Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000930.1 Hibiscus syriacus cultivar Beakdansim tig00001855_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: 196410
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 1 of 2
Found at i:3004 original size:20 final size:20
Alignment explanation
Indices: 2979--3017 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2969 TTTTCAAGGG
2979 CATGCACCGATACACCAATC
1 CATGCACCGATACACCAATC
* *
2999 CATGCATCGATACATCAAT
1 CATGCACCGATACACCAAT
3018 TAATTTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.33, G:0.10, T:0.21
Consensus pattern (20 bp):
CATGCACCGATACACCAATC
Found at i:3069 original size:19 final size:17
Alignment explanation
Indices: 3045--3095 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 17
3035 AATGTATTTT
3045 ATGCATCGATGCACATACC
1 ATGCATCGATGCACA-A-C
* *
3064 ATGCATCGTTGCACAAG
1 ATGCATCGATGCACAAC
3081 ACTGCATCGATGCAC
1 A-TGCATCGATGCAC
3096 TCAGGCTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 1 0.04
18 13 0.46
19 14 0.50
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (17 bp):
ATGCATCGATGCACAAC
Found at i:11585 original size:45 final size:46
Alignment explanation
Indices: 11534--11624 Score: 112
Period size: 45 Copynumber: 2.0 Consensus size: 46
11524 TTGAACATAA
* * *
11534 TGCATTTTATATATCGATGTAC-ATACCAAGCATCGATGCACTCAG
1 TGCATTTGATACATCGATGTACAAGACCAAGCATCGATGCACTCAG
* * * *
11579 TGCATTTGATGCATCGATGTACAAGACTATGCATTGATGCACTCAG
1 TGCATTTGATACATCGATGTACAAGACCAAGCATCGATGCACTCAG
11625 GCTTTTTTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
45 19 0.50
46 19 0.50
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31
Consensus pattern (46 bp):
TGCATTTGATACATCGATGTACAAGACCAAGCATCGATGCACTCAG
Found at i:16973 original size:23 final size:22
Alignment explanation
Indices: 16943--16986 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
16933 ATTTTTTGGT
16943 AAAAAATT-CATTAATATTTTAC
1 AAAAAATTACATTAAT-TTTTAC
*
16965 AAAATAATTACTTTAATTTTTA
1 AAAA-AATTACATTAATTTTTA
16987 TTTTTTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 9 0.47
24 6 0.32
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (22 bp):
AAAAAATTACATTAATTTTTAC
Found at i:18932 original size:10 final size:11
Alignment explanation
Indices: 18889--18934 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 11
18879 TAAAACGTGG
18889 GAAATAATATA
1 GAAATAATATA
*
18900 GAAAGAA-A-A
1 GAAATAATATA
*
18909 GGAATAATATA
1 GAAATAATATA
18920 GAAATAA-ATA
1 GAAATAATATA
18930 GAAAT
1 GAAAT
18935 TTAAATTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
9 6 0.21
10 10 0.34
11 13 0.45
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (11 bp):
GAAATAATATA
Found at i:20691 original size:22 final size:22
Alignment explanation
Indices: 20666--20710 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
20656 AATCCAATTA
20666 CTTTATTCTGGTCCACTAAGTC
1 CTTTATTCTGGTCCACTAAGTC
20688 CTTTATTCTGGTCCACTAAGTC
1 CTTTATTCTGGTCCACTAAGTC
20710 C
1 C
20711 GATACATGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.18, C:0.29, G:0.13, T:0.40
Consensus pattern (22 bp):
CTTTATTCTGGTCCACTAAGTC
Found at i:22810 original size:12 final size:12
Alignment explanation
Indices: 22793--22823 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
22783 AGTAGTTCTC
*
22793 TTTTTTTCTTGT
1 TTTTTTTCTGGT
22805 TTTTTTTCTGGT
1 TTTTTTTCTGGT
22817 TTTTTTT
1 TTTTTTT
22824 TTCCTCTCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.06, G:0.10, T:0.84
Consensus pattern (12 bp):
TTTTTTTCTGGT
Found at i:23257 original size:3 final size:3
Alignment explanation
Indices: 23245--23322 Score: 140
Period size: 3 Copynumber: 26.0 Consensus size: 3
23235 ATATTTGTAT
23245 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
23292 TAA TAA TAA TAA TAA TAAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
23323 AATTAAAATA
Statistics
Matches: 73, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.03
3 68 0.93
4 3 0.04
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:23830 original size:51 final size:45
Alignment explanation
Indices: 23619--24088 Score: 239
Period size: 40 Copynumber: 10.9 Consensus size: 45
23609 ATCTTTAGGA
*
23619 AGGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCTA-
1 AGGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGG--ATCTAG
* ***
23665 AGGGTG---ACCCGGTTCCTACGTGATGAGGAAATCTGG-TC---
1 AGGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGATCTAG
* *
23703 AGGG-GATGACAC-ATCTCCTACGTGATGAGGA-GGTCTGG-TC--G
1 AGGGTGATAACACGGT-TCCTACGTGATGAGGACGG-CTGGATCTAG
*
23744 A-GG-GATGACACGGTTCCTACGTGATGAGGACGGCTGGCCATCTTTAGG
1 AGGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGG--ATC--TA-G
*
23792 AGTGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCTA-
1 AG-GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGG--ATCTAG
* ***
23839 AGGGTG---ACCCGGTTCCTACGTGATGAGGAAATCTGG-TC---
1 AGGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGATCTAG
* * *
23877 AGGG-GATGACACAGCTCCTACGTGATGAGGA-GGTCTGG-TC--G
1 AGGGTGATAACACGGTTCCTACGTGATGAGGACGG-CTGGATCTAG
*
23918 A-GG-GATGACACGGTTCCTACGTGATGAGGACGGCTGGCCATCTTTAGG
1 AGGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGG--ATC--TA-G
*
23966 AGTGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCTA-
1 AG-GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGG--ATCTAG
* *
24013 AGGGTG---ACCCGGCTCCTACGTGATGAGGA-GGTCTGG-T-T-G
1 AGGGTGATAACACGGTTCCTACGTGATGAGGACGG-CTGGATCTAG
* * * *
24052 A-GG-AATGACACGGTTCCTATGTGACGAGGACGGCTGG
1 AGGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGG
24089 CCATCTTTAG
Statistics
Matches: 347, Mismatches: 35, Indels: 90
0.74 0.07 0.19
Matches are distributed among these distances:
37 2 0.01
38 10 0.03
39 3 0.01
40 140 0.40
41 9 0.03
42 2 0.01
43 81 0.23
46 14 0.04
47 4 0.01
48 4 0.01
49 4 0.01
50 4 0.01
51 70 0.20
ACGTcount: A:0.21, C:0.19, G:0.35, T:0.24
Consensus pattern (45 bp):
AGGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGATCTAG
Found at i:24062 original size:174 final size:174
Alignment explanation
Indices: 23534--24041 Score: 853
Period size: 174 Copynumber: 2.9 Consensus size: 174
23524 CATCTAAGGG
* * * ** * *
23534 TGACACGGTTCCTACATGATGAGGAAATATGGTCGAGGGATGACAC--TTCTCATACGTGATGAA
1 TGACACAGCTCCTACGTGATGAGGAGGTCTGGTCGAGGGATGACACGGTTC-C-TACGTGATGAG
*
23597 GA-GTTCTTGGCCATCTTTAGGAAG-GGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTT
64 GACG-GC-TGGCCATCTTTAGG-AGTGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTT
23660 ATCTAAGGGTGACCCGGTTCCTACGTGATGAGGAAATCTGGTCAGGGGA
126 ATCTAAGGGTGACCCGGTTCCTACGTGATGAGGAAATCTGGTCAGGGGA
*
23709 TGACACATCTCCTACGTGATGAGGAGGTCTGGTCGAGGGATGACACGGTTCCTACGTGATGAGGA
1 TGACACAGCTCCTACGTGATGAGGAGGTCTGGTCGAGGGATGACACGGTTCCTACGTGATGAGGA
23774 CGGCTGGCCATCTTTAGGAGTGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCTA
66 CGGCTGGCCATCTTTAGGAGTGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCTA
23839 AGGGTGACCCGGTTCCTACGTGATGAGGAAATCTGGTCAGGGGA
131 AGGGTGACCCGGTTCCTACGTGATGAGGAAATCTGGTCAGGGGA
23883 TGACACAGCTCCTACGTGATGAGGAGGTCTGGTCGAGGGATGACACGGTTCCTACGTGATGAGGA
1 TGACACAGCTCCTACGTGATGAGGAGGTCTGGTCGAGGGATGACACGGTTCCTACGTGATGAGGA
23948 CGGCTGGCCATCTTTAGGAGTGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCTA
66 CGGCTGGCCATCTTTAGGAGTGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCTA
*
24013 AGGGTGACCCGGCTCCTACGTGATGAGGA
131 AGGGTGACCCGGTTCCTACGTGATGAGGA
24042 GGTCTGGTTG
Statistics
Matches: 318, Mismatches: 11, Indels: 9
0.94 0.03 0.03
Matches are distributed among these distances:
173 2 0.01
174 259 0.81
175 52 0.16
176 2 0.01
177 3 0.01
ACGTcount: A:0.22, C:0.19, G:0.33, T:0.25
Consensus pattern (174 bp):
TGACACAGCTCCTACGTGATGAGGAGGTCTGGTCGAGGGATGACACGGTTCCTACGTGATGAGGA
CGGCTGGCCATCTTTAGGAGTGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCTA
AGGGTGACCCGGTTCCTACGTGATGAGGAAATCTGGTCAGGGGA
Found at i:24200 original size:31 final size:28
Alignment explanation
Indices: 24108--24203 Score: 106
Period size: 28 Copynumber: 3.3 Consensus size: 28
24098 GGAGTTATGA
* * *
24108 TTTCAAGAGAAACCGATTCAAAGATTTG
1 TTTCAAAAGAAACAGACTCAAAGATTTG
24136 TTTCAAAAGAAACAGACTCAAAGATTTG
1 TTTCAAAAGAAACAGACTCAAAGATTTG
24164 TTTCAAGAA-AAACA-AGCTCAAAGATAATGTG
1 TTTCAA-AAGAAACAGA-CTCAAAGAT--T-TG
24195 TTTCAAAAG
1 TTTCAAAAG
24204 CAACTGTCTC
Statistics
Matches: 59, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
27 1 0.02
28 45 0.76
29 2 0.03
30 3 0.05
31 8 0.14
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.26
Consensus pattern (28 bp):
TTTCAAAAGAAACAGACTCAAAGATTTG
Found at i:24394 original size:66 final size:63
Alignment explanation
Indices: 24205--24387 Score: 152
Period size: 66 Copynumber: 2.8 Consensus size: 63
24195 TTTCAAAAGC
* ** * *
24205 AACTGTCTCGAAAGAGACAAAATTCGTTTCAAATGAAAC-AACTCAAAAGATGACGTTTAAAGGG
1 AACTGTCTC-AAAGAGACAAAATTCATTTCAAGGGAAACGATCTC-AAAGATGATGTTTAAAGGG
* * * ** * * * * * *
24269 AATTGTCTCAAGCGAGATAAAATTTGTTTTTAAGGGAAACGTTCTCAAATATCGGTGTTTCATGG
1 AACTGTCTCAA-AGAGACAAAA-TTCATTTCAAGGGAAACGATCTCAAAGAT-GATGTTTAAAGG
24334 G
63 G
24335 AAACTGTCTCAAATGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATG
1 -AACTGTCTCAAA-GAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATG
24388 TTTGTTTTGT
Statistics
Matches: 90, Mismatches: 23, Indels: 11
0.73 0.19 0.09
Matches are distributed among these distances:
63 2 0.02
64 16 0.18
65 18 0.20
66 36 0.40
67 18 0.20
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.27
Consensus pattern (63 bp):
AACTGTCTCAAAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATGATGTTTAAAGGG
Found at i:25202 original size:65 final size:66
Alignment explanation
Indices: 25127--25342 Score: 294
Period size: 67 Copynumber: 3.3 Consensus size: 66
25117 AAAGATTTAC
* * * * * *
25127 TTCAAGAGAAACTGTCTCAAGAGATACAAAATTCAT-TTT-AAGAGAAACAGATTCAAAGATTTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAAAATT-TTGTTTCAA-AGAAACAGACTCAAAGATTTT
25190 T-T
64 TGT
*
25192 TTCAAAAGAAAATATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTT-CAAAGAAACAGACTCAAAGATTTTT
25257 GT
65 GT
*
25259 TTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTT-CAAAGAAACAGACTCAAAGATTTTT
25324 GT
65 GT
*
25326 TTCAAAAGAAACAATCT
1 TTCAAAAGAAACTATCT
25343 CAAAGATTTT
Statistics
Matches: 137, Mismatches: 10, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
64 1 0.01
65 31 0.23
66 21 0.15
67 84 0.61
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.30
Consensus pattern (66 bp):
TTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCAAAGAAACAGACTCAAAGATTTTTG
T
Found at i:25226 original size:37 final size:38
Alignment explanation
Indices: 25180--25306 Score: 114
Period size: 37 Copynumber: 3.6 Consensus size: 38
25170 GAAACAGATT
*
25180 CAAAGATTTTTTTTCAAAAGAAAATATCTTAAGAGAGA
1 CAAAGATTTTGTTTCAAAAGAAAATATCTTAAGAGAGA
* **
25218 CAAA-ATTTTGTTTCCAAAG--AA-A-C-----AGACT
1 CAAAGATTTTGTTTCAAAAGAAAATATCTTAAGAGAGA
*
25246 CAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGA
1 CAAAGA-TTTTGTTTCAAAAGAAAATATCTTAAGAGAGA
*
25285 CAAA-ATTTTGTTTCCAAAGAAA
1 CAAAGATTTTGTTTCAAAAGAAA
25307 CAGACTCAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 23
0.68 0.09 0.23
Matches are distributed among these distances:
28 7 0.10
29 1 0.01
30 13 0.19
32 1 0.01
33 2 0.03
34 2 0.03
35 2 0.03
37 29 0.42
38 5 0.07
39 7 0.10
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (38 bp):
CAAAGATTTTGTTTCAAAAGAAAATATCTTAAGAGAGA
Found at i:25257 original size:30 final size:30
Alignment explanation
Indices: 25223--25353 Score: 115
Period size: 30 Copynumber: 4.1 Consensus size: 30
25213 AGAGACAAAA
*
25223 TTTTGTTTCCAAAGAAACAGACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAGACTCAAAGAT
**
25253 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAA-A-
1 TTTTGTTTCAAAAG-AA--A-C-----AGACTCAAAGAT
*
25290 TTTTGTTTCCAAAGAAACAGACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAGACTCAAAGAT
25320 TTTTGTTTCAAAAGAAACA-ATCTCAAAGAT
1 TTTTGTTTCAAAAGAAACAGA-CTCAAAGAT
25350 TTTT
1 TTTT
25354 TTCACAAAAT
Statistics
Matches: 82, Mismatches: 7, Indels: 24
0.73 0.06 0.21
Matches are distributed among these distances:
28 7 0.09
29 2 0.02
30 44 0.54
31 2 0.02
33 2 0.02
34 2 0.02
36 2 0.02
37 13 0.16
38 1 0.01
39 7 0.09
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.34
Consensus pattern (30 bp):
TTTTGTTTCAAAAGAAACAGACTCAAAGAT
Found at i:25275 original size:67 final size:67
Alignment explanation
Indices: 25169--25336 Score: 311
Period size: 67 Copynumber: 2.5 Consensus size: 67
25159 TCATTTTAAG
*
25169 AGAAACAGATTCAAAGATTTTT-TTTCAAAAGAAAATATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAAATATCTTAAGAGAGACAAAATTTTGTTTCC
25233 AA
66 AA
*
25235 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAAATATCTTAAGAGAGACAAAATTTTGTTTCC
25300 AA
66 AA
25302 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAA
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAA
25337 CAATCTCAAA
Statistics
Matches: 99, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
66 21 0.21
67 78 0.79
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.30
Consensus pattern (67 bp):
AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAAATATCTTAAGAGAGACAAAATTTTGTTTCC
AA
Found at i:25362 original size:30 final size:29
Alignment explanation
Indices: 25285--25362 Score: 90
Period size: 30 Copynumber: 2.7 Consensus size: 29
25275 TTAAGAGAGA
25285 CAAA-ATTTTGTTTCC-AAAGAAACAGACT
1 CAAAGATTTT-TTTCCAAAAGAAACAGACT
*
25313 CAAAGATTTTTGTTTCAAAAGAAACA-ATCT
1 CAAAGATTTTT-TTCCAAAAGAAACAGA-CT
25343 CAAAGATTTTTTTCACAAAA
1 CAAAGATTTTTTTC-CAAAA
25363 TTGTCTCAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
28 5 0.12
29 11 0.26
30 27 0.63
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.32
Consensus pattern (29 bp):
CAAAGATTTTTTTCCAAAAGAAACAGACT
Found at i:25417 original size:52 final size:53
Alignment explanation
Indices: 25341--25444 Score: 165
Period size: 52 Copynumber: 2.0 Consensus size: 53
25331 AAGAAACAAT
25341 CTCAAAGATTTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
1 CTCAAAGA-TTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
** *
25395 CTCAAAGA-TTTTTCAGGAAATTGTCTTAAGAGAGACAAAACTTTGTTTCA
1 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
25445 AAAGAAATAG
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
52 39 0.83
54 8 0.17
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (53 bp):
CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
Found at i:25604 original size:28 final size:29
Alignment explanation
Indices: 25441--25596 Score: 210
Period size: 29 Copynumber: 5.4 Consensus size: 29
25431 AAAACTTTGT
* * *
25441 TTCAAAAGAAATAGACTCAAAGATTTTTTT
1 TTCAAAAGAAACAAACTCAAAGA-TTTTTA
25471 TTCAAAAGAAAC-AACTCAAAGATTTTTA
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
* *
25499 TTCAAAAGGAACCAACTCAAAGATTTTTA
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
25528 TTCAAAATG-AACAAACTCAAAGATTTTTA
1 TTCAAAA-GAAACAAACTCAAAGATTTTTA
*
25557 TTCAAAAGGAACAAACTCAAAGATTTTT-
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
*
25585 TTCAAGAGAAAC
1 TTCAAAAGAAAC
25597 TGTCTCAAGA
Statistics
Matches: 116, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
28 27 0.23
29 77 0.66
30 12 0.10
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.29
Consensus pattern (29 bp):
TTCAAAAGAAACAAACTCAAAGATTTTTA
Found at i:25922 original size:36 final size:36
Alignment explanation
Indices: 25836--25939 Score: 124
Period size: 36 Copynumber: 3.0 Consensus size: 36
25826 GAGAAAATGA
* *
25836 TGTCTCAAGCGAGACAAAATTTG-CTTTA-AGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
* ** *
25870 AGTCTCAAATGTGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
*
25906 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAA
25940 ACGATCTCAA
Statistics
Matches: 57, Mismatches: 11, Indels: 3
0.80 0.15 0.04
Matches are distributed among these distances:
34 19 0.33
35 10 0.18
36 28 0.49
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.34
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
Found at i:25948 original size:36 final size:36
Alignment explanation
Indices: 25837--25955 Score: 111
Period size: 36 Copynumber: 3.4 Consensus size: 36
25827 AGAAAATGAT
* *
25837 GTCTCAAGCGAGACAAAATTTG-CTTTA-AGATATA-
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGAGA-AAAC
** * **
25871 GTCTCAAATGTGACAAAATTTGTTTTTAGAGAAATT
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAAC
*
25907 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAAAC
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAAC
*
25942 GATCTCAAGTGAGA
1 G-TCTCAAGCGAGA
25956 TCAACTTTGT
Statistics
Matches: 68, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
34 19 0.28
35 12 0.18
36 37 0.54
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (36 bp):
GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAAC
Found at i:26086 original size:105 final size:101
Alignment explanation
Indices: 25907--26139 Score: 301
Period size: 105 Copynumber: 2.3 Consensus size: 101
25897 TAGAGAAATT
*
25907 GTCTCAAGCGAGAC-AAAGTTTGTTTTTGAGAAAACGATCTCAAGTGAGATCAACTTTGTTTAAT
1 GTCTCAAGCGAGACGAAA-TTTG-TTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAAT
*
25971 GTGAAACAAATTCAAAATTTGGATCTCAAAGGGAAAAG
64 GTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
* *
26009 GTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAACAACAATCT-AAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGACGAAATTTGTTTTG--AG-AA-AACAATCTCAA-GTGAGATCAACTTTG-TT
* * *
26073 TAA-GTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
60 TAATGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
*
26114 GTCTCAAGCGAGACGCAATTTGTTTT
1 GTCTCAAGCGAGACGAAATTTGTTTT
26140 AAAATTCTCA
Statistics
Matches: 116, Mismatches: 8, Indels: 11
0.86 0.06 0.08
Matches are distributed among these distances:
101 5 0.04
102 18 0.16
103 5 0.04
104 4 0.03
105 79 0.68
106 5 0.04
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.30
Consensus pattern (101 bp):
GTCTCAAGCGAGACGAAATTTGTTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATGT
GAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:27853 original size:16 final size:16
Alignment explanation
Indices: 27789--27880 Score: 75
Period size: 16 Copynumber: 5.6 Consensus size: 16
27779 TTTGTCTGTG
27789 TTCTTTGTTCTCTTTTT
1 TTCTTTGTT-TCTTTTT
27806 GTTCTTTGCTTT-TTCTTT
1 -TTCTTTG-TTTCTT-TTT
*
27824 GTT-GTTGTTT-TTTTT
1 -TTCTTTGTTTCTTTTT
*
27839 TT-TTTGCTTTGTTTTT
1 TTCTTTG-TTTCTTTTT
*
27855 TTCTTTGTTTCTCTTT
1 TTCTTTGTTTCTTTTT
27871 TTCTTTGTTT
1 TTCTTTGTTT
27881 TAATTGGATC
Statistics
Matches: 65, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
14 5 0.08
15 6 0.09
16 29 0.45
17 9 0.14
18 14 0.22
19 2 0.03
ACGTcount: A:0.00, C:0.12, G:0.11, T:0.77
Consensus pattern (16 bp):
TTCTTTGTTTCTTTTT
Found at i:27855 original size:13 final size:12
Alignment explanation
Indices: 27801--27864 Score: 62
Period size: 12 Copynumber: 5.2 Consensus size: 12
27791 CTTTGTTCTC
27801 TTTTTGTTCTTTG
1 TTTTT-TTCTTTG
*
27814 -CTTTTTCTTTG
1 TTTTTTTCTTTG
27825 TTGTTGTTT-TTT-
1 TT-TT-TTTCTTTG
27837 TTTTTTTGCTTTG
1 TTTTTTT-CTTTG
27850 TTTTTTTCTTTG
1 TTTTTTTCTTTG
27862 TTT
1 TTT
27865 CTCTTTTTCT
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
10 3 0.07
11 9 0.21
12 16 0.37
13 12 0.28
14 3 0.07
ACGTcount: A:0.00, C:0.08, G:0.12, T:0.80
Consensus pattern (12 bp):
TTTTTTTCTTTG
Found at i:27872 original size:19 final size:19
Alignment explanation
Indices: 27815--27872 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
27805 TGTTCTTTGC
*
27815 TTTTTCTTTGTTGT-TGTTT
1 TTTTTCTTTGTT-TCTCTTT
* *
27834 TTTTT-TTT-TTGCTTTGTT
1 TTTTTCTTTGTTTCTCT-TT
27852 TTTTTCTTTGTTTCTCTTT
1 TTTTTCTTTGTTTCTCTTT
27871 TT
1 TT
27873 CTTTGTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
17 4 0.13
18 10 0.32
19 12 0.39
20 5 0.16
ACGTcount: A:0.00, C:0.09, G:0.10, T:0.81
Consensus pattern (19 bp):
TTTTTCTTTGTTTCTCTTT
Found at i:28580 original size:46 final size:45
Alignment explanation
Indices: 28488--28581 Score: 116
Period size: 46 Copynumber: 2.1 Consensus size: 45
28478 ATAAATACAG
* * * *
28488 TGTTTCAAAGTGGAAAGAATGTTTCAAGGCCTTAAAGAGAGGGAA
1 TGTTTCAAAGTGAAAAGAATATTTCAAGGCCTCAAAGAGAGAGAA
* * *
28533 TGTTTCAAGGTCGAAAAGAATATTTCAAGGTCTCAAAGAGATAGAA
1 TGTTTCAAAGT-GAAAAGAATATTTCAAGGCCTCAAAGAGAGAGAA
28579 TGT
1 TGT
28582 CAAAATTTGG
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
45 10 0.24
46 31 0.76
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.27
Consensus pattern (45 bp):
TGTTTCAAAGTGAAAAGAATATTTCAAGGCCTCAAAGAGAGAGAA
Found at i:29828 original size:31 final size:32
Alignment explanation
Indices: 29772--29833 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
29762 TGACAAAATG
29772 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
29804 ACACAAACAAAAGAGAA-AAATAAGTTAGTA
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTA
29834 CATGTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:33136 original size:3 final size:3
Alignment explanation
Indices: 33124--33176 Score: 90
Period size: 3 Copynumber: 18.0 Consensus size: 3
33114 ATATTTGTAT
*
33124 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAC TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
33171 TAA TAA
1 TAA TAA
33177 AATTAAAATA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:33193 original size:9 final size:10
Alignment explanation
Indices: 33124--33191 Score: 65
Period size: 9 Copynumber: 7.0 Consensus size: 10
33114 ATATTTGTAT
33124 TAATATAATAA
1 TAATA-AATAA
33135 TAAT-AATAA
1 TAATAAATAA
33144 TAAT-AATAA
1 TAATAAATAA
*
33153 TACT-AATAA
1 TAATAAATAA
33162 TAAT-AATAA
1 TAATAAATAA
33171 TAATAAAATTAA
1 TAAT-AAA-TAA
33183 -AATAAATAA
1 TAATAAATAA
33192 AAAAAAGAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
9 37 0.71
10 3 0.06
11 9 0.17
12 3 0.06
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (10 bp):
TAATAAATAA
Found at i:37568 original size:9 final size:9
Alignment explanation
Indices: 37556--37607 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
37546 TAATATTTTG
37556 TATTTAATT
1 TATTTAATT
*
37565 TATTTAA-G
1 TATTTAATT
37573 TATTTAATT
1 TATTTAATT
37582 TATTTAA--
1 TATTTAATT
*
37589 TATTTTATT
1 TATTTAATT
*
37598 TAATTAATT
1 TATTTAATT
37607 T
1 T
37608 TTTTGCATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 6 0.17
8 7 0.20
9 22 0.63
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (9 bp):
TATTTAATT
Found at i:37577 original size:17 final size:17
Alignment explanation
Indices: 37555--37604 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
37545 TTAATATTTT
37555 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
37572 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
* *
37589 -TATTTTATTTAATTAA
1 GTATTTAATTTATTTAA
37605 TTTTTTTGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:38513 original size:2 final size:2
Alignment explanation
Indices: 38506--38539 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
38496 ATTTTTGATA
38506 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
38540 TTGTTTTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39629 original size:25 final size:25
Alignment explanation
Indices: 39601--39660 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
39591 TAGATTTTGT
* *
39601 TTTTTATTATATTTGTATT-TAGTAC
1 TTTTTATTATAGTTGT-TTATAGGAC
* *
39626 TTTTTATTGTAGTTGTTTATTGGAC
1 TTTTTATTATAGTTGTTTATAGGAC
39651 TTTTTATTAT
1 TTTTTATTAT
39661 TTATCATTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
24 2 0.07
25 27 0.93
ACGTcount: A:0.20, C:0.03, G:0.12, T:0.65
Consensus pattern (25 bp):
TTTTTATTATAGTTGTTTATAGGAC
Found at i:45053 original size:31 final size:31
Alignment explanation
Indices: 45015--45170 Score: 217
Period size: 31 Copynumber: 5.0 Consensus size: 31
45005 CCCGAAGGAC
* *
45015 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
45046 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
* *
45077 CAGTCCGTATGTTCCGAAGAACATAGGTAAT
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
45108 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
45139 CAGTCCATATG-TCCAGAAGAACATAGGTAAA
1 CAGTCCATATGTTCC-GAAGAACATAGGTAAA
45170 C
1 C
45171 CCTCGACCCT
Statistics
Matches: 111, Mismatches: 12, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
30 2 0.02
31 108 0.97
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:45112 original size:62 final size:62
Alignment explanation
Indices: 45015--45168 Score: 249
Period size: 62 Copynumber: 2.5 Consensus size: 62
45005 CCCGAAGGAC
* *
45015 CAGTCCATA-GATTCCGAAGAACCTAGGTAATCAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATG-TTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
*
45077 CAGTCCGTATGTTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
45139 CAGTCCATATG-TCCAGAAGAACATAGGTAA
1 CAGTCCATATGTTCC-GAAGAACATAGGTAA
45169 ACCCTCGACC
Statistics
Matches: 86, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
61 3 0.03
62 82 0.95
63 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (62 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:45374 original size:23 final size:24
Alignment explanation
Indices: 45348--45394 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
45338 ATATACTTGT
*
45348 TTTCACATATATA-TTTCATATCA
1 TTTCACATATACACTTTCATATCA
45371 TTTCACATATACACTTTCATATCA
1 TTTCACATATACACTTTCATATCA
45395 CATGCCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTCACATATACACTTTCATATCA
Found at i:46025 original size:21 final size:21
Alignment explanation
Indices: 45995--46039 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
45985 ATTCTGTCGT
* *
45995 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
46016 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
46037 TTG
1 TTG
46040 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:53925 original size:91 final size:91
Alignment explanation
Indices: 53825--54007 Score: 366
Period size: 91 Copynumber: 2.0 Consensus size: 91
53815 GTGATTTATT
53825 GCAAATGATCTCTCTAACAATTAATATCAATTTTTCAAATGCATAACATTTTTTGATAGCTTTAT
1 GCAAATGATCTCTCTAACAATTAATATCAATTTTTCAAATGCATAACATTTTTTGATAGCTTTAT
53890 GCACATGCACTTAAATACAACAATTG
66 GCACATGCACTTAAATACAACAATTG
53916 GCAAATGATCTCTCTAACAATTAATATCAATTTTTCAAATGCATAACATTTTTTGATAGCTTTAT
1 GCAAATGATCTCTCTAACAATTAATATCAATTTTTCAAATGCATAACATTTTTTGATAGCTTTAT
53981 GCACATGCACTTAAATACAACAATTG
66 GCACATGCACTTAAATACAACAATTG
54007 G
1 G
54008 TATTGCATAA
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 92 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.36
Consensus pattern (91 bp):
GCAAATGATCTCTCTAACAATTAATATCAATTTTTCAAATGCATAACATTTTTTGATAGCTTTAT
GCACATGCACTTAAATACAACAATTG
Found at i:58619 original size:16 final size:16
Alignment explanation
Indices: 58600--58652 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
58590 AAATTTAAAA
*
58600 AATTCAAAATATATTT
1 AATTTAAAATATATTT
*
58616 AATTTATAATCATA-TT
1 AATTTAAAAT-ATATTT
*
58632 ATTTTAAAATATATTT
1 AATTTAAAATATATTT
58648 -ATTTA
1 AATTTA
58653 TTTAAAATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
15 7 0.23
16 20 0.67
17 3 0.10
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (16 bp):
AATTTAAAATATATTT
Found at i:58645 original size:15 final size:16
Alignment explanation
Indices: 58605--58651 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
58595 TAAAAAATTC
*
58605 AAAATATATTTAATTT
1 AAAATATATTTATTTT
*
58621 ATAATCATA-TTATTTT
1 AAAAT-ATATTTATTTT
58637 AAAATATATTTATTT
1 AAAATATATTTATTT
58652 ATTTAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 3 0.12
16 20 0.77
17 3 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
AAAATATATTTATTTT
Found at i:58801 original size:2 final size:2
Alignment explanation
Indices: 58794--58845 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
58784 AATTTAAACA
58794 AT AT 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 AT AT
58836 AT AT AT AT AT
1 AT AT AT AT AT
58846 TTACATGACT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60675 original size:3 final size:3
Alignment explanation
Indices: 60667--60717 Score: 56
Period size: 3 Copynumber: 18.3 Consensus size: 3
60657 TATTTATTTC
* *
60667 ATA ATA ATA AT- ATA AT- ATA ATA ATA ATA ATA A-A ACA A-A TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
60711 ATA ATA A
1 ATA ATA A
60718 ATAAAACAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 7 0.17
3 35 0.83
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:60691 original size:19 final size:17
Alignment explanation
Indices: 60667--60722 Score: 67
Period size: 19 Copynumber: 3.1 Consensus size: 17
60657 TATTTATTTC
60667 ATAATAATAATATAATATA
1 ATAATAATAATA-AATA-A
*
60686 ATAATAATAATAAAACAA
1 ATAATAATAAT-AAATAA
60704 ATTAATAATAATAAATAA
1 A-TAATAATAATAAATAA
60722 A
1 A
60723 ACAAATGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 8 0.24
19 24 0.73
20 1 0.03
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (17 bp):
ATAATAATAATAAATAA
Found at i:60695 original size:22 final size:22
Alignment explanation
Indices: 60684--60728 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 22
60674 TAATATAATA
60684 TAATAATAATAATAAAACAAAT
1 TAATAATAATAATAAAACAAAT
60706 TAATAATAATAAATAAAACAAAT
1 TAATAATAAT-AATAAAACAAAT
60729 GAAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (22 bp):
TAATAATAATAATAAAACAAAT
Found at i:61189 original size:112 final size:111
Alignment explanation
Indices: 61060--61694 Score: 949
Period size: 112 Copynumber: 5.7 Consensus size: 111
61050 AGAATTATGC
61060 AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAG-TTGAACAAGTTCTTCTCATTATGAACTTCTTC-TTCTTCTTCAGATGAGTTCTTCTCAT
* *
61125 TATGAACTCTCTCTAACAAGTTGATCCATCGAGTGATGAATTCGAGCG
64 TATGAACTCTCTCTAACAAGTTGATCCATCGAATGATGAATTCAAGCG
* *
61173 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-ACTTTCTTCAAATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-TTCTTCAGATGAGTTCTTCTCATT
* *
61237 ATGAACTCAAC-CTAACAATGCTGATCCATCGAATGATGAATTCAAGCG
65 ATGAACTC-TCTCTAACAA-GTTGATCCATCGAATGATGAATTCAAGCG
61285 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-TTCTTCAGATGAGTTCTTCTCATT
* * *
61350 ATGAACTCT-TCCGGAA-ATGTTGATCCATCGAATGATGAATTCAAGTG
65 ATGAACTCTCT-C-TAACAAGTTGATCCATCGAATGATGAATTCAAGCG
*
61397 AAAATTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TTCTTCTTCAGATGAGTTCTTCTCATT
* **
61462 ATGAACTCTCTCTAACAAGTTGATCCATCGAGTGATGAATTTGAGCG
65 ATGAACTCTCTCTAACAAGTTGATCCATCGAATGATGAATTCAAGCG
* *
61509 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-ACTTTCTTCAAATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-TTCTTCAGATGAGTTCTTCTCATT
* *
61573 ATGAACTCGAC-CTAACAATGCTGATCCATCGAATGATGAATTCAAGCG
65 ATGAACTC-TCTCTAACAA-GTTGATCCATCGAATGATGAATTCAAGCG
*
61621 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAATTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-TTCTTCAGATGAGTTCTTCTCATT
61686 ATGAACTCT
65 ATGAACTCT
61695 TCCGGAAATG
Statistics
Matches: 476, Mismatches: 32, Indels: 29
0.89 0.06 0.05
Matches are distributed among these distances:
110 2 0.00
111 78 0.16
112 318 0.67
113 76 0.16
114 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (111 bp):
AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTCTCTCTAACAAGTTGATCCATCGAATGATGAATTCAAGCG
Found at i:61681 original size:336 final size:336
Alignment explanation
Indices: 61066--61722 Score: 1278
Period size: 336 Copynumber: 2.0 Consensus size: 336
61056 ATGCAAAAGA
61066 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAA
61131 CTCTCTCTAACAAGTTGATCCATCGAGTGATGAATTCGAGCGAAAAGTTGAACAAGTTCTTCTCA
66 CTCTCTCTAACAAGTTGATCCATCGAGTGATGAATTCGAGCGAAAAGTTGAACAAGTTCTTCTCA
61196 TTATGAACTTCTTCACTTTCTTCAAATGAGTTCTTCTCATTATGAACTCAACCTAACAATGCTGA
131 TTATGAACTTCTTCACTTTCTTCAAATGAGTTCTTCTCATTATGAACTCAACCTAACAATGCTGA
61261 TCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCT
196 TCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCT
*
61326 TTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCCGGAAATGTTGATCCATCGAATGATGAATT
261 TTCTTCAGATGAATTCTTCTCATTATGAACTCTTCCGGAAATGTTGATCCATCGAATGATGAATT
61391 CAAGTGAAAAT
326 CAAGTGAAAAT
61402 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAA
*
61467 CTCTCTCTAACAAGTTGATCCATCGAGTGATGAATTTGAGCGAAAAGTTGAACAAGTTCTTCTCA
66 CTCTCTCTAACAAGTTGATCCATCGAGTGATGAATTCGAGCGAAAAGTTGAACAAGTTCTTCTCA
*
61532 TTATGAACTTCTTCACTTTCTTCAAATGAGTTCTTCTCATTATGAACTCGACCTAACAATGCTGA
131 TTATGAACTTCTTCACTTTCTTCAAATGAGTTCTTCTCATTATGAACTCAACCTAACAATGCTGA
61597 TCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCT
196 TCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCT
*
61662 TTCTTCAGATGAATTCTTCTCATTATGAACTCTTCCGGAAATGTTGATCCATTGAATGATG
261 TTCTTCAGATGAATTCTTCTCATTATGAACTCTTCCGGAAATGTTGATCCATCGAATGATG
61723 GATTTGAATC
Statistics
Matches: 317, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
336 317 1.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.37
Consensus pattern (336 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAA
CTCTCTCTAACAAGTTGATCCATCGAGTGATGAATTCGAGCGAAAAGTTGAACAAGTTCTTCTCA
TTATGAACTTCTTCACTTTCTTCAAATGAGTTCTTCTCATTATGAACTCAACCTAACAATGCTGA
TCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCT
TTCTTCAGATGAATTCTTCTCATTATGAACTCTTCCGGAAATGTTGATCCATCGAATGATGAATT
CAAGTGAAAAT
Found at i:62156 original size:22 final size:22
Alignment explanation
Indices: 62131--62204 Score: 112
Period size: 22 Copynumber: 3.4 Consensus size: 22
62121 AATAAAGCTT
* *
62131 TCATATTTGAAAAGAGAATTTA
1 TCATCTTTGAAAAGAGAATCTA
*
62153 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
62175 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
62197 TCATCTTT
1 TCATCTTT
62205 CAAGAGTGTA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:64813 original size:83 final size:83
Alignment explanation
Indices: 64674--65169 Score: 847
Period size: 83 Copynumber: 6.0 Consensus size: 83
64664 TCTACTATGA
64674 GCAAATTCATCTTCCAAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAAAGAACA
1 GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCC-AACCAGATCAGATAACTCAAAGAACA
64738 CTTCCAGAAGATGCTATTG
65 CTTCCAGAAGATGCTATTG
*
64757 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAAAGAACA
1 GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCC-AACCAGATCAGATAACTCAAAGAACA
*
64821 TTTCCAGAAGATGCTA-TG
65 CTTCCAGAAGATGCTATTG
*
64839 AGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACA
1 -GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACA
64904 CTTCCAGAAGATGCTATTG
65 CTTCCAGAAGATGCTATTG
*
64923 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
64988 TTCCAGAAGATGCTATTG
66 TTCCAGAAGATGCTATTG
* * *
65006 GCAAATTTATCTTCTAAATTAAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
*
65071 TTCCAAAAGATGCTA-TG
66 TTCCAGAAGATGCTATTG
*
65088 AGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACA
1 -GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACA
65153 CTTCCAGAAGATGCTAT
65 CTTCCAGAAGATGCTAT
65170 GAAGCACATT
Statistics
Matches: 393, Mismatches: 15, Indels: 9
0.94 0.04 0.02
Matches are distributed among these distances:
82 4 0.01
83 385 0.98
84 4 0.01
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (83 bp):
GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
TTCCAGAAGATGCTATTG
Found at i:70751 original size:14 final size:14
Alignment explanation
Indices: 70717--70770 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
70707 TTGTGCAATA
* *
70717 CAAATGCAAAGATG
1 CAAATGTAAATATG
70731 CCAAATGTAAATATG
1 -CAAATGTAAATATG
70746 CAAATGTAAA-ATTG
1 CAAATGTAAATA-TG
*
70760 TAAATGTAAAT
1 CAAATGTAAAT
70771 TATTTAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
13 1 0.03
14 21 0.62
15 12 0.35
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:72896 original size:16 final size:16
Alignment explanation
Indices: 72877--72929 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
72867 AAATTTAAAA
*
72877 AATTCAAAATATATTT
1 AATTTAAAATATATTT
*
72893 AATTTATAATCATA-TT
1 AATTTAAAAT-ATATTT
*
72909 ATTTTAAAATATATTT
1 AATTTAAAATATATTT
72925 -ATTTA
1 AATTTA
72930 TTTAAAATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
15 7 0.23
16 20 0.67
17 3 0.10
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (16 bp):
AATTTAAAATATATTT
Found at i:72922 original size:15 final size:16
Alignment explanation
Indices: 72882--72928 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
72872 TAAAAAATTC
*
72882 AAAATATATTTAATTT
1 AAAATATATTTATTTT
*
72898 ATAATCATA-TTATTTT
1 AAAAT-ATATTTATTTT
72914 AAAATATATTTATTT
1 AAAATATATTTATTT
72929 ATTTAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 3 0.12
16 20 0.77
17 3 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
AAAATATATTTATTTT
Found at i:73079 original size:2 final size:2
Alignment explanation
Indices: 73072--73107 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
73062 ATTTAAACAA
73072 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
73108 TACATGACTA
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:74937 original size:3 final size:3
Alignment explanation
Indices: 74929--74976 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
74919 TATTTATTTC
* *
74929 ATA ATA ATA AT- ATA AT- ATA ATA ATA ATA A-A ACA A-A TTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
74973 ATA A
1 ATA A
74977 ATAAAACAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 7 0.18
3 32 0.82
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:74953 original size:19 final size:18
Alignment explanation
Indices: 74929--74981 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 18
74919 TATTTATTTC
74929 ATAATAAT-AATATAATATA
1 ATAATAATAAATA-AAT-TA
*
74948 ATAATAATAAAACAAATTA
1 ATAATAAT-AAATAAATTA
74967 ATAATAATAAATAAA
1 ATAATAATAAATAAA
74982 ACAAATGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 6 0.20
19 18 0.60
20 3 0.10
21 3 0.10
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
ATAATAATAAATAAATTA
Found at i:75005 original size:23 final size:23
Alignment explanation
Indices: 74956--75005 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
74946 TAATAATAAT
* * * * *
74956 AAAACAAATTAATAATAATAAAT
1 AAAACAAATGAAAAAAAACAAAA
74979 AAAACAAATGAAAAAAAACAAAA
1 AAAACAAATGAAAAAAAACAAAA
75002 AAAA
1 AAAA
75006 AACTAGTGTC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.78, C:0.06, G:0.02, T:0.14
Consensus pattern (23 bp):
AAAACAAATGAAAAAAAACAAAA
Found at i:76873 original size:24 final size:23
Alignment explanation
Indices: 76812--76877 Score: 64
Period size: 22 Copynumber: 2.9 Consensus size: 23
76802 CATTTGTTTT
* *
76812 TTATAGAAATTATA-TGA-AATAA
1 TTATAAAAATTATATTTATAAT-A
*
76834 TTATAAAACTTATATTTATAATA
1 TTATAAAAATTATATTTATAATA
*
76857 TTATAAAAATATTTATTTATA
1 TTATAAAAAT-TATATTTATA
76878 TTTTAAAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 12 0.33
23 12 0.33
24 12 0.33
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (23 bp):
TTATAAAAATTATATTTATAATA
Found at i:76916 original size:19 final size:18
Alignment explanation
Indices: 76894--76952 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 18
76884 AATACAATTA
76894 ATTATTTATTTGAAATAAT
1 ATTATTTATTT-AAATAAT
76913 ATTA-TT-TTTAAAT--T
1 ATTATTTATTTAAATAAT
76927 ATCTATTTAATTTTAAATAAT
1 AT-TATTT-A-TTTAAATAAT
76948 ATTAT
1 ATTAT
76953 ACGGAACCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
14 3 0.09
15 2 0.06
16 6 0.18
17 3 0.09
18 2 0.06
19 11 0.33
20 3 0.09
21 3 0.09
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (18 bp):
ATTATTTATTTAAATAAT
Found at i:77113 original size:34 final size:37
Alignment explanation
Indices: 77073--77150 Score: 99
Period size: 34 Copynumber: 2.2 Consensus size: 37
77063 ATTTAAAAAA
*
77073 ATAAATAAACATTTTAAAAT-ATTT-TTAT-AATATT
1 ATAAATAAACATTTTAAAATAATTTAATATAAATATT
* * *
77107 ATAAATAAACTTTTTAGAATAATTTAATATAAATTTT
1 ATAAATAAACATTTTAAAATAATTTAATATAAATATT
77144 ATAAATA
1 ATAAATA
77151 CATAAAAGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 18 0.49
35 4 0.11
36 3 0.08
37 12 0.32
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (37 bp):
ATAAATAAACATTTTAAAATAATTTAATATAAATATT
Found at i:77120 original size:22 final size:23
Alignment explanation
Indices: 77093--77147 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
77083 ATTTTAAAAT
77093 ATTTTTATAAT-ATTATAA-ATAA
1 ATTTTTATAATAATT-TAATATAA
*
77115 ACTTTTTAGAATAATTTAATATAA
1 A-TTTTTATAATAATTTAATATAA
77139 A-TTTTATAA
1 ATTTTTATAA
77148 ATACATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
22 8 0.29
23 12 0.43
24 8 0.29
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
ATTTTTATAATAATTTAATATAA
Found at i:82129 original size:22 final size:23
Alignment explanation
Indices: 82087--82129 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
82077 ATAATCTGGT
*
82087 TTTTATATAAAACTAATCTAAAA
1 TTTTATATAAAACAAATCTAAAA
82110 TTTTAT-TAAAA-AAATACTAA
1 TTTTATATAAAACAAAT-CTAA
82130 GCAAAATGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 3 0.17
22 9 0.50
23 6 0.33
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (23 bp):
TTTTATATAAAACAAATCTAAAA
Found at i:92360 original size:54 final size:56
Alignment explanation
Indices: 92240--92360 Score: 149
Period size: 54 Copynumber: 2.2 Consensus size: 56
92230 CTTGGGTCCG
* * *
92240 AGACATTGGTGCAAGCGTCCGACAAGGAGGTTCAAGATAAAGTATCGGTCTTGCCA
1 AGACATTGGTGCAAACGTCCGACAAGGAGGTTCAAGACAAAGTATCGGTCTTGACA
* * * *
92296 TGACATTGGTGCAAATGTCCGATATGGA-GTT-AAGACAAAGTATCGAG-CTTGACA
1 AGACATTGGTGCAAACGTCCGACAAGGAGGTTCAAGACAAAGTATCG-GTCTTGACA
92350 AGACATTGGTG
1 AGACATTGGTG
92361 TAAGTATTCT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
54 29 0.52
55 4 0.07
56 23 0.41
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Consensus pattern (56 bp):
AGACATTGGTGCAAACGTCCGACAAGGAGGTTCAAGACAAAGTATCGGTCTTGACA
Found at i:94698 original size:3 final size:3
Alignment explanation
Indices: 94683--94734 Score: 63
Period size: 3 Copynumber: 17.3 Consensus size: 3
94673 ACTATCATGC
*
94683 ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT AACTT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -A-TT ATT
94728 ATT ATT A
1 ATT ATT A
94735 ATTCTAACTA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 4 0.09
3 35 0.81
4 2 0.05
5 2 0.05
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:100351 original size:63 final size:64
Alignment explanation
Indices: 100252--100378 Score: 229
Period size: 63 Copynumber: 2.0 Consensus size: 64
100242 TTGCTAAAAG
*
100252 GGGTAAACTTCATTTTGGCTCCCTCTGTTTT-GAAAAACATTCAATTTGGTCCCCAAATCGGTT
1 GGGTAAACTTCATTTTGGCTCCCTCTGTTTTAAAAAAACATTCAATTTGGTCCCCAAATCGGTT
*
100315 GGGTAAACTTCATTTTGGCTCCCTCTGTTTTAAAAAAACATTTAATTTGGTCCCCAAATCGGTT
1 GGGTAAACTTCATTTTGGCTCCCTCTGTTTTAAAAAAACATTCAATTTGGTCCCCAAATCGGTT
100379 TAATTCCCTT
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
63 31 0.51
64 30 0.49
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (64 bp):
GGGTAAACTTCATTTTGGCTCCCTCTGTTTTAAAAAAACATTCAATTTGGTCCCCAAATCGGTT
Found at i:100865 original size:125 final size:122
Alignment explanation
Indices: 100736--100975 Score: 419
Period size: 125 Copynumber: 1.9 Consensus size: 122
100726 ATTATATGTA
*
100736 TATATTATTTTTAATTTAACTATTACTATTATCTTCTTTTTACTAAGTTATATGTATATATATAT
1 TATATTATTTTTAATTTAACTATTACTATTATCTTCTTTTTACTAA-TT-TATATATATATATAT
*
100801 ATATTACGTTATTATTA-TATATACGTATACTTTTTTTTTCTTCATTGATTATTATATACG
64 AT-TTACGTTATTATTATTATATACGTATAC-TCTTTTTTCTTCATTGATTATTATATACG
100861 TATATTATTTTTAATTTAACTATTACTATTATCTTCTTTTTACTAATTTATATATATATATATAT
1 TATATTATTTTTAATTTAACTATTACTATTATCTTCTTTTTACTAATTTATATATATATATATAT
100926 TTACGTTATTATTATTATATACGTATACTCTTTTTTCTTCATTGATTATT
66 TTACGTTATTATTATTATATACGTATACTCTTTTTTCTTCATTGATTATT
100976 TTTGCTTAAT
Statistics
Matches: 112, Mismatches: 2, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
122 35 0.31
123 29 0.26
124 2 0.02
125 46 0.41
ACGTcount: A:0.30, C:0.09, G:0.04, T:0.57
Consensus pattern (122 bp):
TATATTATTTTTAATTTAACTATTACTATTATCTTCTTTTTACTAATTTATATATATATATATAT
TTACGTTATTATTATTATATACGTATACTCTTTTTTCTTCATTGATTATTATATACG
Found at i:113149 original size:105 final size:105
Alignment explanation
Indices: 112472--113141 Score: 1277
Period size: 105 Copynumber: 6.4 Consensus size: 105
112462 AGGTTTTACC
112472 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGGCAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGGCAACGTAAGTTCAACTTCACG
112537 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
112577 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGGCAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGGCAACGTAAGTTCAACTTCACG
112642 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
112682 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGGCAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGGCAACGTAAGTTCAACTTCACG
*
112747 ATGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
112787 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGGCAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGGCAACGTAAGTTCAACTTCACG
*
112852 ACGAAGGGACCGCTGGTTGTCAACGAACTTTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
112892 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGGCAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGGCAACGTAAGTTCAACTTCACG
112957 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
* * *
112997 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGGCAACGTAAGTTCAACTTCACG
* *
113062 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
113102 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
113142 GAAACAACAC
Statistics
Matches: 556, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 556 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.24
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGGCAACGTAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
Found at i:114787 original size:17 final size:16
Alignment explanation
Indices: 114751--114789 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
114741 TATATTACTC
*
114751 ATATTTGCTTTTTTTT
1 ATATTTTCTTTTTTTT
114767 -TATTTTCTTTGTTTTT
1 ATATTTTCTTT-TTTTT
114783 ATATTTT
1 ATATTTT
114790 TATGGATGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 9 0.45
16 5 0.25
17 6 0.30
ACGTcount: A:0.13, C:0.05, G:0.05, T:0.77
Consensus pattern (16 bp):
ATATTTTCTTTTTTTT
Found at i:115093 original size:120 final size:125
Alignment explanation
Indices: 114867--115120 Score: 428
Period size: 120 Copynumber: 2.0 Consensus size: 125
114857 TGTTTTACAA
*
114867 ATTATTATATATGTATATATTATTTTTAATTTAACTATTACTATTATCTTCTTTTTACTAAGTTA
1 ATTATTATATACG-ATATATTATTTTTAATTTAACTATTACTATTATCTTCTTTTTACTAA--TA
*
114932 TATGTATATATATATATATTTACGTTATTATTATTATATACGTATACTTTTTTTTCTTCATTG
63 TATGTATATATATATATATTTACGTTATTATTATTATATACGTATACTCTTTTTTCTTCATTG
114995 ATTATTATATACG-TATATTATTTTTAATTTAACTATTACTATTATCTTCTTTTTACT-A-AT-T
1 ATTATTATATACGATATATTATTTTTAATTTAACTATTACTATTATCTTCTTTTTACTAATATAT
115056 -TATATATATATATATTTACGTTATTATTATTATATACGTATACTCTTTTTTCTTCATTG
66 GTATATATATATATATTTACGTTATTATTATTATATACGTATACTCTTTTTTCTTCATTG
115115 ATTATT
1 ATTATT
115121 TTTGCTTAAT
Statistics
Matches: 124, Mismatches: 2, Indels: 8
0.93 0.01 0.06
Matches are distributed among these distances:
120 64 0.52
121 1 0.01
122 2 0.02
125 1 0.01
126 44 0.35
128 12 0.10
ACGTcount: A:0.30, C:0.09, G:0.04, T:0.57
Consensus pattern (125 bp):
ATTATTATATACGATATATTATTTTTAATTTAACTATTACTATTATCTTCTTTTTACTAATATAT
GTATATATATATATATTTACGTTATTATTATTATATACGTATACTCTTTTTTCTTCATTG
Found at i:117395 original size:29 final size:29
Alignment explanation
Indices: 117346--117449 Score: 147
Period size: 29 Copynumber: 3.6 Consensus size: 29
117336 ACCCGACCCA
117346 GTGACATTTT-GGAATTATTTTGAAAAAG
1 GTGACATTTTGGGAATTATTTTGAAAAAG
* *
117374 GTGATATTTTGGGAATTATTTTGAAAAAT
1 GTGACATTTTGGGAATTATTTTGAAAAAG
*
117403 GTAACATTTTGGGAATTATTTTGAAAAAAG
1 GTGACATTTTGGGAATTATTTTG-AAAAAG
* *
117433 GTGATATTTTGGAAATT
1 GTGACATTTTGGGAATT
117450 TGTTAAACAC
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
28 9 0.14
29 38 0.58
30 19 0.29
ACGTcount: A:0.36, C:0.02, G:0.21, T:0.41
Consensus pattern (29 bp):
GTGACATTTTGGGAATTATTTTGAAAAAG
Found at i:117543 original size:106 final size:107
Alignment explanation
Indices: 117358--117550 Score: 264
Period size: 106 Copynumber: 1.8 Consensus size: 107
117348 GACATTTTGG
* * *
117358 AATTATTTTGAAAAAGGTGATATTTTGGGAATTATTTTGAAAAATGTAACATTTTGGGAATTATT
1 AATTATTTTGAAAAAGATGACATTTTGGGAATTATTTTGAAAAATGTAACATTTTGAGAATTATT
117423 TTGAAAAAAGGTGATAT-TTTGGAAATTTGTTAAACACGGGT
66 TTGAAAAAAGGTGATATATTTGGAAATTTGTTAAACACGGGT
* * * * * *
117464 AATTATTTTTAAAATGATGACATTTTGGGAATTA-TTTGTAAAATGGTGATATTTTGATAATTAT
1 AATTATTTTGAAAAAGATGACATTTTGGGAATTATTTTGAAAAAT-GTAACATTTTGAGAATTAT
* *
117528 TTTTAATAAAGGTGATATATTTG
65 TTTGAAAAAAGGTGATATATTTG
117551 TAATTTTCGA
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
105 9 0.12
106 61 0.82
107 4 0.05
ACGTcount: A:0.36, C:0.02, G:0.19, T:0.43
Consensus pattern (107 bp):
AATTATTTTGAAAAAGATGACATTTTGGGAATTATTTTGAAAAATGTAACATTTTGAGAATTATT
TTGAAAAAAGGTGATATATTTGGAAATTTGTTAAACACGGGT
Found at i:117544 original size:30 final size:28
Alignment explanation
Indices: 117462--117555 Score: 107
Period size: 29 Copynumber: 3.2 Consensus size: 28
117452 TTAAACACGG
* *
117462 GTAATTATTTTTAAAATGATGACATTTT
1 GTAATTATTTTTAAAATGGTGATATTTT
* *
117490 GGGAATTATTTGTAAAATGGTGATATTTT
1 -GTAATTATTTTTAAAATGGTGATATTTT
*
117519 GATAATTATTTTTAATAAAGGTGATATATTT
1 G-TAATTATTTTTAA-AATGGTGATAT-TTT
117550 GTAATT
1 GTAATT
117556 TTCGAATGTG
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
28 1 0.02
29 35 0.64
30 15 0.27
31 4 0.07
ACGTcount: A:0.35, C:0.01, G:0.16, T:0.48
Consensus pattern (28 bp):
GTAATTATTTTTAAAATGGTGATATTTT
Found at i:121919 original size:28 final size:28
Alignment explanation
Indices: 121879--121932 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
121869 TGTGAGTTTT
*
121879 GGCTTCAAGAAGTGTCATTTTTGGGGCA
1 GGCTTCAAGAAGTATCATTTTTGGGGCA
*
121907 GGCTTCAAGAAGTATCGTTTTTGGGG
1 GGCTTCAAGAAGTATCATTTTTGGGG
121933 TAGATTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.20, C:0.13, G:0.33, T:0.33
Consensus pattern (28 bp):
GGCTTCAAGAAGTATCATTTTTGGGGCA
Found at i:124925 original size:29 final size:29
Alignment explanation
Indices: 124883--125067 Score: 139
Period size: 29 Copynumber: 6.4 Consensus size: 29
124873 GACCCGACCC
*
124883 AGTGATATTTTGGGAATTATTTTGAAAAA
1 AGTGACATTTTGGGAATTATTTTGAAAAA
124912 AGTGACATTTTGGGAATTATTTTGAAAATTA
1 AGTGACATTTTGGGAATTATTTTGAAAA--A
* *
124943 A-TGACGTTTT-GG-ATT-TTTTTAAAAA
1 AGTGACATTTTGGGAATTATTTTGAAAAA
* * * *
124968 CAATGACATTCTGGTAATTATTTT-TAAAA
1 -AGTGACATTTTGGGAATTATTTTGAAAAA
* *
124997 TGATGACATTTTGGGAATTA-TTTGTAAAAT
1 AG-TGACATTTTGGGAATTATTTTG-AAAAA
* * * *
125027 GGTGATATTTTGGTAATTATTTTTAATAAA
1 AGTGACATTTTGGGAATTATTTTGAA-AAA
* *
125057 GGTGATATTTT
1 AGTGACATTTT
125068 TGTAATTTTC
Statistics
Matches: 126, Mismatches: 18, Indels: 23
0.75 0.11 0.14
Matches are distributed among these distances:
25 1 0.01
26 1 0.01
27 15 0.12
28 7 0.06
29 68 0.54
30 32 0.25
31 2 0.02
ACGTcount: A:0.34, C:0.03, G:0.18, T:0.45
Consensus pattern (29 bp):
AGTGACATTTTGGGAATTATTTTGAAAAA
Found at i:126834 original size:21 final size:21
Alignment explanation
Indices: 126804--126856 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
126794 GTTTCCAGAT
126804 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACATCGACTA
* *
126825 TCGCAGCGCGAACTTCGACTA
1 TCGCAACGCGAACATCGACTA
*
126846 TCGCAATGCGA
1 TCGCAACGCGA
126857 TTTTCCAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.32, G:0.23, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAACATCGACTA
Found at i:126876 original size:19 final size:19
Alignment explanation
Indices: 126852--126918 Score: 62
Period size: 21 Copynumber: 3.3 Consensus size: 19
126842 ACTATCGCAA
126852 TGCGATTTTCCAAATTCGT
1 TGCGATTTTCCAAATTCGT
** *
126871 TGCGATAGTCCAAGTTCGCGT
1 TGCGATTTTCCAAATT--CGT
*
126892 TGCGATTTATTCCAAATTCAT
1 TGCGA-TT-TTCCAAATTCGT
126913 TGCGAT
1 TGCGAT
126919 AGTCCAAGTT
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
19 13 0.35
20 1 0.03
21 15 0.41
22 1 0.03
23 7 0.19
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.37
Consensus pattern (19 bp):
TGCGATTTTCCAAATTCGT
Found at i:126894 original size:21 final size:21
Alignment explanation
Indices: 126868--126986 Score: 147
Period size: 21 Copynumber: 5.8 Consensus size: 21
126858 TTTCCAAATT
126868 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* *
126889 CGTTGCGATTTATTCCAAATT--
1 CGTTGCGA--TAGTCCAAGTTCG
*
126910 CATTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
126931 CGTTGCGATAGTCCAAGTT--
1 CGTTGCGATAGTCCAAGTTCG
* *
126950 TGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
126971 CGTTGCGATAGTCCAA
1 CGTTGCGATAGTCCAA
126987 AATCGCAACG
Statistics
Matches: 82, Mismatches: 10, Indels: 12
0.79 0.10 0.12
Matches are distributed among these distances:
19 26 0.32
21 47 0.57
23 9 0.11
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAGTTCG
Found at i:126957 original size:40 final size:40
Alignment explanation
Indices: 126860--126987 Score: 193
Period size: 40 Copynumber: 3.1 Consensus size: 40
126850 AATGCGATTT
*
126860 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTAT
1 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGA--TAG
*
126902 TCCAAATTCATTGCGATAGTCCAAGTTCGCGTTGCGATAG
1 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAG
* * *
126942 TCCAAGTTTGTTGCGATAGTCGAAGTTCGCGTTGCGATAG
1 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAG
126982 TCCAAA
1 TCCAAA
126988 ATCGCAACGA
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
40 43 0.54
42 36 0.46
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.32
Consensus pattern (40 bp):
TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAG
Found at i:126992 original size:21 final size:21
Alignment explanation
Indices: 126860--126992 Score: 125
Period size: 21 Copynumber: 6.5 Consensus size: 21
126850 AATGCGATTT
126860 TCCAAATT--CGTTGCGATAG
1 TCCAAATTCGCGTTGCGATAG
* *
126879 TCCAAGTTCGCGTTGCGATTTAT
1 TCCAAATTCGCGTTGCGA--TAG
*
126902 TCCAAATT--CATTGCGATAG
1 TCCAAATTCGCGTTGCGATAG
*
126921 TCCAAGTTCGCGTTGCGATAG
1 TCCAAATTCGCGTTGCGATAG
* *
126942 TCCAAGTT--TGTTGCGATAG
1 TCCAAATTCGCGTTGCGATAG
* *
126961 TCGAAGTTCGCGTTGCGATAG
1 TCCAAATTCGCGTTGCGATAG
*
126982 TCCAAAATCGC
1 TCCAAATTCGC
126993 AACGACTGGT
Statistics
Matches: 93, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
19 33 0.35
21 51 0.55
23 9 0.10
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (21 bp):
TCCAAATTCGCGTTGCGATAG
Found at i:127882 original size:21 final size:21
Alignment explanation
Indices: 127856--127967 Score: 92
Period size: 19 Copynumber: 5.4 Consensus size: 21
127846 ATTTTGGACT
127856 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* *
127877 ATCGCAACGCGAACTTGGACT--
1 ATCGCAA--CGAATTTGGAATAA
* *
127898 ATCGCAACGAACTTGGACT--
1 ATCGCAACGAATTTGGAATAA
* *
127917 ATCGCAACAAATTTGGAGTAA
1 ATCGCAACGAATTTGGAATAA
127938 ATCGCAACGCGAATTTGG-A-AA
1 ATCGCAA--CGAATTTGGAATAA
127959 ATCGCAACG
1 ATCGCAACG
127968 CGAACTTCGA
Statistics
Matches: 78, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
19 30 0.38
21 30 0.38
23 18 0.23
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:127944 original size:61 final size:62
Alignment explanation
Indices: 127849--127987 Score: 208
Period size: 61 Copynumber: 2.2 Consensus size: 62
127839 CGTTGCGATT
* **
127849 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAA-CGAAC
1 TTGGACTATCGCAACAAATTTGGAATAAATCGCAACGCGAACTTGGAAAATCGCAACCGAAC
* *
127910 TTGGACTATCGCAACAAATTTGGAGTAAATCGCAACGCGAATTTGGAAAATCGCAACGCGAAC
1 TTGGACTATCGCAACAAATTTGGAATAAATCGCAACGCGAACTTGGAAAATCGCAAC-CGAAC
*
127973 TTCGACTATCGCAAC
1 TTGGACTATCGCAAC
127988 GCGAACTTGG
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
61 51 0.73
63 19 0.27
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.22
Consensus pattern (62 bp):
TTGGACTATCGCAACAAATTTGGAATAAATCGCAACGCGAACTTGGAAAATCGCAACCGAAC
Found at i:127968 original size:21 final size:21
Alignment explanation
Indices: 127849--128013 Score: 162
Period size: 21 Copynumber: 8.0 Consensus size: 21
127839 CGTTGCGATT
*
127849 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
*
127868 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
127891 TTGGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
* *
127910 TTGGACTATCGCAA--CAAAT
1 TTGGACTATCGCAACGCGAAC
* *
127929 TTGGAGTAAATCGCAACGCGAAT
1 TTGGACT--ATCGCAACGCGAAC
**
127952 TTGGAAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
127973 TTCGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
127994 TTGGACTATCGCAATGCGAA
1 TTGGACTATCGCAACGCGAA
128014 TATGTAAATC
Statistics
Matches: 123, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
19 34 0.28
21 70 0.57
23 19 0.15
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.21
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:128054 original size:21 final size:21
Alignment explanation
Indices: 128028--128074 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
128018 TAAATCGCAG
128028 TGCGATAGTCGAAGTTCACGT
1 TGCGATAGTCGAAGTTCACGT
*
128049 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCACGT
128070 TGCGA
1 TGCGA
128075 ATCTGGAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.32, T:0.28
Consensus pattern (21 bp):
TGCGATAGTCGAAGTTCACGT
Found at i:128231 original size:2 final size:2
Alignment explanation
Indices: 128224--128269 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
128214 TTTCTCTACA
128224 AT AT 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 AT AT
128266 AT AT
1 AT AT
128270 TTTTTTTTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:132432 original size:23 final size:24
Alignment explanation
Indices: 132400--132463 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 24
132390 ATTCTTATTG
132400 AATTAATCGAAACTTATAAA-TTA
1 AATTAATCGAAACTTATAAATTTA
* *
132423 AATTAGTCGATACTTATAAATTTTA
1 AATTAATCGAAACTTATAAA-TTTA
*
132448 AATTAATCAAAACTTA
1 AATTAATCGAAACTTA
132464 CAATGTTTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 18 0.53
25 16 0.47
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.38
Consensus pattern (24 bp):
AATTAATCGAAACTTATAAATTTA
Found at i:139773 original size:21 final size:21
Alignment explanation
Indices: 139719--139767 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
139709 AATCGTAACC
*
139719 CGATTTTCCAAATTCTCGTTG
1 CGATTTTCCAAATTCGCGTTG
139740 CGATTTTCCAAATTCGCGTTG
1 CGATTTTCCAAATTCGCGTTG
139761 CGATTTT
1 CGATTTT
139768 AGAAATCGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.18, C:0.22, G:0.16, T:0.43
Consensus pattern (21 bp):
CGATTTTCCAAATTCGCGTTG
Found at i:139782 original size:20 final size:20
Alignment explanation
Indices: 139770--139845 Score: 91
Period size: 20 Copynumber: 3.8 Consensus size: 20
139760 GCGATTTTAG
*
139770 AAATCGCAATGCGAATATGT
1 AAATCGCAATGCGATTATGT
*
139790 AAATCGCAATGCGATTCTG-
1 AAATCGCAATGCGATTATGT
* *
139809 ACTATCGCAATGCGAATATGT
1 A-AATCGCAATGCGATTATGT
*
139830 AAATCGCAACGCGATT
1 AAATCGCAATGCGATT
139846 CTGACTATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 1 0.02
20 44 0.96
21 1 0.02
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.25
Consensus pattern (20 bp):
AAATCGCAATGCGATTATGT
Found at i:139859 original size:20 final size:20
Alignment explanation
Indices: 139792--139897 Score: 99
Period size: 20 Copynumber: 5.2 Consensus size: 20
139782 GAATATGTAA
*
139792 ATCGCAATGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* * * *
139812 ATCGCAATGCGAATATGTA-A
1 ATCGCAACGCGATTCTG-ACT
139832 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* **
139852 ATCACAACGCGATAAT-ACGT
1 ATCGCAACGCGATTCTGAC-T
139872 AATCGCAACGCGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
139893 ATCGC
1 ATCGC
139898 GTTGCGATAA
Statistics
Matches: 68, Mismatches: 13, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
19 3 0.04
20 48 0.71
21 15 0.22
22 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:139905 original size:41 final size:42
Alignment explanation
Indices: 139772--139927 Score: 180
Period size: 40 Copynumber: 3.9 Consensus size: 42
139762 GATTTTAGAA
* *
139772 ATCGCAATGCG--AATATGTAAATCGCAATGCGATTCTGACT
1 ATCGCAATGCGATAATACGTAAATCGCAACGCGATTCTGACT
*
139812 ATCGCAATGCG--AATATGTAAATCGCAACGCGATTCTGACT
1 ATCGCAATGCGATAATACGTAAATCGCAACGCGATTCTGACT
* *
139852 ATCACAACGCGATAATACGT-AATCGCAACGCGATTCTGACT
1 ATCGCAATGCGATAATACGTAAATCGCAACGCGATTCTGACT
** * * *
139893 ATCGCGTTGCGATAATAC-AAAATCACAATGCGATT
1 ATCGCAATGCGATAATACGTAAATCGCAACGCGATT
139928 TTCAAAGCGT
Statistics
Matches: 102, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
40 48 0.47
41 48 0.47
42 6 0.06
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (42 bp):
ATCGCAATGCGATAATACGTAAATCGCAACGCGATTCTGACT
Found at i:140086 original size:22 final size:22
Alignment explanation
Indices: 140071--140165 Score: 145
Period size: 22 Copynumber: 4.3 Consensus size: 22
140061 CTACGGCGAC
*
140071 ATCCGTCCCCATCTACGACAAA
1 ATCCGTCCCCATCTCCGACAAA
*
140093 ATTCGTCCCCATCTCCGACAAA
1 ATCCGTCCCCATCTCCGACAAA
140115 ATCCGTCCCCATCTCCGACAAA
1 ATCCGTCCCCATCTCCGACAAA
* * *
140137 ATCCATCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACAAA
140159 ATCCGTC
1 ATCCGTC
140166 TATCTCCATC
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 66 1.00
ACGTcount: A:0.26, C:0.43, G:0.11, T:0.20
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACAAA
Found at i:142543 original size:20 final size:20
Alignment explanation
Indices: 142520--142568 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
142510 GAAACTTAAA
142520 ATCGCAACGCGGAA-ATGACT
1 ATCGCAACGC-GAATATGACT
*
142540 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATATGACT
*
142560 ATCACAACG
1 ATCGCAACG
142569 GGATAATCGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 3 0.12
20 23 0.88
ACGTcount: A:0.35, C:0.27, G:0.20, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAATATGACT
Found at i:142633 original size:19 final size:18
Alignment explanation
Indices: 142606--142663 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
142596 CGCAACACGA
*
142606 ATTTAGTTTCGCGTTGCG
1 ATTTTGTTTCGCGTTGCG
142624 ATTTTGGTTTCGCGTTGCG
1 ATTTT-GTTTCGCGTTGCG
* *
142643 ATTTTATTTCGCATTGCG
1 ATTTTGTTTCGCGTTGCG
142661 ATT
1 ATT
142664 ATCTGGTTGC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
18 18 0.50
19 18 0.50
ACGTcount: A:0.12, C:0.16, G:0.24, T:0.48
Consensus pattern (18 bp):
ATTTTGTTTCGCGTTGCG
Found at i:142654 original size:18 final size:18
Alignment explanation
Indices: 142607--142663 Score: 78
Period size: 19 Copynumber: 3.1 Consensus size: 18
142597 GCAACACGAA
142607 TTTAGTTTCGCGTTGCGAT
1 TTTA-TTTCGCGTTGCGAT
*
142626 TTTGGTTTCGCGTTGCGAT
1 TTT-ATTTCGCGTTGCGAT
*
142645 TTTATTTCGCATTGCGAT
1 TTTATTTCGCGTTGCGAT
142663 T
1 T
142664 ATCTGGTTGC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 14 0.41
19 20 0.59
ACGTcount: A:0.11, C:0.16, G:0.25, T:0.49
Consensus pattern (18 bp):
TTTATTTCGCGTTGCGAT
Found at i:142698 original size:20 final size:20
Alignment explanation
Indices: 142670--142747 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 20
142660 GATTATCTGG
* * *
142670 TTGCTATAGTCAAATTCGCC
1 TTGCGATAGTCAATTTCGCA
**
142690 TTGCGATAGTCAATTTCGTG
1 TTGCGATAGTCAATTTCGCA
* *
142710 TTGTGATAGTCATTTTCGCA
1 TTGCGATAGTCAATTTCGCA
*
142730 TTGCGATAGTCATTTTCG
1 TTGCGATAGTCAATTTCG
142748 TGTTGCGATT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.41
Consensus pattern (20 bp):
TTGCGATAGTCAATTTCGCA
Found at i:142734 original size:40 final size:40
Alignment explanation
Indices: 142675--142752 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
142665 TCTGGTTGCT
*
142675 ATAGTCAAATTCGCCTTGCGATAGTCAATTTCGTGTTGTG
1 ATAGTCAAATTCGCATTGCGATAGTCAATTTCGTGTTGTG
** *
142715 ATAGTCATTTTCGCATTGCGATAGTCATTTTCGTGTTG
1 ATAGTCAAATTCGCATTGCGATAGTCAATTTCGTGTTG
142753 CGATTTTAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.41
Consensus pattern (40 bp):
ATAGTCAAATTCGCATTGCGATAGTCAATTTCGTGTTGTG
Found at i:142753 original size:20 final size:20
Alignment explanation
Indices: 142690--142756 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
142680 CAAATTCGCC
*
142690 TTGCGATAGTCAATTTCGTG
1 TTGCGATAGTCATTTTCGTG
* **
142710 TTGTGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGTG
142730 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCATTTTCGTG
142750 TTGCGAT
1 TTGCGAT
142757 TTTAAGTTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.18, C:0.15, G:0.24, T:0.43
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGTG
Found at i:143232 original size:21 final size:21
Alignment explanation
Indices: 143206--143292 Score: 77
Period size: 21 Copynumber: 4.1 Consensus size: 21
143196 GCCCGACTCA
143206 CCTATCATCGTTCAAGAGGCC
1 CCTATCATCGTTCAAGAGGCC
* *
143227 CCTATCATCCCTT-AAGAGTCC
1 CCTATCAT-CGTTCAAGAGGCC
* * *
143248 CCTCTTACCGTTCAAGAGGCC
1 CCTATCATCGTTCAAGAGGCC
* * * *
143269 TCTGTCATCGTTGAAGAGGTC
1 CCTATCATCGTTCAAGAGGCC
143290 CCT
1 CCT
143293 CCCACCATTC
Statistics
Matches: 50, Mismatches: 14, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
20 3 0.06
21 44 0.88
22 3 0.06
ACGTcount: A:0.21, C:0.33, G:0.18, T:0.28
Consensus pattern (21 bp):
CCTATCATCGTTCAAGAGGCC
Found at i:144644 original size:14 final size:14
Alignment explanation
Indices: 144623--144661 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
144613 TTGCTTGTTT
144623 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
144637 AGTTGATTTGTAAA
1 AATTGATTTGTAAA
144651 AATTGATTTGT
1 AATTGATTTGT
144662 TTAATTGATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:144669 original size:13 final size:13
Alignment explanation
Indices: 144623--144677 Score: 65
Period size: 14 Copynumber: 4.1 Consensus size: 13
144613 TTGCTTGTTT
144623 AATTGATTTGTAA
1 AATTGATTTGTAA
144636 AAGTTGATTTGTAAA
1 AA-TTGATTTGT-AA
**
144651 AATTGATTTGTTT
1 AATTGATTTGTAA
*
144664 AATTGATGTGTAA
1 AATTGATTTGTAA
144677 A
1 A
144678 TAATTCTTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
13 13 0.37
14 18 0.51
15 4 0.11
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.45
Consensus pattern (13 bp):
AATTGATTTGTAA
Found at i:144682 original size:28 final size:29
Alignment explanation
Indices: 144622--144682 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 29
144612 TTTGCTTGTT
*
144622 TAATTGATTTGTAAAAGTTGATTTGTAAA
1 TAATTGATTTGTAAAAGTTGATGTGTAAA
**
144651 -AATTGATTTGTTTAA-TTGATGTGTAAA
1 TAATTGATTTGTAAAAGTTGATGTGTAAA
144678 TAATT
1 TAATT
144683 CTTATTTGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 11 0.39
28 17 0.61
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (29 bp):
TAATTGATTTGTAAAAGTTGATGTGTAAA
Found at i:144956 original size:20 final size:20
Alignment explanation
Indices: 144798--145180 Score: 254
Period size: 20 Copynumber: 19.9 Consensus size: 20
144788 GCGATTTTCT
* *
144798 CGTTGCGATAGTCAAACTCC
1 CGTTGCGATAGTCAAATTCG
* *
144818 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCG
*
144838 CGTTGCGATAGTCAAAATCG
1 CGTTGCGATAGTCAAATTCG
** * * *
144858 CAATGCGAAAGACAAAATCG
1 CGTTGCGATAGTCAAATTCG
*** *
144878 CAACGCGAAAGTC-AATTCG
1 CGTTGCGATAGTCAAATTCG
* * *
144897 CGTTGCGATGGTCTAATACG
1 CGTTGCGATAGTCAAATTCG
* *
144917 CTTTGCGAT--T----TTCT
1 CGTTGCGATAGTCAAATTCG
*
144931 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
* *
144951 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCG
* *
144971 CGTTGCGATAGTCAAAATCA
1 CGTTGCGATAGTCAAATTCG
** *
144991 CAATGCGAAAGTC-AATTCG
1 CGTTGCGATAGTCAAATTCG
* * * *
145010 CATTGCGATGGTCTAATACG
1 CGTTGCGATAGTCAAATTCG
* *
145030 CTTTGCGAT--T----TTCT
1 CGTTGCGATAGTCAAATTCG
* *
145044 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCG
* *
145064 CGTTGCGGTCGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
145084 TGTTGCGATAGTGAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
145104 CGTTGCGATAGTCAAATTTG
1 CGTTGCGATAGTCAAATTCG
* * *
145124 TGTTACTATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
145144 CGTTGCGATAGTCAAATTTG
1 CGTTGCGATAGTCAAATTCG
* *
145164 CATTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
145181 GAATGTATAA
Statistics
Matches: 286, Mismatches: 63, Indels: 28
0.76 0.17 0.07
Matches are distributed among these distances:
14 20 0.07
16 2 0.01
18 2 0.01
19 27 0.09
20 235 0.82
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:145068 original size:133 final size:133
Alignment explanation
Indices: 144764--145119 Score: 358
Period size: 133 Copynumber: 2.7 Consensus size: 133
144754 AGGCAAAAGA
* * * * ** * *
144764 CGTTACGATAGTCTAATACGCTTTGCGATTTTCTCGTTGCGATAGTCAAACTCCCGTTGCGATAA
1 CGTTGCGATGGTCTAATACGATATGCGAAATTCACGTTGCGATAGTCAAATTCCCGTTGCGATAA
*
144829 TCAAATTCACGTTGCGATAGTCAAAATCGCAATGCGAAAGACAAAATCGCAACGCGAAAGTCAAT
66 TCAAATTCACGTTGCGATAGTCAAAATCACAATGCGAAAGACAAAATCGCAACGCGAAAGTCAAT
*
144894 TCG
131 ACG
* * ** *
144897 CGTTGCGATGGTCTAATACGCTTTGCGATTTTCTCGTTGCGATAGTCAAATTCCCGTTGCGATAA
1 CGTTGCGATGGTCTAATACGATATGCGAAATTCACGTTGCGATAGTCAAATTCCCGTTGCGATAA
* * ** **
144962 TCAAATTCACGTTGCGATAGTCAAAATCACAATGCGAAAGTC-AATTCGCATTGCGATGGTCTAA
66 TCAAATTCACGTTGCGATAGTCAAAATCACAATGCGAAAGACAAAATCGCAACGCGAAAGTC-AA
145026 TACG
130 TACG
* ** ** * * * **
145030 CTTTGCGATTTTCTCGTTGCGATAAT-C-AAATTCACGTTGCGGTCGTCAAATTCGTGTTGCGAT
1 CGTTGCGATGGTCT-AATACGAT-ATGCGAAATTCACGTTGCGATAGTCAAATTCCCGTTGCGAT
* * *
145093 AGTGAAATTCGCGTTGCGATAGTCAAA
64 AATCAAATTCACGTTGCGATAGTCAAA
145120 TTTGTGTTAC
Statistics
Matches: 191, Mismatches: 29, Indels: 6
0.85 0.13 0.03
Matches are distributed among these distances:
132 14 0.07
133 171 0.90
134 5 0.03
135 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (133 bp):
CGTTGCGATGGTCTAATACGATATGCGAAATTCACGTTGCGATAGTCAAATTCCCGTTGCGATAA
TCAAATTCACGTTGCGATAGTCAAAATCACAATGCGAAAGACAAAATCGCAACGCGAAAGTCAAT
ACG
Found at i:145111 original size:113 final size:113
Alignment explanation
Indices: 144818--145118 Score: 422
Period size: 113 Copynumber: 2.7 Consensus size: 113
144808 GTCAAACTCC
* ** * * *
144818 CGTTGCGATAATCAAATTCACGTTGCGATAGTCAAAATCGCAATGCGAAAGACAAAATCGCAACG
1 CGTTGCGATAATCAAATTCACGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAAATCGCAATG
*
144883 CGAAAGTCAATTCGCGTTGCGATGGTCTAATACGCTTTGCGATTTTCT
66 CGAAAGTCAATTCGCATTGCGATGGTCTAATACGCTTTGCGATTTTCT
* * * * *
144931 CGTTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCACGTTGCGATAGTCAAAATCACAATG
1 CGTTGCGATAATCAAATTCACGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAAATCGCAATG
144996 CGAAAGTCAATTCGCATTGCGATGGTCTAATACGCTTTGCGATTTTCT
66 CGAAAGTCAATTCGCATTGCGATGGTCTAATACGCTTTGCGATTTTCT
* * * * * **
145044 CGTTGCGATAATCAAATTCACGTTGCGGTCGTCAAATTCGTGTTGCGATAGTGAAATTCGCGTTG
1 CGTTGCGATAATCAAATTCACGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAAATCGCAATG
*
145109 CGATAGTCAA
66 CGAAAGTCAA
145119 ATTTGTGTTA
Statistics
Matches: 163, Mismatches: 25, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
113 163 1.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.29
Consensus pattern (113 bp):
CGTTGCGATAATCAAATTCACGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAAATCGCAATG
CGAAAGTCAATTCGCATTGCGATGGTCTAATACGCTTTGCGATTTTCT
Found at i:145403 original size:140 final size:140
Alignment explanation
Indices: 145151--145433 Score: 503
Period size: 140 Copynumber: 2.0 Consensus size: 140
145141 TCGCGTTGCG
*
145151 ATAGTCAAATTTGCATTGCGATATTCAAATGAATGTATAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTTGCATTGCGATATTCAAATGAATGTATAACAAGTGATAACAACTGAACAGATCA
* *
145216 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACAGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAAATCAAGTTACTAATAAATGCCTAACAGAAAATGTTAAAAGTTTACACATAA
145281 AATACACATA
131 AATACACATA
* * *
145291 ATAGTCAAATTTGCGTTGCGATATTCAAATGAATGTGTAACAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTTGCATTGCGATATTCAAATGAATGTATAACAAGTGATAACAACTGAACAGATCA
*
145356 TAGCAATGTTCAAAATCAAGTTACTAATAAATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAAATCAAGTTACTAATAAATGCCTAACAGAAAATGTTAAAAGTTTACACATAA
145421 AATACACATA
131 AATACACATA
145431 ATA
1 ATA
145434 AAATGTTTGC
Statistics
Matches: 136, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
140 136 1.00
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.28
Consensus pattern (140 bp):
ATAGTCAAATTTGCATTGCGATATTCAAATGAATGTATAACAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAAATCAAGTTACTAATAAATGCCTAACAGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:147845 original size:24 final size:24
Alignment explanation
Indices: 147794--147845 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
147784 ATCTGAGTAT
** *
147794 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
147818 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
147842 TGAC
1 TGAC
147846 TAGTACCCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:148699 original size:20 final size:20
Alignment explanation
Indices: 148652--148699 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
148642 GAAATTCAGT
*
148652 GTTGCGAAAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
148672 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
148692 GTTGCGAT
1 GTTGCGAT
148700 TACGTATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:148720 original size:21 final size:21
Alignment explanation
Indices: 148687--148742 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
148677 GATAGTCAGA
*
148687 ATCGCGTTGCGATTACGTATT
1 ATCGCATTGCGATTACGTATT
* *
148708 ATCGCATTACGATTATGTATT
1 ATCGCATTGCGATTACGTATT
148729 ATCGCATTGCGATT
1 ATCGCATTGCGATT
148743 TTCTAAAATC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (21 bp):
ATCGCATTGCGATTACGTATT
Found at i:148753 original size:21 final size:20
Alignment explanation
Indices: 148729--148802 Score: 67
Period size: 21 Copynumber: 3.6 Consensus size: 20
148719 ATTATGTATT
148729 ATCGCATTGCGATTTTCTAAA
1 ATCGCATTGCGATTTTC-AAA
* **
148750 ATCGCGTTGCGAATTTGGAAA
1 ATCGCATTGCG-ATTTTCAAA
* * **
148771 ATCGCAATACGATAGTCAAA
1 ATCGCATTGCGATTTTCAAA
148791 ATCGCATTGCGA
1 ATCGCATTGCGA
148803 ATCTGGAAAC
Statistics
Matches: 40, Mismatches: 12, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
20 15 0.38
21 21 0.52
22 4 0.10
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.28
Consensus pattern (20 bp):
ATCGCATTGCGATTTTCAAA
Found at i:148852 original size:19 final size:19
Alignment explanation
Indices: 148828--148864 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
148818 TGCGATAATG
*
148828 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
*
148847 GAGATCGTATTGCGATTT
1 GAGATCGCATTGCGATTT
148865 TATTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.35
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:149314 original size:138 final size:138
Alignment explanation
Indices: 149148--149405 Score: 471
Period size: 138 Copynumber: 1.9 Consensus size: 138
149138 TTTACATAGA
149148 AAATTTAGTGACTAAATTGTAGTTTTTTAAAATTTGCAAAGGCAAAGATGAAAAGTGGATTTTTA
1 AAATTTAGTGACTAAATTGTAGTTTTTTAAAATTTGCAAAGGCAAAGATGAAAAGTGGATTTTTA
* *
149213 TTTGTTCATATAGGAATTTGAAATATTAAAAGGGGTGATAGTACAATGGAAAGTTTAACATTAAA
66 TTTGTTCATATAGGAATTTGAAATATTAAAAGGGATGACAGTACAATGGAAAGTTTAACATTAAA
149278 TGAATTTT
131 TGAATTTT
*
149286 AAATTTAGTGACTAAATTGTAGTTTTTTAAAATTTGCAAAGGCAAAGATGGAAAGTGGATTTTTA
1 AAATTTAGTGACTAAATTGTAGTTTTTTAAAATTTGCAAAGGCAAAGATGAAAAGTGGATTTTTA
* *
149351 TTTGTTCATATTGGAATTTGAAATATTAAAAGGGATGACAGTACAATGGCAAGTT
66 TTTGTTCATATAGGAATTTGAAATATTAAAAGGGATGACAGTACAATGGAAAGTT
149406 GAAATTATCA
Statistics
Matches: 115, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
138 115 1.00
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (138 bp):
AAATTTAGTGACTAAATTGTAGTTTTTTAAAATTTGCAAAGGCAAAGATGAAAAGTGGATTTTTA
TTTGTTCATATAGGAATTTGAAATATTAAAAGGGATGACAGTACAATGGAAAGTTTAACATTAAA
TGAATTTT
Found at i:151835 original size:19 final size:19
Alignment explanation
Indices: 151811--151906 Score: 122
Period size: 19 Copynumber: 5.1 Consensus size: 19
151801 TATGCATTTG
*
151811 GCTATGAATTTGAAAATAA
1 GCTATGAATCTGAAAATAA
* *
151830 GCTATGAATCTGACAGTAA
1 GCTATGAATCTGAAAATAA
* * *
151849 GCTATGAATTTGACAGTAA
1 GCTATGAATCTGAAAATAA
151868 GCTATGAATCTGAAAATAA
1 GCTATGAATCTGAAAATAA
151887 GCTATGAATCT-AGAAATAA
1 GCTATGAATCTGA-AAATAA
151906 G
1 G
151907 TTCTGATTCA
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
18 1 0.01
19 68 0.99
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.28
Consensus pattern (19 bp):
GCTATGAATCTGAAAATAA
Found at i:167411 original size:2 final size:2
Alignment explanation
Indices: 167404--167434 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
167394 AACACCGTCT
*
167404 TC TC TC TC TC TC TC TC TC TC TC TC TC CC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
167435 TATGGTTAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:167762 original size:20 final size:20
Alignment explanation
Indices: 167739--167778 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
167729 CATTGTCCAC
167739 CCCGACAGGAGTTTGTTCAA
1 CCCGACAGGAGTTTGTTCAA
167759 CCCGACAGGAGTTTGTTCAA
1 CCCGACAGGAGTTTGTTCAA
167779 GTGATAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (20 bp):
CCCGACAGGAGTTTGTTCAA
Found at i:169441 original size:32 final size:33
Alignment explanation
Indices: 169396--169462 Score: 102
Period size: 32 Copynumber: 2.0 Consensus size: 33
169386 ATTAAGCCCT
169396 AAACCATAAAACATTACATTAA-AGAGATAAAAAC
1 AAACCAT-AAACATTACATTAAGA-AGATAAAAAC
169430 AAACCAT-AACATTACATTAAGAAGATAAAAAC
1 AAACCATAAACATTACATTAAGAAGATAAAAAC
169462 A
1 A
169463 TTACATATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
32 24 0.75
33 1 0.03
34 7 0.22
ACGTcount: A:0.61, C:0.15, G:0.06, T:0.18
Consensus pattern (33 bp):
AAACCATAAACATTACATTAAGAAGATAAAAAC
Found at i:170296 original size:32 final size:32
Alignment explanation
Indices: 170244--170504 Score: 112
Period size: 32 Copynumber: 7.8 Consensus size: 32
170234 TTTTATAATA
* *
170244 AAGTGATATATCATTGAAAAGTTTATGAAATG
1 AAGTGATATATCACTAAAAAGTTTATGAAATG
* *
170276 AAGTTATATATCACTAAAAAGTTTATGAAGTG
1 AAGTGATATATCACTAAAAAGTTTATGAAATG
* ** * *
170308 AAGTAAT-TAGGAACTAAAAGGTTTATGTCATTATGTATT
1 AAGTGATATA-TCACTAAAAAGTTTATG--A--A---ATG
* * * * ** *
170347 AAATGGTTTATGAGAAAAAGACGTTTTTCTGAAATG
1 AAGTGATATATCACTAAAA-A-G-T-TTATGAAATG
*
170383 AAGTGATATATCATTAAAAAGTTTATGAAATG
1 AAGTGATATATCACTAAAAAGTTTATGAAATG
* * ** *
170415 AAGTTATATATCACTGAAATTTTTTTGAAATG
1 AAGTGATATATCACTAAAAAGTTTATGAAATG
* * * * *
170447 AAGTAATTAGAT-ACTGAAATGTTTTTCTGAAATG
1 AAGTGA-TATATCACTAAAAAG--TTTATGAAATG
* *
170481 AAGTAATATATCACTGAAAAGTTT
1 AAGTGATATATCACTAAAAAGTTT
170505 CTTTTCATAA
Statistics
Matches: 173, Mismatches: 39, Indels: 34
0.70 0.16 0.14
Matches are distributed among these distances:
31 2 0.01
32 99 0.57
33 9 0.05
34 26 0.15
35 1 0.01
36 16 0.09
39 11 0.06
40 2 0.01
41 2 0.01
42 1 0.01
43 4 0.02
ACGTcount: A:0.41, C:0.05, G:0.17, T:0.36
Consensus pattern (32 bp):
AAGTGATATATCACTAAAAAGTTTATGAAATG
Found at i:170427 original size:139 final size:137
Alignment explanation
Indices: 170132--170470 Score: 414
Period size: 139 Copynumber: 2.5 Consensus size: 137
170122 GATATAATAC
* * * * * * * *
170132 TGAAATGAAGTGATACATCACTGAAAAGTTTCTAAAGTGAAGTGATTGGGCACTGAAAAGTTTTT
1 TGAAATGAAGTTATATATCACTGAAAAGTTTATGAAGTGAAGTAATTAGGAACTGAAAAGTTTAT
* * * * *
170197 GTGATTGTGTATTAAATGGTGCATGAGAAAAGGTTTTTTTTATAATAAAGTGATATATCATTGAA
66 GTCATTATGTATTAAATGGTGCATGAGAAAAGGTTTTTCTGATAATAAAGTGATATATCATTAAA
170262 AAGTTTA
131 AAGTTTA
*
170269 TGAAATGAAGTTATATATCACTAAAAAGTTTATGAAGTGAAGTAATTAGGAACT-AAAAGGTTTA
1 TGAAATGAAGTTATATATCACTGAAAAGTTTATGAAGTGAAGTAATTAGGAACTGAAAA-GTTTA
** *
170333 TGTCATTATGTATTAAATGGTTTATGAGAAAAAGACGTTTTTCTGA-AATGAAGTGATATATCAT
65 TGTCATTATGTATTAAATGGTGCATGAG-AAAAG--GTTTTTCTGATAATAAAGTGATATATCAT
170397 TAAAAAGTTTA
127 TAAAAAGTTTA
** * * *
170408 TGAAATGAAGTTATATATCACTGAAATTTTTTTGAAATGAAGTAATTA-GATACTGAAATGTTT
1 TGAAATGAAGTTATATATCACTGAAAAGTTTATGAAGTGAAGTAATTAGGA-ACTGAAAAGTTT
170471 TTCTGAAATG
Statistics
Matches: 173, Mismatches: 23, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
136 4 0.02
137 74 0.43
138 7 0.04
139 77 0.45
140 11 0.06
ACGTcount: A:0.39, C:0.05, G:0.19, T:0.36
Consensus pattern (137 bp):
TGAAATGAAGTTATATATCACTGAAAAGTTTATGAAGTGAAGTAATTAGGAACTGAAAAGTTTAT
GTCATTATGTATTAAATGGTGCATGAGAAAAGGTTTTTCTGATAATAAAGTGATATATCATTAAA
AAGTTTA
Found at i:170472 original size:34 final size:33
Alignment explanation
Indices: 170369--170509 Score: 137
Period size: 32 Copynumber: 4.2 Consensus size: 33
170359 AGAAAAAGAC
* * * *
170369 GTTTTTCTGAAATGAAGTGATATATCATTAAAAA
1 GTTTTTTTGAAATGAAGTAATATATCACT-GAAA
* *
170403 G--TTTATGAAATGAAGTTATATATCACTGAAA
1 GTTTTTTTGAAATGAAGTAATATATCACTGAAA
*
170434 -TTTTTTTGAAATGAAGTAATTAGAT-ACTGAAA
1 GTTTTTTTGAAATGAAGTAA-TATATCACTGAAA
*
170466 TGTTTTTCTGAAATGAAGTAATATATCACTGAAAA
1 -GTTTTTTTGAAATGAAGTAATATATCACTG-AAA
170501 GTTTCTTTT
1 GTTT-TTTT
170510 CATAAACTTT
Statistics
Matches: 89, Mismatches: 10, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
31 3 0.03
32 45 0.51
33 8 0.09
34 27 0.30
35 6 0.07
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.40
Consensus pattern (33 bp):
GTTTTTTTGAAATGAAGTAATATATCACTGAAA
Found at i:175551 original size:12 final size:13
Alignment explanation
Indices: 175521--175552 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
175511 TTTCGGATTA
175521 CCAAAATAGTGAT
1 CCAAAATAGTGAT
175534 CC-AAATA-TGAT
1 CCAAAATAGTGAT
175545 CCAAAATA
1 CCAAAATA
175553 ATTGAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 6 0.33
12 10 0.56
13 2 0.11
ACGTcount: A:0.50, C:0.19, G:0.09, T:0.22
Consensus pattern (13 bp):
CCAAAATAGTGAT
Found at i:176943 original size:24 final size:27
Alignment explanation
Indices: 176888--176956 Score: 108
Period size: 24 Copynumber: 2.6 Consensus size: 27
176878 ATATGTATCA
176888 AATATTGAGGCACAAAACCATCGATCTT
1 AATATTGAGGCACAAAACCA-CGATCTT
176916 AATATTGAGGCACAAAA-C-C-ATCTT
1 AATATTGAGGCACAAAACCACGATCTT
176940 AATATTGAGGCACAAAA
1 AATATTGAGGCACAAAA
176957 GATTGATTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
24 22 0.54
25 1 0.02
27 1 0.02
28 17 0.41
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.23
Consensus pattern (27 bp):
AATATTGAGGCACAAAACCACGATCTT
Found at i:177838 original size:2 final size:2
Alignment explanation
Indices: 177831--177856 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
177821 ATAAAACCCA
177831 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
177857 TCTTTTTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:178055 original size:18 final size:18
Alignment explanation
Indices: 178032--178066 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
178022 TGCATATATA
*
178032 TATATATAAGTATAAATT
1 TATATATAAATATAAATT
178050 TATATATAAATATAAAT
1 TATATATAAATATAAAT
178067 ATGCATAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (18 bp):
TATATATAAATATAAATT
Found at i:180915 original size:48 final size:48
Alignment explanation
Indices: 180840--180931 Score: 157
Period size: 48 Copynumber: 1.9 Consensus size: 48
180830 TTGGGCCAGG
* *
180840 ATAATTTTGAATGTTATTAATAATCATATATTATTGCTACGTACCGGA
1 ATAATTTTGAATGTTATGAATAATCATATACTATTGCTACGTACCGGA
*
180888 ATAATTTTGAATGTTATGAATATTCATATACTATTGCTACGTAC
1 ATAATTTTGAATGTTATGAATAATCATATACTATTGCTACGTAC
180932 GTGAACATGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.42
Consensus pattern (48 bp):
ATAATTTTGAATGTTATGAATAATCATATACTATTGCTACGTACCGGA
Done.