Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006944.1 Hibiscus syriacus cultivar Beakdansim tig00017846_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: 68353
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:81 original size:3 final size:3
Alignment explanation
Indices: 75--588 Score: 597
Period size: 3 Copynumber: 176.3 Consensus size: 3
65 GAGGAGGAGG
75 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG- AGA AG- AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
*
121 AGA AGA AGA AG- AGA AGA AAA AGA A-A AG- AGAA AGA AGAA AGA AG-
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG-A AGA AG-A AGA AGA
*
164 AGA GAGA AAA AG- AGA AGA AGA AGA A-A AGAA AGA AGA A-A AGA ATG-
1 AGA -AGA AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA AGA AGA A-GA
*
208 AGA AGA TG- AGA AG- AGAA AGA AGA AGA AGA AGA AGA AG- AGA AGA
1 AGA AGA AGA AGA AGA AG-A AGA AGA AGA AGA AGA AGA AGA AGA AGA
*
251 AGA AGA AGA AGA AGA AGA AGA AG- AGA A-A AGA AGA AGA AGA GGA AG-
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
*
296 AGA AGA AGA GGA AGA AGAA AGA AG- AGA AGA AGA AGA AG- AGA AG-
1 AGA AGA AGA AGA AGA AG-A AGA AGA AGA AGA AGA AGA AGA AGA AGA
* *
339 AGA AGA A-A AGA GGA AGA A-A AG- AGA AGA GAGA AGA AGA GGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA -AGA AGA AGA AGA AGA
382 AGA AGA AGA AGA AGA AGA AG- AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* *
429 AGA AGA AGA AGA AGA AGA AGA GGA AGA AGA AGA AGA AGA AGA GGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* * * * * * *
477 AGA GGA AGA GGA AGA GGA AGA GGA AGA GGA AGA AGA GGA AGA GGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* * * * *
525 AGA GGA AGA AAA AGA AGA AGA GGA AGA AAA AGA AGA AGA GGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
*
573 GGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA A
589 AGGGATCAAA
Statistics
Matches: 436, Mismatches: 44, Indels: 62
0.80 0.08 0.11
Matches are distributed among these distances:
2 44 0.10
3 372 0.85
4 20 0.05
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:638 original size:105 final size:105
Alignment explanation
Indices: 529--734 Score: 304
Period size: 105 Copynumber: 2.0 Consensus size: 105
519 GGAAGAAGAG
* * *
529 GAAGAAAAAGAAGAAGAGGAAGAAAAAGAAGAAGAGGAAGAAGAGGAAGAAGAAGAAGAAAGGGA
1 GAAGAAAAAGAAGAAGAAGAAGAAAAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAAGGGA
594 TCAAACCTACTTAATTTTTGAACCGGTGACTAAATTTGAA
66 TCAAACCTACTTAATTTTTGAACCGGTGACTAAATTTGAA
* ** * * * * * *
634 GAAGAAGAAGAAGAAGAAGAAGATGATGATGATGAAGAATAAGAAGAGGAGGAAGAAGAAAGGGA
1 GAAGAAAAAGAAGAAGAAGAAGAAAAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAAGGGA
699 TCAAACCTACTTAATTTTTGAACCGGTGACTAAATT
66 TCAAACCTACTTAATTTTTGAACCGGTGACTAAATT
735 CCGGTGACCA
Statistics
Matches: 89, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
105 89 1.00
ACGTcount: A:0.50, C:0.07, G:0.28, T:0.16
Consensus pattern (105 bp):
GAAGAAAAAGAAGAAGAAGAAGAAAAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAAGGGA
TCAAACCTACTTAATTTTTGAACCGGTGACTAAATTTGAA
Found at i:639 original size:3 final size:3
Alignment explanation
Indices: 631--693 Score: 63
Period size: 3 Copynumber: 21.0 Consensus size: 3
621 GACTAAATTT
* * * * *
631 GAA GAA GAA GAA GAA GAA GAA GAA GAT GAT GAT GAT GAA GAA TAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* *
679 GAG GAG GAA GAA GAA
1 GAA GAA GAA GAA GAA
694 AGGGATCAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.57, C:0.00, G:0.35, T:0.08
Consensus pattern (3 bp):
GAA
Found at i:2293 original size:18 final size:19
Alignment explanation
Indices: 2256--2299 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
2246 ATTAGTGAAG
*
2256 TTTTTAAAGTTTTGATATT
1 TTTTTAAAGATTTGATATT
2275 TTTTTAAAGATTTGA-ATT
1 TTTTTAAAGATTTGATATT
2293 TTTTTAA
1 TTTTTAA
2300 TATAATAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (19 bp):
TTTTTAAAGATTTGATATT
Found at i:5486 original size:23 final size:23
Alignment explanation
Indices: 5460--5520 Score: 113
Period size: 23 Copynumber: 2.7 Consensus size: 23
5450 TTGATATACA
5460 TGAGCTATGTGAATATGTGATTC
1 TGAGCTATGTGAATATGTGATTC
*
5483 TGAGCTATATGAATATGTGATTC
1 TGAGCTATGTGAATATGTGATTC
5506 TGAGCTATGTGAATA
1 TGAGCTATGTGAATA
5521 CCTGTCTGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.30, C:0.08, G:0.25, T:0.38
Consensus pattern (23 bp):
TGAGCTATGTGAATATGTGATTC
Found at i:5859 original size:23 final size:22
Alignment explanation
Indices: 5811--5874 Score: 85
Period size: 23 Copynumber: 2.9 Consensus size: 22
5801 GGTTCTACAC
* *
5811 GGTCATTCGGGACA-TATATGT
1 GGTCCTTCGGGACATTTTATGT
5832 GGTCCTTCGGGACAATTTTATGT
1 GGTCCTTCGGGAC-ATTTTATGT
*
5855 TGTCCTTCGGGACATTTTAT
1 GGTCCTTCGGGACATTTTAT
5875 ACGACACACA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 12 0.32
22 8 0.21
23 18 0.47
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (22 bp):
GGTCCTTCGGGACATTTTATGT
Found at i:8775 original size:18 final size:18
Alignment explanation
Indices: 8749--8794 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
8739 TTTTCAAGTA
*
8749 TGTGGTTCCCCTCCTCCG
1 TGTGCTTCCCCTCCTCCG
8767 TGTGCTTCCCCTCCTCCG
1 TGTGCTTCCCCTCCTCCG
8785 TGTGCTTCCC
1 TGTGCTTCCC
8795 TTCACCGCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.00, C:0.46, G:0.20, T:0.35
Consensus pattern (18 bp):
TGTGCTTCCCCTCCTCCG
Found at i:9523 original size:3 final size:3
Alignment explanation
Indices: 9515--9589 Score: 87
Period size: 3 Copynumber: 24.7 Consensus size: 3
9505 ACATGTAAAT
**
9515 TAA TAA TAA TAA TAA TAA GCA TAA TAA TAA TAA TAA TAA TAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
* ** *
9561 TAA TAA TGA TAA CGA TAA TAA TAT TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
9590 TTTTTATAGA
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
3 56 0.95
4 3 0.05
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:12633 original size:21 final size:21
Alignment explanation
Indices: 12608--12655 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
12598 CCTAATATTG
12608 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
12629 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
12650 TAATGT
1 CAATGT
12656 TTGAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:17289 original size:21 final size:21
Alignment explanation
Indices: 17264--17332 Score: 129
Period size: 21 Copynumber: 3.3 Consensus size: 21
17254 CCTAATATTG
17264 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
17285 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
17306 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
17327 TAATGT
1 CAATGT
17333 TTGAAAATTA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:17831 original size:20 final size:20
Alignment explanation
Indices: 17793--17832 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
17783 CTTCTATATA
* * *
17793 TTATTTTTTTAATTGAAATT
1 TTATTTTATTAAATAAAATT
17813 TTATTTTATTAAATAAAATT
1 TTATTTTATTAAATAAAATT
17833 AAGAATTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (20 bp):
TTATTTTATTAAATAAAATT
Found at i:22167 original size:3 final size:3
Alignment explanation
Indices: 22149--22247 Score: 137
Period size: 3 Copynumber: 33.3 Consensus size: 3
22139 TTTAATATAT
* * *
22149 TAA TAA TGA TAG TAA TAA TGA TAA TAA TAA TAA TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
22196 TAT TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
22244 TAA T
1 TAA T
22248 GGATAAAAAT
Statistics
Matches: 83, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
2 2 0.02
3 81 0.98
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:23335 original size:113 final size:113
Alignment explanation
Indices: 22562--23318 Score: 1356
Period size: 113 Copynumber: 6.7 Consensus size: 113
22552 AGAATTATGC
* * * * *
22562 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTTAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * * * *
22627 TATGAAC-TTCTCTGGAAAAGATAATCCATCAATTGATGAATTCAAGT
66 TATGAACTTTCTCTGGAAAGGCTGATCCATCAAATGATGGACTCAGGT
22674 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
22738 TATGAACTTTCTCTGGAAATGCTGATCCATCAAATGATGGACTCAGGT
66 TATGAACTTTCTCTGGAAAGGCTGATCCATCAAATGATGGACTCAGGT
22786 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
22851 TATGAACTTTCTCTAGAAAGGCTGATCCATCAAATGATGGACTCAGGT
66 TATGAACTTTCTCTGGAAAGGCTGATCCATCAAATGATGGACTCAGGT
22899 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
22964 TATGAACTTTCTCTGGAAAGGCTGATCCATCAAATGATGGACTCAGGT
66 TATGAACTTTCTCTGGAAAGGCTGATCCATCAAATGATGGACTCAGGT
23012 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
23077 TATGAACTTTCTCTGGAAATGCTGATCCATCAAATGATGGACTCAGGT
66 TATGAACTTTCTCTGGAAAGGCTGATCCATCAAATGATGGACTCAGGT
23125 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
23190 TATGAACTTTCTCTGGAAAGGCTGATCCATCAAATGATGGACTCAGGT
66 TATGAACTTTCTCTGGAAAGGCTGATCCATCAAATGATGGACTCAGGT
*
23238 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTTTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
23303 TATGAACTTTCTCTGG
66 TATGAACTTTCTCTGG
23319 CAAAAATAAT
Statistics
Matches: 626, Mismatches: 17, Indels: 3
0.97 0.03 0.00
Matches are distributed among these distances:
111 30 0.05
112 110 0.18
113 486 0.78
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAGGCTGATCCATCAAATGATGGACTCAGGT
Found at i:24131 original size:82 final size:81
Alignment explanation
Indices: 23992--24460 Score: 645
Period size: 82 Copynumber: 5.7 Consensus size: 81
23982 GTTCCTACTA
* *
23992 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTTATCTT-TCAAAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGACAAATTCATCTTCT-AAAT
24056 TCAATGATTATTCTCTCC
64 TCAATGATTATTCTCTCC
* * * *
24074 AACCAAATCAGATAACTCAAAGAACACTTACAGAAGATGCTATTGACAAAGTCATCTTCTAAACT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGACAAATTCATCTTCTAAATT
* *
24139 CAATGATTGTTCTGTCC
65 CAATGATTATTCTCTCC
* * *
24156 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGATATGGCAAATTCATCTTCTAAACTC
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGACAAATTCATCTTCTAAATTC
* *
24221 AATGCTTGATTCTGTCC
66 AATGATT-ATTCTCTCC
* * *
24238 AATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTACGAGCAAATTCATATTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA-CAAATTCATCTTCTAAATT
*
24303 CAATGATTGTT-TCTGCC
65 CAATGATTATTCTCT-CC
* *
24320 AAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACAAATTCATATTCTAAAT
1 -AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG-ACAAATTCATCTTCTAAAT
*
24385 TCAATGATTATTCTATCC
64 TCAATGATTATTCTCTCC
* *
24403 AACCAGATCAGATAACTCAAAGAACATTTCCAGAAGATGCTATGAACACATTCATCTT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG-ACAAATTCATCTT
24461 TCAGTTAATG
Statistics
Matches: 349, Mismatches: 31, Indels: 14
0.89 0.08 0.04
Matches are distributed among these distances:
81 29 0.08
82 218 0.62
83 99 0.28
84 3 0.01
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.28
Consensus pattern (81 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGACAAATTCATCTTCTAAATTC
AATGATTATTCTCTCC
Found at i:24436 original size:247 final size:247
Alignment explanation
Indices: 23995--24460 Score: 708
Period size: 247 Copynumber: 1.9 Consensus size: 247
23985 CCTACTAAAC
* * *
23995 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTTATCTTTCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATCGGCAAATTCATATTTCAAATTCAA
24060 TGATTATTCTCTCCAACCAAATCAGATAACTCAAAGAACACTTACAGAAGATGCTATTGACAAAG
66 TGATTATTCTCTCCAACCAAATCAGATAACTCAAAGAACACTTACAGAAGATGCTATTGACAAAG
* * *
24125 TCATCTTCTAAACTCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGA
131 TCATATTCTAAACTCAATGATTATTCTATCCAACCAGATCAGATAACTCAAAGAACACTTCCAGA
*
24190 AGATGATATG-GCAAATTCATCTTCTAAACTCAATGCTTGATTCTGTCCAAT
196 AGATGATATGAACAAATTCATCTTCTAAACTCAATGCTTGATTCTGTCCAAT
24241 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-CGAGCAAATTCATA-TTCTAAATTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATCG-GCAAATTCATATTTC-AAATTC
* * * *
24304 AATGATTGTT-TCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAA
64 AATGATTATTCTCT-CC-AACCAAATCAGATAACTCAAAGAACACTTACAGAAGATGCTATTG-A
* * *
24367 CAAATTCATATTCTAAATTCAATGATTATTCTATCCAACCAGATCAGATAACTCAAAGAACATTT
126 CAAAGTCATATTCTAAACTCAATGATTATTCTATCCAACCAGATCAGATAACTCAAAGAACACTT
* *
24432 CCAGAAGATGCTATGAACACATTCATCTT
191 CCAGAAGATGATATGAACAAATTCATCTT
24461 TCAGTTAATG
Statistics
Matches: 198, Mismatches: 16, Indels: 10
0.88 0.07 0.04
Matches are distributed among these distances:
245 7 0.04
246 67 0.34
247 113 0.57
248 11 0.06
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.28
Consensus pattern (247 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATCGGCAAATTCATATTTCAAATTCAA
TGATTATTCTCTCCAACCAAATCAGATAACTCAAAGAACACTTACAGAAGATGCTATTGACAAAG
TCATATTCTAAACTCAATGATTATTCTATCCAACCAGATCAGATAACTCAAAGAACACTTCCAGA
AGATGATATGAACAAATTCATCTTCTAAACTCAATGCTTGATTCTGTCCAAT
Found at i:25264 original size:16 final size:16
Alignment explanation
Indices: 25243--25282 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
25233 GAATTTCCAA
25243 AAATAAATTG-ACTCTC
1 AAATAAATTGAACT-TC
*
25259 AAATAAATTGAACTTG
1 AAATAAATTGAACTTC
25275 AAATAAAT
1 AAATAAAT
25283 AGAATTGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 19 0.86
17 3 0.14
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (16 bp):
AAATAAATTGAACTTC
Found at i:25618 original size:8 final size:8
Alignment explanation
Indices: 25597--25634 Score: 53
Period size: 7 Copynumber: 5.0 Consensus size: 8
25587 CTTGACCCAC
25597 CTTTTTTT
1 CTTTTTTT
*
25605 C-CTTTTT
1 CTTTTTTT
25612 CTTTTTTT
1 CTTTTTTT
25620 C-TTTTTT
1 CTTTTTTT
25627 CTTTTTTT
1 CTTTTTTT
25635 TCTCCTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
7 13 0.50
8 13 0.50
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (8 bp):
CTTTTTTT
Found at i:25637 original size:16 final size:15
Alignment explanation
Indices: 25597--25634 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
25587 CTTGACCCAC
*
25597 CTTTTTTTCCTTTTT
1 CTTTTTTTCTTTTTT
25612 CTTTTTTTCTTTTTT
1 CTTTTTTTCTTTTTT
25627 CTTTTTTT
1 CTTTTTTT
25635 TCTCCTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
CTTTTTTTCTTTTTT
Found at i:25647 original size:16 final size:16
Alignment explanation
Indices: 25598--25648 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
25588 TTGACCCACC
25598 TTTTTT-TCCTTTTTCT
1 TTTTTTCTCCTTTTT-T
*
25614 TTTTTTCT-TTTTTCTT
1 TTTTTTCTCCTTTT-TT
25630 TTTTTTCTCCTTTTTT
1 TTTTTTCTCCTTTTTT
25646 TTT
1 TTT
25649 CAAGCATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
16 24 0.80
17 6 0.20
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTTCTCCTTTTTT
Found at i:32923 original size:14 final size:15
Alignment explanation
Indices: 32904--32935 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
32894 ATTTTTTTCA
32904 AATTTTAA-TTAATG
1 AATTTTAACTTAATG
32918 AATTTTAACTTAATG
1 AATTTTAACTTAATG
32933 AAT
1 AAT
32936 AAAATAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (15 bp):
AATTTTAACTTAATG
Found at i:38394 original size:3 final size:3
Alignment explanation
Indices: 38366--38498 Score: 185
Period size: 3 Copynumber: 43.7 Consensus size: 3
38356 TATATATGTT
* * * *
38366 TAA TATA TAT TAA TAA TGA TAG TAA TAA TGA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
38412 TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAT TAA TAA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
38460 TAA TAA TAA TAA TAA TAA TAA TATA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TA
38499 TGGATAAAAA
Statistics
Matches: 114, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
3 108 0.95
4 6 0.05
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:39227 original size:32 final size:32
Alignment explanation
Indices: 39186--39264 Score: 149
Period size: 32 Copynumber: 2.5 Consensus size: 32
39176 TATACGAGGT
39186 GAGGTCGCCATGCAGACGAGCCAGCCAATGGA
1 GAGGTCGCCATGCAGACGAGCCAGCCAATGGA
*
39218 GAGGTCGCCATGCAAACGAGCCAGCCAATGGA
1 GAGGTCGCCATGCAGACGAGCCAGCCAATGGA
39250 GAGGTCGCCATGCAG
1 GAGGTCGCCATGCAG
39265 TCTGGGCGAC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.28, C:0.28, G:0.34, T:0.10
Consensus pattern (32 bp):
GAGGTCGCCATGCAGACGAGCCAGCCAATGGA
Found at i:39355 original size:29 final size:29
Alignment explanation
Indices: 39251--39345 Score: 163
Period size: 29 Copynumber: 3.3 Consensus size: 29
39241 GCCAATGGAG
* **
39251 AGGTCGCCATGCAGTCTGGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
39280 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
39309 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
39338 AGGTCGCC
1 AGGTCGCC
39346 CCGGCGTCCC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.14, C:0.31, G:0.33, T:0.23
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:39445 original size:50 final size:50
Alignment explanation
Indices: 39372--39488 Score: 188
Period size: 50 Copynumber: 2.4 Consensus size: 50
39362 CCCGAGACCA
39372 TGCATG-C-ACATGCA-GCCAAGATAACTTCACGTGCTCCTGCTCCCCGC
1 TGCATGCCTACATGCATGCCAAGATAACTTCACGTGCTCCTGCTCCCCGC
*
39419 TGCATGCCTGCATGCATGCCAAGATAACTTCACGTGCTCCTGCTCCCCGC
1 TGCATGCCTACATGCATGCCAAGATAACTTCACGTGCTCCTGCTCCCCGC
*
39469 TGTATGCCTACA-GCATGCCA
1 TGCATGCCTACATGCATGCCA
39489 TGTGATCCTA
Statistics
Matches: 64, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
47 6 0.09
48 1 0.02
49 14 0.22
50 43 0.67
ACGTcount: A:0.21, C:0.37, G:0.20, T:0.23
Consensus pattern (50 bp):
TGCATGCCTACATGCATGCCAAGATAACTTCACGTGCTCCTGCTCCCCGC
Found at i:39724 original size:16 final size:18
Alignment explanation
Indices: 39703--39741 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
39693 GGAGATAAGG
*
39703 TAAATTTGTTTA-TATT-
1 TAAATTAGTTTATTATTA
39719 TAAATTAGTTTATTATTA
1 TAAATTAGTTTATTATTA
39737 TAAAT
1 TAAAT
39742 GTTAATTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 11 0.55
17 4 0.20
18 5 0.25
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
TAAATTAGTTTATTATTA
Found at i:39889 original size:47 final size:48
Alignment explanation
Indices: 39846--39937 Score: 120
Period size: 46 Copynumber: 2.0 Consensus size: 48
39836 TTATATAGTT
*
39846 AAAAAA-TAATTAATTAGTTTGTT-TT-GTT-AATAGTTAGTTATATAA
1 AAAAAATTAATTAAATAGTTT-TTGTTAGTTAAATAGTTAGTTATATAA
*
39891 AAAAAATTATTTAAATAGTTTTTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAAATTAATTAAATAGTTTTTGTTAGTTAAATAGTT-AGTTATAT
39938 TTGTTTGTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
45 8 0.20
46 14 0.35
47 3 0.08
48 7 0.17
49 8 0.20
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (48 bp):
AAAAAATTAATTAAATAGTTTTTGTTAGTTAAATAGTTAGTTATATAA
Found at i:41640 original size:23 final size:24
Alignment explanation
Indices: 41609--41654 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
41599 GATTAATTAC
41609 TAATATTATTAA-TAATGATTTAA
1 TAATATTATTAACTAATGATTTAA
*
41632 TAATTTTATTAATCTAATGATTT
1 TAATATTATTAA-CTAATGATTT
41655 GATATTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 11 0.55
25 9 0.45
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.52
Consensus pattern (24 bp):
TAATATTATTAACTAATGATTTAA
Found at i:41935 original size:18 final size:18
Alignment explanation
Indices: 41912--41975 Score: 74
Period size: 18 Copynumber: 3.4 Consensus size: 18
41902 AATATAAATA
41912 AAACAAAATATTTTTTTT
1 AAACAAAATATTTTTTTT
* * *
41930 AAACAACATTAAATATTTTT
1 AAACAA-AAT-ATTTTTTTT
*
41950 AAACACAATATTTTTTTT
1 AAACAAAATATTTTTTTT
41968 AAACAAAA
1 AAACAAAA
41976 ATTATCTCGC
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
18 20 0.56
19 4 0.11
20 12 0.33
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (18 bp):
AAACAAAATATTTTTTTT
Found at i:42065 original size:14 final size:14
Alignment explanation
Indices: 42046--42072 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42036 CACATACACA
42046 ACAACAAAAAATAG
1 ACAACAAAAAATAG
42060 ACAACAAAAAATA
1 ACAACAAAAAATA
42073 ATAAATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.15, G:0.04, T:0.07
Consensus pattern (14 bp):
ACAACAAAAAATAG
Found at i:42065 original size:17 final size:17
Alignment explanation
Indices: 42043--42075 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
42033 TTACACATAC
42043 ACAACAACAAAA-AATAG
1 ACAACAA-AAAATAATAG
42060 ACAACAAAAAATAATA
1 ACAACAAAAAATAATA
42076 AATTACTCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.73, C:0.15, G:0.03, T:0.09
Consensus pattern (17 bp):
ACAACAAAAAATAATAG
Found at i:42502 original size:21 final size:21
Alignment explanation
Indices: 42469--42517 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
42459 AATATAATAT
*
42469 ATAACTTAAACTAACCAACTA
1 ATAACTTAAACTAACAAACTA
* *
42490 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
42511 ATTAACT
1 A-TAACT
42518 AGATTTTAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:42988 original size:35 final size:35
Alignment explanation
Indices: 42948--43015 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
42938 TGGATGCAAC
*
42948 GCATGCATGAGTGATACAGTTAAAGCTTGGTCGTT
1 GCATGCATGAGTGATACAGTTAAAGCTGGGTCGTT
*
42983 GCATGCATGAGTGCTACAGTTAAAGCTGGGTCG
1 GCATGCATGAGTGATACAGTTAAAGCTGGGTCG
43016 CGATGCAGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.25, C:0.16, G:0.31, T:0.28
Consensus pattern (35 bp):
GCATGCATGAGTGATACAGTTAAAGCTGGGTCGTT
Found at i:43072 original size:12 final size:12
Alignment explanation
Indices: 43055--43079 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43045 TCCATGGCGA
43055 CCTACCACCTAC
1 CCTACCACCTAC
43067 CCTACCACCTAC
1 CCTACCACCTAC
43079 C
1 C
43080 ATGTCGTCGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.60, G:0.00, T:0.16
Consensus pattern (12 bp):
CCTACCACCTAC
Found at i:43412 original size:29 final size:29
Alignment explanation
Indices: 43370--43454 Score: 145
Period size: 29 Copynumber: 2.9 Consensus size: 29
43360 AAATAATGAT
*
43370 GGACGCCGGGCGTGCATGGCGTCCT-TATA
1 GGACGCCGGGCGTGCATGGCGACCTATA-A
43399 GGACGCCGGGCGTGCATGGCGACCTATAA
1 GGACGCCGGGCGTGCATGGCGACCTATAA
43428 GGACGCCGGGCGTGCATGGCGACCTAT
1 GGACGCCGGGCGTGCATGGCGACCTAT
43455 GTTGCCACTG
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
29 52 0.96
30 2 0.04
ACGTcount: A:0.16, C:0.28, G:0.39, T:0.16
Consensus pattern (29 bp):
GGACGCCGGGCGTGCATGGCGACCTATAA
Found at i:47127 original size:24 final size:24
Alignment explanation
Indices: 47076--47127 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
47066 TTAAATATCC
* *
47076 AAAA-TTTAATTTGATTATAATAT
1 AAAATTTTAATTTGAATATAACAT
47099 AAAATTTTAATTTGAATATAACAT
1 AAAATTTTAATTTGAATATAACAT
*
47123 TAAAT
1 AAAAT
47128 ATCTCAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (24 bp):
AAAATTTTAATTTGAATATAACAT
Found at i:47141 original size:32 final size:32
Alignment explanation
Indices: 47104--47169 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 32
47094 AATATAAAAT
** *
47104 TTTAATTTGAATATAACATTAAATATCTCAAA
1 TTTAATTCAAATACAACATTAAATATCTCAAA
* *
47136 TTTAATTCAAATACAACTTTAAATATCTTAAA
1 TTTAATTCAAATACAACATTAAATATCTCAAA
47168 TT
1 TT
47170 AATATAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.45, C:0.11, G:0.02, T:0.42
Consensus pattern (32 bp):
TTTAATTCAAATACAACATTAAATATCTCAAA
Found at i:47529 original size:24 final size:24
Alignment explanation
Indices: 47484--47529 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
47474 GTTATATTTG
* * *
47484 AATTAAATTTTTATTCTATAATCA
1 AATTAAATTTTGAATATATAATCA
*
47508 AATTAAATTTTGAATATTTAAT
1 AATTAAATTTTGAATATATAAT
47530 ACTATATTTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.50
Consensus pattern (24 bp):
AATTAAATTTTGAATATATAATCA
Found at i:52977 original size:25 final size:26
Alignment explanation
Indices: 52943--52992 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
52933 ATAAGACGCT
*
52943 AAAAATGAC-ATTTTATTATTGTCAC
1 AAAAATGACAATTTAATTATTGTCAC
*
52968 AAAAGTGACAATTTAATTATTGTCA
1 AAAAATGACAATTTAATTATTGTCA
52993 TGTTTGAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (26 bp):
AAAAATGACAATTTAATTATTGTCAC
Found at i:53698 original size:2 final size:2
Alignment explanation
Indices: 53693--53722 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
53683 AAATTGAAGA
53693 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
53723 TGAGTTGGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58451 original size:13 final size:13
Alignment explanation
Indices: 58404--58451 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
58394 TTAAAGTCAA
58404 CGAGTTGAC-ACAG
1 CGAGTTGACTA-AG
*
58417 CGAGTTGACTCAG
1 CGAGTTGACTAAG
*
58430 TGAG-TGACTAAG
1 CGAGTTGACTAAG
58442 CGAGTTGACT
1 CGAGTTGACT
58452 CAGTTCGACC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 10 0.34
13 19 0.66
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (13 bp):
CGAGTTGACTAAG
Found at i:63494 original size:35 final size:35
Alignment explanation
Indices: 63447--63583 Score: 163
Period size: 36 Copynumber: 3.9 Consensus size: 35
63437 AAAAAATGAA
63447 CACTTGAATCGAAAGTG-CGACG-TCTCCTTCCATT
1 CACTTGAATCGAAAGTGCCGACGCT-TCCTTCCATT
* *
63481 CGACTTGAATCGAAAGTGCCGATGCTTCCTTCCGTT
1 C-ACTTGAATCGAAAGTGCCGACGCTTCCTTCCATT
* * *
63517 CAGTTTGAATCGGAAGTGCCGATGCTTCCTTCCATT
1 CA-CTTGAATCGAAAGTGCCGACGCTTCCTTCCATT
* *
63553 CACTTGAATCGGAAGTG-CGACGTTTCCTTCC
1 CACTTGAATCGAAAGTGCCGACGCTTCCTTCC
63584 GTTATTCTTG
Statistics
Matches: 91, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
34 13 0.14
35 31 0.34
36 46 0.51
37 1 0.01
ACGTcount: A:0.20, C:0.28, G:0.21, T:0.31
Consensus pattern (35 bp):
CACTTGAATCGAAAGTGCCGACGCTTCCTTCCATT
Found at i:63535 original size:71 final size:70
Alignment explanation
Indices: 63450--63586 Score: 188
Period size: 71 Copynumber: 1.9 Consensus size: 70
63440 AAATGAACAC
*
63450 TTGAATCGAAAGTG-CGACG-TCTCCTTCCATTCGACTTGAATCGAAAGTGCCGATGCTTCCTTC
1 TTGAATCGAAAGTGCCGACGCT-TCCTTCCATTC-ACTTGAATCGAAAGTG-CGACGCTTCCTTC
63513 CGTTCAGT
63 CGTTCAGT
* * * *
63521 TTGAATCGGAAGTGCCGATGCTTCCTTCCATTCACTTGAATCGGAAGTGCGACGTTTCCTTCCGT
1 TTGAATCGAAAGTGCCGACGCTTCCTTCCATTCACTTGAATCGAAAGTGCGACGCTTCCTTCCGT
63586 T
66 T
63587 ATTCTTGTTC
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
70 15 0.25
71 28 0.47
72 15 0.25
73 1 0.02
ACGTcount: A:0.20, C:0.26, G:0.22, T:0.32
Consensus pattern (70 bp):
TTGAATCGAAAGTGCCGACGCTTCCTTCCATTCACTTGAATCGAAAGTGCGACGCTTCCTTCCGT
TCAGT
Done.