Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004399.1 Hibiscus syriacus cultivar Beakdansim tig00009647_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: 100870
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:4540 original size:19 final size:19
Alignment explanation
Indices: 4513--4550 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
4503 CTTCAATTTT
4513 CTTTCTTTTCTT-TTCTTTG
1 CTTTCTTTT-TTCTTCTTTG
*
4532 CTTTTTTTTTTCTTCTTTG
1 CTTTCTTTTTTCTTCTTTG
4551 TGAGTGCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.00, C:0.18, G:0.05, T:0.76
Consensus pattern (19 bp):
CTTTCTTTTTTCTTCTTTG
Found at i:18741 original size:18 final size:18
Alignment explanation
Indices: 18718--18757 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
18708 AATAGGCCAG
*
18718 GCCTGGGCCTGTTTAAAA
1 GCCTGGGCCTATTTAAAA
18736 GCCT-GGCCTATTTAAAA
1 GCCTGGGCCTATTTAAAA
18753 GCCTG
1 GCCTG
18758 TTTAAAAGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.28
Consensus pattern (18 bp):
GCCTGGGCCTATTTAAAA
Found at i:18756 original size:12 final size:12
Alignment explanation
Indices: 18741--18774 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
18731 TAAAAGCCTG
*
18741 GCCTATTTAAAA
1 GCCTGTTTAAAA
18753 GCCTGTTTAAAA
1 GCCTGTTTAAAA
18765 GCCTGTTTAA
1 GCCTGTTTAA
18775 CAATAAACAT
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:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (12 bp):
GCCTGTTTAAAA
Found at i:18943 original size:41 final size:41
Alignment explanation
Indices: 18898--18983 Score: 127
Period size: 41 Copynumber: 2.1 Consensus size: 41
18888 CAGGCTTATA
* *
18898 AGGCTTTTTAATAGGCCTAAGCCTGGCCTGTTTAGTTAAAT
1 AGGCTTTTAAAAAGGCCTAAGCCTGGCCTGTTTAGTTAAAT
** *
18939 AGGCTTTTAAAAAGGCCTGGGCTTGGCCTGTTTAGTTAAAT
1 AGGCTTTTAAAAAGGCCTAAGCCTGGCCTGTTTAGTTAAAT
18980 AGGC
1 AGGC
18984 CAGGCCAGGC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (41 bp):
AGGCTTTTAAAAAGGCCTAAGCCTGGCCTGTTTAGTTAAAT
Found at i:20616 original size:133 final size:133
Alignment explanation
Indices: 20217--20708 Score: 684
Period size: 133 Copynumber: 3.7 Consensus size: 133
20207 CATATACGAT
* * *
20217 GAATCGAGCAAGAAGTTGACGCTGATCCAACTCCTTCTACGATGGATTTGAGCGAAAATAAAAAT
1 GAATCGAGCAAAAAGTTGATGCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAAAT
* * * * * * * * *
20282 GTTGATCCACCTCCTTCTGTGATGGAAATCGAATGATATATCGATGCTTATCTACCTCCTTCTGT
66 GTCGATCCACCTCATTCTGTGATGG-AATCGAACGAGATGTTGGTACTGATCTACCTCCTTCTGT
20347 GATA
130 GATA
* * * *
20351 GAATCGAG-ATAAAAGTTGATGATGATCCAACTCCTTATGCGATGGAATTAAGCGAAAAT-AAAA
1 GAATCGAGCA-AAAAGTTGATGCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAAA
* * *
20414 TGTCGATTCACCTCATTCTGTGATGGAATCGAACGAGATGTTGGTATTGATATACCTCCTTCTGT
65 TGTCGATCCACCTCATTCTGTGATGGAATCGAACGAGATGTTGGTACTGATCTACCTCCTTCTGT
20479 GATA
130 GATA
* *
20483 GAATCGAGCAAAAAGTTGATGCTGATCCAACTCCTTCTGTGACGGATTTGAGCGAAAATAAAAAT
1 GAATCGAGCAAAAAGTTGATGCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAAAT
* *
20548 GTCAATCCACCTCATTCTGTGATGGAATCGAACGAGATGTTGGTACTGATCTACCTTCTTCTGTG
66 GTCGATCCACCTCATTCTGTGATGGAATCGAACGAGATGTTGGTACTGATCTACCTCCTTCTGTG
20613 ATA
131 ATA
* **
20616 GAATCGAGCAAAAAGTTGATGTTGATCCAACTTATTCTGCGATGGATTTGAGC-AAAATAAAAAT
1 GAATCGAGCAAAAAGTTGATGCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAAAT
* * *
20680 GTTGATCCATCTCCTTCTGTGATGGAATC
66 GTCGATCCACCTCATTCTGTGATGGAATC
20709 AAAATGTCGA
Statistics
Matches: 316, Mismatches: 39, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
132 121 0.38
133 145 0.46
134 50 0.16
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (133 bp):
GAATCGAGCAAAAAGTTGATGCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAAAT
GTCGATCCACCTCATTCTGTGATGGAATCGAACGAGATGTTGGTACTGATCTACCTCCTTCTGTG
ATA
Found at i:20642 original size:44 final size:44
Alignment explanation
Indices: 20280--20708 Score: 181
Period size: 44 Copynumber: 9.7 Consensus size: 44
20270 GAAAATAAAA
* * * *
20280 ATGTTGATCCACCTCCTTCTGTGATGGAAATCGAATG-ATATA-TCG
1 ATGTTGATCTACCTCCTTCTGTGATGG-AATCG-A-GCAAAAAGTTG
*
20325 ATGCTT-ATCTACCTCCTTCTGTGATAGAATCGAG-ATAAAAGTTG
1 ATG-TTGATCTACCTCCTTCTGTGATGGAATCGAGCA-AAAAGTTG
* * * * * ** * **
20369 ATGATGATCCAACTCCTTATGCGATGGAATTAAGCGAAAA-TAAA
1 ATGTTGATCTACCTCCTTCTGTGATGGAATCGAGCAAAAAGT-TG
* * * * * *
20413 ATGTCGAT-TCACCTCATTCTGTGATGGAATCGAACGAGATGTTG
1 ATGTTGATCT-ACCTCCTTCTGTGATGGAATCGAGCAAAAAGTTG
* * * *
20457 GTATTGATATACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTG
1 ATGTTGATCTACCTCCTTCTGTGATGGAATCGAGCAAAAAGTTG
* * * * * * ***
20501 ATGCTGATCCAACTCCTTCTGTGACGGATTTGAGCGAAAATA-AAA
1 ATGTTGATCTACCTCCTTCTGTGATGGAATCGAGC-AAAA-AGTTG
** * * * * * *
20546 ATGTCAATCCACCTCATTCTGTGATGGAATCGAACGAGATGTTG
1 ATGTTGATCTACCTCCTTCTGTGATGGAATCGAGCAAAAAGTTG
* ** * *
20590 GTACTGATCTACCTTCTTCTGTGATAGAATCGAGCAAAAAGTTG
1 ATGTTGATCTACCTCCTTCTGTGATGGAATCGAGCAAAAAGTTG
* * ** * * * ***
20634 ATGTTGATCCAACTTATTCTGCGATGGATTTGAGCAAAATA-AAA
1 ATGTTGATCTACCTCCTTCTGTGATGGAATCGAGCAAAA-AGTTG
* *
20678 ATGTTGATCCATCTCCTTCTGTGATGGAATC
1 ATGTTGATCTACCTCCTTCTGTGATGGAATC
20709 AAAATGTCGA
Statistics
Matches: 272, Mismatches: 99, Indels: 27
0.68 0.25 0.07
Matches are distributed among these distances:
42 2 0.01
43 5 0.02
44 207 0.76
45 55 0.20
46 3 0.01
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.31
Consensus pattern (44 bp):
ATGTTGATCTACCTCCTTCTGTGATGGAATCGAGCAAAAAGTTG
Found at i:20787 original size:33 final size:33
Alignment explanation
Indices: 20677--21053 Score: 470
Period size: 33 Copynumber: 11.3 Consensus size: 33
20667 GCAAAATAAA
* * * ***
20677 AATGTTGATCCATCTCCTTCTGTGATGGAATCAA
1 AATGTCGATCCACCTCTTTCTGTGATGG-ATTTG
*
20711 AATGTCGATCCATCTCTTTCTGTGATGGATTTG
1 AATGTCGATCCACCTCTTTCTGTGATGGATTTG
* *
20744 AAATGTCGATCCACCTCTTTATGTAATGGATTTG
1 -AATGTCGATCCACCTCTTTCTGTGATGGATTTG
*
20778 AATGTCGATCCACCTCTTTCTGTGATGGA-TTA
1 AATGTCGATCCACCTCTTTCTGTGATGGATTTG
*
20810 ACATGTCGATCCAACTCTTTCTGTGATGGATTTG
1 A-ATGTCGATCCACCTCTTTCTGTGATGGATTTG
*
20844 AACGTCGATCCACCTCTTTCTGTGATGGATTTG
1 AATGTCGATCCACCTCTTTCTGTGATGGATTTG
* *
20877 AATGTCAATCCACCTCTTTCTGTGATGGATTTAA
1 AATGTCGATCCACCTCTTTCTGTGATGGATTT-G
* *
20911 AATGTC-AGTCCACCTCTTTCTATTATGGATTTG
1 AATGTCGA-TCCACCTCTTTCTGTGATGGATTTG
*
20944 AAATATCGATCCACCTCTTTCTGTGATGGATTTG
1 -AATGTCGATCCACCTCTTTCTGTGATGGATTTG
* * *
20978 AATGTCGATCCACCTCGTTCTATGATGGATATG
1 AATGTCGATCCACCTCTTTCTGTGATGGATTTG
** *
21011 AAATGTAAATCCACCTCTTTCTGGGATGGATTTG
1 -AATGTCGATCCACCTCTTTCTGTGATGGATTTG
21045 AATGTCGAT
1 AATGTCGAT
21054 TCTGATCTAC
Statistics
Matches: 299, Mismatches: 36, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
32 3 0.01
33 153 0.51
34 142 0.47
35 1 0.00
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (33 bp):
AATGTCGATCCACCTCTTTCTGTGATGGATTTG
Found at i:20795 original size:67 final size:67
Alignment explanation
Indices: 20676--21053 Score: 494
Period size: 67 Copynumber: 5.6 Consensus size: 67
20666 AGCAAAATAA
* * * *** *
20676 AAATGTTGATCCATCTCCTTCTGTGATGGAATCAAAATGTCGATCCATCTCTTTCTGTGATGGAT
1 AAATGTCGATCCACCTCTTTCTGTGATGG-ATTTGAATGTCGATCCACCTCTTTCTGTGATGGAT
20741 TTG
65 TTG
* *
20744 AAATGTCGATCCACCTCTTTATGTAATGGATTTGAATGTCGATCCACCTCTTTCTGTGATGGA-T
1 AAATGTCGATCCACCTCTTTCTGTGATGGATTTGAATGTCGATCCACCTCTTTCTGTGATGGATT
20808 T-
66 TG
* *
20809 AACATGTCGATCCAACTCTTTCTGTGATGGATTTGAACGTCGATCCACCTCTTTCTGTGATGGAT
1 AA-ATGTCGATCCACCTCTTTCTGTGATGGATTTGAATGTCGATCCACCTCTTTCTGTGATGGAT
20874 TTG
65 TTG
* * * *
20877 -AATGTCAATCCACCTCTTTCTGTGATGGATTTAAAATGTC-AGTCCACCTCTTTCTATTATGGA
1 AAATGTCGATCCACCTCTTTCTGTGATGGATTT-GAATGTCGA-TCCACCTCTTTCTGTGATGGA
20940 TTTG
64 TTTG
* * * *
20944 AAATATCGATCCACCTCTTTCTGTGATGGATTTGAATGTCGATCCACCTCGTTCTATGATGGATA
1 AAATGTCGATCCACCTCTTTCTGTGATGGATTTGAATGTCGATCCACCTCTTTCTGTGATGGATT
21009 TG
66 TG
** *
21011 AAATGTAAATCCACCTCTTTCTGGGATGGATTTGAATGTCGAT
1 AAATGTCGATCCACCTCTTTCTGTGATGGATTTGAATGTCGAT
21054 TCTGATCTAC
Statistics
Matches: 274, Mismatches: 29, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
65 2 0.01
66 89 0.32
67 128 0.47
68 55 0.20
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.38
Consensus pattern (67 bp):
AAATGTCGATCCACCTCTTTCTGTGATGGATTTGAATGTCGATCCACCTCTTTCTGTGATGGATT
TG
Found at i:26705 original size:21 final size:21
Alignment explanation
Indices: 26672--26712 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
26662 TTCTGGGCAA
* *
26672 GGGAATCGGTACCCATTCAAG
1 GGGAACCGATACCCATTCAAG
*
26693 GGGAACCGATACCCCTTCAA
1 GGGAACCGATACCCATTCAA
26713 ACGACAAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.17
Consensus pattern (21 bp):
GGGAACCGATACCCATTCAAG
Found at i:28371 original size:149 final size:149
Alignment explanation
Indices: 28191--28494 Score: 590
Period size: 149 Copynumber: 2.0 Consensus size: 149
28181 GAGTCGAGGG
28191 TCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGGAAGACACAT
1 TCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGGAAGACACAT
*
28256 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
28321 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
28340 TCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGGAAGACACAT
1 TCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGGAAGACACAT
*
28405 ACTTGATCCTTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
28470 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
28489 TCTACG
1 TCTACG
28495 GGGCACTTCG
Statistics
Matches: 153, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGGAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:28517 original size:23 final size:23
Alignment explanation
Indices: 28473--28517 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
28463 ATCATTATAT
*
28473 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
28496 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
28518 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:40680 original size:15 final size:15
Alignment explanation
Indices: 40660--40741 Score: 74
Period size: 15 Copynumber: 5.0 Consensus size: 15
40650 ATAACATGCA
40660 ATGAAAATTTTGTAC
1 ATGAAAATTTTGTAC
40675 ATGAAAATTTTGTACC
1 ATGAAAATTTTGTA-C
* * *
40691 AATTGGATAAGTTTAGTGATT
1 -A-T-GA-AAATTTTGT-A-C
40712 ATGAAAATTTTGTAC
1 ATGAAAATTTTGTAC
40727 ATGAAAATTTTGTAC
1 ATGAAAATTTTGTAC
40742 CAATTGGATA
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
15 29 0.54
16 2 0.04
17 8 0.15
18 3 0.06
19 3 0.06
20 8 0.15
21 1 0.02
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.40
Consensus pattern (15 bp):
ATGAAAATTTTGTAC
Found at i:40722 original size:52 final size:52
Alignment explanation
Indices: 40660--40765 Score: 212
Period size: 52 Copynumber: 2.0 Consensus size: 52
40650 ATAACATGCA
40660 ATGAAAATTTTGTACATGAAAATTTTGTACCAATTGGATAAGTTTAGTGATT
1 ATGAAAATTTTGTACATGAAAATTTTGTACCAATTGGATAAGTTTAGTGATT
40712 ATGAAAATTTTGTACATGAAAATTTTGTACCAATTGGATAAGTTTAGTGATT
1 ATGAAAATTTTGTACATGAAAATTTTGTACCAATTGGATAAGTTTAGTGATT
40764 AT
1 AT
40766 TTTATAACTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.41
Consensus pattern (52 bp):
ATGAAAATTTTGTACATGAAAATTTTGTACCAATTGGATAAGTTTAGTGATT
Found at i:43344 original size:2 final size:2
Alignment explanation
Indices: 43337--43361 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
43327 TTCCTTTATT
43337 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 T
43362 TTTATGTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:47731 original size:39 final size:39
Alignment explanation
Indices: 47660--47737 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
47650 CCCGGAATAT
* *
47660 TACCCGGGGACGCATCTGCTACTAAAGGGAAAGTAGCAC
1 TACCCGGGGACGCATCTGCTACCAAAGCGAAAGTAGCAC
* * *
47699 TACCCGGGGACTCA-CTCGTTACCAAAGCGAAAGTTGCAC
1 TACCCGGGGACGCATCT-GCTACCAAAGCGAAAGTAGCAC
47738 CTGCTGCGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
38 2 0.06
39 31 0.94
ACGTcount: A:0.29, C:0.28, G:0.26, T:0.17
Consensus pattern (39 bp):
TACCCGGGGACGCATCTGCTACCAAAGCGAAAGTAGCAC
Found at i:47860 original size:21 final size:21
Alignment explanation
Indices: 47814--47870 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
47804 ACTTTGATGA
*
47814 AGAAGATAAAGCTAAAAAGAT
1 AGAAGATAAAGATAAAAAGAT
* *
47835 GGAAGA-AAAGATAAAAATATT
1 AGAAGATAAAGATAAAAAGA-T
*
47856 AGAAGATCAA-ATAAA
1 AGAAGATAAAGATAAA
47871 GATGGTCCAG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 11 0.38
21 16 0.55
22 2 0.07
ACGTcount: A:0.63, C:0.04, G:0.18, T:0.16
Consensus pattern (21 bp):
AGAAGATAAAGATAAAAAGAT
Found at i:54445 original size:1 final size:1
Alignment explanation
Indices: 54439--54466 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
54429 TCCTAAGTTG
54439 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
54467 CGTTTAGGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:55447 original size:105 final size:105
Alignment explanation
Indices: 55264--55877 Score: 1095
Period size: 105 Copynumber: 5.8 Consensus size: 105
55254 AGGTTTTACC
55264 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
55329 ACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTC-AATTT
*
55370 -AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
55434 ACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
55474 CAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
55539 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
55579 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
55644 ACGAAGGGACCGCTGGTTGTCAACAAATATTTCTCAATGT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
55684 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
55749 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* * ***
55789 CAGAGCCAATTTCAGCTTCACAACGAAGGATATTGGACTCAAGACAGTACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
**
55854 ACGAAGGGACCGCTGACTGTCAAC
66 ACGAAGGGACCGCTGGTTGTCAAC
55878 CGTCAACTTC
Statistics
Matches: 491, Mismatches: 16, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
104 5 0.01
105 486 0.99
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:59283 original size:13 final size:13
Alignment explanation
Indices: 59265--59299 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
59255 CGTGTCATAA
59265 ATTTATGACACGC
1 ATTTATGACACGC
*
59278 ATTTATGACGCGC
1 ATTTATGACACGC
*
59291 ATTAATGAC
1 ATTTATGAC
59300 GTTATTTGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Consensus pattern (13 bp):
ATTTATGACACGC
Found at i:59465 original size:85 final size:85
Alignment explanation
Indices: 59311--59561 Score: 384
Period size: 85 Copynumber: 3.0 Consensus size: 85
59301 TTATTTGAGT
*
59311 GTCATTGAAGCCCCCGTCATAAATTAAGATG--ACACATTTCTGCGTCATAAATTTATGACACGC
1 GTCATTGAAGCCCCCGTCATAAATTAAGATGACACACATTTGTGCGTCATAAATTTATGACACGC
*
59374 ATGTATGACTTATATTGCGC
66 ATGTATGACTTACATTGCGC
59394 GTCATTGAAGCCCCCGTCATAAATTAAGATGACACACATTTGTGCGTCATAAATTTATGACACGC
1 GTCATTGAAGCCCCCGTCATAAATTAAGATGACACACATTTGTGCGTCATAAATTTATGACACGC
59459 ATGTATGACTTACATTGCGC
66 ATGTATGACTTACATTGCGC
* * * * *
59479 GTCATTGAAGCCACCGTCATAAATCT--GCTTGACATACATTTGTGTGTCATAAACTTATGACAC
1 GTCATTGAAGCCCCCGTCATAAAT-TAAG-ATGACACACATTTGTGCGTCATAAATTTATGACAC
*
59542 GCATATATGACTTACATTGC
64 GCATGTATGACTTACATTGC
59562 ATGTCATTAA
Statistics
Matches: 156, Mismatches: 8, Indels: 6
0.92 0.05 0.04
Matches are distributed among these distances:
83 31 0.20
84 1 0.01
85 123 0.79
86 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (85 bp):
GTCATTGAAGCCCCCGTCATAAATTAAGATGACACACATTTGTGCGTCATAAATTTATGACACGC
ATGTATGACTTACATTGCGC
Found at i:61059 original size:12 final size:12
Alignment explanation
Indices: 61042--61072 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
61032 ATATATTGAT
61042 AATCAAATGAAA
1 AATCAAATGAAA
61054 AATCAAATGAAA
1 AATCAAATGAAA
*
61066 AAACAAA
1 AATCAAA
61073 CCCGAGATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.71, C:0.10, G:0.06, T:0.13
Consensus pattern (12 bp):
AATCAAATGAAA
Found at i:61674 original size:39 final size:38
Alignment explanation
Indices: 61565--61681 Score: 103
Period size: 39 Copynumber: 3.0 Consensus size: 38
61555 CTCGTCCTCC
* ** *
61565 TCCTTTGCGGTGTTCCTTCCTCCTTTTCTTTCTTTCTTTA
1 TCCTTTGCGGTGTCCCTT-CTCC-TTTCCCTCTTTCTTTT
* * *
61605 ACTCTTT--GGTGTCCCTTATTCTTTCTCCTCTTTCTTTT
1 TC-CTTTGCGGTGTCCCTTCTCCTTTC-CCTCTTTCTTTT
*
61643 TCCTTTGCGGTGTCCCTTCTCCTTTACCCTCTTCCTTTT
1 TCCTTTGCGGTGTCCCTTCTCCTTT-CCCTCTTTCTTTT
61682 CTTTCTCTTT
Statistics
Matches: 61, Mismatches: 11, Indels: 11
0.73 0.13 0.13
Matches are distributed among these distances:
37 8 0.13
38 12 0.20
39 35 0.57
40 2 0.03
41 4 0.07
ACGTcount: A:0.03, C:0.32, G:0.09, T:0.55
Consensus pattern (38 bp):
TCCTTTGCGGTGTCCCTTCTCCTTTCCCTCTTTCTTTT
Found at i:65349 original size:15 final size:15
Alignment explanation
Indices: 65329--65372 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
65319 TCCTTATTTA
*
65329 ACGTTTTCTTCTTTG
1 ACGTTTTCTTCTTAG
65344 ACGTTTTCTTCTTAG
1 ACGTTTTCTTCTTAG
*
65359 ACGTTGTCTTCTTA
1 ACGTTTTCTTCTTA
65373 CCCCGTGAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.11, C:0.20, G:0.14, T:0.55
Consensus pattern (15 bp):
ACGTTTTCTTCTTAG
Found at i:83650 original size:41 final size:41
Alignment explanation
Indices: 83605--83686 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
83595 GTCCAAATAA
83605 TACTCGTATAAACACTATGGATCATATAACATGCCAATTGT
1 TACTCGTATAAACACTATGGATCATATAACATGCCAATTGT
83646 TACTCGTATAAACACTATGGATCATATAACATGCCAATTGT
1 TACTCGTATAAACACTATGGATCATATAACATGCCAATTGT
83687 ATCTCAAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.32
Consensus pattern (41 bp):
TACTCGTATAAACACTATGGATCATATAACATGCCAATTGT
Found at i:84203 original size:19 final size:19
Alignment explanation
Indices: 84179--84223 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
84169 TGAACCCTAA
*
84179 CTTGAATCTCATTTAGGGT
1 CTTGAATCACATTTAGGGT
84198 CTTGAATCACATTTAGGGT
1 CTTGAATCACATTTAGGGT
84217 CTTGAAT
1 CTTGAAT
84224 TAACTTACCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (19 bp):
CTTGAATCACATTTAGGGT
Found at i:85749 original size:117 final size:120
Alignment explanation
Indices: 85601--85820 Score: 320
Period size: 117 Copynumber: 1.9 Consensus size: 120
85591 TGAGCAAAAT
* ** *
85601 AAAAAAATGTTGAGGTCGAGGGAGAAATAGATAAGATTATTGGGTCGACATTGATGAATTGAAGA
1 AAAAAAATGTTGAGGTCGAGAGAGAAATAGATAAGATTATTGGGTCGACACAGATAAATTGAAGA
* *
85666 G-G-TTTTTTTT-ATACAAAAAGTTTAAGTTAGGAGTGTGGGTCCTGAGTAGAAG
66 GAGTTTTTTTTTGATACAAAAAATTTAAGTCAGGAGTGTGGGTCCTGAGTAGAAG
* * *
85718 AAAAAATTGTTGAGGTCTAGAGAGAAGTAGATAAGATTATTGGGTCGACACAGATAAATTGAAGA
1 AAAAAAATGTTGAGGTCGAGAGAGAAATAGATAAGATTATTGGGTCGACACAGATAAATTGAAGA
* *
85783 GAGTTTTTTTTTGTTACAAAAAATTTATGTCAGGAGTG
66 GAGTTTTTTTTTGATACAAAAAATTTAAGTCAGGAGTG
85821 ACTCTCCCAG
Statistics
Matches: 89, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
117 59 0.66
118 1 0.01
119 8 0.09
120 21 0.24
ACGTcount: A:0.37, C:0.05, G:0.27, T:0.31
Consensus pattern (120 bp):
AAAAAAATGTTGAGGTCGAGAGAGAAATAGATAAGATTATTGGGTCGACACAGATAAATTGAAGA
GAGTTTTTTTTTGATACAAAAAATTTAAGTCAGGAGTGTGGGTCCTGAGTAGAAG
Found at i:88965 original size:17 final size:17
Alignment explanation
Indices: 88943--88984 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
88933 AACGGTCGAC
88943 CGTTGACCGTTGACCT-G
1 CGTTGACCGTTGA-CTGG
88960 CGTTGACCGTTGACTGG
1 CGTTGACCGTTGACTGG
88977 CGTTGACC
1 CGTTGACC
88985 ACTGTTAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 2 0.08
17 22 0.92
ACGTcount: A:0.12, C:0.29, G:0.31, T:0.29
Consensus pattern (17 bp):
CGTTGACCGTTGACTGG
Found at i:90141 original size:18 final size:18
Alignment explanation
Indices: 90114--90149 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
90104 ATGACTGAAG
* *
90114 TAAATGATAAGTTTGGAC
1 TAAATAATAAGATTGGAC
90132 TAAATAATAAGATTGGAC
1 TAAATAATAAGATTGGAC
90150 GGAAGAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (18 bp):
TAAATAATAAGATTGGAC
Found at i:90241 original size:26 final size:26
Alignment explanation
Indices: 90212--90273 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
90202 CAAGCCCAGG
*
90212 AATGAATGGATATCCTCAATCTTTGA
1 AATGAATGGATATCCTCAAGCTTTGA
* *
90238 AATGAATGAATATCCTTAAGCTTTGA
1 AATGAATGGATATCCTCAAGCTTTGA
90264 AATGAATGGA
1 AATGAATGGA
90274 AAAACATTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (26 bp):
AATGAATGGATATCCTCAAGCTTTGA
Found at i:93793 original size:17 final size:17
Alignment explanation
Indices: 93771--93803 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
93761 TGACTTTGAC
93771 TGAAAAGTCAAATTTTT
1 TGAAAAGTCAAATTTTT
*
93788 TGAAAAGTCATATTTT
1 TGAAAAGTCAAATTTT
93804 ATGTTTTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.42
Consensus pattern (17 bp):
TGAAAAGTCAAATTTTT
Done.