Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000143.1 Hibiscus syriacus cultivar Beakdansim tig00000258_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: 79360
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:2174 original size:2 final size:2
Alignment explanation
Indices: 2167--2192 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2157 GTTTTATTAT
2167 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
2193 GAATTATTTG
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):
TA
Found at i:6081 original size:35 final size:35
Alignment explanation
Indices: 6037--6108 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
6027 CCACCGAAAG
6037 TGGCCTCCAAATCCACCAAAATTGCCCACCAATTT
1 TGGCCTCCAAATCCACCAAAATTGCCCACCAATTT
* * *
6072 TGGCTTCCAAATCCACTAAAATTGCCTACCAATTT
1 TGGCCTCCAAATCCACCAAAATTGCCCACCAATTT
6107 TG
1 TG
6109 ACTTTTCCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.31, C:0.32, G:0.10, T:0.28
Consensus pattern (35 bp):
TGGCCTCCAAATCCACCAAAATTGCCCACCAATTT
Found at i:8514 original size:37 final size:37
Alignment explanation
Indices: 8473--8554 Score: 103
Period size: 37 Copynumber: 2.2 Consensus size: 37
8463 TTTGTTGTTT
8473 CCACCGAA-AATGGCCTCCAAAATCCACCGAAAATTAC
1 CCACC-AATAATGGCCTCCAAAATCCACCGAAAATTAC
** * *
8510 CCACCAATTTTGGCTTCCAAAATCCACCGAAAATTAT
1 CCACCAATAATGGCCTCCAAAATCCACCGAAAATTAC
*
8547 CCATCAAT
1 CCACCAAT
8555 TTTGACTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
36 2 0.05
37 37 0.95
ACGTcount: A:0.38, C:0.33, G:0.09, T:0.21
Consensus pattern (37 bp):
CCACCAATAATGGCCTCCAAAATCCACCGAAAATTAC
Found at i:8555 original size:37 final size:37
Alignment explanation
Indices: 8483--8558 Score: 125
Period size: 37 Copynumber: 2.1 Consensus size: 37
8473 CCACCGAAAA
8483 TGGCCTCCAAAATCCACCGAAAATTACCCACCAATTT
1 TGGCCTCCAAAATCCACCGAAAATTACCCACCAATTT
* * *
8520 TGGCTTCCAAAATCCACCGAAAATTATCCATCAATTT
1 TGGCCTCCAAAATCCACCGAAAATTACCCACCAATTT
8557 TG
1 TG
8559 ACTTTTCCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.34, C:0.30, G:0.09, T:0.26
Consensus pattern (37 bp):
TGGCCTCCAAAATCCACCGAAAATTACCCACCAATTT
Found at i:11556 original size:13 final size:13
Alignment explanation
Indices: 11538--11564 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
11528 ATAGTTGAAG
11538 AGTCTTCATATGC
1 AGTCTTCATATGC
11551 AGTCTTCATATGC
1 AGTCTTCATATGC
11564 A
1 A
11565 CGTGTGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (13 bp):
AGTCTTCATATGC
Found at i:17607 original size:17 final size:17
Alignment explanation
Indices: 17585--17617 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
17575 ACATTCAAAT
*
17585 AAATAATTAGTTATAAA
1 AAATAATTAGGTATAAA
17602 AAATAATTAGGTATAA
1 AAATAATTAGGTATAA
17618 TTGAGGGGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (17 bp):
AAATAATTAGGTATAAA
Found at i:18879 original size:3 final size:3
Alignment explanation
Indices: 18871--18922 Score: 77
Period size: 3 Copynumber: 17.3 Consensus size: 3
18861 TTCTTCACTT
* * *
18871 TAA TAA TAA TAA TAA TAC TAA TAC TAA TAC TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
18919 TAA T
1 TAA T
18923 TAAGGAGACG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:26480 original size:33 final size:33
Alignment explanation
Indices: 26433--26527 Score: 81
Period size: 32 Copynumber: 2.9 Consensus size: 33
26423 GAAATTGAAA
* * *
26433 TTAACCTGAACCGAAAGA-AACTTGAACCA-AAT
1 TTAACCCGATCCGAAAGACAACTCGAA-CATAAT
26465 TGTAACCCGATCCGAAA-ACAACTCGAACATAAT
1 T-TAACCCGATCCGAAAGACAACTCGAACATAAT
* * * *
26498 TTATCCCGATCCAAAAG-CAACCCGAGCATA
1 TTAACCCGATCCGAAAGACAACTCGAACATA
26528 TTGAAATTGA
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
32 28 0.54
33 24 0.46
ACGTcount: A:0.42, C:0.27, G:0.13, T:0.18
Consensus pattern (33 bp):
TTAACCCGATCCGAAAGACAACTCGAACATAAT
Found at i:29920 original size:37 final size:36
Alignment explanation
Indices: 29879--29955 Score: 91
Period size: 37 Copynumber: 2.1 Consensus size: 36
29869 AGGTGGTAAC
* * *
29879 ATTTATAACATTAGATAGCTGAATAATTCAAAAAATA
1 ATTTATAACATTAAAAACCTGAATAATT-AAAAAATA
* * *
29916 ATTTATAATATTAAAAACCTGAATCATTTAAAAATA
1 ATTTATAACATTAAAAACCTGAATAATTAAAAAATA
29952 ATTT
1 ATTT
29956 TATATACCAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
36 11 0.32
37 23 0.68
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.36
Consensus pattern (36 bp):
ATTTATAACATTAAAAACCTGAATAATTAAAAAATA
Found at i:30045 original size:23 final size:24
Alignment explanation
Indices: 30012--30062 Score: 95
Period size: 23 Copynumber: 2.2 Consensus size: 24
30002 TAATTAATCC
30012 TAATAATAATAAAGATGAAGAGTA
1 TAATAATAATAAAGATGAAGAGTA
30036 TAAT-ATAATAAAGATGAAGAGTA
1 TAATAATAATAAAGATGAAGAGTA
30059 TAAT
1 TAAT
30063 TTAGTATCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 23 0.85
24 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.16, T:0.27
Consensus pattern (24 bp):
TAATAATAATAAAGATGAAGAGTA
Found at i:31481 original size:31 final size:31
Alignment explanation
Indices: 31443--31513 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
31433 TAAAATATTT
31443 AATTTAACCTCT-ACACATTAGATAAAACATC
1 AATTTAACCTCTGA-ACATTAGATAAAACATC
* * * * *
31474 AATTTAACATTTGAACTTTAGATAAAATATT
1 AATTTAACCTCTGAACATTAGATAAAACATC
31505 AATTTAACC
1 AATTTAACC
31514 ATTCAATTCG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
31 32 0.97
32 1 0.03
ACGTcount: A:0.45, C:0.15, G:0.04, T:0.35
Consensus pattern (31 bp):
AATTTAACCTCTGAACATTAGATAAAACATC
Found at i:34405 original size:18 final size:19
Alignment explanation
Indices: 34366--34406 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
34356 ATTTAAAAAT
* *
34366 TAAATTAATATGAATGAGA
1 TAAAATAATATGAATGAAA
34385 TAAAATAATAT-AATGAAA
1 TAAAATAATATGAATGAAA
34403 TAAA
1 TAAA
34407 CAATATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (19 bp):
TAAAATAATATGAATGAAA
Found at i:34413 original size:17 final size:18
Alignment explanation
Indices: 34372--34413 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
34362 AAATTAAATT
* *
34372 AATATGAATGAGATAAAAT
1 AATAT-AATGAAATAAAAC
34391 AATATAATGAAAT-AAAC
1 AATATAATGAAATAAAAC
34408 AATATA
1 AATATA
34414 TAAACATACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 9 0.43
18 7 0.33
19 5 0.24
ACGTcount: A:0.62, C:0.02, G:0.10, T:0.26
Consensus pattern (18 bp):
AATATAATGAAATAAAAC
Found at i:34575 original size:16 final size:16
Alignment explanation
Indices: 34554--34588 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
34544 TAAAAAAAAC
* *
34554 AAAAGGACTAAATTAT
1 AAAAGGACAAAATAAT
34570 AAAAGGACAAAATAAT
1 AAAAGGACAAAATAAT
34586 AAA
1 AAA
34589 GCATAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.66, C:0.06, G:0.11, T:0.17
Consensus pattern (16 bp):
AAAAGGACAAAATAAT
Found at i:35323 original size:121 final size:121
Alignment explanation
Indices: 35109--35351 Score: 477
Period size: 121 Copynumber: 2.0 Consensus size: 121
35099 ACTGAGATTT
35109 ACCCTTTTTGAAAAATAAGCAGAAGGCTCCCCACTGAAACGACGCCGTTTCGCTCAAGGTATAAA
1 ACCCTTTTTGAAAAATAAGCAGAAGGCTCCCCACTGAAACGACGCCGTTTCGCTCAAGGTATAAA
35174 TGGCCCTTTTAACCCCCAAACCGACCATTTGTTTCATTTTACACAAAAGGAGAGAG
66 TGGCCCTTTTAACCCCCAAACCGACCATTTGTTTCATTTTACACAAAAGGAGAGAG
*
35230 ACCCTTTTTGAAAAATACGCAGAAGGCTCCCCACTGAAACGACGCCGTTTCGCTCAAGGTATAAA
1 ACCCTTTTTGAAAAATAAGCAGAAGGCTCCCCACTGAAACGACGCCGTTTCGCTCAAGGTATAAA
35295 TGGCCCTTTTAACCCCCAAACCGACCATTTGTTTCATTTTACACAAAAGGAGAGAG
66 TGGCCCTTTTAACCCCCAAACCGACCATTTGTTTCATTTTACACAAAAGGAGAGAG
35351 A
1 A
35352 GAATGAGAGA
Statistics
Matches: 121, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
121 121 1.00
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (121 bp):
ACCCTTTTTGAAAAATAAGCAGAAGGCTCCCCACTGAAACGACGCCGTTTCGCTCAAGGTATAAA
TGGCCCTTTTAACCCCCAAACCGACCATTTGTTTCATTTTACACAAAAGGAGAGAG
Found at i:36204 original size:3 final size:3
Alignment explanation
Indices: 36196--36264 Score: 77
Period size: 3 Copynumber: 22.7 Consensus size: 3
36186 TTTGTATATC
* * * *
36196 AAT AAT AAT AAT AAA AAT AAT ATT AAT AAT AAT TAT AAT TAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
36244 AATT AA- AAT AAAT AAT AAT AA
1 AA-T AAT AAT -AAT AAT AAT AA
36265 AAAAGACCCG
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
2 2 0.04
3 47 0.85
4 6 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:36767 original size:132 final size:134
Alignment explanation
Indices: 36487--36787 Score: 439
Period size: 132 Copynumber: 2.3 Consensus size: 134
36477 GATGAGAATA
*
36487 TCTAGTTAGGGGATGACACTGCTCATACGTGATGAAGAGTTCTTGGCCATCTTTAGGAAGGGTGA
1 TCTAGTTAGGGGATGACACGGCTCATACGTGATGAAGAGTTCTTGGCCATCTTTAGGAAGGGTGA
** * * *
36552 TAACTCAGTTCCTACGTGATGAGGACGGTTGGTTATCAAGGGTGACACGGCTCTTATGTGATGAG
66 TAACTCAGTTCCTACGTGATGAGGACGGCAGGTTATCAAGGGTGACACGGCTCCTACGTGATGAA
36617 GAGG
131 GAGG
*
36621 TCTAG-TCGGTGGATGACACGGCTCATACGTGATGAAGAGTTC-TGGCCATCTTTAGGAAGGGTG
1 TCTAGTTAGG-GGATGACACGGCTCATACGTGATGAAGAGTTCTTGGCCATCTTTAGGAAGGGTG
*
36684 ATAA-TC-GATTCCTACGTGATGAGGACGGCAGGTTATCAAGGGTGACATGGCTCCTACGTGATG
65 ATAACTCAG-TTCCTACGTGATGAGGACGGCAGGTTATCAAGGGTGACACGGCTCCTACGTGATG
36747 AAGAGG
129 AAGAGG
* * * * *
36753 TCTGGTTAAGGGATGACACGGTTCCTACGCGATGA
1 TCTAGTTAGGGGATGACACGGCTCATACGTGATGA
36788 GGATGGTAGG
Statistics
Matches: 150, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
131 1 0.01
132 83 0.55
133 30 0.20
134 36 0.24
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.27
Consensus pattern (134 bp):
TCTAGTTAGGGGATGACACGGCTCATACGTGATGAAGAGTTCTTGGCCATCTTTAGGAAGGGTGA
TAACTCAGTTCCTACGTGATGAGGACGGCAGGTTATCAAGGGTGACACGGCTCCTACGTGATGAA
GAGG
Found at i:36863 original size:29 final size:29
Alignment explanation
Indices: 36816--36963 Score: 99
Period size: 28 Copynumber: 4.8 Consensus size: 29
36806 AGGGATAATG
*
36816 GTTTCAAGAGAAATC-GACTCAAAGATGAT
1 GTTTCAAAAGAAA-CAGACTCAAAGATGAT
* *
36845 GTTTCAAAAGAAACAGACTTAAAGATAATGGT
1 GTTTCAAAAGAAACAGACTCAAAG---ATGAT
36877 GTTTCAAAAGAAAC-GACTCAAAGATGGCAAATTTT
1 GTTTCAAAAGAAACAGACTCAAAGAT-G---A---T
* *
36912 GTTTCCAAAGAAACAAACTCAAAGATG-T
1 GTTTCAAAAGAAACAGACTCAAAGATGAT
36940 -TTCTCAAAAGAAACA-ATCTCAAAG
1 GTT-TCAAAAGAAACAGA-CTCAAAG
36964 GTTGGTTTTT
Statistics
Matches: 97, Mismatches: 8, Indels: 29
0.72 0.06 0.22
Matches are distributed among these distances:
27 3 0.03
28 22 0.23
29 21 0.22
31 8 0.08
32 18 0.19
35 15 0.15
36 10 0.10
ACGTcount: A:0.45, C:0.15, G:0.16, T:0.24
Consensus pattern (29 bp):
GTTTCAAAAGAAACAGACTCAAAGATGAT
Found at i:37135 original size:29 final size:30
Alignment explanation
Indices: 37062--37364 Score: 180
Period size: 29 Copynumber: 9.8 Consensus size: 30
37052 CTTAAATATT
37062 TTTCAAAA-AGAACAGACTCAAAGA--TTT-
1 TTTCAAAAGA-AACAGACTCAAAGATTTTTG
* *
37089 TCTCAAAAGAAACA-ACTCAAAGATTTTTA
1 TTTCAAAAGAAACAGACTCAAAGATTTTTG
*
37118 TTTCAAAAGAAAC-GACTCAAAGACTTTTG
1 TTTCAAAAGAAACAGACTCAAAGATTTTTG
* * *
37147 TTTCAAGAGAAATAGACTCAAAAATGGGTTTTG
1 TTTCAAAAGAAACAGACTCAAAGAT---TTTTG
**
37180 TTTCAAGGGAAACA-ATCTCAAAGGTATTAAATTTTG
1 TTTCAAAAGAAACAGA-CTCAAA-G-A-T---TTTTG
*
37216 TTTCCAAAGAAACAGACTCAAAGA-TTTT-
1 TTTCAAAAGAAACAGACTCAAAGATTTTTG
* * * * * *
37244 TCTCAAAAGAAACTGTCTTAAGAGAGACAAAATTTTA
1 TTTCAAAAGAAACAGAC-TCA-A-AG----ATTTTTG
*
37281 TTTCAAAAGAAACAAACTC--AGATTTTTG
1 TTTCAAAAGAAACAGACTCAAAGATTTTTG
*
37309 TTTAAAAAGAAACAGACTCAAAGATTTTTTTG
1 TTTCAAAAGAAACAGACTCAAAGA--TTTTTG
*
37341 TTTCAAAAGAAA-TGACTCAAAGAT
1 TTTCAAAAGAAACAGACTCAAAGAT
37365 GACGTTTAAA
Statistics
Matches: 216, Mismatches: 33, Indels: 52
0.72 0.11 0.17
Matches are distributed among these distances:
26 9 0.04
27 11 0.05
28 39 0.18
29 43 0.20
30 13 0.06
31 12 0.06
32 20 0.09
33 23 0.11
34 1 0.00
35 3 0.01
36 28 0.13
37 14 0.06
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.29
Consensus pattern (30 bp):
TTTCAAAAGAAACAGACTCAAAGATTTTTG
Found at i:37317 original size:28 final size:30
Alignment explanation
Indices: 37276--37352 Score: 95
Period size: 28 Copynumber: 2.6 Consensus size: 30
37266 AGAGACAAAA
*
37276 TTTTATTTCAAAAGAAACAAACTC-AGA-T
1 TTTTGTTTCAAAAGAAACAAACTCAAGATT
* *
37304 TTTTGTTTAAAAAGAAACAGACTCAAAGATTT
1 TTTTGTTTCAAAAGAAACAAACTC-AAGA-TT
37336 TTTTGTTTCAAAAGAAA
1 TTTTGTTTCAAAAGAAA
37353 TGACTCAAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 21 0.51
30 3 0.07
32 17 0.41
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.35
Consensus pattern (30 bp):
TTTTGTTTCAAAAGAAACAAACTCAAGATT
Found at i:37358 original size:31 final size:32
Alignment explanation
Indices: 37303--37364 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
37293 CAAACTCAGA
37303 TTTTTGTTTAAAAAGAAACAGACTCAAAGATT
1 TTTTTGTTTAAAAAGAAACAGACTCAAAGATT
* *
37335 TTTTTGTTTCAAAAGAAA-TGACTCAAAGAT
1 TTTTTGTTTAAAAAGAAACAGACTCAAAGAT
37365 GACGTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 11 0.39
32 17 0.61
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (32 bp):
TTTTTGTTTAAAAAGAAACAGACTCAAAGATT
Found at i:37490 original size:32 final size:33
Alignment explanation
Indices: 37439--37501 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
37429 TCGATGTTTC
* *
37439 AAGAGAAACAAACTGAAAGATGTT-TTTGTTCA
1 AAGAAAAACAAACTCAAAGATGTTGTTTGTTCA
* *
37471 AAGAAAAACATACTCAAAGATTTTGTTTGTT
1 AAGAAAAACAAACTCAAAGATGTTGTTTGTT
37502 TTGTTTCAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 20 0.77
33 6 0.23
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.32
Consensus pattern (33 bp):
AAGAAAAACAAACTCAAAGATGTTGTTTGTTCA
Found at i:37603 original size:65 final size:62
Alignment explanation
Indices: 37533--37670 Score: 186
Period size: 62 Copynumber: 2.2 Consensus size: 62
37523 CAAAGATGGT
37533 AAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTCTTAAAAGAAACTGTCTCAAAAGAGACA
1 AAATTTTGTTTCCAAAGAAACAGACTCAAAGA-TTTTC--AAAAGAAACTGTCTCAAAAGAGACA
* * * * **
37598 AAATTTTGTTTCCAAAGAAACATATTCAATGATTTTCAAAAGAAATTGTCTCATGAGAGACA
1 AAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTCAAAAGAAACTGTCTCAAAAGAGACA
*
37660 AAACTTTGTTT
1 AAATTTTGTTT
37671 TTCAGAAAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
62 32 0.48
64 5 0.08
65 29 0.44
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (62 bp):
AAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTCAAAAGAAACTGTCTCAAAAGAGACA
Found at i:37706 original size:100 final size:101
Alignment explanation
Indices: 37592--37774 Score: 271
Period size: 100 Copynumber: 1.8 Consensus size: 101
37582 TGTCTCAAAA
* * * *
37592 GAGACAAAATTTTGTTTCCAAAGAAACATATTCAATGA-TT-TTCAAAAGAAATTGTCTCATGAG
1 GAGACAAAATTTTGTTTCCAAAGAAACAAATTCAAAGATTTCTTCAAAAGAAACTGTCTCAAGAG
*
37655 AGACAAAACTTTGTTTTTCAGAAAATTTTATCTAAGT
66 AAACAAAA-TTTGTTTTTCAGAAAATTTTATCTAAGT
37692 GAGACAAAATTTTGTTTCCAAAGAAACAAATTCAAAGATTTTTCTTCAAAAGAAACTGTCTCAAG
1 GAGACAAAATTTTGTTTCCAAAGAAACAAATTCAAAGA--TTTCTTCAAAAGAAACTGTCTCAAG
*
37757 GGAAACAAAATTTGTTTT
64 AGAAACAAAATTTGTTTT
37775 AATAGAAACG
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
100 36 0.49
103 10 0.14
104 27 0.37
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (101 bp):
GAGACAAAATTTTGTTTCCAAAGAAACAAATTCAAAGATTTCTTCAAAAGAAACTGTCTCAAGAG
AAACAAAATTTGTTTTTCAGAAAATTTTATCTAAGT
Found at i:37803 original size:30 final size:28
Alignment explanation
Indices: 37769--37854 Score: 73
Period size: 30 Copynumber: 2.9 Consensus size: 28
37759 AAACAAAATT
* *
37769 TGTTTTAATAGAAACGATCTCAAAGGTAGG
1 TGTTTTAA-AGAAACGA-CTCAAAGATAGA
* * *
37799 TGTTTCAAGAGAAACTAACTTAAAGATAGA
1 TGTTTTAA-AGAAAC-GACTCAAAGATAGA
*
37829 TGTTTCTAAAGAAAGGACTCAAAGAT
1 TGTTT-TAAAGAAACGACTCAAAGAT
37855 TTTTTTCACG
Statistics
Matches: 44, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
29 9 0.20
30 32 0.73
31 3 0.07
ACGTcount: A:0.42, C:0.10, G:0.20, T:0.28
Consensus pattern (28 bp):
TGTTTTAAAGAAACGACTCAAAGATAGA
Found at i:38196 original size:36 final size:35
Alignment explanation
Indices: 38156--38265 Score: 159
Period size: 36 Copynumber: 3.1 Consensus size: 35
38146 ATAATTTGGA
*
38156 AAATTGTCTCAAGTGAGACAACATTTGTTTTTAGAG
1 AAATTGTCTCAAGCGAGACAA-ATTTGTTTTTAGAG
* *
38192 AAATTGTCTCAAACGAGACAAAAATTGTTTTTAGAG
1 AAATTGTCTCAAGCGAGAC-AAATTTGTTTTTAGAG
38228 AAATTGTCTCAAGCGAGACAAAGTTTGTTTTT-GAG
1 AAATTGTCTCAAGCGAGACAAA-TTTGTTTTTAGAG
38263 AAA
1 AAA
38266 ACAATATCAA
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
35 9 0.13
36 56 0.84
37 2 0.03
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (35 bp):
AAATTGTCTCAAGCGAGACAAATTTGTTTTTAGAG
Found at i:39001 original size:4 final size:4
Alignment explanation
Indices: 38992--39037 Score: 92
Period size: 4 Copynumber: 11.5 Consensus size: 4
38982 TAAATGTTTG
38992 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
39038 TGATATATGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:40376 original size:12 final size:12
Alignment explanation
Indices: 40355--40458 Score: 52
Period size: 12 Copynumber: 8.0 Consensus size: 12
40345 CTTTGTCCTC
40355 TTTTTGTTCTTTG
1 TTTTT-TTCTTTG
40368 TTTTTTTCTTT-
1 TTTTTTTCTTTG
40379 TTTTATTTGCTTT-
1 TTTT-TTT-CTTTG
* * *
40392 TTATTTGCTTTT
1 TTTTTTTCTTTG
*
40404 TTCTCTTTGCTCTTTA
1 TT-T-TTT--TCTTTG
40420 TTTTTCTT-TGTTG
1 TTTTT-TTCT-TTG
40433 TTTTTATTTCTTTG
1 -TTTT-TTTCTTTG
40447 TTTTTTTCTTTG
1 TTTTTTTCTTTG
40459 CTCTTTGCTT
Statistics
Matches: 73, Mismatches: 6, Indels: 25
0.70 0.06 0.24
Matches are distributed among these distances:
11 8 0.11
12 22 0.30
13 19 0.26
14 14 0.19
15 4 0.05
16 6 0.08
ACGTcount: A:0.04, C:0.11, G:0.09, T:0.77
Consensus pattern (12 bp):
TTTTTTTCTTTG
Found at i:40379 original size:21 final size:20
Alignment explanation
Indices: 40353--40393 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
40343 CTCTTTGTCC
* *
40353 TCTTTTTGTTCTTTGTTTTTT
1 TCTTTTT-TTATTTGCTTTTT
40374 TCTTTTTTTATTTGCTTTTT
1 TCTTTTTTTATTTGCTTTTT
40394 ATTTGCTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.02, C:0.10, G:0.07, T:0.80
Consensus pattern (20 bp):
TCTTTTTTTATTTGCTTTTT
Found at i:40392 original size:11 final size:11
Alignment explanation
Indices: 40378--40404 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
40368 TTTTTTTCTT
40378 TTTTTATTTGC
1 TTTTTATTTGC
40389 TTTTTATTTGC
1 TTTTTATTTGC
40400 TTTTT
1 TTTTT
40405 TCTCTTTGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.78
Consensus pattern (11 bp):
TTTTTATTTGC
Found at i:40429 original size:17 final size:16
Alignment explanation
Indices: 40399--40464 Score: 59
Period size: 17 Copynumber: 4.2 Consensus size: 16
40389 TTTTTATTTG
*
40399 CTTTTTTCTCTTTGCT
1 CTTTTTTTTCTTTGCT
*
40415 CTTTATTTTTCTTTGTT
1 CTTT-TTTTTCTTTGCT
*
40432 GTTTTTATTTCTTTG--
1 CTTTTT-TTTCTTTGCT
40447 --TTTTTTTCTTTGCT
1 CTTTTTTTTCTTTGCT
40461 CTTT
1 CTTT
40465 GCTTTTTTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
12 8 0.20
13 4 0.10
16 8 0.20
17 21 0.51
ACGTcount: A:0.03, C:0.15, G:0.08, T:0.74
Consensus pattern (16 bp):
CTTTTTTTTCTTTGCT
Found at i:40488 original size:46 final size:49
Alignment explanation
Indices: 40395--40498 Score: 119
Period size: 46 Copynumber: 2.2 Consensus size: 49
40385 TTGCTTTTTA
* *
40395 TTTGCTTTTTTCTCTTTGCTCTTTATTTTTCTTTGTTGTTTTTA-TT-TC
1 TTTG-TTTTTTCTCTTTGCTCTTTATTTTTCTTCGTTGTTTTAATTTCTC
*
40443 TTTGTTTTTT-TCTTTGCTCTTTGCTTTTT-TTCGTT-TCTTTAATTTCTC
1 TTTGTTTTTTCTCTTTGCTCTTT-ATTTTTCTTCGTTGT-TTTAATTTCTC
40491 TTTGTTTT
1 TTTGTTTT
40499 GATTTGATCT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
45 1 0.02
46 21 0.43
47 13 0.27
48 14 0.29
ACGTcount: A:0.04, C:0.14, G:0.09, T:0.73
Consensus pattern (49 bp):
TTTGTTTTTTCTCTTTGCTCTTTATTTTTCTTCGTTGTTTTAATTTCTC
Found at i:42339 original size:205 final size:204
Alignment explanation
Indices: 41974--42353 Score: 476
Period size: 205 Copynumber: 1.9 Consensus size: 204
41964 CCTTGAAAAA
* * *
41974 TGATGCCCCTCAATGCTCTATAACCTAACTCGGTTAATTCCCCAGCAGTGGTGAAATCGGTGCAC
1 TGATGCCCCTCAATGCTCTATAACCTAACTCGGTTAATGCCCCAGCAATGGTGAAATCGGTACAC
* * * * * * *
42039 CGCTTCTTGATAACTAGCGATGAAATGATTGTAGATGAGAGTCTACTATTAGATGACTCTTTGGC
66 CGCTCCTTGATAACTAGCGATGAAATAATTGTAGA-GAAAGTCTAATATTAGATGACTCCTCGGA
* *
42104 TCAATGGATCAACGTTTCAGTCTCGAATGTTGTAGATCTTCGAGCTGCTTTATCTCGTATCTTCG
130 TCAATGGATCAACGTTTCAGTCTCGAATGTTGCACATCTTCGAGCTGCTTTATCTCGTATCTTCG
42169 TATTTGGAAC
195 TATTTGGAAC
* * * * * *
42179 TGATGCCCCTCAATGCTCTGTAACCTAACTTGGTTAATGCCCCTGTAATGGTGAAGTCGGTACAT
1 TGATGCCCCTCAATGCTCTATAACCTAACTCGGTTAATGCCCCAGCAATGGTGAAATCGGTACAC
* * * * *
42244 CGCTCCTTGATAACTAGCTATGAAATAATTGTAG-GCAAAGCTTTAATGTTGGATTACTCCTCGG
66 CGCTCCTTGATAACTAGCGATGAAATAATTGTAGAG-AAAG-TCTAATATTAGATGACTCCTCGG
* * *
42308 ATCAATGGATTATC-TTTCTAGTCTTGAATGTTGCACATCTTCGAGC
129 ATCAATGGATCAACGTTTC-AGTCTCGAATGTTGCACATCTTCGAGC
42354 AAGTCTCATT
Statistics
Matches: 146, Mismatches: 26, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
203 1 0.01
204 7 0.05
205 138 0.95
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (204 bp):
TGATGCCCCTCAATGCTCTATAACCTAACTCGGTTAATGCCCCAGCAATGGTGAAATCGGTACAC
CGCTCCTTGATAACTAGCGATGAAATAATTGTAGAGAAAGTCTAATATTAGATGACTCCTCGGAT
CAATGGATCAACGTTTCAGTCTCGAATGTTGCACATCTTCGAGCTGCTTTATCTCGTATCTTCGT
ATTTGGAAC
Found at i:44323 original size:18 final size:19
Alignment explanation
Indices: 44284--44324 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
44274 ATTTAAAAAT
* *
44284 TAAATTAATATGAATGAGA
1 TAAAATAATATGAATGAAA
44303 TAAAATAATAT-AATGAAA
1 TAAAATAATATGAATGAAA
44321 TAAA
1 TAAA
44325 CAATATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (19 bp):
TAAAATAATATGAATGAAA
Found at i:44331 original size:17 final size:18
Alignment explanation
Indices: 44290--44331 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
44280 AAATTAAATT
* *
44290 AATATGAATGAGATAAAAT
1 AATAT-AATGAAATAAAAC
44309 AATATAATGAAAT-AAAC
1 AATATAATGAAATAAAAC
44326 AATATA
1 AATATA
44332 TAAACATACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 9 0.43
18 7 0.33
19 5 0.24
ACGTcount: A:0.62, C:0.02, G:0.10, T:0.26
Consensus pattern (18 bp):
AATATAATGAAATAAAAC
Found at i:44487 original size:16 final size:16
Alignment explanation
Indices: 44466--44500 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
44456 TAAAAAAAAC
* *
44466 AAAAGGACTAAATTAT
1 AAAAGGACAAAATAAT
44482 AAAAGGACAAAATAAT
1 AAAAGGACAAAATAAT
44498 AAA
1 AAA
44501 GCATAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.66, C:0.06, G:0.11, T:0.17
Consensus pattern (16 bp):
AAAAGGACAAAATAAT
Found at i:47241 original size:20 final size:22
Alignment explanation
Indices: 47216--47273 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
47206 TTCCCATTGA
47216 AGTGCATCGATGCATTC-TT-C
1 AGTGCATCGATGCATTCTTTAC
47236 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTCTTT-AC
47259 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
47274 CTACCATGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
23 2 0.06
24 13 0.38
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTTAC
Found at i:48607 original size:3 final size:3
Alignment explanation
Indices: 48593--48644 Score: 61
Period size: 3 Copynumber: 17.0 Consensus size: 3
48583 TCAATAAAAG
* *
48593 TAA TAG TAA TAA TAA TTA TAA TAA TAA TAA TAA TTAA -AA TAAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA T-AA TAA
48639 TAA TAA
1 TAA TAA
48645 AAAGACCCGG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
2 2 0.05
3 34 0.81
4 6 0.14
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:51754 original size:24 final size:24
Alignment explanation
Indices: 51717--51768 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
51707 AGAAAACTTC
* *
51717 AATGACAATCGTAAGGACAATGAT
1 AATGACAATCGTAAAGACAATGAA
*
51741 AATGACAA-CGGTAAAGATAATGAA
1 AATGACAATC-GTAAAGACAATGAA
51765 AATG
1 AATG
51769 GTTATATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.50, C:0.10, G:0.21, T:0.19
Consensus pattern (24 bp):
AATGACAATCGTAAAGACAATGAA
Found at i:54346 original size:57 final size:57
Alignment explanation
Indices: 54252--54370 Score: 163
Period size: 57 Copynumber: 2.1 Consensus size: 57
54242 AGACATGACA
*
54252 GGGATATAAATCCCATACAGAAATAGGACGGGATATAATCCCATAT-AGAAA-CAGGAC
1 GGGATATAAATCCCATACAGAAACAGGACGGGATATAATCCCAT-TCA-AAATCAGGAC
* *
54309 GGGATAT-AATCCCATATAGAAACAGGACGGGGATATAATCTCATTCAAAATCAGGAC
1 GGGATATAAATCCCATACAGAAACAGGAC-GGGATATAATCCCATTCAAAATCAGGAC
54366 GGGAT
1 GGGAT
54371 GTTGCCCTCC
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
56 23 0.41
57 33 0.59
ACGTcount: A:0.41, C:0.17, G:0.23, T:0.19
Consensus pattern (57 bp):
GGGATATAAATCCCATACAGAAACAGGACGGGATATAATCCCATTCAAAATCAGGAC
Found at i:54363 original size:29 final size:28
Alignment explanation
Indices: 54252--54370 Score: 161
Period size: 28 Copynumber: 4.2 Consensus size: 28
54242 AGACATGACA
* *
54252 GGGATATAAATCCCATACAGAAATAGGAC
1 GGGATAT-AATCCCATATAGAAACAGGAC
54281 GGGATATAATCCCATATAGAAACAGGAC
1 GGGATATAATCCCATATAGAAACAGGAC
54309 GGGATATAATCCCATATAGAAACAGGAC
1 GGGATATAATCCCATATAGAAACAGGAC
*
54337 GGGGATATAATCTCAT-TCA-AAATCAGGAC
1 -GGGATATAATCCCATAT-AGAAA-CAGGAC
54366 GGGAT
1 GGGAT
54371 GTTGCCCTCC
Statistics
Matches: 84, Mismatches: 3, Indels: 7
0.89 0.03 0.07
Matches are distributed among these distances:
28 56 0.67
29 28 0.33
ACGTcount: A:0.41, C:0.17, G:0.23, T:0.19
Consensus pattern (28 bp):
GGGATATAATCCCATATAGAAACAGGAC
Found at i:54436 original size:71 final size:71
Alignment explanation
Indices: 54317--54503 Score: 198
Period size: 71 Copynumber: 2.6 Consensus size: 71
54307 ACGGGATATA
** * * *
54317 ATCCCATATAGAAACAGGACGGGGATATAATCTCATTCAAAATCAGGAC-GGGATGTTGCCCTCC
1 ATCCCATGCAGAAACAGGAC-GGGATATAATCTCATGCAAAATCAGGACAGAGATGTTACCC-CC
54381 -ATAAAGG
64 TATAAAGG
* * *
54388 ATCCCATGCAGAAACAGGACGGGAATATAATCTCATGCATAATTAGGACATAGATGTTACCCCCT
1 ATCCCATGCAGAAACAGGACGGG-ATATAATCTCATGCAAAATCAGGACAGAGATGTTACCCCCT
* *
54453 GTAAGGG
65 ATAAAGG
* * ** *
54460 ATCCCATGCAAAAACATGACAAGATATAATCCCATGCAAAATCA
1 ATCCCATGCAGAAACAGGACGGGATATAATCTCATGCAAAATCA
54504 ACCATGCAGA
Statistics
Matches: 96, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
70 3 0.03
71 60 0.62
72 33 0.34
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (71 bp):
ATCCCATGCAGAAACAGGACGGGATATAATCTCATGCAAAATCAGGACAGAGATGTTACCCCCTA
TAAAGG
Found at i:54510 original size:42 final size:42
Alignment explanation
Indices: 54463--54543 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
54453 GTAAGGGATC
*
54463 CCATGCAAAAACATGACAAGATATAATCCCATGCAAAATCAA
1 CCATGCAAAAACATGACAAGATATAATCACATGCAAAATCAA
* *
54505 CCATGCAGAAACATGACGAGATATAATCACATGCAAAAT
1 CCATGCAAAAACATGACAAGATATAATCACATGCAAAAT
54544 TAGGACGGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.48, C:0.22, G:0.12, T:0.17
Consensus pattern (42 bp):
CCATGCAAAAACATGACAAGATATAATCACATGCAAAATCAA
Found at i:54708 original size:41 final size:40
Alignment explanation
Indices: 54663--54790 Score: 148
Period size: 40 Copynumber: 3.1 Consensus size: 40
54653 ATAGCAGCAT
* *
54663 TTTAGCAGCATTTTTAGAACAAACGCCGCTAAAGACTATAC
1 TTTAGCAGCGTTTTTAG-ACAAACGCCGCTAAAGACTGTAC
** * *
54704 TTTAGTGGCGTTTTTACACAAACGCTGCTAAAGACTGTAC
1 TTTAGCAGCGTTTTTAGACAAACGCCGCTAAAGACTGTAC
* * *
54744 TTTAGCAACGTTTTTAGACAAAATGCCGCTAAATACTCGTAC
1 TTTAGCAGCGTTTTTAGAC-AAACGCCGCTAAAGACT-GTAC
54786 TTTAG
1 TTTAG
54791 TGGTGTTTTT
Statistics
Matches: 72, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
40 36 0.50
41 27 0.38
42 9 0.12
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.31
Consensus pattern (40 bp):
TTTAGCAGCGTTTTTAGACAAACGCCGCTAAAGACTGTAC
Found at i:55803 original size:43 final size:43
Alignment explanation
Indices: 55735--56148 Score: 408
Period size: 43 Copynumber: 9.7 Consensus size: 43
55725 ATGGTAATTA
** *
55735 GCGGCGTTTGTATTAAAAAACGCCGCTATAGATTTGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTT
* * * *
55778 GTGGCGTTTATATCCAAAAATGCCGCTATAGATCTGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTT
* * *
55821 GCGGCATTTGTATCCAAAAACGCCGCAATAGATATGAACTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTT
* *
55864 ACGGCGTTTGTATCCTAAAACGCCGCTATAGATATGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTT
* * * * *
55907 GCGGCGTTTGTAT-CAAAAATGCCACTATAGATCTTACCTATT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTT
* * *
55949 ACGACGTTTGTATCCAAAAACGCCGCTATTGATATGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTT
* * * *
55992 GCGGCGTTTATATCCAAAAATGCCGTTATAGATATGATCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTT
* *** * *
56035 GCGGCATTTGTGAAATAAAAACGCCGCTATAGATCTCAACC---T
1 GCGGCGTTTGT-ATCCAAAAACGCCGCTATAGATAT-GACCTTTT
** * *
56077 GCGGTATTTGT-TTCAAAAACGCCGCTATAGA-ACTTGACTTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATA--TGACCTTTT
* * *
56120 GCGGCGTTTTTATTTCACAAACGCCGCTA
1 GCGGCGTTTGTA-TCCAAAAACGCCGCTA
56149 ACATTAGCGA
Statistics
Matches: 300, Mismatches: 61, Indels: 18
0.79 0.16 0.05
Matches are distributed among these distances:
40 19 0.06
41 1 0.00
42 45 0.15
43 200 0.67
44 18 0.06
45 17 0.06
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (43 bp):
GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTT
Found at i:55984 original size:128 final size:129
Alignment explanation
Indices: 55736--56045 Score: 424
Period size: 128 Copynumber: 2.4 Consensus size: 129
55726 TGGTAATTAG
** * * *
55736 CGGCGTTTGTATTAAAAAACGCCGCTATAGATTTGACCTTTTGTGGCGTTTATATCCAAAAATGC
1 CGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTATCCAAAAATGC
* * * *
55801 CGCTATAGATCTGACCTTTTGCGGCATTTGTATCCAAAAACGCCGCAATAGATATGAACTTTTA
66 CACTATAGATCTGACCTATTACGACATTTGTATCCAAAAACGCCGCAATAGATATGAACTTTTA
*
55865 CGGCGTTTGTATCCTAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTAT-CAAAAATGC
1 CGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTATCCAAAAATGC
* * * * * *
55929 CACTATAGATCTTACCTATTACGACGTTTGTATCCAAAAACGCCGCTATTGATATGACCTTTTG
66 CACTATAGATCTGACCTATTACGACATTTGTATCCAAAAACGCCGCAATAGATATGAACTTTTA
* * * * *
55993 CGGCGTTTATATCCAAAAATGCCGTTATAGATATGATCTTTTGCGGCATTTGT
1 CGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGT
56046 GAAATAAAAA
Statistics
Matches: 159, Mismatches: 22, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
128 110 0.69
129 49 0.31
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.34
Consensus pattern (129 bp):
CGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTATCCAAAAATGC
CACTATAGATCTGACCTATTACGACATTTGTATCCAAAAACGCCGCAATAGATATGAACTTTTA
Found at i:56087 original size:128 final size:126
Alignment explanation
Indices: 55735--56148 Score: 422
Period size: 128 Copynumber: 3.2 Consensus size: 126
55725 ATGGTAATTA
* ** * * * *
55735 GCGGCGTTTGTATTAAAAAACGCCGCTATAGATTTGACCTTTTGTGGCGTTTATATCCAAAAATG
1 GCGGCGTTTATATCCAAAAACGCCGCTATAGATATGACCTTTTGCGGCATTTGTAT-CAAAAATG
* * *
55800 CCGCTATAGATCTGACCTTTTGCGGCATTTGTATCCAAAAACGCCGCAATAGATATGAACTTTT
65 CCGCTATAGATCTAACC--TTGCGGCATTTGTATCCAAAAACGCCGCTATAGATATGACCTTTT
* * * *
55864 ACGGCGTTTGTATCCTAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTATCAAAAATGC
1 GCGGCGTTTATATCCAAAAACGCCGCTATAGATATGACCTTTTGCGGCATTTGTATCAAAAATGC
* * * * * *
55929 CACTATAGATCTTACCTATTACGACGTTTGTATCCAAAAACGCCGCTATTGATATGACCTTTT
66 CGCTATAGATCTAACC--TTGCGGCATTTGTATCCAAAAACGCCGCTATAGATATGACCTTTT
* * *
55992 GCGGCGTTTATATCCAAAAATGCCGTTATAGATATGATCTTTTGCGGCATTTGTGAAAT-AAAAA
1 GCGGCGTTTATATCCAAAAACGCCGCTATAGATATGACCTTTTGCGGCATTTGT---ATCAAAAA
* * * *
56056 CGCCGCTATAGATCTCAACC-TGCGGTATTTGT-TTCAAAAACGCCGCTATAGA-ACTTGACTTT
63 TGCCGCTATAGATCT-AACCTTGCGGCATTTGTATCCAAAAACGCCGCTATAGATA--TGACCTT
56118 TT
125 TT
* * *
56120 GCGGCGTTTTTATTTCACAAACGCCGCTA
1 GCGGCGTTTATA-TCCAAAAACGCCGCTA
56149 ACATTAGCGA
Statistics
Matches: 240, Mismatches: 38, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
126 1 0.00
127 18 0.08
128 137 0.57
129 61 0.25
130 18 0.08
131 5 0.02
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (126 bp):
GCGGCGTTTATATCCAAAAACGCCGCTATAGATATGACCTTTTGCGGCATTTGTATCAAAAATGC
CGCTATAGATCTAACCTTGCGGCATTTGTATCCAAAAACGCCGCTATAGATATGACCTTTT
Found at i:66093 original size:6 final size:6
Alignment explanation
Indices: 66082--66107 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
66072 AAAAGAATCA
66082 TTGATT TTGATT TTGATT TTGATT TT
1 TTGATT TTGATT TTGATT TTGATT TT
66108 TCATCCATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.69
Consensus pattern (6 bp):
TTGATT
Found at i:68762 original size:19 final size:19
Alignment explanation
Indices: 68738--68781 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
68728 AACATATTTT
68738 TGTAAAAAACTTGTAGTGG
1 TGTAAAAAACTTGTAGTGG
*
68757 TGTAAATAACTTGTAGTGG
1 TGTAAAAAACTTGTAGTGG
*
68776 AGTAAA
1 TGTAAA
68782 CATCCAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.32
Consensus pattern (19 bp):
TGTAAAAAACTTGTAGTGG
Found at i:74406 original size:29 final size:29
Alignment explanation
Indices: 74373--74447 Score: 114
Period size: 29 Copynumber: 2.6 Consensus size: 29
74363 TTTCTGATTC
* ** *
74373 TGCATGAGATTAATTCTTTGTCCTTATTT
1 TGCATGGGATTAATTCCATGTCCTAATTT
74402 TGCATGGGATTAATTCCATGTCCTAATTT
1 TGCATGGGATTAATTCCATGTCCTAATTT
74431 TGCATGGGATTAATTCC
1 TGCATGGGATTAATTCC
74448 CCGTCATGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.23, C:0.16, G:0.17, T:0.44
Consensus pattern (29 bp):
TGCATGGGATTAATTCCATGTCCTAATTT
Found at i:74460 original size:29 final size:29
Alignment explanation
Indices: 74373--74494 Score: 104
Period size: 29 Copynumber: 4.2 Consensus size: 29
74363 TTTCTGATTC
* ***
74373 TGCATGAGATTAATTCTTTGTCCT-TATTT
1 TGCATGGGATTAATTCCCCGTCCTGT-TTT
** **
74402 TGCATGGGATTAATTCCATGTCCTAATTT
1 TGCATGGGATTAATTCCCCGTCCTGTTTT
*
74431 TGCATGGGATTAATTCCCCGTCATGTTTT
1 TGCATGGGATTAATTCCCCGTCCTGTTTT
* * *
74460 TGCATAGGA-TCATATCCCCGTCCTGTTTC
1 TGCATGGGATTAAT-TCCCCGTCCTGTTTT
74489 TGCATG
1 TGCATG
74495 AGATCATATC
Statistics
Matches: 77, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
28 3 0.04
29 74 0.96
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (29 bp):
TGCATGGGATTAATTCCCCGTCCTGTTTT
Found at i:74499 original size:29 final size:29
Alignment explanation
Indices: 74445--74519 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
74435 TGGGATTAAT
* *
74445 TCCCCGTCATGTTTTTGCATAGGATCATA
1 TCCCCGTCCTGTTTCTGCATAGGATCATA
74474 TCCCCGTCCTGTTTCTGCAT-GAGATCATA
1 TCCCCGTCCTGTTTCTGCATAG-GATCATA
* * *
74503 TCTCTGTCCTATTTCTG
1 TCCCCGTCCTGTTTCTG
74520 TTTGGGATCC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
28 1 0.03
29 39 0.98
ACGTcount: A:0.16, C:0.28, G:0.16, T:0.40
Consensus pattern (29 bp):
TCCCCGTCCTGTTTCTGCATAGGATCATA
Found at i:74528 original size:29 final size:29
Alignment explanation
Indices: 74421--74528 Score: 85
Period size: 29 Copynumber: 3.7 Consensus size: 29
74411 TTAATTCCAT
*
74421 GTCCTAATTT-TGCATGGGATTA-ATTCCCC
1 GTCCT-ATTTCTGCATGGGATCATA-TCCCC
* * * *
74450 GTCATGTTTTTGCATAGGATCATATCCCC
1 GTCCTATTTCTGCATGGGATCATATCCCC
* * * *
74479 GTCCTGTTTCTGCATGAGATCATATCTCT
1 GTCCTATTTCTGCATGGGATCATATCCCC
**
74508 GTCCTATTTCTGTTTGGGATC
1 GTCCTATTTCTGCATGGGATC
74529 CTCTTCGGAT
Statistics
Matches: 63, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
28 3 0.05
29 59 0.94
30 1 0.02
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.41
Consensus pattern (29 bp):
GTCCTATTTCTGCATGGGATCATATCCCC
Found at i:76885 original size:19 final size:19
Alignment explanation
Indices: 76846--76890 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
76836 TTATAATTAA
*
76846 TTTATATGAATATTTGGAT
1 TTTATATGAATATTTGCAT
* *
76865 TTTATATGATTATTTTCAT
1 TTTATATGAATATTTGCAT
76884 TTCTATA
1 TT-TATA
76891 ATTTTGATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.29, C:0.04, G:0.09, T:0.58
Consensus pattern (19 bp):
TTTATATGAATATTTGCAT
Found at i:78487 original size:20 final size:20
Alignment explanation
Indices: 78462--78500 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
78452 TCTGATGACC
*
78462 TTGGTAAGGAGATCTGACTT
1 TTGGTAAGGAGAACTGACTT
78482 TTGGTAAGGAGAACTGACT
1 TTGGTAAGGAGAACTGACT
78501 GTCTTGCTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.31, T:0.31
Consensus pattern (20 bp):
TTGGTAAGGAGAACTGACTT
Found at i:79032 original size:23 final size:23
Alignment explanation
Indices: 78998--79088 Score: 94
Period size: 23 Copynumber: 4.0 Consensus size: 23
78988 CACCACAGCT
* *
78998 CGTATAAATGCATCAAAGTGCCA
1 CGTAGAAATGCACCAAAGTGCCA
* * *
79021 CGTAGAATTGCACCATAGTGCCG
1 CGTAGAAATGCACCAAAGTGCCA
** *
79044 CGTAGAAATGCACTGAAGT-CCG
1 CGTAGAAATGCACCAAAGTGCCA
*
79066 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCAAAGTGCCA
79089 TATAAGATTG
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
22 21 0.38
23 35 0.62
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCAAAGTGCCA
Done.