Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002711.1 Hibiscus syriacus cultivar Beakdansim tig00005594_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: 66285
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:466 original size:21 final size:22
Alignment explanation
Indices: 431--472 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
421 ATATAATATT
431 TTTTATTATTAAATG-ATTAAC
1 TTTTATTATTAAATGAATTAAC
452 TTTTATTATCT-AATGAATTAA
1 TTTTATTAT-TAAATGAATTAA
473 AAAATAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (22 bp):
TTTTATTATTAAATGAATTAAC
Found at i:1195 original size:31 final size:32
Alignment explanation
Indices: 1145--1206 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
1135 TATCAATACT
*
1145 ATAAAAATATTAATGTTAAT-ATAATAATAAA
1 ATAAAAATATTAATGTTAATAATAAAAATAAA
*
1176 ATAAAAATATATCAT-TTAATAATAAAAATAA
1 ATAAAAATAT-TAATGTTAATAATAAAAATAA
1207 TATTATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 15 0.56
32 12 0.44
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.34
Consensus pattern (32 bp):
ATAAAAATATTAATGTTAATAATAAAAATAAA
Found at i:2398 original size:10 final size:10
Alignment explanation
Indices: 2379--2408 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
2369 TTCACCGCAC
2379 CAAATCCTCT
1 CAAATCCTCT
*
2389 CAAATTCTCT
1 CAAATCCTCT
2399 CAAATCCTCT
1 CAAATCCTCT
2409 AAAAACCCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.30, C:0.37, G:0.00, T:0.33
Consensus pattern (10 bp):
CAAATCCTCT
Found at i:2466 original size:17 final size:18
Alignment explanation
Indices: 2446--2480 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
2436 TTTATAAGGT
2446 ATATTTTGTTA-TATTTA
1 ATATTTTGTTAGTATTTA
2463 ATATTTTGTTAGTATTTA
1 ATATTTTGTTAGTATTTA
2481 TTTAATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.63
Consensus pattern (18 bp):
ATATTTTGTTAGTATTTA
Found at i:2484 original size:22 final size:20
Alignment explanation
Indices: 2457--2513 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 20
2447 TATTTTGTTA
**
2457 TATTTAATATTTTGTTAGTATT
1 TATTTAATATTTAATTA-T-TT
2479 TATTTAATTATTTAATTATTT
1 TATTTAA-TATTTAATTATTT
2500 TATTTAAATATTTA
1 TATTT-AATATTTA
2514 TTTTTTTGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 13 0.42
22 10 0.32
23 8 0.26
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (20 bp):
TATTTAATATTTAATTATTT
Found at i:4863 original size:105 final size:104
Alignment explanation
Indices: 4661--4858 Score: 244
Period size: 105 Copynumber: 1.9 Consensus size: 104
4651 GTCGATGACT
* *
4661 CATCGGATTCGAGTATTTTGACCATCTCTAATTTTGACGGGGTTGTTCTCGGTGACTTTATATGC
1 CATCGGATTCGAGTATTTTGACCATCTCTAATTTTGACGCGGTTGTTCTCGATGACTTTATATGC
*
4726 ATCTGTGCTGTGCTTACTTGATCTTGCTGTTTTCTGAACC
66 ATCTGTGC-GTGCTGACTTGATCTTGCTGTTTTCTGAACC
* * * * * *
4766 CATCGGGTTCGGGTATTTTGGCCATCTCTAGTTTT-AGCTCGGTTGTTCTCGATGAATTTATATA
1 CATCGGATTCGAGTATTTTGACCATCTCTAATTTTGA-CGCGGTTGTTCTCGATG-ACTT-TATA
4830 TGCATCTGTGC-T-C-GA-TTGATCTTGCTGTT
63 TGCATCTGTGCGTGCTGACTTGATCTTGCTGTT
4859 GTTTTTCTCG
Statistics
Matches: 81, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
102 14 0.17
103 1 0.01
104 2 0.02
105 46 0.57
106 3 0.04
107 15 0.19
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (104 bp):
CATCGGATTCGAGTATTTTGACCATCTCTAATTTTGACGCGGTTGTTCTCGATGACTTTATATGC
ATCTGTGCGTGCTGACTTGATCTTGCTGTTTTCTGAACC
Found at i:7170 original size:29 final size:29
Alignment explanation
Indices: 7137--7206 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
7127 CATATTTTGG
* *
7137 TTAGTGACCAAAATATAAATTTTG-AAAGT
1 TTAGTGACCAAAATAGAAA-TTGGAAAAGT
* * *
7166 TTAGTGGCTAAAGTAGAAATTGGAAAAGT
1 TTAGTGACCAAAATAGAAATTGGAAAAGT
*
7195 TTAGGGACCAAA
1 TTAGTGACCAAA
7207 GGGTAATTTT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
28 3 0.09
29 29 0.91
ACGTcount: A:0.43, C:0.07, G:0.21, T:0.29
Consensus pattern (29 bp):
TTAGTGACCAAAATAGAAATTGGAAAAGT
Found at i:9105 original size:24 final size:24
Alignment explanation
Indices: 9004--9098 Score: 129
Period size: 24 Copynumber: 4.0 Consensus size: 24
8994 CACTGAAGTG
* * *
9004 CCACATAG-ATTTGTCTCAAAGGA
1 CCACGTAGAATTTGTCCCGAAGGA
* *
9027 ACGCGTAGAATTTGTCCCGAAGGA
1 CCACGTAGAATTTGTCCCGAAGGA
9051 CCACGTAGAATTTGTCCCGAAGGA
1 CCACGTAGAATTTGTCCCGAAGGA
*
9075 CCACGTAGAATTTATCCCGAAGGA
1 CCACGTAGAATTTGTCCCGAAGGA
9099 TTGCGTATAA
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
23 5 0.08
24 58 0.92
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.22
Consensus pattern (24 bp):
CCACGTAGAATTTGTCCCGAAGGA
Found at i:13521 original size:12 final size:12
Alignment explanation
Indices: 13493--13536 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
13483 AAGTACTTAT
*
13493 TATGAATATGAAA
1 TATGAAAATG-AA
13506 TATGAAAATGAA
1 TATGAAAATGAA
**
13518 TATGTGAATGAA
1 TATGAAAATGAA
13530 TATGAAA
1 TATGAAA
13537 GTTGAAAATG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 17 0.65
13 9 0.35
ACGTcount: A:0.52, C:0.00, G:0.18, T:0.30
Consensus pattern (12 bp):
TATGAAAATGAA
Found at i:18376 original size:2 final size:2
Alignment explanation
Indices: 18369--18395 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
18359 CTAATTTTCT
18369 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
18396 TTTTATCTTC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:19206 original size:14 final size:14
Alignment explanation
Indices: 19187--19218 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
19177 CTATAATTGG
19187 TTTTTCGAAAAATA
1 TTTTTCGAAAAATA
*
19201 TTTTTCGAAAAATG
1 TTTTTCGAAAAATA
19215 TTTT
1 TTTT
19219 CCTAATTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.50
Consensus pattern (14 bp):
TTTTTCGAAAAATA
Found at i:19437 original size:30 final size:27
Alignment explanation
Indices: 19380--19437 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 27
19370 CTCAAAACAT
**
19380 TATTATTTTATATATTTAATATTAATA
1 TATTATTTTATATATTTAATAAAAATA
19407 TATTATTTTAGTATCATTTTAATAAAAATA
1 TATTATTTTA-TAT-A-TTTAATAAAAATA
19437 T
1 T
19438 TAATTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 10 0.38
28 3 0.12
29 1 0.04
30 12 0.46
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (27 bp):
TATTATTTTATATATTTAATAAAAATA
Found at i:19490 original size:21 final size:21
Alignment explanation
Indices: 19422--19490 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
19412 TTTTAGTATC
19422 ATTTTAATAA-A-AATATTA-
1 ATTTTAATAATATAATATTAT
* *
19440 ATTATTAA-ATTATATTTATTGAT
1 ATT-TTAATAATATA-ATATT-AT
19463 AATTTTAATAATATAATATTAT
1 -ATTTTAATAATATAATATTAT
19485 ATTTTA
1 ATTTTA
19491 TTATTTTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
18 4 0.10
19 5 0.13
20 1 0.03
21 10 0.26
22 3 0.08
23 8 0.21
24 8 0.21
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (21 bp):
ATTTTAATAATATAATATTAT
Found at i:19655 original size:21 final size:22
Alignment explanation
Indices: 19610--19652 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
19600 TATTGAATTG
*
19610 TTAAATATTTAATATATATTCC
1 TTAAATATATAATATATATTCC
19632 TTAAA-ATATAATATAATATTC
1 TTAAATATATAATAT-ATATTC
19653 TTATTTTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (22 bp):
TTAAATATATAATATATATTCC
Found at i:19686 original size:16 final size:16
Alignment explanation
Indices: 19665--19717 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 16
19655 ATTTTGATAT
19665 TTTAATAATATTATTA
1 TTTAATAATATTATTA
19681 TTTAATAAATAATTAATATA
1 TTTAAT-AAT-ATT-AT-TA
*
19701 GTTAATAATA-TATTA
1 TTTAATAATATTATTA
19716 TT
1 TT
19718 CTTTTTTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
15 3 0.10
16 8 0.26
17 4 0.13
18 4 0.13
19 5 0.16
20 7 0.23
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
TTTAATAATATTATTA
Found at i:19693 original size:20 final size:20
Alignment explanation
Indices: 19668--19734 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
19658 TTGATATTTT
19668 AATAATATTATTATTTAATA
1 AATAATATTATTATTTAATA
* *
19688 AATAAT-TAATATAGTTAATA
1 AATAATATTAT-TATTTAATA
* * *
19708 ATATATTATTCTTTTTTAATA
1 A-ATAATATTATTATTTAATA
19729 AATAAT
1 AATAAT
19735 CAATATAATT
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 3 0.08
20 19 0.53
21 12 0.33
22 2 0.06
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (20 bp):
AATAATATTATTATTTAATA
Found at i:19851 original size:14 final size:14
Alignment explanation
Indices: 19808--19862 Score: 60
Period size: 14 Copynumber: 3.9 Consensus size: 14
19798 AATTATAGAT
19808 ATAATATTTTAAT-A
1 ATAATA-TTTAATAA
*
19822 ATAATATTGACATAA
1 ATAATATTTA-ATAA
19837 ATAATATTTAATAA
1 ATAATATTTAATAA
*
19851 ATTATA-TTAATA
1 ATAATATTTAATA
19863 TTTTAAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
13 9 0.25
14 17 0.47
15 10 0.28
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (14 bp):
ATAATATTTAATAA
Found at i:19863 original size:20 final size:20
Alignment explanation
Indices: 19838--19900 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
19828 TTGACATAAA
19838 TAATATTTAATAAATTATAT
1 TAATATTTAATAAATTATAT
*
19858 TAATATTTTA-AAATTATTAT
1 TAATATTTAATAAATTA-TAT
* * *
19878 TATTTTGTTAATAAATAATAT
1 TAATAT-TTAATAAATTATAT
19899 TA
1 TA
19901 TTTATTGTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
19 6 0.17
20 16 0.46
21 8 0.23
22 5 0.14
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TAATATTTAATAAATTATAT
Found at i:20907 original size:41 final size:44
Alignment explanation
Indices: 20861--20945 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
20851 TTATATATAC
20861 ATATAACA-AAC-CT-ATTATAATTATTTTTTTTCTTTTTTATT
1 ATATAACAGAACTCTAATTATAATTATTTTTTTTCTTTTTTATT
* * *
20902 ATATAATAGCACTCTAATTGTAATTATTTTTTTTCTTTTTTATT
1 ATATAACAGAACTCTAATTATAATTATTTTTTTTCTTTTTTATT
20946 GGAGGGTATG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 7 0.18
42 2 0.05
43 2 0.05
44 27 0.71
ACGTcount: A:0.29, C:0.09, G:0.02, T:0.59
Consensus pattern (44 bp):
ATATAACAGAACTCTAATTATAATTATTTTTTTTCTTTTTTATT
Found at i:39324 original size:6 final size:6
Alignment explanation
Indices: 39313--39360 Score: 60
Period size: 6 Copynumber: 8.0 Consensus size: 6
39303 GAAAGTGGAG
* * * *
39313 GAGGAT GAGGAT GAGGAT GAGGAT GACGAG GAGGAC GATGAT GAGGAT
1 GAGGAT GAGGAT GAGGAT GAGGAT GAGGAT GAGGAT GAGGAT GAGGAT
39361 TAACAAAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.33, C:0.04, G:0.48, T:0.15
Consensus pattern (6 bp):
GAGGAT
Found at i:57572 original size:27 final size:25
Alignment explanation
Indices: 57525--57580 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
57515 TATTTTAAAA
*
57525 TTATAATTATGAAAAATATATATTAAT
1 TTATAATTATGAAAAA-A-ATATTTAT
*
57552 TTATATTTAT-AAATAAAATATTTAT
1 TTATAATTATGAAA-AAAATATTTAT
57577 TTAT
1 TTAT
57581 TTAGAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 11 0.42
26 4 0.15
27 11 0.42
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
TTATAATTATGAAAAAAATATTTAT
Found at i:57666 original size:158 final size:159
Alignment explanation
Indices: 57463--57787 Score: 573
Period size: 159 Copynumber: 2.0 Consensus size: 159
57453 TATAAATTGT
* * *
57463 CTCTTATTATTAGAAATTAAAACTTCAAAATATATTTAATTTATAATCCTATTATTTTAAAATTA
1 CTCTT-TTATTAAAAATTAAAAATTCAAAATATATTTAATTTATAATCCTATAATTTTAAAATTA
57528 TAATTATGAAAAATATATATTAA-TT-TATATTTATAAATAAAATATTTATTTATTTAGAAATAT
65 TAATTATGAAAAATATATA-TAATTTATATATTTATAAATAAAATATTTATTTATTTAGAAATAT
57591 CAGAAAAAGACTTCTAGGTGCCTTAAGACAG
129 CAGAAAAAGACTTCTAGGTGCCTTAAGACAG
*
57622 TTCTTTTATTAAAAATTAAAAATTCAAAATATATTTAATTTATAATCCTATAATTTTAAAATTAT
1 CTCTTTTATTAAAAATTAAAAATTCAAAATATATTTAATTTATAATCCTATAATTTTAAAATTAT
57687 AATTATGAAAAATATATATAATTTATATATTTATAAATAAAATATTTATTTATTTAGAAATATCA
66 AATTATGAAAAATATATATAATTTATATATTTATAAATAAAATATTTATTTATTTAGAAATATCA
*
57752 GAAAATGACTTCTAGGTGCCTTAAGACAG
131 GAAAAAGACTTCTAGGTGCCTTAAGACAG
57781 CTCTTTT
1 CTCTTTT
57788 TCTCGATATT
Statistics
Matches: 158, Mismatches: 6, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
157 3 0.02
158 77 0.49
159 78 0.49
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.42
Consensus pattern (159 bp):
CTCTTTTATTAAAAATTAAAAATTCAAAATATATTTAATTTATAATCCTATAATTTTAAAATTAT
AATTATGAAAAATATATATAATTTATATATTTATAAATAAAATATTTATTTATTTAGAAATATCA
GAAAAAGACTTCTAGGTGCCTTAAGACAG
Found at i:57841 original size:159 final size:157
Alignment explanation
Indices: 57516--57842 Score: 446
Period size: 159 Copynumber: 2.1 Consensus size: 157
57506 TAATCCTATT
57516 ATTTTAAAATTATAATTATGAAAAATATATATTAATTTATATTTATAAATAAAATATTTATTTAT
1 ATTTTAAAATTATAATTATGAAAAATATATATTAATTTATATTTATAAATAAAATATTTATTTAT
* *
57581 TTAGAAATATCAGAAAAAGACTTCTAGGTGCCTTAAGACAGTTCTTTTATTAAAAATTAAAAATT
66 TTAGAAATATCAGAAAAAGACTTCTAGGTGCCTTAAGACAGCTCTTTTATTAAAAATTAAAAAAT
* * * * ** *
57646 CAAAATATATTTAATTTATAATCCTATA
131 CAAAAAATAATTAA-TAACAATAATAGA
57674 ATTTTAAAATTATAATTATGAAAAATATATA-TAATTTATATATTTATAAATAAAATATTTATTT
1 ATTTTAAAATTATAATTATGAAAAATATATATTAA-TT-TATATTTATAAATAAAATATTTATTT
* ** *
57738 ATTTAGAAATATCAGAAAATGACTTCTAGGTGCCTTAAGACAGCTCTTTT-TCTCGATATTAAAA
64 ATTTAGAAATATCAGAAAAAGACTTCTAGGTGCCTTAAGACAGCTCTTTTAT-TAAAAATTAAAA
57802 AAT-AAATAAATAATTAA-AACAATTAATAGA
128 AATCAAA-AAATAATTAATAACAA-TAATAGA
57832 ATTTATAAAAT
1 ATTT-TAAAAT
57843 AGGATATTTA
Statistics
Matches: 150, Mismatches: 13, Indels: 11
0.86 0.07 0.06
Matches are distributed among these distances:
157 6 0.04
158 45 0.30
159 99 0.66
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.40
Consensus pattern (157 bp):
ATTTTAAAATTATAATTATGAAAAATATATATTAATTTATATTTATAAATAAAATATTTATTTAT
TTAGAAATATCAGAAAAAGACTTCTAGGTGCCTTAAGACAGCTCTTTTATTAAAAATTAAAAAAT
CAAAAAATAATTAATAACAATAATAGA
Found at i:59436 original size:3 final size:3
Alignment explanation
Indices: 59428--59471 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
59418 TATATATATT
* * *
59428 TAA TAA TAA TAA TAA TAA TATA TTA TAT TAA TAA TAA TTA TAA T
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA T
59472 TATTATTATG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
3 32 0.94
4 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
TAA
Found at i:59448 original size:28 final size:27
Alignment explanation
Indices: 59413--59480 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 27
59403 ATGTAATTTG
59413 TAATATATA-TATATTTAATAATAATAA
1 TAATATATATTATA-TTAATAATAATAA
*
59440 TAATAATATATTATATTAATAATAATTA
1 TAAT-ATATATTATATTAATAATAATAA
59468 TAAT-TATTATTAT
1 TAATATA-TATTAT
59481 GAAAAAATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
26 2 0.05
27 10 0.27
28 21 0.57
29 4 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
TAATATATATTATATTAATAATAATAA
Found at i:59478 original size:22 final size:22
Alignment explanation
Indices: 59434--59479 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
59424 TATTTAATAA
59434 TAATAATAATAATATATTATAT
1 TAATAATAATAATATATTATAT
*
59456 TAATAATAATTATA-ATTATTAT
1 TAATAATAATAATATATTA-TAT
59478 TA
1 TA
59480 TGAAAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TAATAATAATAATATATTATAT
Found at i:59712 original size:76 final size:76
Alignment explanation
Indices: 59595--60153 Score: 897
Period size: 76 Copynumber: 7.5 Consensus size: 76
59585 GATGAAAATG
* * * * *
59595 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGG-CTTTGAAAACATCAAAAAGC
59660 TCCCGAAGGCTT
65 TCCCGAAGGCTT
* *
59672 TTTGGAAACATCATGCACTGTAGGAC-TACAGATGACCCGAAGG-TTTGAAAACATCAAAAAAGC
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATC-AAAAAGC
*
59735 TCCCAAAGGCTT
65 TCCCGAAGGCTT
59747 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
59812 CCCGAAGGCTT
66 CCCGAAGGCTT
*
59823 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
59888 CCCGAAGGC-T
66 CCCGAAGGCTT
* *
59898 TTTGG--ACATCATGCACTGCATGACTTA-AGATGACCCTAAGGTTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
59960 CCCGAAGGCTT
66 CCCGAAGGCTT
*
59971 TTTGG-AA-A-CAT-CACTGCAGGACTTACAGATGACCCTAAGGCTTTGGAAACATCAAAAAAGC
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATC-AAAAAGC
60032 TCCCGAAGGCTT
65 TCCCGAAGGCTT
*
60044 TTTGGAAACATCATGCACTGTA-GACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
60108 CCCGAAGGCTT
66 CCCGAAGGCTT
60119 TTTGGAAACATCATGCACTGCAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATG
60154 TGGGAAATAG
Statistics
Matches: 453, Mismatches: 17, Indels: 25
0.92 0.03 0.05
Matches are distributed among these distances:
71 13 0.03
72 71 0.16
73 51 0.11
74 15 0.03
75 90 0.20
76 172 0.38
77 41 0.09
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:60055 original size:148 final size:153
Alignment explanation
Indices: 59595--60153 Score: 908
Period size: 148 Copynumber: 3.7 Consensus size: 153
59585 GATGAAAATG
* * * * *
59595 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGG-CTTTGAAAACATCAAAAAGC
* *
59660 TCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGAC-TACAGATGACCCGAAGG-TTTGAAAA
65 TCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAA
*
59723 CATCAAAAAAGCTCCCAAAGGCTT
130 CATCAAAAAAGCTCCCGAAGGCTT
59747 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
59812 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
59877 ATC-AAAAAGCTCCCGAAGGC-T
131 ATCAAAAAAGCTCCCGAAGGCTT
* *
59898 TTTGG--ACATCATGCACTGCATGACTTA-AGATGACCCTAAGGTTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
59960 CCCGAAGGCTTTTTGG-AA-A-CAT-CACTGCAGGACTTACAGATGACCCTAAGGCTTTGGAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
60021 ATCAAAAAAGCTCCCGAAGGCTT
131 ATCAAAAAAGCTCCCGAAGGCTT
*
60044 TTTGGAAACATCATGCACTGTA-GACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
60108 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
60154 TGGGAAATAG
Statistics
Matches: 383, Mismatches: 13, Indels: 22
0.92 0.03 0.05
Matches are distributed among these distances:
144 40 0.10
145 20 0.05
146 7 0.02
147 8 0.02
148 114 0.30
149 23 0.06
150 1 0.00
151 66 0.17
152 92 0.24
153 12 0.03
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (153 bp):
TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
ATCAAAAAAGCTCCCGAAGGCTT
Found at i:60461 original size:152 final size:150
Alignment explanation
Indices: 60179--60463 Score: 376
Period size: 152 Copynumber: 1.9 Consensus size: 150
60169 TAAGTAAGAA
* * * * * *
60179 ACTATGAAAATCGTTTTCTTACTTTTCAATAATTTCATTTTAGAAAAGATTGAATGAGAAACTAT
1 ACTAAGAAAATCGTTTTCTTACTTTTCAACAATTT-ATTTTAGAAAAAAATAAATGACAAACTAT
* *
60244 GGAAATCATTTTCTCATTATTTTCAAAATAACATGTTAATTGGGTAACATGCCCCAATCTCAAGA
65 GAAAATCATTTTCTCATTATTTTCAAAATAACATGTTAATTGGGTAACATGACCCAATCTCAAGA
60309 TAAGGCTGTTGGAAATAGTTT
130 TAAGGCTGTTGGAAATAGTTT
60330 ACTAAGAAAATCGTTTTCTTACTTTTCAACAA-TT-TTTTAGAAAAAAAATAAATGACAAACTAT
1 ACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTATTTTAG-AAAAAAATAAATGACAAACTAT
* * * ** * *
60393 GAAAATCGTTTTCTTATTCTGTTTTTTTAAATAACATGTTGATTGGGTAACATGACCCAATCTGA
65 GAAAATCATTTTCTCA-T-T-ATTTTCAAAATAACATGTTAATTGGGTAACATGACCCAATCTCA
60458 AGATAA
127 AGATAA
60464 TGCTCATTTT
Statistics
Matches: 115, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
148 6 0.05
149 31 0.27
150 3 0.03
151 31 0.27
152 44 0.38
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (150 bp):
ACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTATTTTAGAAAAAAATAAATGACAAACTATG
AAAATCATTTTCTCATTATTTTCAAAATAACATGTTAATTGGGTAACATGACCCAATCTCAAGAT
AAGGCTGTTGGAAATAGTTT
Found at i:61497 original size:54 final size:54
Alignment explanation
Indices: 61371--61528 Score: 184
Period size: 54 Copynumber: 3.0 Consensus size: 54
61361 ATAATCATTG
* * * *
61371 GTTCGTAAAACATTTGACAATACATTCATCTTTTCCTGTGGTTTCTG-TC-GA-
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCTTGTGGCTTCTGCTCAGAT
* * *
61422 GAT-GTAAAACATTTGAAAACACATT-ATTCCTTTCTTGTAGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCA-TCCTTTCTTGTGGCTTCTGCTCAGAT
*
61475 GTTCGTAAAGCATTTGACAACACATTCATCCTTT-TCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCT-TGTGGCTTCTGCTCAGAT
61529 TTCTCAATTA
Statistics
Matches: 89, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
49 1 0.01
50 35 0.39
51 4 0.04
52 2 0.02
53 3 0.03
54 43 0.48
55 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCTTGTGGCTTCTGCTCAGAT
Found at i:65785 original size:9 final size:8
Alignment explanation
Indices: 65770--65884 Score: 87
Period size: 8 Copynumber: 14.5 Consensus size: 8
65760 CAATTTCTCC
65770 CTTTTTTT
1 CTTTTTTT
65778 CATTTTTTTT
1 C--TTTTTTT
*
65788 CATTTTTT
1 CTTTTTTT
* *
65796 CCTTTTTC
1 CTTTTTTT
65804 CTTTTTTT
1 CTTTTTTT
65812 -TCTTTTTT
1 CT-TTTTTT
65820 -TTTTTTT
1 CTTTTTTT
*
65827 CTTTTTTC
1 CTTTTTTT
*
65835 CTTTTTCT
1 CTTTTTTT
*
65843 C-ATTTTT
1 CTTTTTTT
*
65850 CTTTTTCAT
1 CTTTTT-TT
65859 C-TTTTTT
1 CTTTTTTT
65866 C-TTTTTT
1 CTTTTTTT
*
65873 CTTTCTTT
1 CTTTTTTT
65881 CTTT
1 CTTT
65885 GCTGGATTTT
Statistics
Matches: 86, Mismatches: 14, Indels: 14
0.75 0.12 0.12
Matches are distributed among these distances:
7 21 0.24
8 55 0.64
9 2 0.02
10 8 0.09
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.79
Consensus pattern (8 bp):
CTTTTTTT
Found at i:65786 original size:10 final size:10
Alignment explanation
Indices: 65771--65795 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
65761 AATTTCTCCC
65771 TTTTTTTCAT
1 TTTTTTTCAT
65781 TTTTTTTCAT
1 TTTTTTTCAT
65791 TTTTT
1 TTTTT
65796 CCTTTTTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTTCAT
Found at i:65832 original size:46 final size:46
Alignment explanation
Indices: 65782--65881 Score: 130
Period size: 46 Copynumber: 2.2 Consensus size: 46
65772 TTTTTTCATT
* ** *
65782 TTTTTTCATTTTT-TCCTTTTTCCTTTTTTTTCTTTTTTTTTTTTTC
1 TTTTTTCATTTTTCTCATTTTT-CTTTTTCATCTTTTTTCTTTTTTC
*
65828 TTTTTTCCTTTTTCTCATTTTTCTTTTTCATCTTTTTTCTTTTTTC
1 TTTTTTCATTTTTCTCATTTTTCTTTTTCATCTTTTTTCTTTTTTC
65874 TTTCTTTC
1 TTT-TTTC
65882 TTTGCTGGAT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
46 36 0.77
47 11 0.23
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (46 bp):
TTTTTTCATTTTTCTCATTTTTCTTTTTCATCTTTTTTCTTTTTTC
Found at i:65894 original size:46 final size:46
Alignment explanation
Indices: 65798--65901 Score: 122
Period size: 46 Copynumber: 2.2 Consensus size: 46
65788 CATTTTTTCC
** * *
65798 TTTTTCCTTTTTTTTCTTTTTTTTTTTTTCTTTTTTCCTTTTTCTCA
1 TTTTT-CTTTTTCATCTTTTTTCTTTTTTCTTTTTTCCTTTTGCTCA
*
65845 TTTTTCTTTTTCATCTTTTTTCTTTTTTCTTTCTTT-C-TTTGCTGGA
1 TTTTTCTTTTTCATCTTTTTTCTTTTTTCTTT-TTTCCTTTTGCT-CA
65891 TTTTTCTTTTT
1 TTTTTCTTTTT
65902 TCTTTCTTTG
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
45 5 0.10
46 37 0.74
47 8 0.16
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.78
Consensus pattern (46 bp):
TTTTTCTTTTTCATCTTTTTTCTTTTTTCTTTTTTCCTTTTGCTCA
Found at i:65906 original size:7 final size:7
Alignment explanation
Indices: 65782--65884 Score: 98
Period size: 7 Copynumber: 13.4 Consensus size: 7
65772 TTTTTTCATT
65782 TTTTTTC
1 TTTTTTC
65789 ATTTTTTCC
1 -TTTTTT-C
*
65798 TTTTTCCTT
1 TTTTT--TC
65807 TTTTTTC
1 TTTTTTC
*
65814 TTTTTTT
1 TTTTTTC
65821 TTTTTTC
1 TTTTTTC
65828 TTTTTTCC
1 TTTTTT-C
65836 TTTTTCTC
1 TTTTT-TC
*
65844 ATTTTTC
1 TTTTTTC
65851 TTTTTCATC
1 TTTTT--TC
65860 TTTTTTC
1 TTTTTTC
65867 TTTTTTC
1 TTTTTTC
65874 TTTCTTTC
1 TTT-TTTC
65882 TTT
1 TTT
65885 GCTGGATTTT
Statistics
Matches: 81, Mismatches: 6, Indels: 16
0.79 0.06 0.16
Matches are distributed among these distances:
7 37 0.46
8 29 0.36
9 14 0.17
10 1 0.01
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTTTC
Done.