Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004505.1 Hibiscus syriacus cultivar Beakdansim tig00009939_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: 85080
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:2813 original size:19 final size:19
Alignment explanation
Indices: 2789--2839 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
2779 ACCAACTAAA
2789 TCGCAATGCGATCGATAAT
1 TCGCAATGCGATCGATAAT
2808 TCGCAATGCGATCGATAAT
1 TCGCAATGCGATCGATAAT
*
2827 TCGCAACGCGATC
1 TCGCAATGCGATC
2840 TCTGGTATCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (19 bp):
TCGCAATGCGATCGATAAT
Found at i:2986 original size:20 final size:20
Alignment explanation
Indices: 2930--3000 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
2920 GTGATTTTCC
*
2930 GACTATCGCAATGCGAATAT
1 GACTATCGCAATGCGATTAT
*
2950 GTA-AATCGCAATGCGATTAT
1 G-ACTATCGCAATGCGATTAT
*
2970 GACTATCGCAATGCGATTCT
1 GACTATCGCAATGCGATTAT
*
2990 GACTGTCGCAA
1 GACTATCGCAA
3001 CACTGAATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
19 1 0.02
20 42 0.95
21 1 0.02
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (20 bp):
GACTATCGCAATGCGATTAT
Found at i:5482 original size:3 final size:3
Alignment explanation
Indices: 5474--5528 Score: 67
Period size: 3 Copynumber: 18.7 Consensus size: 3
5464 CATGCACACT
* * * *
5474 TAA TAA TAA TAT TAC TAA TAT TAA TAA TAA TAA TAA TAA TAA TAA T-T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5521 TAA TAA TA
1 TAA TAA TA
5529 TTCTTTAACC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
2 1 0.02
3 43 0.98
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:5494 original size:9 final size:9
Alignment explanation
Indices: 5477--5530 Score: 74
Period size: 9 Copynumber: 6.1 Consensus size: 9
5467 GCACACTTAA
5477 TAATAATAT
1 TAATAATAT
*
5486 TACTAATAT
1 TAATAATAT
*
5495 TAATAATAA
1 TAATAATAT
*
5504 TAATAATAA
1 TAATAATAT
5513 TAATAAT-T
1 TAATAATAT
5521 TAATAATAT
1 TAATAATAT
5530 T
1 T
5531 CTTTAACCCT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
8 7 0.17
9 33 0.82
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (9 bp):
TAATAATAT
Found at i:6033 original size:108 final size:111
Alignment explanation
Indices: 5844--6051 Score: 368
Period size: 108 Copynumber: 1.9 Consensus size: 111
5834 TTGGAAATGG
5844 CAATCCCCCAAGTGAGGTGTCACTGATTCGAAATGCTGTGAATCGAGTGATAGGTCAAACAAGCT
1 CAATCCCCCAAGTGAGGTGTCACTGATTCGAAATGCTGTGAATCGAGTGATAGGTCAAACAAGCT
5909 CTTCTCATTATGAACTTC-T-TC-CTCTGTCGGATATTGAAAATTT
66 CTTCTCATTATGAACTTCTTCTCACTCTGTCGGATATTGAAAATTT
* * *
5952 CAATCCCTCAAGTGAGGTGTCACTGATTTGAAATGCTGTGAATCGAGTGATAGGTCGAACAAGCT
1 CAATCCCCCAAGTGAGGTGTCACTGATTCGAAATGCTGTGAATCGAGTGATAGGTCAAACAAGCT
6017 CTTCTCATTATGAACTTCTTCTCACTCTGTCGGAT
66 CTTCTCATTATGAACTTCTTCTCACTCTGTCGGAT
6052 GAGTTCTTCT
Statistics
Matches: 94, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
108 80 0.85
109 1 0.01
110 2 0.02
111 11 0.12
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (111 bp):
CAATCCCCCAAGTGAGGTGTCACTGATTCGAAATGCTGTGAATCGAGTGATAGGTCAAACAAGCT
CTTCTCATTATGAACTTCTTCTCACTCTGTCGGATATTGAAAATTT
Found at i:6641 original size:15 final size:15
Alignment explanation
Indices: 6616--6689 Score: 95
Period size: 14 Copynumber: 5.2 Consensus size: 15
6606 AAACCCTCAC
6616 TTTTCTCTTTTCATTT
1 TTTTCT-TTTTCATTT
6632 TTTTCTTTTTCATTT
1 TTTTCTTTTTCATTT
*
6647 TTTTC-ATTT--TTT
1 TTTTCTTTTTCATTT
6659 TTTTCTTTTTCA-TT
1 TTTTCTTTTTCATTT
6673 TTTT-TTTTTCATTT
1 TTTTCTTTTTCATTT
6687 TTT
1 TTT
6690 ATTTGTTTCT
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
12 8 0.15
13 10 0.19
14 14 0.27
15 14 0.27
16 6 0.12
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTCTTTTTCATTT
Found at i:6678 original size:18 final size:18
Alignment explanation
Indices: 6646--6680 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
6636 CTTTTTCATT
6646 TTTTTCATTTTTTTTTTC
1 TTTTTCATTTTTTTTTTC
6664 TTTTTCATTTTTTTTTT
1 TTTTTCATTTTTTTTTT
6681 TCATTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.06, C:0.09, G:0.00, T:0.86
Consensus pattern (18 bp):
TTTTTCATTTTTTTTTTC
Found at i:6687 original size:27 final size:28
Alignment explanation
Indices: 6623--6689 Score: 95
Period size: 27 Copynumber: 2.4 Consensus size: 28
6613 CACTTTTCTC
6623 TTTTCATTTTTTTCTTTTTCATTTTTTTCA
1 TTTTCA-TTTTTTCTTTTTCATTTTTTT-A
6653 TTTT--TTTTTTCTTTTTCATTTTTTT-
1 TTTTCATTTTTTCTTTTTCATTTTTTTA
6678 TTTTCATTTTTT
1 TTTTCATTTTTT
6690 ATTTGTTTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
25 4 0.11
27 27 0.77
30 4 0.11
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.82
Consensus pattern (28 bp):
TTTTCATTTTTTCTTTTTCATTTTTTTA
Found at i:6702 original size:15 final size:15
Alignment explanation
Indices: 6616--6704 Score: 76
Period size: 15 Copynumber: 5.7 Consensus size: 15
6606 AAACCCTCAC
*
6616 TTTTCTCTTTTCATTT
1 TTTTCT-TTTTTATTT
*
6632 TTTTCTTTTTCATTT
1 TTTTCTTTTTTATTT
6647 TTTTCATTTTTT-TTT
1 TTTTC-TTTTTTATTT
6662 TCTTT-TTCATTTT-TTT
1 T-TTTCTT--TTTTATTT
6678 TTTTCATTTTTTATTT
1 TTTTC-TTTTTTATTT
*
6694 GTTTCTTTTTT
1 TTTTCTTTTTT
6705 CTTCAAGCAT
Statistics
Matches: 64, Mismatches: 2, Indels: 15
0.79 0.02 0.19
Matches are distributed among these distances:
14 2 0.03
15 31 0.48
16 29 0.45
17 2 0.03
ACGTcount: A:0.07, C:0.11, G:0.01, T:0.81
Consensus pattern (15 bp):
TTTTCTTTTTTATTT
Found at i:16139 original size:23 final size:23
Alignment explanation
Indices: 16113--16158 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
16103 AACATATTAA
*
16113 GTAGCGCTTATATAATGTAATAG
1 GTAGCACTTATATAATGTAATAG
16136 GTAGCACTTATATAATGTAATAG
1 GTAGCACTTATATAATGTAATAG
16159 ACATTTAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.35
Consensus pattern (23 bp):
GTAGCACTTATATAATGTAATAG
Found at i:16680 original size:73 final size:72
Alignment explanation
Indices: 16555--16690 Score: 188
Period size: 73 Copynumber: 1.9 Consensus size: 72
16545 TATAAATGTA
* * *
16555 TCGACACTTTATGGTTGCACCCTTTTTGGTATTCATTCTGGACCAAAAGTATCGACACAAATTTA
1 TCGACACTTTATGGTTGCACCCTTTGTGGCATTCATGCTGGACCAAAAGTATCGACACAAATTTA
16620 TCAAGTG
66 TCAAGTG
16627 TCGACACTTTATGCG-TGCACCTCGTTTGT-GCATTCATGCTGGA-CAATAAGTATCGACACAAA
1 TCGACACTTTATG-GTTGCACC-C-TTTGTGGCATTCATGCTGGACCAA-AAGTATCGACACAAA
16689 TT
62 TT
16691 ACACAAGTAT
Statistics
Matches: 57, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
72 22 0.39
73 31 0.54
74 4 0.07
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (72 bp):
TCGACACTTTATGGTTGCACCCTTTGTGGCATTCATGCTGGACCAAAAGTATCGACACAAATTTA
TCAAGTG
Found at i:16698 original size:73 final size:72
Alignment explanation
Indices: 16552--16703 Score: 186
Period size: 73 Copynumber: 2.1 Consensus size: 72
16542 TTTTATAAAT
* * *
16552 GTATCGACACTTTATGGTTGCACCCTTTTTGGTATTCATTCTGGACCAAAAGTATCGACACAAAT
1 GTATCGACACTTTATGGTTGCACCCTTTGTGGCATTCATGCTGGACCAAAAGTATCGACACAAAT
*
16617 TTATCAA
66 TTAACAA
*
16624 GTGTCGACACTTTATGCG-TGCACCTCGTTTGT-GCATTCATGCTGGA-CAATAAGTATCGACAC
1 GTATCGACACTTTATG-GTTGCACC-C-TTTGTGGCATTCATGCTGGACCAA-AAGTATCGACAC
16686 AAA-TTACACAA
62 AAATTTA-ACAA
16697 GTATCGA
1 GTATCGA
16704 TACATTATAT
Statistics
Matches: 69, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
72 27 0.39
73 38 0.55
74 4 0.06
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.32
Consensus pattern (72 bp):
GTATCGACACTTTATGGTTGCACCCTTTGTGGCATTCATGCTGGACCAAAAGTATCGACACAAAT
TTAACAA
Found at i:22266 original size:2 final size:2
Alignment explanation
Indices: 22261--22289 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
22251 TATATTCATC
22261 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22290 CCACGCATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22663 original size:31 final size:31
Alignment explanation
Indices: 22616--22680 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
22606 GAACCTCGGC
* *
22616 AACTGTCTATAGGTCTCG-AAGAACCTAGGTA
1 AACTGTCCATAGGTCTCGAAAG-ACATAGGTA
*
22647 AACTGTCCATATGTCTCGAAAGACATAGGTA
1 AACTGTCCATAGGTCTCGAAAGACATAGGTA
22678 AAC
1 AAC
22681 CCTCGACTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 27 0.90
32 3 0.10
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (31 bp):
AACTGTCCATAGGTCTCGAAAGACATAGGTA
Found at i:26579 original size:33 final size:33
Alignment explanation
Indices: 26542--26607 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
26532 CATCTTAAGA
*
26542 TCACCCCTTAACACCTCAACTTCTTTCACCACT
1 TCACCCCTCAACACCTCAACTTCTTTCACCACT
*
26575 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCTCAACTTCTTTCACCACT
26608 CCATCTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.23, C:0.47, G:0.00, T:0.30
Consensus pattern (33 bp):
TCACCCCTCAACACCTCAACTTCTTTCACCACT
Found at i:26666 original size:21 final size:21
Alignment explanation
Indices: 26641--26684 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
26631 CCCCTTATGC
26641 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
* *
26662 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
26683 CT
1 CT
26685 TGATTGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.32, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCGACT
Found at i:27090 original size:19 final size:22
Alignment explanation
Indices: 27057--27116 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 22
27047 ATAGCGCAAC
27057 CTACA-TTTATAATAAAATT-TA
1 CTACATTTTAT-ATAAAATTATA
27078 -TA-ATTTTATATAATAATTATA
1 CTACATTTTATATAA-AATTATA
27099 CTATCATTTTATATAAAA
1 CTA-CATTTTATATAAAA
27117 ACACAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
19 5 0.15
20 11 0.33
21 2 0.06
22 2 0.06
23 2 0.06
24 11 0.33
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (22 bp):
CTACATTTTATATAAAATTATA
Found at i:28963 original size:20 final size:19
Alignment explanation
Indices: 28908--28954 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
28898 TACGGTAGCG
28908 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
28927 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
28948 TTTTACC
1 TTTTACC
28955 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:29336 original size:11 final size:11
Alignment explanation
Indices: 29320--29344 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
29310 ATTTGGTAAT
29320 ACCGTATATTA
1 ACCGTATATTA
29331 ACCGTATATTA
1 ACCGTATATTA
29342 ACC
1 ACC
29345 CATCTTTCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (11 bp):
ACCGTATATTA
Found at i:41199 original size:18 final size:17
Alignment explanation
Indices: 41162--41199 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
41152 AACTATGTAT
*
41162 AATGTAAGATATTTAGA
1 AATGTAAGATATTTAAA
41179 AATGTAAGATATTTTAAA
1 AATGTAAGATA-TTTAAA
41197 AAT
1 AAT
41200 AAAAAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (17 bp):
AATGTAAGATATTTAAA
Found at i:44730 original size:21 final size:23
Alignment explanation
Indices: 44685--44727 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
44675 AAAGTTAAAA
* *
44685 AATATATATTTGATAAATTGAAG
1 AATATATATTTGAAAAATAGAAG
44708 AATAT-TATTTGAAAAATAGA
1 AATATATATTTGAAAAATAGA
44728 GAAAAATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (23 bp):
AATATATATTTGAAAAATAGAAG
Found at i:45250 original size:23 final size:24
Alignment explanation
Indices: 45224--45291 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 24
45214 GTTTGTTTTG
*
45224 TGTTCGCGAACATGTTAGTTTA-A
1 TGTTCGCAAACATGTTAGTTTATA
* ** *
45247 TGTTTGTTAACATGTTCGTTTATA
1 TGTTCGCAAACATGTTAGTTTATA
* *
45271 TATTCGCAAACAT-TTTGTTTA
1 TGTTCGCAAACATGTTAGTTTA
45292 GCGTTATCGA
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
23 25 0.71
24 10 0.29
ACGTcount: A:0.25, C:0.12, G:0.16, T:0.47
Consensus pattern (24 bp):
TGTTCGCAAACATGTTAGTTTATA
Found at i:45763 original size:2 final size:2
Alignment explanation
Indices: 45756--45803 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
45746 TGTATGTATG
45756 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
45798 TA TA TA
1 TA TA TA
45804 AAGTTCGATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:57388 original size:16 final size:16
Alignment explanation
Indices: 57338--57388 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
57328 ATTTGGTTCA
57338 CGGAATGTAAGATTAC
1 CGGAATGTAAGATTAC
**
57354 CGGCGAAAATAAGATTAC
1 C-G-GAATGTAAGATTAC
*
57372 CGGAATGTAACATTAC
1 CGGAATGTAAGATTAC
57388 C
1 C
57389 TAACACATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
16 13 0.46
17 2 0.07
18 13 0.46
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.22
Consensus pattern (16 bp):
CGGAATGTAAGATTAC
Found at i:57553 original size:11 final size:11
Alignment explanation
Indices: 57537--57562 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
57527 TAACAAGTTG
57537 AATTCTACTAT
1 AATTCTACTAT
57548 AATTCTACTAT
1 AATTCTACTAT
57559 AATT
1 AATT
57563 AATTTATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (11 bp):
AATTCTACTAT
Found at i:60734 original size:7 final size:7
Alignment explanation
Indices: 60718--60748 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
60708 CCAAAATCGT
*
60718 TTCGATA
1 TTCGAAA
60725 TTCGAAA
1 TTCGAAA
60732 TTCGAAA
1 TTCGAAA
60739 TTCGAAA
1 TTCGAAA
60746 TTC
1 TTC
60749 AAGACTCTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (7 bp):
TTCGAAA
Found at i:67510 original size:24 final size:24
Alignment explanation
Indices: 67482--67530 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
67472 TTACAAAATG
67482 ATAAAATTATGAATTTTAACTTTT
1 ATAAAATTATGAATTTTAACTTTT
67506 ATAAAATTATGAATTTTAACTTTT
1 ATAAAATTATGAATTTTAACTTTT
67530 A
1 A
67531 ATACTTACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (24 bp):
ATAAAATTATGAATTTTAACTTTT
Found at i:69177 original size:170 final size:170
Alignment explanation
Indices: 68895--69236 Score: 684
Period size: 170 Copynumber: 2.0 Consensus size: 170
68885 AATAAGAGCC
68895 TACCATTTTTGAATATGCGCAAATAAAGAACTAAAGTTTTTTACATCAATATTTTTCAATTATTC
1 TACCATTTTTGAATATGCGCAAATAAAGAACTAAAGTTTTTTACATCAATATTTTTCAATTATTC
68960 TTTGACAGATTTGAAAATCAAGGGTGAATGAGGTGCGGAGTGAATTTTCAATTAAAAGTTTCAAG
66 TTTGACAGATTTGAAAATCAAGGGTGAATGAGGTGCGGAGTGAATTTTCAATTAAAAGTTTCAAG
69025 TTCAAGTCAAGTTAATTTATTCTTTTAATAATGAATAATA
131 TTCAAGTCAAGTTAATTTATTCTTTTAATAATGAATAATA
69065 TACCATTTTTGAATATGCGCAAATAAAGAACTAAAGTTTTTTACATCAATATTTTTCAATTATTC
1 TACCATTTTTGAATATGCGCAAATAAAGAACTAAAGTTTTTTACATCAATATTTTTCAATTATTC
69130 TTTGACAGATTTGAAAATCAAGGGTGAATGAGGTGCGGAGTGAATTTTCAATTAAAAGTTTCAAG
66 TTTGACAGATTTGAAAATCAAGGGTGAATGAGGTGCGGAGTGAATTTTCAATTAAAAGTTTCAAG
69195 TTCAAGTCAAGTTAATTTATTCTTTTAATAATGAATAATA
131 TTCAAGTCAAGTTAATTTATTCTTTTAATAATGAATAATA
69235 TA
1 TA
69237 AAAAATATAC
Statistics
Matches: 172, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
170 172 1.00
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (170 bp):
TACCATTTTTGAATATGCGCAAATAAAGAACTAAAGTTTTTTACATCAATATTTTTCAATTATTC
TTTGACAGATTTGAAAATCAAGGGTGAATGAGGTGCGGAGTGAATTTTCAATTAAAAGTTTCAAG
TTCAAGTCAAGTTAATTTATTCTTTTAATAATGAATAATA
Found at i:83329 original size:31 final size:28
Alignment explanation
Indices: 83248--83325 Score: 77
Period size: 28 Copynumber: 2.7 Consensus size: 28
83238 CCTCATAAAG
*
83248 TTATACTATATGTTCATATAATCTCATT
1 TTATACTATATGTTCATATTATCTCATT
* * *
83276 TTATCCTATAAG-TCATACTTATCTTATCT
1 TTATACTATATGTTCATA-TTATCTCAT-T
*
83305 CTTATTCTATATGTTCATATT
1 -TTATACTATATGTTCATATT
83326 TATCATATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
27 5 0.12
28 17 0.43
29 1 0.03
30 12 0.30
31 5 0.12
ACGTcount: A:0.28, C:0.17, G:0.04, T:0.51
Consensus pattern (28 bp):
TTATACTATATGTTCATATTATCTCATT
Found at i:83610 original size:20 final size:20
Alignment explanation
Indices: 83477--83610 Score: 85
Period size: 20 Copynumber: 6.7 Consensus size: 20
83467 AATGACCAAC
**
83477 AAATCGCAACGCGAAAT--A
1 AAATCGCAACGCGATTTCCA
**
83495 AAATCGCAACGCGATCCCCA
1 AAATCGCAACGCGATTTCCA
* **
83515 GAATCGCAAATC-AGTTTCCA
1 AAATCGCAACGCGA-TTTCCA
**
83535 AAATCGCAACGCGATTCTTAA
1 AAATCGCAACGCGATT-TCCA
* * *
83556 AAATCGCAATGCGATAGTACA
1 AAATCGCAACGCGAT-TTCCA
* **
83577 AATTCGCATTGCGATTTCCA
1 AAATCGCAACGCGATTTCCA
83597 AAATCGCAACGCGA
1 AAATCGCAACGCGA
83611 ATATGAAATC
Statistics
Matches: 86, Mismatches: 24, Indels: 10
0.72 0.20 0.08
Matches are distributed among these distances:
18 14 0.16
19 1 0.01
20 39 0.45
21 32 0.37
ACGTcount: A:0.38, C:0.26, G:0.16, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGATTTCCA
Found at i:83812 original size:20 final size:20
Alignment explanation
Indices: 83597--83825 Score: 212
Period size: 20 Copynumber: 11.5 Consensus size: 20
83587 GCGATTTCCA
**
83597 AAATCGCAACGCGAATATG-
1 AAATCGCAACGCGAATCCGT
*
83616 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATC-CGT
*
83636 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
83656 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATCCGT
* **
83676 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGAATCCGT
* *
83696 AAATTC-CAATGCGTATCCGT
1 AAA-TCGCAACGCGAATCCGT
* *
83716 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
***
83736 AAATCGCAACAATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
83756 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
83776 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
83796 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
*
83816 AAATCACAAC
1 AAATCGCAAC
83826 ACTAAAATTT
Statistics
Matches: 178, Mismatches: 27, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
19 17 0.10
20 158 0.89
21 3 0.02
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Done.