Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003977.1 Hibiscus syriacus cultivar Beakdansim tig00008636_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: 174717
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3515 original size:2 final size:2
Alignment explanation
Indices: 3502--3534 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3492 ACCCAAATTT
*
3502 TA TA TT 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 T
3535 GATTGATCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:14337 original size:202 final size:203
Alignment explanation
Indices: 13991--14402 Score: 745
Period size: 202 Copynumber: 2.0 Consensus size: 203
13981 GTGTTGGTTG
13991 GATTTGTCAAAAATTTCATTGATTGTCTTTGTCTTGTTGAATATTGTTTGGAATGCTATGCTTGT
1 GATTTGTCAAAAATTTCATTGATTGTCTTTGTCTTGTTGAATATTGTTTGGAATGCTATGCTTGT
*
14056 TTGGGAACACATGATTGTTTAGTTTAGGATATTCTTGATAGCGAATAGCATGAATTGTGATCAAG
66 TTGGGAACACATGATTGTTTAGGTTAGGATATTCTTGATAGCGAATAGCATGAATTGTGATCAAG
** *
14121 TTGGTACTTTTGTGATATCCCATGGTTTTATTGATTGAAATGTGATTAGCTTGATGCA-AAATAA
131 TTGGTACTTTTGTGATATCCCATGGTTTTATTGATTGAAATGTGATTAGCTCAATGCAGAAACAA
14185 TTTGGTGA
196 TTTGGTGA
*
14193 GATTTGTCAAAAATTTCATTGATTGTCTTTGTCTTGTTGAATATTGTTTGGAATGCTATGTTTGT
1 GATTTGTCAAAAATTTCATTGATTGTCTTTGTCTTGTTGAATATTGTTTGGAATGCTATGCTTGT
14258 TTGGGAACACATGATTGTTTAGGTTAGGATATTCTTGATAGCGAATAGCATGAATTGTGATCAAG
66 TTGGGAACACATGATTGTTTAGGTTAGGATATTCTTGATAGCGAATAGCATGAATTGTGATCAAG
* *
14323 TTGGTACTTTTGTGATATTCCATGGTTTTATTGGTTGAAATGTGATTAGCTCAATGCATGAAACA
131 TTGGTACTTTTGTGATATCCCATGGTTTTATTGATTGAAATGTGATTAGCTCAATGCA-GAAACA
14388 ATTTGGTGA
195 ATTTGGTGA
14397 GATTTG
1 GATTTG
14403 AGCCTTTAAG
Statistics
Matches: 201, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
202 182 0.91
204 19 0.09
ACGTcount: A:0.26, C:0.09, G:0.23, T:0.42
Consensus pattern (203 bp):
GATTTGTCAAAAATTTCATTGATTGTCTTTGTCTTGTTGAATATTGTTTGGAATGCTATGCTTGT
TTGGGAACACATGATTGTTTAGGTTAGGATATTCTTGATAGCGAATAGCATGAATTGTGATCAAG
TTGGTACTTTTGTGATATCCCATGGTTTTATTGATTGAAATGTGATTAGCTCAATGCAGAAACAA
TTTGGTGA
Found at i:18307 original size:23 final size:23
Alignment explanation
Indices: 18273--18318 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
18263 CATTATTATA
* *
18273 TGGCACTCCGGTGTAATTCTACG
1 TGGCACTCCGGTGCAATTATACG
*
18296 TGGCACTTCGGTGCAATTATACG
1 TGGCACTCCGGTGCAATTATACG
18319 AGTTGTGGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (23 bp):
TGGCACTCCGGTGCAATTATACG
Found at i:30815 original size:58 final size:59
Alignment explanation
Indices: 30702--30815 Score: 146
Period size: 59 Copynumber: 1.9 Consensus size: 59
30692 CAAATTCTAT
* *
30702 AATATTATAATATATAAAATATATCAATTTAAATCATAAAATATATTTTATTTATTTAA
1 AATATTATAATATATAAAATATAACAATTTAAATCATAAAATATATATTATTTATTTAA
*
30761 AATATT-TAATATAATAAAATATAACATTTTTAAATC-TATAAATA-A-ATTATTTATT
1 AATATTATAATAT-ATAAAATATAACA-ATTTAAATCATA-AAATATATATTATTTATT
30816 ATATAATTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
58 15 0.31
59 21 0.43
60 13 0.27
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (59 bp):
AATATTATAATATATAAAATATAACAATTTAAATCATAAAATATATATTATTTATTTAA
Found at i:31015 original size:16 final size:17
Alignment explanation
Indices: 30984--31017 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
30974 TTTAATATTA
*
30984 ATTTTAACTCTAAAAAT
1 ATTTTAAATCTAAAAAT
31001 ATTTTAAAT-TAAAAAT
1 ATTTTAAATCTAAAAAT
31017 A
1 A
31018 ATTTCTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTTTAAATCTAAAAAT
Found at i:31021 original size:17 final size:18
Alignment explanation
Indices: 30982--31026 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
30972 TATTTAATAT
*
30982 TAATTTTAACTCTAAAAA
1 TAATTTTAAATCTAAAAA
31000 T-ATTTTAAAT-TAAAAA
1 TAATTTTAAATCTAAAAA
31016 TAATTTCTAAA
1 TAATTT-TAAA
31027 ATGAAATACT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 7 0.29
17 12 0.50
18 5 0.21
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATTTTAAATCTAAAAA
Found at i:37499 original size:39 final size:39
Alignment explanation
Indices: 37437--37511 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
37427 CTTTGCTAAC
37437 TTCCAAAAAAATATAATTGGTTATTTATATCTAAAAGAA
1 TTCCAAAAAAATATAATTGGTTATTTATATCTAAAAGAA
* * *
37476 TTCCTAAAAATTATAATTTGTTATTTATATCTAAAA
1 TTCCAAAAAAATATAATTGGTTATTTATATCTAAAA
37512 TATTATTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.41
Consensus pattern (39 bp):
TTCCAAAAAAATATAATTGGTTATTTATATCTAAAAGAA
Found at i:38987 original size:2 final size:2
Alignment explanation
Indices: 38980--39042 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
38970 ATAAAGATTC
38980 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
39022 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
39043 CTAGTTAGGG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:42142 original size:30 final size:30
Alignment explanation
Indices: 42106--42166 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
42096 TCAGCAGATG
*
42106 TGCATGGAA-GCGTGGATCTCTCGGCGTCTT
1 TGCATGGAAGGC-TGGATATCTCGGCGTCTT
42136 TGCATGGAAGGCTGGATATCTCGGCGTCTT
1 TGCATGGAAGGCTGGATATCTCGGCGTCTT
42166 T
1 T
42167 AACGCAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 27 0.93
31 2 0.07
ACGTcount: A:0.15, C:0.21, G:0.33, T:0.31
Consensus pattern (30 bp):
TGCATGGAAGGCTGGATATCTCGGCGTCTT
Found at i:42257 original size:34 final size:34
Alignment explanation
Indices: 42219--42303 Score: 143
Period size: 34 Copynumber: 2.5 Consensus size: 34
42209 TATGATTGAT
* *
42219 CTCTCGGCGTCTTTAGTTGGATTCTTCATGGGAA
1 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
42253 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
1 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
*
42287 ATCTCGGCGTCTTCAGT
1 CTCTCGGCGTCTTCAGT
42304 GCTGTGCATG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.15, C:0.24, G:0.25, T:0.36
Consensus pattern (34 bp):
CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
Found at i:42425 original size:23 final size:23
Alignment explanation
Indices: 42399--42442 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
42389 TGAGCAGGGG
*
42399 CTGCACGTCTGCATGTGGGGGTC
1 CTGCACGTCTGCATGTAGGGGTC
42422 CTGCACGTCTGCATGTAGGGG
1 CTGCACGTCTGCATGTAGGGG
42443 CATGCAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.11, C:0.25, G:0.39, T:0.25
Consensus pattern (23 bp):
CTGCACGTCTGCATGTAGGGGTC
Found at i:43159 original size:173 final size:173
Alignment explanation
Indices: 42870--43229 Score: 607
Period size: 173 Copynumber: 2.1 Consensus size: 173
42860 TTGTAAAGTT
*
42870 TTAGGGA-CTGTTTTGTAAAATTTAAGGAATTTAAGGAATAAGAGTAAATTATTAAAAGTTGCTA
1 TTAGGGATC-GTTTTGTAAAATTTAAGGAATTTAAGGAATAAGAGTAAATTATAAAAAGTTGCTA
*
42934 TACTATGCTGGAATTTAGTATTAGTATGCTTAATTGGTTAAATTTGAAAGAATTTATAAATTTA-
65 TACTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTTGAAAGAATTTATAAATTTAG
*
42998 TGGATTAAATTGCTAAGTTTGAAAATGTTGAGAACCAAATAGTAA
130 T-GATTAAATTGCAAAGTTTGAAAATGTTGAGAACCAAATAGTAA
* * *
43043 TTAGGGATCGTTTTGTAAAATTTGAGGAATTTAAGGAATTAGAGTAAATTATAAAAAGTTGGTAT
1 TTAGGGATCGTTTTGTAAAATTTAAGGAATTTAAGGAATAAGAGTAAATTATAAAAAGTTGCTAT
*
43108 ACTATGCTTGAATTTAGTATTAATATGCTTAATTGGTTAAATTTGAAAGAATTTATAAATTTAGT
66 ACTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTTGAAAGAATTTATAAATTTAGT
*
43173 GATTAAATTGCAAAGTTTGAAAATGTTGAGAAGCAAATAGTAA
131 GATTAAATTGCAAAGTTTGAAAATGTTGAGAACCAAATAGTAA
*
43216 TTAGGGATCATTTT
1 TTAGGGATCGTTTT
43230 ATATTTGATG
Statistics
Matches: 176, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
173 174 0.99
174 2 0.01
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.38
Consensus pattern (173 bp):
TTAGGGATCGTTTTGTAAAATTTAAGGAATTTAAGGAATAAGAGTAAATTATAAAAAGTTGCTAT
ACTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTTGAAAGAATTTATAAATTTAGT
GATTAAATTGCAAAGTTTGAAAATGTTGAGAACCAAATAGTAA
Found at i:45299 original size:37 final size:37
Alignment explanation
Indices: 45255--45495 Score: 340
Period size: 37 Copynumber: 6.3 Consensus size: 37
45245 ATTTAAATCA
*
45255 TTAAATCATTAAAGTAATTATTATTAAAGCATTAAAG
1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
45292 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
* * *
45329 -TAATTATTATTAAAGCATTAAAGTTAAATCATTAAATCATTAAAA
1 TTAA--ATCATTAAAG---T-AA-TT--ATTATTAAATCATTAAAG
*
45374 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAA
1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
45411 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
45448 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
*
45485 TTAAATAATTA
1 TTAAATCATTA
45496 TTATTAAATC
Statistics
Matches: 186, Mismatches: 8, Indels: 20
0.87 0.04 0.09
Matches are distributed among these distances:
36 3 0.02
37 136 0.73
38 9 0.05
39 2 0.01
40 2 0.01
41 2 0.01
42 2 0.01
43 2 0.01
44 9 0.05
45 16 0.09
46 3 0.02
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (37 bp):
TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
Found at i:45311 original size:23 final size:22
Alignment explanation
Indices: 45247--45448 Score: 115
Period size: 23 Copynumber: 8.7 Consensus size: 22
45237 GGGCATGTAT
*
45247 TTAAATCATTAAA-TCATTAAA
1 TTAAATCATTAAAGTAATTAAA
* * *
45268 GTAATTATTATTAAAG-CATTAAA
1 TTAA--ATCATTAAAGTAATTAAA
*
45291 GTTAAATCATTAAAGTAATTATTA
1 -TTAAATCATTAAAGTAATTA-AA
*
45315 TTAAATCATTAAAGTAATTATTA
1 TTAAATCATTAAAGTAATTA-AA
* * *
45338 TTAAAGCATTAAAGTTAAAT-CA
1 TTAAATCATTAAAG-TAATTAAA
*
45360 TTAAATCATTAAAATTAAATCATTAAA
1 TTAAATCATT-AAAGT--A--ATTAAA
* * *
45387 GTAATTATTATTAAA-TCATTAAAA
1 TTAA--ATCATTAAAGTAATT-AAA
*
45411 TTAAATCATTAAAGTAATTATTA
1 TTAAATCATTAAAGTAATTA-AA
45434 TTAAATCATTAAAGT
1 TTAAATCATTAAAGT
45449 TAAATCATTA
Statistics
Matches: 143, Mismatches: 20, Indels: 34
0.73 0.10 0.17
Matches are distributed among these distances:
21 3 0.02
22 29 0.20
23 81 0.57
24 15 0.10
26 2 0.01
27 5 0.03
28 3 0.02
29 5 0.03
ACGTcount: A:0.50, C:0.06, G:0.05, T:0.40
Consensus pattern (22 bp):
TTAAATCATTAAAGTAATTAAA
Found at i:45376 original size:14 final size:14
Alignment explanation
Indices: 45247--45537 Score: 122
Period size: 14 Copynumber: 20.8 Consensus size: 14
45237 GGGCATGTAT
45247 TTAAATCATTAAATCA
1 TTAAATCATTAAA--A
* **
45263 TTAAAGTAATTATTA
1 TTAAA-TCATTAAAA
* *
45278 TTAAAGCATTAAAG
1 TTAAATCATTAAAA
45292 TTAAATCATT-AAA
1 TTAAATCATTAAAA
* *
45305 GTAATTATTATTAAATCA
1 TTAA--ATCATTAAA--A
* **
45323 TTAAAGTAATTATTA
1 TTAAA-TCATTAAAA
* *
45338 TTAAAGCATTAAAG
1 TTAAATCATTAAAA
45352 TTAAATCATTAAATCA
1 TTAAATCATTAAA--A
45368 TTAAA--ATTAAATCA
1 TTAAATCATTAAA--A
* **
45382 TTAAAGTAATTATTA
1 TTAAA-TCATTAAAA
45397 TTAAATCATTAAAA
1 TTAAATCATTAAAA
45411 TTAAATCATT-AAA
1 TTAAATCATTAAAA
* *
45424 GT-AATTATT---A
1 TTAAATCATTAAAA
*
45434 TTAAATCATTAAAG
1 TTAAATCATTAAAA
45448 TTAAATCATT-AAA
1 TTAAATCATTAAAA
* *
45461 GT-AATTATT---A
1 TTAAATCATTAAAA
*
45471 TTAAATCATTAAAG
1 TTAAATCATTAAAA
* **
45485 TTAAATAATTATTA
1 TTAAATCATTAAAA
*
45499 TTAAATCATTAAAT
1 TTAAATCATTAAAA
* *
45513 TTAAATAATTAAAT
1 TTAAATCATTAAAA
*
45527 TTAAATAATTA
1 TTAAATCATTA
45538 TTATTAAATA
Statistics
Matches: 207, Mismatches: 48, Indels: 42
0.70 0.16 0.14
Matches are distributed among these distances:
10 4 0.02
11 12 0.06
12 12 0.06
13 12 0.06
14 113 0.55
15 23 0.11
16 13 0.06
17 14 0.07
18 4 0.02
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (14 bp):
TTAAATCATTAAAA
Found at i:45393 original size:9 final size:8
Alignment explanation
Indices: 45352--45537 Score: 70
Period size: 8 Copynumber: 25.4 Consensus size: 8
45342 AGCATTAAAG
*
45352 TTAAATCA
1 TTAAATAA
*
45360 TTAAATCA
1 TTAAATAA
45368 TT-AA-AA
1 TTAAATAA
*
45374 TTAAATCA
1 TTAAATAA
45382 TTAAAGTAA
1 TTAAA-TAA
*
45391 TT--ATTA
1 TTAAATAA
*
45397 TTAAATCA
1 TTAAATAA
45405 TT-AA-AA
1 TTAAATAA
*
45411 TTAAATCA
1 TTAAATAA
45419 TTAAAGTAA
1 TTAAA-TAA
*
45428 TT--ATTA
1 TTAAATAA
*
45434 TTAAATCA
1 TTAAATAA
*
45442 TT-AA-AG
1 TTAAATAA
*
45448 TTAAATCA
1 TTAAATAA
45456 TTAAAGTAA
1 TTAAA-TAA
*
45465 TT--ATTA
1 TTAAATAA
*
45471 TTAAATCA
1 TTAAATAA
*
45479 TT-AA-AG
1 TTAAATAA
45485 TTAAATAA
1 TTAAATAA
*
45493 TT--ATTA
1 TTAAATAA
*
45499 TTAAATCA
1 TTAAATAA
45507 TTAAAT--
1 TTAAATAA
45513 TTAAATAA
1 TTAAATAA
45521 TTAAAT--
1 TTAAATAA
45527 TTAAATAA
1 TTAAATAA
45535 TTA
1 TTA
45538 TTATTAAATA
Statistics
Matches: 133, Mismatches: 22, Indels: 46
0.66 0.11 0.23
Matches are distributed among these distances:
6 39 0.29
7 19 0.14
8 63 0.47
9 12 0.09
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (8 bp):
TTAAATAA
Found at i:45400 original size:74 final size:72
Alignment explanation
Indices: 45337--45546 Score: 263
Period size: 74 Copynumber: 2.9 Consensus size: 72
45327 AGTAATTATT
*
45337 ATTAAAGCATTAAAGTTAAATCATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAAA
1 ATTAAATCATTAAAGTTAAATCATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAAA
45402 TCATTAAA
66 TCATT-AA
* *
45410 ATTAAATCATTAAAG-TAATTATTATTAAATCATTAAAGTTAAATCATTAAAGTAATTATTATTA
1 ATTAAATCATTAAAGTTAA--ATCATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTA
45474 AATCATTAA
64 AATCATTAA
* *
45483 AGTTAAATAATTATTA-TTAAATCATTAAAT--TTAAATAATTAAAT--TTAAA-TAATTATTAT
1 A-TTAAATCATTA-AAGTTAAATCATTAAATCATT-AA-AATTAAATCATTAAAGTAATTATTAT
45542 TAAAT
62 TAAAT
45547 ATGTACTCGA
Statistics
Matches: 123, Mismatches: 7, Indels: 17
0.84 0.05 0.12
Matches are distributed among these distances:
70 15 0.12
71 7 0.06
72 5 0.04
73 33 0.27
74 59 0.48
75 4 0.03
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (72 bp):
ATTAAATCATTAAAGTTAAATCATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAAA
TCATTAA
Found at i:45475 original size:119 final size:118
Alignment explanation
Indices: 45254--45483 Score: 365
Period size: 119 Copynumber: 1.9 Consensus size: 118
45244 TATTTAAATC
*
45254 ATTAAATCATTAAAGTAATTATTATTAAAGCATTAAAGTTAAATCATTAAAGTAATTATTATTAA
1 ATTAAATCATTAAAGTAATTATTATTAAAGCATTAAAATTAAATCATTAAAGTAATTATTATTAA
* *
45319 ATCATTAAAGTAATTATTATTAAAGCATTAAAGTTAAATCATTAAATCATTAAA
66 ATCATTAAAGTAA-TATCATTAAAGAATTAAAGTTAAATCATTAAATCATTAAA
*
45373 ATTAAATCATTAAAGTAATTATTATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAA
1 ATTAAATCATTAAAGTAATTATTATTAAAGCATTAAAATTAAATCATTAAAGTAATTATTATTAA
*
45438 ATCATTAAAGTTAA-ATCATTAAAGTAATTATTA-TTAAATCATTAAA
66 ATCATTAAAG-TAATATCATTAAAG-AATTA-AAGTTAAATCATTAAA
45484 GTTAAATAAT
Statistics
Matches: 103, Mismatches: 5, Indels: 6
0.90 0.04 0.05
Matches are distributed among these distances:
118 9 0.09
119 90 0.87
120 4 0.04
ACGTcount: A:0.50, C:0.06, G:0.05, T:0.40
Consensus pattern (118 bp):
ATTAAATCATTAAAGTAATTATTATTAAAGCATTAAAATTAAATCATTAAAGTAATTATTATTAA
ATCATTAAAGTAATATCATTAAAGAATTAAAGTTAAATCATTAAATCATTAAA
Found at i:49061 original size:42 final size:42
Alignment explanation
Indices: 48997--49084 Score: 158
Period size: 42 Copynumber: 2.1 Consensus size: 42
48987 AACAAATCTC
*
48997 ACGCTTCAGGCGAATCTAACGCTTCGGCCCCAAAGCATACAG
1 ACGCTTCAGGCGAATCTAACGCTTCGGCCACAAAGCATACAG
*
49039 ACGCTTCAGGCGAATCTCACGCTTCGGCCACAAAGCATACAG
1 ACGCTTCAGGCGAATCTAACGCTTCGGCCACAAAGCATACAG
49081 ACGC
1 ACGC
49085 ATGCAGAATG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.28, C:0.34, G:0.22, T:0.16
Consensus pattern (42 bp):
ACGCTTCAGGCGAATCTAACGCTTCGGCCACAAAGCATACAG
Found at i:50296 original size:36 final size:37
Alignment explanation
Indices: 50249--50324 Score: 127
Period size: 36 Copynumber: 2.1 Consensus size: 37
50239 ATTGATCAAT
*
50249 TTATTGATTTTGAAACTTTAGTGG-GAAAATGAAAAC
1 TTATTGATTTTGAAACTTTAGTGGAAAAAATGAAAAC
*
50285 TTATTGCTTTTGAAACTTTAGTGGAAAAAATGAAAAC
1 TTATTGATTTTGAAACTTTAGTGGAAAAAATGAAAAC
50322 TTA
1 TTA
50325 CTCAAACATT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
36 23 0.62
37 14 0.38
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (37 bp):
TTATTGATTTTGAAACTTTAGTGGAAAAAATGAAAAC
Found at i:50476 original size:31 final size:31
Alignment explanation
Indices: 50427--50503 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
50417 TTTAAGTCTC
* * *
50427 AGTGACCACATCTTAATTATATAAAAACGAA
1 AGTGACCAAATATTAATTAAATAAAAACGAA
* * *
50458 AGTGGCCAAATATTAATTAAATAAAGATGAA
1 AGTGACCAAATATTAATTAAATAAAAACGAA
*
50489 AGTGATCAAATATTA
1 AGTGACCAAATATTA
50504 TATTTTTTAA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.27
Consensus pattern (31 bp):
AGTGACCAAATATTAATTAAATAAAAACGAA
Found at i:52423 original size:51 final size:51
Alignment explanation
Indices: 52314--52435 Score: 163
Period size: 51 Copynumber: 2.4 Consensus size: 51
52304 TAAGTTGCGA
* *
52314 AAACGAAATTTACGTTGCGATAATTGTGTTTACCTATATCGGTAATTAGCG
1 AAACGAAATTCACGTTGCGATAATTGTGTTTACCTATATCGGTAATTAACG
** * *
52365 AAACGAAATTCGTGTTGCGATAGTTGTGTTTACCTATATCGGTAATTAATG
1 AAACGAAATTCACGTTGCGATAATTGTGTTTACCTATATCGGTAATTAACG
***
52416 TTGCGAAATTCACGTTGCGA
1 AAACGAAATTCACGTTGCGA
52436 AAACAAAATT
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (51 bp):
AAACGAAATTCACGTTGCGATAATTGTGTTTACCTATATCGGTAATTAACG
Found at i:52458 original size:20 final size:20
Alignment explanation
Indices: 52421--52458 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
52411 TAATGTTGCG
*
52421 AAATTCACGTTGCGAAAACA
1 AAATTCACGTTGCAAAAACA
*
52441 AAATTCATGTTGCAAAAA
1 AAATTCACGTTGCAAAAA
52459 TTTCTATGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.16, G:0.13, T:0.24
Consensus pattern (20 bp):
AAATTCACGTTGCAAAAACA
Found at i:56194 original size:24 final size:26
Alignment explanation
Indices: 56159--56212 Score: 78
Period size: 24 Copynumber: 2.2 Consensus size: 26
56149 CTAATAAAAA
56159 AATATTTATCTAATGA-AA-ATTTTT
1 AATATTTATCTAATGATAATATTTTT
56183 AATATATT-TCTAATGATAATATTTTT
1 AATAT-TTATCTAATGATAATATTTTT
56209 AATA
1 AATA
56213 ACTATTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 13 0.48
25 4 0.15
26 10 0.37
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (26 bp):
AATATTTATCTAATGATAATATTTTT
Found at i:56412 original size:21 final size:21
Alignment explanation
Indices: 56363--56403 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
56353 TGCAATGAAC
56363 CCTAAACCTTAAATCATAAAA
1 CCTAAACCTTAAATCATAAAA
*
56384 CCTAAACCTTAAATTATAAA
1 CCTAAACCTTAAATCATAAA
56404 CATTAAACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (21 bp):
CCTAAACCTTAAATCATAAAA
Found at i:56431 original size:28 final size:28
Alignment explanation
Indices: 56379--56432 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
56369 CCTTAAATCA
*
56379 TAAAACCTAAACCTTAAATTATAAACAT
1 TAAAACCTAAACCTTAAACTATAAACAT
* *
56407 TAAACCCTAAACCTTAAACTCTAAAC
1 TAAAACCTAAACCTTAAACTATAAAC
56433 CCTGAATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (28 bp):
TAAAACCTAAACCTTAAACTATAAACAT
Found at i:58493 original size:23 final size:23
Alignment explanation
Indices: 58467--58554 Score: 99
Period size: 23 Copynumber: 3.8 Consensus size: 23
58457 AGCTCGTATA
58467 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
58490 AATTTGTC-CCGAAG-GACCGCGTAG
1 AA-TTG-CACCGAAGTG-CCACGTAG
58514 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* * *
58537 AAATGCATCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
58555 TATATGATTT
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
22 1 0.02
23 34 0.62
24 19 0.35
25 1 0.02
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:68579 original size:22 final size:21
Alignment explanation
Indices: 68537--68576 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
68527 GAGTTTGTTT
*
68537 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
68558 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
68577 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:74588 original size:23 final size:23
Alignment explanation
Indices: 74562--74649 Score: 90
Period size: 23 Copynumber: 3.8 Consensus size: 23
74552 AGCTCGTATA
74562 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* **
74585 AATTTGTC-CCGAAAG-ACCGTGTAG
1 AA-TTG-CACCG-AAGTGCCACGTAG
74609 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
74632 AAATGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
74650 TATAAGATTT
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
22 4 0.08
23 30 0.58
24 14 0.27
25 4 0.08
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:77275 original size:24 final size:24
Alignment explanation
Indices: 77231--77277 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
77221 ATAAAGAACC
*
77231 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
77255 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
77278 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:80601 original size:19 final size:20
Alignment explanation
Indices: 80579--80622 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
80569 GAGAAAAGGT
80579 AAAAGTTAA-AATGAAAGAG
1 AAAAGTTAATAATGAAAGAG
* *
80598 AAAAATTAATAATGAAAGAT
1 AAAAGTTAATAATGAAAGAG
80618 AAAAG
1 AAAAG
80623 AAAAAGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAAGTTAATAATGAAAGAG
Found at i:87514 original size:24 final size:24
Alignment explanation
Indices: 87470--87516 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
87460 ATAAAGAACC
*
87470 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
87494 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
87517 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:89985 original size:11 final size:11
Alignment explanation
Indices: 89969--89997 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
89959 GAGTTTGAGT
89969 TCGAGCTTCGA
1 TCGAGCTTCGA
89980 TCGAGCTTCGA
1 TCGAGCTTCGA
89991 TCGAGCT
1 TCGAGCT
89998 CCTAAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.17, C:0.28, G:0.28, T:0.28
Consensus pattern (11 bp):
TCGAGCTTCGA
Found at i:91496 original size:4 final size:4
Alignment explanation
Indices: 91489--91513 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
91479 ATATTTTTCA
91489 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
91514 CAAAATACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:94941 original size:61 final size:60
Alignment explanation
Indices: 94819--94931 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 60
94809 TGAATGAGTG
* * * *
94819 TTTTGTAATTTTTAATATTTGGAAATTCAATAAAATAATATCTTATAATTTTAAAAATAT
1 TTTTGTAATTTTTAATAATTGGAAATTCAACAAAATAATATCTTATAAGTCTAAAAATAT
* *
94879 TTTTTTAATTTTTTATAATTGAGAAATTCAACAAAATAATA-C-TATATAGTCTA
1 TTTTGTAATTTTTAATAATTG-GAAATTCAACAAAATAATATCTTATA-AGTCTA
94932 GAGATTATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
59 4 0.09
60 23 0.51
61 18 0.40
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (60 bp):
TTTTGTAATTTTTAATAATTGGAAATTCAACAAAATAATATCTTATAAGTCTAAAAATAT
Found at i:97083 original size:60 final size:60
Alignment explanation
Indices: 96958--97113 Score: 176
Period size: 60 Copynumber: 2.6 Consensus size: 60
96948 ATTGATTCTT
* * * * *
96958 AAACTTTTAAATATTTTAATTTCATCCAT-AAATTATGACTATCATTCTAAATTAGTCCTC
1 AAACTTTTGAACATTTTAATTTCATCC-TCAAACTATGACTATCATTCTAAATCAATCCTC
*
97018 AAACTTTTGAACATTTTAGTTTCATCCTCAAACTATGACCT-TCATTCTAAATCAAT-CTCC
1 AAACTTTTGAACATTTTAATTTCATCCTCAAACTATGA-CTATCATTCTAAATCAATCCT-C
* *
97078 GAACTTTTTGAACATTCTAATTTCATCC-CAAACTAT
1 AAAC-TTTTGAACATTTTAATTTCATCCTCAAACTAT
97114 ACGCATATAC
Statistics
Matches: 83, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
59 3 0.04
60 57 0.69
61 23 0.28
ACGTcount: A:0.34, C:0.21, G:0.04, T:0.40
Consensus pattern (60 bp):
AAACTTTTGAACATTTTAATTTCATCCTCAAACTATGACTATCATTCTAAATCAATCCTC
Found at i:97334 original size:60 final size:60
Alignment explanation
Indices: 97241--97395 Score: 161
Period size: 60 Copynumber: 2.6 Consensus size: 60
97231 TTTGGGTATA
* ** * * *
97241 AAATTGGAATATTCAAAAGTTTGGGGACCAATTTTGAAAGAGGGTCATAATCTAG-GGATG
1 AAATTAGAATATTCAAAAGTTTAAGAACCAATTTAGAAAGAGAGTCATAAT-TAGAGGATG
* * *
97301 AAATTAGAATATTCAAAAGTTTAAGAACTAATTTAGAATGAGAGTCATAATTTGAGGATG
1 AAATTAGAATATTCAAAAGTTTAAGAACCAATTTAGAAAGAGAGTCATAATTAGAGGATG
* * * *
97361 AAATTAAAATATTAAAAAATTTCAAG-ATCAATTTA
1 AAATTAGAATATTCAAAAGTTT-AAGAACCAATTTA
97396 AAATAAAGAT
Statistics
Matches: 79, Mismatches: 14, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
59 2 0.03
60 74 0.94
61 3 0.04
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.31
Consensus pattern (60 bp):
AAATTAGAATATTCAAAAGTTTAAGAACCAATTTAGAAAGAGAGTCATAATTAGAGGATG
Found at i:97411 original size:60 final size:60
Alignment explanation
Indices: 97296--97414 Score: 143
Period size: 60 Copynumber: 2.0 Consensus size: 60
97286 CATAATCTAG
* * * * *
97296 GGATGAAATTAGAATATTCAAAAGTTTAAGAACTAATTTAGAATGAGAGTCATAATTTGA
1 GGATGAAATTAAAATATTAAAAAATTTAAGAACTAATTTAAAATAAGAGTCATAATTTGA
* *
97356 GGATGAAATTAAAATATTAAAAAATTTCAAGATC-AATTTAAAATAA-AGATTATAATTTG
1 GGATGAAATTAAAATATTAAAAAATTT-AAGAACTAATTTAAAATAAGAG-TCATAATTTG
97415 GAGATATATG
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
59 2 0.04
60 43 0.86
61 5 0.10
ACGTcount: A:0.49, C:0.04, G:0.14, T:0.33
Consensus pattern (60 bp):
GGATGAAATTAAAATATTAAAAAATTTAAGAACTAATTTAAAATAAGAGTCATAATTTGA
Found at i:98146 original size:2 final size:2
Alignment explanation
Indices: 98139--98175 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
98129 GGGACATGTG
98139 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 T
98176 TGGAGATAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:108681 original size:112 final size:109
Alignment explanation
Indices: 108540--108760 Score: 370
Period size: 112 Copynumber: 2.0 Consensus size: 109
108530 AAGAAAGTTA
108540 CTGTGTATACATATTGCAACATTCCATGCAACAGTAATTAGACAGAAACTACGTACTGTGCTTCT
1 CTGTGTATACATATTGCAACATTCCATGCAACAGTAATTAGACAGAAACTACGTACTGTG---CT
* *
108605 TGTATATTTTTTGCTAGTGATTGAATATCATGAATCGGATCACTATT
63 TGTATATTTTCTGCTAGTGATGGAATATCATGAATCGGATCACTATT
* *
108652 CTGTGTATACATATTGCAACATTCCATGCAACAGTGATTATACAGAAACTACGTACTGTGCTTGT
1 CTGTGTATACATATTGCAACATTCCATGCAACAGTAATTAGACAGAAACTACGTACTGTGCTTGT
*
108717 ATATTTTCTGCTGGTGATGGAATATCATGAATCGGATCACTATT
66 ATATTTTCTGCTAGTGATGGAATATCATGAATCGGATCACTATT
108761 TGTTTACCCT
Statistics
Matches: 104, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
109 46 0.44
112 58 0.56
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (109 bp):
CTGTGTATACATATTGCAACATTCCATGCAACAGTAATTAGACAGAAACTACGTACTGTGCTTGT
ATATTTTCTGCTAGTGATGGAATATCATGAATCGGATCACTATT
Found at i:109480 original size:28 final size:28
Alignment explanation
Indices: 109420--109485 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 28
109410 TCAAAAACTT
*
109420 ATTTTGTAACTTTCAATAGTCAAAGGACT
1 ATTTTGTAACTTTC-ATAGTCAAAGGACC
* *
109449 ATTTTGTAACTTTC-TCAGTCGAGGGACC
1 ATTTTGTAACTTTCAT-AGTCAAAGGACC
109477 ATTTATGTA
1 ATTT-TGTA
109486 TTTTACCTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 1 0.03
28 13 0.41
29 18 0.56
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (28 bp):
ATTTTGTAACTTTCATAGTCAAAGGACC
Found at i:111234 original size:39 final size:39
Alignment explanation
Indices: 111183--111271 Score: 178
Period size: 39 Copynumber: 2.3 Consensus size: 39
111173 TTTCAGGATA
111183 TAGCGGCGTTTACATTAAAAAAGCCACAAAATGATACTT
1 TAGCGGCGTTTACATTAAAAAAGCCACAAAATGATACTT
111222 TAGCGGCGTTTACATTAAAAAAGCCACAAAATGATACTT
1 TAGCGGCGTTTACATTAAAAAAGCCACAAAATGATACTT
111261 TAGCGGCGTTT
1 TAGCGGCGTTT
111272 TTACAACAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (39 bp):
TAGCGGCGTTTACATTAAAAAAGCCACAAAATGATACTT
Found at i:111380 original size:42 final size:41
Alignment explanation
Indices: 111328--111426 Score: 119
Period size: 41 Copynumber: 2.4 Consensus size: 41
111318 TAGAGTTATT
* * * *
111328 TTTAGTGGCGTTTTGT-CGACAAGCGTCGCAACAGAGTAGTAA
1 TTTAGTGGCGTTTT-TACG-CAAACGCCACAACAAAGTAGTAA
* *
111370 TTTAGCGGCGTTTTTATGCAAACGCCACAACAAAGTAGTAA
1 TTTAGTGGCGTTTTTACGCAAACGCCACAACAAAGTAGTAA
111411 TTTAGTGGCGTTTTTA
1 TTTAGTGGCGTTTTTA
111427 TAAAAAAAAG
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
41 35 0.71
42 14 0.29
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.32
Consensus pattern (41 bp):
TTTAGTGGCGTTTTTACGCAAACGCCACAACAAAGTAGTAA
Found at i:113678 original size:22 final size:22
Alignment explanation
Indices: 113647--113699 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
113637 TTGTTTTTAT
*
113647 GGTTTCGAATAGAAAAATAATA
1 GGTTTTGAATAGAAAAATAATA
* *
113669 GGTTTTGAATAGGAAAATATTA
1 GGTTTTGAATAGAAAAATAATA
*
113691 GCTTTTGAA
1 GGTTTTGAA
113700 AACGTGAAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.42, C:0.04, G:0.21, T:0.34
Consensus pattern (22 bp):
GGTTTTGAATAGAAAAATAATA
Found at i:118044 original size:17 final size:17
Alignment explanation
Indices: 118022--118058 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
118012 GGGAGGGAAG
118022 TGGAACAAAAATCAAAA
1 TGGAACAAAAATCAAAA
118039 TGGAACAAAAATCAAAA
1 TGGAACAAAAATCAAAA
118056 TGG
1 TGG
118059 GAGGGCAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.59, C:0.11, G:0.16, T:0.14
Consensus pattern (17 bp):
TGGAACAAAAATCAAAA
Found at i:118228 original size:28 final size:28
Alignment explanation
Indices: 118188--118250 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
118178 AATGTATTCT
*
118188 TTGTGTGCAGGTCGAATAGAACCATTGA
1 TTGTGTTCAGGTCGAATAGAACCATTGA
118216 TTGTGTTCAGGTCGAATAGAACCATTGA
1 TTGTGTTCAGGTCGAATAGAACCATTGA
118244 -TGTGTTC
1 TTGTGTTC
118251 TGTGCTTTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 7 0.21
28 27 0.79
ACGTcount: A:0.25, C:0.14, G:0.27, T:0.33
Consensus pattern (28 bp):
TTGTGTTCAGGTCGAATAGAACCATTGA
Found at i:118863 original size:2 final size:2
Alignment explanation
Indices: 118856--118891 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
118846 TAGCTACGGG
118856 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
118892 CTCAGTTTTC
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):
TA
Found at i:121705 original size:29 final size:31
Alignment explanation
Indices: 121637--121702 Score: 98
Period size: 33 Copynumber: 2.1 Consensus size: 31
121627 TATTCAAAGT
*
121637 TTGGCCACCAACCAAGATGAAATTTCCAATAAG
1 TTGGCCACCAACCAAGATGAAATTTCC-A-AAC
121670 TTGGCCACCAACCAAGATGAAATTTCC-AAC
1 TTGGCCACCAACCAAGATGAAATTTCCAAAC
121700 TTG
1 TTG
121703 CCAACTTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 5 0.16
33 27 0.84
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (31 bp):
TTGGCCACCAACCAAGATGAAATTTCCAAAC
Found at i:122846 original size:64 final size:63
Alignment explanation
Indices: 122713--122869 Score: 176
Period size: 64 Copynumber: 2.5 Consensus size: 63
122703 TTGTTTAAGG
* * * * * *
122713 TGCATCGATGCACATGCAGTGCATCGATGCATGAATTTAAATAGAAACATCGAATGTGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCAATTTAAATACAAACATCGAATGTGATATA
*
122776 TGCATCGATGCATAAGGAGTGCATCGATGCATCTCCA-TTAAATACAAACATCGAATAG-GATAT
1 TGCATCGATGCATAAGGAGTGCATCGATGCA--TCAATTTAAATACAAACATCGAAT-GTGATAT
122839 A
63 A
*
122840 TGCATCGATGCAT-GGTGTAGTGCATCGATG
1 TGCATCGATGCATAAG-G-AGTGCATCGATG
122870 AATACCTTCA
Statistics
Matches: 81, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
63 29 0.36
64 37 0.46
65 15 0.19
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCAATTTAAATACAAACATCGAATGTGATATA
Found at i:124475 original size:25 final size:25
Alignment explanation
Indices: 124441--124509 Score: 129
Period size: 25 Copynumber: 2.8 Consensus size: 25
124431 GAGTAGAGGG
*
124441 TCTACGCGGTCCTTTGGGACAATAT
1 TCTACGCGGTCCTTCGGGACAATAT
124466 TCTACGCGGTCCTTCGGGACAATAT
1 TCTACGCGGTCCTTCGGGACAATAT
124491 TCTACGCGGTCCTTCGGGA
1 TCTACGCGGTCCTTCGGGA
124510 TATATATATA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.17, C:0.28, G:0.26, T:0.29
Consensus pattern (25 bp):
TCTACGCGGTCCTTCGGGACAATAT
Found at i:124668 original size:23 final size:23
Alignment explanation
Indices: 124624--124668 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
124614 ATCATTATAT
*
124624 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
124647 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
124669 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:140789 original size:3 final size:3
Alignment explanation
Indices: 140781--140816 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
140771 TTTACGGCCC
140781 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
140817 CTGCAACGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:146644 original size:2 final size:2
Alignment explanation
Indices: 146637--146679 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
146627 AGTAACTATT
146637 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
146679 T
1 T
146680 CTCAATACAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:147959 original size:14 final size:15
Alignment explanation
Indices: 147908--147957 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
147898 TTAATTCATC
147908 TAAATAATTAGTGTT
1 TAAATAATTAGTGTT
* *
147923 TACATAATTTA-TATT
1 TAAATAA-TTAGTGTT
147938 TAAAT-ATTAGTGTT
1 TAAATAATTAGTGTT
147952 TAAATA
1 TAAATA
147958 TTTGATAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
13 3 0.11
14 9 0.32
15 13 0.46
16 3 0.11
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (15 bp):
TAAATAATTAGTGTT
Found at i:147971 original size:29 final size:29
Alignment explanation
Indices: 147909--147972 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
147899 TAATTCATCT
* * *
147909 AAATAATTAGTGTTTACATAATTTATATTT
1 AAAT-ATTAGTGTTTAAATAATTTATAATA
147939 AAATATTAGTGTTTAAAT-ATTTGATAATA
1 AAATATTAGTGTTTAAATAATTT-ATAATA
147968 AAATA
1 AAATA
147973 ATGGTTTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 4 0.13
29 22 0.73
30 4 0.13
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (29 bp):
AAATATTAGTGTTTAAATAATTTATAATA
Found at i:149548 original size:2 final size:2
Alignment explanation
Indices: 149541--149570 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
149531 ATGGATATGC
*
149541 CT CT CT CT CT CT CT CT CT CT CT AT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
149571 AAATGTATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:151179 original size:28 final size:28
Alignment explanation
Indices: 151126--151182 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
151116 TCGTCGTCGC
**
151126 TTTCAAGCATTGACTCGGCGACATAATG
1 TTTCAAGCATTGACTCAACGACATAATG
*
151154 TTTCAAGCATTGACTCAACGATATAATG
1 TTTCAAGCATTGACTCAACGACATAATG
151182 T
1 T
151183 AAACAAAGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (28 bp):
TTTCAAGCATTGACTCAACGACATAATG
Found at i:152383 original size:29 final size:29
Alignment explanation
Indices: 152349--152407 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
152339 CCTAAATTAA
152349 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
152378 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
152407 T
1 T
152408 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:157069 original size:29 final size:29
Alignment explanation
Indices: 157035--157093 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
157025 CCTAAATTAA
*
157035 TTTGATGTCATTGCTTACGTCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
157064 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
157093 T
1 T
157094 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.22, C:0.14, G:0.15, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:159430 original size:2 final size:2
Alignment explanation
Indices: 159378--159421 Score: 61
Period size: 2 Copynumber: 21.5 Consensus size: 2
159368 AAATTATTTG
* *
159378 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT TT GAT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
159421 A
1 A
159422 AGTTATATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 36 0.97
3 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:162283 original size:35 final size:34
Alignment explanation
Indices: 162198--162284 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
162188 AAAATAATTT
* *
162198 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGA
* *
162232 TAAATGATAACCAAATTACAATAACTGATATTAAATGA
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGA
162270 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
162285 ACTGAAATAC
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.55
36 1 0.02
37 4 0.09
38 10 0.23
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGA
Found at i:163513 original size:20 final size:20
Alignment explanation
Indices: 163488--163533 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
163478 AACTATAATC
163488 TAAAATCAATTTTTAAACAT
1 TAAAATCAATTTTTAAACAT
*
163508 TAAAATCGATTTTTAAACAT
1 TAAAATCAATTTTTAAACAT
*
163528 CAAAAT
1 TAAAAT
163534 AATCCAACGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.37
Consensus pattern (20 bp):
TAAAATCAATTTTTAAACAT
Found at i:168227 original size:21 final size:21
Alignment explanation
Indices: 168203--168268 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
168193 CTCGCCTTCT
168203 GTAGTACCGATCTTCTGGTGA
1 GTAGTACCGATCTTCTGGTGA
* * ** **
168224 GTAGGAACGATCCGCCT--TCT
1 GTAGTACCGAT-CTTCTGGTGA
168244 GTAGTACCGATCTTCTGGTGA
1 GTAGTACCGATCTTCTGGTGA
168265 GTAG
1 GTAG
168269 GAACGATCCC
Statistics
Matches: 30, Mismatches: 12, Indels: 6
0.62 0.25 0.12
Matches are distributed among these distances:
19 3 0.10
20 10 0.33
21 14 0.47
22 3 0.10
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (21 bp):
GTAGTACCGATCTTCTGGTGA
Found at i:168275 original size:21 final size:21
Alignment explanation
Indices: 168210--168276 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
168200 TCTGTAGTAC
168210 CGATCTTCTGGTGAGTAGGAA
1 CGATCTTCTGGTGAGTAGGAA
** ** * *
168231 CGATCCGCCT--TCTGTAGTAC
1 CGAT-CTTCTGGTGAGTAGGAA
168251 CGATCTTCTGGTGAGTAGGAA
1 CGATCTTCTGGTGAGTAGGAA
168272 CGATC
1 CGATC
168277 CCGCCTTCTA
Statistics
Matches: 31, Mismatches: 12, Indels: 6
0.63 0.24 0.12
Matches are distributed among these distances:
19 3 0.10
20 10 0.32
21 15 0.48
22 3 0.10
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.28
Consensus pattern (21 bp):
CGATCTTCTGGTGAGTAGGAA
Found at i:168313 original size:83 final size:84
Alignment explanation
Indices: 168170--168366 Score: 270
Period size: 83 Copynumber: 2.4 Consensus size: 84
168160 TACTGTGACT
* ** * * *
168170 ATCATCTGGAGAGTAGGAACGATCTCGCCTTCTGTAGTACCGATCTTCTGGTGAGTAGGAACGAT
1 ATCATCTGGTGAGTAGGAACGATCTCGCCTTCTACAGTACCGATCATCTCGTGAATAGGAACGAT
* *
168235 -CCGCCTTCTGTAGTACCG
66 CCCGCCTTCTATAGCACCG
* * *
168253 ATCTTCTGGTGAGTAGGAACGATCCCGCCTTCTACAGTATCGATCATCTCGTGAATAGGAACGAT
1 ATCATCTGGTGAGTAGGAACGATCTCGCCTTCTACAGTACCGATCATCTCGTGAATAGGAACGAT
*
168318 CCCGCCTTCTATAGCATCG
66 CCCGCCTTCTATAGCACCG
*
168337 ATCATCAGGTGAGTAGGAACGATCTCGCCT
1 ATCATCTGGTGAGTAGGAACGATCTCGCCT
168367 ACGGTAGTAA
Statistics
Matches: 98, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
83 56 0.57
84 42 0.43
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.27
Consensus pattern (84 bp):
ATCATCTGGTGAGTAGGAACGATCTCGCCTTCTACAGTACCGATCATCTCGTGAATAGGAACGAT
CCCGCCTTCTATAGCACCG
Found at i:168452 original size:42 final size:42
Alignment explanation
Indices: 168170--168441 Score: 278
Period size: 42 Copynumber: 6.5 Consensus size: 42
168160 TACTGTGACT
* * *
168170 ATCATCTGGAGAGTAGGAACGATCTCGCCTTCTGTAGTACCG
1 ATCATCTGGTGAGTAGGAACGATCCCGCCTTCTGTAGTATCG
* *
168212 ATCTTCTGGTGAGTAGGAACGAT-CCGCCTTCTGTAGTACCG
1 ATCATCTGGTGAGTAGGAACGATCCCGCCTTCTGTAGTATCG
* **
168253 ATCTTCTGGTGAGTAGGAACGATCCCGCCTTCTACAGTATCG
1 ATCATCTGGTGAGTAGGAACGATCCCGCCTTCTGTAGTATCG
* * * *
168295 ATCATCTCGTGAATAGGAACGATCCCGCCTTCTATAGCATCG
1 ATCATCTGGTGAGTAGGAACGATCCCGCCTTCTGTAGTATCG
* * * *
168337 ATCATCAGGTGAGTAGGAACGATCTCGCCTACGGTAGTAAT-G
1 ATCATCTGGTGAGTAGGAACGATCCCGCCTTCTGTAGT-ATCG
* * * * * * * * *
168379 TTCATCTGGAGTGTAAGACCTATCCCGTCTTCTGTAGCATCT
1 ATCATCTGGTGAGTAGGAACGATCCCGCCTTCTGTAGTATCG
* *
168421 ATCATCAGGAGAGTAGGAACG
1 ATCATCTGGTGAGTAGGAACG
168442 GTCACGTCTT
Statistics
Matches: 189, Mismatches: 38, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
41 42 0.22
42 145 0.77
43 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (42 bp):
ATCATCTGGTGAGTAGGAACGATCCCGCCTTCTGTAGTATCG
Found at i:168468 original size:84 final size:84
Alignment explanation
Indices: 168316--168470 Score: 193
Period size: 84 Copynumber: 1.8 Consensus size: 84
168306 AATAGGAACG
* * * * *
168316 ATCCCGCCTTCTATAGCATCGATCATCAGGTGAGTAGGAACGATCTCGCCTACGGTAGTAATGTT
1 ATCCCGCCTTCTATAGCATCGATCATCAGGAGAGTAGGAACGATCACGCCTACCGTAGTAACGGT
168381 CATCTGGAGTGTAAGACCT
66 CATCTGGAGTGTAAGACCT
* * * * * * **
168400 ATCCCGTCTTCTGTAGCATCTATCATCAGGAGAGTAGGAACGGTCACGTCTTCCGTAGTTGCGGT
1 ATCCCGCCTTCTATAGCATCGATCATCAGGAGAGTAGGAACGATCACGCCTACCGTAGTAACGGT
168465 CATCTG
66 CATCTG
168471 AACAAATACT
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
84 58 1.00
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.28
Consensus pattern (84 bp):
ATCCCGCCTTCTATAGCATCGATCATCAGGAGAGTAGGAACGATCACGCCTACCGTAGTAACGGT
CATCTGGAGTGTAAGACCT
Done.