Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000941.1 Hibiscus syriacus cultivar Beakdansim tig00001880_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: 75108
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:1136 original size:42 final size:42
Alignment explanation
Indices: 1080--1179 Score: 121
Period size: 42 Copynumber: 2.4 Consensus size: 42
1070 CGCATACTAT
* *
1080 CAACAAAGATTAGTGACAAAAACAATTATCATCACAAA-TAGC
1 CAACTAAGACTAGTGACAAAAACAATTATCATCACAAATTA-C
* * * *
1122 CAACTAAGACTAGTGACAAAAATAATTATCGTTAGAAATTAC
1 CAACTAAGACTAGTGACAAAAACAATTATCATCACAAATTAC
*
1164 CAACTAAAACTAGTGA
1 CAACTAAGACTAGTGA
1180 AAATATTTTC
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
42 48 0.96
43 2 0.04
ACGTcount: A:0.50, C:0.17, G:0.11, T:0.22
Consensus pattern (42 bp):
CAACTAAGACTAGTGACAAAAACAATTATCATCACAAATTAC
Found at i:4725 original size:19 final size:18
Alignment explanation
Indices: 4677--4725 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
4667 TTCCTATTAT
*
4677 TTTAATATTTAAATAATG
1 TTTAATATTTAAATAATC
* *
4695 TTTCACATTTAAATAGATC
1 TTTAATATTTAAATA-ATC
4714 TTTAATATTTAA
1 TTTAATATTTAA
4726 TGTTATTTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 13 0.52
19 12 0.48
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (18 bp):
TTTAATATTTAAATAATC
Found at i:6181 original size:2 final size:2
Alignment explanation
Indices: 6174--6211 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
6164 CAATAATGCG
6174 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
6212 TCAAATTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8489 original size:2 final size:2
Alignment explanation
Indices: 8484--8510 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
8474 TATATGATTA
8484 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
8511 CTTTAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14359 original size:2 final size:2
Alignment explanation
Indices: 14352--14383 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
14342 TAAATATTTA
14352 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
14384 TAAATGATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16040 original size:17 final size:17
Alignment explanation
Indices: 16008--16041 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
15998 TCTATTTGAA
* *
16008 AATTTTGACTTTTAATT
1 AATTTTGAATTGTAATT
16025 AATTTTGAATTGTAATT
1 AATTTTGAATTGTAATT
16042 TTATAAATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.03, G:0.09, T:0.56
Consensus pattern (17 bp):
AATTTTGAATTGTAATT
Found at i:17439 original size:35 final size:35
Alignment explanation
Indices: 17393--17465 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
17383 ACAAATTGGG
17393 AGTTGGGCAAAGCAAATGAATGCATTGATGGAGGT
1 AGTTGGGCAAAGCAAATGAATGCATTGATGGAGGT
17428 AGTTGGGCAAAGCAAATGAATGCATTGATGGAGGT
1 AGTTGGGCAAAGCAAATGAATGCATTGATGGAGGT
17463 AGT
1 AGT
17466 GACCCTATGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.34, C:0.08, G:0.34, T:0.23
Consensus pattern (35 bp):
AGTTGGGCAAAGCAAATGAATGCATTGATGGAGGT
Found at i:20416 original size:31 final size:31
Alignment explanation
Indices: 20380--20459 Score: 151
Period size: 31 Copynumber: 2.6 Consensus size: 31
20370 AGTCAAAAAA
*
20380 TAGTTTAGGCACTTATTTGGAGAAAACAATG
1 TAGTTTAGACACTTATTTGGAGAAAACAATG
20411 TAGTTTAGACACTTATTTGGAGAAAACAATG
1 TAGTTTAGACACTTATTTGGAGAAAACAATG
20442 TAGTTTAGACACTTATTT
1 TAGTTTAGACACTTATTT
20460 TGGTATTAAG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.36
Consensus pattern (31 bp):
TAGTTTAGACACTTATTTGGAGAAAACAATG
Found at i:26361 original size:20 final size:20
Alignment explanation
Indices: 26336--26426 Score: 72
Period size: 20 Copynumber: 5.0 Consensus size: 20
26326 TAAATTAAAT
*
26336 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
*
26356 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTA
* *
26376 ATT--CT---ATTAG--TT-
1 ATTAGATAGAATCAGTTTTA
* *
26388 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCAGTTTTA
26408 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
26427 TTATTCTATT
Statistics
Matches: 54, Mismatches: 9, Indels: 16
0.68 0.11 0.20
Matches are distributed among these distances:
12 3 0.06
13 2 0.04
14 1 0.02
15 4 0.07
17 3 0.06
18 1 0.02
19 2 0.04
20 38 0.70
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:26413 original size:52 final size:52
Alignment explanation
Indices: 26335--26482 Score: 271
Period size: 53 Copynumber: 2.8 Consensus size: 52
26325 CTAAATTAAA
*
26335 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
26387 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAG-TTTTTATTCTATTAGT
26440 TATTAGATAGGATCATTTTTAATTAGATAGAATCA-TTTTTATT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATT
26483 ATGTTGCTAA
Statistics
Matches: 94, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
51 8 0.09
52 35 0.37
53 51 0.54
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.48
Consensus pattern (52 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
Found at i:26466 original size:20 final size:20
Alignment explanation
Indices: 26441--26480 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
26431 TCTATTAGTT
*
26441 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCATTTTTA
26461 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
26481 TTATGTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:31070 original size:20 final size:20
Alignment explanation
Indices: 31045--31135 Score: 72
Period size: 20 Copynumber: 5.0 Consensus size: 20
31035 TAAATTAAAT
*
31045 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
*
31065 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTA
* *
31085 ATT--CT---ATTAG--TT-
1 ATTAGATAGAATCAGTTTTA
* *
31097 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCAGTTTTA
31117 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
31136 TTATTCTATT
Statistics
Matches: 54, Mismatches: 9, Indels: 16
0.68 0.11 0.20
Matches are distributed among these distances:
12 3 0.06
13 2 0.04
14 1 0.02
15 4 0.07
17 3 0.06
18 1 0.02
19 2 0.04
20 38 0.70
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:31122 original size:52 final size:52
Alignment explanation
Indices: 31044--31191 Score: 271
Period size: 53 Copynumber: 2.8 Consensus size: 52
31034 CTAAATTAAA
*
31044 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
31096 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAG-TTTTTATTCTATTAGT
31149 TATTAGATAGGATCATTTTTAATTAGATAGAATCA-TTTTTATT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATT
31192 ATGTTGCTAA
Statistics
Matches: 94, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
51 8 0.09
52 35 0.37
53 51 0.54
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.48
Consensus pattern (52 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
Found at i:31175 original size:20 final size:20
Alignment explanation
Indices: 31150--31189 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
31140 TCTATTAGTT
*
31150 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCATTTTTA
31170 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
31190 TTATGTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:34317 original size:3 final size:3
Alignment explanation
Indices: 34309--34375 Score: 52
Period size: 3 Copynumber: 23.0 Consensus size: 3
34299 TTAATTACTA
* *
34309 TAT TAT TA- TAT TAT TA- TAT TAT AAT TATT TAT TA- TAT T-T AAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
* *
34351 AAT TAA TAT TAT TAAT TAT TAT TAT
1 TAT TAT TAT TAT T-AT TAT TAT TAT
34376 ATTCATTTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
2 7 0.13
3 39 0.75
4 6 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:34326 original size:16 final size:15
Alignment explanation
Indices: 34267--34375 Score: 80
Period size: 13 Copynumber: 8.0 Consensus size: 15
34257 ATTTACAAAA
34267 TATATTATA-ATTAT
1 TATATTATATATTAT
* *
34281 T-T-TTATAAAATAT
1 TATATTATATATTAT
* *
34294 T-TATTTTA-ATTAC
1 TATATTATATATTAT
34307 TATATTATTATATTAT
1 TATATTA-TATATTAT
34323 TATATTATA-ATTAT
1 TATATTATATATTAT
*
34337 T-TATTATAT-TTAA
1 TATATTATATATTAT
34350 TA-ATTA-ATATTAT
1 TATATTATATATTAT
34363 TA-ATTAT-TATTAT
1 TATATTATATATTAT
34376 ATTCATTTAA
Statistics
Matches: 78, Mismatches: 8, Indels: 19
0.74 0.08 0.18
Matches are distributed among these distances:
12 7 0.09
13 41 0.53
14 15 0.19
15 4 0.05
16 11 0.14
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (15 bp):
TATATTATATATTAT
Found at i:34511 original size:13 final size:13
Alignment explanation
Indices: 34493--34529 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
34483 GGTTACATCG
34493 CCCTTCGCAATCA
1 CCCTTCGCAATCA
*
34506 CCCTTCGCAATCG
1 CCCTTCGCAATCA
*
34519 CCCTTCTCAAT
1 CCCTTCGCAAT
34530 GCACGATGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.19, C:0.46, G:0.08, T:0.27
Consensus pattern (13 bp):
CCCTTCGCAATCA
Found at i:36500 original size:51 final size:51
Alignment explanation
Indices: 36424--36574 Score: 223
Period size: 51 Copynumber: 3.0 Consensus size: 51
36414 CCAACCAGCT
* * *
36424 GGTGACTGTGTAGCTCCACCGAATCAG-CTGGTTTCGGTGTCGCCGACTGCG
1 GGTGACTGCGTAGCTCCACCGAATCAGCCT-GTTTCGGTATCGCCGACTGCC
* *
36475 GGTGACCGCGTAGCTCCATCGAATCAGCCTGTTTCGGTATCGCCGACTGCC
1 GGTGACTGCGTAGCTCCACCGAATCAGCCTGTTTCGGTATCGCCGACTGCC
* *
36526 GGTGACTGCGCAGCTCCACCGGATCAGCCTGTTTCGGTATCGCCGACTG
1 GGTGACTGCGTAGCTCCACCGAATCAGCCTGTTTCGGTATCGCCGACTG
36575 TCGGCGATGC
Statistics
Matches: 90, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
51 88 0.98
52 2 0.02
ACGTcount: A:0.15, C:0.31, G:0.30, T:0.24
Consensus pattern (51 bp):
GGTGACTGCGTAGCTCCACCGAATCAGCCTGTTTCGGTATCGCCGACTGCC
Found at i:38928 original size:2 final size:2
Alignment explanation
Indices: 38921--38946 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38911 ACATACATAC
38921 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
38947 CTTCATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39815 original size:42 final size:41
Alignment explanation
Indices: 39768--40030 Score: 306
Period size: 42 Copynumber: 6.3 Consensus size: 41
39758 TGAAAAGAAG
*
39768 ATCGCAACGCGATCTTCCAAGAATCGCAATGCGATTCATAAA
1 ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCA-AAA
*
39810 ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCCAAGA
1 ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATT-CAAAA
* * *
39852 ATCGCAACCCGA--TT-CAGAAAATCGCAACGCGATTCCAAGA
1 ATCGCAACGCGATCTTCCA-AGAATCGCAACGCGATT-CAAAA
*
39892 ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAA
1 ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCA-AAA
*
39934 ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAA
1 ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCA-AAA
*
39976 ATCGCAACGCGA--TT-C-AGTAAATCGCAACGCGATCTTCCAAGA
1 ATCGCAACGCGATCTTCCAAG--AATCGCAACGCGA--TT-CAAAA
40018 ATCGCAACGCGAT
1 ATCGCAACGCGAT
40031 TAAGAAAATC
Statistics
Matches: 199, Mismatches: 10, Indels: 23
0.86 0.04 0.10
Matches are distributed among these distances:
38 2 0.01
39 3 0.02
40 50 0.25
41 1 0.01
42 138 0.69
43 5 0.03
ACGTcount: A:0.36, C:0.28, G:0.19, T:0.17
Consensus pattern (41 bp):
ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAAAA
Found at i:39816 original size:62 final size:61
Alignment explanation
Indices: 39709--40004 Score: 223
Period size: 62 Copynumber: 4.8 Consensus size: 61
39699 GACCAACAAA
* * * *
39709 ATCGCAACGCGATAT-CAA-AACCGCAACGCGATTTAGAAAAGCGCAACGTTGAAAAGAAG
1 ATCGCAACGCGATTTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGTTGAAAAGAAG
* * ***
39768 ATCGCAACGCGATCTTCCAAGAATCGCAATGCGATTCATAAAATCGCAACGCGATCTTCCAAG-A
1 ATCGCAACGCGAT-TTCCAAGAATCGCAACGCGATTCAGAAAATCGCAA--CG-T-TGAAAAGAA
39832 -
61 G
* * ****
39832 ATCGCAACGCGA-TTCCAAGAATCGCAACCCGATTCAGAAAATCGCAACG-CGATTCCAAG
1 ATCGCAACGCGATTTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGTTGAAAAGAAG
* ***
39891 AATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATCTTCCAAG-
1 -ATCGCAACGCGAT-TTCCAAGAATCGCAACGCGATTCAGAAAATCGCAA--CG-T-TGAAAAGA
39955 A-
60 AG
*** *
39956 ATCGCAACGCGATTAAGAA-AATCGCAACGCGATTCAGTAAATCGCAACG
1 ATCGCAACGCGATTTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACG
40005 CGATCTTCCA
Statistics
Matches: 187, Mismatches: 33, Indels: 33
0.74 0.13 0.13
Matches are distributed among these distances:
58 1 0.01
59 13 0.07
60 17 0.09
61 3 0.02
62 114 0.61
63 3 0.02
64 29 0.16
65 2 0.01
66 5 0.03
ACGTcount: A:0.38, C:0.27, G:0.19, T:0.17
Consensus pattern (61 bp):
ATCGCAACGCGATTTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGTTGAAAAGAAG
Found at i:39883 original size:104 final size:102
Alignment explanation
Indices: 39763--40081 Score: 423
Period size: 104 Copynumber: 3.1 Consensus size: 102
39753 AACGTTGAAA
* * * *
39763 AGAAGATCGCAACGCGATCTTCCAAGAATCGCAATGCGA-TT-CATAAAATCGCAACGCGATCTT
1 AGAAAATCGCAACGCGA--TTCCAAGAATCGCAACGCGACTTCCA-AGAATCGCAACGCGAT-TA
** *
39826 CCAAGAATCGCAACGCGA-TTCCAAGAATCGCAACCCGATTC
62 AGAA-AATCGCAACGCGACTTCCAAGAATCGCAACGCGATTC
39867 AGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGA
1 AGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGA-CTTCCAAGAATCGCAACGCGATTAAGA
*
39932 AAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTA
65 AAATCGCAACGCGA-CTTCCAAGAATCGCAACGCGATTC
39971 AGAAAATCGCAACGCGATT-C-AGTAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAA
1 AGAAAATCGCAACGCGATTCCAAG--AATCGCAACGCGA-CTTCCAAGAATCGCAACGCGATTAA
*
40034 GAAAATCGCAATGCGATCTTCCAAGAATCGCAACGCGATTC
63 GAAAATCGCAACGCGA-CTTCCAAGAATCGCAACGCGATTC
40075 AGAAAAT
1 AGAAAAT
40082 GAGTAAATTC
Statistics
Matches: 198, Mismatches: 10, Indels: 14
0.89 0.05 0.06
Matches are distributed among these distances:
102 34 0.17
103 4 0.02
104 158 0.80
105 2 0.01
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.18
Consensus pattern (102 bp):
AGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGACTTCCAAGAATCGCAACGCGATTAAGAA
AATCGCAACGCGACTTCCAAGAATCGCAACGCGATTC
Found at i:39950 original size:124 final size:123
Alignment explanation
Indices: 39708--40030 Score: 445
Period size: 124 Copynumber: 2.6 Consensus size: 123
39698 TGACCAACAA
* * * * ****
39708 AATCGCAACGCGATATCAA-AACCGCAACGCGATTTAGAAAAGCGCAACGTTGAAAAGAAG-ATC
1 AATCGCAACGCGAT-TCAAGAATCGCAACGCGATTCAGAAAATCGCAACG-CGATTCCAAGAATC
* * *
39771 GCAACGCGATCTTCCAAGAATCGCAATGCGATTCATAAAATCGCAACGCGATCTTCCAAG
64 GCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATCTTCCAAG
*
39831 AATCGCAACGCGATTCCAAGAATCGCAACCCGATTCAGAAAATCGCAACGCGATTCCAAGAATCG
1 AATCGCAACGCGATT-CAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGATTCCAAGAATCG
39896 CAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATCTTCCAAG
65 CAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATCTTCCAAG
*
39955 AATCGCAACGCGATT-AAGAAAATCGCAACGCGATTCAGTAAATCGCAACGCGATCTTCCAAGAA
1 AATCGCAACGCGATTCAAG--AATCGCAACGCGATTCAGAAAATCGCAACGCGA--TTCCAAGAA
40019 TCGCAACGCGAT
62 TCGCAACGCGAT
40031 TAAGAAAATC
Statistics
Matches: 179, Mismatches: 14, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
122 4 0.02
123 22 0.12
124 132 0.74
126 21 0.12
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.17
Consensus pattern (123 bp):
AATCGCAACGCGATTCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGATTCCAAGAATCGC
AACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATCTTCCAAG
Found at i:40005 original size:62 final size:62
Alignment explanation
Indices: 39789--40072 Score: 380
Period size: 62 Copynumber: 4.5 Consensus size: 62
39779 ATCTTCCAAG
* *
39789 AATCGCAATGCGATTCATAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCCAAG--
1 AATCGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATT--AAGAA
* ***
39851 AATCGCAACCCGATTCAGAAAATCGCAACGCGA--TTCCAAGAATCGCAACGCGATCTTCCAA
1 AATCGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGAT-TAAGAA
*
39912 GAATCGCAACGCGATTAAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAA
1 -AATCGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAA
*
39975 AATCGCAACGCGATTCAGTAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAA
1 AATCGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAA
* *
40037 AATCGCAATGCGATCTTCCA-AGAATCGCAACGCGAT
1 AATCGCAACGCGA--TT-CAGAAAATCGCAACGCGAT
40073 TCAGAAAATG
Statistics
Matches: 197, Mismatches: 16, Indels: 16
0.86 0.07 0.07
Matches are distributed among these distances:
60 21 0.11
61 1 0.01
62 133 0.68
63 3 0.02
64 37 0.19
65 2 0.01
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.18
Consensus pattern (62 bp):
AATCGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAA
Found at i:40031 original size:42 final size:41
Alignment explanation
Indices: 39706--40081 Score: 287
Period size: 42 Copynumber: 9.1 Consensus size: 41
39696 AATGACCAAC
* * *
39706 AAAATCGCAACGCGATAT-CAA-AACCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTCCAAGAATCGCAACGCGATTCAG
* ***
39745 AAAAGCGCAA--CG-TTGAAAAGAAGATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGATTTCCAAG-A-ATCGCAACGCGA--TT-CAG
* * *
39787 AGAATCGCAATGCGA-TT-CATAAAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGATTTCCA-AGAATCGCAACGCGA--TT-CAG
* *
39829 AGAATCGCAACGCGA-TTCCAAGAATCGCAACCCGATTCAG
1 AAAATCGCAACGCGATTTCCAAGAATCGCAACGCGATTCAG
39869 AAAATCGCAACGCGA-TTCCAAGAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGATTTCCAAGAATCGCAACGCGA--TT-CAG
* ***
39911 AGAATCGCAACGCGATTAAGAA-AATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGATTTCCAAGAATCGCAACGCGA--TT-CAG
* ***
39953 AGAATCGCAACGCGATTAAGAA-AATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTTCCAAGAATCGCAACGCGATTCAG
* *
39993 TAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGAT-TTCCAAGAATCGCAACGCGATTCAG
*
40035 AAAATCGCAATGCGATCTTCCAAGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGAT-TTCCAAGAATCGCAACGCGATTCAG
40077 AAAAT
1 AAAAT
40082 GAGTAAATTC
Statistics
Matches: 288, Mismatches: 29, Indels: 37
0.81 0.08 0.10
Matches are distributed among these distances:
36 1 0.00
37 4 0.01
39 14 0.05
40 62 0.22
41 3 0.01
42 190 0.66
43 10 0.03
44 4 0.01
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (41 bp):
AAAATCGCAACGCGATTTCCAAGAATCGCAACGCGATTCAG
Found at i:40188 original size:6 final size:6
Alignment explanation
Indices: 40177--40263 Score: 174
Period size: 6 Copynumber: 14.5 Consensus size: 6
40167 GACACGTATT
40177 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
40225 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
40264 CGAGACGAGA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 81 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:40844 original size:6 final size:5
Alignment explanation
Indices: 40752--40840 Score: 124
Period size: 5 Copynumber: 16.6 Consensus size: 5
40742 CGCCGCCGTC
40752 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGGG TCGGG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TC-GGG TCGGG
40803 TCGGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCG
1 TCGGG TCG-GG TCG-GG TCG-GG TCG-GG TCG-GG TCG
40841 TGGTAATACG
Statistics
Matches: 82, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
5 48 0.59
6 34 0.41
ACGTcount: A:0.00, C:0.19, G:0.56, T:0.25
Consensus pattern (5 bp):
TCGGG
Found at i:40996 original size:20 final size:20
Alignment explanation
Indices: 40940--41377 Score: 326
Period size: 20 Copynumber: 21.2 Consensus size: 20
40930 GAATTTACTC
*
40940 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
40960 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
*
40982 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
41002 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
**
41024 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
**
41046 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
*
41066 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
41086 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
**
41108 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
*
41128 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
41148 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
*
41170 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
*
41190 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
*
41210 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
** *
41230 ATTCTTGGAAGATCGCATTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
* * *
41252 ATTTTATGAATCGCATTGCG
1 ATTTTCTAAATCGCGTTGCG
* * *
41272 ATTTTATGAATCGCATTGCG
1 ATTTTCTAAATCGCGTTGCG
** *
41292 ATTCTTGGAAGATCGTGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
* ** *
41314 ATCTTCT-TTTCAACGTTGCG
1 ATTTTCTAAATC-GCGTTGCG
*
41334 CTTTTCTAAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
* * *
41354 GTTTT-GATATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
41373 ATTTT
1 ATTTT
41378 GTTGGTCATT
Statistics
Matches: 350, Mismatches: 52, Indels: 33
0.80 0.12 0.08
Matches are distributed among these distances:
19 22 0.06
20 185 0.53
21 35 0.10
22 108 0.31
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.39
Consensus pattern (20 bp):
ATTTTCTAAATCGCGTTGCG
Found at i:40999 original size:42 final size:42
Alignment explanation
Indices: 40940--41321 Score: 353
Period size: 42 Copynumber: 9.2 Consensus size: 42
40930 GAATTTACTC
40940 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
40982 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
***
41024 ATTCTTGGAAGATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
41066 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
***
41108 A--TTCTTGGAATCGCGTTGCGATT-TTCTTA-ATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
*** *
41148 ATTCTTGGAAGATCGCGTTGCGATT-TTCTG-A-ATCGCGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCGATTCTT-GGAAGATCGCGTTGCG
* *
41190 ATTTTCTGAATCGCGTTGCGATT-TTCTG-A-ATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTT-GGAAGATCGCGTTGCG
*** * * *
41230 ATTCTTGGAAGATCGCATTGCGATT-TT--ATGAATCGCATTGCG
1 ATT-TTCTTA-ATCGCGTTGCGATTCTTGGAAG-ATCGCGTTGCG
* * * *
41272 ATTTTATGAATCGCATTGCGATTCTTGGAAGATCGTGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
*
41314 ATCTTCTT
1 ATTTTCTT
41322 TTCAACGTTG
Statistics
Matches: 289, Mismatches: 32, Indels: 38
0.81 0.09 0.11
Matches are distributed among these distances:
40 84 0.29
41 19 0.07
42 159 0.55
43 8 0.03
44 19 0.07
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.38
Consensus pattern (42 bp):
ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
Found at i:41089 original size:62 final size:62
Alignment explanation
Indices: 40940--41377 Score: 481
Period size: 62 Copynumber: 7.1 Consensus size: 62
40930 GAATTTACTC
40940 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTT--AATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGA--TTCTTGGAATCGCGTTGCG
***
41002 ATTCTTGGAAGATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTCTTGGAATCGCGTTGCG
41066 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTCTTGGAATCGCGTTGCG
*
41128 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATT-TTCTGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTCTT-GGAATCGCGTTGCG
* * *
41190 ATTTTCTGAATCGCGTTGCGATT-TTCTG-A-ATCGCGTTGCGATTCTTGGAAGATCGCATTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTT-GGAAGATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
* * * * * *
41252 ATTTTATGAATCGCATTGCGATT-TT--ATGAATCGCATTGCGATTCTTGGAAGATCGTGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAAG-ATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
* * * * ** *
41314 ATCTTCTT-TTCAACGTTGCGCTT-TTCTAA-ATCGCGTTGCGGTT-TT-GATATCGCGTTGCG
1 ATTTTCTTAATC-GCGTTGCGATTCTTGGAAGATCGCGTTGCGATTCTTGGA-ATCGCGTTGCG
41373 ATTTT
1 ATTTT
41378 GTTGGTCATT
Statistics
Matches: 331, Mismatches: 30, Indels: 33
0.84 0.08 0.08
Matches are distributed among these distances:
59 15 0.05
60 16 0.05
61 12 0.04
62 232 0.70
63 6 0.02
64 50 0.15
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.39
Consensus pattern (62 bp):
ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTCTTGGAATCGCGTTGCG
Found at i:41333 original size:82 final size:79
Alignment explanation
Indices: 41013--41377 Score: 305
Period size: 82 Copynumber: 4.4 Consensus size: 79
41003 TTCTTGGAAG
*
41013 ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTCTT-GGAATCGCGTTGCGATTTTCTT--A
1 ATCGCGTTGCGATT-TTTG-A-ATCGCGTTGCGATT-TTCGGAATCGCGTTGCGA--TTCTTGGA
*** *
41075 ATCGCGTTGCGATTCTT-GGAA
60 AGATCGTTGCGATT-TTCTG-A
* **
41096 GATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAAGAT
1 -ATCGCGTTGCGATT-TTTGAATCGCGTTGCGATTTTCGGAATCGCGTTGCGATTCTTGGAAGAT
41161 CGCGTTGCGATTTTCTGA
64 --CGTTGCGATTTTCTGA
*
41179 ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAGATC
1 ATCGCGTTGCGATTTT-TGAATCGCGTTGCGATTTTCGGAATCGCGTTGCGATTCTTGGAAGATC
*
41244 GCATTGCGATTTTATGA
65 G--TTGCGATTTTCTGA
* * * ***
41261 ATCGCATTGCGATTTTATGAATCGCATTGCGATTCTT-GGAAGATCGTGTTGCGATCTTCTTTTC
1 ATCGCGTTGCGATTTT-TGAATCGCGTTGCGATT-TTCGG-A-ATCGCGTTGCGA--TTCTTGGA
* *
41325 A-A-CGTTGCGCTTTTCTAA
60 AGATCGTTGCGATTTTCTGA
*
41343 ATCGCGTTGCG-GTTTTGATATCGCGTTGCGATTTT
1 ATCGCGTTGCGATTTTTGA-ATCGCGTTGCGATTTT
41378 GTTGGTCATT
Statistics
Matches: 243, Mismatches: 23, Indels: 34
0.81 0.08 0.11
Matches are distributed among these distances:
80 12 0.05
81 20 0.08
82 154 0.63
83 7 0.03
84 43 0.18
85 1 0.00
86 6 0.02
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (79 bp):
ATCGCGTTGCGATTTTTGAATCGCGTTGCGATTTTCGGAATCGCGTTGCGATTCTTGGAAGATCG
TTGCGATTTTCTGA
Found at i:41593 original size:2 final size:2
Alignment explanation
Indices: 41586--41617 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
41576 CTTTAGTTCG
41586 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
41618 TTGATTAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45660 original size:29 final size:29
Alignment explanation
Indices: 45625--45695 Score: 142
Period size: 29 Copynumber: 2.4 Consensus size: 29
45615 TCCCCAAGCA
45625 TAGGTCGCCATGCCCTCTGGGCGACCTTG
1 TAGGTCGCCATGCCCTCTGGGCGACCTTG
45654 TAGGTCGCCATGCCCTCTGGGCGACCTTG
1 TAGGTCGCCATGCCCTCTGGGCGACCTTG
45683 TAGGTCGCCATGC
1 TAGGTCGCCATGC
45696 ACTCCCTCCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.11, C:0.34, G:0.31, T:0.24
Consensus pattern (29 bp):
TAGGTCGCCATGCCCTCTGGGCGACCTTG
Found at i:45761 original size:14 final size:14
Alignment explanation
Indices: 45739--45785 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
45729 CCTCGCATAG
*
45739 CTCGCTCGGATGGC
1 CTCGGTCGGATGGC
45753 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
* *
45767 CTAGATCGGATGGC
1 CTCGGTCGGATGGC
45781 CTCGG
1 CTCGG
45786 ATGCTCTCAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.11, C:0.30, G:0.38, T:0.21
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:47368 original size:16 final size:16
Alignment explanation
Indices: 47349--47398 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
47339 AAGTATCTAA
47349 TTTAACTAAAGAATAG
1 TTTAACTAAAGAATAG
* * *
47365 TTTAA--ATA-CATAA
1 TTTAACTAAAGAATAG
47378 TTTAACTAAAGAATAG
1 TTTAACTAAAGAATAG
47394 TTTAA
1 TTTAA
47399 GCACCTAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
13 8 0.32
14 2 0.08
15 2 0.08
16 13 0.52
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.36
Consensus pattern (16 bp):
TTTAACTAAAGAATAG
Found at i:47369 original size:29 final size:29
Alignment explanation
Indices: 47336--47399 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
47326 CATATAATGA
47336 TTTAAGTATC-TAATTTAACTAAAGAATAG
1 TTTAAGTA-CATAATTTAACTAAAGAATAG
*
47365 TTTAAATACATAATTTAACTAAAGAATAG
1 TTTAAGTACATAATTTAACTAAAGAATAG
47394 TTTAAG
1 TTTAAG
47400 CACCTAAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 1 0.03
29 31 0.97
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (29 bp):
TTTAAGTACATAATTTAACTAAAGAATAG
Found at i:54363 original size:23 final size:23
Alignment explanation
Indices: 54337--54380 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
54327 ATAGGCTACC
* * *
54337 TATTAGTTTTTTAATGTTTTTAT
1 TATTACTTTTATAATCTTTTTAT
54360 TATTACTTTTATAATCTTTTT
1 TATTACTTTTATAATCTTTTT
54381 CCTATTTTGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.68
Consensus pattern (23 bp):
TATTACTTTTATAATCTTTTTAT
Found at i:54386 original size:23 final size:23
Alignment explanation
Indices: 54335--54386 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
54325 AAATAGGCTA
* * *
54335 CCTATTAGTTTTTTAATGTTTTT
1 CCTATTACTTTTATAATCTTTTT
**
54358 ATTATTACTTTTATAATCTTTTT
1 CCTATTACTTTTATAATCTTTTT
54381 CCTATT
1 CCTATT
54387 TTGCAGTCCA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.21, C:0.12, G:0.04, T:0.63
Consensus pattern (23 bp):
CCTATTACTTTTATAATCTTTTT
Found at i:65334 original size:64 final size:64
Alignment explanation
Indices: 65238--65388 Score: 180
Period size: 64 Copynumber: 2.4 Consensus size: 64
65228 AACCAGATAT
* * * * * *
65238 CTTTTAATATTTAAATTTAAACAAATAATATTTTTAATTTGACATATTC-AAAAGATATAATCAC
1 CTTTTAATATTCAAAATTAAATAAATAATA-TTTTAATTTGAAATATTCAAAAAGATACAATAAC
* * * * *
65302 CTTTTACTATTCAAACTTAAATAGATACTATTTTAATTTGAAATATTCAAAAAGATACAATAAT
1 CTTTTAATATTCAAAATTAAATAAATAATATTTTAATTTGAAATATTCAAAAAGATACAATAAC
65366 C-TTTAATATTCAAAATTAAATAA
1 CTTTTAATATTCAAAATTAAATAA
65389 GTAACAAATA
Statistics
Matches: 73, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
63 36 0.49
64 37 0.51
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.40
Consensus pattern (64 bp):
CTTTTAATATTCAAAATTAAATAAATAATATTTTAATTTGAAATATTCAAAAAGATACAATAAC
Found at i:65349 original size:63 final size:63
Alignment explanation
Indices: 65240--65387 Score: 172
Period size: 63 Copynumber: 2.3 Consensus size: 63
65230 CCAGATATCT
* * * * * * * *
65240 TTTAATATTTAAATTTAAACAAATAATATTTTTAATTTGACATATTC-AAAAGATATAATCACC
1 TTTAATATTCAAAATTAAATAGATACTA-TTTTAATTTGAAATATTCAAAAAGATACAATAACC
* * *
65303 TTTTACTATTCAAACTTAAATAGATACTATTTTAATTTGAAATATTCAAAAAGATACAATAATC
1 -TTTAATATTCAAAATTAAATAGATACTATTTTAATTTGAAATATTCAAAAAGATACAATAACC
65367 TTTAATATTCAAAATTAAATA
1 TTTAATATTCAAAATTAAATA
65388 AGTAACAAAT
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
63 36 0.51
64 35 0.49
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (63 bp):
TTTAATATTCAAAATTAAATAGATACTATTTTAATTTGAAATATTCAAAAAGATACAATAACC
Found at i:69022 original size:29 final size:29
Alignment explanation
Indices: 68969--69053 Score: 89
Period size: 29 Copynumber: 2.9 Consensus size: 29
68959 AACCCAACCC
**
68969 ATAGGTCGCCATGCACTCCCAGCGACCTC
1 ATAGGTCGCCATGCACTCCCAGCGACCAA
* ***
68998 CTAGGTCGCCATGCACTCTGGGCGACCAA
1 ATAGGTCGCCATGCACTCCCAGCGACCAA
* * *
69027 AGAGGTCGCCATGCACGCCCGGCGACC
1 ATAGGTCGCCATGCACTCCCAGCGACC
69054 TTGTCTCCTT
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.20, C:0.39, G:0.27, T:0.14
Consensus pattern (29 bp):
ATAGGTCGCCATGCACTCCCAGCGACCAA
Found at i:69235 original size:29 final size:29
Alignment explanation
Indices: 69198--69254 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
69188 GGGTTAAAAG
* *
69198 CTTGGTCACCGGGCGTGCATGGCGACCTC
1 CTTGGTCACCCGGAGTGCATGGCGACCTC
69227 CTTGGTCACCCGGAGTGCATGGCGACCT
1 CTTGGTCACCCGGAGTGCATGGCGACCT
69255 AGGAGGTTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.12, C:0.33, G:0.33, T:0.21
Consensus pattern (29 bp):
CTTGGTCACCCGGAGTGCATGGCGACCTC
Found at i:70552 original size:20 final size:20
Alignment explanation
Indices: 70529--70573 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
70519 TAGTTCCATT
70529 ACCTTCTATGA-AGTTTTAAA
1 ACCTTCT-TGAGAGTTTTAAA
* *
70549 ACCTTCTTTAGTGTTTTAAA
1 ACCTTCTTGAGAGTTTTAAA
70569 ACCTT
1 ACCTT
70574 TCACAATGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.44
Consensus pattern (20 bp):
ACCTTCTTGAGAGTTTTAAA
Found at i:70634 original size:20 final size:20
Alignment explanation
Indices: 70611--70652 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
70601 ATCTAGGACG
70611 TTCCAAAATATTCTAAAACT
1 TTCCAAAATATTCTAAAACT
* * *
70631 TTCCATAATGTTCTAAACCT
1 TTCCAAAATATTCTAAAACT
70651 TT
1 TT
70653 TTATTGTGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.21, G:0.02, T:0.40
Consensus pattern (20 bp):
TTCCAAAATATTCTAAAACT
Found at i:70934 original size:60 final size:60
Alignment explanation
Indices: 70813--70935 Score: 167
Period size: 60 Copynumber: 2.0 Consensus size: 60
70803 GTCTATCAAT
* * * *
70813 TATATAGTATTGTTTTATTAAGTCTATCGACTATTAAAAGTTATAAAATGATTATTGGAC
1 TATAGAGTATTGTTTTATTAAGTCCATCGACTATTAAAAGTTATAAAATGATCACTGGAC
* * *
70873 TATAGAGTATTGTTTTGTTGAGTCCATCGACTATTAAAAGTTATAAAATGGTCACCT-GAC
1 TATAGAGTATTGTTTTATTAAGTCCATCGACTATTAAAAGTTATAAAATGATCA-CTGGAC
70933 TAT
1 TAT
70936 TCATTGTCAA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
60 54 0.98
61 1 0.02
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (60 bp):
TATAGAGTATTGTTTTATTAAGTCCATCGACTATTAAAAGTTATAAAATGATCACTGGAC
Done.