Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006629.1 Hibiscus syriacus cultivar Beakdansim tig00016287_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: 83574
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1123 original size:4 final size:4
Alignment explanation
Indices: 1114--1176 Score: 67
Period size: 4 Copynumber: 16.0 Consensus size: 4
1104 TGTAGAACAC
* * *
1114 GTAT GTAT GTAT GTAT GTAT GTAT GTAT G-AT GCAT GGAT ATAT G-ATT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTA-T
*
1161 GTAT ATAT GTAT GTAT
1 GTAT GTAT GTAT GTAT
1177 ACATATTGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
3 4 0.08
4 45 0.90
5 1 0.02
ACGTcount: A:0.29, C:0.02, G:0.24, T:0.46
Consensus pattern (4 bp):
GTAT
Found at i:1288 original size:21 final size:21
Alignment explanation
Indices: 1264--1307 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1254 ATATCATACT
*
1264 TACATATATGCAT-CAATATCA
1 TACATATATACATAC-ATATCA
1285 TACATATATACATACATATCA
1 TACATATATACATACATATCA
1306 TA
1 TA
1308 TATTAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.34
Consensus pattern (21 bp):
TACATATATACATACATATCA
Found at i:1309 original size:17 final size:17
Alignment explanation
Indices: 1283--1342 Score: 65
Period size: 17 Copynumber: 3.7 Consensus size: 17
1273 GCATCAATAT
1283 CATA-CATATATACATA
1 CATATCATATATACATA
1299 CATATCATATATTA-ATA
1 CATATCATATA-TACATA
*
1316 -A-ATTATATATACATA
1 CATATCATATATACATA
*
1331 CATAACATATAT
1 CATATCATATAT
1343 TAATAAATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
14 2 0.06
15 10 0.28
16 6 0.17
17 16 0.44
18 2 0.06
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (17 bp):
CATATCATATATACATA
Found at i:1329 original size:32 final size:32
Alignment explanation
Indices: 1288--1359 Score: 126
Period size: 32 Copynumber: 2.2 Consensus size: 32
1278 AATATCATAC
*
1288 ATATATACATACATATCATATATTAATAAATT
1 ATATATACATACATAACATATATTAATAAATT
1320 ATATATACATACATAACATATATTAATAAATT
1 ATATATACATACATAACATATATTAATAAATT
*
1352 ATACATAC
1 ATATATAC
1360 GTAAGTACAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (32 bp):
ATATATACATACATAACATATATTAATAAATT
Found at i:2340 original size:13 final size:13
Alignment explanation
Indices: 2289--2341 Score: 56
Period size: 13 Copynumber: 4.1 Consensus size: 13
2279 CATTTAATAA
2289 AATTA-AATTAAT
1 AATTATAATTAAT
*
2301 GATTATAATTGAA-
1 AATTATAATT-AAT
*
2314 AATTTTAATCTAAT
1 AATTATAAT-TAAT
2328 AATTATAATTAAT
1 AATTATAATTAAT
2341 A
1 A
2342 TAGAAAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
12 4 0.12
13 18 0.55
14 11 0.33
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (13 bp):
AATTATAATTAAT
Found at i:2359 original size:39 final size:42
Alignment explanation
Indices: 2316--2416 Score: 118
Period size: 43 Copynumber: 2.5 Consensus size: 42
2306 TAATTGAAAA
*
2316 TTTTAATCTAATAATTATAATTAAT-AT-A-GAAAATAATTT
1 TTTTAATCTAATAATTATAATTAATAATAATGAAAATAAGTT
* * *
2355 TTTTAATCTAATGATCATAATTAATAAATAATGAAAGTAAGTT
1 TTTTAATCTAATAATTATAATTAAT-AATAATGAAAATAAGTT
* *
2398 TATTAATTTAATAATTATA
1 TTTTAATCTAATAATTATA
2417 TTTAGATTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
39 23 0.46
41 2 0.04
42 1 0.02
43 24 0.48
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.45
Consensus pattern (42 bp):
TTTTAATCTAATAATTATAATTAATAATAATGAAAATAAGTT
Found at i:3685 original size:19 final size:18
Alignment explanation
Indices: 3643--3681 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
3633 AACACTTTTG
3643 AAATCCCTACCAACCCTT
1 AAATCCCTACCAACCCTT
*
3661 AAATCCCTACCAGCCCTT
1 AAATCCCTACCAACCCTT
3679 AAA
1 AAA
3682 ATCCTTACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.36, C:0.41, G:0.03, T:0.21
Consensus pattern (18 bp):
AAATCCCTACCAACCCTT
Found at i:5208 original size:19 final size:19
Alignment explanation
Indices: 5184--5255 Score: 83
Period size: 19 Copynumber: 3.8 Consensus size: 19
5174 ACCTTTCTTT
*
5184 ATTTTCATATTCATAACTC
1 ATTTTCAGATTCATAACTC
* * *
5203 ATTTTCAAATTCATAATTT
1 ATTTTCAGATTCATAACTC
5222 ATTTTCAGATT-ATAACTC
1 ATTTTCAGATTCATAACTC
*
5240 TTTTTTCAGATTCATA
1 -ATTTTCAGATTCATA
5256 GCACAATGTA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
18 5 0.11
19 36 0.82
20 3 0.07
ACGTcount: A:0.32, C:0.15, G:0.03, T:0.50
Consensus pattern (19 bp):
ATTTTCAGATTCATAACTC
Found at i:5224 original size:38 final size:38
Alignment explanation
Indices: 5181--5255 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
5171 TTCACCTTTC
*
5181 TTTATTTTCATATTCATAACTC-ATTTTCAAATTCATAA
1 TTTATTTTCAGATT-ATAACTCTATTTTCAAATTCATAA
* *
5219 TTTATTTTCAGATTATAACTCTTTTTTCAGATTCATA
1 TTTATTTTCAGATTATAACTCTATTTTCAAATTCATA
5256 GCACAATGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 7 0.21
38 26 0.79
ACGTcount: A:0.31, C:0.15, G:0.03, T:0.52
Consensus pattern (38 bp):
TTTATTTTCAGATTATAACTCTATTTTCAAATTCATAA
Found at i:7862 original size:29 final size:31
Alignment explanation
Indices: 7798--7870 Score: 80
Period size: 29 Copynumber: 2.4 Consensus size: 31
7788 AAAATTATAT
*
7798 TTTTGGTCC-CTAAAGTTTTGCAAAGTTTATA
1 TTTTGG-CCACTAAAGTTTTGCAAAGTTTACA
* *
7829 CTTTGGCCACTAAA-TTTT-CAAATTTTACA
1 TTTTGGCCACTAAAGTTTTGCAAAGTTTACA
*
7858 TTTTGGTCACTAA
1 TTTTGGCCACTAA
7871 CAAAAAATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 20 0.56
30 6 0.17
31 10 0.28
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.44
Consensus pattern (31 bp):
TTTTGGCCACTAAAGTTTTGCAAAGTTTACA
Found at i:15199 original size:20 final size:20
Alignment explanation
Indices: 15174--15213 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
15164 TTTTGGTGCA
*
15174 GAGGGAATCGATCCCCCCTT
1 GAGGGAACCGATCCCCCCTT
*
15194 GAGGGAACCGATTCCCCCTT
1 GAGGGAACCGATCCCCCCTT
15214 TAAAGGGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.35, G:0.25, T:0.20
Consensus pattern (20 bp):
GAGGGAACCGATCCCCCCTT
Found at i:15255 original size:21 final size:21
Alignment explanation
Indices: 15217--15256 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
15207 CCCCCTTTAA
**
15217 AGGGGAACCGATTGCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
15238 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
15257 TAGGGTTCTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.38, G:0.28, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:19956 original size:53 final size:53
Alignment explanation
Indices: 19899--19999 Score: 157
Period size: 53 Copynumber: 1.9 Consensus size: 53
19889 CCATCCAAAC
* * * *
19899 AAACATTAAAATATAACATACATTTGAATCAAATATTAGGTTATCATCTAAGT
1 AAACATTAAAATATAACATACATTCGAATCAAACAGTAGGTTACCATCTAAGT
*
19952 AAACATTAATATATAACATACATTCGAATCAAACAGTAGGTTACCATC
1 AAACATTAAAATATAACATACATTCGAATCAAACAGTAGGTTACCATC
20000 CAACCAAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.31
Consensus pattern (53 bp):
AAACATTAAAATATAACATACATTCGAATCAAACAGTAGGTTACCATCTAAGT
Found at i:22952 original size:57 final size:55
Alignment explanation
Indices: 22844--22953 Score: 130
Period size: 57 Copynumber: 2.0 Consensus size: 55
22834 TCTTCGTCAT
* * *
22844 CTTCTTCAACTTCATCCTTTCTATACTTCATCTTGAAGTACATTCTGTACTTCCA
1 CTTCTTCAACTTCATCCTTTCTATACTTCATCTTCAAGTACATCCTCTACTTCCA
* * * * *
22899 CTTCTTCAATTTCATCCTCTATTTCTACTTCATCTTCTATTACATCCTCTACTTC
1 CTTCTTCAACTTCATCCT-T-TCTATACTTCATCTTCAAGTACATCCTCTACTTC
22954 TAATTTTTCA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
55 17 0.38
56 1 0.02
57 27 0.60
ACGTcount: A:0.20, C:0.31, G:0.03, T:0.46
Consensus pattern (55 bp):
CTTCTTCAACTTCATCCTTTCTATACTTCATCTTCAAGTACATCCTCTACTTCCA
Found at i:23433 original size:15 final size:16
Alignment explanation
Indices: 23394--23426 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
23384 ACTACATTAG
23394 TTAAAGTATACAATAA
1 TTAAAGTATACAATAA
23410 TTAAAGTATAC-ATAA
1 TTAAAGTATACAATAA
23425 TT
1 TT
23427 TTAGTATGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (16 bp):
TTAAAGTATACAATAA
Found at i:40741 original size:27 final size:27
Alignment explanation
Indices: 40698--40868 Score: 279
Period size: 27 Copynumber: 6.3 Consensus size: 27
40688 TCCTACCTCG
*
40698 CAGTTCACCCTGCTCTGACCGCTCATA
1 CAGTACACCCTGCTCTGACCGCTCATA
* *
40725 TAGTACACCTTGCTCTGACCGCTCATA
1 CAGTACACCCTGCTCTGACCGCTCATA
*
40752 CAGTACACCCTACTCTGACCGCTCATA
1 CAGTACACCCTGCTCTGACCGCTCATA
*
40779 CAGTACACCCTGCTCTGATCGCTCATA
1 CAGTACACCCTGCTCTGACCGCTCATA
*
40806 CAGTACACCCTGCTCTGATCGCTCATA
1 CAGTACACCCTGCTCTGACCGCTCATA
*
40833 TAGTACACCCTGCTCTGACCGCTCATA
1 CAGTACACCCTGCTCTGACCGCTCATA
40860 CAGTACACC
1 CAGTACACC
40869 ACTATCACCA
Statistics
Matches: 133, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 133 1.00
ACGTcount: A:0.23, C:0.38, G:0.14, T:0.25
Consensus pattern (27 bp):
CAGTACACCCTGCTCTGACCGCTCATA
Found at i:44112 original size:20 final size:21
Alignment explanation
Indices: 44074--44113 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
44064 ATAAAAATAA
* *
44074 TTTTTCAAAAATTTCATTTTG
1 TTTTTCAAAAATCTAATTTTG
44095 TTTTTC-AAAATCTAATTTT
1 TTTTTCAAAAATCTAATTTT
44114 TCCTTCACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.30, C:0.10, G:0.03, T:0.57
Consensus pattern (21 bp):
TTTTTCAAAAATCTAATTTTG
Found at i:47208 original size:31 final size:31
Alignment explanation
Indices: 47172--47230 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
47162 TAAATTTCAG
47172 AAAAGA-AAAATAATAAATATAAA-AAAAAGTT
1 AAAAGAGAAAATAA-AAATA-AAACAAAAAGTT
47203 AAAAGAGAAAATAAAAATAAAACAAAAA
1 AAAAGAGAAAATAAAAATAAAACAAAAA
47231 TAAAAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 3 0.12
31 16 0.62
32 7 0.27
ACGTcount: A:0.78, C:0.02, G:0.07, T:0.14
Consensus pattern (31 bp):
AAAAGAGAAAATAAAAATAAAACAAAAAGTT
Found at i:47242 original size:7 final size:6
Alignment explanation
Indices: 47172--47285 Score: 74
Period size: 6 Copynumber: 18.7 Consensus size: 6
47162 TAAATTTCAG
* * * *
47172 AAAAGA AAAATA ATAAATA TAAAA-A AAAGTT AAAAGA GAAAATA AAAAT-
1 AAAATA AAAATA A-AAATA -AAAATA AAAATA AAAATA -AAAATA AAAATA
* * * *
47221 AAAACA AAAATA AAAATA AAAA-A AGAAGTGG AAAATA AAAATA AAAAAA
1 AAAATA AAAATA AAAATA AAAATA A-AAAT-A AAAATA AAAATA AAAATA
47270 TAAAAT- AAAATA AAAA
1 -AAAATA AAAATA AAAA
47286 ATTGTTAAAT
Statistics
Matches: 83, Mismatches: 15, Indels: 20
0.70 0.13 0.17
Matches are distributed among these distances:
5 14 0.17
6 47 0.57
7 20 0.24
8 2 0.02
ACGTcount: A:0.78, C:0.01, G:0.07, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:47243 original size:25 final size:24
Alignment explanation
Indices: 47215--47285 Score: 79
Period size: 25 Copynumber: 2.9 Consensus size: 24
47205 AAGAGAAAAT
47215 AAAAATAAAACAAAAATAAAAATAA
1 AAAAATAAAA-AAAAATAAAAATAA
* ***
47240 AAAAAGAAGTGGAAAATAAAAATAA
1 AAAAATAA-AAAAAAATAAAAATAA
*
47265 AAAAATAAAATAAAATAAAAA
1 AAAAATAAAAAAAAATAAAAA
47286 ATTGTTAAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
24 10 0.27
25 27 0.73
ACGTcount: A:0.80, C:0.01, G:0.06, T:0.13
Consensus pattern (24 bp):
AAAAATAAAAAAAAATAAAAATAA
Found at i:47416 original size:11 final size:11
Alignment explanation
Indices: 47400--47445 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 11
47390 TTGAAAAGGT
47400 ATAATAAAATA
1 ATAATAAAATA
47411 ATAAT-AAATA
1 ATAATAAAATA
* **
47421 AAAAGGAAAT-
1 ATAATAAAATA
47431 ATAATAAAATA
1 ATAATAAAATA
47442 ATAA
1 ATAA
47446 ATAATAGTAG
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
10 15 0.54
11 13 0.46
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (11 bp):
ATAATAAAATA
Found at i:47512 original size:18 final size:18
Alignment explanation
Indices: 47491--47533 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
47481 GTTATTTTTA
*
47491 AAATAAAAGATAGA-AATT
1 AAATAAAAGA-AAATAATT
47509 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAATAATT
47527 AAATAAA
1 AAATAAA
47534 TAATCTAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.09
18 21 0.91
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAATAATT
Found at i:48940 original size:42 final size:41
Alignment explanation
Indices: 48893--49371 Score: 133
Period size: 42 Copynumber: 11.2 Consensus size: 41
48883 TTTAAATGAC
48893 TCCCCTTCACGGGAAATCCAAGTGGTATATTCCTCAGGTGGT
1 TCCCCTTCACGGGAAA-CCAAGTGGTATATTCCTCAGGTGGT
* * * ** **
48935 TCCCCTTTACGGGTCTGAACCAAGTGGGATGA-T-CTTTGGATGAC
1 TCCCCTTCACGGG---AAACCAAGTGGTAT-ATTCCTCAGG-TGGT
* * *
48979 TCCCCTTCATGGGAAAGCCATGTGATATATTCCTCAGGTGGT
1 TCCCCTTCACGGGAAA-CCAAGTGGTATATTCCTCAGGTGGT
* ** **
49021 TCCCCTT-AGCGGGTCTGAACCAAGTGAGATGATATTTGT-A--TGAC
1 TCCCCTTCA-CGGG---AAACCAAGTG-G-T-ATATTCCTCAGGTGGT
* *
49065 TCCCCTTCACGGGAAAACCATGTGGTATATTCCTCAAGTGGT
1 TCCCCTTCACGGG-AAACCAAGTGGTATATTCCTCAGGTGGT
* * * * * **
49107 TCCCCTTCGCGGGTCTGAACCAAGTGAG-ATGA-TCTTTAGATGAC
1 TCCCCTTCACGGG---AAACCAAGTG-GTAT-ATTCCTCAGGTGGT
* * * *
49151 TCCCCTTCACGGGAAAGACATGAGGTATATTCCTCATGTGGT
1 TCCCCTTCACGGGAAA-CCAAGTGGTATATTCCTCAGGTGGT
* * ** **
49193 TCCCCTTCATGGGTCTGAACCAAGTGAG-ATGA-T-CTTTGGATGAC
1 TCCCCTTCACGGG---AAACCAAGTG-GTAT-ATTCCTCAGG-TGGT
* * * * *
49237 TCCCCTTCACGGGAAAGACATGGGGTATATTACACAGGTGGT
1 TCCCCTTCACGGGAAA-CCAAGTGGTATATTCCTCAGGTGGT
** **
49279 TCCCCTT-AGCGGGTTTAAACCAAGTGAG-ATGATT--TTTGGATGAC
1 TCCCCTTCA-CGGG---AAACCAAGTG-GTAT-ATTCCTCAGG-TGGT
*
49323 TCCCCTTCACGGGAAAGCCATGTGGTATATTCCTCAGGTGGT
1 TCCCCTTCACGGGAAA-CCAAGTGGTATATTCCTCAGGTGGT
49365 TCCCCTT
1 TCCCCTT
49372 AGTGGGTCTG
Statistics
Matches: 303, Mismatches: 86, Indels: 96
0.62 0.18 0.20
Matches are distributed among these distances:
39 6 0.02
40 2 0.01
41 21 0.07
42 116 0.38
43 19 0.06
44 111 0.37
45 20 0.07
46 2 0.01
47 6 0.02
ACGTcount: A:0.23, C:0.24, G:0.25, T:0.29
Consensus pattern (41 bp):
TCCCCTTCACGGGAAACCAAGTGGTATATTCCTCAGGTGGT
Found at i:49026 original size:86 final size:86
Alignment explanation
Indices: 48888--49628 Score: 1026
Period size: 86 Copynumber: 8.6 Consensus size: 86
48878 AATTCTTTAA
* *
48888 ATGACTCCCCTTCACGGGAAATCCAAGTGGTATATTCCTCAGGTGGTTCCCCTTTACGGGTCTGA
1 ATGACTCCCCTTCACGGGAAAGCCATGTGGTATATTCCTCAGGTGGTTCCCCTTTACGGGTCTGA
*
48953 ACCAAGTGGGATGATCTTTGG
66 ACCAAGTGAGATGATCTTTGG
* *
48974 ATGACTCCCCTTCATGGGAAAGCCATGTGATATATTCCTCAGGTGGTTCCCC-TTAGCGGGTCTG
1 ATGACTCCCCTTCACGGGAAAGCCATGTGGTATATTCCTCAGGTGGTTCCCCTTTA-CGGGTCTG
* *
49038 AACCAAGTGAGATGATATTTGT
65 AACCAAGTGAGATGATCTTTGG
* * **
49060 ATGACTCCCCTTCACGGGAAAACCATGTGGTATATTCCTCAAGTGGTTCCCCTTCGCGGGTCTGA
1 ATGACTCCCCTTCACGGGAAAGCCATGTGGTATATTCCTCAGGTGGTTCCCCTTTACGGGTCTGA
*
49125 ACCAAGTGAGATGATCTTTAG
66 ACCAAGTGAGATGATCTTTGG
* * * * *
49146 ATGACTCCCCTTCACGGGAAAGACATGAGGTATATTCCTCATGTGGTTCCCCTTCATGGGTCTGA
1 ATGACTCCCCTTCACGGGAAAGCCATGTGGTATATTCCTCAGGTGGTTCCCCTTTACGGGTCTGA
49211 ACCAAGTGAGATGATCTTTGG
66 ACCAAGTGAGATGATCTTTGG
* * * * * *
49232 ATGACTCCCCTTCACGGGAAAGACATGGGGTATATTACACAGGTGGTTCCCC-TTAGCGGGTTTA
1 ATGACTCCCCTTCACGGGAAAGCCATGTGGTATATTCCTCAGGTGGTTCCCCTTTA-CGGGTCTG
*
49296 AACCAAGTGAGATGATTTTTGG
65 AACCAAGTGAGATGATCTTTGG
*
49318 ATGACTCCCCTTCACGGGAAAGCCATGTGGTATATTCCTCAGGTGGTTCCCC-TTAGTGGGTCTG
1 ATGACTCCCCTTCACGGGAAAGCCATGTGGTATATTCCTCAGGTGGTTCCCCTTTA-CGGGTCTG
* *
49382 AACTAGGTGAGATGATCTTTGG
65 AACCAAGTGAGATGATCTTTGG
* * * * ** *
49404 ATGACTCCCCTTCACCGGAAAGTCATGTGGTACATTCTTCAGGTGGTTCCCCTTCGCGGGTCTAA
1 ATGACTCCCCTTCACGGGAAAGCCATGTGGTATATTCCTCAGGTGGTTCCCCTTTACGGGTCTGA
49469 ACCAAGTGAGATGATCTTTGG
66 ACCAAGTGAGATGATCTTTGG
** * *
49490 ATGACTCCCCTTCACATGAAAGCCATATGGTATATTCCTCAGGTGGTTCCCC-TTA-GAAAGTCT
1 ATGACTCCCCTTCACGGGAAAGCCATGTGGTATATTCCTCAGGTGGTTCCCCTTTACG--GGTCT
* *
49553 AAACCAACTGAGATGAT-TTTGG
64 GAACCAAGTGAGATGATCTTTGG
*
49575 ATGACTCCCCTTCACGAGAAAGCCATGTGGTATATTCCTCAGGTGGTTCCCCTT
1 ATGACTCCCCTTCACGGGAAAGCCATGTGGTATATTCCTCAGGTGGTTCCCCTT
49629 AGCGAGTCTG
Statistics
Matches: 583, Mismatches: 65, Indels: 14
0.88 0.10 0.02
Matches are distributed among these distances:
84 1 0.00
85 60 0.10
86 520 0.89
87 2 0.00
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.29
Consensus pattern (86 bp):
ATGACTCCCCTTCACGGGAAAGCCATGTGGTATATTCCTCAGGTGGTTCCCCTTTACGGGTCTGA
ACCAAGTGAGATGATCTTTGG
Found at i:49157 original size:44 final size:44
Alignment explanation
Indices: 48935--49249 Score: 142
Period size: 44 Copynumber: 7.3 Consensus size: 44
48925 CTCAGGTGGT
* * *
48935 TCCCCTTTACGGGTCTGAACCAAGTGGGATGATCTTTGGATGAC
1 TCCCCTTCACGGGTCTGAACCAAGTGAGATGATCTTTAGATGAC
* * * * * * * **
48979 TCCCCTTCATGGG---AAAGCCATGTGATAT-ATTCCTCAGGTGGT
1 TCCCCTTCACGGGTCTGAA-CCAAGTGAGATGA-TCTTTAGATGAC
*
49021 TCCCCTT-AGCGGGTCTGAACCAAGTGAGATGATATTT-GTATGAC
1 TCCCCTTCA-CGGGTCTGAACCAAGTGAGATGATCTTTAG-ATGAC
** * * * **
49065 TCCCCTTCACGGG--AAAACCATGTG-GTAT-ATTCCTCA-AGTGGT
1 TCCCCTTCACGGGTCTGAACCAAGTGAG-ATGA-TCTTTAGA-TGAC
*
49107 TCCCCTTCGCGGGTCTGAACCAAGTGAGATGATCTTTAGATGAC
1 TCCCCTTCACGGGTCTGAACCAAGTGAGATGATCTTTAGATGAC
*** * * **
49151 TCCCCTTCACGGGAAAG-A-C-A-TGAGGTAT-ATTCCTCATG-TGGT
1 TCCCCTTCACGGGTCTGAACCAAGTGA-G-ATGA-TCTTTA-GATGAC
* *
49193 TCCCCTTCATGGGTCTGAACCAAGTGAGATGATCTTTGGATGAC
1 TCCCCTTCACGGGTCTGAACCAAGTGAGATGATCTTTAGATGAC
49237 TCCCCTTCACGGG
1 TCCCCTTCACGGG
49250 AAAGACATGG
Statistics
Matches: 187, Mismatches: 56, Indels: 56
0.63 0.19 0.19
Matches are distributed among these distances:
40 3 0.02
41 10 0.05
42 72 0.39
43 5 0.03
44 84 0.45
45 10 0.05
46 3 0.02
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.29
Consensus pattern (44 bp):
TCCCCTTCACGGGTCTGAACCAAGTGAGATGATCTTTAGATGAC
Found at i:49346 original size:258 final size:258
Alignment explanation
Indices: 48881--49638 Score: 1140
Period size: 258 Copynumber: 2.9 Consensus size: 258
48871 CGGTCATAAT
* ** * *
48881 TCTTTAAATGACTCCCCTTCACGGGAAATCCAAGTGGTATATTCCTCAGGTGGTTCCCCTTTACG
1 TCTTTAGATGACTCCCCTTCACGGGAAAGACATGTGGTATATTCCTCAGGTGGTTCCCCTTCACG
* * *
48946 GGTCTGAACCAAGTGGGATGATCTTTGGATGACTCCCCTTCATGGGAAAGCCATGTGATATATTC
66 GGTCTGAACCAAGTGAGATGATCTTTGGATGACTCCCCTTCACGGGAAAGCCATGTGGTATATTC
* * *
49011 CTCAGGTGGTTCCCCTTAGCGGGTCTGAACCAAGTGAGATGATATTTGTATGACTCCCCTTCACG
131 CTCAGGTGGTTCCCCTTAGCGGGTCTAAACCAAGTGAGATGATTTTTGGATGACTCCCCTTCACG
* * *
49076 GGAAAACCATGTGGTATATTCCTCAAGTGGTTCCCCTTCGCGGGTCTGAACCAAGTGAGATGA
196 GGAAAGCCATGTGGTATATTCCTCAGGTGGTTCCCCTTAGCGGGTCTGAACCAAGTGAGATGA
* * *
49139 TCTTTAGATGACTCCCCTTCACGGGAAAGACATGAGGTATATTCCTCATGTGGTTCCCCTTCATG
1 TCTTTAGATGACTCCCCTTCACGGGAAAGACATGTGGTATATTCCTCAGGTGGTTCCCCTTCACG
* * *
49204 GGTCTGAACCAAGTGAGATGATCTTTGGATGACTCCCCTTCACGGGAAAGACATGGGGTATATTA
66 GGTCTGAACCAAGTGAGATGATCTTTGGATGACTCCCCTTCACGGGAAAGCCATGTGGTATATTC
* *
49269 CACAGGTGGTTCCCCTTAGCGGGTTTAAACCAAGTGAGATGATTTTTGGATGACTCCCCTTCACG
131 CTCAGGTGGTTCCCCTTAGCGGGTCTAAACCAAGTGAGATGATTTTTGGATGACTCCCCTTCACG
* * *
49334 GGAAAGCCATGTGGTATATTCCTCAGGTGGTTCCCCTTAGTGGGTCTGAACTAGGTGAGATGA
196 GGAAAGCCATGTGGTATATTCCTCAGGTGGTTCCCCTTAGCGGGTCTGAACCAAGTGAGATGA
* * * * * *
49397 TCTTTGGATGACTCCCCTTCACCGGAAAGTCATGTGGTACATTCTTCAGGTGGTTCCCCTTCGCG
1 TCTTTAGATGACTCCCCTTCACGGGAAAGACATGTGGTATATTCCTCAGGTGGTTCCCCTTCACG
* ** *
49462 GGTCTAAACCAAGTGAGATGATCTTTGGATGACTCCCCTTCACATGAAAGCCATATGGTATATTC
66 GGTCTGAACCAAGTGAGATGATCTTTGGATGACTCCCCTTCACGGGAAAGCCATGTGGTATATTC
*** *
49527 CTCAGGTGGTTCCCCTTAGAAAGTCTAAACCAACTGAGATGA-TTTTGGATGACTCCCCTTCACG
131 CTCAGGTGGTTCCCCTTAGCGGGTCTAAACCAAGTGAGATGATTTTTGGATGACTCCCCTTCACG
* *
49591 AGAAAGCCATGTGGTATATTCCTCAGGTGGTTCCCCTTAGCGAGTCTG
196 GGAAAGCCATGTGGTATATTCCTCAGGTGGTTCCCCTTAGCGGGTCTG
49639 TATTGGGACC
Statistics
Matches: 450, Mismatches: 50, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
257 67 0.15
258 383 0.85
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.29
Consensus pattern (258 bp):
TCTTTAGATGACTCCCCTTCACGGGAAAGACATGTGGTATATTCCTCAGGTGGTTCCCCTTCACG
GGTCTGAACCAAGTGAGATGATCTTTGGATGACTCCCCTTCACGGGAAAGCCATGTGGTATATTC
CTCAGGTGGTTCCCCTTAGCGGGTCTAAACCAAGTGAGATGATTTTTGGATGACTCCCCTTCACG
GGAAAGCCATGTGGTATATTCCTCAGGTGGTTCCCCTTAGCGGGTCTGAACCAAGTGAGATGA
Found at i:59913 original size:16 final size:16
Alignment explanation
Indices: 59894--59932 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
59884 ATAAATGCAT
59894 GATGCATGAAATGTTC
1 GATGCATGAAATGTTC
59910 GATGCATGAAATGTTC
1 GATGCATGAAATGTTC
*
59926 GAGGCAT
1 GATGCAT
59933 TGATCCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.28
Consensus pattern (16 bp):
GATGCATGAAATGTTC
Found at i:61038 original size:20 final size:20
Alignment explanation
Indices: 61013--61057 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
61003 CTGAGTTCTC
61013 CTTGCTGGTGCCCCCTTGGG
1 CTTGCTGGTGCCCCCTTGGG
61033 CTTGCTGGTGCCCCCTTGGG
1 CTTGCTGGTGCCCCCTTGGG
61053 CTTGC
1 CTTGC
61058 CAGACCCTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.33, T:0.31
Consensus pattern (20 bp):
CTTGCTGGTGCCCCCTTGGG
Found at i:62170 original size:18 final size:18
Alignment explanation
Indices: 62149--62191 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
62139 GTTGTTTTTA
62149 AAATAAAAGATAAA-AATT
1 AAATAAAAGA-AAATAATT
62167 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAATAATT
62185 AAATAAA
1 AAATAAA
62192 TAATCTAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAATAATT
Found at i:62899 original size:12 final size:13
Alignment explanation
Indices: 62882--62910 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
62872 AATGATAAAA
62882 TAAAATAATATT-
1 TAAAATAATATTC
62894 TAAAATAATATTC
1 TAAAATAATATTC
62907 TAAA
1 TAAA
62911 TTCTAATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATAATATTC
Found at i:64037 original size:39 final size:39
Alignment explanation
Indices: 63994--64112 Score: 145
Period size: 39 Copynumber: 3.1 Consensus size: 39
63984 TTTAAAAAAT
*
63994 AATTTAGAATGTTAATGTAAAATAATTTAAGAAATTAAA
1 AATTTAGAATGTTAATGTAAAATAATTTAAGAAATTATA
* * *
64033 AATTTAGAATGTT-GTGGTAGCAA-AATTTAAGAAATTATG
1 AATTTAGAATGTTAAT-GTA-AAATAATTTAAGAAATTATA
* *
64072 AATTTAGAATGTTAAAGTGAAATAATTTAA-AAATTATA
1 AATTTAGAATGTTAATGTAAAATAATTTAAGAAATTATA
64110 AAT
1 AAT
64113 AAACATTTAA
Statistics
Matches: 67, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
38 13 0.19
39 52 0.78
40 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.13, T:0.36
Consensus pattern (39 bp):
AATTTAGAATGTTAATGTAAAATAATTTAAGAAATTATA
Found at i:64500 original size:13 final size:13
Alignment explanation
Indices: 64484--64508 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
64474 ATTTTTTTTT
64484 AAAAATATTTTAA
1 AAAAATATTTTAA
64497 AAAAATATTTTA
1 AAAAATATTTTA
64509 TTTTTAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAAATATTTTAA
Found at i:64527 original size:29 final size:29
Alignment explanation
Indices: 64472--64530 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
64462 TGTCATGTTC
** *
64472 ATATTTTTTTTTAAAAATATTTTAAAAAA
1 ATATTTTTTTTTAAAAATAAATAAAAAAA
64501 ATATTTTATTTTTAAAAA-AAATAAAAAAA
1 ATATTTT-TTTTTAAAAATAAATAAAAAAA
64530 A
1 A
64531 ATATAACCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
ATATTTTTTTTTAAAAATAAATAAAAAAA
Found at i:64529 original size:30 final size:29
Alignment explanation
Indices: 64472--64534 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 29
64462 TGTCATGTTC
* * **
64472 ATATTTTTTTTTAAAAATATTTTAAAAAA
1 ATATTTTTTTTTAAAAAAAATAAAAAAAA
64501 ATATTTTATTTTTAAAAAAAATAAAAAAAA
1 ATATTTT-TTTTTAAAAAAAATAAAAAAAA
64531 ATAT
1 ATAT
64535 AACCATGATA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 7 0.24
30 22 0.76
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
ATATTTTTTTTTAAAAAAAATAAAAAAAA
Found at i:64800 original size:2 final size:2
Alignment explanation
Indices: 64793--64842 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
64783 TTAATATCTT
64793 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
64835 TA TA TA TA
1 TA TA TA TA
64843 AAGGTTTATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:64906 original size:17 final size:19
Alignment explanation
Indices: 64884--64923 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
64874 TATGTGCATA
64884 TTCAAACCA-T-AAGCAAC
1 TTCAAACCATTGAAGCAAC
64901 TTCAAACCATTGAAGCAAC
1 TTCAAACCATTGAAGCAAC
64920 TTCA
1 TTCA
64924 GCTTGTTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 9 0.43
18 1 0.05
19 11 0.52
ACGTcount: A:0.42, C:0.28, G:0.07, T:0.23
Consensus pattern (19 bp):
TTCAAACCATTGAAGCAAC
Found at i:66329 original size:22 final size:22
Alignment explanation
Indices: 66301--66351 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
66291 ACTTTAATTC
66301 TAAATTCAAAGAATTTTGTATT
1 TAAATTCAAAGAATTTTGTATT
66323 TAAATTCAAAGAATTTTGTATT
1 TAAATTCAAAGAATTTTGTATT
66345 TAAATTC
1 TAAATTC
66352 GGTGGCGTAA
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:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (22 bp):
TAAATTCAAAGAATTTTGTATT
Found at i:72833 original size:21 final size:19
Alignment explanation
Indices: 72781--72835 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 19
72771 TAAATTAATT
*
72781 TTATTAAATAATTTATTTA
1 TTATAAAATAATTTATTTA
* *
72800 TTA-AACATGATTTATTATA
1 TTATAAAATAATTTATT-TA
72819 TTATAAAATTAATTTAT
1 TTATAAAA-TAATTTAT
72836 ATTTAAGTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
18 10 0.36
19 8 0.29
20 3 0.11
21 7 0.25
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (19 bp):
TTATAAAATAATTTATTTA
Found at i:72941 original size:2 final size:2
Alignment explanation
Indices: 72934--72972 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
72924 TATTTGAGAT
72934 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
72973 TAAATTCCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:73108 original size:19 final size:19
Alignment explanation
Indices: 73084--73165 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 19
73074 TTAGTAAGTT
73084 GGGAAATTGGAAATTTAGA
1 GGGAAATTGGAAATTTAGA
73103 GGGAAATTGGGAAATTTTGTGAATAGA
1 GGGAAATT-GGAAA---T-T---TAGA
73130 GGGAAATT-GAGAATTTAGA
1 GGGAAATTGGA-AATTTAGA
73149 GGGAAATTGAGAAATTT
1 GGGAAATTG-GAAATTT
73166 TGAGAATAGA
Statistics
Matches: 52, Mismatches: 0, Indels: 21
0.71 0.00 0.29
Matches are distributed among these distances:
19 20 0.38
20 10 0.19
21 2 0.04
22 1 0.02
23 2 0.04
24 1 0.02
25 2 0.04
26 2 0.04
27 12 0.23
ACGTcount: A:0.40, C:0.00, G:0.32, T:0.28
Consensus pattern (19 bp):
GGGAAATTGGAAATTTAGA
Found at i:73129 original size:27 final size:27
Alignment explanation
Indices: 73099--73184 Score: 89
Period size: 27 Copynumber: 3.5 Consensus size: 27
73089 ATTGGAAATT
*
73099 TAGAGGGAAATTGGGAAATTTTGTGAA
1 TAGAGGGAAATTGAGAAATTTTGTGAA
73126 TAGAGGGAAATTGAG-AA---T-T---
1 TAGAGGGAAATTGAGAAATTTTGTGAA
*
73145 TAGAGGGAAATTGAGAAATTTTGAGAA
1 TAGAGGGAAATTGAGAAATTTTGTGAA
*
73172 TAGAGGAAAATTG
1 TAGAGGGAAATTG
73185 GGAATTTAGA
Statistics
Matches: 48, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
19 15 0.31
20 2 0.04
22 1 0.02
23 2 0.04
26 2 0.04
27 26 0.54
ACGTcount: A:0.42, C:0.00, G:0.31, T:0.27
Consensus pattern (27 bp):
TAGAGGGAAATTGAGAAATTTTGTGAA
Found at i:73137 original size:46 final size:46
Alignment explanation
Indices: 73050--73255 Score: 186
Period size: 46 Copynumber: 4.3 Consensus size: 46
73040 TTTATTTGAG
* * *
73050 AATTTAGAGGAAAATTAGGAAATTTTAGT--A-AGTTGGGAAATTGGA
1 AATTTAGAGGGAAATTGGGAAATTTT-GTGAATAG-AGGGAAATTGGA
73095 AATTTAGAGGGAAATTGGGAAATTTTGTGAATAGAGGGAAATT-GA
1 AATTTAGAGGGAAATTGGGAAATTTTGTGAATAGAGGGAAATTGGA
* * * *
73140 GAATTTAGAGGGAAATTGAGAAATTTTGAGAATAGAGGAAAATTGGG
1 -AATTTAGAGGGAAATTGGGAAATTTTGTGAATAGAGGGAAATTGGA
* * * *
73187 AATTTAGAAGGAAATTTTGGGAATATAAATTTTGGGAATAGATGGAAATTAGA
1 AATTTAGAGGGAAA--TTGGG-----AAATTTTGTGAATAGAGGGAAATTGGA
*
73240 AATTTAGAGTGAAATT
1 AATTTAGAGGGAAATT
73256 TTGGGAAGTT
Statistics
Matches: 133, Mismatches: 16, Indels: 18
0.80 0.10 0.11
Matches are distributed among these distances:
44 2 0.02
45 26 0.20
46 62 0.47
47 3 0.02
48 4 0.03
51 2 0.02
53 34 0.26
ACGTcount: A:0.42, C:0.00, G:0.28, T:0.30
Consensus pattern (46 bp):
AATTTAGAGGGAAATTGGGAAATTTTGTGAATAGAGGGAAATTGGA
Found at i:73218 original size:15 final size:15
Alignment explanation
Indices: 73198--73226 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
73188 ATTTAGAAGG
73198 AAATTTTGGGAATAT
1 AAATTTTGGGAATAT
73213 AAATTTTGGGAATA
1 AAATTTTGGGAATA
73227 GATGGAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (15 bp):
AAATTTTGGGAATAT
Found at i:73218 original size:53 final size:53
Alignment explanation
Indices: 73160--73262 Score: 147
Period size: 53 Copynumber: 1.9 Consensus size: 53
73150 GGAAATTGAG
* *
73160 AAATTTTGAGAATAGA-GGAAAATTGGGAATTTAGAAG-GAAATTTTGGGAATAT
1 AAATTTTGAGAATAGATGG-AAATTAGAAATTTAG-AGTGAAATTTTGGGAATAT
*
73213 AAATTTTGGGAATAGATGGAAATTAGAAATTTAGAGTGAAATTTTGGGAA
1 AAATTTTGAGAATAGATGGAAATTAGAAATTTAGAGTGAAATTTTGGGAA
73263 GTTGGGAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
52 2 0.04
53 41 0.91
54 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.26, T:0.31
Consensus pattern (53 bp):
AAATTTTGAGAATAGATGGAAATTAGAAATTTAGAGTGAAATTTTGGGAATAT
Found at i:73281 original size:37 final size:37
Alignment explanation
Indices: 73213--73292 Score: 92
Period size: 37 Copynumber: 2.1 Consensus size: 37
73203 TTGGGAATAT
*
73213 AAATTTTGGGAATAGATGGAAATTAGAAATTTAGAGTG
1 AAATTTTGGGAATAGA-GGAAATTAGAAATTTAGAGGG
* *
73251 AAATTTTGGGAAGTTG-GGAAATT-GAGAATTTAGTGGG
1 AAATTTTGGGAA-TAGAGGAAATTAGA-AATTTAGAGGG
73288 AAATT
1 AAATT
73293 GGGATATATA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
36 2 0.05
37 21 0.57
38 12 0.32
39 2 0.05
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.33
Consensus pattern (37 bp):
AAATTTTGGGAATAGAGGAAATTAGAAATTTAGAGGG
Found at i:73736 original size:199 final size:200
Alignment explanation
Indices: 73391--73753 Score: 543
Period size: 199 Copynumber: 1.8 Consensus size: 200
73381 AACCTAATTT
* * *
73391 TCTCTCATTGGTGTGTTGTTCATCTTATTTCTTTTTCGTCTTTGTTGATCAGCAGCGACACCAAC
1 TCTCTCATTGGTGTGTCGTTCATCTTATTTCTTTTCCGTCTTTGTTGATCAGCAACGACACCAAC
***
73456 TTTAATGTTGGTTGCCGACCGTTGGTATTCTTTATTTTCTTTTTATTTTCTATAATGTATCTCTA
66 TTTAATGTTGGTTGCCGACCGCCAGTATTCTTTATTTTCTTTTTATTTTCTATAATGTATCTCTA
*
73521 TTTTCTTTTC-TTTTTTTATTTTTAATAAGTCTCCATGTGTTGCACGTTTTCATCTGCCTTTATG
131 TTTTCTTTTCTTTTTTTTATTTTCAATAAGTCTCCATGTGTTGCACGTTTTCATCTGCCTTTATG
73585 ACACG
196 ACACG
* * * *
73590 TCTCTCATTTGTGTGTCGTTCATCTCT-TTTCTTTTCCGTCTTTGTTGATCGGCAATGGCACCAA
1 TCTCTCATTGGTGTGTCGTTCATCT-TATTTCTTTTCCGTCTTTGTTGATCAGCAACGACACCAA
* * *
73654 CTTTAATGGTT-GTTGTCGATCGCCAGTATTCTTTATTTTCTTTTTATTTTCTATAATGTATCTT
65 CTTTAAT-GTTGGTTGCCGACCGCCAGTATTCTTTATTTTCTTTTTATTTTCTATAATGTATCTC
*
73718 TATTTTCTTTTGTTTTTTTTTATTTTCAATAAGTCT
129 TATTTTCTTTT-CTTTTTTTTATTTTCAATAAGTCT
73754 GTCTGTGTTG
Statistics
Matches: 145, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
199 120 0.83
200 4 0.03
201 21 0.14
ACGTcount: A:0.16, C:0.18, G:0.13, T:0.53
Consensus pattern (200 bp):
TCTCTCATTGGTGTGTCGTTCATCTTATTTCTTTTCCGTCTTTGTTGATCAGCAACGACACCAAC
TTTAATGTTGGTTGCCGACCGCCAGTATTCTTTATTTTCTTTTTATTTTCTATAATGTATCTCTA
TTTTCTTTTCTTTTTTTTATTTTCAATAAGTCTCCATGTGTTGCACGTTTTCATCTGCCTTTATG
ACACG
Found at i:73738 original size:10 final size:10
Alignment explanation
Indices: 73685--73744 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
73675 GCCAGTATTC
73685 TTTATTTTCTT
1 TTTATTTTC-T
73696 TTTATTTTCT
1 TTTATTTTCT
* * *
73706 ATAATGTATC-
1 TTTAT-TTTCT
73716 TTTATTTTCT
1 TTTATTTTCT
* *
73726 TTTGTTTTTT
1 TTTATTTTCT
73736 TTTATTTTC
1 TTTATTTTC
73745 AATAAGTCTG
Statistics
Matches: 37, Mismatches: 10, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
9 3 0.08
10 22 0.59
11 12 0.32
ACGTcount: A:0.13, C:0.08, G:0.03, T:0.75
Consensus pattern (10 bp):
TTTATTTTCT
Found at i:74277 original size:2 final size:2
Alignment explanation
Indices: 74270--74397 Score: 208
Period size: 2 Copynumber: 65.5 Consensus size: 2
74260 AAAACAAATA
74270 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
* * *
74312 AT AT AT AT AT AT AT AT AT AT AT AT -T TT AT AT GT TT 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
74353 -T AT AT AT A- 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
74393 AT AT A
1 AT AT A
74398 CTTATATTGT
Statistics
Matches: 119, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
1 3 0.03
2 116 0.97
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.52
Consensus pattern (2 bp):
AT
Found at i:74496 original size:10 final size:9
Alignment explanation
Indices: 74470--74504 Score: 54
Period size: 10 Copynumber: 3.9 Consensus size: 9
74460 TTCATCATAC
74470 ATATTATAT
1 ATATTATAT
74479 -TATTATAT
1 ATATTATAT
74487 ATATTAATAT
1 ATATT-ATAT
74497 ATATTATA
1 ATATTATA
74505 ATTGTTTCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 8 0.33
9 7 0.29
10 9 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
ATATTATAT
Done.