Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003624.1 Hibiscus syriacus cultivar Beakdansim tig00007665_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: 85071
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:1220 original size:36 final size:37
Alignment explanation
Indices: 1148--1248 Score: 134
Period size: 36 Copynumber: 2.8 Consensus size: 37
1138 GTGCTTGTGG
* * * *
1148 ATCCTATCTTTAGGAGTTTAAAACATAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
*
1185 ATCCTATTTTTAGGAG-TTGAATCCTAGCAGAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1221 ATCCTATTTTT-GAGAGTTTGAATCCTAG
1 ATCCTATTTTTAG-GAGTTTGAATCCTAG
1249 TACGAAAAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
35 1 0.02
36 30 0.53
37 26 0.46
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.39
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
Found at i:1667 original size:171 final size:174
Alignment explanation
Indices: 1302--1771 Score: 736
Period size: 171 Copynumber: 2.7 Consensus size: 174
1292 GAATTTTAAC
1302 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAA-T
1 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATT--AAAAATTATATAAAATT
1366 TTATTTTATAATTATATATTATTTAAATTAATTTAAATTGTTTTTTTAATTAAAAAATATTAATA
64 TTATTTTATAATTATATATTATTTAAATTAATTTAAATTG--TTTTTAATTAAAAAATATT-ATA
1431 TTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATA
126 -TATATATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATA
*
1481 ATTTAAGATCCAATAACTTTAAAACCTAAATCAATATTAATTAATTAAAAATTATATAAAATTTT
1 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAATTATATAAAATTTT
*
1546 ATTTTATAATGATATATTATTTAAATTAATTGTAAATTGTTTTTAATTAAAAAATA-T-TA-A-A
66 ATTTTATAATTATATATTATTTAAATTAATT-TAAATTGTTTTTAATTAAAAAATATTATATATA
* *
1607 TATAACATATGGGCTAAGCCCAAACCATTTAAAACTCAATTGATA
130 TATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATA
*
1652 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAATTTATATGAAATTT
1 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAA-TTATATAAAATTT
* *
1717 TATTTTAAAATTATATATTATTTAAATTAATTATAAACTT-TTTTTGAATTTAAAA
65 TATTTTATAATTATATATTATTTAAATTAATT-TAAA-TTGTTTTT-AATTAAAAA
1772 CATTTTTTAT
Statistics
Matches: 276, Mismatches: 10, Indels: 16
0.91 0.03 0.05
Matches are distributed among these distances:
171 94 0.34
172 52 0.19
173 10 0.04
174 2 0.01
176 1 0.00
177 32 0.12
178 33 0.12
179 52 0.19
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (174 bp):
ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAATTATATAAAATTTT
ATTTTATAATTATATATTATTTAAATTAATTTAAATTGTTTTTAATTAAAAAATATTATATATAT
ATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATA
Found at i:3952 original size:18 final size:19
Alignment explanation
Indices: 3929--3971 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
3919 CAGTAATCAT
*
3929 ATTCC-CTGGTAATTTTAC
1 ATTCCACTGGTAATCTTAC
3947 ATTCCCACTGGTAATCTTAC
1 ATT-CCACTGGTAATCTTAC
3967 ATTCC
1 ATTCC
3972 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 4 0.18
20 15 0.68
ACGTcount: A:0.23, C:0.28, G:0.09, T:0.40
Consensus pattern (19 bp):
ATTCCACTGGTAATCTTAC
Found at i:3959 original size:20 final size:20
Alignment explanation
Indices: 3934--3971 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3924 ATCATATTCC
*
3934 CTGGTAATTTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
3954 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
3972 GTGAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:7444 original size:31 final size:32
Alignment explanation
Indices: 7409--7470 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
7399 TTTTTTAAAT
7409 TTATAAAATAATCATTACA-TTTATCAAATTG
1 TTATAAAATAATCATTACATTTTATCAAATTG
* * *
7440 TTATATAATAATCATTATATTTTATTAAATT
1 TTATAAAATAATCATTACATTTTATCAAATT
7471 TGTACATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 17 0.63
32 10 0.37
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (32 bp):
TTATAAAATAATCATTACATTTTATCAAATTG
Found at i:21977 original size:2 final size:2
Alignment explanation
Indices: 21972--21999 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21962 TTTATTATTA
21972 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
22000 CCACTATGCA
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:33485 original size:22 final size:23
Alignment explanation
Indices: 33443--33494 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
33433 GAGTCGAGGG
* * *
33443 TTTCATAGGTCATTCGTGACATA
1 TTTCATAGGTCATACGGGACAAA
*
33466 -TTCATAGGTCCTACGGGACAAA
1 TTTCATAGGTCATACGGGACAAA
33488 TTTCATA
1 TTTCATA
33495 TGCCGCTCAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (23 bp):
TTTCATAGGTCATACGGGACAAA
Found at i:34065 original size:21 final size:21
Alignment explanation
Indices: 34023--34065 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
34013 GTAGCAGTAT
* **
34023 TGTAGCATGGTATCGGTACCC
1 TGTAGCAGGGTATCAATACCC
*
34044 TGTAGCAGGGTATCAATGCCC
1 TGTAGCAGGGTATCAATACCC
34065 T
1 T
34066 ATTTGTAATC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.23, G:0.28, T:0.28
Consensus pattern (21 bp):
TGTAGCAGGGTATCAATACCC
Found at i:37619 original size:2 final size:2
Alignment explanation
Indices: 37614--37654 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
37604 ATACTAAGAA
37614 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
37655 AATTTATAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:37739 original size:18 final size:19
Alignment explanation
Indices: 37704--37742 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
37694 TTGATTAAAT
*
37704 TTTAAATTAAACATTTTAA
1 TTTAAAATAAACATTTTAA
37723 TTTAAAATAAA-ATTTTAA
1 TTTAAAATAAACATTTTAA
37741 TT
1 TT
37743 AATTATGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTAAAATAAACATTTTAA
Found at i:40524 original size:28 final size:29
Alignment explanation
Indices: 40474--40531 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
40464 GTCGAAGATG
40474 TTAGAAAAAAAAAACAAATAAT-AATAAA
1 TTAGAAAAAAAAAACAAATAATAAATAAA
* *
40502 TTAGGAAAAAAAAA-TAATAAATAAATAAA
1 TTAGAAAAAAAAAACAAAT-AATAAATAAA
40531 T
1 T
40532 GAATATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 3 0.12
28 16 0.62
29 7 0.27
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (29 bp):
TTAGAAAAAAAAAACAAATAATAAATAAA
Found at i:40644 original size:13 final size:13
Alignment explanation
Indices: 40626--40665 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
40616 TGAGATAGGG
*
40626 AAAAATAAAAATA
1 AAAAATAATAATA
*
40639 AAAAATAATATTA
1 AAAAATAATAATA
40652 AAAAATAATAATA
1 AAAAATAATAATA
40665 A
1 A
40666 TTAGAACGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAAATAATAATA
Found at i:40768 original size:13 final size:14
Alignment explanation
Indices: 40745--40774 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
40735 TATGGGAAAG
40745 AAATAATAATAATA
1 AAATAATAATAATA
40759 AAATAA-AATAATA
1 AAATAATAATAATA
40772 AAA
1 AAA
40775 ATAGATGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AAATAATAATAATA
Found at i:42097 original size:13 final size:13
Alignment explanation
Indices: 42079--42104 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42069 GGTGAATAAT
42079 AATAAATAAAAAC
1 AATAAATAAAAAC
42092 AATAAATAAAAAC
1 AATAAATAAAAAC
42105 TATATAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (13 bp):
AATAAATAAAAAC
Found at i:42253 original size:33 final size:33
Alignment explanation
Indices: 42163--42262 Score: 89
Period size: 33 Copynumber: 3.0 Consensus size: 33
42153 TATATATAAA
* * *
42163 TTTTCAAAAATGTTTTTTCAAAAAAAACTA-ATA-A
1 TTTTTAAAAATG--TTTT-AAAAAAAATTATATATT
**
42197 TTTTTAAAAATGTTATT-TTAAAAATTATATATT
1 TTTTTAAAAATGTT-TTAAAAAAAATTATATATT
*
42230 TTTTTAAAAATGTTTTAAAAAAAATTTTATATT
1 TTTTTAAAAATGTTTTAAAAAAAATTATATATT
42263 ATATATAAGT
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
31 7 0.13
32 7 0.13
33 29 0.54
34 11 0.20
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (33 bp):
TTTTTAAAAATGTTTTAAAAAAAATTATATATT
Found at i:42335 original size:36 final size:35
Alignment explanation
Indices: 42198--42413 Score: 167
Period size: 36 Copynumber: 6.0 Consensus size: 35
42188 AACTAATAAT
42198 TTTTAAAAATGTTATTTTAAAAATTATATA-T-T-T-
1 TTTTAAAAATG-T-TTTTAAAAATTATATATTATATG
* *
42231 TTTTAAAAATGTTTTAAAAAAAATTTTATATTATATATAAG
1 TTTTAAAAATGTTTT--TAAAAA--TTATA-TAT-TATATG
*
42272 TTTTCAAAAATG-TTCTAAAAATTATATATTATATG
1 TTTT-AAAAATGTTTTTAAAAATTATATATTATATG
* *
42307 TTTTCAAAATGTTTTTCAAAAATTATATATTATATAT
1 TTTTAAAAATGTTTTT-AAAAATTATATATTATAT-G
* *
42344 TTTTAAAAATG-TTTTGAAAATATATATAATATATAG
1 TTTTAAAAATGTTTTTAAAAAT-TATATATTATAT-G
* **
42380 TTTTTAAAA-GTGTTTTAAAAACCATATATTATAT
1 TTTTAAAAATGT-TTTTAAAAATTATATATTATAT
42414 ACGTATTTTC
Statistics
Matches: 149, Mismatches: 17, Indels: 31
0.76 0.09 0.16
Matches are distributed among these distances:
31 3 0.02
32 1 0.01
33 16 0.11
34 6 0.04
35 23 0.15
36 57 0.38
37 23 0.15
38 1 0.01
39 6 0.04
41 6 0.04
42 7 0.05
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (35 bp):
TTTTAAAAATGTTTTTAAAAATTATATATTATATG
Found at i:42370 original size:72 final size:70
Alignment explanation
Indices: 42196--42414 Score: 198
Period size: 72 Copynumber: 3.0 Consensus size: 70
42186 AAAACTAATA
* *
42196 ATTTTTAAAAATGTTATTTTAAAAAT-TATATAT-T-T-TTTTAAAAATGTTTTAAAAAAAATTT
1 ATTTTTAAAAATG---TTTTAAAAATATATATATATATGTTTTAAAAATGTTTT--TAAAAATTA
42257 TATATTATAT
61 TATATTATAT
* *
42267 ATAAGTTTTCAAAAATGTTCTAAAAAT-TATATATTATATGTTTTCAAAATGTTTTTCAAAAATT
1 AT---TTTT-AAAAATGTTTTAAAAATATATATA-TATATGTTTTAAAAATGTTTTT-AAAAATT
42331 ATATATTATAT
60 ATATATTATAT
* * **
42342 ATTTTTAAAAATGTTTTGAAAATATATATAATATATAGTTTTTAAAA-GTGTTTTAAAAACCATA
1 ATTTTTAAAAATGTTTTAAAAATATATAT-ATATAT-GTTTTAAAAATGT-TTTTAAAAATTATA
42406 TATTATAT
63 TATTATAT
42414 A
1 A
42415 CGTATTTTCA
Statistics
Matches: 126, Mismatches: 9, Indels: 25
0.79 0.06 0.16
Matches are distributed among these distances:
71 17 0.13
72 48 0.38
73 15 0.12
74 5 0.04
75 27 0.21
76 14 0.11
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (70 bp):
ATTTTTAAAAATGTTTTAAAAATATATATATATATGTTTTAAAAATGTTTTTAAAAATTATATAT
TATAT
Found at i:42384 original size:37 final size:37
Alignment explanation
Indices: 42230--42414 Score: 164
Period size: 37 Copynumber: 4.9 Consensus size: 37
42220 ATTATATATT
* *
42230 TTTTTAAAAATGTTTTAAAAAAAATTTTATATTATATATAAG
1 TTTTTAAAAATGTTTT---AAAAA-TATATATAATATAT-AG
* * *
42272 TTTTCAAAAATGTTCTAAAAAT-TATATATTATAT-G
1 TTTTTAAAAATGTTTTAAAAATATATATAATATATAG
* *
42307 -TTTTCAAAATGTTTTTCAAAAAT-TATATATTATATA-
1 TTTTTAAAAATG-TTTT-AAAAATATATATAATATATAG
*
42343 TTTTTAAAAATGTTTTGAAAATATATATAATATATAG
1 TTTTTAAAAATGTTTTAAAAATATATATAATATATAG
* * *
42380 TTTTTAAAAGTGTTTTAAAAACCATATATTATATA
1 TTTTTAAAAATGTTTTAAAAA-TATATATAATATA
42415 CGTATTTTCA
Statistics
Matches: 122, Mismatches: 14, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
34 9 0.07
35 9 0.07
36 34 0.28
37 39 0.32
38 12 0.10
39 5 0.04
42 14 0.11
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.47
Consensus pattern (37 bp):
TTTTTAAAAATGTTTTAAAAATATATATAATATATAG
Found at i:42414 original size:36 final size:37
Alignment explanation
Indices: 42220--42414 Score: 168
Period size: 36 Copynumber: 5.2 Consensus size: 37
42210 TATTTTAAAA
* * * *
42220 ATTATATATTTTTTTAAAAATGTTTTAAAAAAAATTTTAT
1 ATTATATA-GTTTTCAAAAATGTTTT--CAAAAATTATAT
*
42260 ATTATATATAAGTTTTCAAAAATGTTCT-AAAAATTATAT
1 A-T-TATAT-AGTTTTCAAAAATGTTTTCAAAAATTATAT
42299 ATTATAT-GTTTTC-AAAATGTTTTTCAAAAATTATAT
1 ATTATATAGTTTTCAAAAATG-TTTTCAAAAATTATAT
* *
42335 ATTATATA-TTTTTAAAAATGTTTT-GAAAATATATAT
1 ATTATATAGTTTTCAAAAATGTTTTCAAAAAT-TATAT
* * * **
42371 AATATATAGTTTTTAAAAGTGTTTT-AAAAACCATAT
1 ATTATATAGTTTTCAAAAATGTTTTCAAAAATTATAT
42407 ATTATATA
1 ATTATATA
42415 CGTATTTTCA
Statistics
Matches: 133, Mismatches: 13, Indels: 22
0.79 0.08 0.13
Matches are distributed among these distances:
34 6 0.05
35 14 0.11
36 49 0.37
37 30 0.23
38 1 0.01
39 11 0.08
40 1 0.01
41 1 0.01
42 19 0.14
43 1 0.01
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (37 bp):
ATTATATAGTTTTCAAAAATGTTTTCAAAAATTATAT
Found at i:43212 original size:84 final size:83
Alignment explanation
Indices: 43071--43718 Score: 685
Period size: 84 Copynumber: 7.9 Consensus size: 83
43061 ACCTCGAAGT
* * * * * *
43071 TGAGTGTAATCGAACCCGAGGGTCTTTGG---CAGATAGCCCTTCTCGACTTAAGCTATGCTGCA
1 TGAGCGTAGTCGAACTCGAAGGTCTTTGGTTCCAGATAACCCTTCTCGACTTAAGTTATGCTGCA
*
43133 AATGATGTGCCTTAGAGC
66 AATGATGTGCCTTCGAGC
* * * *
43151 TGAGCGTAGTCGAACTCGAAGGTCTTTTGG-TCATAGATAACCCTTCTAGCCTTGAGTTATGCTG
1 TGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTC-CAGATAACCCTTCTCGACTTAAGTTATGCTG
* * *
43215 TAAATGATGTGCCCTCGAAGT
64 CAAATGATGTGCCTTCG-AGC
* * ** * * *
43236 TGAGTGTAATCGAACTCGGGGGTCTTTGG---CAGATAGCCCTTTTCGACTTAAGCTATGCTGCA
1 TGAGCGTAGTCGAACTCGAAGGTCTTTGGTTCCAGATAACCCTTCTCGACTTAAGTTATGCTGCA
*
43298 AATGATGTGCCTTAGAGC
66 AATGATGTGCCTTCGAGC
* *
43316 TGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTATGTTATGCTGC
1 TGAGCGTAGTCGAACTCGAAGGTCTTTGGTT-CCAGATAACCCTTCTCGACTTAAGTTATGCTGC
*
43381 AAATGATGTGCCCTCGAAGC
65 AAATGATGTGCCTTCG-AGC
* * ** *
43401 TGAGTGTAATCGAACTCGGGGGTCTTTGG---CAGATAGCCCTTCTCGACTTAAGTTATGCTGCA
1 TGAGCGTAGTCGAACTCGAAGGTCTTTGGTTCCAGATAACCCTTCTCGACTTAAGTTATGCTGCA
43463 AATGATGTGCCGTT-GAGC
66 AATGATGTGCC-TTCGAGC
* * * *
43481 TGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGCCAGACAACCCTTCTAGACTTAAGTTGTGCTGC
1 TGAGCGTAGTCGAACTCGAAGGTCTTTGGTT-CCAGATAACCCTTCTCGACTTAAGTTATGCTGC
* *
43546 AAATGATATGCCTTGGAGC
65 AAATGATGTGCCTTCGAGC
* * *
43565 TGAGCGTAGCCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGTTGC
1 TGAGCGTAGTCGAACTCGAAGGTCTTTGGTT-CCAGATAACCCTTCTCGACTTAAGTTATGCTGC
*
43630 AAATGATGTGCCCTCGAAGC
65 AAATGATGTGCCTTCG-AGC
* * ** * * *
43650 TGAGTGTAATCGAACTCGGGGGGTCTTTGG---CAGATAGCCCTTCTCGACTTAAGCTATACTGC
1 TGAGCGTAGTCGAACTC-GAAGGTCTTTGGTTCCAGATAACCCTTCTCGACTTAAGTTATGCTGC
43712 AAATGAT
65 AAATGAT
43719 TTGGTTTTTA
Statistics
Matches: 475, Mismatches: 75, Indels: 34
0.81 0.13 0.06
Matches are distributed among these distances:
80 74 0.16
81 86 0.18
82 36 0.08
83 2 0.00
84 200 0.42
85 67 0.14
86 10 0.02
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.29
Consensus pattern (83 bp):
TGAGCGTAGTCGAACTCGAAGGTCTTTGGTTCCAGATAACCCTTCTCGACTTAAGTTATGCTGCA
AATGATGTGCCTTCGAGC
Found at i:43298 original size:165 final size:164
Alignment explanation
Indices: 43026--43718 Score: 833
Period size: 165 Copynumber: 4.2 Consensus size: 164
43016 TGACAAATAG
* * * * * * * *
43026 CCCTTCTTGCCTTGAGCTATGTTGTAAATGATATGACCTCGAAGTTGAGTGTAATCGAACCCGAG
1 CCCTTCTAGACTTGAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAG
43091 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGC
66 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGC
*
43156 GTAGTCGAACTCGAAGGTCTTTTGG-TCATAGATAA
131 GTAGTCGAACTCGAAGGTC-TTTGGTTC-CAGATAA
* * * * *
43191 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGTTGAGTGTAATCGAACTCGGG
1 CCCTTCTAGACTTGAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAG
*
43256 GGTCTTTGGCAGATAGCCCTTTTCGACTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGC
66 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGC
*
43321 GTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAA
131 GTAGTCGAACTCGAAGGTCTTTGGTT-CCAGATAA
* * *
43356 CCCTTCTCGACTT-ATGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGG
1 CCCTTCTAGACTTGA-GTTATGCTGCAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGA
*
43420 GGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCGTT-GAGCTGA
65 GGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC-TTAGAGCTGA
* *
43484 GCGTAGTCGAACTCAAAGGTCTTTGGTTGCCAGACAA
129 GCGTAGTCGAACTCGAAGGTCTTTGGTT-CCAGATAA
* * * * * ** *
43521 CCCTTCTAGACTTAAGTTGTGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAGCCGAACTCGAA
1 CCCTTCTAGACTTGAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAG
* * * * *
43585 GGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGTTGCAAATGATGTGCCCTCGAAGC
66 GGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTAG-AGC
* * ** *
43650 TGAGTGTAATCGAACTCGGGGGGTCTTTGG---CAGATAG
126 TGAGCGTAGTCGAACTC-GAAGGTCTTTGGTTCCAGATAA
* * * *
43687 CCCTTCTCGACTTAAGCTATACTGCAAATGAT
1 CCCTTCTAGACTTGAGTTATGCTGCAAATGAT
43719 TTGGTTTTTA
Statistics
Matches: 473, Mismatches: 43, Indels: 23
0.88 0.08 0.04
Matches are distributed among these distances:
164 32 0.07
165 329 0.70
166 37 0.08
167 1 0.00
168 47 0.10
169 18 0.04
170 9 0.02
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (164 bp):
CCCTTCTAGACTTGAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAG
GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGC
GTAGTCGAACTCGAAGGTCTTTGGTTCCAGATAA
Found at i:43379 original size:249 final size:248
Alignment explanation
Indices: 43096--43718 Score: 813
Period size: 249 Copynumber: 2.5 Consensus size: 248
43086 CCGAGGGTCT
* * * * * *
43096 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTAG-AGCTGAGCGTAG
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
* * *
43160 TCGAACTCGAAGGTCTTTTGGTCATAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
66 TCGAACTCGAAGGTC-TTTGG-C--AGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
* * *** * * * *
43225 GCCCTCGAAGTTGAGTGTAATCGAACTCGGGGGTCTTT-G-G-CAGATAGCCCTTTTCGACTTAA
127 GCCCTCG-AGCTGAGCGTAATCGAACTCAAAGGTCTTTGGTGCCAGACAACCCTTCTAGACTTAA
* *
43287 GCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
191 GCTATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGCCGAACTCGAAGGTCTTTGG
*
43345 TTGGCAGATAACCCTTCTCGACTTATGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
** * * *
43410 TCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCG
66 TCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCC
* * * *
43475 TTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGCCAGACAACCCTTCTAGACTTAAGTTG
131 TCGAGCTGAGCGTAATCGAACTCAAAGGTCTTTGG-TGCCAGACAACCCTTCTAGACTTAAGCTA
*
43540 TGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGCCGAACTCGAAGGTCTTTGG
195 TGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGCCGAACTCGAAGGTCTTTGG
*
43594 TTGGCAGATAACCCTTCTCGACTTAAGTTATGTTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
** * * * *
43659 TCGAACTCGGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGAT
66 TCGAACTC-GAAGGTCTTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGAT
43719 TTGGTTTTTA
Statistics
Matches: 333, Mismatches: 35, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
245 24 0.07
246 41 0.12
248 2 0.01
249 194 0.58
250 72 0.22
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (248 bp):
TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
TCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCC
TCGAGCTGAGCGTAATCGAACTCAAAGGTCTTTGGTGCCAGACAACCCTTCTAGACTTAAGCTAT
GCTGCAAATGATATGCCTTAGAGCTGAGCGTAGCCGAACTCGAAGGTCTTTGG
Found at i:46867 original size:17 final size:19
Alignment explanation
Indices: 46829--46872 Score: 65
Period size: 17 Copynumber: 2.4 Consensus size: 19
46819 TTAGTTAATG
46829 AATGCAAAGAAATAACAAA
1 AATGCAAAGAAATAACAAA
*
46848 AATGCAAAG-AA-AATAAA
1 AATGCAAAGAAATAACAAA
46865 AATGCAAA
1 AATGCAAA
46873 ATGTCTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 13 0.54
18 2 0.08
19 9 0.38
ACGTcount: A:0.68, C:0.09, G:0.11, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAATAACAAA
Found at i:47567 original size:15 final size:16
Alignment explanation
Indices: 47547--47577 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
47537 TGCAAATGAT
47547 GAGAAC-AAAATAAAA
1 GAGAACAAAAATAAAA
47562 GAGAACAAAAATAAAA
1 GAGAACAAAAATAAAA
47578 AGAGTTAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.74, C:0.06, G:0.13, T:0.06
Consensus pattern (16 bp):
GAGAACAAAAATAAAA
Found at i:48771 original size:24 final size:27
Alignment explanation
Indices: 48741--48796 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 27
48731 CGAGATAGGG
48741 AAAAATAAAAATAA-A-AA-GAATATT
1 AAAAATAAAAATAATAGAACGAATATT
*
48765 AAAAATAATAATAATTAGAACGAATATT
1 AAAAATAAAAATAA-TAGAACGAATATT
48793 AAAA
1 AAAA
48797 CGTTAACTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 13 0.48
26 1 0.04
27 2 0.07
28 11 0.41
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (27 bp):
AAAAATAAAAATAATAGAACGAATATT
Found at i:48879 original size:13 final size:14
Alignment explanation
Indices: 48856--48885 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
48846 TATGTTAAAG
48856 AAATAATAATAATA
1 AAATAATAATAATA
48870 AAATAA-AATAATA
1 AAATAATAATAATA
48883 AAA
1 AAA
48886 ATAGATGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AAATAATAATAATA
Found at i:50207 original size:13 final size:13
Alignment explanation
Indices: 50189--50214 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
50179 GGTGAATAAT
50189 AATAAATAAAAAC
1 AATAAATAAAAAC
50202 AATAAATAAAAAC
1 AATAAATAAAAAC
50215 TATATAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (13 bp):
AATAAATAAAAAC
Found at i:50334 original size:33 final size:33
Alignment explanation
Indices: 50269--50376 Score: 105
Period size: 35 Copynumber: 3.2 Consensus size: 33
50259 CTATATACTA
*
50269 TATATAAATTTTCAAAAATGTTTTTTCAAAAAAAAC
1 TATAT-AATTTTAAAAAATGTTTTTT--AAAAAAAC
*
50305 TA-ATAATTTTAAAAAATGTTATTTT--AAAAAT
1 TATATAATTTTAAAAAATGTT-TTTTAAAAAAAC
* *
50336 TATATAATTTTTTAAAAATGTTTTTTTAAAAAAAT
1 TATATAA-TTTTAAAAAATG-TTTTTTAAAAAAAC
50371 TATATA
1 TATATA
50377 TTATATATAA
Statistics
Matches: 63, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
31 7 0.11
32 4 0.06
33 15 0.24
34 17 0.27
35 18 0.29
36 2 0.03
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (33 bp):
TATATAATTTTAAAAAATGTTTTTTAAAAAAAC
Found at i:50376 original size:35 final size:34
Alignment explanation
Indices: 50269--50376 Score: 123
Period size: 34 Copynumber: 3.2 Consensus size: 34
50259 CTATATACTA
* * *
50269 TATATAAATTTTCAAAAATGTTTTTTCAAAAAAAAC
1 TATAT-AATTTTAAAAAATGTTTTTT-TAAAAAAAT
*
50305 TA-ATAATTTTAAAAAATGTTATTTT--AAAAAT
1 TATATAATTTTAAAAAATGTTTTTTTAAAAAAAT
*
50336 TATATAATTTTTTAAAAATGTTTTTTTAAAAAAAT
1 TATATAA-TTTTAAAAAATGTTTTTTTAAAAAAAT
50371 TATATA
1 TATATA
50377 TTATATATAA
Statistics
Matches: 62, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
31 7 0.11
32 4 0.06
33 17 0.27
34 18 0.29
35 14 0.23
36 2 0.03
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (34 bp):
TATATAATTTTAAAAAATGTTTTTTTAAAAAAAT
Found at i:50401 original size:77 final size:73
Alignment explanation
Indices: 50307--50527 Score: 192
Period size: 70 Copynumber: 3.0 Consensus size: 73
50297 AAAAAAACTA
*
50307 ATAATTTTAAAAAATGTTATTTTAAAAATTATATA-AT-T-TTTTAAAAATGTTTTTTTAAAAAA
1 ATAATTTTAAAAAATG---TTCTAAAAATTATATATATATGTTTTAAAAATG--TTTTT-AAAAA
50369 ATTATATATTATAT
60 ATTATATATTATAT
* * *
50383 ATAAGTTTTCAAAAATGTTCTAAAAATTATATATTATATGTTTTCAAAATGTTTTTCAAAAATTA
1 ATAA-TTTTAAAAAATGTTCTAAAAATTATATA-TATATGTTTTAAAAATGTTTTTAAAAAATTA
50448 TATA-T-TAT
64 TATATTATAT
* * * **
50456 AT-ATTTT-AAAAATGTTTTGAAAA-TATATAATATATAGTTTTTAAAA-GTGTTTT-AAAAACC
1 ATAATTTTAAAAAATGTTCTAAAAATTATAT-ATATAT-GTTTTAAAAATGT-TTTTAAAAAATT
50516 ATATATTATAT
63 ATATATTATAT
50527 A
1 A
50528 CGTATTTTCA
Statistics
Matches: 126, Mismatches: 9, Indels: 25
0.79 0.06 0.16
Matches are distributed among these distances:
69 22 0.17
70 29 0.23
71 8 0.06
72 1 0.01
73 5 0.04
74 16 0.13
75 12 0.10
76 11 0.09
77 12 0.10
78 10 0.08
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (73 bp):
ATAATTTTAAAAAATGTTCTAAAAATTATATATATATGTTTTAAAAATGTTTTTAAAAAATTATA
TATTATAT
Found at i:50432 original size:111 final size:113
Alignment explanation
Indices: 50244--50473 Score: 267
Period size: 111 Copynumber: 2.0 Consensus size: 113
50234 AACTATTTCT
*
50244 TTTTTTTAAAAAAAACTATATACTATATATAAATTTTCAAAAATGTTTTTTCAAAAAAAACTAAT
1 TTTTTTTAAAAAAAACTATATACTATATATAAATTTTCAAAAATG-TTTCTCAAAAAAAACTAAT
*
50309 AATTTTAAAAAATGTTATTTTAAAAATTATATA-AT-T-TTTTAAAAATG
65 AATTTTAAAAAATGTT-TTTCAAAAATTATATATATATATTTTAAAAATG
* * * * *
50356 TTTTTTT-AAAAAAATTATATATTATATATAAGTTTTCAAAAATG-TTCT-AAAAATTATA-TAT
1 TTTTTTTAAAAAAAACTATATACTATATATAAATTTTCAAAAATGTTTCTCAAAAA--AAACTAA
**
50417 TATATGTTTTCAAAATGTTTTTCAAAAATTATATATTATATATTTTAAAAATG
64 TA-AT-TTTAAAAAATGTTTTTCAAAAATTATATA-TATATATTTTAAAAATG
50470 TTTT
1 TTTT
50474 GAAAATATAT
Statistics
Matches: 101, Mismatches: 9, Indels: 14
0.81 0.07 0.11
Matches are distributed among these distances:
108 5 0.05
109 7 0.07
110 19 0.19
111 45 0.45
112 9 0.09
113 1 0.01
114 15 0.15
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (113 bp):
TTTTTTTAAAAAAAACTATATACTATATATAAATTTTCAAAAATGTTTCTCAAAAAAAACTAATA
ATTTTAAAAAATGTTTTTCAAAAATTATATATATATATTTTAAAAATG
Found at i:50451 original size:36 final size:35
Alignment explanation
Indices: 50311--50526 Score: 169
Period size: 36 Copynumber: 6.0 Consensus size: 35
50301 AAACTAATAA
50311 TTTTAAAAAATGTTATTTTAAAAATTATATA--AT-T-
1 TTTT-AAAAATG-T-TTTTAAAAATTATATATTATATG
50345 TTTTAAAAATGTTTTTTTAAAAAAATTATATATTATATATAAG
1 TTTTAAAAATG--TTTTT--AAAAATTATATA-T-TATAT--G
*
50388 TTTTCAAAAATG-TTCTAAAAATTATATATTATATG
1 TTTT-AAAAATGTTTTTAAAAATTATATATTATATG
* *
50423 TTTTCAAAATGTTTTTCAAAAATTATATATTATATA
1 TTTTAAAAATGTTTTT-AAAAATTATATATTATATG
* *
50459 TTTTAAAAATG-TTTTGAAAA-TATATAATATATAG
1 TTTTAAAAATGTTTTTAAAAATTATATATTATAT-G
* **
50493 TTTTTAAAA-GTGTTTTAAAAACCATATATTATAT
1 TTTTAAAAATGT-TTTTAAAAATTATATATTATAT
50527 ACGTATTTTC
Statistics
Matches: 152, Mismatches: 12, Indels: 34
0.77 0.06 0.17
Matches are distributed among these distances:
33 23 0.15
34 24 0.16
35 32 0.21
36 38 0.25
37 5 0.03
38 1 0.01
39 14 0.09
40 1 0.01
41 3 0.02
43 4 0.03
44 7 0.05
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (35 bp):
TTTTAAAAATGTTTTTAAAAATTATATATTATATG
Found at i:50527 original size:36 final size:36
Alignment explanation
Indices: 50365--50527 Score: 183
Period size: 36 Copynumber: 4.5 Consensus size: 36
50355 GTTTTTTTAA
*
50365 AAAAATTATATATTATATATAAGTTTTCAAAAATGTTCT
1 AAAAATTATATA-T-TATAT-AGTTTTCAAAAATGTTTT
50404 AAAAATTATATATTATAT-GTTTTC-AAAATGTTTTT
1 AAAAATTATATATTATATAGTTTTCAAAAATG-TTTT
50439 CAAAAATTATATATTATATA-TTTT-AAAAATGTTTT
1 -AAAAATTATATATTATATAGTTTTCAAAAATGTTTT
* * * *
50474 GAAAA-TATATAATATATAGTTTTTAAAAGTGTTTT
1 AAAAATTATATATTATATAGTTTTCAAAAATGTTTT
**
50509 AAAAACCATATATTATATA
1 AAAAATTATATATTATATA
50528 CGTATTTTCA
Statistics
Matches: 110, Mismatches: 7, Indels: 17
0.82 0.05 0.13
Matches are distributed among these distances:
33 12 0.11
34 14 0.13
35 27 0.25
36 39 0.35
37 5 0.05
38 1 0.01
39 12 0.11
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (36 bp):
AAAAATTATATATTATATAGTTTTCAAAAATGTTTT
Found at i:51564 original size:20 final size:20
Alignment explanation
Indices: 51539--51592 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
51529 TCCTACGCTG
*
51539 CCTTTCTTCCCTTTTATCCT
1 CCTTTCCTCCCTTTTATCCT
*
51559 CCTTTCCTCCCTTTTCTCCT
1 CCTTTCCTCCCTTTTATCCT
51579 CCTTTCCTCCCTTT
1 CCTTTCCTCCCTTT
51593 CCCTTATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.02, C:0.46, G:0.00, T:0.52
Consensus pattern (20 bp):
CCTTTCCTCCCTTTTATCCT
Found at i:63409 original size:2 final size:2
Alignment explanation
Indices: 63402--63434 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
63392 TCTATCTATC
63402 TA TA 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 TA TA T
63435 GTTTGAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:69974 original size:20 final size:20
Alignment explanation
Indices: 69922--69975 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
69912 AACTTAATAT
*
69922 TATTATTTTTAAAATATTAAAA
1 TATTATTTTT--ATTATTAAAA
*
69944 TAATT-TATTTATTATTAAAA
1 T-ATTATTTTTATTATTAAAA
69964 TATTATTTTTAT
1 TATTATTTTTAT
69976 AATTTTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
19 3 0.11
20 16 0.59
22 5 0.19
23 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTATTTTTATTATTAAAA
Found at i:70041 original size:26 final size:27
Alignment explanation
Indices: 69990--70041 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
69980 TTATTAATAA
* *
69990 AAATAAAAATATTGATATATTTTATTG
1 AAATAAAAATATTGATAAATTATATTG
70017 AAATAAAAATATT-ATAAATTATATT
1 AAATAAAAATATTGATAAATTATATT
70042 AATTATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (27 bp):
AAATAAAAATATTGATAAATTATATTG
Found at i:70101 original size:23 final size:23
Alignment explanation
Indices: 70071--70122 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
70061 AGTGTTATAT
70071 TATATTTTAAAAATATTAATTAA
1 TATATTTTAAAAATATTAATTAA
* * *
70094 TATATTTTAAATATCTTCATTAA
1 TATATTTTAAAAATATTAATTAA
*
70117 AATATT
1 TATATT
70123 ATTAGATTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATTAA
Found at i:70192 original size:54 final size:52
Alignment explanation
Indices: 70134--70260 Score: 132
Period size: 54 Copynumber: 2.4 Consensus size: 52
70124 TTAGATTATT
* *
70134 TTATTAATATTAAATATATAAATAATATTATTCATTATTAATAATTTAATA-ATA
1 TTATTAATATAAAATATATAAATAATA-AATT--TTATTAATAATTTAATATATA
** * *
70188 TTATTTCTATGAAAT-TAATAAATAATAAATTTTATTAATAATTTATTATATA
1 TTATTAATATAAAATAT-ATAAATAATAAATTTTATTAATAATTTAATATATA
*
70240 TTATTAAAATAAAAATATATA
1 TTATTAATAT-AAAATATATA
70261 TCTTATATTA
Statistics
Matches: 60, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
51 16 0.27
52 10 0.17
53 11 0.18
54 23 0.38
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (52 bp):
TTATTAATATAAAATATATAAATAATAAATTTTATTAATAATTTAATATATA
Found at i:70334 original size:20 final size:20
Alignment explanation
Indices: 70296--70335 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
70286 TTTATTATAA
*
70296 TATTAAAATATATATTAAAT
1 TATTAAAATATATAATAAAT
70316 TATTAGAAATAT-TAATAAAT
1 TATTA-AAATATATAATAAAT
70336 ATTTTTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (20 bp):
TATTAAAATATATAATAAAT
Found at i:70395 original size:24 final size:25
Alignment explanation
Indices: 70348--70396 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
70338 TTTTATAATT
*
70348 AATATTTTGATTAAAACTATATTAA
1 AATATTTTGATTAAAACTAAATTAA
* *
70373 AATATTTT-ATTAATATTAAATTAA
1 AATATTTTGATTAAAACTAAATTAA
70397 TAAAATTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (25 bp):
AATATTTTGATTAAAACTAAATTAA
Found at i:74354 original size:10 final size:10
Alignment explanation
Indices: 74335--74395 Score: 77
Period size: 10 Copynumber: 6.1 Consensus size: 10
74325 CATTTAATAA
*
74335 ATAAATGAAC
1 ATAAACGAAC
74345 ATAAACGAAC
1 ATAAACGAAC
**
74355 ACGAACGAAC
1 ATAAACGAAC
74365 ATAAACGAAC
1 ATAAACGAAC
**
74375 ACGAACGAAC
1 ATAAACGAAC
74385 ATAAACGAAC
1 ATAAACGAAC
74395 A
1 A
74396 ACACAAACAC
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
10 42 1.00
ACGTcount: A:0.57, C:0.21, G:0.13, T:0.08
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:74366 original size:20 final size:20
Alignment explanation
Indices: 74341--74395 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
74331 ATAAATAAAT
74341 GAACATAAACGAACACGAAC
1 GAACATAAACGAACACGAAC
74361 GAACATAAACGAACACGAAC
1 GAACATAAACGAACACGAAC
74381 GAACATAAACGAACA
1 GAACATAAACGAACA
74396 ACACAAACAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.56, C:0.24, G:0.15, T:0.05
Consensus pattern (20 bp):
GAACATAAACGAACACGAAC
Found at i:74679 original size:14 final size:16
Alignment explanation
Indices: 74660--74691 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
74650 ACCCTCTGTT
74660 CGAACATA-AAT-GAA
1 CGAACATATAATCGAA
74674 CGAACATATAATCGAA
1 CGAACATATAATCGAA
74690 CG
1 CG
74692 TTCACGAACG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 3 0.19
16 5 0.31
ACGTcount: A:0.50, C:0.19, G:0.16, T:0.16
Consensus pattern (16 bp):
CGAACATATAATCGAA
Found at i:80944 original size:2 final size:2
Alignment explanation
Indices: 80939--80963 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
80929 CACTAAGAAT
80939 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
80964 TGATATAAGA
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
Done.