGGTT
44455 GAGCTGGGTA
Statistics
Matches: 123, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 123 1.00
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.39
Consensus pattern (81 bp):
AAGAATTTGAAAATATTTTCAAAATTATTTCAAGCATTGGTTAATGAGGATGAGGCAGATAATTA
TTTCAAAATTATTTTC
Found at i:44350 original size:20 final size:20
Alignment explanation
Indices: 44315--44357 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
44305 GCAGATAATT
44315 ATTTCAAAATTATTTTCAAGA
1 ATTTCAAAATTATTTTCAA-A
*
44336 ATTTGAAAA-TATTTTCAAA
1 ATTTCAAAATTATTTTCAAA
44355 ATT
1 ATT
44358 ATTTCAAGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 9 0.43
21 8 0.38
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (20 bp):
ATTTCAAAATTATTTTCAAA
Found at i:44408 original size:11 final size:11
Alignment explanation
Indices: 44392--44445 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
44382 TGAGGCAGAT
44392 AATTATTTCAA
1 AATTATTTCAA
44403 AATTATTTTCAA
1 AATTA-TTTCAA
* *
44415 GA--ATTTGAA
1 AATTATTTCAA
44424 AA-TATTTTCAA
1 AATTA-TTTCAA
44435 AATTATTTCAA
1 AATTATTTCAA
44446 GCATTGGTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
9 6 0.17
10 2 0.06
11 18 0.51
12 9 0.26
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (11 bp):
AATTATTTCAA
Found at i:44431 original size:20 final size:20
Alignment explanation
Indices: 44396--44438 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
44386 GCAGATAATT
44396 ATTTCAAAATTATTTTCAAGA
1 ATTTCAAAATTATTTTCAA-A
*
44417 ATTTGAAAA-TATTTTCAAA
1 ATTTCAAAATTATTTTCAAA
44436 ATT
1 ATT
44439 ATTTCAAGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 9 0.43
21 8 0.38
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (20 bp):
ATTTCAAAATTATTTTCAAA
Found at i:50079 original size:8 final size:8
Alignment explanation
Indices: 50068--50121 Score: 74
Period size: 8 Copynumber: 6.8 Consensus size: 8
50058 AAAAAATAAT
50068 TTAAAATA
1 TTAAAATA
50076 TTAAAATA
1 TTAAAATA
*
50084 TTAAAAAA
1 TTAAAATA
*
50092 TTAAAATC
1 TTAAAATA
50100 TATAAAATA
1 T-TAAAATA
50109 TTAAAATA
1 TTAAAATA
50117 -TAAAA
1 TTAAAA
50122 AAAAATAGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
7 5 0.12
8 29 0.71
9 7 0.17
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (8 bp):
TTAAAATA
Found at i:50081 original size:33 final size:31
Alignment explanation
Indices: 50039--50126 Score: 88
Period size: 33 Copynumber: 2.7 Consensus size: 31
50029 TTTTATCTTT
*
50039 AAAT-TTAAAAAATAAAAATAAAAAATAATTTA
1 AAATATTAAAAAATAAAAA-AAAAAAT-ATATA
* * *
50071 AAATATTAAAATATTAAAAAATTAAAATCTATA
1 AAATATTAAAA-AATAAAAAA-AAAAATATATA
*
50104 AAATATTAAAATATAAAAAAAAA
1 AAATATTAAAAAATAAAAAAAAA
50127 TAGAATACCT
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
31 2 0.04
32 11 0.24
33 21 0.46
34 12 0.26
ACGTcount: A:0.70, C:0.01, G:0.00, T:0.28
Consensus pattern (31 bp):
AAATATTAAAAAATAAAAAAAAAAATATATA
Found at i:50122 original size:8 final size:8
Alignment explanation
Indices: 50039--50122 Score: 57
Period size: 8 Copynumber: 10.4 Consensus size: 8
50029 TTTTATCTTT
*
50039 AAATTTAA
1 AAATATAA
50047 AAA-ATAA
1 AAATATAA
50054 AAATA-AA
1 AAATATAA
*
50061 AAATAATTTA
1 AAAT-A-TAA
*
50071 AAATATTA
1 AAATATAA
50079 AAATATTAA
1 AAATA-TAA
*
50088 AAA-ATTA
1 AAATATAA
*
50095 AAATCTATA
1 AAATATA-A
*
50104 AAATATTA
1 AAATATAA
50112 AAATATAA
1 AAATATAA
50120 AAA
1 AAA
50123 AAAATAGAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
7 17 0.28
8 26 0.43
9 12 0.20
10 5 0.08
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (8 bp):
AAATATAA
Found at i:50123 original size:17 final size:17
Alignment explanation
Indices: 50070--50123 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
50060 AAAATAATTT
*
50070 AAAATATTAAAATATTA
1 AAAATATTAAAATATAA
* *
50087 AAAA-ATTAAAATCTAT
1 AAAATATTAAAATATAA
50103 AAAATATTAAAATATAA
1 AAAATATTAAAATATAA
50120 AAAA
1 AAAA
50124 AAATAGAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
16 13 0.42
17 18 0.58
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAATATTAAAATATAA
Found at i:50426 original size:7 final size:8
Alignment explanation
Indices: 50410--50562 Score: 70
Period size: 8 Copynumber: 18.8 Consensus size: 8
50400 TTTTGATTTT
50410 TTTTATAA
1 TTTTATAA
50418 TTTTA-AA
1 TTTTATAA
*
50425 -TTTATCA
1 TTTTATAA
50432 TTTTATAGA
1 TTTTATA-A
* **
50441 TTTTGTTT
1 TTTTATAA
*
50449 TTTTAAAA
1 TTTTATAA
50457 TTTT-TAA
1 TTTTATAA
*
50464 TTTTATAT
1 TTTTATAA
50472 TTATTATTTAA
1 TT-TTA--TAA
50483 TTTTTATATA
1 -TTTTATA-A
* *
50493 TTTAATAG
1 TTTTATAA
50501 TGTTT-TAA
1 T-TTTATAA
*
50509 TTTTTGTAA
1 -TTTTATAA
50518 TTTTAT-A
1 TTTTATAA
50525 TTTTA-AA
1 TTTTATAA
50532 TTTTA-AA
1 TTTTATAA
50539 TTTTAAATAA
1 TTTT--ATAA
50549 TTTCT-TAA
1 TTT-TATAA
50557 TTTTAT
1 TTTTAT
50563 TTTATTTTCT
Statistics
Matches: 110, Mismatches: 17, Indels: 36
0.67 0.10 0.22
Matches are distributed among these distances:
6 4 0.04
7 28 0.25
8 40 0.36
9 24 0.22
10 6 0.05
11 6 0.05
12 2 0.02
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.63
Consensus pattern (8 bp):
TTTTATAA
Found at i:50480 original size:14 final size:15
Alignment explanation
Indices: 50450--50499 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 15
50440 ATTTTGTTTT
* *
50450 TTTAAAATTTTTA-A
1 TTTAATATTTATATA
*
50464 TTTTATATTTAT-TA
1 TTTAATATTTATATA
*
50478 TTTAATTTTTATATA
1 TTTAATATTTATATA
50493 TTTAATA
1 TTTAATA
50500 GTGTTTTAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
14 20 0.71
15 8 0.29
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTAATATTTATATA
Found at i:50535 original size:14 final size:14
Alignment explanation
Indices: 50516--50546 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
50506 TAATTTTTGT
*
50516 AATTTTATATTTTA
1 AATTTTAAATTTTA
50530 AATTTTAAATTTTA
1 AATTTTAAATTTTA
50544 AAT
1 AAT
50547 AATTTCTTAA
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
AATTTTAAATTTTA
Found at i:50955 original size:60 final size:60
Alignment explanation
Indices: 50874--51006 Score: 151
Period size: 60 Copynumber: 2.2 Consensus size: 60
50864 AAGGGTAAAG
* * * * *
50874 TATATAAATGGTCCTTTGACTAT-GTAATACTACTTTGTTGAGTCCCTCGAATATTAGAAGT
1 TATA-AAATGGTCCTTCGACTATAGGAAGA-TACTTTGTTGAGTCCCTCGAATATTAAAAAT
** * * *
50935 TATAAAATGGTCCTTCGACTATAGGGCGATGCTTTGTTGAGTCCCTTGACTATTAAAAAT
1 TATAAAATGGTCCTTCGACTATAGGAAGATACTTTGTTGAGTCCCTCGAATATTAAAAAT
50995 TATAAAATGGTC
1 TATAAAATGGTC
51007 ACTCGATTAT
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
60 55 0.90
61 6 0.10
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (60 bp):
TATAAAATGGTCCTTCGACTATAGGAAGATACTTTGTTGAGTCCCTCGAATATTAAAAAT
Found at i:58448 original size:4 final size:4
Alignment explanation
Indices: 58439--58466 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
58429 AATATAAATT
58439 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
58467 AAAATAATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:65160 original size:13 final size:14
Alignment explanation
Indices: 65134--65162 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
65124 ATCATAAATT
65134 TTATATGCTATATA
1 TTATATGCTATATA
65148 TTATATG-TATATA
1 TTATATGCTATATA
65161 TT
1 TT
65163 GTAGTATAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.55
Consensus pattern (14 bp):
TTATATGCTATATA
Found at i:71159 original size:2 final size:2
Alignment explanation
Indices: 71152--71177 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
71142 TCATTTATCC
71152 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
71178 CCCTTGTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:71391 original size:10 final size:9
Alignment explanation
Indices: 71374--71440 Score: 55
Period size: 10 Copynumber: 6.7 Consensus size: 9
71364 AACACAGAGC
71374 AAAAAAAAG
1 AAAAAAAAG
71383 AATAAAAAAG
1 AA-AAAAAAG
71393 AAATTAAAGAA-
1 AAA--AAA-AAG
71404 AAGAAAAAAG
1 AA-AAAAAAG
71414 AGAAACAAAGAG
1 A-AAA-AAA-AG
71426 AAAAAAAAG
1 AAAAAAAAG
71435 AAAAAA
1 AAAAAA
71441 TGGACGATAA
Statistics
Matches: 49, Mismatches: 0, Indels: 18
0.73 0.00 0.27
Matches are distributed among these distances:
9 13 0.27
10 18 0.37
11 12 0.24
12 6 0.12
ACGTcount: A:0.81, C:0.01, G:0.13, T:0.04
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:71417 original size:9 final size:9
Alignment explanation
Indices: 71405--71440 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
71395 ATTAAAGAAA
71405 AGAAAAAAG
1 AGAAAAAAG
71414 AGAAACAAAG
1 AGAAA-AAAG
*
71424 AGAAAAAAA
1 AGAAAAAAG
71433 AGAAAAAA
1 AGAAAAAA
71441 TGGACGATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 16 0.64
10 9 0.36
ACGTcount: A:0.81, C:0.03, G:0.17, T:0.00
Consensus pattern (9 bp):
AGAAAAAAG
Found at i:71427 original size:24 final size:23
Alignment explanation
Indices: 71373--71439 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 23
71363 AAACACAGAG
71373 CAAAA-AAAAGAATAAAAAAGAAA
1 CAAAAGAAAAGAA-AAAAAAGAAA
** *
71396 TTAAAGAAAAGAAAAAAGAGAAA
1 CAAAAGAAAAGAAAAAAAAGAAA
*
71419 CAAAGAGAAAAAAAAGAAAAA
1 CAAA-AGAAAAGAAA-AAAAA
71440 ATGGACGATA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
23 14 0.41
24 16 0.47
25 4 0.12
ACGTcount: A:0.79, C:0.03, G:0.13, T:0.04
Consensus pattern (23 bp):
CAAAAGAAAAGAAAAAAAAGAAA
Found at i:71428 original size:33 final size:33
Alignment explanation
Indices: 71374--71438 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
71364 AACACAGAGC
**
71374 AAAAAAAAGAATAAAAAAGAAATTAAAGAAAAG
1 AAAAAAAAGAATAAAAAAGAAAAAAAAGAAAAG
* *
71407 AAAAAAGAGAA-ACAAAGAGAAAAAAAAGAAAA
1 AAAAAAAAGAATA-AAAAAGAAAAAAAAGAAAA
71439 AATGGACGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 1 0.04
33 26 0.96
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.05
Consensus pattern (33 bp):
AAAAAAAAGAATAAAAAAGAAAAAAAAGAAAAG
Found at i:72882 original size:43 final size:43
Alignment explanation
Indices: 72835--72950 Score: 151
Period size: 43 Copynumber: 2.7 Consensus size: 43
72825 GCCATCCATA
*
72835 ATTTCAACTCCACGACGGAGGATATCGTACCAATGGATCCACG
1 ATTTCAACTCCACGACGGAGGATATCGTACCAATAGATCCACG
* * *
72878 ATTTCAACTCCACGACGGAGGATATCGTGCCCATATATCCACG
1 ATTTCAACTCCACGACGGAGGATATCGTACCAATAGATCCACG
* * * * *
72921 GTTTCAACTTCACGATGAAGGAAATCGTAC
1 ATTTCAACTCCACGACGGAGGATATCGTAC
72951 ACACAAGCAG
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 63 1.00
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (43 bp):
ATTTCAACTCCACGACGGAGGATATCGTACCAATAGATCCACG
Found at i:73253 original size:43 final size:43
Alignment explanation
Indices: 73162--73286 Score: 146
Period size: 43 Copynumber: 2.9 Consensus size: 43
73152 ACGAAGGCGC
* *
73162 CATCCATAATTTCAACTCTACGACGGAGGATATCGTACCAATG
1 CATCCATGATTTCAACTCTACGACGGAGGATATCGTACCAATA
* *
73205 GATCCATGATTTCAACTCTACGACGGAGGATATCGTGCTC-ATA
1 CATCCATGATTTCAACTCTACGACGGAGGATATCGTAC-CAATA
* * * *
73248 CATCCACGGTTTCAACT-TCACGACGAAGGAAATCGTACC
1 CATCCATGATTTCAACTCT-ACGACGGAGGATATCGTACC
73287 CACAAGCAGC
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
42 2 0.03
43 67 0.96
44 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.25
Consensus pattern (43 bp):
CATCCATGATTTCAACTCTACGACGGAGGATATCGTACCAATA
Found at i:73325 original size:335 final size:335
Alignment explanation
Indices: 72712--73562 Score: 1468
Period size: 335 Copynumber: 2.5 Consensus size: 335
72702 TGCAGCTTTT
* * * *
72712 AGAGCCAATTTCAACTTCATGACGAAGGATATTGGACTCAAAATAGCACAAGCTTGGATTTCAAC
1 AGAGCCAATTTTAACTTCATGGCGAAGGATATTGGACTCGAAACAGCACAAGCTTGGATTTCAAC
*
72777 TTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCAAGACGAAGGCGCCATCCATAATTTCAA
66 TTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGCGCCATCCATAATTTCAA
72842 CTCCACGACGGAGGATATCGTACCAATGGATCCACGATTTCAACTCCACGACGGAGGATATCGTG
131 CTCCACGACGGAGGATATCGTACCAATGGATCCACGATTTCAACTCCACGACGGAGGATATCGTG
* *
72907 CCCATATATCCACGGTTTCAACTTCACGATGAAGGAAATCGTACACACAAGCAGCATTCATCTCT
196 CCCATACATCCACGGTTTCAACTTCACGACGAAGGAAATCGTACACACAAGCAGCATTCATCTCT
72972 AGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAAGGAGTGTCTGTCAATAAACT
261 AGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAAGGAGTGTCTGTCAATAAACT
73037 TTCCAGTTTC
326 TTCCAGTTTC
73047 AGAGCCAATTTTAACTTCATGGCGAAGGATATTGGACTCGAAACAGCACAAGCTTGGATTTCAAC
1 AGAGCCAATTTTAACTTCATGGCGAAGGATATTGGACTCGAAACAGCACAAGCTTGGATTTCAAC
73112 TTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGCGCCATCCATAATTTCAA
66 TTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGCGCCATCCATAATTTCAA
* * *
73177 CTCTACGACGGAGGATATCGTACCAATGGATCCATGATTTCAACTCTACGACGGAGGATATCGTG
131 CTCCACGACGGAGGATATCGTACCAATGGATCCACGATTTCAACTCCACGACGGAGGATATCGTG
* * *
73242 CTCATACATCCACGGTTTCAACTTCACGACGAAGGAAATCGTACCCACAAGCAGCATTTATCTCT
196 CCCATACATCCACGGTTTCAACTTCACGACGAAGGAAATCGTACACACAAGCAGCATTCATCTCT
*
73307 AGATTGGATTTTAACTTCACGACGAAGGATATCCAACTCAAAGAAGGAGTGTCTGTCAATAAACT
261 AGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAAGGAGTGTCTGTCAATAAACT
73372 TTCCAGTTTC
326 TTCCAGTTTC
* *
73382 AGAGCCAATTTTAACTTCACGGCGAAGGATATTGGACTCGAAACAACACAAGCTTGGATTTCAAC
1 AGAGCCAATTTTAACTTCATGGCGAAGGATATTGGACTCGAAACAGCACAAGCTTGGATTTCAAC
* * *
73447 TTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGATGAAGGCGCCATCCATGATTCCAA
66 TTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGCGCCATCCATAATTTCAA
* * * *** *
73512 CTCCACGACAGAGGATATCGTGCCCACACATCCACGATTTCAACTTCACGA
131 CTCCACGACGGAGGATATCGTACCAATGGATCCACGATTTCAACTCCACGA
73563 TGAAGGGAAT
Statistics
Matches: 487, Mismatches: 29, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
335 487 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.24
Consensus pattern (335 bp):
AGAGCCAATTTTAACTTCATGGCGAAGGATATTGGACTCGAAACAGCACAAGCTTGGATTTCAAC
TTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGCGCCATCCATAATTTCAA
CTCCACGACGGAGGATATCGTACCAATGGATCCACGATTTCAACTCCACGACGGAGGATATCGTG
CCCATACATCCACGGTTTCAACTTCACGACGAAGGAAATCGTACACACAAGCAGCATTCATCTCT
AGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAAGGAGTGTCTGTCAATAAACT
TTCCAGTTTC
Found at i:73963 original size:35 final size:36
Alignment explanation
Indices: 73884--74030 Score: 215
Period size: 36 Copynumber: 4.1 Consensus size: 36
73874 AGACATCCAC
73884 GAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTT
1 GAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTT
* *
73921 GAAACAAATTTCGTCTCTCTTGAGACA-TTTTTCTT
1 GAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
* *
73956 GAAACAAATTTTGTCTCTCATGAGACAGTTTCCCTT
1 GAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
* * *
73992 GAAACAAATTTTATATCTTTTGAGACAGTTTCTCTT
1 GAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
74028 GAA
1 GAA
74031 GCATCATTTG
Statistics
Matches: 98, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
35 32 0.33
36 58 0.59
37 8 0.08
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (36 bp):
GAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
Found at i:73987 original size:71 final size:73
Alignment explanation
Indices: 73884--74030 Score: 217
Period size: 71 Copynumber: 2.0 Consensus size: 73
73874 AGACATCCAC
* * * *
73884 GAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACA-
1 GAAACAAAGTTTTGTCTCTCATGAGACAGTTTCCCTTGAAACAAATTTCATATCTCTTGAGACAG
*
73948 TTTTTCTT
66 TTTCTCTT
* *
73956 GAAACAAA-TTTTGTCTCTCATGAGACAGTTTCCCTTGAAACAAATTTTATATCTTTTGAGACAG
1 GAAACAAAGTTTTGTCTCTCATGAGACAGTTTCCCTTGAAACAAATTTCATATCTCTTGAGACAG
74020 TTTCTCTT
66 TTTCTCTT
74028 GAA
1 GAA
74031 GCATCATTTG
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
71 49 0.73
72 18 0.27
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (73 bp):
GAAACAAAGTTTTGTCTCTCATGAGACAGTTTCCCTTGAAACAAATTTCATATCTCTTGAGACAG
TTTCTCTT
Found at i:74455 original size:9 final size:9
Alignment explanation
Indices: 74431--74463 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
74421 GTTCGGGATA
74431 TAATATTAT
1 TAATATTAT
74440 T-ATATTAT
1 TAATATTAT
74448 TAATATTAT
1 TAATATTAT
74457 TAATATT
1 TAATATT
74464 GTTTATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
TAATATTAT
Found at i:76454 original size:13 final size:14
Alignment explanation
Indices: 76428--76456 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
76418 ATCATAAATT
76428 TTATATGCTATATA
1 TTATATGCTATATA
76442 TTATATG-TATATA
1 TTATATGCTATATA
76455 TT
1 TT
76457 GTAGTATAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.55
Consensus pattern (14 bp):
TTATATGCTATATA
Found at i:90330 original size:18 final size:18
Alignment explanation
Indices: 90291--90324 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
90281 ACAAAAAGAT
*
90291 AAATAAAACGACATTCGA
1 AAATAAAACGAAATTCGA
90309 AAATAAAA-GAAATTCG
1 AAATAAAACGAAATTCG
90325 TCAAATTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.59, C:0.12, G:0.12, T:0.18
Consensus pattern (18 bp):
AAATAAAACGAAATTCGA
Found at i:92330 original size:60 final size:59
Alignment explanation
Indices: 92219--92332 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 59
92209 TATCAATCTA
* **
92219 TCATTCTAAATTAGTCCTTAAACTTTTAAGCATTTCAATTTCATCCCAAACTATGACCT
1 TCATTCTAAATTAATCCCCAAACTTTTAAGCATTTCAATTTCATCCCAAACTATGACCT
* *
92278 TCATTCTAAATTAATCCCCAAACTTTTTGAGCA-TTCTAATTTTATCCCAAACTAT
1 TCATTCTAAATTAATCCCCAAAC-TTTTAAGCATTTC-AATTTCATCCCAAACTAT
92333 ATGTATATAC
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 23 0.48
60 25 0.52
ACGTcount: A:0.32, C:0.24, G:0.04, T:0.39
Consensus pattern (59 bp):
TCATTCTAAATTAATCCCCAAACTTTTAAGCATTTCAATTTCATCCCAAACTATGACCT
Found at i:94410 original size:187 final size:185
Alignment explanation
Indices: 94054--94556 Score: 737
Period size: 187 Copynumber: 2.7 Consensus size: 185
94044 GGGCGTGACA
* *
94054 CAATTCTTTTTCAGTTTTCTGCCATAAAAAAGAGATAAACGAATATTATAGAATAAACTAAAAAA
1 CAATTCTTTTTCAGTTTTCTGCCAGAAAAAAGAGAGAAACGAATATTATAGAA-AAACTAAAAAA
94119 TGGGTTCCTTGAATTTGAAGAAGATGGTTCAAGAGGAGATCATAGAGAGATGGGTGGTGAATTCA
65 TGGGTTCCTTGAATTTGAAGAAGATGGTTCAAGAGGAGATCATAGAGAGATGGGTGGTGAATTCA
* * *
94184 AGCTCAAAGATTTATTCAGAAACATTCATAAACACATGGTGTGCATGCATCAAATC
130 AGCTCAAAGATTTATTCAGAAACATTCACAAAAACATGGTATGCATGCATCAAATC
* * *
94240 CAATTGTTTTTCAGATTTCTGCCAGCAAAAAAGAGAGAAACGAATGTTATAGAAGAAACTAAAAA
1 CAATTCTTTTTCAGTTTTCTGCCAG-AAAAAAGAGAGAAACGAATATTATAGAA-AAACTAAAAA
* *
94305 ATGGGTTCCTTGAATTTGAAG-AGAATTGTCCAAGAGGAGATCATAGAGAGATGGGTGGTGAATT
64 ATGGGTTCCTTGAATTTGAAGAAG-ATGGTTCAAGAGGAGATCATAGAGAGATGGGTGGTGAATT
* *
94369 CAAGCTCAAAGTTTTATTCAGAAATATTCACAAAAACATGGTATGCATGCATCAAATC
128 CAAGCTCAAAGATTTATTCAGAAACATTCACAAAAACATGGTATGCATGCATCAAATC
* * * * *
94427 CAATTCCTTTGCAGTTTTCTACCAGAAAAACGAGGGAGAAACGAATATTATAGAATAA--AAAAA
1 CAATTCTTTTTCAGTTTTCTGCCAGAAAAA--AGAGAGAAACGAATATTATAGAAAAACTAAAAA
* * *
94490 A--GGTTCTTTGAATTTGAAGAAGATGGTTCAAAAGGAGATCATAGAGAGATGGGTGGTGAATCC
64 ATGGGTTCCTTGAATTTGAAGAAGATGGTTCAAGAGGAGATCATAGAGAGATGGGTGGTGAATTC
94553 AAGC
129 AAGC
94557 GTATATTCTT
Statistics
Matches: 286, Mismatches: 26, Indels: 13
0.88 0.08 0.04
Matches are distributed among these distances:
183 58 0.20
184 2 0.01
185 6 0.02
186 29 0.10
187 170 0.59
188 21 0.07
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.27
Consensus pattern (185 bp):
CAATTCTTTTTCAGTTTTCTGCCAGAAAAAAGAGAGAAACGAATATTATAGAAAAACTAAAAAAT
GGGTTCCTTGAATTTGAAGAAGATGGTTCAAGAGGAGATCATAGAGAGATGGGTGGTGAATTCAA
GCTCAAAGATTTATTCAGAAACATTCACAAAAACATGGTATGCATGCATCAAATC
Found at i:113375 original size:12 final size:12
Alignment explanation
Indices: 113358--113382 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
113348 ATATGCAAAA
113358 CTCGACTCGATT
1 CTCGACTCGATT
113370 CTCGACTCGATT
1 CTCGACTCGATT
113382 C
1 C
113383 GAAAAAGTTT
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:0.16, C:0.36, G:0.16, T:0.32
Consensus pattern (12 bp):
CTCGACTCGATT
Found at i:123449 original size:15 final size:16
Alignment explanation
Indices: 123426--123464 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
123416 AGATTATGAG
123426 TTTGAGGATTTAA-GAT
1 TTTG-GGATTTAACGAT
123442 TTTGGGATTTAACGAT
1 TTTGGGATTTAACGAT
*
123458 TTAGGGA
1 TTTGGGA
123465 GATTTAGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.28, C:0.03, G:0.28, T:0.41
Consensus pattern (16 bp):
TTTGGGATTTAACGAT
Found at i:130231 original size:21 final size:21
Alignment explanation
Indices: 130189--130231 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
130179 TTTCTGGGCT
* *
130189 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
130210 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
130231 A
1 A
130232 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:133814 original size:105 final size:105
Alignment explanation
Indices: 133604--134901 Score: 2076
Period size: 105 Copynumber: 12.4 Consensus size: 105
133594 GTATTGTTCC
* * ** * * **
133604 GGAGCCCAATATCATTCACTGTGAAGTTGAAATTGGCTCCGAAATTGAGAAGTTGTCGGTTGACA
1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACA
** ****
133669 GTCAGCGGTCCCTTCGTCGTGAAGTTGAACTTATACTGTCT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* ** *
133710 TGAGTCCAATATCCTTCGCGGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATATTTGTTGACAA
1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAA
133775 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
133815 GGAGTCCAATATCCTTCATGGTGAAGTTGAAATTGGCTCTGAAATTGAG-AATGTTTGTTGACAA
1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAA
133879 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* **
133919 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGAATCTG-AA-T--GAAAT-TTTGTTGACAA
1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAA
*
133979 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
134019 GGAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACA
* * *
134084 ACCAGCGGTCCCTTCGTTGTGAAGTTGAACATGCGTTGTTT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
134125 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGT-TGTTGTTGACA
1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGT-TTGTTGACA
134189 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * *
134230 GAAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGT-TGTTGTTGACA
1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGT-TTGTTGACA
**
134294 GGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
*
134335 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AATTGGAGAAATGTTTGGTGACA
1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GAGAAATGTTTGTTGACA
134399 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
*
134440 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAA
1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAA
134505 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
*
134545 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AATTGGAGAAATGTTTGGTGACA
1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GAGAAATGTTTGTTGACA
134609 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
134650 GGAGTCCAATATCCTTCGTTGTGAAGCTGAAATTGGCTCTGAACTTGAGAAATGTTTGTTGACAA
1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAA
134715 CCAGCGGTCCCTTCGTCGTGAAGTTTGAACTTGCGTTGTCT
66 CCAGCGGTCCCTTCGTCGTGAAG-TTGAACTTGCGTTGTCT
* *
134756 GGAGTCCAATATCCTTCGTTGTGAAGCTGAAATTGGCTCTGAACTTGAGAAATGTTTGTTGACAA
1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAA
134821 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
134861 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
134902 GGTAAAACCT
Statistics
Matches: 1118, Mismatches: 60, Indels: 29
0.93 0.05 0.02
Matches are distributed among these distances:
100 88 0.08
101 5 0.00
102 2 0.00
103 2 0.00
104 101 0.09
105 667 0.60
106 253 0.23
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (105 bp):
GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
Done.