Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004573.1 Hibiscus syriacus cultivar Beakdansim tig00010181_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: 147978
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:12465 original size:38 final size:38
Alignment explanation
Indices: 12414--12492 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 38
12404 CTTTTTTCAT
* *
12414 TATCGGGTTAAGTATCCTTTGTGGTTCCATATAATTGC
1 TATCGGGTTAAGTATCCTTTGTGGTTCCACATAATTAC
12452 TATCGGGTTAAGTATCCTTTGTGGTTCCACATAATTAC
1 TATCGGGTTAAGTATCCTTTGTGGTTCCACATAATTAC
12490 TAT
1 TAT
12493 GGCTATCTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42
Consensus pattern (38 bp):
TATCGGGTTAAGTATCCTTTGTGGTTCCACATAATTAC
Found at i:26357 original size:8 final size:8
Alignment explanation
Indices: 26339--26382 Score: 54
Period size: 8 Copynumber: 5.4 Consensus size: 8
26329 TGAACCCCTC
26339 TTTTA-TT
1 TTTTATTT
26346 TTTTATTTT
1 TTTTA-TTT
26355 TTTTATTT
1 TTTTATTT
26363 TTTTATTT
1 TTTTATTT
*
26371 GTTTTCTTT
1 -TTTTATTT
26380 TTT
1 TTT
26383 GCTCTATCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
7 5 0.15
8 14 0.42
9 14 0.42
ACGTcount: A:0.09, C:0.02, G:0.02, T:0.86
Consensus pattern (8 bp):
TTTTATTT
Found at i:26358 original size:9 final size:9
Alignment explanation
Indices: 26344--26382 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
26334 CCCTCTTTTA
26344 TTTTTTATT
1 TTTTTTATT
26353 TTTTTTA-T
1 TTTTTTATT
26361 TTTTTTATT
1 TTTTTTATT
* *
26370 TGTTTTCTT
1 TTTTTTATT
26379 TTTT
1 TTTT
26383 GCTCTATCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
8 8 0.31
9 18 0.69
ACGTcount: A:0.08, C:0.03, G:0.03, T:0.87
Consensus pattern (9 bp):
TTTTTTATT
Found at i:26366 original size:17 final size:17
Alignment explanation
Indices: 26339--26382 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
26329 TGAACCCCTC
*
26339 TTTTA-TTTTTTATTTT
1 TTTTATTTTTTTATTTG
26355 TTTTATTTTTTTATTTG
1 TTTTATTTTTTTATTTG
*
26372 TTTTCTTTTTT
1 TTTTATTTTTT
26383 GCTCTATCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.09, C:0.02, G:0.02, T:0.86
Consensus pattern (17 bp):
TTTTATTTTTTTATTTG
Found at i:36477 original size:16 final size:17
Alignment explanation
Indices: 36438--36482 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
36428 ATATTTTGAG
*
36438 GGAATTGAAATCTGTGAA
1 GGAATTGGAATC-GTGAA
*
36456 GAAATTGGAATC-TGAA
1 GGAATTGGAATCGTGAA
36472 GGAATTGGAAT
1 GGAATTGGAAT
36483 TCGAATCTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.58
18 10 0.42
ACGTcount: A:0.40, C:0.04, G:0.29, T:0.27
Consensus pattern (17 bp):
GGAATTGGAATCGTGAA
Found at i:37137 original size:28 final size:27
Alignment explanation
Indices: 37078--37138 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
37068 AACCTGACAC
* * * *
37078 CGACCCGAATATCACACTTAAAATACC
1 CGACCCAAATATCAAACTTAAAAAACA
37105 CGACCCAAATATCAAACTTAAAAAAACA
1 CGACCCAAATATCAAACTT-AAAAAACA
37133 CGACCC
1 CGACCC
37139 GACCTGATCC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 17 0.59
28 12 0.41
ACGTcount: A:0.46, C:0.33, G:0.07, T:0.15
Consensus pattern (27 bp):
CGACCCAAATATCAAACTTAAAAAACA
Found at i:39105 original size:54 final size:54
Alignment explanation
Indices: 38929--39237 Score: 194
Period size: 54 Copynumber: 5.7 Consensus size: 54
38919 AAAATGACTA
* * * * *
38929 AGCACCTCTGTACTT-AAGTCTAGAATCTGGTACCTCTGTTCTTCGTAATGATTA
1 AGCACCTTTGTGCTTCAA-TCTAGAATCTGGCACCTCTGTTCTTTGTAATGATTG
* * * * * * ** *
38983 AGCACCTATGTGCTTCAAT-TGAAAAACCGACACTTCT-TTGCTGTTAAAAATGACTG
1 AGCACCTTTGTGCTTCAATCT-AGAATCTGGCACCTCTGTT-CT-TT-GTAATGATTG
* * *
39039 ATCACCTGTGTGCTTCAGTCTAGAATCTGGCACCTCTGTTCTTTGTAATGATTG
1 AGCACCTTTGTGCTTCAATCTAGAATCTGGCACCTCTGTTCTTTGTAATGATTG
* * * * * * ** *
39093 AGCACTTTTGTGCTTCAAACTAGGATCTGGAACCTATGTGCTTTGGGATTATTG
1 AGCACCTTTGTGCTTCAATCTAGAATCTGGCACCTCTGTTCTTTGTAATGATTG
* * * * ** **
39147 AGCACCTTTGTGCTTCAATCTAAAAT-TTGTACCTATGAGCTTTAAAATTGATTG
1 AGCACCTTTGTGCTTCAATCTAGAATCTGGCACCTCTGTTCTTTGTAA-TGATTG
* * * *
39201 AACACCTCTGTGCATCAATCTAGAGTCTGGCACCTCT
1 AGCACCTTTGTGCTTCAATCTAGAATCTGGCACCTCT
39238 ATGCTCTGAT
Statistics
Matches: 191, Mismatches: 55, Indels: 17
0.73 0.21 0.06
Matches are distributed among these distances:
53 18 0.09
54 123 0.64
55 12 0.06
56 35 0.18
57 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.35
Consensus pattern (54 bp):
AGCACCTTTGTGCTTCAATCTAGAATCTGGCACCTCTGTTCTTTGTAATGATTG
Found at i:41748 original size:23 final size:23
Alignment explanation
Indices: 41722--41765 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
41712 TATTAAGTAC
**
41722 CGCTTATATAATGTAATAGGTAG
1 CGCTTATATAATAAAATAGGTAG
41745 CGCTTATATAATAAAATAGGT
1 CGCTTATATAATAAAATAGGT
41766 TAATTACTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (23 bp):
CGCTTATATAATAAAATAGGTAG
Found at i:41838 original size:87 final size:87
Alignment explanation
Indices: 41689--42081 Score: 572
Period size: 87 Copynumber: 4.5 Consensus size: 87
41679 ATTTAACCGA
* * * *
41689 AAATATTACCAAGTACAATAACATATTAAGTACCGCTTATATAATGTAATAGGTAGCGCTTATAT
1 AAATATTATCAAGCACAATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCACTTATAT
*
41754 AATAAAATAGGTTAATTACTGG
66 AATAAAATAGGTTAATTACTAG
* *
41776 AAATATTATCAAGCACAATAATATATTAGGTACCGCTTATATAATGTAAT-GTGTATCACTTATA
1 AAATATTATCAAGCACAATAACATATTAGGTACCGCTTATATAATGTAATAG-GTAGCACTTATA
* *
41840 TAATAAAATAGGTTAATTAATGG
65 TAATAAAATAGGTTAATTACTAG
* * *
41863 AAATATTATCAAACACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATAT
1 AAATATTATCAAGCACAATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCACTTATAT
41928 AATAAAATAGGTTAATTACTAG
66 AATAAAATAGGTTAATTACTAG
* * * *
41950 AAACATTATCAAGCACAATAACATATTAGGTATCACTTATATAATGTAATAGGTAACACTTATAT
1 AAATATTATCAAGCACAATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCACTTATAT
*
42015 AATAAAATAAGTTAATTACTAG
66 AATAAAATAGGTTAATTACTAG
* * * * *
42037 AAACATTATCAAGCACAATAACGTAATAAGTAACGCTTATATAAT
1 AAATATTATCAAGCACAATAACATATTAGGTACCGCTTATATAAT
42082 AAAATATGTT
Statistics
Matches: 278, Mismatches: 26, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
86 1 0.00
87 276 0.99
88 1 0.00
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (87 bp):
AAATATTATCAAGCACAATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCACTTATAT
AATAAAATAGGTTAATTACTAG
Found at i:41915 original size:23 final size:23
Alignment explanation
Indices: 41889--41939 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
41879 AATAACATAT
**
41889 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
41912 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
41935 TAGGT
1 TAGGT
41940 TAATTACTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.37, C:0.08, G:0.22, T:0.33
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:42023 original size:23 final size:23
Alignment explanation
Indices: 41976--42023 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
41966 AATAACATAT
* **
41976 TAGGTATCACTTATATAATGTAA
1 TAGGTAACACTTATATAATAAAA
41999 TAGGTAACACTTATATAATAAAA
1 TAGGTAACACTTATATAATAAAA
42022 TA
1 TA
42024 AGTTAATTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.35
Consensus pattern (23 bp):
TAGGTAACACTTATATAATAAAA
Found at i:42649 original size:21 final size:23
Alignment explanation
Indices: 42599--42651 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
42589 TAAACACTTT
*
42599 AAAATAATATTATTTCTTAACAA
1 AAAATATTATTATTTCTTAACAA
42622 AATAATATTATTATTT-TTAA-AA
1 AA-AATATTATTATTTCTTAACAA
*
42644 TAAATATT
1 AAAATATT
42652 TCAAATTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 6 0.22
22 3 0.11
23 6 0.22
24 12 0.44
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (23 bp):
AAAATATTATTATTTCTTAACAA
Found at i:42994 original size:199 final size:198
Alignment explanation
Indices: 42654--43089 Score: 644
Period size: 199 Copynumber: 2.2 Consensus size: 198
42644 TAAATATTTC
*
42654 AAATTTACCTATTACATTATAATTATCTGTTTCGATGTTTTTGGGATCGATACAATTTTTAAATG
1 AAATTTACCTATTACATTATAATTATCAGTTTCGATGTTTTTGGGATCGATAC-ATTTTTAAATG
*
42719 TATCGACACTTTATGTGTGCACCTCGTTGGGCATTCATTCTGGAAAAAAGTATCGACACAAACTT
65 TATCGACACTTTATGTATGCACCTCGTTGGGCATTCATTCTGGAAAAAAGTATCGACACAAACTT
*
42784 AAAATGTGTCGATACATTATGTAGACATATTTTCTCATAAAACCGGTATATTTATACCGAG-TAC
130 AAAATGTGTCGATACATTATGTAGACATATTCTCTCATAAAACCGGTATATTTATACCG-GTTAC
42848 ATTAT
194 ATTAT
* * *
42853 AAATTTACCTATTACATTGTAATTATCAGTTTCAATGTTTTTGTGATCGATAC-TTTTAATAAAT
1 AAATTTACCTATTACATTATAATTATCAGTTTCGATGTTTTTGGGATCGATACATTTT--TAAAT
* * * ***
42917 GTATCGACACTTTATGTATGCACCTCGTTTGGCATTCATTCTGGACAAATGTATCGACAC-TTTT
64 GTATCGACACTTTATGTATGCACCTCGTTGGGCATTCATTCTGGAAAAAAGTATCGACACAAACT
* * * *
42981 TAAATTTGTGTCGATACATTATGTTGACCTATTCTCTCATAAAATCGGTATATTTATACCGGTTA
129 TAAA-ATGTGTCGATACATTATGTAGACATATTCTCTCATAAAACCGGTATATTTATACCGGTTA
*
43046 CATTGT
193 CATTAT
*
43052 AAATTTACCTATTACATTATAATTATCGGTTTCGATGT
1 AAATTTACCTATTACATTATAATTATCAGTTTCGATGT
43090 AACATATGTG
Statistics
Matches: 213, Mismatches: 20, Indels: 8
0.88 0.08 0.03
Matches are distributed among these distances:
197 4 0.02
198 6 0.03
199 203 0.95
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (198 bp):
AAATTTACCTATTACATTATAATTATCAGTTTCGATGTTTTTGGGATCGATACATTTTTAAATGT
ATCGACACTTTATGTATGCACCTCGTTGGGCATTCATTCTGGAAAAAAGTATCGACACAAACTTA
AAATGTGTCGATACATTATGTAGACATATTCTCTCATAAAACCGGTATATTTATACCGGTTACAT
TAT
Found at i:43225 original size:31 final size:30
Alignment explanation
Indices: 43190--43271 Score: 80
Period size: 30 Copynumber: 2.7 Consensus size: 30
43180 AATAAATATT
*
43190 AAATATAATTTATAATAATTTTATT-TTAATA
1 AAATATAA-TAATAATAATTTT-TTATTAATA
* *
43221 AAATATAATAATCATAATTTTTTATTTATA
1 AAATATAATAATAATAATTTTTTATTAATA
43251 AAATTATAGAT-ATAAT-ATTTT
1 AAA-TATA-ATAATAATAATTTT
43272 AATAGTAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
29 2 0.05
30 24 0.55
31 16 0.36
32 2 0.05
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (30 bp):
AAATATAATAATAATAATTTTTTATTAATA
Found at i:44495 original size:13 final size:13
Alignment explanation
Indices: 44477--44507 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
44467 CCTTCACATG
44477 TTATACTATATGA
1 TTATACTATATGA
44490 TTATACTATATGA
1 TTATACTATATGA
44503 TTATA
1 TTATA
44508 TAAGTGTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (13 bp):
TTATACTATATGA
Found at i:46297 original size:15 final size:15
Alignment explanation
Indices: 46277--46306 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
46267 CATCGTTAAA
46277 AAAATCGACATACTT
1 AAAATCGACATACTT
*
46292 AAAATCGACGTACTT
1 AAAATCGACATACTT
46307 TTTATTTTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.27
Consensus pattern (15 bp):
AAAATCGACATACTT
Found at i:49188 original size:194 final size:191
Alignment explanation
Indices: 48863--49249 Score: 706
Period size: 194 Copynumber: 2.0 Consensus size: 191
48853 CAAATGCAAT
48863 GCGGGTAGAATGGTTATAGTCCCCTAGCACCTTAGGCGATAACCTACATAAGACAAAATGTCACT
1 GCGGGTAGAATGGTTATAGTCCCCTAGCACCTTAGGCGATAACCTACATAAGACAAAATGTCACT
48928 CTAATGCATCCCAACAGGTTTTGATGTAATAAATAGAAGAAACAGCTCCAGGTTTAATAAAATAA
66 CTAATGCATCCCAACAGGTTTTGATGTAATAAATAGAAGAAACAGCTCCAGGTTTAATAAAATAA
48993 AAAACCTCCCCACAGACAGCTTC-AAAAAGAGTCTAATCA-ATCATGAGTAACCTGCAGAGC
131 AAAACCTCCCCACAGACAGCTTCAAAAAAGAGTCTAA-CACATCATGAGTAACCTGCAGAGC
49053 GCGGGTAGAATGGTTATAGTCCCCTAGCAACCTTAGGCGATAAACCTACATAAGACAAAATGTCA
1 GCGGGTAGAATGGTTATAGTCCCCTAGC-ACCTTAGGCGAT-AACCTACATAAGACAAAATGTCA
49118 CTCTAAATGCATCCCAAACAGGTTTTGATGTAATAAATAGAAGAAACAGCTCCAGGTTTAATAAA
64 CTCT-AATGCATCCC-AACAGGTTTTGATGTAATAAATAGAAGAAACAGCTCCAGGTTTAATAAA
49183 ATAAAAAACCTCCCCACAGACAGCTTCAAAAAAGAGTCTAACATCATCATGAGTAACCTGCAGAG
127 ATAAAAAACCTCCCCACAGACAGCTTCAAAAAAGAGTCTAACA-CATCATGAGTAACCTGCAGAG
49248 C
191 C
49249 G
1 G
49250 TAATATCACA
Statistics
Matches: 190, Mismatches: 0, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
190 28 0.15
191 12 0.06
192 27 0.14
193 10 0.05
194 78 0.41
195 13 0.07
196 22 0.12
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (191 bp):
GCGGGTAGAATGGTTATAGTCCCCTAGCACCTTAGGCGATAACCTACATAAGACAAAATGTCACT
CTAATGCATCCCAACAGGTTTTGATGTAATAAATAGAAGAAACAGCTCCAGGTTTAATAAAATAA
AAAACCTCCCCACAGACAGCTTCAAAAAAGAGTCTAACACATCATGAGTAACCTGCAGAGC
Found at i:51850 original size:18 final size:17
Alignment explanation
Indices: 51827--51861 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
51817 TAGAACATAA
51827 TTTTAATGGCTTCAAAAT
1 TTTTAATGGCTT-AAAAT
51845 TTTTAATGGCTTAAAAT
1 TTTTAATGGCTTAAAAT
51862 ACAATTAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (17 bp):
TTTTAATGGCTTAAAAT
Found at i:52003 original size:33 final size:33
Alignment explanation
Indices: 51963--52032 Score: 106
Period size: 33 Copynumber: 2.1 Consensus size: 33
51953 GTTTATAACA
* *
51963 TAATGAATAATTATGA-GACCATTTTATAACTTT
1 TAATGAATAATCA-GATAACCATTTTATAACTTT
51996 TAATGAATAATCAGATAACCATTTTATAACTTT
1 TAATGAATAATCAGATAACCATTTTATAACTTT
52029 TAAT
1 TAAT
52033 AATTAAGAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 2 0.06
33 32 0.94
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.41
Consensus pattern (33 bp):
TAATGAATAATCAGATAACCATTTTATAACTTT
Found at i:52571 original size:62 final size:61
Alignment explanation
Indices: 52500--52620 Score: 172
Period size: 62 Copynumber: 1.9 Consensus size: 61
52490 TATTTTAGTA
*
52500 TATGAATGCAATATTGGATTTAATAATTTTTTAGTCTTA-TTGTTGTTGAAAAGTGTTTCAAG
1 TATGAATGCAATATTGGATTTAATAA-TTTTTAGT-TTAGTTGCTGTTGAAAAGTGTTTCAAG
* *
52562 TATGAATGCAATATTGGATTTCATTATTTTTAGTTTAGTGTTGCTGTTGAAAAGTGTTT
1 TATGAATGCAATATTGGATTTAATAATTTTTAGTTTA--GTTGCTGTTGAAAAGTGTTT
52621 TTTAAAAAGT
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
60 3 0.06
61 8 0.15
62 24 0.45
63 18 0.34
ACGTcount: A:0.28, C:0.05, G:0.19, T:0.48
Consensus pattern (61 bp):
TATGAATGCAATATTGGATTTAATAATTTTTAGTTTAGTTGCTGTTGAAAAGTGTTTCAAG
Found at i:55027 original size:5 final size:5
Alignment explanation
Indices: 55017--55255 Score: 101
Period size: 5 Copynumber: 47.4 Consensus size: 5
55007 ACTCTATAAA
* *
55017 AATAT AATAT -ATA- AATAT ATTAT GATAT ACATAAT AGATAT -ATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT A-AT-AT A-ATAT AATAT
* * * ** * *
55062 AATACCAT AATAC CATA- AATAT -ATAT ATATAA AATAT TGTAT ACTGT
1 AAT---AT AATAT AATAT AATAT AATAT A-ATAT AATAT AATAT AATAT
* *
55109 AAATAT AATAT AATAAT ATTAT AATAT AA-AT -ATAG AATAT -ATAT AATAT
1 AA-TAT AATAT AAT-AT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
* **
55158 AAATAT ATATAT AATACT -ATAT AATAT AATAT -ATAA AAT-T TTTAT
1 -AATAT A-ATAT AATA-T AATAT AATAT AATAT AATAT AATAT AATAT
*
55203 TATAT AATAT AATA- ATATAAT AATAT AATCAT AATAT -ATA- ATATAT
1 AATAT AATAT AATAT A-AT-AT AATAT AAT-AT AATAT AATAT A-ATAT
55249 AATAT AA
1 AATAT AA
55256 CAATATAATT
Statistics
Matches: 178, Mismatches: 27, Indels: 58
0.68 0.10 0.22
Matches are distributed among these distances:
3 1 0.01
4 33 0.19
5 97 0.54
6 36 0.20
7 6 0.03
8 5 0.03
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:55036 original size:2 final size:2
Alignment explanation
Indices: 55018--55254 Score: 80
Period size: 2 Copynumber: 129.5 Consensus size: 2
55008 CTCTATAAAA
* * *
55018 AT AT A- AT AT AT AA AT AT AT -T AT GAT AT AC AT A- AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT
* * * *
55058 AT AT A- AT ACC AT A- AT ACC AT AA AT AT AT AT AT AT A- AA AT AT
1 AT AT AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
* * *
55099 -T GT AT ACT GT AA AT AT A- AT AT A- AT A- AT AT -T AT A- AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
55136 AA AT AT AG A- AT AT AT AT A- AT AT AA AT AT AT AT AT A- AT ACT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* * *
55176 AT AT A- AT AT A- AT AT AT A- AA AT TT TT AT -T AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55213 A- AT A- AT AT A- AT A- AT AT A- AT CAT A- AT AT AT A- 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
55249 A- AT AT A
1 AT AT AT A
55255 ACAATATAAT
Statistics
Matches: 175, Mismatches: 26, Indels: 68
0.65 0.10 0.25
Matches are distributed among these distances:
1 28 0.16
2 138 0.79
3 9 0.05
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.40
Consensus pattern (2 bp):
AT
Found at i:55246 original size:98 final size:100
Alignment explanation
Indices: 55068--55249 Score: 241
Period size: 98 Copynumber: 1.8 Consensus size: 100
55058 ATATAATACC
* *
55068 ATAATACCATAAATATATATATATAAAATATTGTATACTGTAAATATAATATAATAATATTATAA
1 ATAATACCATAAATATATATATATAAAATATTGTATACTATAAATATAATATAATAATAATATAA
55133 TATAAATATAGAATATATATAATATAAATATATAT
66 TATAAATATAGAATATATATAATATAAATATATAT
* *
55168 ATAATACTATATAATATA-ATATATAAAAT-TT-T-TATTATATAATATAATA-ATATAATAATA
1 ATAATACCATA-AATATATATATATAAAATATTGTATACTATA-AATATAATATA-ATAATAATA
*
55228 TAATCAT-AATATATAATATATA
63 TAAT-ATAAATATAGAATATATA
55250 ATATAACAAT
Statistics
Matches: 73, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
97 6 0.08
98 36 0.49
99 4 0.05
100 21 0.29
101 6 0.08
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.41
Consensus pattern (100 bp):
ATAATACCATAAATATATATATATAAAATATTGTATACTATAAATATAATATAATAATAATATAA
TATAAATATAGAATATATATAATATAAATATATAT
Found at i:55291 original size:82 final size:77
Alignment explanation
Indices: 55128--55296 Score: 184
Period size: 77 Copynumber: 2.1 Consensus size: 77
55118 ATAATAATAT
*
55128 TATAATATAAATATAGAATATATATAATATAAATATATATATAATACTATATAATATAATATATA
1 TATAATATAAATATAGAATATATATAATATAAATATATATATAATACTATACAATATAATATATA
* *
55193 AAATTTTTATTA
66 AAATTATTACTA
*
55205 TATAATAT-AATAATATAATA-ATATAATCATAATATATAATATATAATA-TA-ACAATATAATT
1 TATAATATAAAT-ATAGAATATATATAAT-ATAA-ATAT-ATATATAATACTATACAATATAA--
*
55266 TATAATAAAGTATATTACTA
60 TAT-ATAAAAT-TATTACTA
55286 CTATAATATAA
1 -TATAATATAA
55297 GGCTAATAAT
Statistics
Matches: 77, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
76 10 0.13
77 27 0.35
78 6 0.08
79 13 0.17
80 6 0.08
81 6 0.08
82 8 0.10
83 1 0.01
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (77 bp):
TATAATATAAATATAGAATATATATAATATAAATATATATATAATACTATACAATATAATATATA
AAATTATTACTA
Found at i:55350 original size:16 final size:15
Alignment explanation
Indices: 55329--55380 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
55319 ATTCTTTAAT
*
55329 ATATAACATGTATATA
1 ATATAACATATATA-A
*
55345 ATATAATATATATAA
1 ATATAACATATATAA
* *
55360 ATATTATATATATAA
1 ATATAACATATATAA
55375 TATATA
1 -ATATA
55381 TTGTACACTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
15 15 0.48
16 16 0.52
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (15 bp):
ATATAACATATATAA
Found at i:55379 original size:36 final size:36
Alignment explanation
Indices: 55079--55380 Score: 117
Period size: 39 Copynumber: 8.0 Consensus size: 36
55069 TAATACCATA
* *
55079 AATAT-ATATATATAAAATATTGTATACTGTAA-ATAT
1 AATATAATATATAT-AAATATTATATA-TATAATATAT
* *
55115 AATATAATA-ATATTATAATA-TAAATATAGAATATATAT
1 AATATAATATATA-TA-AATATTATATATA-TA-ATATAT
*
55153 AATATAAATATATATATAATACTATATAATATAATATAT
1 AATAT-AATATATATA-AATATTATAT-ATATAATATAT
* * * *
55192 AAAAT-TTTTATTATATAATATAATA-ATATAATAATAT
1 AATATAATATA-TATA-AATATTATATATATAAT-ATAT
* * * *
55229 AATCATAATATATAATATATAATATAACAATATAATTTAT
1 AAT-ATAATATAT-ATAAATATTAT-A-TATATAATATAT
* *
55269 AATA-AAGTATAT-T-ACTACTATA-ATATAAGGCTA-AT
1 AATATAA-TATATATAAATATTATATATATAA---TATAT
* * *
55304 AATCT-ATACTATATAATTCTT-TAATATATAACATGTATAT
1 AATATAATA-TATATAAATATTAT-ATATAT-A-A--TATAT
55344 AATATAATATATATAAATATTATATATATAATATAT
1 AATATAATATATATAAATATTATATATATAATATAT
55380 A
1 A
55381 TTGTACACTA
Statistics
Matches: 202, Mismatches: 31, Indels: 66
0.68 0.10 0.22
Matches are distributed among these distances:
33 6 0.03
34 2 0.01
35 11 0.05
36 35 0.17
37 23 0.11
38 36 0.18
39 38 0.19
40 37 0.18
41 14 0.07
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (36 bp):
AATATAATATATATAAATATTATATATATAATATAT
Found at i:56853 original size:148 final size:147
Alignment explanation
Indices: 56563--56863 Score: 550
Period size: 148 Copynumber: 2.0 Consensus size: 147
56553 CGAATTGCCC
56563 CGTAGAATTGCACCGTAGTGCCATATAATATGTCCATAAGGACCACATAGAATTCCTTAAGAATC
1 CGTAGAATTGCACCGTAGTGCCATATAATATGTCCATAAGGACCACATAGAATTCCTTAAGAATC
* *
56628 ATATACTATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGGATATACA
66 ATATACTATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATACA
*
56693 TATGTCCTAAAGAACCG
131 TATGTCCCAAAGAACCG
56710 CGTAGAATTGCACCGTAGTGCCATAT-ATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAAT-ATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
56774 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
65 CATATAC-TATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
56839 CATATGTCCCAAAGAACCG
129 CATATGTCCCAAAGAACCG
56858 CGTAGA
1 CGTAGA
56864 CCCTCTACCC
Statistics
Matches: 149, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
146 2 0.01
147 68 0.46
148 79 0.53
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.28
Consensus pattern (147 bp):
CGTAGAATTGCACCGTAGTGCCATATAATATGTCCATAAGGACCACATAGAATTCCTTAAGAATC
ATATACTATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATACA
TATGTCCCAAAGAACCG
Found at i:57480 original size:67 final size:66
Alignment explanation
Indices: 57341--57490 Score: 201
Period size: 66 Copynumber: 2.2 Consensus size: 66
57331 TTTTTCTCAT
* * * * *
57341 GGGGAATCGGTTCCCCCCCTGGGGGTATCGGTTCCCCTCTAACATTCTGGAATTTCATGTCCGTT
1 GGGGTATCGGTT-CCCCCCTGGGGGTATCGATTCCCCTCTAACATTCTGGAAATTCATATCCATT
57406 GA
65 GA
* * * *
57408 GGGGTATCGGTTCCCCCCTTGGGGTATTGATTCCCCTCTAGCATTCTGGAAATTCATATTCATTG
1 GGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAACATTCTGGAAATTCATATCCATTG
57473 A
66 A
57474 GAGGGTATCGGTTCCCC
1 G-GGGTATCGGTTCCCC
57491 TTGAATGGGT
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
66 47 0.64
67 26 0.36
ACGTcount: A:0.16, C:0.27, G:0.26, T:0.31
Consensus pattern (66 bp):
GGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAACATTCTGGAAATTCATATCCATTG
A
Found at i:63827 original size:149 final size:149
Alignment explanation
Indices: 63557--63860 Score: 581
Period size: 149 Copynumber: 2.0 Consensus size: 149
63547 CGAAGTACCC
63557 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
* *
63622 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGGATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
*
63687 CATATGTCCTAAAGAACCG
131 CATATGTCCCAAAGAACCG
63706 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
63771 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
63836 CATATGTCCCAAAGAACCG
131 CATATGTCCCAAAGAACCG
63855 CGTAGA
1 CGTAGA
63861 CCCTCTACCC
Statistics
Matches: 152, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCAAAGAACCG
Found at i:64457 original size:67 final size:67
Alignment explanation
Indices: 64338--64489 Score: 205
Period size: 67 Copynumber: 2.3 Consensus size: 67
64328 TTTTTCTCAT
* * * * *
64338 GGGGGAATCGGTTCCCCCCCTGGGGGTATCGGTTCCCCTCTAACATTATGGAATTTCATGTCCGT
1 GGGGGTATCGGTT-CCCCCCTGGGGGTATCGATTCCCCTCTAACATTATGGAAATTCATATCCAT
64403 TGA
65 TGA
* * * *
64406 GGGGGTATCGGTTCCCCCCTTGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATTCATT
1 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAACATTATGGAAATTCATATCCATT
64471 GA
66 GA
*
64473 GAGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
64490 TTGAATGGGT
Statistics
Matches: 74, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
67 62 0.84
68 12 0.16
ACGTcount: A:0.16, C:0.26, G:0.27, T:0.30
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAACATTATGGAAATTCATATCCATT
GA
Found at i:76528 original size:33 final size:33
Alignment explanation
Indices: 76441--76531 Score: 155
Period size: 33 Copynumber: 2.8 Consensus size: 33
76431 GACACAGTGG
* *
76441 TTCGATTGCTTACTATTTATTATAAATTTTCCT
1 TTCGATTGCTTATTATTTATTTTAAATTTTCCT
*
76474 TTCGATCGCTTATTATTTATTTTAAATTTTCCT
1 TTCGATTGCTTATTATTTATTTTAAATTTTCCT
76507 TTCGATTGCTTATTATTTATTTTAA
1 TTCGATTGCTTATTATTTATTTTAA
76532 TTTGTCCAGT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.23, C:0.13, G:0.07, T:0.57
Consensus pattern (33 bp):
TTCGATTGCTTATTATTTATTTTAAATTTTCCT
Found at i:80268 original size:22 final size:22
Alignment explanation
Indices: 80240--80290 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
80230 CTTACCGCAT
80240 GTCCTTATGCTATAAGTATAAG
1 GTCCTTATGCTATAAGTATAAG
80262 GTCCTTATGCTATAAGTATAAG
1 GTCCTTATGCTATAAGTATAAG
80284 GTCCTTA
1 GTCCTTA
80291 CTAGGTGCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (22 bp):
GTCCTTATGCTATAAGTATAAG
Found at i:83282 original size:17 final size:17
Alignment explanation
Indices: 83236--83282 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
83226 CTGTTGAGCG
*
83236 TTGACTGACCGTTGACCT
1 TTGACTGA-CGTTGACCA
*
83254 TTGA-TCGGCGTTGACCA
1 TTGACT-GACGTTGACCA
83271 TTGACTGACGTT
1 TTGACTGACGTT
83283 AACTTTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
17 18 0.75
18 6 0.25
ACGTcount: A:0.17, C:0.23, G:0.26, T:0.34
Consensus pattern (17 bp):
TTGACTGACGTTGACCA
Found at i:84655 original size:20 final size:21
Alignment explanation
Indices: 84630--84669 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
84620 CAGCAAAACA
*
84630 AGTCTT-TAGTGACGTTTTTT
1 AGTCTTATAGCGACGTTTTTT
*
84650 AGTCTTATAGCGGCGTTTTT
1 AGTCTTATAGCGACGTTTTT
84670 AAGCGCCGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.15, C:0.12, G:0.23, T:0.50
Consensus pattern (21 bp):
AGTCTTATAGCGACGTTTTTT
Found at i:84879 original size:43 final size:43
Alignment explanation
Indices: 84832--84986 Score: 115
Period size: 43 Copynumber: 3.7 Consensus size: 43
84822 CGTTAATTAT
* * * *
84832 CTTGTCTTTAGTAGCCTTTTTTGCGACAAACACCGCTAATTCG
1 CTTGTCTTTAGTGGCATTTTTTGCCACAAACACCACTAATTCG
* * * * * *
84875 CTTG----TAATGGCTTTTTTTTCTACAAACGCCACTAATTCT
1 CTTGTCTTTAGTGGCATTTTTTGCCACAAACACCACTAATTCG
* *
84914 CTTGTCTTTAGTGGCATTTTTTGCCACAAA-ATCTACTAATTCT
1 CTTGTCTTTAGTGGCATTTTTTGCCACAAACA-CCACTAATTCG
* * **
84957 ATTGTTTTTAGTGGCGCTTTTT-CCACAAAC
1 CTTGTCTTTAGTGGCATTTTTTGCCACAAAC
84987 GTTGCTAATT
Statistics
Matches: 88, Mismatches: 18, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
39 31 0.35
42 7 0.08
43 50 0.57
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.42
Consensus pattern (43 bp):
CTTGTCTTTAGTGGCATTTTTTGCCACAAACACCACTAATTCG
Found at i:84996 original size:42 final size:42
Alignment explanation
Indices: 84906--85046 Score: 167
Period size: 43 Copynumber: 3.3 Consensus size: 42
84896 ACAAACGCCA
* * *
84906 CTAATTCTCTTGTCTTTAGTGGCATTTTTTGCCACAAAATCTA
1 CTAATTCTATTGTCTTTAGTGGCGTTTTTTGCCACAAAAT-TG
* * *
84949 CTAATTCTATTGTTTTTAGTGGCGCTTTTT-CCACAAACGTTG
1 CTAATTCTATTGTCTTTAGTGGCGTTTTTTGCCACAAA-ATTG
* * *
84991 CTAATTCTATTGTCTTTAGTAGTGTTTTTTGCCATAAAATTCG
1 CTAATTCTATTGTCTTTAGTGGCGTTTTTTGCCACAAAATT-G
85034 CTAATTCTATTGT
1 CTAATTCTATTGT
85047 TTTCAATGAC
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
42 36 0.43
43 47 0.57
ACGTcount: A:0.22, C:0.18, G:0.13, T:0.47
Consensus pattern (42 bp):
CTAATTCTATTGTCTTTAGTGGCGTTTTTTGCCACAAAATTG
Found at i:89311 original size:129 final size:130
Alignment explanation
Indices: 89171--89417 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
89161 TATTTATATA
*
89171 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCA-TTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * *
89235 TTAGCACATGATCATGACACGTGTCATTGGTGACACGTGTTACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
89300 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * * *
89365 TTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCTCCTAATTA
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTA
89418 GAAGAAAATT
Statistics
Matches: 109, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
129 43 0.39
130 66 0.61
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:89448 original size:130 final size:128
Alignment explanation
Indices: 89185--89448 Score: 298
Period size: 130 Copynumber: 2.0 Consensus size: 128
89175 ATTTGGTCCT
* *
89185 AAATTAAATAAAATTTAATAAATTAATCATTAATTAGGATCTGACATGTGTTAGCACATGATCAT
1 AAATTAAATAAAATTTAATAAATTAATCATTAATCAGGATCTGACATGTGTTAACACATGATCAT
* * *** * * **** *
89250 GACACGTGTCATTGGTGACACGTGTTACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 GACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
89314 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCA-TTAATCAGGATCTGACATGTGTTAACACATGATCA
* * * * *
89379 TGATATGTGTTATTGGTGACACATGTCACCTCCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
65 TGACACGTGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
89443 -A
127 CA
89444 AAATT
1 AAATT
89449 TGGGTCTTGG
Statistics
Matches: 112, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
129 29 0.26
130 70 0.62
132 8 0.07
133 5 0.04
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (128 bp):
AAATTAAATAAAATTTAATAAATTAATCATTAATCAGGATCTGACATGTGTTAACACATGATCAT
GACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:89775 original size:28 final size:27
Alignment explanation
Indices: 89744--89806 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
89734 AGTTGATACA
*
89744 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
89772 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
89800 ATATTTT
1 ATATTTT
89807 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:89905 original size:16 final size:18
Alignment explanation
Indices: 89884--89917 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
89874 ATTTATTATT
89884 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
89900 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
89918 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:90064 original size:21 final size:21
Alignment explanation
Indices: 90039--90088 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
90029 ATATTACCTT
*
90039 AAATTGAAGTATTTTAGAATT
1 AAATTGAAGTATTTTAGAATA
*
90060 TAATTGAAGTATTTTAGAATA
1 AAATTGAAGTATTTTAGAATA
90081 AAATTGAA
1 AAATTGAA
90089 TTACTTTGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.40
Consensus pattern (21 bp):
AAATTGAAGTATTTTAGAATA
Found at i:90305 original size:29 final size:29
Alignment explanation
Indices: 90253--90310 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
90243 GCAAACGGAA
* *
90253 TAAATGTTGGGGGACTGTATTGCAAGTTT
1 TAAATGTTGGGGGACTGAAATGCAAGTTT
90282 TAAATGTTGGGGGACCT-AAATGCAAGTTT
1 TAAATGTTGGGGGA-CTGAAATGCAAGTTT
90311 CAGAAATGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.28, C:0.09, G:0.29, T:0.34
Consensus pattern (29 bp):
TAAATGTTGGGGGACTGAAATGCAAGTTT
Found at i:90587 original size:82 final size:82
Alignment explanation
Indices: 90480--90768 Score: 324
Period size: 82 Copynumber: 3.5 Consensus size: 82
90470 TATTATAGCG
* * * * *
90480 TTTGTAAAAAAATACCGCTATAGTACTACTTTGTTGTGGCGTTAT-TTCAAAAAAATGCCACTAT
1 TTTGTATAAAAACACCGCTAAAGTACTACTTTATTGTGGCGTT-TGTTGAAAAAAA-GCCACTAT
*
90544 AGATTAA-CCTATTGCGGTA
64 AGATGAACCCTATTGCGG-A
* * *
90563 TTTGTAT-AAAACACCGCTAAAGTACTACTTTATTATGACGTTTGTTGAAAAACA-CCACTATAG
1 TTTGTATAAAAACACCGCTAAAGTACTACTTTATTGTGGCGTTTGTTGAAAAAAAGCCACTATAG
*
90626 ATGAATCCTATTGCGGA
66 ATGAACCCTATTGCGGA
* * * *
90643 GTTTGTATAAAAACGCCGCTAAAGTATTACTCTATTGCGGCGTTTGTTGAAAAAAAG-CACTATA
1 -TTTGTATAAAAACACCGCTAAAGTACTACTTTATTGTGGCGTTTGTTGAAAAAAAGCCACTATA
*
90707 GATGAACCCTATTGCGGCG
65 GATGAACCCTATTGCGG-A
*
90726 TTTGTATAAAAACGCCGCTAAAGT--TACTATT-TTGTGGCGTTTG
1 TTTGTATAAAAACACCGCTAAAGTACTACT-TTATTGTGGCGTTTG
90769 GAATATAAAC
Statistics
Matches: 179, Mismatches: 20, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
80 29 0.16
81 19 0.11
82 125 0.70
83 6 0.03
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (82 bp):
TTTGTATAAAAACACCGCTAAAGTACTACTTTATTGTGGCGTTTGTTGAAAAAAAGCCACTATAG
ATGAACCCTATTGCGGA
Found at i:90647 original size:41 final size:41
Alignment explanation
Indices: 90601--90738 Score: 147
Period size: 41 Copynumber: 3.4 Consensus size: 41
90591 TTTATTATGA
90601 CGTTTGT-TGAAAAACACCACTATAGATGAATCCTATTGCGG
1 CGTTTGTAT-AAAAACACCACTATAGATGAATCCTATTGCGG
* * * * * *
90642 AGTTTGTATAAAAACGCCGCTAAAGTATTACT-CTATTGCGG
1 CGTTTGTATAAAAACACCACTATAG-ATGAATCCTATTGCGG
* * *
90683 CGTTTGT-TGAAAAAAAGCACTATAGATGAACCCTATTGCGG
1 CGTTTGTAT-AAAAACACCACTATAGATGAATCCTATTGCGG
90724 CGTTTGTATAAAAAC
1 CGTTTGTATAAAAAC
90739 GCCGCTAAAG
Statistics
Matches: 76, Mismatches: 16, Indels: 10
0.75 0.16 0.10
Matches are distributed among these distances:
40 4 0.05
41 66 0.87
42 6 0.08
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (41 bp):
CGTTTGTATAAAAACACCACTATAGATGAATCCTATTGCGG
Found at i:93760 original size:24 final size:24
Alignment explanation
Indices: 93733--93782 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
93723 ATAAAGAACC
*
93733 AAAATAAA-CTTAAACATATCATTA
1 AAAATAAAGCTTAAACAT-CCATTA
*
93757 AAAATAAAGTTTAAACATCCATTA
1 AAAATAAAGCTTAAACATCCATTA
93781 AA
1 AA
93783 CCAATCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAAGCTTAAACATCCATTA
Found at i:97072 original size:3 final size:3
Alignment explanation
Indices: 97064--97088 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
97054 GAATAGGGTT
97064 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
97089 CCTTTTTTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:97360 original size:31 final size:31
Alignment explanation
Indices: 97299--97360 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 31
97289 TATTGTTATG
*
97299 TTATAATTTTTTGATATATTTATAATATTAA
1 TTATAATTTTTTGATATATTTATAAAATTAA
97330 TTATAA-TTTTTG-TAATATTTATAAAAATTAA
1 TTATAATTTTTTGAT-ATATTTAT-AAAATTAA
97361 AATGTGACCG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 1 0.04
30 14 0.50
31 13 0.46
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (31 bp):
TTATAATTTTTTGATATATTTATAAAATTAA
Found at i:98678 original size:19 final size:19
Alignment explanation
Indices: 98636--98687 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
98626 TTTAAAGATT
* *
98636 TAAAATTTATAAAATTATAT
1 TAAAATTTAT-AAATAATAA
98656 TAAAATTTATAAATAATAA
1 TAAAATTTATAAATAATAA
98675 T-AAATATTATAAA
1 TAAAAT-TTATAAA
98688 CTTGAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 4 0.14
19 15 0.52
20 10 0.34
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAAATTTATAAATAATAA
Found at i:100411 original size:194 final size:194
Alignment explanation
Indices: 100172--100605 Score: 593
Period size: 194 Copynumber: 2.2 Consensus size: 194
100162 ATTGAAATTT
* * * * * **
100172 GTATCGATACTTTTCTAAATATATGCACCAAATTATCGATACTTTAGGAATTTTAAAA-AATTGT
1 GTATCGATACTTTTATAAGTATATGTATCATATTATCGATACTTTAGGAA-TTTAAAAGAATTAA
* * * * *
100236 AATAATAGCGCATATAAAGTATCGATACTTTATAAACATGTATCGATACATAACAATATTACAGG
65 AATAATAGCGCATATAAAGTATCCATACTTTAGAAACATGTATCAATACATAACAATATAACAAG
* *
100301 TAAAAATATGA-AAAAGTCGGTTTCAATATGAAAAAACCGGTAAAGAGCAATCGGATATGTTGAA
130 TAAAAATATGACAAAA-CCAGTTTCAATATGAAAAAACCGGTAAAGAGCAATCGGATATGTTGAA
100365 G
194 G
* * *
100366 GTATCGATACTTTTATAAGTATATATATCATACTATCGATACTTTATGAATTTAAAAGAATTAAA
1 GTATCGATACTTTTATAAGTATATGTATCATATTATCGATACTTTAGGAATTTAAAAGAATTAAA
* * * *
100431 ATAGTAGCGCCTATAAAGTATCCATACTTTAGAAATATGTATCAATACATGACAATATAACAAGT
66 ATAATAGCGCATATAAAGTATCCATACTTTAGAAACATGTATCAATACATAACAATATAACAAGT
* * * *
100496 TAAAATATGACAAAACCAGTTTCAATATGACAAAACCGGTAAAGCGCTATCGGATATGTTGAAG
131 AAAAATATGACAAAACCAGTTTCAATATGAAAAAACCGGTAAAGAGCAATCGGATATGTTGAAG
* *
100560 GTATCGATACTTTAATAAGTGTATGTATCATATTATCGATACTTTA
1 GTATCGATACTTTTATAAGTATATGTATCATATTATCGATACTTTA
100606 AAAAGAAAAA
Statistics
Matches: 209, Mismatches: 29, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
193 7 0.03
194 198 0.95
195 4 0.02
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.32
Consensus pattern (194 bp):
GTATCGATACTTTTATAAGTATATGTATCATATTATCGATACTTTAGGAATTTAAAAGAATTAAA
ATAATAGCGCATATAAAGTATCCATACTTTAGAAACATGTATCAATACATAACAATATAACAAGT
AAAAATATGACAAAACCAGTTTCAATATGAAAAAACCGGTAAAGAGCAATCGGATATGTTGAAG
Found at i:101259 original size:19 final size:19
Alignment explanation
Indices: 101201--101269 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
101191 TTATAAAGTG
101201 ATATTATAGGTAGAAAATAA
1 ATATTATAGGTAGAAAAT-A
* * * *
101221 ATATTGATA-CTTGTATATA
1 ATATT-ATAGGTAGAAAATA
101240 ATATTATAGGTAGAAAATA
1 ATATTATAGGTAGAAAATA
*
101259 ATATTGTAGGT
1 ATATTATAGGT
101270 TATATAAATG
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
18 3 0.08
19 22 0.58
20 10 0.26
21 3 0.08
ACGTcount: A:0.45, C:0.01, G:0.16, T:0.38
Consensus pattern (19 bp):
ATATTATAGGTAGAAAATA
Found at i:101320 original size:231 final size:231
Alignment explanation
Indices: 100909--101325 Score: 701
Period size: 231 Copynumber: 1.8 Consensus size: 231
100899 AAATAGGGGT
*
100909 TTTATGGGTTTGGGGGTTTCAAAGCAAAGAAGGATTTCAGACCGATTAGAGTTAGAAAGTGATAT
1 TTTATGGGTTTGGGGATTTCAAAGCAAAGAAGGATTTCAGACCGATTAGAGTTAGAAAGTGATAT
*
100974 TATAGGTAGAAAATAAATATCGATACTTGTATATAATATTATAGGTAGAAAATGATATTGTAGGT
66 TATAGGTAGAAAATAAATATCGATACTTGTATATAATATTATAGGTAGAAAATAATATTGTAGGT
* *
101039 TGTATAAATGTACTGATACTTGTAGTAGAGAGTATTCCCATTCGTTTGAAGGAAACCCTAGTTTT
131 TATATAAATGTACTGATACTTGTAATAGAGAGTATTCCCATTCGTTTGAAGGAAACCCTAGTTTT
101104 TTTTAGTATTATAGTAATCATAAATAGGGATTAGGG
196 TTTTAGTATTATAGTAATCATAAATAGGGATTAGGG
** ** *
101140 TTTATGGGTTTGGGGATTTTGAAGCAAAGAAGGATTTGGGACCGATTAGAGTTATAAAGTGATAT
1 TTTATGGGTTTGGGGATTTCAAAGCAAAGAAGGATTTCAGACCGATTAGAGTTAGAAAGTGATAT
*
101205 TATAGGTAGAAAATAAATATTGATACTTGTATATAATATTATAGGTAGAAAATAATATTGTAGGT
66 TATAGGTAGAAAATAAATATCGATACTTGTATATAATATTATAGGTAGAAAATAATATTGTAGGT
** *
101270 TATATAAATGTA-TCGATACTTGTAATAGAGAGTATTCTGATTCTTTTGAAGGAAAC
131 TATATAAATGTACT-GATACTTGTAATAGAGAGTATTCCCATTCGTTTGAAGGAAAC
101326 TGTTTTACTA
Statistics
Matches: 172, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
230 1 0.01
231 171 0.99
ACGTcount: A:0.36, C:0.06, G:0.22, T:0.35
Consensus pattern (231 bp):
TTTATGGGTTTGGGGATTTCAAAGCAAAGAAGGATTTCAGACCGATTAGAGTTAGAAAGTGATAT
TATAGGTAGAAAATAAATATCGATACTTGTATATAATATTATAGGTAGAAAATAATATTGTAGGT
TATATAAATGTACTGATACTTGTAATAGAGAGTATTCCCATTCGTTTGAAGGAAACCCTAGTTTT
TTTTAGTATTATAGTAATCATAAATAGGGATTAGGG
Found at i:104377 original size:13 final size:13
Alignment explanation
Indices: 104359--104420 Score: 61
Period size: 13 Copynumber: 4.8 Consensus size: 13
104349 TGCGTCATAA
*
104359 ATTTATGACGCGC
1 ATTTATGACGCAC
* *
104372 ATTTATGGCACAC
1 ATTTATGACGCAC
*
104385 ATTTATGACACAC
1 ATTTATGACGCAC
* **
104398 ATTTATGATGCGT
1 ATTTATGACGCAC
104411 ATTTATGACG
1 ATTTATGACG
104421 TTCATTGAGC
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (13 bp):
ATTTATGACGCAC
Found at i:109947 original size:15 final size:15
Alignment explanation
Indices: 109927--109957 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
109917 GATACTCGAA
109927 ACCCTTCTCTTGAAC
1 ACCCTTCTCTTGAAC
109942 ACCCTTCTCTTGAAC
1 ACCCTTCTCTTGAAC
109957 A
1 A
109958 ACAAAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.39, G:0.06, T:0.32
Consensus pattern (15 bp):
ACCCTTCTCTTGAAC
Found at i:110861 original size:201 final size:195
Alignment explanation
Indices: 110489--112059 Score: 1121
Period size: 200 Copynumber: 8.0 Consensus size: 195
110479 TTTCGATCCT
* * ** * * *
110489 TTTTGTCCAGTATGCTTCCCAAACTGGAAGTAAAAAGAAAATATCGATACATGTATGAAAAATAT
1 TTTT-TCCAGTATGCATCCTAAACAAGAAGTAAAAAGAAAGTATCGATACAAGTATG-AAAGTAT
* * * * * *
110554 CAATTCTTAAAAATTCGAAATCGATTAACTTAAAGTAATAAGTAAATTTACAATGTTATCGATAA
64 CAATTCTTAAAACTTCGAAACCGATT-ATTTAAAGTAATAGGTAAATTTACAATG-TAGCGGTAA
* * ** * * *
110619 AAAGATA-CATGTTT-ATGATAAAATATATTAACATAAAGTATCGATACTTTTTGTATGTGTACC
127 AAATATACCA-GTTTAATGACAAAATACGTAAACATAAAGTATCGATACTTTTTGTATTTGTATC
110682 GATAC
191 GATAC
* *
110687 TTTCTTCCAGTATGTATCCTAAACTTAAGTAAGTAAAAAGAAAGTATCAATACAAGTATGAAATG
1 TTT-TTCCAGTATGCATCCTAAAC--AAG-AAGTAAAAAGAAAGTATCGATACAAGTATGAAA-G
* *
110752 TATCAATTCTTAAAACTTTGAAACCGATTATTTGAAGGTAATAGGTAAATTTACAATGTAGCGGT
61 TATCAATTCTTAAAACTTCGAAACCGATTATTT-AAAGTAATAGGTAAATTTACAATGTAGCGGT
* *
110817 AAAAATATACCAGTTTAATGACAAGATACGTAAACATAAAGTATCAATAC--TTTGTATTTGTAT
125 AAAAATATACCAGTTTAATGACAAAATACGTAAACATAAAGTATCGATACTTTTTGTATTTGTAT
*
110880 CGATATT
190 CGATA-C
* * * * * *
110887 TTTTGTCCAGTATGCATCCTAAACGAGATGCACACATAAAGTATCGATACACA-TATGAGAAGTA
1 TTTT-TCCAGTATGCATCCTAAACAAGAAGTAAAAAGAAAGTATCGATACA-AGTATGA-AAGTA
* * *
110951 TCGATTC-TGAAACTTCGAAACCGATTAGTATAAAGTAATAGGTAAATTTACAATGTAAGCGGTA
63 TCAATTCTTAAAACTTCGAAACCGATTA-TTTAAAGTAATAGGTAAATTTACAATGT-AGCGGTA
** *
111015 AAAATATACTGGTTTAATGACAAAATACGTAAACACAAAGTATCGATACTTTTTGTATTTGTATC
126 AAAATATACCAGTTTAATGACAAAATACGTAAACATAAAGTATCGATACTTTTTGTATTTGTATC
111080 GATAC
191 GATAC
* * ** * * * *
111085 TAATTTTCCAGTATGCTTTCC-AAACTAG-A-TACACGCAGAAAGTATTGATTC---T-TAAAAC
1 T--TTTTCCAGTATGC-ATCCTAAACAAGAAGTA-A-AAAGAAAGTATCGATACAAGTATGAAAG
** ** * * ** * * * *
111143 T-T-AGAAACTTATTAGTAT--AAA--GTAATAGATAAA-T-TTA--TAATATATGC--GGTA--
61 TATCA-ATTCTTAAAACT-TCGAAACCG-ATTATTTAAAGTAATAGGTAA-ATTTACAATGTAGC
* * *
111194 --AA--AATATA-CATGTTTAATGACAAAATACATAAACACAAAGTATCGATACTTTTTGTATTT
122 GGTAAAAATATACCA-GTTTAATGACAAAATACGTAAACATAAAGTATCGATACTTTTTGTATTT
111254 GTATCGATAC
186 GTATCGATAC
* * * ** * * *** * *
111264 TAATTGTCCAATATGCTTTCC-AAACTTGATGCACGCAGAAAGTATCAATACATGTATGAGAAGT
1 T--TTTTCCAGTATGC-ATCCTAAACAAGAAGTAAAAAGAAAGTATCGATACAAGTATGA-AAGT
*
111328 ATCAATTCTTAAAACTTCGAAACCGATTAGTATAAAGTAATAGGTAAATTTA-AA---A----T-
62 ATCAATTCTTAAAACTTCGAAACCGATTA-TTTAAAGTAATAGGTAAATTTACAATGTAGCGGTA
* * *
111384 ATAATATACCAGTTTAATGACAAGATACGTAAACATAAAGTATCGATACTTTTTGTATGTGTATC
126 AAAATATACCAGTTTAATGACAAAATACGTAAACATAAAGTATCGATACTTTTTGTATTTGTATC
111449 GATAC
191 GATAC
* * * * * **
111454 TTTTTGTCTAGTATGCATCCCAAACGAG-A-TACACACATAAAGTATCGATACACTTATGTAAAG
1 -TTTT-TCCAGTATGCATCCTAAACAAGAAGTA-A-AAAGAAAGTATCGATACAAGTATG-AAAG
* * * * * *
111517 TATCGATTCTTAAAACTTCAAAACCAATTAATTTAAGGTAATAGGTAAATTTACAAGGTTAGAGG
61 TATCAATTCTTAAAACTTCGAAACCGATT-ATTTAAAGTAATAGGTAAATTTACAATG-TAGCGG
* * *
111582 TAAAAATATACCGGTTTAAAGACAAAATACGTAAACATGAAGTATCGATACTTTTTGTATTTGTA
124 TAAAAATATACCAGTTTAATGACAAAATACGTAAACATAAAGTATCGATACTTTTTGTATTTGTA
111647 TCGATAC
189 TCGATAC
** * * * *** * *
111654 TTTTTTGTCCAGTATGTTTTCC-AAACTAGATGCACGCAGAAAGTATCGATACACGTACGATAAG
1 --TTTT-TCCAGTATG-CATCCTAAACAAGAAGTAAAAAGAAAGTATCGATACAAGTATGA-AAG
* * ** * *
111718 TATCGATTCTTAAAACTTCAAAACTAATTAATATAAAGTAATAGGTAAATTTACAATGTAAGTGG
61 TATCAATTCTTAAAACTTCGAAACCGATT-ATTTAAAGTAATAGGTAAATTTACAATGT-AGCGG
* * * * * *
111783 TAAAAATATACCGGTTTAGTGAAAAAATACGTAAACACAAAGTATCAATACTTTTTGTATGTGTA
124 TAAAAATATACCAGTTTAATGACAAAATACGTAAACATAAAGTATCGATACTTTTTGTATTTGTA
111848 TCGATAC
189 TCGATAC
* * * * *** * * *
111855 TTTTTGTCCAGTATGCTTTCC-AAACTAGATGCATGTAGAAAGTATCGATACACGTACGAGAGGT
1 -TTTT-TCCAGTATGC-ATCCTAAACAAGAAGTAAAAAGAAAGTATCGATACAAGTATGA-AAGT
* * * * *
111919 ATCGATTCTTAAAAATTCAAAACCGATTAGTATAAAGTAATAAGTAAATTTACAATGTAAGCGGT
62 ATCAATTCTTAAAACTTCGAAACCGATTA-TTTAAAGTAATAGGTAAATTTACAATGT-AGCGGT
* * * *
111984 AAAAATATA-CATGTTTAATGACAAAATACGTAAACACAAAGTATCAATATTTTTTGTATGTGTA
125 AAAAATATACCA-GTTTAATGACAAAATACGTAAACATAAAGTATCGATACTTTTTGTATTTGTA
112048 TCGATAC
189 TCGATAC
112055 TTTTT
1 TTTTT
112060 GTCTAGTATG
Statistics
Matches: 1135, Mismatches: 162, Indels: 152
0.78 0.11 0.10
Matches are distributed among these distances:
179 103 0.09
181 2 0.00
182 1 0.00
183 2 0.00
184 4 0.00
185 9 0.01
186 6 0.01
187 6 0.01
188 11 0.01
189 9 0.01
190 145 0.13
191 16 0.01
192 6 0.01
193 6 0.01
194 6 0.01
195 4 0.00
196 43 0.04
197 86 0.08
198 26 0.02
199 72 0.06
200 298 0.26
201 270 0.24
202 3 0.00
203 1 0.00
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (195 bp):
TTTTTCCAGTATGCATCCTAAACAAGAAGTAAAAAGAAAGTATCGATACAAGTATGAAAGTATCA
ATTCTTAAAACTTCGAAACCGATTATTTAAAGTAATAGGTAAATTTACAATGTAGCGGTAAAAAT
ATACCAGTTTAATGACAAAATACGTAAACATAAAGTATCGATACTTTTTGTATTTGTATCGATAC
Found at i:111178 original size:179 final size:178
Alignment explanation
Indices: 110946--111309 Score: 577
Period size: 179 Copynumber: 2.0 Consensus size: 178
110936 CACATATGAG
* * * *
110946 AAGTATCGATTCTGAAACTTCGAAACCGATTAGTATAAAGTAATAGGTAAATTTACAATGTAAGC
1 AAGTATCGATTCTAAAACTTAGAAACCGATTAGTATAAAGTAATAGATAAATTTACAATATAAGC
*
111011 GGTAAAAATATAC-TGGTTTAATGACAAAATACGTAAACACAAAGTATCGATACTTTTTGTATTT
66 GGTAAAAATATACAT-GTTTAATGACAAAATACATAAACACAAAGTATCGATACTTTTTGTATTT
* *
111075 GTATCGATACTAATTTTCCAGTATGCTTTCCAAACTAGATACACGCAGA
130 GTATCGATACTAATTGTCCAATATGCTTTCCAAACTAGATACACGCAGA
* ** * *
111124 AAGTATTGATTCTTAAAACTTAGAAACTTATTAGTATAAAGTAATAGATAAATTTATAATATATG
1 AAGTATCGATTC-TAAAACTTAGAAACCGATTAGTATAAAGTAATAGATAAATTTACAATATAAG
111189 CGGTAAAAATATACATGTTTAATGACAAAATACATAAACACAAAGTATCGATACTTTTTGTATTT
65 CGGTAAAAATATACATGTTTAATGACAAAATACATAAACACAAAGTATCGATACTTTTTGTATTT
* *
111254 GTATCGATACTAATTGTCCAATATGCTTTCCAAACTTGATGCACGCAGA
130 GTATCGATACTAATTGTCCAATATGCTTTCCAAACTAGATACACGCAGA
111303 AAGTATC
1 AAGTATC
111310 AATACATGTA
Statistics
Matches: 169, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
178 11 0.07
179 157 0.93
180 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (178 bp):
AAGTATCGATTCTAAAACTTAGAAACCGATTAGTATAAAGTAATAGATAAATTTACAATATAAGC
GGTAAAAATATACATGTTTAATGACAAAATACATAAACACAAAGTATCGATACTTTTTGTATTTG
TATCGATACTAATTGTCCAATATGCTTTCCAAACTAGATACACGCAGA
Found at i:111649 original size:200 final size:199
Alignment explanation
Indices: 111154--112069 Score: 1170
Period size: 200 Copynumber: 4.6 Consensus size: 199
111144 TAGAAACTTA
* * * **
111154 TTAGTATAAAGTAATAGATAAATTTATAA-TATATGCGGTAAAAATATACATGTTTAATGACAAA
1 TTAGTATAAAGTAATAGGTAAATTTACAAGTA-A-GAGGTAAAAATATACCGGTTTAATGACAAA
* * ** *
111218 ATACATAAACACAAAGTATCGATACTTTTTGTATTTGTATCGATACTAATTGTCCAATATGCTTT
64 ATACGTAAACACAAAGTATCGATACTTTTTGTATGTGTATCGATACTTTTTGTCCAGTATGCTTT
* * * * * *
111283 CCAAACTTGATGCACGCAGAAAGTATCAATACATGTATGAGAAGTATCAATTCTTAAAACTTCGA
129 CCAAACTAGATGCACGCAGAAAGTATCGATACACGTACGAGAAGTATCGATTCTTAAAACTTCAA
*
111348 AACCGA
194 AACCAA
* * *
111354 TTAGTATAAAGTAATAGGTAAATTT---A--AA-A--T-ATAATATACCAGTTTAATGACAAGAT
1 TTAGTATAAAGTAATAGGTAAATTTACAAGTAAGAGGTAAAAATATACCGGTTTAATGACAAAAT
* * * *
111410 ACGTAAACATAAAGTATCGATACTTTTTGTATGTGTATCGATACTTTTTGTCTAGTATGCATCCC
66 ACGTAAACACAAAGTATCGATACTTTTTGTATGTGTATCGATACTTTTTGTCCAGTATGCTTTCC
* * * * * *
111475 AAACGAGATACACACATAAAGTATCGATACACTTATGTA-AAGTATCGATTCTTAAAACTTCAAA
131 AAACTAGATGCACGCAGAAAGTATCGATACACGTACG-AGAAGTATCGATTCTTAAAACTTCAAA
111539 ACCAA
195 ACCAA
* * * * *
111544 TTAATTTAAGGTAATAGGTAAATTTACAAGGTTAGAGGTAAAAATATACCGGTTTAAAGACAAAA
1 TTAGTATAAAGTAATAGGTAAATTTACAA-GTAAGAGGTAAAAATATACCGGTTTAATGACAAAA
** * *
111609 TACGTAAACATGAAGTATCGATACTTTTTGTATTTGTATCGATACTTTTTTGTCCAGTATGTTTT
65 TACGTAAACACAAAGTATCGATACTTTTTGTATGTGTATCGATAC-TTTTTGTCCAGTATGCTTT
*
111674 CCAAACTAGATGCACGCAGAAAGTATCGATACACGTACGATAAGTATCGATTCTTAAAACTTCAA
129 CCAAACTAGATGCACGCAGAAAGTATCGATACACGTACGAGAAGTATCGATTCTTAAAACTTCAA
*
111739 AACTAA
194 AACCAA
* * * *
111745 TTAATATAAAGTAATAGGTAAATTTACAATGTAAGTGGTAAAAATATACCGGTTTAGTGAAAAAA
1 TTAGTATAAAGTAATAGGTAAATTTACAA-GTAAGAGGTAAAAATATACCGGTTTAATGACAAAA
*
111810 TACGTAAACACAAAGTATCAATACTTTTTGTATGTGTATCGATACTTTTTGTCCAGTATGCTTTC
65 TACGTAAACACAAAGTATCGATACTTTTTGTATGTGTATCGATACTTTTTGTCCAGTATGCTTTC
* * * *
111875 CAAACTAGATGCATGTAGAAAGTATCGATACACGTACGAGAGGTATCGATTCTTAAAAATTCAAA
130 CAAACTAGATGCACGCAGAAAGTATCGATACACGTACGAGAAGTATCGATTCTTAAAACTTCAAA
*
111940 ACCGA
195 ACCAA
* * **
111945 TTAGTATAAAGTAATAAGTAAATTTACAATGTAAGCGGTAAAAATATACATGTTTAATGACAAAA
1 TTAGTATAAAGTAATAGGTAAATTTACAA-GTAAGAGGTAAAAATATACCGGTTTAATGACAAAA
* * *
112010 TACGTAAACACAAAGTATCAATATTTTTTGTATGTGTATCGATACTTTTTGTCTAGTATG
65 TACGTAAACACAAAGTATCGATACTTTTTGTATGTGTATCGATACTTTTTGTCCAGTATG
112070 AAAACACCGA
Statistics
Matches: 627, Mismatches: 76, Indels: 26
0.86 0.10 0.04
Matches are distributed among these distances:
190 156 0.25
191 2 0.00
193 1 0.00
195 1 0.00
196 2 0.00
197 2 0.00
199 1 0.00
200 287 0.46
201 175 0.28
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.33
Consensus pattern (199 bp):
TTAGTATAAAGTAATAGGTAAATTTACAAGTAAGAGGTAAAAATATACCGGTTTAATGACAAAAT
ACGTAAACACAAAGTATCGATACTTTTTGTATGTGTATCGATACTTTTTGTCCAGTATGCTTTCC
AAACTAGATGCACGCAGAAAGTATCGATACACGTACGAGAAGTATCGATTCTTAAAACTTCAAAA
CCAA
Found at i:111668 original size:21 final size:21
Alignment explanation
Indices: 111622--111668 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
111612 GTAAACATGA
**
111622 AGTATCGATACTTTTTGTATT
1 AGTATCGATACTTTTTGTACC
*
111643 TGTATCGATACTTTTTTGT-CC
1 AGTATCGATAC-TTTTTGTACC
111664 AGTAT
1 AGTAT
111669 GTTTTCCAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.21, C:0.13, G:0.15, T:0.51
Consensus pattern (21 bp):
AGTATCGATACTTTTTGTACC
Found at i:111923 original size:401 final size:390
Alignment explanation
Indices: 111123--112069 Score: 1189
Period size: 401 Copynumber: 2.4 Consensus size: 390
111113 ATACACGCAG
* * ** * * **
111123 AAAGTATTGATTCTTAAAACTT-AGAAACTTATTAGTATAAAGTAAT-AGATAAATTTATAATAT
1 AAAGTATCGATTCTTAAAAATTCA-AAACCAATTAATATAAAGTAATAAG-TAAATTTACAAGGT
* * *
111186 ATGCGGTAAAAATATACATGTTTAATGACAAAATACATAAACACAAAGTATCGATACTTTTTGTA
64 AAGAGGTAAAAATATACATGTTTAATGACAAAATACGTAAACACAAAGTATCGATACTTTTTGTA
** * *
111251 TTTGTATCGATACTAATTGTCCAATATGCTTTCCAAACTTGATGCACGCAGAAAGTATCAATACA
129 TTTGTATCGATACTTTTTGTCCAGTATGCTTTCCAAACTAGATGCACGCAGAAAGTATCAATACA
* * * * *
111316 TGTATGAGAAGTATCAATTCTTAAAACTTCGAAACCGATTAGTATAAAGTAATAGGTAAATTTAA
194 CGTACGAGAAGTATCAATTCTTAAAACTTCAAAACCAATTAATATAAAGTAATAGGTAAATTTAA
* * * * *
111381 AATATAATATACCAGTTTAATGACAAGATACGTAAACATAAAGTATCGATACTTTTTGTATGTGT
259 AATAAAATATACCAGTTTAATGAAAAAATACGTAAACACAAAGTATCAATACTTTTTGTATGTGT
* * * *
111446 ATCGATACTTTTTGTCTAGTATGCATCCCAAACGAGATACACACATAAAGTATCGATACACTTAT
324 ATCGATACTTTTTGTCCAGTATGCATCCCAAACGAGATACACACAGAAAGTATCGATACACGTAC
111511 GT
389 GT
* * * * *
111513 AAAGTATCGATTCTTAAAACTTCAAAACCAATTAATTTAAGGTAATAGGTAAATTTACAAGGTTA
1 AAAGTATCGATTCTTAAAAATTCAAAACCAATTAATATAAAGTAATAAGTAAATTTACAAGGTAA
** * **
111578 GAGGTAAAAATATACCGGTTTAAAGACAAAATACGTAAACATGAAGTATCGATACTTTTTGTATT
66 GAGGTAAAAATATACATGTTTAATGACAAAATACGTAAACACAAAGTATCGATACTTTTTGTATT
* *
111643 TGTATCGATACTTTTTTGTCCAGTATGTTTTCCAAACTAGATGCACGCAGAAAGTATCGATACAC
131 TGTATCGATAC-TTTTTGTCCAGTATGCTTTCCAAACTAGATGCACGCAGAAAGTATCAATACAC
* * *
111708 GTACGATAAGTATCGATTCTTAAAACTTCAAAACTAATTAATATAAAGTAATAGGTAAATTTACA
195 GTACGAGAAGTATCAATTCTTAAAACTTCAAAACCAATTAATATAAAGTAATAGGTAAATTT--A
* *
111773 ATGTAAGTGGTAAAAATATACCGGTTTAGTGAAAAAATACGTAAACACAAAGTATCAATACTTTT
258 A---AA----T-AAAATATACCAGTTTAATGAAAAAATACGTAAACACAAAGTATCAATACTTTT
* * * * ***
111838 TGTATGTGTATCGATACTTTTTGTCCAGTATGCTTTCCAAACTAGATGCATGTAGAAAGTATCGA
315 TGTATGTGTATCGATACTTTTTGTCCAGTATGCATCCCAAACGAGATACACACAGAAAGTATCGA
111903 TACACGTACG-
380 TACACGTACGT
* * * *
111913 AGAGGTATCGATTCTTAAAAATTCAAAACCGATTAGTATAAAGTAATAAGTAAATTTACAATGTA
1 A-AAGTATCGATTCTTAAAAATTCAAAACCAATTAATATAAAGTAATAAGTAAATTTACAAGGTA
* * *
111978 AGCGGTAAAAATATACATGTTTAATGACAAAATACGTAAACACAAAGTATCAATATTTTTTGTAT
65 AGAGGTAAAAATATACATGTTTAATGACAAAATACGTAAACACAAAGTATCGATACTTTTTGTAT
* *
112043 GTGTATCGATACTTTTTGTCTAGTATG
130 TTGTATCGATACTTTTTGTCCAGTATG
112070 AAAACACCGA
Statistics
Matches: 473, Mismatches: 70, Indels: 18
0.84 0.12 0.03
Matches are distributed among these distances:
390 118 0.25
391 103 0.22
393 2 0.00
396 2 0.00
400 16 0.03
401 232 0.49
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (390 bp):
AAAGTATCGATTCTTAAAAATTCAAAACCAATTAATATAAAGTAATAAGTAAATTTACAAGGTAA
GAGGTAAAAATATACATGTTTAATGACAAAATACGTAAACACAAAGTATCGATACTTTTTGTATT
TGTATCGATACTTTTTGTCCAGTATGCTTTCCAAACTAGATGCACGCAGAAAGTATCAATACACG
TACGAGAAGTATCAATTCTTAAAACTTCAAAACCAATTAATATAAAGTAATAGGTAAATTTAAAA
TAAAATATACCAGTTTAATGAAAAAATACGTAAACACAAAGTATCAATACTTTTTGTATGTGTAT
CGATACTTTTTGTCCAGTATGCATCCCAAACGAGATACACACAGAAAGTATCGATACACGTACGT
Found at i:114860 original size:15 final size:15
Alignment explanation
Indices: 114840--114869 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
114830 AAGAGAAGAA
114840 AACATTGTTATGTAT
1 AACATTGTTATGTAT
*
114855 AACATTGTTTTGTAT
1 AACATTGTTATGTAT
114870 GTATGTTTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (15 bp):
AACATTGTTATGTAT
Found at i:115131 original size:6 final size:6
Alignment explanation
Indices: 115120--115261 Score: 97
Period size: 6 Copynumber: 23.7 Consensus size: 6
115110 TTTATGCAGT
* * * *
115120 TTTCAA TTTCAA TTTCAGA -CTGAA TTTCAT TTTCAA TTTCAA TTTTAA
1 TTTCAA TTTCAA TTTCA-A TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
*** * * * * *
115168 TTTGTG TTTCAA TTTTAA TATCAA TTTTAA TTTGAG TTTCAA TTTCAA
1 TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
* * * * * * *
115216 TATCAA TTTTAA TTTTAA TTTGAG TTTGAA TTTTAA TTTCAA TTTC
1 TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTC
115262 GGCCCCACTA
Statistics
Matches: 104, Mismatches: 30, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
5 1 0.01
6 102 0.98
7 1 0.01
ACGTcount: A:0.30, C:0.10, G:0.06, T:0.54
Consensus pattern (6 bp):
TTTCAA
Found at i:115254 original size:30 final size:31
Alignment explanation
Indices: 115119--115260 Score: 139
Period size: 30 Copynumber: 4.5 Consensus size: 31
115109 ATTTATGCAG
* * *
115119 TTTTCAATTTCAATTTCAGA-CTGAATTTC-A
1 TTTTCAATTTCAATTTTA-ATTTGAGTTTCAA
*
115149 TTTTCAATTTCAATTTTAATTTGTGTTTCAA
1 TTTTCAATTTCAATTTTAATTTGAGTTTCAA
*
115180 TTTT-AATATCAATTTTAATTTGAGTTTCAA
1 TTTTCAATTTCAATTTTAATTTGAGTTTCAA
* *
115210 TTTCAATATCAATTTTAATTTTAATTTGAGTTTGAA
1 -TT---T-TCAATTTCAATTTTAATTTGAGTTTCAA
115246 TTTT-AATTTCAATTT
1 TTTTCAATTTCAATTT
115261 CGGCCCCACT
Statistics
Matches: 94, Mismatches: 10, Indels: 16
0.78 0.08 0.13
Matches are distributed among these distances:
29 1 0.01
30 57 0.61
31 8 0.09
32 1 0.01
34 1 0.01
35 3 0.03
36 23 0.24
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.54
Consensus pattern (31 bp):
TTTTCAATTTCAATTTTAATTTGAGTTTCAA
Found at i:115781 original size:3 final size:3
Alignment explanation
Indices: 115773--115806 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
115763 CTAAATTATC
* *
115773 TCT TCT TCT TCT ACT ACT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
115807 TCCCGTGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.06, C:0.32, G:0.00, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:117364 original size:22 final size:22
Alignment explanation
Indices: 117325--117369 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
117315 ATTATGCCAG
* ** *
117325 TTTGATTAAAAGGTTAAATGCC
1 TTTGAGTAAAAGACTAAAAGCC
117347 TTTGAGTAAAAGACTAAAAGCC
1 TTTGAGTAAAAGACTAAAAGCC
117369 T
1 T
117370 AGATGTGCAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (22 bp):
TTTGAGTAAAAGACTAAAAGCC
Found at i:117370 original size:82 final size:81
Alignment explanation
Indices: 117107--117424 Score: 404
Period size: 81 Copynumber: 3.9 Consensus size: 81
117097 ACTGTTCTAA
* * * *
117107 AGTAAAAGACTAAAAGCCTAGCTGCGCATTTGACAAAAAGGTGT-ATATTATCCCAGTTAGATGA
1 AGTAAAAGACTAAAAGCCTAGATGTGCATTTGACAGAAAGGTGTCA-ATTATGCCAGTTAGATGA
117171 AAGGTTAAATACCTTTG
65 AAGGTTAAATACCTTTG
* ** * * * * *
117188 AGTAAAAGATTAATGGCCTAGTTGTGCATTTGATATAAAGGTGTCAATGATGTCAGTTAGATGAA
1 AGTAAAAGACTAAAAGCCTAGATGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
117253 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* ** * *
117269 AGTAAAAGATTAATGGCCTAGATGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTTGATTAA
1 AGTAAAAGACTAAAAGCCTAGATGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA-TGA
*
117334 AAGGTTAAATGCCTTTG
65 AAGGTTAAATACCTTTG
* * * *
117351 AGTAAAAGACTAAAAGCCTAGATGTGCATTTGGCAGAAATGTGTCAATCATGCCAGTTAGACGAA
1 AGTAAAAGACTAAAAGCCTAGATGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
*
117416 ACGTTAAAT
66 AGGTTAAAT
117425 GCTCTAGACG
Statistics
Matches: 207, Mismatches: 28, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
81 134 0.65
82 73 0.35
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.29
Consensus pattern (81 bp):
AGTAAAAGACTAAAAGCCTAGATGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
AGGTTAAATACCTTTG
Found at i:117379 original size:163 final size:162
Alignment explanation
Indices: 117107--117424 Score: 413
Period size: 163 Copynumber: 2.0 Consensus size: 162
117097 ACTGTTCTAA
* *
117107 AGTAAAAGACTAAAAGCCTAGCTGCGCATTTGACAAAAAGGTGTATATTATCCCAGTTAGATGAA
1 AGTAAAAGACTAAAAGCCTAGATGCGCATTTGACAAAAAGGTGTATATTATCCCAGTTAGATAAA
* ** * * * *
117172 AGGTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGATATAAAGGTGTCAATG
66 AGGTTAAATACCTTTGAGTAAAAGACTAAAAGCCTAGATGTGCATTTGACAGAAAGGTGTCAATC
* * *
117237 ATGTCAGTTAGATGAAAGGTTAAATACCTTTG
131 ATGCCAGTTAGACGAAACGTTAAATACCTTTG
* ** * * * *
117269 AGTAAAAGATTAATGGCCTAGATGTGCATTTGACAGAAAGGTGTCA-ATTATGCCAGTTTGATTA
1 AGTAAAAGACTAAAAGCCTAGATGCGCATTTGACAAAAAGGTGT-ATATTATCCCAGTTAGA-TA
* * *
117333 AAAGGTTAAATGCCTTTGAGTAAAAGACTAAAAGCCTAGATGTGCATTTGGCAGAAATGTGTCAA
64 AAAGGTTAAATACCTTTGAGTAAAAGACTAAAAGCCTAGATGTGCATTTGACAGAAAGGTGTCAA
117398 TCATGCCAGTTAGACGAAACGTTAAAT
129 TCATGCCAGTTAGACGAAACGTTAAAT
117425 GCTCTAGACG
Statistics
Matches: 132, Mismatches: 22, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
162 51 0.39
163 81 0.61
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.29
Consensus pattern (162 bp):
AGTAAAAGACTAAAAGCCTAGATGCGCATTTGACAAAAAGGTGTATATTATCCCAGTTAGATAAA
AGGTTAAATACCTTTGAGTAAAAGACTAAAAGCCTAGATGTGCATTTGACAGAAAGGTGTCAATC
ATGCCAGTTAGACGAAACGTTAAATACCTTTG
Found at i:119321 original size:19 final size:19
Alignment explanation
Indices: 119284--119321 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
119274 AATTTTAAAC
*
119284 CGGTTAAAATTTGACAAAA
1 CGGTTAAAATTTGAAAAAA
119303 CGGTTAAAATTTGAAAAAA
1 CGGTTAAAATTTGAAAAAA
119322 TCAATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.08, G:0.16, T:0.26
Consensus pattern (19 bp):
CGGTTAAAATTTGAAAAAA
Found at i:119408 original size:21 final size:21
Alignment explanation
Indices: 119382--119433 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
119372 CGCCTATAAA
119382 GTATCGATACCTAAGAAACAT
1 GTATCGATACCTAAGAAACAT
119403 GTATCGATACCTAAGAAACAT
1 GTATCGATACCTAAGAAACAT
119424 GTATCGATAC
1 GTATCGATAC
119434 TTAACAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.25
Consensus pattern (21 bp):
GTATCGATACCTAAGAAACAT
Found at i:122292 original size:2 final size:2
Alignment explanation
Indices: 122285--122365 Score: 162
Period size: 2 Copynumber: 40.5 Consensus size: 2
122275 AAATGAATCG
122285 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
122327 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
122366 AGTAATAGGT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:123126 original size:23 final size:24
Alignment explanation
Indices: 123081--123126 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
123071 ATCAGCTTTA
* *
123081 ATAATGCGCTACTTATTACGTTAC
1 ATAATGCGCTACCTAATACGTTAC
*
123105 ATAAT-CGCTACCTAATATGTTA
1 ATAATGCGCTACCTAATACGTTA
123127 TTATGGTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.37
Consensus pattern (24 bp):
ATAATGCGCTACCTAATACGTTAC
Found at i:123187 original size:226 final size:224
Alignment explanation
Indices: 122784--123395 Score: 789
Period size: 226 Copynumber: 2.7 Consensus size: 224
122774 TTTTAGGCGT
* * * ** * *
122784 TAATATTGATAATAAATCAAGTAATTAACCTATTCTGTTATCGTTGGATTTCTAAGGTCTCATCA
1 TAATAATGATAATAAATTAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAA-GCCCCATCA
* *
122849 GCTTTAATAATGCGCTACATATTACGTTACAT-ATGTGATACCTAATATGTTATTATGGTTGATA
65 GCTTTAATAATGCGCTACATATTACGTTACATAAT-CGCTACCTAATATGTTATTATGGTTGATA
** * *
122913 ATGTTTCTGGTAATTAACCGATTATGTTATTGTCAAATTTCTAAGGCTCCATCAACTTAAACTTT
129 ATGTTTCCAGTAATTAACCG-TTATGTTATCGTCAAATTTCCAAGGCTCCATCAACTTAAACTTT
* *
122978 GATAACATTTTAAGTGTTGCCTAATATGTTGA
193 GATAACATTTTAAGTGTTACCTAATATGTTAA
* *
123010 TAATAATGATAATAAATTAAGTAACTAACCTATTTTGCTATCGTCAGATTTCTAAGACCCCATCA
1 TAATAATGATAATAAATTAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAG-CCCCATCA
*
123075 GCTTTAATAATGCGCTACTTATTACGTTACATAATCGCTACCTAATATGTTATTATGGTTGATAA
65 GCTTTAATAATGCGCTACATATTACGTTACATAATCGCTACCTAATATGTTATTATGGTTGATAA
* ** *
123140 TGTTTCCAGTAATTAATCTGTTATGTTATCGTCGGATTTCCAAGGCTCCATCAGCTTAAACTTTG
130 TGTTTCCAGTAATTAA-CCGTTATGTTATCGTCAAATTTCCAAGGCTCCATCAACTTAAACTTTG
*
123205 ATAACATTTTAGGTGTTACCTAATATGTTAA
194 ATAACATTTTAAGTGTTACCTAATATGTTAA
* * * * *
123236 TAATACTAATAACAAATTAAGTAATTAACCTATTTTGTTATCGTCAGATTTTCAAAGCTCCAT-A
1 TAATAATGATAATAAATTAAGTAATTAACCTATTTTGTTATCGTCAGA-TTTCTAAGCCCCATCA
* * * * * * *
123300 TGCTTTAA-AAAGATGCTACATATTACATTATATAAGCGCTACCTAATATATTATTATGCTTGAT
65 -GCTTTAATAATG-CGCTACATATTACGTTACATAATCGCTACCTAATATGTTATTATGGTTGAT
* *
123364 AATGTTTCCATTAATTAACCGGTTATATTATC
128 AATGTTTCCAGTAATTAACC-GTTATGTTATC
123396 ATTTATATTT
Statistics
Matches: 338, Mismatches: 41, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
225 6 0.02
226 321 0.95
227 11 0.03
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.40
Consensus pattern (224 bp):
TAATAATGATAATAAATTAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGCCCCATCAG
CTTTAATAATGCGCTACATATTACGTTACATAATCGCTACCTAATATGTTATTATGGTTGATAAT
GTTTCCAGTAATTAACCGTTATGTTATCGTCAAATTTCCAAGGCTCCATCAACTTAAACTTTGAT
AACATTTTAAGTGTTACCTAATATGTTAA
Found at i:133066 original size:29 final size:30
Alignment explanation
Indices: 133033--133119 Score: 74
Period size: 29 Copynumber: 3.0 Consensus size: 30
133023 GAAAATATAT
133033 TATTTGAAGTTAAAGATAATAACAAAAT-G
1 TATTTGAAGTTAAAGATAATAACAAAATAG
* * * *
133062 TATTTTTAAGTTAATA-A-AACAATAAAATAT
1 TA-TTTGAAGTTAA-AGATAATAACAAAATAG
* *
133092 TACTTGATGTT-AAGATAATAACAAAATA
1 TATTTGAAGTTAAAGATAATAACAAAATA
133120 TTTTTTAAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
27 1 0.02
28 2 0.05
29 27 0.61
30 13 0.30
31 1 0.02
ACGTcount: A:0.52, C:0.05, G:0.09, T:0.34
Consensus pattern (30 bp):
TATTTGAAGTTAAAGATAATAACAAAATAG
Found at i:133143 original size:57 final size:59
Alignment explanation
Indices: 133021--133148 Score: 172
Period size: 57 Copynumber: 2.2 Consensus size: 59
133011 TAACTTAAGG
* * * *
133021 AAGAA-AATATATTATTTGAAGTTAAAGATAATAACAAAATGTATTTTTAAGTTAATAA
1 AAGAATAAAATATTACTTGAAGTTAAAGATAATAACAAAATATATTTTTAAATTAATAA
* * *
133079 AACAATAAAATATTACTTGATGTT-AAGATAATAACAAAATAT-TTTTTAAATTGATAA
1 AAGAATAAAATATTACTTGAAGTTAAAGATAATAACAAAATATATTTTTAAATTAATAA
133136 AAGAATAAAATAT
1 AAGAATAAAATAT
133149 ATTTTTAAGT
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
57 25 0.41
58 21 0.34
59 15 0.25
ACGTcount: A:0.53, C:0.03, G:0.09, T:0.35
Consensus pattern (59 bp):
AAGAATAAAATATTACTTGAAGTTAAAGATAATAACAAAATATATTTTTAAATTAATAA
Found at i:133168 original size:2 final size:2
Alignment explanation
Indices: 133163--133198 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
133153 TTAAGTTAAA
133163 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
133199 TTAATAAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:134541 original size:28 final size:28
Alignment explanation
Indices: 134510--134572 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 28
134500 GTTAGATATG
* *
134510 AAAATTATTATTTGA-ATTTAAATTAATT
1 AAAA-TATTATTTAATATTTAAATCAATT
* *
134538 AAAATATTTTTTAATATTTGAATCAATT
1 AAAATATTATTTAATATTTAAATCAATT
134566 -AAATATT
1 AAAATATT
134573 TGAATGAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 15 0.50
28 15 0.50
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (28 bp):
AAAATATTATTTAATATTTAAATCAATT
Found at i:134572 original size:17 final size:18
Alignment explanation
Indices: 134550--134591 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
134540 AATATTTTTT
134550 AATATTTGAATCAATT-A
1 AATATTTGAATCAATTCA
*
134567 AATATTTGAATGAATTCA
1 AATATTTGAATCAATTCA
134585 AATATTT
1 AATATTT
134592 TAAAAATGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (18 bp):
AATATTTGAATCAATTCA
Found at i:134636 original size:16 final size:17
Alignment explanation
Indices: 134615--134647 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
134605 AGTAAATAGT
134615 ATTTGAA-AAACTAAAA
1 ATTTGAATAAACTAAAA
*
134631 ATTTGAATAAATTAAAA
1 ATTTGAATAAACTAAAA
134648 TAAAACTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.30
Consensus pattern (17 bp):
ATTTGAATAAACTAAAA
Found at i:135538 original size:45 final size:46
Alignment explanation
Indices: 135474--135581 Score: 139
Period size: 45 Copynumber: 2.4 Consensus size: 46
135464 AGGTGCACTA
* *
135474 AGAGTGCATCGATTCATCAAGTGCATTCGATG-TTTCA-AAATAGCC
1 AGAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-AGCC
* *
135519 AGAGTGCATCGATGCATCAAATGTATTCGATGTTTTCATAAAATCC
1 AGAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAGCC
**
135565 TCAGTGCATCGATGCAT
1 AGAGTGCATCGATGCAT
135582 GGTATGTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
45 29 0.53
46 23 0.42
47 3 0.05
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (46 bp):
AGAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAGCC
Found at i:136346 original size:14 final size:14
Alignment explanation
Indices: 136327--136354 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
136317 TCAAGCATTT
136327 AACAATCCAAAACA
1 AACAATCCAAAACA
136341 AACAATCCAAAACA
1 AACAATCCAAAACA
136355 TAAAAAACAA
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:0.64, C:0.29, G:0.00, T:0.07
Consensus pattern (14 bp):
AACAATCCAAAACA
Found at i:138294 original size:43 final size:43
Alignment explanation
Indices: 138244--138345 Score: 125
Period size: 43 Copynumber: 2.4 Consensus size: 43
138234 AAACCCAACT
* *
138244 GATGCATCGATGCA-TGGCCTTGTGCATCGATGCACATTCAAG
1 GATGCATCGATGCACTGGCATGGTGCATCGATGCACATTCAAG
* * ** *
138286 GCGTGCATCGGTGCACTTTCATGGTGTATCGATGCACATTCAAG
1 G-ATGCATCGATGCACTGGCATGGTGCATCGATGCACATTCAAG
138330 GATGCATCGATGCACT
1 GATGCATCGATGCACT
138346 ATTAGGTGTA
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
42 1 0.02
43 24 0.49
44 24 0.49
ACGTcount: A:0.23, C:0.24, G:0.26, T:0.27
Consensus pattern (43 bp):
GATGCATCGATGCACTGGCATGGTGCATCGATGCACATTCAAG
Found at i:138295 original size:23 final size:22
Alignment explanation
Indices: 138265--138344 Score: 99
Period size: 22 Copynumber: 3.6 Consensus size: 22
138255 GCATGGCCTT
138265 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
138287 CGTGCATCGGTGCACTTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
138309 GTGTATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
*
138331 ATGCATCGATGCAC
1 GTGCATCGATGCAC
138345 TATTAGGTGT
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
21 15 0.32
22 16 0.34
23 16 0.34
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:138319 original size:44 final size:42
Alignment explanation
Indices: 138269--138363 Score: 138
Period size: 44 Copynumber: 2.2 Consensus size: 42
138259 GGCCTTGTGC
* *
138269 ATCGATGCACATTCAAGGCGTGCATCGGTGCACT-TTCATGGTGT
1 ATCGATGCACATTCAAGG-ATGCATCGATGCACTATT-A-GGTGT
138313 ATCGATGCACATTCAAGGATGCATCGATGCACTATTAGGTGT
1 ATCGATGCACATTCAAGGATGCATCGATGCACTATTAGGTGT
138355 ATCGATGCA
1 ATCGATGCA
138364 TGAAGCACAA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
42 14 0.29
43 14 0.29
44 20 0.42
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.28
Consensus pattern (42 bp):
ATCGATGCACATTCAAGGATGCATCGATGCACTATTAGGTGT
Found at i:138321 original size:21 final size:20
Alignment explanation
Indices: 138265--138363 Score: 92
Period size: 21 Copynumber: 4.7 Consensus size: 20
138255 GCATGGCCTT
138265 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTC-A-G
* *
138287 CGTGCATCGGTGCACTTTCATG
1 -GTGCATCGATGCACATTCA-G
*
138309 GTGTATCGATGCACATTCAAG
1 GTGCATCGATGCACATTC-AG
138330 GATGCATCGATGCACTATT-AG
1 G-TGCATCGATGCAC-ATTCAG
*
138351 GTGTATCGATGCA
1 GTGCATCGATGCA
138364 TGAAGCACAA
Statistics
Matches: 65, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
20 11 0.17
21 20 0.31
22 15 0.23
23 19 0.29
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.28
Consensus pattern (20 bp):
GTGCATCGATGCACATTCAG
Found at i:139566 original size:65 final size:65
Alignment explanation
Indices: 139449--139642 Score: 191
Period size: 65 Copynumber: 3.0 Consensus size: 65
139439 TTGGACCCTT
* * *
139449 AATGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATTCGTGGATGGTGCATCGATGCATCA
1 AATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGATGGTGCATCGATGCATCA
* * *
139513 AATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATTGATGCATGGTAT-GTGCATCGATGCAT
1 AATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATGG-ATGGTGCATCGATGCAT
*
139576 GA
64 CA
** ** ** *
139578 AATGCATTCGATG--TTCAATTTAATTCATGGTGCATCGATGCATGGATTGGTGCATCGGTGCAT
1 AATGCATTCGATGTTTTCAAAAT-AGCCACAGTGCATCGATGCATGGA-TGGTGCATCGATGCAT
139641 CA
64 CA
139643 CTTTGATAAA
Statistics
Matches: 107, Mismatches: 16, Indels: 13
0.79 0.12 0.10
Matches are distributed among these distances:
62 1 0.01
63 5 0.05
64 32 0.30
65 64 0.60
66 5 0.05
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.32
Consensus pattern (65 bp):
AATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGATGGTGCATCGATGCATCA
Found at i:140677 original size:21 final size:21
Alignment explanation
Indices: 140653--140696 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
140643 TCGGAGGAGG
*
140653 AGGAGGAGCACGAGAAGAGCT
1 AGGAGCAGCACGAGAAGAGCT
* *
140674 AGGAGCAGCTCGTGAAGAGCT
1 AGGAGCAGCACGAGAAGAGCT
140695 AG
1 AG
140697 CTCCCGGAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.16, G:0.41, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAAGAGCT
Found at i:142245 original size:23 final size:22
Alignment explanation
Indices: 142218--142297 Score: 90
Period size: 23 Copynumber: 3.6 Consensus size: 22
142208 TCATGGACTT
142218 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
142240 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
* *
142262 GTGTATCAATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
*
142284 ATGCATCGATGCAC
1 GTGCATCGATGCAC
142298 TGTTAGGTGT
Statistics
Matches: 45, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
21 14 0.31
22 15 0.33
23 16 0.36
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Done.