Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004876.1 Hibiscus syriacus cultivar Beakdansim tig00010990_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: 110493
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2676 original size:31 final size:33
Alignment explanation
Indices: 2599--2686 Score: 126
Period size: 33 Copynumber: 2.7 Consensus size: 33
2589 TAGAAATTTT
* *
2599 ATCTTGGTTGGTGGCCAATTTATTGGAAAATTC
1 ATCTTGGTTGGTGGCCAACTTATTGGAAAAATC
2632 ATCTTGGTTGGTGGCCAACTTATTGGAAAAATC
1 ATCTTGGTTGGTGGCCAACTTATTGGAAAAATC
* *
2665 -T-TTGGTAGGTGGCTAACTTATT
1 ATCTTGGTTGGTGGCCAACTTATT
2687 TTTCATCTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
31 19 0.37
32 1 0.02
33 31 0.61
ACGTcount: A:0.24, C:0.12, G:0.25, T:0.39
Consensus pattern (33 bp):
ATCTTGGTTGGTGGCCAACTTATTGGAAAAATC
Found at i:6319 original size:34 final size:35
Alignment explanation
Indices: 6263--6337 Score: 91
Period size: 34 Copynumber: 2.2 Consensus size: 35
6253 CTTATATCGT
*
6263 TCCTTATCATATACTTACTCTTTTTCTTGTACCAA
1 TCCTTATCATATACTTACTCTTTTTCCTGTACCAA
* * *
6298 TCCTT-TCACTATA-TTATTCTTTTTCCTGTATCAT
1 TCCTTATCA-TATACTTACTCTTTTTCCTGTACCAA
6332 TCCTTA
1 TCCTTA
6338 CAGTGTACTG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
34 25 0.74
35 9 0.26
ACGTcount: A:0.20, C:0.25, G:0.03, T:0.52
Consensus pattern (35 bp):
TCCTTATCATATACTTACTCTTTTTCCTGTACCAA
Found at i:6639 original size:65 final size:65
Alignment explanation
Indices: 6558--7012 Score: 696
Period size: 65 Copynumber: 7.0 Consensus size: 65
6548 AATCTTTGCA
* *
6558 GTATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAATCATATGAGTGATATGTATT
1 GTATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATCTGTATT
* * * *
6623 GTATTCAATTATCACTCCACCTTATGCACCACAAAGGTATATTAGTCATATGAGTGATCTATATT
1 GTATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATCTGTATT
** * *
6688 GTACACAATTATCACTCCACCTCATGCACCATAAAGGTACATGAATCATATGAGTGATCTGTATT
1 GTATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATCTGTATT
** * *
6753 GTATTCAATTATCACTCCATTTCATGCACCACAAAGGTACATGAGTCATGTGAGTGATTTGTATT
1 GTATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATCTGTATT
* * * *
6818 GTATTCAATTATCATTCCACCTCATACACCACAAAGATACATGAGTCATATGAGTGATCTGTACT
1 GTATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATCTGTATT
* * *
6883 GTATTCAATTATCACTCGAACC-CATGTACCACAAAGGTACATGAGTCATATGAGTGATATGTAT
1 GTATTCAATTATCACTC-CACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATCTGTAT
6947 T
65 T
*
6948 GTATTCAATTATCACTCCATCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATCTGTATT
1 GTATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATCTGTATT
7013 CAAGTCTAGT
Statistics
Matches: 347, Mismatches: 41, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
64 2 0.01
65 342 0.99
66 3 0.01
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.32
Consensus pattern (65 bp):
GTATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATCTGTATT
Found at i:7952 original size:65 final size:65
Alignment explanation
Indices: 7877--8324 Score: 709
Period size: 65 Copynumber: 6.9 Consensus size: 65
7867 GATATTTGCA
* * **
7877 GTATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAATAATACATATT
1 GTATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATATGTATT
* * * *
7942 GTATTCAATTATCACTCCACCTTATGCACCACAAAGGTATATTAGTCATATGGGTGATATGTATT
1 GTATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATATGTATT
* * * *
8007 GTATAT-AATTATCACTCCACCTCATACACTACAAAGGTACATGAGTCATATGAGTGATTTGTAC
1 GTAT-TCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATATGTAT
8071 T
65 T
*
8072 GTATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATTTGTATT
1 GTATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATATGTATT
*
8137 GTATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATATGCATT
1 GTATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATATGTATT
* * * *
8202 GTATTCAATTATCACTCGACCCCATGCACCACAAAGGTATATGAGTCATATGAGTGATATGTGTT
1 GTATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATATGTATT
*
8267 GTATTCAATTATCACTCCATCTCATGCACCACAAAGGTACATGAGTCATATGAGTGAT
1 GTATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGAT
8325 CTATACTTAT
Statistics
Matches: 351, Mismatches: 30, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
64 1 0.00
65 349 0.99
66 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (65 bp):
GTATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATATGTATT
Found at i:15702 original size:28 final size:28
Alignment explanation
Indices: 15670--15726 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
15660 TGCCATTGCC
15670 AACATTACCATTAACAATCAAGGAGCTT
1 AACATTACCATTAACAATCAAGGAGCTT
15698 AACATTACCATTAACAATCAAGGAGCTT
1 AACATTACCATTAACAATCAAGGAGCTT
15726 A
1 A
15727 CTTCTTATGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.44, C:0.21, G:0.11, T:0.25
Consensus pattern (28 bp):
AACATTACCATTAACAATCAAGGAGCTT
Found at i:17579 original size:2 final size:2
Alignment explanation
Indices: 17572--17599 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
17562 TATTGACAAC
17572 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
17600 CATGCATACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19803 original size:25 final size:25
Alignment explanation
Indices: 19775--19824 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
19765 GACCAAATCT
19775 TAACTTTTATGAAATTAAATAACAA
1 TAACTTTTATGAAATTAAATAACAA
19800 TAACTTTTATGAAATTAAATAACAA
1 TAACTTTTATGAAATTAAATAACAA
19825 CGATGTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.36
Consensus pattern (25 bp):
TAACTTTTATGAAATTAAATAACAA
Found at i:27794 original size:16 final size:16
Alignment explanation
Indices: 27773--27804 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
27763 ATTAATATAG
*
27773 TTAATATTATCTTTTT
1 TTAATATTATATTTTT
27789 TTAATATTATATTTTT
1 TTAATATTATATTTTT
27805 AATTTAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (16 bp):
TTAATATTATATTTTT
Found at i:27861 original size:20 final size:20
Alignment explanation
Indices: 27789--27861 Score: 57
Period size: 20 Copynumber: 3.8 Consensus size: 20
27779 TTATCTTTTT
* *
27789 TTAATATTATATTTTTAAT-
1 TTAATATAATAATTTTAATA
27808 TTAATAATAATGAA---TAATA
1 TTAAT-ATAAT-AATTTTAATA
*
27827 TTAAT-TTATACATTTTAATA
1 TTAATATAATA-ATTTTAATA
27847 TTAATATAATAATTT
1 TTAATATAATAATTT
27862 AGTATTATGT
Statistics
Matches: 42, Mismatches: 4, Indels: 15
0.69 0.07 0.25
Matches are distributed among these distances:
16 1 0.02
17 4 0.10
18 4 0.10
19 10 0.24
20 18 0.43
21 5 0.12
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (20 bp):
TTAATATAATAATTTTAATA
Found at i:28120 original size:30 final size:30
Alignment explanation
Indices: 28084--28144 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
28074 AAATATCATA
*
28084 AAATAATTTATTTTACGTAAAATAATTTTT
1 AAATAATTTATTTTACATAAAATAATTTTT
* *
28114 AAATAATTTATTTTACATAAATTATTTTTT
1 AAATAATTTATTTTACATAAAATAATTTTT
28144 A
1 A
28145 GAAAATCAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (30 bp):
AAATAATTTATTTTACATAAAATAATTTTT
Found at i:35801 original size:2 final size:2
Alignment explanation
Indices: 35787--35819 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
35777 AATAAATTTG
35787 TA TA TA -A TCA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA T
35820 GTTCATTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:36786 original size:6 final size:6
Alignment explanation
Indices: 36775--36808 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
36765 TGTAATTCCC
36775 CTATTT CTATTT CTATTT CTATTT CTATTT CTAT
1 CTATTT CTATTT CTATTT CTATTT CTATTT CTAT
36809 CTACAATGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.65
Consensus pattern (6 bp):
CTATTT
Found at i:37618 original size:42 final size:43
Alignment explanation
Indices: 37546--37633 Score: 151
Period size: 42 Copynumber: 2.1 Consensus size: 43
37536 TAGATGTATC
37546 TCAAATGAAGCAAAAAATTGAGAGAAAACTTGGAGCTTCTATT
1 TCAAATGAAGCAAAAAATTGAGAGAAAACTTGGAGCTTCTATT
* *
37589 TCAAATGAAGC-AAAAATTGAGAGATAACTTGGAGCTTTTATT
1 TCAAATGAAGCAAAAAATTGAGAGAAAACTTGGAGCTTCTATT
37631 TCA
1 TCA
37634 TGTTTAAGTC
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
42 32 0.74
43 11 0.26
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.28
Consensus pattern (43 bp):
TCAAATGAAGCAAAAAATTGAGAGAAAACTTGGAGCTTCTATT
Found at i:40073 original size:19 final size:19
Alignment explanation
Indices: 40049--40086 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
40039 TCTTCTCTTG
40049 AGGCCATTTCAACACAAAT
1 AGGCCATTTCAACACAAAT
40068 AGGCCATTTCAACACAAAT
1 AGGCCATTTCAACACAAAT
40087 TCTTCAACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.26, G:0.11, T:0.21
Consensus pattern (19 bp):
AGGCCATTTCAACACAAAT
Found at i:42036 original size:29 final size:29
Alignment explanation
Indices: 41992--42063 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
41982 TAGGAGGGAA
* *
41992 TGCATGGTGACCTACAAGGTCGCCAGGAG
1 TGCATGGCGACTTACAAGGTCGCCAGGAG
42021 TGCATGGCGACTTACAAGGTCGCCAGGAG
1 TGCATGGCGACTTACAAGGTCGCCAGGAG
* *
42050 GGCATGACGACTTA
1 TGCATGGCGACTTA
42064 TGCTTGGGGA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.25, C:0.24, G:0.33, T:0.18
Consensus pattern (29 bp):
TGCATGGCGACTTACAAGGTCGCCAGGAG
Found at i:45970 original size:15 final size:15
Alignment explanation
Indices: 45950--46001 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
45940 ATATTTAGCT
*
45950 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
*
45965 GGGCGGGCGGATACG
1 GGGCGGGCGGATGCG
*
45980 GGGCGGGCAGATGCG
1 GGGCGGGCGGATGCG
45995 GGGCGGG
1 GGGCGGG
46002 TAATGTCTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.10, C:0.17, G:0.65, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:52259 original size:84 final size:84
Alignment explanation
Indices: 52125--52312 Score: 268
Period size: 84 Copynumber: 2.2 Consensus size: 84
52115 CTGAATGAAA
* * *
52125 TCGAACTCGTTAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
1 TCGAACTCG-AAGGTCTTTGGTTAGCAAATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
52190 TGCCTCGGAGCTGAGAGTAG
65 TGCCTCGGAGCTGAGAGTAG
* * * *
52210 TCGAACTCGAAGGTCTTTGGTTAGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTTAGCAAATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
* * *
52275 GCCTTGGAGTTGAGCGTAG
66 GCCTCGGAGCTGAGAGTAG
*
52294 TCGAACTCAAAGGTCTTTG
1 TCGAACTCGAAGGTCTTTG
52313 TGTTTCAAGA
Statistics
Matches: 92, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
84 83 0.90
85 9 0.10
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (84 bp):
TCGAACTCGAAGGTCTTTGGTTAGCAAATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
GCCTCGGAGCTGAGAGTAG
Found at i:52350 original size:34 final size:34
Alignment explanation
Indices: 52309--52428 Score: 190
Period size: 34 Copynumber: 3.6 Consensus size: 34
52299 CTCAAAGGTC
52309 TTTGTGTTTCAAGAGAAAC-ATTTTCAAAGGTTTT
1 TTTGTGTTTCAAGAGAAACGA-TTTCAAAGGTTTT
*
52343 TTTGTGTTTCAAGAGGAACGATTTCAAAGG-TTT
1 TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTTT
*
52376 TTTGTGTTTCAAGAGAAACGATTTCAAAGATTTT
1 TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTTT
*
52410 TTTGTGTTTAAAGAGAAAC
1 TTTGTGTTTCAAGAGAAAC
52429 TGTCTCTATG
Statistics
Matches: 80, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
33 31 0.39
34 48 0.60
35 1 0.01
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.41
Consensus pattern (34 bp):
TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTTT
Found at i:52410 original size:67 final size:66
Alignment explanation
Indices: 52300--52424 Score: 198
Period size: 67 Copynumber: 1.9 Consensus size: 66
52290 GTAGTCGAAC
* *
52300 TCAAAGGTCTTTGTGTTTCAAGAGAAACATTTTCAAAGGTTTTTTTGTGTTTCAAGAGGAACGAT
1 TCAAAGGTCTTTGTGTTTCAAGAGAAACATTTTCAAAGATTTTTTTGTGTTTAAAGAGGAACGAT
52365 T
66 T
*
52366 TCAAAGGTTTTTTGTGTTTCAAGAGAAACGA-TTTCAAAGATTTTTTTGTGTTTAAAGAG
1 TCAAAGG-TCTTTGTGTTTCAAGAGAAAC-ATTTTCAAAGATTTTTTTGTGTTTAAAGAG
52425 AAACTGTCTC
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
66 7 0.13
67 46 0.85
68 1 0.02
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.41
Consensus pattern (66 bp):
TCAAAGGTCTTTGTGTTTCAAGAGAAACATTTTCAAAGATTTTTTTGTGTTTAAAGAGGAACGAT
T
Found at i:52522 original size:21 final size:21
Alignment explanation
Indices: 52496--52560 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
52486 GGAAACTGTC
52496 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
** *
52517 TC-A-AGAG---AAA-CCGTC
1 TCAAGAGAGACAAAATTTGTT
52532 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
52553 TCAAGAGA
1 TCAAGAGA
52561 AATTGTCTCA
Statistics
Matches: 32, Mismatches: 6, Indels: 12
0.64 0.12 0.24
Matches are distributed among these distances:
15 4 0.12
16 4 0.12
17 4 0.12
19 4 0.12
20 4 0.12
21 12 0.38
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.23
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTT
Found at i:52527 original size:36 final size:36
Alignment explanation
Indices: 52479--52583 Score: 183
Period size: 36 Copynumber: 2.9 Consensus size: 36
52469 TTGGTTGGTA
*
52479 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
*
52515 TTTCAAGAGAAACCGTCTCAAGAGAGACAAAATTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
*
52551 TTTCAAGAGAAATTGTCTCAAGAGAGACAAAAT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT
52584 CTTTAGTTTC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 65 1.00
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (36 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
Found at i:53304 original size:106 final size:106
Alignment explanation
Indices: 52976--54161 Score: 1807
Period size: 106 Copynumber: 11.2 Consensus size: 106
52966 TTCGTCGTAG
* * * * * * * *
52976 AGTTGAAATTGGTTCTGGAACTAGAAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAG
1 AGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
* * *
53041 TTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCATTGTGA
66 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
* * * * *
53082 AGTTGAAATCGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTTGTGAA
1 AGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCG-TCGTGAA
* *
53147 GTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGCTGTGA
65 GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
53189 AGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
1 AGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
* **
53254 TTGAACTTGCATTGTCTGGAGTCCAATATCCTTCACTGTGA
66 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
*
53295 AGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
1 AGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
* * *
53360 TTGAACTTGCATTGTCTTGAGTCCAATATCCTTCGCTGTGA
66 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
* *
53401 AGTTGAAATTGACTCTGAAATTGGGAAATTGTTTATTAACAACCAGCGGTCCCTTCGTCGTGAAG
1 AGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
*
53466 TTAAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
66 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
53507 AGTTGAAATTGGCTCTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAA
1 AGTTGAAATTGGCTC-TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAA
53572 GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
65 GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
* * * *
53614 AGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTTACAACCAGCGGTCCCTTCGTCGTGAAG
1 AGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
* * *
53679 TTGAACTTGCGTTGTCTTGAGTCCAATATCCTTTGCTGTGA
66 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
* * * * *
53720 AGTTGAAATTGACTTTGAAATTTGAAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTAAAG
1 AGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
53785 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
66 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
* * * *
53826 AGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
1 AGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
*
53891 TTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
66 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
* * *
53932 AGTTGAAATTGGCTCTGATATTGGGAAATTATTTATTGACAACCAGCGGTCCCTTCGTCGTAAAG
1 AGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
53997 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
66 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
* * * *
54038 AGTTGAAATTGTCTCTGAAATTGAGAAGTT-TTTATTGACAACCAGTGGTCCCTTCGTCGTGAAG
1 AGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
* * * * **
54102 TTGAACATGCATTGTCTGGAGTCCAATTTTCTTCGTTGCAA
66 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
* *
54143 AGTTGAAATAGACTCTGAA
1 AGTTGAAATTGGCTCTGAA
54162 TGAAATTGGA
Statistics
Matches: 995, Mismatches: 83, Indels: 5
0.92 0.08 0.00
Matches are distributed among these distances:
105 84 0.08
106 709 0.71
107 202 0.20
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.35
Consensus pattern (106 bp):
AGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
Found at i:53766 original size:425 final size:424
Alignment explanation
Indices: 53001--54161 Score: 1847
Period size: 425 Copynumber: 2.7 Consensus size: 424
52991 TGGAACTAGA
* * * *
53001 AAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCA
1 AAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* * * * *
53066 ATATCCTTCATTGTGAAGTTGAAATCGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCCG
66 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGG
* * *
53131 TCCCTTCGTTTGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAA
131 TCCCTTCG-TCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAA
* *
53196 ATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
195 ATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
* * *
53261 TGCATTGTCTGGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG
260 TGCATTGTCTGGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAAATTGGAAAATTG
* *
53326 TTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTTGAGTCCAATATCC
325 TTTATTGACAACCAGCGGTCCCTTCGTCGTAAAGTTGAACTTGCATTGTCTGGAGTCCAATATCC
* *
53391 TTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGG
390 TTCGCTGTGAAGTTGAAATTGACTCTAAAATTGAG
* * *
53426 AAATTGTTTATTAACAACCAGCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTGTCTGGAGTCCA
1 AAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
53491 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTTGAAATTGGGAAATTGTTTATTGACAACCAGCG
66 ATATCCTTCGTTGTGAAGTTGAAATTGGCTC-TGAAATTGGGAAATTGTTTATTGACAACCAGCG
53556 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAA
130 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAA
* *
53621 ATTGGCTCTGAAATTGAGAAGTTGTTTGTTTACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
195 ATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
* * ** * *
53686 TGCGTTGTCTTGAGTCCAATATCCTTTGCTGTGAAGTTGAAATTGACTTTGAAATTTGAAAATTG
260 TGCATTGTCTGGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAAATTGGAAAATTG
*
53751 TTTATTGACAACCAGCGGTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
325 TTTATTGACAACCAGCGGTCCCTTCGTCGTAAAGTTGAACTTGCATTGTCTGGAGTCCAATATCC
* *
53816 TTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAG
390 TTCGCTGTGAAGTTGAAATTGACTCTAAAATTGAG
* *
53851 AAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCA
1 AAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* *
53916 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGATATTGGGAAATTATTTATTGACAACCAGCGG
66 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGG
*
53981 TCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
131 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
* * *
54046 TTGTCTCTGAAATTGAGAAGTT-TTTATTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACAT
196 TTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
* * ** ** *
54110 GCATTGTCTGGAGTCCAATTTTCTTCGTTGCAAAGTTGAAATAGACTCTGAA
261 GCATTGTCTGGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAA
54162 TGAAATTGGA
Statistics
Matches: 677, Mismatches: 58, Indels: 4
0.92 0.08 0.01
Matches are distributed among these distances:
423 80 0.12
424 117 0.17
425 441 0.65
426 39 0.06
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.35
Consensus pattern (424 bp):
AAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGG
TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
TTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
GCATTGTCTGGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAAATTGGAAAATTGT
TTATTGACAACCAGCGGTCCCTTCGTCGTAAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCT
TCGCTGTGAAGTTGAAATTGACTCTAAAATTGAG
Found at i:61609 original size:2 final size:2
Alignment explanation
Indices: 61602--61627 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
61592 AGTAGGGATG
61602 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
61628 AAAGATGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:66477 original size:29 final size:31
Alignment explanation
Indices: 66444--66507 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 31
66434 CAAATTTTGG
**
66444 TTAGTGATTAAAA-TATAAGTTTTG-AAAA-T
1 TTAGTGACCAAAAGTATAA-TTTTGTAAAAGT
66473 TTAGTGACCAAAAGTATAATTTTGTAAAAGT
1 TTAGTGACCAAAAGTATAATTTTGTAAAAGT
66504 TTAG
1 TTAG
66508 GAACATAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 16 0.53
30 9 0.30
31 5 0.17
ACGTcount: A:0.42, C:0.03, G:0.16, T:0.39
Consensus pattern (31 bp):
TTAGTGACCAAAAGTATAATTTTGTAAAAGT
Found at i:66887 original size:15 final size:15
Alignment explanation
Indices: 66867--66895 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
66857 TTTGACTATG
66867 GATATTTTAATGGAA
1 GATATTTTAATGGAA
66882 GATATTTTAATGGA
1 GATATTTTAATGGA
66896 TAATGGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (15 bp):
GATATTTTAATGGAA
Found at i:72877 original size:37 final size:37
Alignment explanation
Indices: 72833--72937 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
72823 CATTTTCGTC
72833 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
72870 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
72907 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
72938 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:73333 original size:18 final size:17
Alignment explanation
Indices: 73294--73336 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
73284 ATTATATGGA
73294 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
73310 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
73328 TATTATTAT
1 TATTATTAT
73337 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:79183 original size:183 final size:183
Alignment explanation
Indices: 78875--79411 Score: 959
Period size: 183 Copynumber: 2.9 Consensus size: 183
78865 ATTAAATCCG
*
78875 TAAAGCTGAGCTATTCCACTAAGGTAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGAAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
*
78940 ATAGATTATATTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTACTT
66 ATAGATTATATTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
79005 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
79058 TAAAGCTGAGCTATTCCACTAAGGAAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGAAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
* * *
79123 ATAGATTATGTTCAAACTATGACACTGCTCAGACACTTGGCAATTCAGTGTTTGCTCCACTGCTT
66 ATAGATTATATTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
*
79188 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
* *
79241 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGAAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGAAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
* *
79306 ATAGATTACATTCAAA-TCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
66 ATAGATTATATTCAAACT-ATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
*
79370 TTTGTCAGGTCAAAGACTTTGTGATGAGATGAACCCTTCAGT
130 TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGT
79412 TAAACCTGAT
Statistics
Matches: 338, Mismatches: 15, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
182 1 0.00
183 337 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGAAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTATATTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
Found at i:80632 original size:36 final size:36
Alignment explanation
Indices: 80592--80708 Score: 90
Period size: 36 Copynumber: 3.1 Consensus size: 36
80582 ATACTTTGTC
80592 TCACTTGAGACTGTTTTTCTCGAAAGAAGATTTATT
1 TCACTTGAGACTGTTTTTCTCGAAAGAAGATTTATT
** * ** * * *
80628 TCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTC
1 TCACTTGAGACTGTTTTTCTCGAAAGAAGATTTATT
* * * *
80664 TCGCTTGAGGCCGTTTTCACTCGAAAGAAGGCATTTCATT
1 TCACTTGAGACTGTTTT-TCTCGAAAGAA-G-ATTT-ATT
80704 TCACT
1 TCACT
80709 CAAGGCTGTT
Statistics
Matches: 56, Mismatches: 21, Indels: 4
0.69 0.26 0.05
Matches are distributed among these distances:
36 39 0.70
37 7 0.12
38 1 0.02
39 4 0.07
40 5 0.09
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.38
Consensus pattern (36 bp):
TCACTTGAGACTGTTTTTCTCGAAAGAAGATTTATT
Found at i:80645 original size:72 final size:75
Alignment explanation
Indices: 80551--80725 Score: 209
Period size: 72 Copynumber: 2.4 Consensus size: 75
80541 ATGCAGATGA
* * * *
80551 TTATCTCACTCAA-ATTAGTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGACTGTTTT-TCTC
1 TTATTTCACTCAAGATT-GTTTTTCTTAAAACA-AGATTTGTCTCACTTGAGACCGTTTTCACTC
80613 GAAAGAA-G-AT
64 GAAAGAAGGCAT
* *
80623 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGGCCGTTTTCACTCGA
1 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGA
80688 AAGAAGGCAT
66 AAGAAGGCAT
**
80698 TTCATTTCACTCAAGGCTGTTTTT-TTAA
1 TT-ATTTCACTCAAGATTGTTTTTCTTAA
80726 GAAGATTTTA
Statistics
Matches: 89, Mismatches: 8, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
71 1 0.01
72 47 0.53
73 13 0.15
74 1 0.01
75 8 0.09
76 19 0.21
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (75 bp):
TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGA
AAGAAGGCAT
Found at i:80879 original size:39 final size:39
Alignment explanation
Indices: 80819--80893 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
80809 CCTTGAAATT
* *
80819 AATTTTTTCTCTCCTGTGATAGTTTCCCTCGAAACAGAA
1 AATTTTGTCTCTCCTGAGATAGTTTCCCTCGAAACAGAA
* *
80858 AATTTTGTCTC-CCTTGAGATAGTTTCTCTTGAAACA
1 AATTTTGTCTCTCC-TGAGATAGTTTCCCTCGAAACA
80894 TAAACAGTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 2 0.06
39 29 0.94
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.40
Consensus pattern (39 bp):
AATTTTGTCTCTCCTGAGATAGTTTCCCTCGAAACAGAA
Found at i:80962 original size:105 final size:104
Alignment explanation
Indices: 80797--81104 Score: 478
Period size: 105 Copynumber: 3.0 Consensus size: 104
80787 CAGTTTCTCT
* * *
80797 TGAAAACATTTCCCTTGAAATTAATTTTTTCTCTCCTGTGATAGTTTCCCTCGAAACAGAAAATT
1 TGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAATT
*
80862 TTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAACAG
66 TTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACAG
*
80901 TGAAAACATTTCCCTTGAAATGATTTTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
1 TGAAAACATTTCCCTTGAAATGA-ATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
*
80966 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACAT
65 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACAG
* * * *
81006 TGAAAACATTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAGTTTCCCTTGAAA-TG--AATT
1 TGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAATT
**
81068 TTGTCTCCCTTGAGACAGTTTCTCTCCAAACATAAAC
66 TTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAC
81105 TTTAAAAACA
Statistics
Matches: 190, Mismatches: 13, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
101 39 0.21
103 1 0.01
104 51 0.27
105 99 0.52
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (104 bp):
TGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAATT
TTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACAG
Found at i:81061 original size:36 final size:36
Alignment explanation
Indices: 81014--81089 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 36
81004 ATTGAAAACA
* *
81014 TTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAG
1 TTTCCCTTGAAATGAATTTTATCTCCCTTGAGACAG
*
81050 TTTCCCTTGAAATGAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAATGAATTTTATCTCCCTTGAGACAG
81086 TTTC
1 TTTC
81090 TCTCCAAACA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.42
Consensus pattern (36 bp):
TTTCCCTTGAAATGAATTTTATCTCCCTTGAGACAG
Found at i:81483 original size:105 final size:105
Alignment explanation
Indices: 81289--81919 Score: 896
Period size: 105 Copynumber: 6.0 Consensus size: 105
81279 ATATCGTGAC
* * * * ** * * *
81289 ACTCGAGACAACACAAGTTCAACTTCACAATGAAGGGATGGCTGGTTGTCAAAAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTC-AACAACAACTTCCC
81354 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
81395 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
81460 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
81500 ACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGGTCCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
* *
81565 ATCTCAGAGCTAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
81605 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
*
81670 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
81710 ACTCTAGACAACGCAAGTTCAACTCCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
* *
81771 A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * ** * * * *
81810 ACTCGAGACAACACAAGTTCAACTTCAAAACGAATGGA-CGACTGGTTGTCAACAAATAATTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGCTTGTCAAC-AACAACTTCC
** * * *
81874 CTGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
64 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
81916 ACTC
1 ACTC
81920 GGAACAATGC
Statistics
Matches: 482, Mismatches: 36, Indels: 14
0.91 0.07 0.03
Matches are distributed among these distances:
99 2 0.00
100 78 0.16
101 3 0.01
102 3 0.01
103 4 0.01
104 3 0.01
105 309 0.64
106 80 0.17
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (105 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:82554 original size:37 final size:37
Alignment explanation
Indices: 82460--82556 Score: 122
Period size: 37 Copynumber: 2.6 Consensus size: 37
82450 CATTTTCGTC
82460 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* ** * *
82497 TTGTTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * *
82534 CTACTAAGATTTAAATTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
82557 GATATGATCC
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:82960 original size:18 final size:17
Alignment explanation
Indices: 82921--82963 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
82911 ATTATATGGA
82921 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
82937 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
82955 TATTATTAT
1 TATTATTAT
82964 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:84268 original size:21 final size:20
Alignment explanation
Indices: 84244--84297 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
84234 TATATAATAT
84244 ATATTAAATAATAATAATTAA
1 ATATTAAATAATAATAATT-A
*
84265 ATATTTAAAT-TTAATAATTA
1 ATA-TTAAATAATAATAATTA
*
84285 ATA-AAAATAATAA
1 ATATTAAATAATAA
84298 AATAAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 4 0.14
19 3 0.11
20 4 0.14
21 11 0.39
22 6 0.21
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATATTAAATAATAATAATTA
Found at i:85422 original size:17 final size:17
Alignment explanation
Indices: 85402--85441 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
85392 TAAATTACAT
85402 TTTTATGTTTTAAAGTA
1 TTTTATGTTTTAAAGTA
85419 TTTTATGTTTTAAAGTA
1 TTTTATGTTTTAAAGTA
85436 TTTTAT
1 TTTTAT
85442 AACATTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (17 bp):
TTTTATGTTTTAAAGTA
Found at i:90239 original size:81 final size:81
Alignment explanation
Indices: 90104--90266 Score: 290
Period size: 81 Copynumber: 2.0 Consensus size: 81
90094 CCTCCAATGC
90104 GTTCCAGTTGTGATACTGTACAGGAGCACGGTAAAGAAGAAACGGGCCGTCAACTAGGCTTTCAT
1 GTTCCAGTTGTGATACTGTACAGGAGCACGGTAAAGAAGAAACGGGCCGTCAACTAGGCTTTCAT
90169 GGCCCTCTACGCCTTT
66 GGCCCTCTACGCCTTT
* * * *
90185 GTTCCGGTTGTGATACTGTACAGGAGCACGGTAAAGAAGAAACGGGCTGTCAACTCGGCTTTTAT
1 GTTCCAGTTGTGATACTGTACAGGAGCACGGTAAAGAAGAAACGGGCCGTCAACTAGGCTTTCAT
90250 GGCCCTCTACGCCTTT
66 GGCCCTCTACGCCTTT
90266 G
1 G
90267 CCGCCGCTCT
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 78 1.00
ACGTcount: A:0.23, C:0.24, G:0.27, T:0.26
Consensus pattern (81 bp):
GTTCCAGTTGTGATACTGTACAGGAGCACGGTAAAGAAGAAACGGGCCGTCAACTAGGCTTTCAT
GGCCCTCTACGCCTTT
Found at i:99662 original size:33 final size:35
Alignment explanation
Indices: 99592--99670 Score: 108
Period size: 36 Copynumber: 2.3 Consensus size: 35
99582 GATTACCATA
*
99592 TTACATATTACATTAAGGAGATAAAAACAACAAACC
1 TTACACATTACATTAAGGAGAT-AAAACAACAAACC
*
99628 TTACACATTACGTTAAGGAGAT-AAA-AACAAACC
1 TTACACATTACATTAAGGAGATAAAACAACAAACC
*
99661 TTAAACATTA
1 TTACACATTA
99671 AATAAAATCT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
33 17 0.43
34 3 0.08
36 20 0.50
ACGTcount: A:0.51, C:0.16, G:0.09, T:0.24
Consensus pattern (35 bp):
TTACACATTACATTAAGGAGATAAAACAACAAACC
Found at i:100629 original size:30 final size:31
Alignment explanation
Indices: 100558--100632 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 31
100548 ATAAAAAACT
*
100558 ATATT-CAATTA--AAAACATTACATTAAAC
1 ATATTACAATTATTAAAACATTACATTAAAA
* * *
100586 ATA-AAGAAATATTAAAACATTACA-TAAAA
1 ATATTACAATTATTAAAACATTACATTAAAA
100615 ATATTACAATTATTAAAA
1 ATATTACAATTATTAAAA
100633 TCTAACGATG
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
28 7 0.19
29 7 0.19
30 22 0.61
ACGTcount: A:0.59, C:0.09, G:0.01, T:0.31
Consensus pattern (31 bp):
ATATTACAATTATTAAAACATTACATTAAAA
Found at i:101085 original size:21 final size:21
Alignment explanation
Indices: 101043--101085 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
101033 ATAACTCTAC
*
101043 GGGCTCGATATGTAACCTTGT
1 GGGCTCGATATGTAACCATGT
101064 GGGCTCGATATGTAACCATGT
1 GGGCTCGATATGTAACCATGT
101085 G
1 G
101086 ATGGTGACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (21 bp):
GGGCTCGATATGTAACCATGT
Found at i:102074 original size:20 final size:20
Alignment explanation
Indices: 102049--102087 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
102039 TTTTCAAGGG
102049 CATGCACCGATGCACCAATC
1 CATGCACCGATGCACCAATC
* *
102069 CATGCATCGATGCATCAAT
1 CATGCACCGATGCACCAAT
102088 TAATTTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.33, G:0.15, T:0.21
Consensus pattern (20 bp):
CATGCACCGATGCACCAATC
Found at i:102155 original size:20 final size:19
Alignment explanation
Indices: 102114--102165 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
102104 GAATGCATTT
102114 TATGCATCGATG--CATAC
1 TATGCATCGATGCACATAC
*
102131 CATGCATCGATGCACAATAC
1 TATGCATCGATGCAC-ATAC
102151 TATGCATCGATGCAC
1 TATGCATCGATGCAC
102166 TCAGGCTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 11 0.37
19 1 0.03
20 18 0.60
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (19 bp):
TATGCATCGATGCACATAC
Done.