Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018040.1 Corchorus olitorius cultivar O-4 contig18073, 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: 97604
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:11 original size:2 final size:2
Alignment explanation
Indices: 5--42 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1 CAGG
5 AT AT AT AT AT 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 AT AT AT AT AT
43 TGTCACAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:764 original size:13 final size:13
Alignment explanation
Indices: 748--775 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
738 AACCTACACA
748 AAATTAAATTAAG
1 AAATTAAATTAAG
761 AAATTAAATTAAG
1 AAATTAAATTAAG
774 AA
1 AA
776 CCAAAACAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (13 bp):
AAATTAAATTAAG
Found at i:1478 original size:115 final size:115
Alignment explanation
Indices: 1261--1560 Score: 288
Period size: 115 Copynumber: 2.6 Consensus size: 115
1251 AATTTGTAAC
* * ** * *
1261 GCCTAAAAATGTTAGAATCAGTCAACTAGTACAATTTGTAACGCCTGAAATTGTTAGAATCAGCC
1 GCCTAAAAATATTAGAATCAATCAACTAGTACAATTTGTAACGCCTGAAATTAATACAATCACCC
1326 AATCACAATCCGTAACGCATGAAAAATATAGCCAACCAATCTAGCTTAAT
66 AATCACAATCCGTAACGCATGAAAAATATAGCCAACCAATCTAGCTTAAT
* * *
1376 GCCTAAAAATATTAGAATCAATCGACTGGTACAATTTGTAACGCTTGAAA-TAATACAATCAACC
1 GCCTAAAAATATTAGAATCAATCAACTAGTACAATTTGTAACGCCTGAAATTAATACAATC-ACC
* * * * * *
1440 CATAAAT-ACAATCTGTAACGCATG-AAAAT-TAGCTAACCAGTATAACTTGTAAC
65 C---AATCACAATCCGTAACGCATGAAAAATATAGCCAACCAATCTAGC-T-TAAT
** * * * * *
1493 GCCTACGAATGTTGGAATCAGTCAACAAGTACAATTTGTAACGCCTTGAAATGT--TACAATCAG
1 GCCTAAAAATATTAGAATCAATCAACTAGTACAATTTGTAACGCC-TGAAAT-TAATACAATCAC
1556 CCAAT
64 CCAAT
1561 TTAGACAATA
Statistics
Matches: 151, Mismatches: 25, Indels: 19
0.77 0.13 0.10
Matches are distributed among these distances:
114 10 0.07
115 61 0.40
116 6 0.04
117 58 0.38
118 15 0.10
120 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26
Consensus pattern (115 bp):
GCCTAAAAATATTAGAATCAATCAACTAGTACAATTTGTAACGCCTGAAATTAATACAATCACCC
AATCACAATCCGTAACGCATGAAAAATATAGCCAACCAATCTAGCTTAAT
Found at i:1511 original size:117 final size:116
Alignment explanation
Indices: 1230--1554 Score: 354
Period size: 117 Copynumber: 2.8 Consensus size: 116
1220 TTTTTCTTAT
* * *
1230 AAAACATTAGCCAATCAGTACAATTTGTAACGCCTAAAAATGTTAGAATCAGTCAACTAGTACAA
1 AAAA-ATTAGCCAACCAGTATAACTTGTAACGCCTAAAAATGTTAGAATCAGTCAACTAGTACAA
* * *
1295 TTTGTAACGCCTGAAATTGTTAGAATC-AGCCAATCACAATCCGTAACGCATG
65 TTTGTAACGCTTGAAA-TGTTACAATCAACCCAATCACAATCCGTAACGCATG
* * * * * * * *
1347 AAAAATATAGCCAACCAATCTAGC-T-TAATGCCTAAAAATATTAGAATCAATCGACTGGTACAA
1 AAAAAT-TAGCCAACCAGTATAACTTGTAACGCCTAAAAATGTTAGAATCAGTCAACTAGTACAA
** *
1410 TTTGTAACGCTTGAAATAATACAATCAACCCATAAAT-ACAATCTGTAACGCATG
65 TTTGTAACGCTTGAAATGTTACAATCAACCC---AATCACAATCCGTAACGCATG
* ** * *
1464 -AAAATTAGCTAACCAGTATAACTTGTAACGCCTACGAATGTTGGAATCAGTCAACAAGTACAAT
1 AAAAATTAGCCAACCAGTATAACTTGTAACGCCTAAAAATGTTAGAATCAGTCAACTAGTACAAT
1528 TTGTAACGCCTTGAAATGTTACAATCA
66 TTGTAACG-CTTGAAATGTTACAATCA
1555 GCCAATTTAG
Statistics
Matches: 168, Mismatches: 32, Indels: 15
0.78 0.15 0.07
Matches are distributed among these distances:
114 7 0.04
115 64 0.38
116 9 0.05
117 69 0.41
118 19 0.11
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.26
Consensus pattern (116 bp):
AAAAATTAGCCAACCAGTATAACTTGTAACGCCTAAAAATGTTAGAATCAGTCAACTAGTACAAT
TTGTAACGCTTGAAATGTTACAATCAACCCAATCACAATCCGTAACGCATG
Found at i:2185 original size:14 final size:14
Alignment explanation
Indices: 2166--2195 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2156 TTATGGATTG
2166 TATCTATGAGTAAT
1 TATCTATGAGTAAT
2180 TATCTATGAGTAAT
1 TATCTATGAGTAAT
2194 TA
1 TA
2196 GCTTGAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (14 bp):
TATCTATGAGTAAT
Found at i:3220 original size:14 final size:15
Alignment explanation
Indices: 3201--3229 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3191 TTGGTTTCTG
3201 AAGGGAAAAA-AAAA
1 AAGGGAAAAAGAAAA
3215 AAGGGAAAAAGAAAA
1 AAGGGAAAAAGAAAA
3230 TACGAATCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (15 bp):
AAGGGAAAAAGAAAA
Found at i:14312 original size:36 final size:36
Alignment explanation
Indices: 14265--14337 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
14255 GCATTGAAGC
14265 ACAGACCGACTAACTATTGTGTAGATAACATGATTA
1 ACAGACCGACTAACTATTGTGTAGATAACATGATTA
14301 ACAGACCGACTAACTATTGTGTAGATAACATGATTA
1 ACAGACCGACTAACTATTGTGTAGATAACATGATTA
14337 A
1 A
14338 GTGCATCATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.27
Consensus pattern (36 bp):
ACAGACCGACTAACTATTGTGTAGATAACATGATTA
Found at i:15403 original size:41 final size:41
Alignment explanation
Indices: 15346--15429 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
15336 ACCAGGAGTC
*
15346 CTAGAATGATAACAAGCAGTCAATATTATACCGAAAACCCA
1 CTAGAATGATAACAAGCAGTCAACATTATACCGAAAACCCA
15387 CTAGAATGATAACAAGCAGTCAACATTATACCGAAAACCCA
1 CTAGAATGATAACAAGCAGTCAACATTATACCGAAAACCCA
15428 CT
1 CT
15430 TTATTACTAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.45, C:0.24, G:0.12, T:0.19
Consensus pattern (41 bp):
CTAGAATGATAACAAGCAGTCAACATTATACCGAAAACCCA
Found at i:22533 original size:12 final size:13
Alignment explanation
Indices: 22516--22544 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
22506 ATTTAAAGTT
22516 AAAAAAG-AGAAA
1 AAAAAAGAAGAAA
22528 AAAAAAGAAGAAA
1 AAAAAAGAAGAAA
22541 AAAA
1 AAAA
22545 TTTGGTGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAGAAA
Found at i:24494 original size:13 final size:13
Alignment explanation
Indices: 24478--24502 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24468 TAATATTCAG
24478 TATATATATATAA
1 TATATATATATAA
24491 TATATATATATA
1 TATATATATATA
24503 TTTCTATAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TATATATATATAA
Found at i:27488 original size:43 final size:43
Alignment explanation
Indices: 27439--27525 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
27429 AATAGACTAA
27439 TTTTTATTTGTCTTTGATGAGGACACTTGTTGGACAAGTAAGT
1 TTTTTATTTGTCTTTGATGAGGACACTTGTTGGACAAGTAAGT
27482 TTTTTATTTGTCTTTGATGAGGACACTTGTTGGACAAGTAAGT
1 TTTTTATTTGTCTTTGATGAGGACACTTGTTGGACAAGTAAGT
27525 T
1 T
27526 GTTGGCTGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.45
Consensus pattern (43 bp):
TTTTTATTTGTCTTTGATGAGGACACTTGTTGGACAAGTAAGT
Found at i:28918 original size:39 final size:39
Alignment explanation
Indices: 28875--28949 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
28865 AAGGAAAAAT
*
28875 AAAAAATTAAGACTTTAGAAATTCTTAAGTCATCAAGGC
1 AAAAAATTAAGACTTTAGAAATTCTCAAGTCATCAAGGC
28914 AAAAAATTAAGACTTTAGAAATTCTCAAGTCATCAA
1 AAAAAATTAAGACTTTAGAAATTCTCAAGTCATCAA
28950 TGCCCATGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.28
Consensus pattern (39 bp):
AAAAAATTAAGACTTTAGAAATTCTCAAGTCATCAAGGC
Found at i:35044 original size:19 final size:18
Alignment explanation
Indices: 35019--35072 Score: 76
Period size: 19 Copynumber: 3.1 Consensus size: 18
35009 ACTGTTTGGC
*
35019 AACTGTACAGATGAGATT
1 AACTGTACAGATTAGATT
35037 ACACTGTACAGATTAGATT
1 A-ACTGTACAGATTAGATT
35056 -A-TGTACAGATTAGATT
1 AACTGTACAGATTAGATT
35072 A
1 A
35073 TACTAATCTC
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
16 15 0.45
17 1 0.03
18 1 0.03
19 16 0.48
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (18 bp):
AACTGTACAGATTAGATT
Found at i:35062 original size:16 final size:16
Alignment explanation
Indices: 35022--35073 Score: 68
Period size: 16 Copynumber: 3.1 Consensus size: 16
35012 GTTTGGCAAC
*
35022 TGTACAGATGAGATTACA
1 TGTACAGATTAGATT--A
35040 CTGTACAGATTAGATTA
1 -TGTACAGATTAGATTA
35057 TGTACAGATTAGATTA
1 TGTACAGATTAGATTA
35073 T
1 T
35074 ACTAATCTCC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
16 17 0.53
17 1 0.03
19 14 0.44
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.35
Consensus pattern (16 bp):
TGTACAGATTAGATTA
Found at i:35229 original size:19 final size:19
Alignment explanation
Indices: 35205--35241 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
35195 TTTGGTTCCA
35205 AAACGGTGGTGAAACGGTC
1 AAACGGTGGTGAAACGGTC
35224 AAACGGTGGTGAAACGGT
1 AAACGGTGGTGAAACGGT
35242 TACAGATAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.14, G:0.38, T:0.16
Consensus pattern (19 bp):
AAACGGTGGTGAAACGGTC
Found at i:35267 original size:2 final size:2
Alignment explanation
Indices: 35260--35299 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
35250 AGGAGCCTTA
35260 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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
35300 GTATTTATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35747 original size:13 final size:13
Alignment explanation
Indices: 35729--35754 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35719 AATTCCAAAT
35729 ATAATATTTATAA
1 ATAATATTTATAA
35742 ATAATATTTATAA
1 ATAATATTTATAA
35755 CATTGAATTA
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATAATATTTATAA
Found at i:49239 original size:21 final size:20
Alignment explanation
Indices: 49205--49252 Score: 87
Period size: 21 Copynumber: 2.4 Consensus size: 20
49195 TATGTATGTG
49205 TTTATTTATTTATCATCTTC
1 TTTATTTATTTATCATCTTC
49225 TTTATTTACTTTATCATCTTC
1 TTTATTTA-TTTATCATCTTC
49246 TTTATTT
1 TTTATTT
49253 TGAAATCGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 8 0.30
21 19 0.70
ACGTcount: A:0.19, C:0.15, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTATTTATTTATCATCTTC
Found at i:49325 original size:17 final size:17
Alignment explanation
Indices: 49303--49335 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
49293 TTTTTTGTTT
*
49303 GAAAATCTGGATTTATG
1 GAAAATCTAGATTTATG
49320 GAAAATCTAGATTTAT
1 GAAAATCTAGATTTAT
49336 TTATATATGG
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:0.18, T:0.36
Consensus pattern (17 bp):
GAAAATCTAGATTTATG
Found at i:49750 original size:32 final size:34
Alignment explanation
Indices: 49708--49778 Score: 119
Period size: 32 Copynumber: 2.1 Consensus size: 34
49698 CCAAGCTGCT
*
49708 GCTGCCAAGCTCAAGGACGTGTTCAGC-TTGCAA
1 GCTGCCAAGCTCAAGGACGTGTTCAACTTTGCAA
49741 -CTGCCAAGCTCAAGGACGTGTTCAACTTTGCAA
1 GCTGCCAAGCTCAAGGACGTGTTCAACTTTGCAA
49774 GCTGC
1 GCTGC
49779 TGCTGCCAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
32 25 0.71
33 6 0.17
34 4 0.11
ACGTcount: A:0.24, C:0.28, G:0.25, T:0.23
Consensus pattern (34 bp):
GCTGCCAAGCTCAAGGACGTGTTCAACTTTGCAA
Found at i:49859 original size:23 final size:21
Alignment explanation
Indices: 49825--49867 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
49815 AATGTGAAGC
49825 ACAAATGAAAATTTGGAATTTGA
1 ACAAATGAAAA-TT-GAATTTGA
49848 ACAAATTG-AAATTGAATTTG
1 ACAAA-TGAAAATTGAATTTG
49868 GGGTGTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 7 0.37
22 2 0.11
23 8 0.42
24 2 0.11
ACGTcount: A:0.47, C:0.05, G:0.16, T:0.33
Consensus pattern (21 bp):
ACAAATGAAAATTGAATTTGA
Found at i:54044 original size:17 final size:17
Alignment explanation
Indices: 54022--54056 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
54012 TCTTTTGAAT
54022 TTTCGGTTTTTCAATTC
1 TTTCGGTTTTTCAATTC
54039 TTTCGGTTTTTCAATTC
1 TTTCGGTTTTTCAATTC
54056 T
1 T
54057 AACCTAGATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.17, G:0.11, T:0.60
Consensus pattern (17 bp):
TTTCGGTTTTTCAATTC
Found at i:55213 original size:29 final size:29
Alignment explanation
Indices: 55180--55256 Score: 145
Period size: 29 Copynumber: 2.7 Consensus size: 29
55170 GGTCATTTAG
55180 GGGGCATTTTGGTCATTTTCAAAAATTCA
1 GGGGCATTTTGGTCATTTTCAAAAATTCA
55209 GGGGCATTTTGGTCATTTTCAAAAATTCA
1 GGGGCATTTTGGTCATTTTCAAAAATTCA
*
55238 GGGGCATTTTGATCATTTT
1 GGGGCATTTTGGTCATTTT
55257 AAGTTCACAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.40
Consensus pattern (29 bp):
GGGGCATTTTGGTCATTTTCAAAAATTCA
Found at i:60617 original size:14 final size:14
Alignment explanation
Indices: 60590--60629 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
60580 TTGAATGAGA
* *
60590 GAAGACGAGGGTAG
1 GAAGATGAGAGTAG
60604 GAAGATGAGAGTAG
1 GAAGATGAGAGTAG
60618 GAAGATGAGAGT
1 GAAGATGAGAGT
60630 GTGTATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.40, C:0.03, G:0.45, T:0.12
Consensus pattern (14 bp):
GAAGATGAGAGTAG
Found at i:60882 original size:19 final size:19
Alignment explanation
Indices: 60846--60885 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
60836 ATTGGCTGCA
**
60846 ATTGGATCTTGTTTGTTTG
1 ATTGGATCTTGTAAGTTTG
60865 ATTGGATCTTGTAAGTTTG
1 ATTGGATCTTGTAAGTTTG
60884 AT
1 AT
60886 AGATCCTATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.17, C:0.05, G:0.25, T:0.53
Consensus pattern (19 bp):
ATTGGATCTTGTAAGTTTG
Found at i:61519 original size:20 final size:20
Alignment explanation
Indices: 61494--61534 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
61484 AAAAAGAGCA
61494 CCAATTTGCAAATCAAATGC
1 CCAATTTGCAAATCAAATGC
*
61514 CCAATTTGTAAATCAAATGC
1 CCAATTTGCAAATCAAATGC
61534 C
1 C
61535 TTGTATTTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.24, G:0.10, T:0.27
Consensus pattern (20 bp):
CCAATTTGCAAATCAAATGC
Found at i:62834 original size:69 final size:69
Alignment explanation
Indices: 62613--63189 Score: 903
Period size: 69 Copynumber: 8.4 Consensus size: 69
62603 GGAATTGAAC
* * *
62613 TTGGCTTATGGAAAAGCCCATGTTGCTTGGGTGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATGTTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
62678 GAGT
66 GAGT
* * *
62682 TTGGCTTGATGGAAAAGCCTACGTGGCTTGGATGGAACCAAGGCTTGAACTG---CGTATAGAAA
1 TTGGCTTG-TGGAAAAGCCTATGTTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAA
62744 CGAGT
65 CGAGT
* * *
62749 TTGGCTTGTGGAAAAGCCTATGTTGCTTGGATGAAACCAATGCTTGAACTGACTCATATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATGTTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
62814 GAGT
66 GAGT
* *
62818 TTGGCTTGTGGAAAAGCCTATGTTGCTTGGATGGAACCAAGGCTTGAACTGACTTGTATGGAAAT
1 TTGGCTTGTGGAAAAGCCTATGTTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
62883 GAGT
66 GAGT
* * *
62887 TTGGCTTGTGGAAAAGCCTATGTTGTTTGGATGGAACCAAGGCTTAAACTGGCTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATGTTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
62952 GAGT
66 GAGT
62956 TTGGCTTGTGGAAAAGCCTATGTTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATGTTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
63021 GAGT
66 GAGT
63025 TTGGCTTGTGGAAAAGCCTACT-TTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAA
1 TTGGCTTGTGGAAAAGCCTA-TGTTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAA
63089 CGAGT
65 CGAGT
* ** * * * *
63094 TTAGCTTGTGGAAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTT-AACTAACCCGTATGGGAA
1 TTGGCTTGTGG-AAAAGCCTATGTTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAA
63158 CGAGT
65 CGAGT
63163 TTGGCTTGTGGAAAAGCCTATGTTGCT
1 TTGGCTTGTGGAAAAGCCTATGTTGCT
63190 AATTGACTCG
Statistics
Matches: 465, Mismatches: 36, Indels: 15
0.90 0.07 0.03
Matches are distributed among these distances:
66 39 0.08
67 22 0.05
68 13 0.03
69 322 0.69
70 69 0.15
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (69 bp):
TTGGCTTGTGGAAAAGCCTATGTTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
GAGT
Found at i:64635 original size:51 final size:51
Alignment explanation
Indices: 64522--64672 Score: 193
Period size: 51 Copynumber: 3.0 Consensus size: 51
64512 TTAAATGCCC
* * * *
64522 TTTGAAAAGCGAAGTTTGATCTTGGACTCAC-AAATGGAATGCAACCTTT-C
1 TTTGAAAAGCGAATTTTGATCTTGGACTCACAAAATGGAAAGCAA-TTTTAT
** *
64572 CCTGACAAGCGAATTTTGATCTTGGACTCACAAAATGGAAAGCAATTTTAT
1 TTTGAAAAGCGAATTTTGATCTTGGACTCACAAAATGGAAAGCAATTTTAT
*
64623 TTTGAAAAGCGAATTTTGATCTTGGGCTCA-AAAA-GGAAAGCAATTTTAT
1 TTTGAAAAGCGAATTTTGATCTTGGACTCACAAAATGGAAAGCAATTTTAT
64672 T
1 T
64673 GTAAAACTCT
Statistics
Matches: 88, Mismatches: 11, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
49 16 0.18
50 34 0.39
51 38 0.43
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.31
Consensus pattern (51 bp):
TTTGAAAAGCGAATTTTGATCTTGGACTCACAAAATGGAAAGCAATTTTAT
Found at i:66810 original size:4 final size:4
Alignment explanation
Indices: 66783--67127 Score: 84
Period size: 4 Copynumber: 89.0 Consensus size: 4
66773 GACCAAAAAG
* * * *
66783 ATTT TTTT A-TT ATTT ATTC A-TT ATTT ATCT ATTT ATTT ATTT -TTA
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
* * * * * **
66828 ACTATT ATCT ATTT ATTT A-CT AATT ATCT ATTT ATTT TTTT AAACT A-TT
1 A-T-TT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT -ATTT ATTT
* * * **
66877 ATCT ATTT ATTT A-CT ATTT ATTT -TTT -TTT ATTT TTTT CAACT A-TT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT -ATTT ATTT
* * * *
66922 ATCT ACTT ATTT A-CT ATTT ATCTT -TTT ATTT A-TT -TTT AATT A-TT
1 ATTT ATTT ATTT ATTT ATTT AT-TT ATTT ATTT ATTT ATTT ATTT ATTT
* * * * ** *
66966 ATCT ATTT ATTT A-CT ATTT ATTTT TTTT ATTT ATTA ATTT A-GC AATT
1 ATTT ATTT ATTT ATTT ATTT A-TTT ATTT ATTT ATTT ATTT ATTT ATTT
* ** **
67013 ATTT ATTT ATTT A-TT AATT A-TT A-TT ATCCTT -TTT AGCT ACCT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT AT--TT ATTT ATTT ATTT ATTT
* * * * * * * **
67059 ATCT A-TT ATTCT CTGT ATCT ATTT ATCT CTAT ACCT ATTT ATTTT ATTT
1 ATTT ATTT ATT-T ATTT ATTT ATTT ATTT ATTT ATTT ATTT A-TTT ATTT
67108 ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT
67128 TAAACTTATT
Statistics
Matches: 243, Mismatches: 69, Indels: 58
0.66 0.19 0.16
Matches are distributed among these distances:
3 48 0.20
4 175 0.72
5 16 0.07
6 4 0.02
ACGTcount: A:0.26, C:0.09, G:0.01, T:0.65
Consensus pattern (4 bp):
ATTT
Found at i:66853 original size:19 final size:19
Alignment explanation
Indices: 66803--66864 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
66793 TATTTATTCA
* *
66803 TTATTTATCTATTTATTTAT
1 TTATTTA-CTAATTATCTAT
*
66823 TT-TTAACT-ATTATCTAT
1 TTATTTACTAATTATCTAT
66840 TTATTTACTAATTATCTAT
1 TTATTTACTAATTATCTAT
66859 TTATTT
1 TTATTT
66865 TTTTAAACTA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 9 0.25
18 7 0.19
19 18 0.50
20 2 0.06
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (19 bp):
TTATTTACTAATTATCTAT
Found at i:66855 original size:44 final size:44
Alignment explanation
Indices: 66789--67025 Score: 275
Period size: 44 Copynumber: 5.3 Consensus size: 44
66779 AAAGATTTTT
* *
66789 TTAT-TATTTATTCATTATTTATCTATTTATTTATTTTTAACTA
1 TTATCTATTTATTTACTATTTATCTATTTATTTATTTTTAACTA
* *
66832 TTATCTATTTATTTACTAATTATCTATTTATTT-TTTTAAACTA
1 TTATCTATTTATTTACTATTTATCTATTTATTTATTTTTAACTA
*
66875 TTATCTATTTATTTACTATTTAT-T-TTTTTTTATTTTTTTCAACTA
1 TTATCTATTTATTTACTATTTATCTATTTATTTA--TTTTT-AACTA
* * *
66920 TTATCTACTTATTTACTATTTATCTTTTTATTTATTTTTAATTA
1 TTATCTATTTATTTACTATTTATCTATTTATTTATTTTTAACTA
* * * *
66964 TTATCTATTTATTTACTATTTATTTTTTTTATTTATTAATTTAGCAA
1 TTATCTATTTATTTACTATTTA-TCTATTTATTTATT--TTTAACTA
*
67011 TTATTTATTTATTTA
1 TTATCTATTTATTTA
67026 TTAATTATTA
Statistics
Matches: 168, Mismatches: 16, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
41 6 0.04
42 1 0.01
43 35 0.21
44 54 0.32
45 45 0.27
46 1 0.01
47 26 0.15
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (44 bp):
TTATCTATTTATTTACTATTTATCTATTTATTTATTTTTAACTA
Found at i:66926 original size:88 final size:89
Alignment explanation
Indices: 66789--67037 Score: 310
Period size: 88 Copynumber: 2.8 Consensus size: 89
66779 AAAGATTTTT
* * * *
66789 TTAT-TATTTATTCATTATTTA-TCTATTTATTTATTTTTAACTATTATCTATTTATTTACTAAT
1 TTATCTATTTATTTACTATTTATTTTTTTTATTTATTTTTAACTATTATCTATTTATTTACTAAT
66852 TATCTATTTATTT-TTTTAAACTA
66 TATCTATTTATTTATTTTAAACTA
* * *
66875 TTATCTATTTATTTACTATTTATTTTTTTTTATTT-TTTTCAACTATTATCTACTTATTTACTAT
1 TTATCTATTTATTTACTATTTA-TTTTTTTTATTTATTTTTAACTATTATCTATTTATTTACTAA
* * *
66939 TTATCTTTTTATTTATTTTTAATTA
65 TTATCTATTTATTTATTTTAAACTA
* * * *
66964 TTATCTATTTATTTACTATTTATTTTTTTTATTTATTAATTTAGCAATTATTTATTTATTTATTA
1 TTATCTATTTATTTACTATTTATTTTTTTTATTTATT--TTTAACTATTATCTATTTATTTACTA
67029 ATTAT-TATT
64 ATTATCTATT
67038 ATCCTTTTTA
Statistics
Matches: 138, Mismatches: 18, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
86 4 0.03
87 15 0.11
88 51 0.37
89 41 0.30
90 3 0.02
91 24 0.17
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.65
Consensus pattern (89 bp):
TTATCTATTTATTTACTATTTATTTTTTTTATTTATTTTTAACTATTATCTATTTATTTACTAAT
TATCTATTTATTTATTTTAAACTA
Found at i:66942 original size:11 final size:11
Alignment explanation
Indices: 66928--66988 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
66918 TATTATCTAC
66928 TTATTTACTAT
1 TTATTTACTAT
**
66939 TTATCTTTTTAT
1 TTAT-TTACTAT
* *
66951 TTATTT-TTAA
1 TTATTTACTAT
66961 TTA-TTATCTAT
1 TTATTTA-CTAT
66972 TTATTTACTAT
1 TTATTTACTAT
66983 TTATTT
1 TTATTT
66989 TTTTTATTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
9 2 0.05
10 6 0.15
11 21 0.51
12 12 0.29
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.69
Consensus pattern (11 bp):
TTATTTACTAT
Found at i:67006 original size:32 final size:35
Alignment explanation
Indices: 66936--67036 Score: 102
Period size: 32 Copynumber: 2.9 Consensus size: 35
66926 ACTTATTTAC
*
66936 TATTTATCTTTTTATTTATTTTTAATTATTATCTATT
1 TATTTATCTATTTATTTATTTTTAATTATTA--TATT
*
66973 TATTTA-CTATTTATTT-TTTTTATTTATTA-ATT
1 TATTTATCTATTTATTTATTTTTAATTATTATATT
***
67005 TAGCAAT-TATTTATTTATTTATTAATTATTAT
1 TATTTATCTATTTATTTATTT-TTAATTATTAT
67037 TATCCTTTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
32 15 0.28
33 3 0.06
34 9 0.17
35 12 0.22
36 9 0.17
37 6 0.11
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.67
Consensus pattern (35 bp):
TATTTATCTATTTATTTATTTTTAATTATTATATT
Found at i:67016 original size:19 final size:19
Alignment explanation
Indices: 66992--67038 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
66982 TTTATTTTTT
66992 TTATTTATTAATTTAGCAA
1 TTATTTATTAATTTAGCAA
* **
67011 TTATTTATTTATTTATTAA
1 TTATTTATTAATTTAGCAA
67030 TTA-TTATTA
1 TTATTTATTA
67039 TCCTTTTTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (19 bp):
TTATTTATTAATTTAGCAA
Found at i:67153 original size:8 final size:8
Alignment explanation
Indices: 67053--67170 Score: 50
Period size: 8 Copynumber: 15.0 Consensus size: 8
67043 TTTTAGCTAC
67053 CTATTTAT
1 CTATTTAT
67061 CTA-TTATT
1 CTATTTA-T
* *
67069 CTCTGTAT
1 CTATTTAT
67077 CTATTTAT
1 CTATTTAT
* * *
67085 CTCTATAC
1 CTATTTAT
67093 CTATTTATT
1 CTATTTA-T
*
67102 TTATTTAT
1 CTATTTAT
*
67110 TTATTTAT
1 CTATTTAT
*
67118 TTATTTAT
1 CTATTTAT
* *
67126 -T-TTAAA
1 CTATTTAT
67132 CTTATTT-T
1 C-TATTTAT
67140 CTTATTTAT
1 C-TATTTAT
67149 CTA-TTA-
1 CTATTTAT
*
67155 CTTTTTAT
1 CTATTTAT
*
67163 ATATTTAT
1 CTATTTAT
67171 TAATAATTTT
Statistics
Matches: 83, Mismatches: 18, Indels: 18
0.70 0.15 0.15
Matches are distributed among these distances:
6 5 0.06
7 10 0.12
8 56 0.67
9 12 0.14
ACGTcount: A:0.25, C:0.11, G:0.01, T:0.64
Consensus pattern (8 bp):
CTATTTAT
Found at i:71216 original size:21 final size:21
Alignment explanation
Indices: 71192--71248 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
71182 ATCCAACATC
71192 TGAGGCAGGCACAAGAAGAAA
1 TGAGGCAGGCACAAGAAGAAA
* ** * *
71213 TGAGACATTCGCAAGAAGAGA
1 TGAGGCAGGCACAAGAAGAAA
*
71234 TGAGGCAGGAACAAG
1 TGAGGCAGGCACAAG
71249 GTGTTATAAA
Statistics
Matches: 26, Mismatches: 10, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.44, C:0.14, G:0.33, T:0.09
Consensus pattern (21 bp):
TGAGGCAGGCACAAGAAGAAA
Found at i:71818 original size:4 final size:4
Alignment explanation
Indices: 71791--72031 Score: 91
Period size: 4 Copynumber: 62.8 Consensus size: 4
71781 TACCAAAAAG
* * * *
71791 ATTT TTTT A-TT ATTT ATTC A-TT ATTT ATCT ATTT ATTT ATTT -TTA
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
* * * * **
71836 ACTATT ATCT ATTT ATTT A-CT ATTT ATCT ATTT ATTT TTTT AAACT A-TT
1 A-T-TT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT -ATTT ATTT
* * * ** *
71885 ATCT ATTT ATTT A-CT ATTT -TTT -TTT ATTT TTTT CAACT A-TT ATCT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT -ATTT ATTT ATTT
* * * *
71930 AGTT ATTT A-CT ATTT ATCTT -TTT ATTT A-TT -TTT AATT A-TT ATCT
1 ATTT ATTT ATTT ATTT AT-TT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
* * * **
71974 ATTT ATTT A-CT ATTT ATTTT TTTT ATTT ATTA ATTT AGCT A-TT ATTT
1 ATTT ATTT ATTT ATTT A-TTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
72021 ATTT ATTT ATT
1 ATTT ATTT ATT
72032 ATTATTATCC
Statistics
Matches: 170, Mismatches: 46, Indels: 42
0.66 0.18 0.16
Matches are distributed among these distances:
3 36 0.21
4 123 0.72
5 9 0.05
6 2 0.01
ACGTcount: A:0.25, C:0.07, G:0.01, T:0.67
Consensus pattern (4 bp):
ATTT
Found at i:71825 original size:8 final size:8
Alignment explanation
Indices: 71812--72121 Score: 64
Period size: 8 Copynumber: 38.6 Consensus size: 8
71802 ATTTATTCAT
71812 TATTTATC
1 TATTTATC
*
71820 TATTTATT
1 TATTTATC
*
71828 TATTTTTAAC
1 TA--TTTATC
71838 TA-TTATC
1 TATTTATC
71845 TATTTATTTAC
1 TATTTA--T-C
71856 TATTTATC
1 TATTTATC
*
71864 TATTTATT
1 TATTTATC
* *
71872 TTTTTAAAC
1 TATTT-ATC
71881 TA-TTATC
1 TATTTATC
71888 TATTTATTTAC
1 TATTTA--T-C
71899 TATTT-T-
1 TATTTATC
* *
71905 TTTTTATT
1 TATTTATC
* *
71913 TTTTTCAAC
1 TATTT-ATC
71922 TA-TTATC
1 TATTTATC
*
71929 TAGTTATTTAC
1 TA-TT-TAT-C
71940 TATTTATC
1 TATTTATC
* *
71948 TTTTTATT
1 TATTTATC
71956 TATTT-T-
1 TATTTATC
*
71962 TAATTAT-
1 TATTTATC
* *
71969 TATCTATT
1 TATTTATC
71977 TATTTA-C
1 TATTTATC
71984 TATTTAT-
1 TATTTATC
*
71991 T-TTT-TT
1 TATTTATC
71997 TATTTAT-
1 TATTTATC
*
72004 TAATTTAGC
1 T-ATTTATC
*
72013 TA-TTATT
1 TATTTATC
*
72020 TATTTATT
1 TATTTATC
72028 TA-TTAT-
1 TATTTATC
72034 TA-TTATCC
1 TATTTAT-C
72042 T-TTTAGCTACC
1 TATTTA--T--C
72053 TATTTATC
1 TATTTATC
72061 TA-TTATTC
1 TATTTA-TC
* *
72069 TCTGTATC
1 TATTTATC
72077 TATTTATC
1 TATTTATC
72085 TATTTATC
1 TATTTATC
* * *
72093 TCTATACC
1 TATTTATC
*
72101 TATTTATT
1 TATTTATC
* *
72109 TTTTTATT
1 TATTTATC
72117 TATTT
1 TATTT
72122 TTTTATTTTA
Statistics
Matches: 225, Mismatches: 41, Indels: 72
0.67 0.12 0.21
Matches are distributed among these distances:
5 1 0.00
6 18 0.08
7 45 0.20
8 113 0.50
9 11 0.05
10 14 0.06
11 19 0.08
12 4 0.02
ACGTcount: A:0.25, C:0.10, G:0.01, T:0.65
Consensus pattern (8 bp):
TATTTATC
Found at i:71825 original size:19 final size:19
Alignment explanation
Indices: 71796--72034 Score: 112
Period size: 19 Copynumber: 12.5 Consensus size: 19
71786 AAAAGATTTT
*
71796 TTTAT-TATTTATTCATTA
1 TTTATCTATTTATTTATTA
71814 TTTATCTATTTATTTATTTTTAA
1 TTTATCTATTTATTTA---TT-A
*
71837 CTATTATCTATTTATTTACTA
1 -T-TTATCTATTTATTTATTA
*
71858 TTTATCTATTTATTTTTTTAAA
1 TTTATCTATTTA-TTTATT--A
*
71880 CTATTATCTATTTATTTACTA
1 -T-TTATCTATTTATTTATTA
*
71901 TTT-T-TTTTTATTT-TT-
1 TTTATCTATTTATTTATTA
* * *
71916 TTCAACTA-TTATCTAGTTA
1 TTTATCTATTTATTTA-TTA
*
71935 TTTA-CTATTTATCTTTTTA
1 TTTATCTATTTAT-TTATTA
71954 TTTAT-T-TTTA---ATTA
1 TTTATCTATTTATTTATTA
*
71968 -TTATCTATTTATTTACTA
1 TTTATCTATTTATTTATTA
* *
71986 TTTATTTTTTTTATTTATTAA
1 TTTA-TCTATTTATTTATT-A
*
72007 TTTAGCTA-TTATTTATTTA
1 TTTATCTATTTATTTA-TTA
72026 TTTAT-TATT
1 TTTATCTATT
72035 ATTATCCTTT
Statistics
Matches: 167, Mismatches: 24, Indels: 59
0.67 0.10 0.24
Matches are distributed among these distances:
13 4 0.02
14 4 0.02
15 6 0.04
16 6 0.04
17 9 0.05
18 20 0.12
19 53 0.32
20 21 0.13
21 7 0.04
22 4 0.02
23 6 0.04
24 12 0.07
25 15 0.09
ACGTcount: A:0.26, C:0.07, G:0.01, T:0.67
Consensus pattern (19 bp):
TTTATCTATTTATTTATTA
Found at i:71860 original size:44 final size:44
Alignment explanation
Indices: 71797--72034 Score: 306
Period size: 44 Copynumber: 5.5 Consensus size: 44
71787 AAAGATTTTT
* * *
71797 TTAT-TATTTATTCATTATTTATCTATTTATTTATTTTTAACTA
1 TTATCTATTTATTTACTATTTATCTTTTTATTTATTTTTAACTA
* *
71840 TTATCTATTTATTTACTATTTATCTATTTATTT-TTTTAAACTA
1 TTATCTATTTATTTACTATTTATCTTTTTATTTATTTTTAACTA
*
71883 TTATCTATTTATTTACTATTT-T-TTTTTATTT-TTTTCAACTA
1 TTATCTATTTATTTACTATTTATCTTTTTATTTATTTTTAACTA
* *
71924 TTATCTAGTTATTTACTATTTATCTTTTTATTTATTTTTAATTA
1 TTATCTATTTATTTACTATTTATCTTTTTATTTATTTTTAACTA
* *
71968 TTATCTATTTATTTACTATTTATTTTTTTTATTTATTAATTTAGCTA
1 TTATCTATTTATTTACTATTTA-TCTTTTTATTTATT--TTTAACTA
* *
72015 TTATTTATTTATTTATTATT
1 TTATCTATTTATTTACTATT
72035 ATTATCCTTT
Statistics
Matches: 174, Mismatches: 14, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
41 37 0.21
42 2 0.01
43 43 0.25
44 55 0.32
45 13 0.07
47 24 0.14
ACGTcount: A:0.26, C:0.07, G:0.01, T:0.66
Consensus pattern (44 bp):
TTATCTATTTATTTACTATTTATCTTTTTATTTATTTTTAACTA
Found at i:71936 original size:84 final size:87
Alignment explanation
Indices: 71797--72004 Score: 289
Period size: 84 Copynumber: 2.4 Consensus size: 87
71787 AAAGATTTTT
* * * * *
71797 TTAT-TATTTATTCATTATTTATCTATTTATTTATTTTTAACTATTATCTATTTATTTACTATTT
1 TTATCTATTTATTTACTATTTAT-TTTTTATTTATTTTCAACTATTATCTAGTTATTTACTATTT
71861 ATCTATTTATTT-TTTTAAACTA
65 ATCTATTTATTTATTTTAAACTA
71883 TTATCTATTTATTTACTATTT-TTTTTTATTT-TTTTCAACTATTATCTAGTTATTTACTATTTA
1 TTATCTATTTATTTACTATTTATTTTTTATTTATTTTCAACTATTATCTAGTTATTTACTATTTA
* * *
71946 TCTTTTTATTTATTTTTAATTA
66 TCTATTTATTTATTTTAAACTA
71968 TTATCTATTTATTTACTATTTATTTTTTTTATTTATT
1 TTATCTATTTATTTACTATTTA--TTTTTTATTTATT
72005 AATTTAGCTA
Statistics
Matches: 108, Mismatches: 8, Indels: 9
0.86 0.06 0.07
Matches are distributed among these distances:
84 40 0.37
85 37 0.34
86 5 0.05
87 14 0.13
88 10 0.09
89 2 0.02
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (87 bp):
TTATCTATTTATTTACTATTTATTTTTTATTTATTTTCAACTATTATCTAGTTATTTACTATTTA
TCTATTTATTTATTTTAAACTA
Found at i:72047 original size:36 final size:34
Alignment explanation
Indices: 71950--72064 Score: 110
Period size: 32 Copynumber: 3.3 Consensus size: 34
71940 TATTTATCTT
**
71950 TTTATTTATTTTTAATTATTATCTATTTATTTACTA
1 TTTATTTATTTTT-ATTATTATCT-TTTAGCTACTA
* *
71986 TTTATTT-TTTTTATTTATTA--ATTTAGCTATTA
1 TTTATTTATTTTTA-TTATTATCTTTTAGCTACTA
72018 TTTATTTATTTATTATTATTATCCTTTTAGCTACCTA
1 TTTATTTATTT-TTATTATTAT-CTTTTAGCTA-CTA
*
72055 TTTATCTATT
1 TTTATTTATT
72065 ATTCTCTGTA
Statistics
Matches: 65, Mismatches: 7, Indels: 13
0.76 0.08 0.15
Matches are distributed among these distances:
32 15 0.23
33 9 0.14
34 4 0.06
35 11 0.17
36 15 0.23
37 11 0.17
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.65
Consensus pattern (34 bp):
TTTATTTATTTTTATTATTATCTTTTAGCTACTA
Found at i:72081 original size:24 final size:24
Alignment explanation
Indices: 72049--72107 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
72039 TCCTTTTAGC
*
72049 TACCTATTTATCTA-TTATTCTCTG
1 TACCTATTTATCTATTTA-TCTCTA
*
72073 TATCTATTTATCTATTTATCTCTA
1 TACCTATTTATCTATTTATCTCTA
72097 TACCTATTTAT
1 TACCTATTTAT
72108 TTTTTTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 28 0.90
25 3 0.10
ACGTcount: A:0.24, C:0.19, G:0.02, T:0.56
Consensus pattern (24 bp):
TACCTATTTATCTATTTATCTCTA
Found at i:72122 original size:12 final size:12
Alignment explanation
Indices: 72101--72129 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
72091 TCTCTATACC
72101 TATTTATTTTTT
1 TATTTATTTTTT
72113 TATTTATTTTTT
1 TATTTATTTTTT
72125 TATTT
1 TATTT
72130 TAAACTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (12 bp):
TATTTATTTTTT
Found at i:72734 original size:26 final size:27
Alignment explanation
Indices: 72696--72746 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
72686 TCCAGGTGTT
*
72696 TTTTTTTCATTTTCTT-TTTTATTTTTC
1 TTTTCTTCATTTT-TTATTTTATTTTTC
72723 TTTTCTTC-TTTTTTATTTTATTTT
1 TTTTCTTCATTTTTTATTTTATTTT
72747 ATTTTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 2 0.09
26 13 0.59
27 7 0.32
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.82
Consensus pattern (27 bp):
TTTTCTTCATTTTTTATTTTATTTTTC
Found at i:72756 original size:13 final size:12
Alignment explanation
Indices: 72694--72757 Score: 65
Period size: 12 Copynumber: 5.1 Consensus size: 12
72684 ATTCCAGGTG
*
72694 TTTTTTTTTCAT
1 TTTTTTTTTTAT
*
72706 TTTCTTTTTTAT
1 TTTTTTTTTTAT
*
72718 TTTTCTTTTCTTCT
1 TTTT-TTTT-TTAT
*
72732 TTTTTATTTTAT
1 TTTTTTTTTTAT
72744 TTTATTTTTTTAT
1 TTT-TTTTTTTAT
72757 T
1 T
72758 ATTGGGAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
12 19 0.45
13 16 0.38
14 7 0.17
ACGTcount: A:0.09, C:0.08, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTTTTTTTAT
Found at i:72759 original size:21 final size:20
Alignment explanation
Indices: 72710--72760 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
72700 TTTCATTTTC
* * *
72710 TTTTTTATTTTTCTTTTCTTC
1 TTTTTTA-TTTTATTTTATTT
72731 TTTTTTATTTTATTTTATTT
1 TTTTTTATTTTATTTTATTT
72751 TTTTATTATT
1 TTTT-TTATT
72761 GGGAAATCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTTTATTTTATTTTATTT
Found at i:73238 original size:76 final size:74
Alignment explanation
Indices: 73136--73281 Score: 204
Period size: 76 Copynumber: 1.9 Consensus size: 74
73126 AGTCACCTCA
* *
73136 AAATCATTGTTTTGACCAAAATTGATTTTG-AAACATCTTTTGATTAAAACACCGTCATTCCTTT
1 AAATCATAGTTTTGACCAAAACTGATTTTGAAAAC-T-TTTTGATTAAAAC-CCGTCATTCCTTT
73200 ACTCACAGCTCG
63 ACTCACAGCTCG
* * * *
73212 AAATCATAGTTTTGACTAAAACTGATTTTGAAAACTTTTTGATTGAAACTCGTCATTCCTTTGCT
1 AAATCATAGTTTTGACCAAAACTGATTTTGAAAACTTTTTGATTAAAACCCGTCATTCCTTTACT
73277 CACAG
66 CACAG
73282 TCCAGATAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
74 19 0.30
75 12 0.19
76 28 0.44
77 4 0.06
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.38
Consensus pattern (74 bp):
AAATCATAGTTTTGACCAAAACTGATTTTGAAAACTTTTTGATTAAAACCCGTCATTCCTTTACT
CACAGCTCG
Found at i:74862 original size:21 final size:22
Alignment explanation
Indices: 74823--74864 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
74813 CTAAGGTTTA
74823 ATGGAATGCATGAACGAATGCC
1 ATGGAATGCATGAACGAATGCC
* *
74845 ATGGCATG-ATGAATGAATGC
1 ATGGAATGCATGAACGAATGC
74865 ATGAGGCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.36, C:0.14, G:0.29, T:0.21
Consensus pattern (22 bp):
ATGGAATGCATGAACGAATGCC
Found at i:78512 original size:14 final size:14
Alignment explanation
Indices: 78493--78532 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
78483 TTGAATGAGA
*
78493 GAAGATGAGGGTAG
1 GAAGATGAGAGTAG
78507 GAAGATGAGAGTAG
1 GAAGATGAGAGTAG
78521 GAAGATGAGAGT
1 GAAGATGAGAGT
78533 CTGTATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.45, T:0.15
Consensus pattern (14 bp):
GAAGATGAGAGTAG
Found at i:78866 original size:16 final size:16
Alignment explanation
Indices: 78845--78886 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
78835 TGGGCTGCAA
*
78845 GTGAGCTGTCCTTTTG
1 GTGAGCTGGCCTTTTG
78861 GTGAGCTGGCCTTTTG
1 GTGAGCTGGCCTTTTG
78877 GTGAGCTGGC
1 GTGAGCTGGC
78887 ATCGATGGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.07, C:0.19, G:0.38, T:0.36
Consensus pattern (16 bp):
GTGAGCTGGCCTTTTG
Found at i:79520 original size:19 final size:19
Alignment explanation
Indices: 79483--79522 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
79473 ATTGGCTGCA
***
79483 ATTGGATCTTGTTTTTTTG
1 ATTGGATCTTGTAAGTTTG
79502 ATTGGATCTTGTAAGTTTG
1 ATTGGATCTTGTAAGTTTG
79521 AT
1 AT
79523 AGATCCTATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.17, C:0.05, G:0.23, T:0.55
Consensus pattern (19 bp):
ATTGGATCTTGTAAGTTTG
Found at i:80163 original size:20 final size:20
Alignment explanation
Indices: 80138--80176 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
80128 AAAAAGAGCA
80138 CCAATTTGCAAATCAAATGC
1 CCAATTTGCAAATCAAATGC
*
80158 CCAATTTGTAAATCAAATG
1 CCAATTTGCAAATCAAATG
80177 TCTTGTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (20 bp):
CCAATTTGCAAATCAAATGC
Found at i:93306 original size:24 final size:24
Alignment explanation
Indices: 93261--93307 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
93251 ACGGTTAAAG
* *
93261 ATAAAAAAAATTAATTTTAAAATA
1 ATAAAAAAAATTAATATAAAAATA
93285 ATAAAATAAAATT-ATATAAAAAT
1 ATAAAA-AAAATTAATATAAAAAT
93308 CTTTTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (24 bp):
ATAAAAAAAATTAATATAAAAATA
Found at i:94189 original size:15 final size:15
Alignment explanation
Indices: 94169--94207 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
94159 TACGTTTTTT
*
94169 AATTTTTATTAAAAA
1 AATTTTAATTAAAAA
*
94184 AATTTTAATTAAAAT
1 AATTTTAATTAAAAA
*
94199 TATTTTAAT
1 AATTTTAAT
94208 CAATTTTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
AATTTTAATTAAAAA
Found at i:95319 original size:17 final size:17
Alignment explanation
Indices: 95297--95338 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
95287 GACCGTTTAT
95297 TATTATATATA-ATTAAA
1 TATTATATATATATT-AA
*
95314 TATTATATATATATTAT
1 TATTATATATATATTAA
95331 TATTATAT
1 TATTATAT
95339 CACATATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 20 0.87
18 3 0.13
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TATTATATATATATTAA
Found at i:95326 original size:21 final size:20
Alignment explanation
Indices: 95294--95332 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
95284 ACCGACCGTT
95294 TATTATTATATATAATTAAA
1 TATTATTATATATAATTAAA
*
95314 TATTATATATATATTATTA
1 TATTAT-TATATATAATTA
95333 TTATATCACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TATTATTATATATAATTAAA
Done.