Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004160.1 Hibiscus syriacus cultivar Beakdansim tig00009098_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: 65640
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:9089 original size:24 final size:24
Alignment explanation
Indices: 9062--9107 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
9052 AATGGAACAT
9062 TATACTTATTAAATAAATGATAAC
1 TATACTTATTAAATAAATGATAAC
9086 TATACTTATTAAATAAATGATA
1 TATACTTATTAAATAAATGATA
9108 TAAAGAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (24 bp):
TATACTTATTAAATAAATGATAAC
Found at i:9210 original size:2 final size:2
Alignment explanation
Indices: 9203--9228 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9193 AATAATTTAA
9203 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
9229 CCAGCTAAGC
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:9366 original size:49 final size:50
Alignment explanation
Indices: 9293--9403 Score: 188
Period size: 49 Copynumber: 2.2 Consensus size: 50
9283 TTAAACAAAT
9293 ATATATATATATATGAACAAAAAAAATCAGTTTACAAGACACATTAAATAA
1 ATATATATATATATGAAC-AAAAAAATCAGTTTACAAGACACATTAAATAA
*
9344 ATATATATATATATGAAC-AAAAAATCAGTTTCCAAGACACATTAAATAA
1 ATATATATATATATGAACAAAAAAATCAGTTTACAAGACACATTAAATAA
*
9393 AAATATATATA
1 ATATATATATA
9404 CGTTTAACAA
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
49 40 0.69
51 18 0.31
ACGTcount: A:0.56, C:0.10, G:0.05, T:0.29
Consensus pattern (50 bp):
ATATATATATATATGAACAAAAAAATCAGTTTACAAGACACATTAAATAA
Found at i:9397 original size:51 final size:52
Alignment explanation
Indices: 9283--9403 Score: 185
Period size: 51 Copynumber: 2.4 Consensus size: 52
9273 CTAAGACATG
* *
9283 TTAAACAAATATATATATATATATGAACAAAAAAAATCAGTTTACAAGACACA
1 TTAAATAAAAATATATATATATATGAAC-AAAAAAATCAGTTTACAAGACACA
*
9336 TTAAAT--AAATATATATATATATGAAC-AAAAAATCAGTTTCCAAGACACA
1 TTAAATAAAAATATATATATATATGAACAAAAAAATCAGTTTACAAGACACA
9385 TTAAATAAAAATATATATA
1 TTAAATAAAAATATATATA
9404 CGTTTAACAA
Statistics
Matches: 63, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
49 28 0.44
51 30 0.48
53 5 0.08
ACGTcount: A:0.56, C:0.10, G:0.05, T:0.29
Consensus pattern (52 bp):
TTAAATAAAAATATATATATATATGAACAAAAAAATCAGTTTACAAGACACA
Found at i:9541 original size:177 final size:183
Alignment explanation
Indices: 9233--9580 Score: 494
Period size: 177 Copynumber: 1.9 Consensus size: 183
9223 ATATATCCAG
**
9233 CTAAGCTATACGTTAAACAAATAAAATATGCCTATTCTTCCTAAGACATGTTAAACAAATATATA
1 CTAAGCTATAC-TTAAACAAATAAAATATGCCTATTCTTCCTAAGACACATT-AACAAATATATA
*
9298 TATATATATGAACAAAAAAAATCAGTTTACAAGACACATTAAATAAATATATATATATATGAACA
64 TATATATATGAAC-AAAAAAATCAGTTTACAAGACACATTAAACAAATATATATATATATGAACA
*
9363 AAAAATCAGTTTCCAAGACACATTAAATAAAAATATATATACGTTTAACAAATAAA
128 AAAAATCAGTTTCCAAGACACATTAAACAAAAATATATATACGTTTAACAAATAAA
*
9419 CTAAGCTATA-TTAAACAAAT-AAATAATGGCTATTCTTCCTAAGACACATT-A-AAA-A-ATAT
1 CTAAGCTATACTTAAACAAATAAAAT-ATGCCTATTCTTCCTAAGACACATTAACAAATATATAT
* * * **
9478 ATGTATATGAAC-AAAGAATCAGTTTCCAAGACATGTTAAACAAATATATATATATATGAACAAA
65 ATATATATGAACAAAAAAATCAGTTTACAAGACACATTAAACAAATATATATATATATGAACAAA
** *
9542 AAATCAGTTTCCAAGACATGTTAAACAAATATATATATA
130 AAATCAGTTTCCAAGACACATTAAACAAAAATATATATA
9581 TATATATGAA
Statistics
Matches: 148, Mismatches: 13, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
177 82 0.55
179 15 0.10
180 1 0.01
181 3 0.02
182 1 0.01
183 4 0.03
184 32 0.22
186 10 0.07
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.29
Consensus pattern (183 bp):
CTAAGCTATACTTAAACAAATAAAATATGCCTATTCTTCCTAAGACACATTAACAAATATATATA
TATATATGAACAAAAAAATCAGTTTACAAGACACATTAAACAAATATATATATATATGAACAAAA
AATCAGTTTCCAAGACACATTAAACAAAAATATATATACGTTTAACAAATAAA
Found at i:9589 original size:102 final size:102
Alignment explanation
Indices: 9474--9689 Score: 378
Period size: 102 Copynumber: 2.1 Consensus size: 102
9464 ACATTAAAAA
* *
9474 ATATATGTATATGAACAAAGAATCAGTTTCCAAGACATGTTAAACAAATATATATATATATGAAC
1 ATATATATATATGAACAAAAAATCAGTTTCCAAGACATGTTAAACAAATATATATATATATGAAC
** *
9539 AAAAAATCAGTTTCCAAGACATGTTAAACAAATATAT
66 AAAAAATCAGTTTCCAAGACACATTAAACAAATAAAT
9576 ATATATATATATGAACAAAAAATCAGTTTCCAAGACATGTTAAACAAATATATATATATATGAAC
1 ATATATATATATGAACAAAAAATCAGTTTCCAAGACATGTTAAACAAATATATATATATATGAAC
*
9641 AAAAAATCAGTTTCCAAGACACATTAAATAAATAAAT
66 AAAAAATCAGTTTCCAAGACACATTAAACAAATAAAT
9678 ATATATATATAT
1 ATATATATATAT
9690 ATATATATAT
Statistics
Matches: 108, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 108 1.00
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.30
Consensus pattern (102 bp):
ATATATATATATGAACAAAAAATCAGTTTCCAAGACATGTTAAACAAATATATATATATATGAAC
AAAAAATCAGTTTCCAAGACACATTAAACAAATAAAT
Found at i:9683 original size:2 final size:2
Alignment explanation
Indices: 9676--9730 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
9666 AAATAAATAA
9676 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
9718 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
9731 CACGTTTAAC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9688 original size:53 final size:49
Alignment explanation
Indices: 9474--9685 Score: 334
Period size: 49 Copynumber: 4.2 Consensus size: 49
9464 ACATTAAAAA
* *
9474 ATATATGTATATGAACAAAGAATCAGTTTCCAAGACATGTTAAACAAAT
1 ATATATATATATGAACAAAAAATCAGTTTCCAAGACATGTTAAACAAAT
9523 ATATATATATATGAACAAAAAATCAGTTTCCAAGACATGTTAAACAAATATAT
1 ATATATATATATGAACAAAAAATCAGTTTCCAAGACATGTTAAAC--A-A-AT
9576 ATATATATATATGAACAAAAAATCAGTTTCCAAGACATGTTAAACAAAT
1 ATATATATATATGAACAAAAAATCAGTTTCCAAGACATGTTAAACAAAT
** *
9625 ATATATATATATGAACAAAAAATCAGTTTCCAAGACACATTAAATAAAT
1 ATATATATATATGAACAAAAAATCAGTTTCCAAGACATGTTAAACAAAT
*
9674 AAATATATATAT
1 ATATATATATAT
9686 ATATATATAT
Statistics
Matches: 153, Mismatches: 6, Indels: 8
0.92 0.04 0.05
Matches are distributed among these distances:
49 102 0.67
50 1 0.01
51 2 0.01
52 1 0.01
53 47 0.31
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.30
Consensus pattern (49 bp):
ATATATATATATGAACAAAAAATCAGTTTCCAAGACATGTTAAACAAAT
Found at i:11638 original size:3 final size:3
Alignment explanation
Indices: 11632--11674 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
11622 TAAATACACT
* *
11632 TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA T-T TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
11675 TTTTTTAACT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 1 0.03
3 34 0.97
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:12835 original size:20 final size:20
Alignment explanation
Indices: 12810--12847 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12800 TTAAGCATTA
* *
12810 TAAAAATCTTAAAATTATCT
1 TAAAAACCTAAAAATTATCT
12830 TAAAAACCTAAAAATTAT
1 TAAAAACCTAAAAATTAT
12848 AAAATGAACT
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:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAAAACCTAAAAATTATCT
Found at i:12863 original size:28 final size:28
Alignment explanation
Indices: 12810--12863 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
12800 TTAAGCATTA
* *
12810 TAAAAATCTTAAAATTATCTTAAAAACC
1 TAAAAATCTTAAAATGAACTTAAAAACC
*
12838 TAAAAAT-TATAAAATGAACTTGAAAA
1 TAAAAATCT-TAAAATGAACTTAAAAA
12864 GAAATTATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 1 0.05
28 21 0.95
ACGTcount: A:0.57, C:0.09, G:0.04, T:0.30
Consensus pattern (28 bp):
TAAAAATCTTAAAATGAACTTAAAAACC
Found at i:13617 original size:58 final size:59
Alignment explanation
Indices: 13492--13624 Score: 144
Period size: 58 Copynumber: 2.3 Consensus size: 59
13482 AAATTTTGGG
* ** * * * *
13492 ACCAATTTAGAATGAGGGTCATAGTTTGGGGATGAAATTGGAATGTTAAAAAGTCTAAGG
1 ACCAATTTAAAATGA-GGTCATAGTTTGAAGATAAAATTAGAATATTAAAAAGTCTAAGA
* **
13552 ACTAATTTAAAATGA-GTCATAGTTTGAAGATAAAATTAGAATATTTTAAAG-CTTAAGA
1 ACCAATTTAAAATGAGGTCATAGTTTGAAGATAAAATTAGAATATTAAAAAGTC-TAAGA
13610 ACCAATTTAAAATGA
1 ACCAATTTAAAATGA
13625 TAATCATAGT
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
57 1 0.02
58 47 0.77
60 13 0.21
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.31
Consensus pattern (59 bp):
ACCAATTTAAAATGAGGTCATAGTTTGAAGATAAAATTAGAATATTAAAAAGTCTAAGA
Found at i:17038 original size:39 final size:39
Alignment explanation
Indices: 16970--17177 Score: 277
Period size: 39 Copynumber: 5.5 Consensus size: 39
16960 TATACAATTT
*
16970 TTTTG-AAAT-TATATATAATATATAGTTTTTGAAAACA
1 TTTTGAAAATATATATATAATATATAATTTTTGAAAACA
* *
17007 TTTTGAATATATATATATAATATATAATTTTTGAAGACA
1 TTTTGAAAATATATATATAATATATAATTTTTGAAAACA
*
17046 TTTTGAAAAAATATATATAATATATAATTTTTGAAAACA
1 TTTTGAAAATATATATATAATATATAATTTTTGAAAACA
* *
17085 TTTTGAAAACATATATATAATATAT-AGTTTTGAAAACA
1 TTTTGAAAATATATATATAATATATAATTTTTGAAAACA
* *
17123 TTTTGAAAAT-T-TATAAAATATATAA-TTTT-AAAACG
1 TTTTGAAAATATATATATAATATATAATTTTTGAAAACA
17158 TTTTAGAAAATATATCATAT
1 TTTT-GAAAATATAT-ATAT
17178 GTATAGGTTT
Statistics
Matches: 152, Mismatches: 12, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
35 9 0.06
36 21 0.14
37 8 0.05
38 25 0.16
39 89 0.59
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (39 bp):
TTTTGAAAATATATATATAATATATAATTTTTGAAAACA
Found at i:17281 original size:4 final size:4
Alignment explanation
Indices: 17211--17274 Score: 76
Period size: 4 Copynumber: 15.8 Consensus size: 4
17201 CGAAATATAT
* *
17211 TTTA TATTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TATG TTTA TTT-
1 TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
*
17259 TTATT TTTA TTTA TTT
1 TT-TA TTTA TTTA TTT
17275 TTATTTAGGT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
3 2 0.04
4 44 0.85
5 6 0.12
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:18532 original size:12 final size:13
Alignment explanation
Indices: 18517--18545 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
18507 AAACATTTTA
18517 TTTTT-TTTTATC
1 TTTTTATTTTATC
18529 TTTTTATTTTATC
1 TTTTTATTTTATC
18542 TTTT
1 TTTT
18546 AACCTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.10, C:0.07, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTATTTTATC
Found at i:19729 original size:28 final size:28
Alignment explanation
Indices: 19693--19747 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
19683 ATCATATTGT
*
19693 TTTCAAACACTTGCTCAACGACATAATG
1 TTTCAAACACTTACTCAACGACATAATG
*
19721 TTTCAAACACTTACTCAACGATATAAT
1 TTTCAAACACTTACTCAACGACATAAT
19748 ATAAACATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.38, C:0.24, G:0.07, T:0.31
Consensus pattern (28 bp):
TTTCAAACACTTACTCAACGACATAATG
Found at i:21985 original size:28 final size:28
Alignment explanation
Indices: 21954--22009 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
21944 TTTAACCATA
21954 ATCTCAGCTTTGCTTCATTGATTTTCAT
1 ATCTCAGCTTTGCTTCATTGATTTTCAT
21982 ATCTCAGCTTTGCTTCATTGATTTTCAT
1 ATCTCAGCTTTGCTTCATTGATTTTCAT
22010 TGCTTAAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.18, C:0.21, G:0.11, T:0.50
Consensus pattern (28 bp):
ATCTCAGCTTTGCTTCATTGATTTTCAT
Found at i:29407 original size:21 final size:18
Alignment explanation
Indices: 29369--29409 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 18
29359 ATATTTGCAA
29369 ATATTAAATTTTAAAAAT
1 ATATTAAATTTTAAAAAT
29387 ATATTCAAAGTTTTCAAAAAT
1 ATATT-AAA-TTTT-AAAAAT
29408 AT
1 AT
29410 TCACCAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 5 0.25
19 3 0.15
20 4 0.20
21 8 0.40
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.41
Consensus pattern (18 bp):
ATATTAAATTTTAAAAAT
Found at i:29411 original size:19 final size:18
Alignment explanation
Indices: 29367--29412 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
29357 TAATATTTGC
29367 AAATATT-AAATTTTAAA
1 AAATATTCAAATTTTAAA
*
29384 AATATATTCAAAGTTTTCAA
1 AA-ATATTCAAA-TTTTAAA
29404 AAATATTCA
1 AAATATTCA
29413 CCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 2 0.08
18 5 0.20
19 10 0.40
20 8 0.32
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (18 bp):
AAATATTCAAATTTTAAA
Found at i:33291 original size:178 final size:180
Alignment explanation
Indices: 32990--33353 Score: 705
Period size: 178 Copynumber: 2.0 Consensus size: 180
32980 AATAAAGAGA
32990 TTTTACGATTCAAATCTATAAAATATGAGATAATATGAACAATCCTAATATATATATATATATAT
1 TTTTACGATTCAAATCTATAAAATATGAGATAATATGAACAATCCTAATATATATATATATATAT
33055 ATATTAGTACATTGACCGTCCGTGATTAATGTTATATGCACCTTTGTTGTAATGTTTAAAAGTAA
66 ATATTAGTACATTGACCGTCCGTGATTAATGTTATATGCACCTTTGTTGTAATGTTTAAAAGTAA
33120 GGAAGGGATGAAACAAAATAGATATGACTTGTTCGAAAATTAAGAATCTT
131 GGAAGGGATGAAACAAAATAGATATGACTTGTTCGAAAATTAAGAATCTT
33170 TTTTACGATTCAAATCTATAAAATATGAGATAATATG-A-AATCCTAATATATATATATATATAT
1 TTTTACGATTCAAATCTATAAAATATGAGATAATATGAACAATCCTAATATATATATATATATAT
33233 ATATTAGTACATTGACCGTCCGTGATTAATGTTATATGCACCTTTGTTGTAATGTTTAAAAGTAA
66 ATATTAGTACATTGACCGTCCGTGATTAATGTTATATGCACCTTTGTTGTAATGTTTAAAAGTAA
33298 GGAAGGGATGAAACAAAATAGATATGACTTGTTCGAAAATTAAGAATCTT
131 GGAAGGGATGAAACAAAATAGATATGACTTGTTCGAAAATTAAGAATCTT
33348 TATTTA
1 T-TTTA
33354 ATCTGATTTT
Statistics
Matches: 183, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
178 141 0.77
179 5 0.03
180 37 0.20
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (180 bp):
TTTTACGATTCAAATCTATAAAATATGAGATAATATGAACAATCCTAATATATATATATATATAT
ATATTAGTACATTGACCGTCCGTGATTAATGTTATATGCACCTTTGTTGTAATGTTTAAAAGTAA
GGAAGGGATGAAACAAAATAGATATGACTTGTTCGAAAATTAAGAATCTT
Found at i:34202 original size:15 final size:15
Alignment explanation
Indices: 34182--34219 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
34172 CTGAACTTAA
34182 ATTTTCTTCAAGTTT
1 ATTTTCTTCAAGTTT
34197 ATTTTCTTCAAGTTT
1 ATTTTCTTCAAGTTT
34212 -TTTT-TTCA
1 ATTTTCTTCA
34220 TTTAGATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 4 0.17
14 4 0.17
15 15 0.65
ACGTcount: A:0.18, C:0.13, G:0.05, T:0.63
Consensus pattern (15 bp):
ATTTTCTTCAAGTTT
Found at i:34946 original size:13 final size:13
Alignment explanation
Indices: 34899--34946 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
34889 GATAAAACAA
34899 TTAAAAATAATAT
1 TTAAAAATAATAT
*
34912 TTAAATAATAAAAT
1 TTAAA-AATAATAT
34926 GATTAAAAATAATAT
1 --TTAAAAATAATAT
34941 TTAAAA
1 TTAAAA
34947 TGGACTGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 11 0.37
14 7 0.23
15 7 0.23
16 5 0.17
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (13 bp):
TTAAAAATAATAT
Found at i:37483 original size:39 final size:39
Alignment explanation
Indices: 37440--37525 Score: 163
Period size: 39 Copynumber: 2.2 Consensus size: 39
37430 CTAGGATGCC
*
37440 TCATTTTGCTATTTTTTCTTCTAATTTTGACATTATGTT
1 TCATTTTGCTATTTTTTCTTCTAAATTTGACATTATGTT
37479 TCATTTTGCTATTTTTTCTTCTAAATTTGACATTATGTT
1 TCATTTTGCTATTTTTTCTTCTAAATTTGACATTATGTT
37518 TCATTTTG
1 TCATTTTG
37526 TTTCAATCTA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.19, C:0.13, G:0.08, T:0.60
Consensus pattern (39 bp):
TCATTTTGCTATTTTTTCTTCTAAATTTGACATTATGTT
Found at i:38961 original size:276 final size:276
Alignment explanation
Indices: 38395--38986 Score: 703
Period size: 276 Copynumber: 2.1 Consensus size: 276
38385 TGAATAATTT
** * * * * *
38395 CATAATTGATTAAAATTAATTACTATTAATATTAGAGCCACTATTTTAGGCCTAATTTTGAATTT
1 CATAATTGATTAAAATTAATTAAGATTAATATTAGAGCCTCCATCTTAGGCATAATTTTCAATTT
** * * *
38460 AGTCCTTAAATTAGTTGAATTCTTAATTTGGTCCTCGCTTTTGTTCGAGGTTCCACTTTAATTAT
66 AGTCCTTAAATTAGGAGAATTCTTAATTTGGTCCCCACTTTTGCTCGAGGTTCCACTTTAATTAT
* * * *
38525 TCGAATTGCATAATTTATTAAAATTAATTAAGATTAATATTAGATCATCCATCTTAGGCCTAATT
131 TCAAATTGCATAATTGATTAAAATTAATTAAGAGTAATATTAGAGCATCCATCTTAGGCCTAATT
* * *
38590 TCACATTTAGTCCTTAAATTAGGAGAATTTCTAATTGGGTCATCGCTTTTTCTCGAGGTTCCAAT
196 TCAAATTTAGTCCTTAAATTAGGAGAATTTCTAATTGGGTCATCGCTTATGCTCGAGGTTCCAAT
* *
38655 TTAATTGTTCGAATCA
261 TTAACTATTCGAATCA
* *
38671 CATAATTGATTAAAATTAATTAGGATTAATATTAGAGCCTCCATCTTAGGTATAA-TTTCACATT
1 CATAATTGATTAAAATTAATTAAGATTAATATTAGAGCCTCCATCTTAGGCATAATTTTCA-ATT
* *
38735 TAGTCCTTGAATTAGGAGAATTCTTAATTTGGTCCCCATTTTTGCTCGAGGTTCCACTTTAATTA
65 TAGTCCTTAAATTAGGAGAATTCTTAATTTGGTCCCCACTTTTGCTCGAGGTTCCACTTTAATTA
* * * ** * **
38800 TTCAAATTGCATAATTGATTAAAAGTTAA-T-AGGGTAATGCTTAGAGCCTCTTTTTTAGGTTTA
130 TTCAAATTGCATAATTGATTAAAA-TTAATTAAGAGTAAT-ATTAGAGCATCCATCTTAGGCCTA
* * * *
38863 ATTTCAAATTTAGTCCTTTAATTTAGGAGAATTTTTAACTT-GGTCCTCGCTTATGCTCGTGGTT
193 ATTTCAAATTTAGTCC-TTAAATTAGGAGAATTTCTAA-TTGGGTCATCGCTTATGCTCGAGGTT
*
38927 CCATTTTAACTATTC-AACTCA
256 CCAATTTAACTATTCGAA-TCA
* * *
38948 -ATAATTCATTAAAAATGATTTAAG-TTAATATTAGAGCCT
1 CATAATTGATT-AAAATTAATTAAGATTAATATTAGAGCCT
38987 ACATTTTTAG
Statistics
Matches: 268, Mismatches: 41, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
275 10 0.04
276 189 0.71
277 67 0.25
278 2 0.01
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (276 bp):
CATAATTGATTAAAATTAATTAAGATTAATATTAGAGCCTCCATCTTAGGCATAATTTTCAATTT
AGTCCTTAAATTAGGAGAATTCTTAATTTGGTCCCCACTTTTGCTCGAGGTTCCACTTTAATTAT
TCAAATTGCATAATTGATTAAAATTAATTAAGAGTAATATTAGAGCATCCATCTTAGGCCTAATT
TCAAATTTAGTCCTTAAATTAGGAGAATTTCTAATTGGGTCATCGCTTATGCTCGAGGTTCCAAT
TTAACTATTCGAATCA
Found at i:38994 original size:139 final size:139
Alignment explanation
Indices: 38390--39003 Score: 638
Period size: 138 Copynumber: 4.4 Consensus size: 139
38380 TTAGATGAAT
* ** *
38390 AATTTCATAATTGATTAAAATTAATTACTATTAATATTAGAGCC-AC-TATTTTAGGCCTAATTT
1 AATTGCATAATTGATTAAAATTAATTAAGATTAATATTAGAGCCTACAT-TTTTAGGTCTAATTT
** ** *
38453 TGAATTTAGTCCTTAAATTAGTTGAATTCTTAATTTGGTCCTCGCTTTTGTTCGAGGTTCCACTT
65 CAAATTTAGTCCTTAAATTAGGAGAATTCTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCACTT
38518 TAATTATTCG
130 TAATTATTCG
* * * * * *
38528 AATTGCATAATTTATTAAAATTAATTAAGATTAATATTAGATCATCCA-TCTTAGGCCTAATTTC
1 AATTGCATAATTGATTAAAATTAATTAAGATTAATATTAGAGCCTACATTTTTAGGTCTAATTTC
* * * * *
38592 ACATTTAGTCCTTAAATTAGGAGAATT-TCTAATTGGGTCATCGCTTTTTCTCGAGGTTCCAATT
66 AAATTTAGTCCTTAAATTAGGAGAATTCT-TAATTTGGTCCTCGCTTTTGCTCGAGGTTCCACTT
*
38656 TAATTGTTCG
130 TAATTATTCG
** * * * *
38666 AATCACATAATTGATTAAAATTAATTAGGATTAATATTAGAGCCTCCA-TCTTAGGTATAATTTC
1 AATTGCATAATTGATTAAAATTAATTAAGATTAATATTAGAGCCTACATTTTTAGGTCTAATTTC
* * * **
38730 ACATTTAGTCCTTGAATTAGGAGAATTCTTAATTTGGTCCCCATTTTTGCTCGAGGTTCCACTTT
66 AAATTTAGTCCTTAAATTAGGAGAATTCTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCACTTT
*
38795 AATTATTCA
131 AATTATTCG
** * * *
38804 AATTGCATAATTGATTAAAAGTTAA-T-AGGGTAATGCTTAGAGCCT-CTTTTTTAGGTTTAATT
1 AATTGCATAATTGATTAAAA-TTAATTAAGATTAAT-ATTAGAGCCTACATTTTTAGGTCTAATT
* * * * * *
38866 TCAAATTTAGTCCTTTAATTTAGGAGAATTTTTAACTTGGTCCTCGCTTATGCTCGTGGTTCCAT
64 TCAAATTTAGTCC-TTAAATTAGGAGAATTCTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCAC
*
38931 TTTAACTATTC-
128 TTTAATTATTCG
* * * * *
38942 AACT-CAATAATTCATTAAAAATGATTTAAG-TTAATATTAGAGCCTACATTTTTAGGTTTAAT
1 AATTGC-ATAATTGATT-AAAATTAATTAAGATTAATATTAGAGCCTACATTTTTAGGTCTAAT
39004 CCTTAGGTTC
Statistics
Matches: 398, Mismatches: 65, Indels: 25
0.82 0.13 0.05
Matches are distributed among these distances:
137 8 0.02
138 307 0.77
139 81 0.20
140 2 0.01
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (139 bp):
AATTGCATAATTGATTAAAATTAATTAAGATTAATATTAGAGCCTACATTTTTAGGTCTAATTTC
AAATTTAGTCCTTAAATTAGGAGAATTCTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCACTTT
AATTATTCG
Found at i:44340 original size:19 final size:19
Alignment explanation
Indices: 44318--44361 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
44308 TCATTCCTTA
*
44318 AGAGAATGCTTAGTGTTTG
1 AGAGAATGCTTAGTGTTCG
*
44337 AGAGAATGCTTATTGTTCG
1 AGAGAATGCTTAGTGTTCG
44356 AGAGAA
1 AGAGAA
44362 ACTAAGATTG
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:0.32, C:0.07, G:0.30, T:0.32
Consensus pattern (19 bp):
AGAGAATGCTTAGTGTTCG
Found at i:45209 original size:21 final size:21
Alignment explanation
Indices: 45169--45221 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
45159 TTTCATAGCA
*
45169 TTTTTGTTTTACTTTTTTATT
1 TTTTTGTTTTACTTTGTTATT
45190 TTTTTAGTTTTAC-TTGTTATT
1 TTTTT-GTTTTACTTTGTTATT
*
45211 TTCCTTGTTTT
1 TT-TTTGTTTT
45222 TAAAGGTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 19 0.68
22 9 0.32
ACGTcount: A:0.09, C:0.08, G:0.08, T:0.75
Consensus pattern (21 bp):
TTTTTGTTTTACTTTGTTATT
Found at i:48326 original size:12 final size:12
Alignment explanation
Indices: 48296--48329 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
48286 TTAAACCCAA
*
48296 TCATGAAGAAAG
1 TCATGATGAAAG
48308 TCATGATGAAAG
1 TCATGATGAAAG
48320 TCATGATGAA
1 TCATGATGAA
48330 GAAATTATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.44, C:0.09, G:0.24, T:0.24
Consensus pattern (12 bp):
TCATGATGAAAG
Found at i:57706 original size:44 final size:44
Alignment explanation
Indices: 57643--57808 Score: 172
Period size: 44 Copynumber: 3.8 Consensus size: 44
57633 GTTTACAGAT
57643 TAGATTCCATCACATAAGGAGGTGGATTAACATTCCCTTTTTGC
1 TAGATTCCATCACATAAGGAGGTGGATTAACATTCCCTTTTTGC
* * * *
57687 TAGATTCCACCACATAAGGAGTTGGATTAACATTACCTTTTCGC
1 TAGATTCCATCACATAAGGAGGTGGATTAACATTCCCTTTTTGC
* * * * * ** *
57731 TCGATTCAATCATATAAGAAGGTAGATTAACA-TCAATATTTTGT
1 TAGATTCCATCACATAAGGAGGTGGATTAACATTCCCT-TTTTGC
* * * *
57775 TCGATTCCATCACAGAAAGAGGTGGATCAACATT
1 TAGATTCCATCACATAAGGAGGTGGATTAACATT
57809 GTCATTTCGC
Statistics
Matches: 97, Mismatches: 23, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
43 2 0.02
44 94 0.97
45 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Consensus pattern (44 bp):
TAGATTCCATCACATAAGGAGGTGGATTAACATTCCCTTTTTGC
Found at i:57801 original size:88 final size:88
Alignment explanation
Indices: 57645--57808 Score: 195
Period size: 88 Copynumber: 1.9 Consensus size: 88
57635 TTACAGATTA
* * * ** * * *
57645 GATTCCATCACATAAGGAGGTGGATTAACATTCCCTTTTTGCTAGATTCCACCACATAAGGAGTT
1 GATTCAATCACATAAGAAGGTAGATTAACATTCAATTTTTGCTAGATTCCACCACAGAAAGAGGT
*
57710 GGATTAACATTACCTTTTCGCTC
66 GGATCAACATTACCTTTTCGCTC
* * * *
57733 GATTCAATCATATAAGAAGGTAGATTAACA-TCAATATTTTGTTCGATTCCATCACAGAAAGAGG
1 GATTCAATCACATAAGAAGGTAGATTAACATTCAAT-TTTTGCTAGATTCCACCACAGAAAGAGG
57797 TGGATCAACATT
65 TGGATCAACATT
57809 GTCATTTCGC
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
87 3 0.05
88 59 0.95
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (88 bp):
GATTCAATCACATAAGAAGGTAGATTAACATTCAATTTTTGCTAGATTCCACCACAGAAAGAGGT
GGATCAACATTACCTTTTCGCTC
Found at i:58194 original size:18 final size:18
Alignment explanation
Indices: 58156--58191 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
58146 AATTTTTAGT
*
58156 TGATAAAAAAGGAAAAAA
1 TGATAAAAAAAGAAAAAA
58174 TGATAAAAAAAAGAAAAA
1 TGAT-AAAAAAAGAAAAA
58192 TGAGGAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.75, C:0.00, G:0.14, T:0.11
Consensus pattern (18 bp):
TGATAAAAAAAGAAAAAA
Found at i:58245 original size:19 final size:19
Alignment explanation
Indices: 58206--58241 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
58196 GAAATTTTGA
58206 AAAAAAAGAGAAAGAAATG
1 AAAAAAAGAGAAAGAAATG
58225 AAAAAAAGAGAAA-AAAT
1 AAAAAAAGAGAAAGAAAT
58242 TGAATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.06
Consensus pattern (19 bp):
AAAAAAAGAGAAAGAAATG
Found at i:58302 original size:26 final size:23
Alignment explanation
Indices: 58250--58308 Score: 75
Period size: 22 Copynumber: 2.5 Consensus size: 23
58240 ATTGAATTTT
*
58250 TTTGAAAAAACGAGAAAAGAAAA
1 TTTGAAAAAAAGAGAAAAGAAAA
58273 -TTGAAAAGAAAGAGAACAAGAGAAA
1 TTTGAAAA-AAAGAGAA-AAGA-AAA
58298 TTTGAAAAAAA
1 TTTGAAAAAAA
58309 TAGATTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
22 7 0.23
23 7 0.23
24 4 0.13
25 6 0.19
26 7 0.23
ACGTcount: A:0.64, C:0.03, G:0.19, T:0.14
Consensus pattern (23 bp):
TTTGAAAAAAAGAGAAAAGAAAA
Found at i:60924 original size:22 final size:22
Alignment explanation
Indices: 60895--60943 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
60885 TGGGTAAAAT
*
60895 TCTAATTTT-TAACTGCTAACA
1 TCTAATTTTCAAACTGCTAACA
*
60916 TGCTAATTTTCAAACTTCTAACA
1 T-CTAATTTTCAAACTGCTAACA
60939 TCTAA
1 TCTAA
60944 CTTATAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 12 0.50
23 11 0.46
ACGTcount: A:0.35, C:0.20, G:0.04, T:0.41
Consensus pattern (22 bp):
TCTAATTTTCAAACTGCTAACA
Found at i:61418 original size:13 final size:13
Alignment explanation
Indices: 61400--61424 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
61390 GGTTACCATA
61400 TCTTTAAATTTAC
1 TCTTTAAATTTAC
61413 TCTTTAAATTTA
1 TCTTTAAATTTA
61425 GATTCCTTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (13 bp):
TCTTTAAATTTAC
Found at i:61782 original size:138 final size:138
Alignment explanation
Indices: 61468--62071 Score: 686
Period size: 138 Copynumber: 4.4 Consensus size: 138
61458 TTAGATGAAC
* * *
61468 AATTGCATAATTAATTAAAATTAATTAGGATTAATATTAGAGCCACTATCTTAGGCCTAATTTCA
1 AATTGCATAATTGATTAAAATTAATTAGGATTAATATTAGAGCCTCCATCTTAGGCCTAATTTCA
* *
61533 CATTTAGTCCTTAAAGTA-G-GAATTCTTAATTTGGTCCTCACTTTTGCTCGAGGTTCCATTTTA
66 CATTTAGTCCTTAAATTAGGAGAATTCTTAATTGGGTCCTCACTTTTGCTCGAGGTTCCATTTTA
61596 ATTATTCG
131 ATTATTCG
* * *
61604 AATTGCATAAATGATTTAAATTAATTAGGATTAATATTAGAGCCTCCATCTTATGCCTAATTTCA
1 AATTGCATAATTGATTAAAATTAATTAGGATTAATATTAGAGCCTCCATCTTAGGCCTAATTTCA
* * * *
61669 CATTTAGTCCTTAAATTAGGAAAATTCTTAATTGGGTCATCACTTTTGCTCGAGGTTTCAATTTA
66 CATTTAGTCCTTAAATTAGGAGAATTCTTAATTGGGTCCTCACTTTTGCTCGAGGTTCCATTTTA
* *
61734 ATTGCTT-A
131 ATT-ATTCG
* * *
61742 AATCGCATAATTTATTAAAATTAATTAGGATCAATATTAGAGCCTCCATCTTAGGCCTAATTTCA
1 AATTGCATAATTGATTAAAATTAATTAGGATTAATATTAGAGCCTCCATCTTAGGCCTAATTTCA
* * * * ** * *
61807 CATTTATTCCTTGAATTAGGAGGATTCTTAATTTGGTCCTCGTTTTTTCTCGAGGTTCCACTTTA
66 CATTTAGTCCTTAAATTAGGAGAATTCTTAATTGGGTCCTCACTTTTGCTCGAGGTTCCATTTTA
61872 ATTATTCG
131 ATTATTCG
* * * * * * ** *
61880 AATTGCATAATTGATTAAAAGTGAA-TAGG-GTAATGTTTAGAGTCTCAATTTTAGGTTTACTTT
1 AATTGCATAATTGATTAAAA-TTAATTAGGATTAAT-ATTAGAGCCTCCATCTTAGGCCTAATTT
* * * * *
61943 CAAACTTAGTCCTTTAATTTAGGAGAATTCTTAATTGGGTCCTCGCTTTTGGTCGAGGTTCCATT
64 CACATTTAGTCC-TTAAATTAGGAGAATTCTTAATTGGGTCCTCACTTTTGCTCGAGGTTCCATT
*
62008 TTAACTATTC-
128 TTAATTATTCG
* * * * *
62018 AACT-CAATAATTCATTACAAATT-ATTAAG-TTAATATTAGAGCCTACATTTTAGG
1 AATTGC-ATAATTGATTA-AAATTAATTAGGATTAATATTAGAGCCTCCATCTTAGG
62072 TTTAATCCTT
Statistics
Matches: 392, Mismatches: 66, Indels: 19
0.82 0.14 0.04
Matches are distributed among these distances:
136 76 0.19
137 24 0.06
138 231 0.59
139 61 0.16
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (138 bp):
AATTGCATAATTGATTAAAATTAATTAGGATTAATATTAGAGCCTCCATCTTAGGCCTAATTTCA
CATTTAGTCCTTAAATTAGGAGAATTCTTAATTGGGTCCTCACTTTTGCTCGAGGTTCCATTTTA
ATTATTCG
Done.