Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002644.1 Hibiscus syriacus cultivar Beakdansim tig00005394_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: 75007
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:374 original size:39 final size:39
Alignment explanation
Indices: 293--377 Score: 120
Period size: 40 Copynumber: 2.2 Consensus size: 39
283 TAGTTTCATA
*
293 TAAACTACTAAATCAAATGTGTATAGGGTTCTACTTAATC
1 TAAACTACTAAATCAAATGTGTATA-GGTTCTAATTAATC
333 TAAACTACTAAATCAAATAG-GATATA-GTTCTAATTAATC
1 TAAACTACTAAATCAAAT-GTG-TATAGGTTCTAATTAATC
372 TAAACT
1 TAAACT
378 TTTAAATGAA
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
39 18 0.43
40 19 0.45
41 5 0.12
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.34
Consensus pattern (39 bp):
TAAACTACTAAATCAAATGTGTATAGGTTCTAATTAATC
Found at i:2953 original size:39 final size:39
Alignment explanation
Indices: 2910--3020 Score: 222
Period size: 39 Copynumber: 2.8 Consensus size: 39
2900 AAAAGGATGA
2910 AGTTATAGTTAATATAAACTACTAAATCAAATAGGAGAG
1 AGTTATAGTTAATATAAACTACTAAATCAAATAGGAGAG
2949 AGTTATAGTTAATATAAACTACTAAATCAAATAGGAGAG
1 AGTTATAGTTAATATAAACTACTAAATCAAATAGGAGAG
2988 AGTTATAGTTAATATAAACTACTAAATCAAATA
1 AGTTATAGTTAATATAAACTACTAAATCAAATA
3021 ATTTACTGCT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 72 1.00
ACGTcount: A:0.50, C:0.08, G:0.13, T:0.30
Consensus pattern (39 bp):
AGTTATAGTTAATATAAACTACTAAATCAAATAGGAGAG
Found at i:3807 original size:17 final size:18
Alignment explanation
Indices: 3785--3828 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 18
3775 CTATGAGGTA
3785 AAAAATAATATCATTA-T
1 AAAAATAATATCATTATT
3802 AAAAAT-ATA--ATTATT
1 AAAAATAATATCATTATT
*
3817 TAAAATAATATC
1 AAAAATAATATC
3829 TAAGTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 7
0.73 0.03 0.23
Matches are distributed among these distances:
14 4 0.18
15 6 0.27
16 6 0.27
17 6 0.27
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAAATAATATCATTATT
Found at i:19323 original size:18 final size:17
Alignment explanation
Indices: 19283--19319 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
19273 TTATTTTTAC
19283 TTTAATTGTTTTACTTA
1 TTTAATTGTTTTACTTA
19300 TTTAATTGATTTTA-TTA
1 TTTAATTG-TTTTACTTA
19317 TTT
1 TTT
19320 TAATATTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.24, C:0.03, G:0.05, T:0.68
Consensus pattern (17 bp):
TTTAATTGTTTTACTTA
Found at i:27961 original size:10 final size:10
Alignment explanation
Indices: 27946--27970 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
27936 TGAAATTACA
27946 TTAATAATTT
1 TTAATAATTT
27956 TTAATAATTT
1 TTAATAATTT
27966 TTAAT
1 TTAAT
27971 GTATTATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TTAATAATTT
Found at i:28205 original size:2 final size:2
Alignment explanation
Indices: 28188--28264 Score: 140
Period size: 2 Copynumber: 39.5 Consensus size: 2
28178 AAAAAACTTA
28188 AT AT A- AT AT A- AT AT 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 AT AT AT AT AT AT AT AT
28228 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28265 GGCGCGCGCG
Statistics
Matches: 73, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.03
2 71 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28502 original size:2 final size:2
Alignment explanation
Indices: 28495--28532 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
28485 CGTCAAATTA
28495 AT AT AT AT AT AT 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 AT AT AT AT AT AT
28533 GTGTGTGTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29724 original size:3 final size:3
Alignment explanation
Indices: 29716--29766 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
29706 CTGTCGTTGC
*
29716 ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
29764 ATT
1 ATT
29767 GCTGCCGAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:30315 original size:24 final size:24
Alignment explanation
Indices: 30299--30354 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
30289 ATTTTATATA
30299 TAATAATATTACATATTTAATTAT
1 TAATAATATTACATATTTAATTAT
* * *
30323 TAATAATTTTATATATTAAATTAAAT
1 TAATAATATTACATATTTAATT--AT
30349 TAATAA
1 TAATAA
30355 AATTTTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 19 0.70
26 8 0.30
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
TAATAATATTACATATTTAATTAT
Found at i:31488 original size:173 final size:172
Alignment explanation
Indices: 31198--31528 Score: 495
Period size: 173 Copynumber: 1.9 Consensus size: 172
31188 GCCTTTTCGT
* ** * *
31198 TCTCTAGATGGGAACTTGGCCCTTATATGTATATACACATTGGGTAAAATTATGGATGAATGGAA
1 TCTCTAGATGGGAACTTGGCCCTTAGACATATATACACATTAGGTAAAATTATGGATGAACGGAA
* * *
31263 ATTTTATGTTAAGGGTGAATTTATAAATTTTTAGAGACATAAATTTATAACATTTT-TGAGGATG
66 ATTTTATGTTAAGGGTGAATTTATAAATCTTTAGAGACATAAATTAATAACATTTTAAG-GGATG
31327 AAAACAAGTTATCAATAGAAAATAGAAAATTTATAATTTTTCA
130 AAAACAAGTTATCAATAGAAAATAGAAAATTTATAATTTTTCA
* *
31370 TCTCTAGTTGGGAACTTGGCCTTTAGACATATATACACATTAGGTAAAATTA-GGTATGAACGGA
1 TCTCTAGATGGGAACTTGGCCCTTAGACATATATACACATTAGGTAAAATTATGG-ATGAACGG-
* *
31434 AAATTTTATGTTAAGGGTGAATTTATGAATCTTTAGAGAGATAAATTAATAACATTTTAAGGGAT
64 AAATTTTATGTTAAGGGTGAATTTATAAATCTTTAGAGACATAAATTAATAACATTTTAAGGGAT
* *
31499 GAAAACATGTTATCAATAGAAAATATAAAA
129 GAAAACAAGTTATCAATAGAAAATAGAAAA
31529 AAAAATCTAA
Statistics
Matches: 142, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
171 2 0.01
172 53 0.37
173 86 0.61
174 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.18, T:0.35
Consensus pattern (172 bp):
TCTCTAGATGGGAACTTGGCCCTTAGACATATATACACATTAGGTAAAATTATGGATGAACGGAA
ATTTTATGTTAAGGGTGAATTTATAAATCTTTAGAGACATAAATTAATAACATTTTAAGGGATGA
AAACAAGTTATCAATAGAAAATAGAAAATTTATAATTTTTCA
Found at i:31761 original size:20 final size:20
Alignment explanation
Indices: 31738--31777 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
31728 ATGATTTATT
31738 ATAAAATATATATTAAAATA
1 ATAAAATATATATTAAAATA
* * *
31758 ATAATATATTTCTTAAAATA
1 ATAAAATATATATTAAAATA
31778 CTATAATAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAAAATATATATTAAAATA
Found at i:31795 original size:22 final size:21
Alignment explanation
Indices: 31737--31795 Score: 52
Period size: 22 Copynumber: 2.8 Consensus size: 21
31727 TATGATTTAT
*
31737 TATAA-AATATATATTAAAATA
1 TATAATAATTTAT-TTAAAATA
*
31758 -ATAATATATTT-CTTAAAATA
1 TATAATA-ATTTATTTAAAATA
31778 CTATAATAATTTATTTAA
1 -TATAATAATTTATTTAA
31796 TATTATTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
20 12 0.40
21 5 0.17
22 13 0.43
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (21 bp):
TATAATAATTTATTTAAAATA
Found at i:31948 original size:51 final size:53
Alignment explanation
Indices: 31892--31999 Score: 130
Period size: 51 Copynumber: 2.1 Consensus size: 53
31882 AATTGGGTAA
* ** * * *
31892 ATTAATTATTTATCAAAATAATTATATTA-TATTATATTATTGAAA-AATATT
1 ATTAATTACTTATCAAAATAAGAATATTATTATTATACTATTAAAATAAAATT
* *
31943 ATTAATTACTTATTAAATTAAGAATATTATTATTATACTATTAAAATAAAATT
1 ATTAATTACTTATCAAAATAAGAATATTATTATTATACTATTAAAATAAAATT
31996 ATTA
1 ATTA
32000 CATTTATATT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
51 24 0.51
52 14 0.30
53 9 0.19
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (53 bp):
ATTAATTACTTATCAAAATAAGAATATTATTATTATACTATTAAAATAAAATT
Found at i:31998 original size:28 final size:27
Alignment explanation
Indices: 31935--31999 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 27
31925 ATATTATTGA
*
31935 AAAATATTATTAATTACTTATTAAATT
1 AAAATATTATTAATTACTTATTAAAAT
*
31962 AAGAATATTATTATTATAC-TATTAAAAT
1 AA-AATATTATTAAT-TACTTATTAAAAT
31990 AAAATTATTA
1 AAAA-TATTA
32000 CATTTATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
27 4 0.12
28 26 0.79
29 3 0.09
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.45
Consensus pattern (27 bp):
AAAATATTATTAATTACTTATTAAAAT
Found at i:33038 original size:23 final size:18
Alignment explanation
Indices: 32994--33057 Score: 110
Period size: 18 Copynumber: 3.6 Consensus size: 18
32984 ACCGGTCACA
32994 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTT
33012 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTT
* *
33030 ACCTGACCCAACCCGTTT
1 ACCCGACCCGACCCGTTT
33048 ACCCGACCCG
1 ACCCGACCCG
33058 TTGACCCGAC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.19, C:0.50, G:0.16, T:0.16
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTT
Found at i:33051 original size:13 final size:13
Alignment explanation
Indices: 33033--33070 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
33023 CCCGTTTACC
*
33033 TGACCCAACCCGT
1 TGACCCGACCCGT
*
33046 TTACCCGACCCGT
1 TGACCCGACCCGT
33059 TGACCCGACCCG
1 TGACCCGACCCG
33071 ACCCGTTGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.18, C:0.47, G:0.18, T:0.16
Consensus pattern (13 bp):
TGACCCGACCCGT
Found at i:33052 original size:31 final size:31
Alignment explanation
Indices: 33016--33096 Score: 117
Period size: 31 Copynumber: 2.6 Consensus size: 31
33006 CCGTTTACCC
* *
33016 GACCCGACCCGTTTACCTGACCCAACCCGTT
1 GACCCGACCCGTTGACCCGACCCAACCCGTT
* *
33047 TACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCAACCCGTT
*
33078 GACTCGACCCGTTGACCCG
1 GACCCGACCCGTTGACCCG
33097 TTGACCGTTG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.17, C:0.46, G:0.20, T:0.17
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCAACCCGTT
Found at i:33069 original size:18 final size:18
Alignment explanation
Indices: 32994--33102 Score: 102
Period size: 18 Copynumber: 6.2 Consensus size: 18
32984 ACCGGTCACA
*
32994 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
*
33012 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
* *
33030 ACCTGACCCAACCCGTT-
1 ACCCGACCCGACCCGTTG
*
33047 ----TACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
33061 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
33079 ACTCGACCCGTTGACCCGTTG
1 ACCCGACCC---GACCCGTTG
33100 ACC
1 ACC
33103 GTTGACCGTC
Statistics
Matches: 76, Mismatches: 7, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
13 11 0.14
18 54 0.71
21 11 0.14
ACGTcount: A:0.17, C:0.47, G:0.18, T:0.17
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:33085 original size:13 final size:13
Alignment explanation
Indices: 33069--33093 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33059 TGACCCGACC
33069 CGACCCGTTGACT
1 CGACCCGTTGACT
33082 CGACCCGTTGAC
1 CGACCCGTTGAC
33094 CCGTTGACCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.40, G:0.24, T:0.20
Consensus pattern (13 bp):
CGACCCGTTGACT
Found at i:33096 original size:8 final size:8
Alignment explanation
Indices: 33083--33129 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 8
33073 CCGTTGACTC
33083 GACCCGTT
1 GACCCGTT
33091 GACCCGTT
1 GACCCGTT
33099 GA-CCGTT
1 GACCCGTT
33106 GACCGTCGTT
1 GACC--CGTT
33116 GACCACTGTT
1 GACC-C-GTT
33126 GACC
1 GACC
33130 AAAACTTTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
7 7 0.21
8 11 0.32
9 1 0.03
10 15 0.44
ACGTcount: A:0.15, C:0.34, G:0.26, T:0.26
Consensus pattern (8 bp):
GACCCGTT
Found at i:33106 original size:15 final size:16
Alignment explanation
Indices: 33086--33119 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
33076 TTGACTCGAC
33086 CCGTTGACC-CGTTGA
1 CCGTTGACCGCGTTGA
33101 CCGTTGACCGTCGTTGA
1 CCGTTGACCG-CGTTGA
33118 CC
1 CC
33120 ACTGTTGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.12, C:0.35, G:0.26, T:0.26
Consensus pattern (16 bp):
CCGTTGACCGCGTTGA
Found at i:34425 original size:18 final size:18
Alignment explanation
Indices: 34399--34433 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
34389 TCGAAAGGAC
*
34399 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
34417 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
34434 CCAGATGGAA
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:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:40062 original size:17 final size:18
Alignment explanation
Indices: 40029--40062 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
40019 TCCATTCTGT
40029 CTTATTATTTAATTCCAA
1 CTTATTATTTAATTCCAA
40047 CTTATTATTT-ATTCCA
1 CTTATTATTTAATTCCA
40063 GACCTTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (18 bp):
CTTATTATTTAATTCCAA
Found at i:41117 original size:27 final size:27
Alignment explanation
Indices: 41065--41117 Score: 63
Period size: 28 Copynumber: 1.9 Consensus size: 27
41055 AGGTAAAATA
*
41065 TGGAAAAACGACTTACCGGGTACGAATT
1 TGGAAAAACGACTTA-CGGATACGAATT
*
41093 TGGAAAAACGAACTT-CGGATTCGAA
1 TGGAAAAACG-ACTTACGGATACGAA
41118 CCCAGGACGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
27 8 0.36
28 10 0.45
29 4 0.18
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.21
Consensus pattern (27 bp):
TGGAAAAACGACTTACGGATACGAATT
Found at i:47273 original size:20 final size:20
Alignment explanation
Indices: 47239--47288 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
47229 TTACAATATT
47239 GATACTTTT-TCAAAAGTATC
1 GATACTTTTAT-AAAAGTATC
* *
47259 GATGCTTTTATAAAATTATC
1 GATACTTTTATAAAAGTATC
47279 GATACTTTTA
1 GATACTTTTA
47289 AATTTAAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (20 bp):
GATACTTTTATAAAAGTATC
Found at i:47485 original size:61 final size:59
Alignment explanation
Indices: 47403--47533 Score: 181
Period size: 61 Copynumber: 2.2 Consensus size: 59
47393 TCGATACTTT
* ** *
47403 TTCAAAAGTATCAATATTTTTAAATTCGAAAGTTAAAATATCATTTTTTTTATTTTTTAAA
1 TTCAAAAGTATCAATACTTTTAAATGAGAAAGTTAAAATATCA--TTTTTCATTTTTTAAA
* *
47464 TTCAAAAGTATCGATACTTTTATATGAGAAAGTTAAAATATCATTTTTCATTTTTTAAA
1 TTCAAAAGTATCAATACTTTTAAATGAGAAAGTTAAAATATCATTTTTCATTTTTTAAA
*
47523 TTCGAAAGTAT
1 TTCAAAAGTAT
47534 GTATAGTTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
59 25 0.40
61 38 0.60
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.46
Consensus pattern (59 bp):
TTCAAAAGTATCAATACTTTTAAATGAGAAAGTTAAAATATCATTTTTCATTTTTTAAA
Found at i:48334 original size:36 final size:38
Alignment explanation
Indices: 48248--48338 Score: 132
Period size: 39 Copynumber: 2.4 Consensus size: 38
48238 AGATGAGTTT
*
48248 AATGTTAAGGTTAACAAATTATAATAGTTGACCTCATAT
1 AATGTTAAGGTTAACAAATTATAATAGTTGA-CTCATAG
* *
48287 AATGTTAAGGTTAACAAATTATAATAGTTGA-T-TTGG
1 AATGTTAAGGTTAACAAATTATAATAGTTGACTCATAG
48323 AATGTTAAGGTTAACA
1 AATGTTAAGGTTAACA
48339 TTCTTGTGCG
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
36 17 0.35
37 1 0.02
39 31 0.63
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.36
Consensus pattern (38 bp):
AATGTTAAGGTTAACAAATTATAATAGTTGACTCATAG
Found at i:48464 original size:77 final size:76
Alignment explanation
Indices: 48336--48665 Score: 263
Period size: 77 Copynumber: 4.2 Consensus size: 76
48326 GTTAAGGTTA
* *
48336 ACATTCTT-GTGCGCAACTCATTTTATTAAAAAAAATATTAACA-TTCTAGATCGTAACCTATTT
1 ACATTCTTAG-GCGCAACCCATTTTATTAATAAAAATATTAACATTTC-AGATCGTAACCTATTT
48399 CTTAGTGAATCATG
64 CTTAGTGAA-CATG
* * * * **
48413 ACATTCTTGGGCACAACCCATTTTCTTAATAAAAATATTAACATTTCAGATCGCAATATATTTCT
1 ACATTCTTAGGCGCAACCCATTTTATTAATAAAAATATTAACATTTCAGATCGTAACCTATTTCT
* *
48478 TAATGAACTAAG
66 TAGTGAAC-ATG
* * ** * * *
48490 ATATTCTTAGGCCCAACTTATTTTACTAA-AAAAATATTTACATTACATTACAGATTGCT-ACCT
1 ACATTCTTAGGCGCAACCCATTTTATTAATAAAAATA-TT--A--ACATTTCAGATCG-TAACCT
*
48553 AATTCTTAGTGAACCATG
60 ATTTCTTAGTGAA-CATG
** * * *** * *
48571 ATGTTCTTAGGCGCAACCTATTTTATTAATAAAAATATTAACATTCCAGATTACAATCTATTTTT
1 ACATTCTTAGGCGCAACCCATTTTATTAATAAAAATATTAACATTTCAGATCGTAACCTATTTCT
*
48636 TTGTGAACCATG
66 TAGTGAA-CATG
*
48648 ACATTTTTAGGCGCAACC
1 ACATTCTTAGGCGCAACC
48666 GTATTTCTTA
Statistics
Matches: 203, Mismatches: 38, Indels: 24
0.77 0.14 0.09
Matches are distributed among these distances:
76 8 0.04
77 128 0.63
78 4 0.02
79 2 0.01
81 53 0.26
82 8 0.04
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (76 bp):
ACATTCTTAGGCGCAACCCATTTTATTAATAAAAATATTAACATTTCAGATCGTAACCTATTTCT
TAGTGAACATG
Found at i:50706 original size:41 final size:41
Alignment explanation
Indices: 50655--50932 Score: 332
Period size: 41 Copynumber: 6.8 Consensus size: 41
50645 AAGTTAAATG
50655 GTGAACTATTGCATATTGTCATGGTTGAATTGGATCGAATA
1 GTGAACTATTGCATATTGTCATGGTTGAATTGGATCGAATA
* * * *
50696 TTGAATTATTGCATATTGTCATGGTTGAATTGGATCAAATG
1 GTGAACTATTGCATATTGTCATGGTTGAATTGGATCGAATA
* *
50737 GTGAAATATTGCATATTGTCATGGTTGAATTGGATCAAATA
1 GTGAACTATTGCATATTGTCATGGTTGAATTGGATCGAATA
*
50778 GTGAACTATTGCATATTATCATGGTTGAATTGGATCGAAT-
1 GTGAACTATTGCATATTGTCATGGTTGAATTGGATCGAATA
* *
50818 G-G---TATTGCATACTGTCATGGTTGAATTGGATCGAATG
1 GTGAACTATTGCATATTGTCATGGTTGAATTGGATCGAATA
* * *
50855 GTGAACTATTACATATTGGAATGATGGAATTGAATTGGATCGAATG
1 GTGAACTATTGCATATT-G--TCATGG--TTGAATTGGATCGAATA
* * * *
50901 GTGAACTATTGTATATTGGCATGATGGAATTG
1 GTGAACTATTGCATATTGTCATGGTTGAATTG
50933 AATTGGATTG
Statistics
Matches: 206, Mismatches: 21, Indels: 20
0.83 0.09 0.08
Matches are distributed among these distances:
36 32 0.16
37 1 0.00
38 1 0.00
39 1 0.00
40 1 0.00
41 128 0.62
42 1 0.00
43 3 0.01
44 5 0.02
45 1 0.00
46 32 0.16
ACGTcount: A:0.30, C:0.08, G:0.25, T:0.37
Consensus pattern (41 bp):
GTGAACTATTGCATATTGTCATGGTTGAATTGGATCGAATA
Found at i:50855 original size:18 final size:18
Alignment explanation
Indices: 50798--50856 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
50788 GCATATTATC
50798 ATGGTTGAATTGGATCGA
1 ATGGTTGAATTGGATCGA
* *
50816 ATGG-T--ATTGCATACTGTC
1 ATGGTTGAATTGGAT-C-G-A
50834 ATGGTTGAATTGGATCGA
1 ATGGTTGAATTGGATCGA
50852 ATGGT
1 ATGGT
50857 GAACTATTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 12
0.66 0.09 0.26
Matches are distributed among these distances:
15 6 0.19
16 1 0.03
17 2 0.06
18 13 0.42
19 2 0.06
20 1 0.03
21 6 0.19
ACGTcount: A:0.25, C:0.08, G:0.31, T:0.36
Consensus pattern (18 bp):
ATGGTTGAATTGGATCGA
Found at i:50891 original size:46 final size:46
Alignment explanation
Indices: 50838--50940 Score: 179
Period size: 46 Copynumber: 2.2 Consensus size: 46
50828 ACTGTCATGG
50838 TTGAATTGGATCGAATGGTGAACTATTACATATTGGAATGATGGAA
1 TTGAATTGGATCGAATGGTGAACTATTACATATTGGAATGATGGAA
** *
50884 TTGAATTGGATCGAATGGTGAACTATTGTATATTGGCATGATGGAA
1 TTGAATTGGATCGAATGGTGAACTATTACATATTGGAATGATGGAA
50930 TTGAATTGGAT
1 TTGAATTGGAT
50941 TGTGAATTAA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 54 1.00
ACGTcount: A:0.32, C:0.06, G:0.27, T:0.35
Consensus pattern (46 bp):
TTGAATTGGATCGAATGGTGAACTATTACATATTGGAATGATGGAA
Found at i:50931 original size:123 final size:122
Alignment explanation
Indices: 50650--50932 Score: 367
Period size: 123 Copynumber: 2.3 Consensus size: 122
50640 AAATCAAGTT
* *
50650 AAATGGTGAACTATTGCATATTGTCATGGTTGAATTGGATCGAATATTGAATTATTGCATATTGT
1 AAATGGTGAACTATTGCATATTGTCATGGTTGAATTGGATCGAATATTG-AGTATTGCATACTGT
*
50715 CATGGTTGAATTGGATCAAATGGTGAAATATTGCATATTGTCATGGTTGAATTGGATC
65 CATGGTTGAATTGGATCAAATGGTGAAATATTACATATTGTCATGGTTGAATTGGATC
* *
50773 AAATAGTGAACTATTGCATATTATCATGGTTGAATTGGATCG-A-A-TG-GTATTGCATACTGTC
1 AAATGGTGAACTATTGCATATTGTCATGGTTGAATTGGATCGAATATTGAGTATTGCATACTGTC
* * *
50834 ATGGTTGAATTGGATCGAATGGTGAACTATTACATATTGGAATGATGGAATTGAATTGGATC
66 ATGGTTGAATTGGATCAAATGGTGAAATATTACATATT-G--TCATGG--TTGAATTGGATC
* * * * *
50896 GAATGGTGAACTATTGTATATTGGCATGATGGAATTG
1 AAATGGTGAACTATTGCATATTGTCATGGTTGAATTG
50933 AATTGGATTG
Statistics
Matches: 140, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
118 48 0.34
119 1 0.01
120 2 0.01
121 6 0.04
122 1 0.01
123 82 0.59
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (122 bp):
AAATGGTGAACTATTGCATATTGTCATGGTTGAATTGGATCGAATATTGAGTATTGCATACTGTC
ATGGTTGAATTGGATCAAATGGTGAAATATTACATATTGTCATGGTTGAATTGGATC
Found at i:52248 original size:14 final size:14
Alignment explanation
Indices: 52229--52259 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
52219 ATAAATAGTT
52229 TAATTTATCTAAAA
1 TAATTTATCTAAAA
52243 TAATTTATCTAAAA
1 TAATTTATCTAAAA
52257 TAA
1 TAA
52260 GAATATTGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (14 bp):
TAATTTATCTAAAA
Found at i:52611 original size:24 final size:21
Alignment explanation
Indices: 52579--52637 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 21
52569 TACATAGGCA
52579 ATGTACCGATACACTAGTGAAGGG
1 ATGTACCGATACACTA-T--AGGG
* *
52603 ATGTACCGATACCCTATAGTG
1 ATGTACCGATACACTATAGGG
52624 -TGTACCGATACACT
1 ATGTACCGATACACT
52638 TCAAAGGGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 13 0.41
21 3 0.09
23 1 0.03
24 15 0.47
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (21 bp):
ATGTACCGATACACTATAGGG
Found at i:53817 original size:18 final size:18
Alignment explanation
Indices: 53794--53828 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
53784 GTTCTTAAGG
*
53794 AGTGGTCCTTCGGGACAT
1 AGTGGTCATTCGGGACAT
*
53812 AGTGGTCATTTGGGACA
1 AGTGGTCATTCGGGACA
53829 AATTTTCAGT
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:0.20, C:0.17, G:0.34, T:0.29
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:56067 original size:182 final size:182
Alignment explanation
Indices: 55760--56127 Score: 605
Period size: 182 Copynumber: 2.0 Consensus size: 182
55750 AAATTATTAT
* *
55760 TTTTTTAATTCAAAAAAATTTATAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAG
1 TTTTTTAATTAAAAAAAATTTACAATTAATTTAAATAATATATAATTATAAAAT-AAAATTTCAG
*
55825 ATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTAGATCTTAAATTATTAATT
65 ATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGATATTAGATCTTAAATTATTAATT
*
55890 G-ATTTTAAATGGTTTGGACTTAGCCCATATGTTATATATAATATATTTAATA
130 GTATTTTAAATGGTTTGGACTAAGCCCATATGTTATATATAATATATTTAATA
*
55942 TTTTTTAATTAAAAAAATAGTTTACAATTAATTTAAATAATATATAATTATAAAAT-AAATTTTA
1 TTTTTTAATTAAAAAAA-A-TTTACAATTAATTTAAATAATATATAATTATAAAATAAAATTTCA
* * *
56006 TATAATTTTTTTAATTAATTAATATTGATTTAGATTTAAAAGATATTGGATCTTAAATTATTAAT
64 GATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGATATTAGATCTTAAATTATTAAT
* *
56071 TGTGTTTTAAATGGTTTGGGCTAAGCCCATATGTTATATATAATATATTTAATA
129 TGTATTTTAAATGGTTTGGACTAAGCCCATATGTTATATATAATATATTTAATA
56125 TTT
1 TTT
56128 AAAATTTAAT
Statistics
Matches: 173, Mismatches: 10, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
182 86 0.50
183 52 0.30
184 35 0.20
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (182 bp):
TTTTTTAATTAAAAAAAATTTACAATTAATTTAAATAATATATAATTATAAAATAAAATTTCAGA
TAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGATATTAGATCTTAAATTATTAATTG
TATTTTAAATGGTTTGGACTAAGCCCATATGTTATATATAATATATTTAATA
Found at i:56863 original size:5 final size:5
Alignment explanation
Indices: 56853--56884 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
56843 AAGAGAGGCA
56853 GAAAG GAAAG GAAAG GAAAG G-AAG GAAAG GAA
1 GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAA
56885 TGATTATGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (5 bp):
GAAAG
Found at i:56879 original size:9 final size:9
Alignment explanation
Indices: 56855--56884 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
56845 GAGAGGCAGA
56855 AAGGAAAGG
1 AAGGAAAGG
56864 AAAGGAAAGG
1 -AAGGAAAGG
56874 AAGGAAAGG
1 AAGGAAAGG
56883 AA
1 AA
56885 TGATTATGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (9 bp):
AAGGAAAGG
Found at i:59398 original size:13 final size:13
Alignment explanation
Indices: 59365--59422 Score: 80
Period size: 13 Copynumber: 4.5 Consensus size: 13
59355 TTTTAAAAGG
* *
59365 TTAAATTAAGAAA
1 TTAAAATAAAAAA
*
59378 TAAAAATAAAAAA
1 TTAAAATAAAAAA
*
59391 CTAAAATAAAAAA
1 TTAAAATAAAAAA
59404 TTAAAATAAAAAA
1 TTAAAATAAAAAA
59417 TTAAAA
1 TTAAAA
59423 AAGGTAATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (13 bp):
TTAAAATAAAAAA
Found at i:60710 original size:4 final size:4
Alignment explanation
Indices: 60703--60735 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
60693 AAAAAGAAAA
60703 AAAT AAAT -AA- AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
60736 ATGTAAATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 4 0.15
4 23 0.85
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:60714 original size:18 final size:18
Alignment explanation
Indices: 60684--60731 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
60674 TAGACCCTAG
*
60684 AAAAAGAAA-AAAAAGAA
1 AAAAATAAATAAAAAGAA
*
60701 AAAAATAAATAAAAATAA
1 AAAAATAAATAAAAAGAA
*
60719 ATAAATAAATAAA
1 AAAAATAAATAAA
60732 TAAAATGTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 8 0.30
18 19 0.70
ACGTcount: A:0.83, C:0.00, G:0.04, T:0.12
Consensus pattern (18 bp):
AAAAATAAATAAAAAGAA
Found at i:60728 original size:22 final size:21
Alignment explanation
Indices: 60690--60736 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
60680 CTAGAAAAAG
60690 AAAAAAAAGAAAAAAATAAAT
1 AAAAAAAAGAAAAAAATAAAT
* *
60711 AAAAATAAATAAATAAATAAAT
1 AAAAA-AAAGAAAAAAATAAAT
60733 AAAA
1 AAAA
60737 TGTAAATGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.15
Consensus pattern (21 bp):
AAAAAAAAGAAAAAAATAAAT
Found at i:60917 original size:37 final size:36
Alignment explanation
Indices: 60872--61249 Score: 487
Period size: 37 Copynumber: 10.2 Consensus size: 36
60862 TTTCAAAATG
*
60872 TTTTCAAAAATAATTTTTCAAAACTATATA-ATATATA
1 TTTTCAAAAAT--GTTTTCAAAACTATATATATATATA
*
60909 TTTTCAAAAATTATTTTCAAAACTATATA-ATATATA
1 TTTTCAAAAA-TGTTTTCAAAACTATATATATATATA
* * *
60945 TTTTCAAAAGTTATTTTCAAAACTATATA-ATATGTA
1 TTTTCAAAA-ATGTTTTCAAAACTATATATATATATA
* *
60981 TTTTCAAAAAGGTTTTTAAAAACTATATATTATATATA
1 TTTTCAAAAATG-TTTTCAAAACTATATA-TATATATA
*
61019 TATTTC-AAAATATTTTCAAAACTATATA-ATATATA
1 T-TTTCAAAAATGTTTTCAAAACTATATATATATATA
*
61054 TTTTCAAAAATGTTTTAAAAAACTATATATTATATATA
1 TTTTCAAAAATGTTTT-CAAAACTATATA-TATATATA
61092 TTTTCAAAAATGTTTTCAAAACTATATATTATATATA
1 TTTTCAAAAATGTTTTCAAAACTATATA-TATATATA
* *
61129 GTTTCAAAAATGTTTTCAAAAACTATGTATTATATATA
1 TTTTCAAAAATGTTTTC-AAAACTATATA-TATATATA
*
61167 TTTTTAAAAATGTTTTCAAAACTATATATTATATATA
1 TTTTCAAAAATGTTTTCAAAACTATATA-TATATATA
61204 TTTTCAAAAATGTTTTCAAAACTATATATTATATATA
1 TTTTCAAAAATGTTTTCAAAACTATATA-TATATATA
61241 TTTTCAAAA
1 TTTTCAAAA
61250 CTATATATTA
Statistics
Matches: 310, Mismatches: 20, Indels: 22
0.88 0.06 0.06
Matches are distributed among these distances:
34 4 0.01
35 17 0.05
36 91 0.29
37 125 0.40
38 69 0.22
39 4 0.01
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (36 bp):
TTTTCAAAAATGTTTTCAAAACTATATATATATATA
Found at i:60953 original size:73 final size:70
Alignment explanation
Indices: 60872--61249 Score: 472
Period size: 75 Copynumber: 5.1 Consensus size: 70
60862 TTTCAAAATG
60872 TTTTCAAAAATAATTTTTCAAAACTATATAATATATATTTTCAAAAATTATTTTCAAAACTATAT
1 TTTTCAAAAAT-A-TTTTCAAAACTATATAATATATATTTTCAAAAA-T-TTTTCAAAACTATAT
60937 A-ATATATA
62 ATATATATA
* * *
60945 TTTTCAAAAGTTATTTTCAAAACTATATAATATGTATTTTCAAAAAGGTTTTTAAAAACTATATA
1 TTTTCAAAA-ATATTTTCAAAACTATATAATATATATTTTCAAAAA--TTTTTCAAAACTATATA
61010 TTATATATA
63 -TATATATA
*
61019 TATTTC-AAAATATTTTCAAAACTATATAATATATATTTTCAAAAATGTTTTAAAAAACTATATA
1 T-TTTCAAAAATATTTTCAAAACTATATAATATATATTTTCAAAAAT-TTTT-CAAAACTATATA
61083 TTATATATA
63 -TATATATA
* * *
61092 TTTTCAAAAATGTTTTCAAAACTATATATTATATATAGTTTCAAAAATGTTTTCAAAAACTATGT
1 TTTTCAAAAATATTTTCAAAACTATATA--ATATATATTTTCAAAAAT-TTTTC-AAAACTATAT
61157 ATTATATATA
62 A-TATATATA
* *
61167 TTTTTAAAAATGTTTTCAAAACTATATATTATATATATTTTCAAAAATGTTTTCAAAACTATATA
1 TTTTCAAAAATATTTTCAAAACTATATA--ATATATATTTTCAAAAAT-TTTTCAAAACTATATA
61232 TTATATATA
63 -TATATATA
61241 TTTTCAAAA
1 TTTTCAAAA
61250 CTATATATTA
Statistics
Matches: 280, Mismatches: 14, Indels: 21
0.89 0.04 0.07
Matches are distributed among these distances:
71 1 0.00
72 55 0.20
73 88 0.31
74 39 0.14
75 97 0.35
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (70 bp):
TTTTCAAAAATATTTTCAAAACTATATAATATATATTTTCAAAAATTTTTCAAAACTATATATAT
ATATA
Found at i:61276 original size:27 final size:25
Alignment explanation
Indices: 61213--61274 Score: 115
Period size: 25 Copynumber: 2.5 Consensus size: 25
61203 ATTTTCAAAA
61213 ATGTTTTCAAAACTATATATTATAT
1 ATGTTTTCAAAACTATATATTATAT
*
61238 ATATTTTCAAAACTATATATTATAT
1 ATGTTTTCAAAACTATATATTATAT
61263 ATGTTTTCAAAA
1 ATGTTTTCAAAA
61275 AATGTTTTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (25 bp):
ATGTTTTCAAAACTATATATTATAT
Found at i:61307 original size:62 final size:62
Alignment explanation
Indices: 61179--61312 Score: 182
Period size: 62 Copynumber: 2.1 Consensus size: 62
61169 TTTAAAAATG
* *
61179 TTTTCAAAACTATATATTATATATATTTTCAAAAATGTTTTCAAAACTATATATTATATATA
1 TTTTCAAAACTATATATTATATATATTTTCAAAAATGTTTTCAAAAATATATATTATACATA
* * *
61241 TTTTCAAAACTATATATTATATATGTTTTCAAAAAATGTTTTCTAAAAAT-TTTGTTATACAT-
1 TTTTCAAAACTATATATTATATATATTTTC-AAAAATGTTTTC-AAAAATATATATTATACATA
61303 TTTTCGAAAA
1 TTTTC-AAAA
61313 TATTTTCAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
62 34 0.53
63 25 0.39
64 5 0.08
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.47
Consensus pattern (62 bp):
TTTTCAAAACTATATATTATATATATTTTCAAAAATGTTTTCAAAAATATATATTATACATA
Found at i:68496 original size:20 final size:20
Alignment explanation
Indices: 68449--68652 Score: 109
Period size: 20 Copynumber: 10.2 Consensus size: 20
68439 AATGACCAAC
* *
68449 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
*
68468 AAAACCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
* * **
68488 AAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTTAG
* **
68508 AAGATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
*
68529 AAGAATCGCAACGCGATTCAG
1 AA-AATCGCAACGCGATTTAG
*
68550 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-TAG
* **
68570 AGAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
*
68591 AAGAATCGCAACGC---TAAG
1 AA-AATCGCAACGCGATTTAG
*
68609 -AAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-TAG
* * *
68628 AGAATCGCAATGCGATTCAG
1 AAAATCGCAACGCGATTTAG
68648 AAAAT
1 AAAAT
68653 GAGTAAATTC
Statistics
Matches: 141, Mismatches: 29, Indels: 29
0.71 0.15 0.15
Matches are distributed among these distances:
16 11 0.08
17 1 0.01
18 1 0.01
19 21 0.15
20 72 0.51
21 11 0.08
22 24 0.17
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:68539 original size:22 final size:20
Alignment explanation
Indices: 68511--68645 Score: 156
Period size: 20 Copynumber: 6.8 Consensus size: 20
68501 TGAAAAGAAG
68511 ATCGCAACGCGATCTTCCAAGA
1 ATCGCAACGCGA--TTCCAAGA
*
68533 ATCGCAACGCGATT-CAGAAA
1 ATCGCAACGCGATTCCA-AGA
68553 ATCGCAACGCGATTCCAAGA
1 ATCGCAACGCGATTCCAAGA
68573 ATCGCAACGCGATCTTCCAAGA
1 ATCGCAACGCGA--TTCCAAGA
68595 ATCGCAACGC---T--AAGAA
1 ATCGCAACGCGATTCCAAG-A
68611 ATCGCAACGCGATTCCAAGA
1 ATCGCAACGCGATTCCAAGA
*
68631 ATCGCAATGCGATTC
1 ATCGCAACGCGATTC
68646 AGAAAATGAG
Statistics
Matches: 100, Mismatches: 3, Indels: 22
0.80 0.02 0.18
Matches are distributed among these distances:
15 3 0.03
16 11 0.11
17 1 0.01
19 3 0.03
20 47 0.47
21 5 0.05
22 30 0.30
ACGTcount: A:0.35, C:0.29, G:0.19, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGATTCCAAGA
Found at i:68552 original size:62 final size:62
Alignment explanation
Indices: 68446--68604 Score: 193
Period size: 62 Copynumber: 2.6 Consensus size: 62
68436 CAAAATGACC
* * * *
68446 AACAA-AATCGCAACGCGAT-AT-CAA-AACCGCAACGCGATTTAGAAAAGCGCAACGTTGAA
1 AACAAGAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAAGCGCAACG-CGAA
* * *
68505 AAGAAG-ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGAT
1 AACAAGAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAAGCGCAACGCGAA
**
68566 TCCAAGAATCGCAACGCGATCTTCCAAGAATCGCAACGC
1 AACAAGAATCGCAACGCGATCTTCCAAGAATCGCAACGC
68605 TAAGAAATCG
Statistics
Matches: 85, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
59 17 0.20
60 1 0.01
61 8 0.09
62 59 0.69
ACGTcount: A:0.39, C:0.27, G:0.19, T:0.14
Consensus pattern (62 bp):
AACAAGAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAAGCGCAACGCGAA
Found at i:68643 original size:58 final size:60
Alignment explanation
Indices: 68511--68643 Score: 216
Period size: 58 Copynumber: 2.2 Consensus size: 60
68501 TGAAAAGAAG
*
68511 ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGATTCCAAGA
1 ATCGCAACGCGATCTTCCAAGAATCGCAACGC-A-TAAGAAAATCGCAACGCGATTCCAAGA
68573 ATCGCAACGCGATCTTCCAAGAATCGCAACGC-TAAG-AAATCGCAACGCGATTCCAAGA
1 ATCGCAACGCGATCTTCCAAGAATCGCAACGCATAAGAAAATCGCAACGCGATTCCAAGA
*
68631 ATCGCAATGCGAT
1 ATCGCAACGCGAT
68644 TCAGAAAATG
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
58 34 0.49
59 3 0.04
62 32 0.46
ACGTcount: A:0.35, C:0.29, G:0.20, T:0.17
Consensus pattern (60 bp):
ATCGCAACGCGATCTTCCAAGAATCGCAACGCATAAGAAAATCGCAACGCGATTCCAAGA
Found at i:68759 original size:6 final size:6
Alignment explanation
Indices: 68748--68803 Score: 105
Period size: 6 Copynumber: 9.5 Consensus size: 6
68738 GACACGTATT
68748 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
68796 ACC-CG ACC
1 ACCACG ACC
68804 CGAGACGAGA
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.10
6 45 0.90
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:69324 original size:6 final size:6
Alignment explanation
Indices: 69288--69351 Score: 93
Period size: 6 Copynumber: 11.5 Consensus size: 6
69278 CGCCGTCTCG
69288 GGTCG- GGTCG- GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
69331 GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGT
69352 AATACGTGTC
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 25 0.43
6 33 0.57
ACGTcount: A:0.00, C:0.17, G:0.55, T:0.28
Consensus pattern (6 bp):
GGTCGT
Found at i:69472 original size:20 final size:20
Alignment explanation
Indices: 69447--69734 Score: 211
Period size: 20 Copynumber: 14.2 Consensus size: 20
69437 GAATTTACTC
*
69447 ATTTTCTGAATCGCATTGCG
1 ATTTTCTGAATCGCGTTGCG
*
69467 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
69487 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
* *
69507 ATTTCCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
69527 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
69547 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
69567 ATTTTCTGAATCGCATTGCG
1 ATTTTCTGAATCGCGTTGCG
*
69587 ATTCTT-GGAAGATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
* * *
69609 ATTCTCTTAATCGCATTGCG
1 ATTTTCTGAATCGCGTTGCG
*
69629 ATTCTT-GGAATATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
69651 ATTTTCTTTTG-A-C-CGTTGCG
1 ATTTTC---TGAATCGCGTTGCG
** *
69671 ATTTTCT-TTTCAACGTTGCG
1 ATTTTCTGAATC-GCGTTGCG
*
69691 ATTTTCTAAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
69711 A-TTT-TGATATCGCGTTGTG
1 ATTTTCTGA-ATCGCGTTGCG
69730 ATTTT
1 ATTTT
69735 GTTGGTCATT
Statistics
Matches: 217, Mismatches: 29, Indels: 44
0.75 0.10 0.15
Matches are distributed among these distances:
17 1 0.00
18 3 0.01
19 17 0.08
20 153 0.71
21 15 0.07
22 27 0.12
25 1 0.00
ACGTcount: A:0.17, C:0.19, G:0.23, T:0.41
Consensus pattern (20 bp):
ATTTTCTGAATCGCGTTGCG
Found at i:69548 original size:60 final size:61
Alignment explanation
Indices: 69447--69631 Score: 250
Period size: 60 Copynumber: 3.0 Consensus size: 61
69437 GAATTTACTC
* ***
69447 ATTTTCTGAATCGCATTGCGATT-TTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTCCTGAATCGCATTGCGATTCTTGGAAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
* *
69507 ATTTCCTTAATCGCGTTGCGATTCTTGG-AATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTCCTGAATCGCATTGCGATTCTTGGAAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
* * *
69567 ATTTTCTGAATCGCATTGCGATTCTTGGAAGATCGCGTTGCGATTCTCT-TAATCGCATTGCG
1 ATTTCCTGAATCGCATTGCGATTCTTGGAA-ATCGCGTTGCGATTCT-TGGAATCGCGTTGCG
69629 ATT
1 ATT
69632 CTTGGAATAT
Statistics
Matches: 111, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
60 77 0.69
61 3 0.03
62 30 0.27
63 1 0.01
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (61 bp):
ATTTCCTGAATCGCATTGCGATTCTTGGAAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
Found at i:70967 original size:22 final size:22
Alignment explanation
Indices: 70942--70989 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
70932 TTGGACCCTA
70942 AAAAAGAAA-AAAAAGAATAAAT
1 AAAAAGAAACAAAAA-AATAAAT
* *
70964 AAAAATAAACAAATAAATAAAT
1 AAAAAGAAACAAAAAAATAAAT
70986 AAAA
1 AAAA
70990 TGTAAATGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.81, C:0.02, G:0.04, T:0.12
Consensus pattern (22 bp):
AAAAAGAAACAAAAAAATAAAT
Found at i:71054 original size:2 final size:2
Alignment explanation
Indices: 71043--71071 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
71033 TTTCATAATC
71043 AT AT -T 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 AT AT
71072 TTGAAAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:71179 original size:36 final size:35
Alignment explanation
Indices: 71135--71433 Score: 269
Period size: 36 Copynumber: 7.9 Consensus size: 35
71125 AAATATTTTT
*
71135 TTTTCAAAACTATATAATATATATTTTCAAAATTTA
1 TTTTCAAAACTATATAATATATATTTTCAAAA-TTG
71171 TTTTCAAAACTATATAATATATATTTTCAAAAATTG
1 TTTTCAAAACTATATAATATATATTTTC-AAAATTG
* * **
71207 TTTCCAAAACTATATAATATGTATTTTCAAAAAGG
1 TTTTCAAAACTATATAATATATATTTTCAAAATTG
71242 TTTTCAAAAACTATATATTATATACAATATATATTTTCTAAAA-TG
1 TTTTC-AAAAC-------TATAT--AATATATATTTTC-AAAATTG
* *
71287 TTTTAAAAAACTATATATTATATATATTTTCAAAAATG
1 TTTTCAAA-ACTATATA--ATATATATTTTCAAAATTG
*
71325 TTTTCAAAACTATATATTATATATATTTTCAAAAATG
1 TTTTCAAAACTATATA--ATATATATTTTCAAAATTG
*
71362 TTTTTAAAAACTATATATTATATATATTTTCAAGAA-TG
1 -TTTTCAAAACTATATA--ATATATATTTTCAA-AATTG
* *
71400 TTTTCAAAACTATCTATTATATATGTTTTCAAAA
1 TTTTCAAAACTA--TATAATATATATTTTCAAAA
71434 AATGGTTTCT
Statistics
Matches: 229, Mismatches: 14, Indels: 40
0.81 0.05 0.14
Matches are distributed among these distances:
35 9 0.04
36 64 0.28
37 61 0.27
38 59 0.26
39 5 0.02
43 5 0.02
44 3 0.01
45 19 0.08
46 4 0.02
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.45
Consensus pattern (35 bp):
TTTTCAAAACTATATAATATATATTTTCAAAATTG
Found at i:71343 original size:37 final size:37
Alignment explanation
Indices: 71268--71490 Score: 277
Period size: 37 Copynumber: 5.9 Consensus size: 37
71258 ATTATATACA
* *
71268 ATATATATTTTCTAAAATGTTTTAAAAAACTATATATT
1 ATATATATTTTCAAAAATGTTTT-CAAAACTATATATT
71306 ATATATATTTTCAAAAATGTTTTCAAAACTATATATT
1 ATATATATTTTCAAAAATGTTTTCAAAACTATATATT
*
71343 ATATATATTTTCAAAAATGTTTTTAAAAACTATATATT
1 ATATATATTTTCAAAAATG-TTTTCAAAACTATATATT
* *
71381 ATATATATTTTCAAGAATGTTTTCAAAACTATCTATT
1 ATATATATTTTCAAAAATGTTTTCAAAACTATATATT
* * *
71418 ATATATGTTTTCAAAAAATGGTTTCTTAAAACTATATGTT
1 ATATATATTTTC-AAAAAT-GTTT-TCAAAACTATATATT
** * *
71458 ATACGT-TTTTCGAAAATATTTTCAAAAACTATA
1 ATATATATTTTCAAAAATGTTTTC-AAAACTATA
71491 CTATATTATT
Statistics
Matches: 164, Mismatches: 16, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
36 1 0.01
37 71 0.43
38 67 0.41
39 9 0.05
40 16 0.10
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (37 bp):
ATATATATTTTCAAAAATGTTTTCAAAACTATATATT
Found at i:71360 original size:75 final size:74
Alignment explanation
Indices: 71268--71490 Score: 295
Period size: 75 Copynumber: 2.9 Consensus size: 74
71258 ATTATATACA
*
71268 ATATATATTTTCTAAAATGTTTTAAAAAACTATATATTATATATATTTTCAAAAATGTTTTCAAA
1 ATATATATTTTCAAAAATGTTTT-AAAAACTATATATTATATATATTTTCAAAAATGTTTTCAAA
71333 ACTATATATT
65 ACTATATATT
*
71343 ATATATATTTTCAAAAATGTTTTTAAAAACTATATATTATATATATTTTCAAGAATGTTTTCAAA
1 ATATATATTTTCAAAAATG-TTTTAAAAACTATATATTATATATATTTTCAAAAATGTTTTCAAA
*
71408 ACTATCTATT
65 ACTATATATT
* * * ** * *
71418 ATATATGTTTTCAAAAAATGGTTTCTTAAAACTATATGTTATACGT-TTTTCGAAAATATTTTCA
1 ATATATATTTTC-AAAAAT-GTTT-TAAAAACTATATATTATATATATTTTCAAAAATGTTTTC-
71482 AAAACTATA
62 AAAACTATA
71491 CTATATTATT
Statistics
Matches: 131, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
75 78 0.60
76 27 0.21
77 26 0.20
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (74 bp):
ATATATATTTTCAAAAATGTTTTAAAAACTATATATTATATATATTTTCAAAAATGTTTTCAAAA
CTATATATT
Found at i:71988 original size:15 final size:15
Alignment explanation
Indices: 71970--71999 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
71960 AAAACCATGT
71970 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
71985 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
72000 GAAATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (15 bp):
TAGATAAAAAGGTAA
Found at i:72006 original size:15 final size:15
Alignment explanation
Indices: 71973--72007 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
71963 ACCATGTTAG
* *
71973 ATAAAAAGGTAATAG
1 ATAAAAAGGTAAGAA
71988 ATAAAAAGGTAAGAA
1 ATAAAAAGGTAAGAA
72003 ATAAA
1 ATAAA
72008 TAAATTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (15 bp):
ATAAAAAGGTAAGAA
Found at i:72151 original size:21 final size:20
Alignment explanation
Indices: 72113--72192 Score: 60
Period size: 21 Copynumber: 3.9 Consensus size: 20
72103 TAAAGAAGAA
72113 AGAAAAAAAAGAAA-AAATAT
1 AGAAAAAAAA-AAATAAATAT
*
72133 AGAAATAAAACAAATAAATA-
1 AGAAA-AAAAAAAATAAATAT
72153 A-AAAAGTAAAAATAATATATATAT
1 AGAAAA--AAAAA-AATA-A-ATAT
72177 A-AAAAAAAAAAATAAA
1 AGAAAAAAAAAAATAAA
72193 AAAAGTAATA
Statistics
Matches: 50, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
18 1 0.02
19 4 0.08
20 14 0.28
21 17 0.34
22 6 0.12
23 3 0.06
24 5 0.10
ACGTcount: A:0.78, C:0.01, G:0.05, T:0.16
Consensus pattern (20 bp):
AGAAAAAAAAAAATAAATAT
Found at i:72164 original size:42 final size:41
Alignment explanation
Indices: 72118--72196 Score: 95
Period size: 42 Copynumber: 1.9 Consensus size: 41
72108 AAGAAAGAAA
* *
72118 AAAAAGAAAAAATATAGAAATAAAACAAATAAATAAAAAAGT
1 AAAAAGAAAAAATATAGAAAAAAAAAAAATAAA-AAAAAAGT
* * * *
72160 AAAAATAATATATATATAAAAAAAAAAAATAAAAAAA
1 AAAAAGAAAAAATATAGAAAAAAAAAAAATAAAAAAA
72197 GTAATATATA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
41 4 0.13
42 27 0.87
ACGTcount: A:0.78, C:0.01, G:0.04, T:0.16
Consensus pattern (41 bp):
AAAAAGAAAAAATATAGAAAAAAAAAAAATAAAAAAAAAGT
Found at i:72165 original size:27 final size:26
Alignment explanation
Indices: 72086--72196 Score: 68
Period size: 28 Copynumber: 4.2 Consensus size: 26
72076 AATAGTAAGT
*
72086 AAAATAAATATAAAAAATAAAGAAGAAAG
1 AAAAT-AA-ATAAAAAATAAA-AATAAAG
* *
72115 AAAAAAAAGAAAAAATATAGAAATAAA-
1 AAAATAAATAAAAAATA-A-AAATAAAG
72142 ACAAATAAATAAAAAAGTAAAAAT-AA-
1 A-AAATAAATAAAAAA-TAAAAATAAAG
* * * *
72168 TATATATATAAAAAAAAAAAATAAA-
1 AAAATAAATAAAAAATAAAAATAAAG
72193 AAAA
1 AAAA
72197 GTAATATATA
Statistics
Matches: 66, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
24 6 0.09
25 16 0.24
26 2 0.03
27 14 0.21
28 21 0.32
29 7 0.11
ACGTcount: A:0.78, C:0.01, G:0.05, T:0.15
Consensus pattern (26 bp):
AAAATAAATAAAAAATAAAAATAAAG
Found at i:72170 original size:38 final size:38
Alignment explanation
Indices: 72082--72200 Score: 111
Period size: 38 Copynumber: 3.2 Consensus size: 38
72072 GATAAATAGT
* * * *
72082 AAGTAAAATAAATATAAAAAATAAAGAAGAAAGA-AAAAA
1 AAGTAAAA-AAATAT-AGAAATAAAAAAAAAAAATAAAAA
* *
72121 AAG--AAAAAATATAGAAATAAAACAAATAAAT-AAAA
1 AAGTAAAAAAATATAGAAATAAAAAAAAAAAATAAAAA
* *
72156 AAGTAAAAATAATATATATATAAAAAAAAAAAATAAAAA
1 AAGTAAAAA-AATATAGAAATAAAAAAAAAAAATAAAAA
72195 AAGTAA
1 AAGTAA
72201 TATATATATA
Statistics
Matches: 65, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
35 19 0.29
36 6 0.09
37 7 0.11
38 20 0.31
39 13 0.20
ACGTcount: A:0.76, C:0.01, G:0.07, T:0.16
Consensus pattern (38 bp):
AAGTAAAAAAATATAGAAATAAAAAAAAAAAATAAAAA
Found at i:72210 original size:39 final size:38
Alignment explanation
Indices: 72117--72218 Score: 111
Period size: 38 Copynumber: 2.7 Consensus size: 38
72107 GAAGAAAGAA
* * * *
72117 AAAAAAG--AAAA-AATATAGAAATAAAACAAATAAAT
1 AAAAAAGTAAAAATAATATATATATAAAAAAAAAAAAT
72152 AAAAAAGTAAAAATAATATATATATAAAAAAAAAAAAT
1 AAAAAAGTAAAAATAATATATATATAAAAAAAAAAAAT
*
72190 AAAAAAAGTAATATATATATATATATATA
1 -AAAAAAGTAA-AAATA-ATATATATATA
72219 TAAATTAATA
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
35 7 0.12
37 4 0.07
38 20 0.36
39 10 0.18
40 4 0.07
41 11 0.20
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.23
Consensus pattern (38 bp):
AAAAAAGTAAAAATAATATATATATAAAAAAAAAAAAT
Found at i:72281 original size:24 final size:24
Alignment explanation
Indices: 72254--72322 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
72244 ATAATATATT
*
72254 TATATATAATCTAAAAAAATAAAA
1 TATATATAATGTAAAAAAATAAAA
* *
72278 TATATACTAAAGT-AAAAAAGAAAA
1 TATATA-TAATGTAAAAAAATAAAA
* *
72302 TACATAAAATGTAAAAAAATA
1 TATATATAATGTAAAAAAATA
72323 TACATGAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
23 4 0.11
24 28 0.78
25 4 0.11
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (24 bp):
TATATATAATGTAAAAAAATAAAA
Found at i:72682 original size:36 final size:36
Alignment explanation
Indices: 72634--72734 Score: 145
Period size: 36 Copynumber: 2.9 Consensus size: 36
72624 ATAGTAGAAC
*
72634 TCTATTCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
72671 T-TATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
* *
72704 TCTATCATATTTTTAGGAGTTTCAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
72735 TAGGACGAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
33 6 0.10
34 25 0.43
36 26 0.45
37 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.45
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:72720 original size:34 final size:33
Alignment explanation
Indices: 72641--72733 Score: 132
Period size: 34 Copynumber: 2.7 Consensus size: 33
72631 AACTCTATTC
*
72641 TATTTTTAGGAGTTTGAATCCTAGCAAAATTTATCC
1 TATTTTTAGGAGTTTGAATCCT---AAAATTTATCA
72677 TATTTTTAGGAGTTTGAATCCTAAAATTCTATCA
1 TATTTTTAGGAGTTTGAATCCTAAAATT-TATCA
*
72711 TATTTTTAGGAGTTTCAATCCTA
1 TATTTTTAGGAGTTTGAATCCTA
72734 GTAGGACGAA
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
33 6 0.11
34 26 0.48
36 22 0.41
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.44
Consensus pattern (33 bp):
TATTTTTAGGAGTTTGAATCCTAAAATTTATCA
Found at i:73688 original size:104 final size:105
Alignment explanation
Indices: 73272--73774 Score: 758
Period size: 104 Copynumber: 4.9 Consensus size: 105
73262 CATTGTTCCA
* * ** * *
73272 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-AACCGGGAA-TTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * * * *
73335 CAGCCGTCCATTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
**
73376 AGTCCAATATCCTTCG-TGTGAAGTTGAAATTGAATCTG-AA-TGA-AA-TT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
73435 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
73475 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTTTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
73540 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
73580 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT-TGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
73644 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
73684 AGTCCAATATCC-TCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
73748 AGCGGACCCTTCG-CGTGAAGTTGAACT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACT
73775 CCAAGTATTT
Statistics
Matches: 370, Mismatches: 22, Indels: 15
0.91 0.05 0.04
Matches are distributed among these distances:
99 62 0.17
100 20 0.05
101 5 0.01
102 3 0.01
103 60 0.16
104 133 0.36
105 87 0.24
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:74422 original size:36 final size:36
Alignment explanation
Indices: 74377--74785 Score: 293
Period size: 36 Copynumber: 11.7 Consensus size: 36
74367 GAAGATTTTG
* *
74377 TGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
74413 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * *
74450 AGTTCCAAAAGAAACTGTCTCAAG-GGGAACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAG-ACAAAATT
* * *** *
74486 TGTTTCAA-AGAAA-----AC-ATATTTA-AATATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
74514 TGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * * *
74549 TATTTCAAGGGAAAATGTCTCAAGAGAGATAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
74585 TATTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * *
74622 TGTTTCAAG-GGAATTATCTCAAGAGAGACGAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAATT
* * * *
74658 TATTTCAAGGGAAATTATCTCAAGAGAGACGAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAATT
* * * * *
74695 TATTTCAAGGGAAA-TGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAATT
*
74723 ATGTTTCAAGAGAAACTGTCTCAAGGGAGA-AAAATT
1 -TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
74759 TGTTTCAAGGGAAAACTGTCTCAAGAG
1 TGTTTCAAGAG-AAACTGTCTCAAGAG
74786 GGGCAAAACT
Statistics
Matches: 301, Mismatches: 46, Indels: 52
0.75 0.12 0.13
Matches are distributed among these distances:
28 14 0.05
29 21 0.07
30 4 0.01
32 1 0.00
34 2 0.01
35 50 0.17
36 124 0.41
37 85 0.28
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:74472 original size:37 final size:36
Alignment explanation
Indices: 74389--74473 Score: 125
Period size: 37 Copynumber: 2.3 Consensus size: 36
74379 TTTCAAGAGT
* * * *
74389 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGA
1 AACTGTCTCAAGAGAGACAAAATTAGTTCCAAAAGA
74425 AACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGA
1 AACTGTCTCAAGAGAGACAAAA-TTAGTTCCAAAAGA
74462 AACTGTCTCAAG
1 AACTGTCTCAAG
74474 GGGAACGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
36 21 0.48
37 23 0.52
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22
Consensus pattern (36 bp):
AACTGTCTCAAGAGAGACAAAATTAGTTCCAAAAGA
Found at i:74660 original size:22 final size:22
Alignment explanation
Indices: 74635--74703 Score: 71
Period size: 22 Copynumber: 3.5 Consensus size: 22
74625 TTCAAGGGAA
74635 TTATCTCAAGAGAGACGAAAAT
1 TTATCTCAAGAGAGACGAAAAT
*
74657 TTATTTC-A-AG-G--G-AAA-
1 TTATCTCAAGAGAGACGAAAAT
74672 TTATCTCAAGAGAGACGAAAAT
1 TTATCTCAAGAGAGACGAAAAT
*
74694 TTATTTCAAG
1 TTATCTCAAG
74704 GGAAATGTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 14
0.69 0.06 0.26
Matches are distributed among these distances:
15 6 0.16
16 4 0.11
17 3 0.08
18 1 0.03
19 1 0.03
20 3 0.08
21 4 0.11
22 15 0.41
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (22 bp):
TTATCTCAAGAGAGACGAAAAT
Found at i:74660 original size:73 final size:71
Alignment explanation
Indices: 74511--74709 Score: 292
Period size: 73 Copynumber: 2.8 Consensus size: 71
74501 ATATTTAAAT
* *
74511 ATTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAATTTATTTCAAGGGAAAATGTCTCAAGAG
1 ATTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGG-AAATATCTCAAGAG
*
74575 AGATAAA
65 AGAGAAA
* *
74582 ATTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAATTATCTCAAGAG
1 ATTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTATTTCAAGGGAAATATCTCAAGAG
74647 AGACGAAA
65 AGA-GAAA
* *
74655 ATTTATTTCAAGGGAAATTATCTCAAGAGAGACGAAAATTTATTTCAAGGGAAAT
1 ATTTATTTCAAGGGAAACTGTCTCAAGAGAGAC-AAAATTTATTTCAAGGGAAAT
74710 GTTTTCAATG
Statistics
Matches: 115, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
71 32 0.28
72 18 0.16
73 61 0.53
74 4 0.03
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.28
Consensus pattern (71 bp):
ATTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAATATCTCAAGAGA
GAGAAA
Done.