Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013460.1 Kokia drynarioides strain JFW-HI SEQ_128486, 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: 105485
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Found at i:1389 original size:205 final size:203
Alignment explanation
Indices: 1011--1689 Score: 881
Period size: 205 Copynumber: 3.3 Consensus size: 203
1001 ATTTCAGTTT
* * *
1011 ACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTTCTTCAACCTGCTTCTCGGTGTCTCATC
1 ACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCGGTATCTCATC
* * *
1076 AGGAAGC-----T-G-AGATTTTGCTCACATCGAGCGTGGATTTGATTTGGTCTTCTTCTCAGTA
66 AGGAAGCTGGGTTCGAAGA-TTTGCTCACA-CGAGAGTGGGTTTGATTTGGTCTTCTTCTCGGTA
* * * ** *
1134 TCTCATCAAGAAGATGACCGCATTGCTAGTTTCAATTCGCTTCTCTATATCTCATCAGGAAGACG
129 TCTCATCAGGAAGATGACTGTATCACTTGTTTCAATTCGCTTCTCTATATCTCATCAGGAAGACG
1199 AATTTGGTCC
194 AATTTGGTCC
* * * * *
1209 ACTTCTCAGTGTTTCATCTGGAAGCTAACCTTTTATTGCTTCGACTTGCTTCTCGGTGTCTCATC
1 ACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCGGTATCTCATC
* *
1274 AAGAAGCTAGGGTTCGAAGATTTGCTCACACAGAGAGTGGGTTTGACTTGGTCTTCTTCTCGGTA
66 AGGAAGCT-GGGTTCGAAGATTTGCTCACAC-GAGAGTGGGTTTGATTTGGTCTTCTTCTCGGTA
* * * *
1339 TCTCATCGGGAAGATGACTGTATCACTTGTTTCAATTCGCTTCCCTATATCTCATCAAGAAGACA
129 TCTCATCAGGAAGATGACTGTATCACTTGTTTCAATTCGCTTCTCTATATCTCATCAGGAAGACG
1404 AATTTGGTCC
194 AATTTGGTCC
* * * **
1414 ACTTCTCAGTATCTCAACAGGAAGCTAACCTTTTACTGCTTCGCCCTGCTTCTTAGTATCTCATC
1 ACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCGGTATCTCATC
* * * * *
1479 AGGAAGCTGGGGTTCGAAGATTCGCTCGA-ATTGAGCAG-GGGTTTGATTTGGTCTTCTTTTTGA
66 AGGAAGCT-GGGTTCGAAGATTTGCTC-ACA-CGAG-AGTGGGTTTGATTTGGTCTTCTTCTCGG
* *
1542 TATCTCATCAGGAAGATGATTGTATCACTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAGA
127 TATCTCATCAGGAAGATGACTGTATCACTTGTTTCAATTCGCTTCTCTATATCTCATCAGGAAGA
*
1607 TGAATTTGGTCC
192 CGAATTTGGTCC
* *
1619 ACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGCCCTACTTCTCGGTATCTCATC
1 ACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCGGTATCTCATC
1684 AGGAAG
66 AGGAAG
1690 ATGACTGTAT
Statistics
Matches: 418, Mismatches: 51, Indels: 17
0.86 0.10 0.03
Matches are distributed among these distances:
198 65 0.16
204 2 0.00
205 345 0.83
206 6 0.01
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.35
Consensus pattern (203 bp):
ACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCGGTATCTCATC
AGGAAGCTGGGTTCGAAGATTTGCTCACACGAGAGTGGGTTTGATTTGGTCTTCTTCTCGGTATC
TCATCAGGAAGATGACTGTATCACTTGTTTCAATTCGCTTCTCTATATCTCATCAGGAAGACGAA
TTTGGTCC
Found at i:5257 original size:17 final size:17
Alignment explanation
Indices: 5235--5267 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
5225 ACCGGCGTCA
5235 AATTGTTTCTTGACTTT
1 AATTGTTTCTTGACTTT
5252 AATTGTTTCTTGACTT
1 AATTGTTTCTTGACTT
5268 CTTCTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.12, G:0.12, T:0.58
Consensus pattern (17 bp):
AATTGTTTCTTGACTTT
Found at i:13175 original size:30 final size:30
Alignment explanation
Indices: 13136--13354 Score: 128
Period size: 30 Copynumber: 7.4 Consensus size: 30
13126 CGGGGGTAAT
* *
13136 ATGGTAATTTTGGGAAATTTTGGGGTTTAAA
1 ATGG-AATTTTTGGAAATTTTGGGGTTAAAA
* * *
13167 ATGGAATTTTTAGAAA-TTCGGGGATAAAA
1 ATGGAATTTTTGGAAATTTTGGGGTTAAAA
* * *
13196 AT-GAGATTTTTGGAAGTTTTAGGGTCAAAA
1 ATGGA-ATTTTTGGAAATTTTGGGGTTAAAA
*
13226 ATGGGATTTTT-GAAAGTTTTGGGG-TAAAA
1 ATGGAATTTTTGGAAA-TTTTGGGGTTAAAA
* ** * * * *
13255 ATGGGATTTTTTTAAGTTTCGAGGTCAAAA
1 ATGGAATTTTTGGAAATTTTGGGGTTAAAA
** *
13285 ATGGGTTTTTTGG-AA-TTCGAGGG-TAAAA
1 ATGGAATTTTTGGAAATTTTG-GGGTTAAAA
** * * *
13313 ATGGGTTTTTTGGAAGTTTTTGGGTCAAAA
1 ATGGAATTTTTGGAAATTTTGGGGTTAAAA
*
13343 ATGGGATTTTTG
1 ATGGAATTTTTG
13355 TACAGTTTAG
Statistics
Matches: 147, Mismatches: 31, Indels: 21
0.74 0.16 0.11
Matches are distributed among these distances:
28 23 0.16
29 52 0.35
30 67 0.46
31 5 0.03
ACGTcount: A:0.30, C:0.03, G:0.28, T:0.39
Consensus pattern (30 bp):
ATGGAATTTTTGGAAATTTTGGGGTTAAAA
Found at i:13225 original size:29 final size:30
Alignment explanation
Indices: 13192--13354 Score: 190
Period size: 30 Copynumber: 5.5 Consensus size: 30
13182 ATTCGGGGAT
*
13192 AAAAATGAGATTTTTGGAAGTTTTAGGGTC
1 AAAAATGGGATTTTTGGAAGTTTTAGGGTC
* *
13222 AAAAATGGGATTTTTGAAAGTTTTGGGGT-
1 AAAAATGGGATTTTTGGAAGTTTTAGGGTC
** *
13251 AAAAATGGGATTTTTTTAAG-TTTCGAGGTC
1 AAAAATGGGATTTTTGGAAGTTTTAG-GGTC
* **
13281 AAAAATGGGTTTTTTGGAA-TTCGAGGGT-
1 AAAAATGGGATTTTTGGAAGTTTTAGGGTC
* *
13309 AAAAATGGGTTTTTTGGAAGTTTTTGGGTC
1 AAAAATGGGATTTTTGGAAGTTTTAGGGTC
13339 AAAAATGGGATTTTTG
1 AAAAATGGGATTTTTG
13355 TACAGTTTAG
Statistics
Matches: 112, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
28 23 0.21
29 30 0.27
30 59 0.53
ACGTcount: A:0.30, C:0.03, G:0.28, T:0.39
Consensus pattern (30 bp):
AAAAATGGGATTTTTGGAAGTTTTAGGGTC
Found at i:13227 original size:59 final size:57
Alignment explanation
Indices: 13164--13354 Score: 231
Period size: 59 Copynumber: 3.3 Consensus size: 57
13154 TTTGGGGTTT
* *
13164 AAAATGGAATTTTTAGAAATTCGGGGATAAAAATGAGATTTTTGGAAGTTTTAGGGTCA
1 AAAATGGGATTTTT-GAAATTCGGGG-TAAAAATGGGATTTTTGGAAGTTTTAGGGTCA
* ** *
13223 AAAATGGGATTTTTGAAAGTTTTGGGGTAAAAATGGGATTTTTTTAAG-TTTCGAGGTCA
1 AAAATGGGATTTTTGAAA--TTCGGGGTAAAAATGGGATTTTTGGAAGTTTTAG-GGTCA
* * * *
13282 AAAATGGGTTTTTTGGAATTCGAGGGTAAAAATGGGTTTTTTGGAAGTTTTTGGGTCA
1 AAAATGGGATTTTTGAAATTCG-GGGTAAAAATGGGATTTTTGGAAGTTTTAGGGTCA
13340 AAAATGGGATTTTTG
1 AAAATGGGATTTTTG
13355 TACAGTTTAG
Statistics
Matches: 113, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
57 3 0.03
58 48 0.42
59 56 0.50
60 6 0.05
ACGTcount: A:0.31, C:0.03, G:0.28, T:0.38
Consensus pattern (57 bp):
AAAATGGGATTTTTGAAATTCGGGGTAAAAATGGGATTTTTGGAAGTTTTAGGGTCA
Found at i:14390 original size:3 final size:3
Alignment explanation
Indices: 14384--14456 Score: 58
Period size: 3 Copynumber: 24.0 Consensus size: 3
14374 TCGACTTTTT
* * * * *
14384 TTA TTA TTA TTA ATA TTA ATA TTAA TTA ATA TTA TCA TTA TTA -CA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA
* *
14429 ATA TTTA TTA TTA TTA ATA TTA TTA TTA
1 TTA -TTA TTA TTA TTA TTA TTA TTA TTA
14457 ATAATCATTT
Statistics
Matches: 54, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
2 1 0.02
3 48 0.89
4 5 0.09
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:15184 original size:52 final size:52
Alignment explanation
Indices: 15127--15238 Score: 136
Period size: 52 Copynumber: 2.2 Consensus size: 52
15117 AATTTTATTT
* * * ** *
15127 ATTTTAATTTTATAATAATTTTAAATT-TGAAAATGAATTTAAACTTAAATTA
1 ATTTTAAATTTAAAATAAATTTAAATTCT-AAAACAAATTTAAACTTAAAATA
*
15179 ATTTTAAATTTAAAATAAATTTAAATTCTAAAACAAATTTAATCTTAAAATA
1 ATTTTAAATTTAAAATAAATTTAAATTCTAAAACAAATTTAAACTTAAAATA
*
15231 AATTTAAA
1 ATTTTAAA
15239 ATGAGTTTGA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
52 50 0.98
53 1 0.02
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (52 bp):
ATTTTAAATTTAAAATAAATTTAAATTCTAAAACAAATTTAAACTTAAAATA
Found at i:15220 original size:35 final size:34
Alignment explanation
Indices: 15146--15238 Score: 107
Period size: 35 Copynumber: 2.7 Consensus size: 34
15136 TTATAATAAT
* ** *
15146 TTTAAATTTGAAAATGAATTTAAACTTAAATTAAT
1 TTTAAATTT-AAAATAAATTTAAACTTAAAACAAA
*
15181 TTTAAATTTAAAATAAATTTAAATTCTAAAACAAA
1 TTTAAATTTAAAATAAATTTAAACT-TAAAACAAA
15216 TTT-AATCTTAAAATAAATTTAAA
1 TTTAAAT-TTAAAATAAATTTAAA
15239 ATGAGTTTGA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
34 17 0.33
35 34 0.67
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (34 bp):
TTTAAATTTAAAATAAATTTAAACTTAAAACAAA
Found at i:15233 original size:17 final size:16
Alignment explanation
Indices: 15129--15237 Score: 83
Period size: 17 Copynumber: 6.3 Consensus size: 16
15119 TTTTATTTAT
* *
15129 TTTAATTTTATAATAAT
1 TTTAA-TTTAAAATAAA
*
15146 TTTAAATTTGAAAATGAA
1 TTT-AATTT-AAAATAAA
* * *
15164 TTTAAACTTAAATTAAT
1 TTT-AATTTAAAATAAA
15181 TTTAAATTTAAAATAAA
1 TTT-AATTTAAAATAAA
*
15198 TTTAAATTCTAAAACAAA
1 TTT-AATT-TAAAATAAA
15216 TTTAATCTTAAAATAAA
1 TTTAAT-TTAAAATAAA
15233 TTTAA
1 TTTAA
15238 AATGAGTTTG
Statistics
Matches: 76, Mismatches: 12, Indels: 8
0.79 0.12 0.08
Matches are distributed among these distances:
17 49 0.64
18 27 0.36
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (16 bp):
TTTAATTTAAAATAAA
Found at i:20959 original size:9 final size:9
Alignment explanation
Indices: 20936--21021 Score: 59
Period size: 10 Copynumber: 9.0 Consensus size: 9
20926 AAACATCATC
20936 AATAAAAAT
1 AATAAAAAT
* *
20945 AGTAATAAT
1 AATAAAAAT
20954 AATAATAACA-
1 AATAA-AA-AT
*
20964 AATAAAACAG
1 AATAAAA-AT
20974 AATAAAAA-
1 AATAAAAAT
20982 AATAAAAAT
1 AATAAAAAT
*
20991 AATGAAAATAA
1 AAT-AAAA-AT
21002 AATAATAAAT
1 AATAA-AAAT
21012 AAATAAAAAT
1 -AATAAAAAT
21022 GTTAAAAGAC
Statistics
Matches: 63, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
8 8 0.13
9 19 0.30
10 24 0.38
11 12 0.19
ACGTcount: A:0.73, C:0.02, G:0.03, T:0.21
Consensus pattern (9 bp):
AATAAAAAT
Found at i:21003 original size:14 final size:15
Alignment explanation
Indices: 20980--21021 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
20970 ACAGAATAAA
20980 AAAATAAAAATAATG
1 AAAATAAAAATAATG
*
20995 AAAAT-AAAATAATAA
1 AAAATAAAAATAAT-G
21010 ATAAATAAAAAT
1 A-AAATAAAAAT
21022 GTTAAAAGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 8 0.35
15 6 0.26
16 4 0.17
17 5 0.22
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.21
Consensus pattern (15 bp):
AAAATAAAAATAATG
Found at i:21020 original size:17 final size:15
Alignment explanation
Indices: 20936--21021 Score: 61
Period size: 15 Copynumber: 5.6 Consensus size: 15
20926 AAACATCATC
* *
20936 AATAAAAATAGTAAT
1 AATAAAAATAATAAA
* *
20951 AATAATAATAACAAA
1 AATAAAAATAATAAA
20966 TAA-AACAGAATAA-AAA
1 -AATAA-A-AATAATAAA
*
20982 AATAAAAATAATGAA
1 AATAAAAATAATAAA
20997 AAT-AAAATAATAAATA
1 AATAAAAATAAT-AA-A
21013 AATAAAAAT
1 AATAAAAAT
21022 GTTAAAAGAC
Statistics
Matches: 56, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
14 13 0.23
15 22 0.39
16 11 0.20
17 10 0.18
ACGTcount: A:0.73, C:0.02, G:0.03, T:0.21
Consensus pattern (15 bp):
AATAAAAATAATAAA
Found at i:21022 original size:28 final size:28
Alignment explanation
Indices: 20948--21022 Score: 68
Period size: 28 Copynumber: 2.8 Consensus size: 28
20938 TAAAAATAGT
*
20948 AATAAT-AAT-AATAACAAAT-AAAACAG
1 AATAATAAATAAATAA-AAATGAAAACAA
* * *
20974 AATAAAAAAATAAA-AATAATGAAAATAA
1 AAT-AATAAATAAATAAAAATGAAAACAA
21002 AATAATAAATAAATAAAAATG
1 AATAATAAATAAATAAAAATG
21023 TTAAAAGACA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
26 3 0.08
27 14 0.37
28 19 0.50
29 2 0.05
ACGTcount: A:0.73, C:0.03, G:0.04, T:0.20
Consensus pattern (28 bp):
AATAATAAATAAATAAAAATGAAAACAA
Found at i:21837 original size:122 final size:120
Alignment explanation
Indices: 21600--21842 Score: 287
Period size: 122 Copynumber: 2.0 Consensus size: 120
21590 TATGTTTGTC
*
21600 CTTGCCAGCCCGTGTGGCTTCGAAGTATAAAAAAAATCGCCCAGTGGTCACACAGTCTAGCACAC
1 CTTGCCAGCCCGTGTGGCTTCGAAGTATAAAAAAAATCGACCAGTGGTCACACAGTCTAGCACAC
*
21665 GCCTGTGTGTCCAGGCTGTGTGCCTCACACAACCATGTTTCAGGTCGTGTGTGAT
66 GCCTGTGTGTCCAGGCTGTGTGCCTCACACAACCATGTTTCAGCTCGTGTGTGAT
* * * * ** * *
21720 CTTGGCAGCCCGTGTGATTCTTCGAAGTGTAGAAAAATATC-ACCAGTGGTCACATGGTCTGGTA
1 CTTGCCAGCCCGTGTG--GCTTCGAAGTATA-AAAAAAATCGACCAGTGGTCACACAGTCTAGCA
* **
21784 CACGCTCT-TGTGTCCAAG-TCGTGTGCCTCACACGGCCATGTTTCAGACT-GTGTGTGAT
63 CACGC-CTGTGTGTCCAGGCT-GTGTGCCTCACACAACCATGTTTCAG-CTCGTGTGTGAT
21842 C
1 C
21843 ACCCTTCGCT
Statistics
Matches: 104, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
120 15 0.14
121 1 0.01
122 77 0.74
123 11 0.11
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.27
Consensus pattern (120 bp):
CTTGCCAGCCCGTGTGGCTTCGAAGTATAAAAAAAATCGACCAGTGGTCACACAGTCTAGCACAC
GCCTGTGTGTCCAGGCTGTGTGCCTCACACAACCATGTTTCAGCTCGTGTGTGAT
Found at i:22787 original size:14 final size:14
Alignment explanation
Indices: 22759--22810 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
22749 AAGTTACGGG
22759 TATGAGTTTAGGGTT
1 TATG-GTTTAGGGTT
22774 TA-GGTTTAAGGGTT
1 TATGGTTT-AGGGTT
*
22788 TATGGTTTGGGGTT
1 TATGGTTTAGGGTT
*
22802 TATGATTTA
1 TATGGTTTA
22811 AGTTTTGGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 4 0.12
14 21 0.66
15 7 0.22
ACGTcount: A:0.19, C:0.00, G:0.33, T:0.48
Consensus pattern (14 bp):
TATGGTTTAGGGTT
Found at i:22810 original size:21 final size:20
Alignment explanation
Indices: 22786--22829 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
22776 GGTTTAAGGG
*
22786 TTTATGGTTTGGGGTTTATGA
1 TTTAAGGTTTGGGGTTTAT-A
* *
22807 TTTAAGTTTTGGGTTTTATA
1 TTTAAGGTTTGGGGTTTATA
22827 TTT
1 TTT
22830 TGGGTTTAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.16, C:0.00, G:0.25, T:0.59
Consensus pattern (20 bp):
TTTAAGGTTTGGGGTTTATA
Found at i:24065 original size:3 final size:3
Alignment explanation
Indices: 24057--24117 Score: 113
Period size: 3 Copynumber: 20.0 Consensus size: 3
24047 AAAGAAAAGA
24057 AAT AAT AAT AAAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
24103 AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT
24118 TGGTTAAGCT
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 54 0.95
4 3 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:26025 original size:11 final size:11
Alignment explanation
Indices: 25997--26045 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 11
25987 CGACTACATT
*
25997 AAATAACAACA
1 AAATAATAACA
26008 AAATAATAACA
1 AAATAATAACA
***
26019 AAATAATAGTG
1 AAATAATAACA
*
26030 AAATAGTAACA
1 AAATAATAACA
26041 AAATA
1 AAATA
26046 GTAAAAACAA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.67, C:0.08, G:0.06, T:0.18
Consensus pattern (11 bp):
AAATAATAACA
Found at i:26075 original size:34 final size:33
Alignment explanation
Indices: 26030--26094 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 33
26020 AATAATAGTG
* *
26030 AAATAGTAACAAAATAGTAAAAACAACAACAATA
1 AAATAGCAACAAAACAGTAAAAA-AACAACAATA
*
26064 AAATAGCAACAAAACAGTAAAAAAATAACAA
1 AAATAGCAACAAAACAGTAAAAAAACAACAA
26095 CTTTTCGGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 7 0.25
34 21 0.75
ACGTcount: A:0.69, C:0.12, G:0.06, T:0.12
Consensus pattern (33 bp):
AAATAGCAACAAAACAGTAAAAAAACAACAATA
Found at i:26744 original size:2 final size:2
Alignment explanation
Indices: 26737--26763 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
26727 ATTTTCAATT
26737 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 T
26764 TGTGATCTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30867 original size:24 final size:24
Alignment explanation
Indices: 30820--30870 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
30810 GAAATTTTTA
** *
30820 TTTATTTTTAAAATATTTATATTT
1 TTTATTTTTAAAATATAAAGATTT
*
30844 TTTATTTTTAAATTATAAAGATTT
1 TTTATTTTTAAAATATAAAGATTT
30868 TTT
1 TTT
30871 TCCTTTTTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (24 bp):
TTTATTTTTAAAATATAAAGATTT
Found at i:34054 original size:96 final size:96
Alignment explanation
Indices: 33880--34071 Score: 248
Period size: 96 Copynumber: 2.0 Consensus size: 96
33870 ATTTTGGGAA
** **
33880 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGTAATATTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCCAAATATTTCA
*
33945 GAATCGAAGAT-AAAGAAACATTGCCTCGATT
66 GAATCGAAGATAAAAG-AACATTACCTCGATT
* *
33976 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAAT-TTTC
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGC-CAAATATTTC
*
34040 -GAAACTCGAA-ATAAAAGAATATTACCTCGATT
65 AG-AA-TCGAAGATAAAAGAACATTACCTCGATT
34072 TTAAAGTCTT
Statistics
Matches: 84, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
95 1 0.01
96 71 0.85
97 12 0.14
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCCAAATATTTCA
GAATCGAAGATAAAAGAACATTACCTCGATT
Found at i:34418 original size:29 final size:30
Alignment explanation
Indices: 34351--34672 Score: 255
Period size: 29 Copynumber: 11.0 Consensus size: 30
34341 GTAATTTTAG
* *
34351 GGAAG-TTCGAGGTTAAAAGATGAAATTTTT
1 GGAAGTTTCGAGGGTAAAA-ATGGAATTTTT
* *
34381 AG-A-TATTCGAGAGTAAAAATGGAATTTTT
1 GGAAGT-TTCGAGGGTAAAAATGGAATTTTT
* * * *
34410 GG-AGTTTCGA-GGTCGAATATAGAGTTTTT
1 GGAAGTTTCGAGGGT-AAAAATGGAATTTTT
**
34439 GGACA--TTCG-GGGGCAAAATGGTAATTTTT
1 GGA-AGTTTCGAGGGTAAAAATGG-AATTTTT
*
34468 GAAAGTTTCG-GGGTCAAAAATGGAATTTTT
1 GGAAGTTTCGAGGGT-AAAAATGGAATTTTT
*
34498 GGAAG-TTCGAGGGTCAAAATGGAATTTTT
1 GGAAGTTTCGAGGGTAAAAATGGAATTTTT
**
34527 GGAAG-TTCG-GGGTAAAAATGGGTTTTTT
1 GGAAGTTTCGAGGGTAAAAATGGAATTTTT
*
34555 GGAAGTTTCGA-GGTCGAAAATGGAATTTTT
1 GGAAGTTTCGAGGGT-AAAAATGGAATTTTT
* *
34585 GGAAG-TTCGGGGGTAAAAATGAAATTTTT
1 GGAAGTTTCGAGGGTAAAAATGGAATTTTT
* * *
34614 AGAAATTTTG-GGGTCAAAAAT-GAAGTTTTT
1 GGAAGTTTCGAGGGT-AAAAATGGAA-TTTTT
*
34644 GGAAG-TTCGAGGGTAAAAATGTAATTTTT
1 GGAAGTTTCGAGGGTAAAAATGGAATTTTT
34673 AGACAATTTA
Statistics
Matches: 234, Mismatches: 37, Indels: 43
0.75 0.12 0.14
Matches are distributed among these distances:
28 29 0.12
29 119 0.51
30 78 0.33
31 8 0.03
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (30 bp):
GGAAGTTTCGAGGGTAAAAATGGAATTTTT
Found at i:34420 original size:59 final size:58
Alignment explanation
Indices: 34351--34675 Score: 258
Period size: 59 Copynumber: 5.6 Consensus size: 58
34341 GTAATTTTAG
* *
34351 GGAAGTTCGAGGTTAAAAGATGAAATTTTTAGATA-TTCGAGAGTAAAAATGGAATTTTT
1 GGAAGTTCGAGGGTAAAA-ATGAAATTTTTAGA-AGTTCGAGGGTAAAAATGGAATTTTT
* * * * **
34410 GG-AGTTTCGA-GGTCGAATAT-AGAGTTTTTGGACA-TTCG-GGGGCAAAATGGTAATTTTT
1 GGAAG-TTCGAGGGT-AAAAATGA-AATTTTTAGA-AGTTCGAGGGTAAAAATGG-AATTTTT
* * * *
34468 GAAAGTTTCG-GGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTCAAAATGGAATTTTT
1 GGAAG-TTCGAGGGT-AAAAATGAAATTTTTAGAAGTTCGAGGGTAAAAATGGAATTTTT
*** * *
34527 GGAAGTTCG-GGGTAAAAATGGGTTTTTTGGAAGTTTCGA-GGTCGAAAATGGAATTTTT
1 GGAAGTTCGAGGGTAAAAATGAAATTTTTAGAAG-TTCGAGGGT-AAAAATGGAATTTTT
* * *
34585 GGAAGTTCGGGGGTAAAAATGAAATTTTTAGAAATTTTG-GGGTCAAAAAT-GAAGTTTTT
1 GGAAGTTCGAGGGTAAAAATGAAATTTTTAG-AAGTTCGAGGGT-AAAAATGGAA-TTTTT
*
34644 GGAAGTTCGAGGGTAAAAATGTAATTTTTAGA
1 GGAAGTTCGAGGGTAAAAATGAAATTTTTAGA
34676 CAATTTAGGG
Statistics
Matches: 223, Mismatches: 28, Indels: 31
0.79 0.10 0.11
Matches are distributed among these distances:
57 31 0.14
58 68 0.30
59 111 0.50
60 13 0.06
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.34
Consensus pattern (58 bp):
GGAAGTTCGAGGGTAAAAATGAAATTTTTAGAAGTTCGAGGGTAAAAATGGAATTTTT
Found at i:34586 original size:146 final size:146
Alignment explanation
Indices: 34351--34675 Score: 419
Period size: 146 Copynumber: 2.2 Consensus size: 146
34341 GTAATTTTAG
*
34351 GGAAGTTCGAGGTTAAAAGATGAAATTTTTAGATATTCGAGAGTAAAAATGGAATTTTTGGAGTT
1 GGAAGTTCGAGGGTAAAA-ATGAAATTTTTAGATATTCGAGAGTAAAAATGGAATTTTTGGAGTT
* * * *
34416 TCGAGGTCGAATATAGAGTTTTTGGACA-TTCGGGGG-CAAAATGGTAATTTTT-GAAAGTTTCG
65 TCGAGGTCGAAAATAGAATTTTTGGA-AGTTCGGGGGTAAAAAT-GAAATTTTTAGAAA-TTTCG
34478 GGGTCAAAAATGGAA-TTTTT
127 GGGTCAAAAAT-GAAGTTTTT
* * * * **
34498 GGAAGTTCGAGGGTCAAAATGGAATTTTTGGA-AGTTCG-GGGTAAAAATGGGTTTTTTGGAAGT
1 GGAAGTTCGAGGGTAAAAATGAAATTTTTAGATA-TTCGAGAGTAAAAATGGAATTTTTGG-AGT
* *
34561 TTCGAGGTCGAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGAAATTTTTAGAAATTTTGGG
64 TTCGAGGTCGAAAATAGAATTTTTGGAAGTTCGGGGGTAAAAATGAAATTTTTAGAAATTTCGGG
34626 GTCAAAAATGAAGTTTTT
129 GTCAAAAATGAAGTTTTT
*
34644 GGAAGTTCGAGGGTAAAAATGTAATTTTTAGA
1 GGAAGTTCGAGGGTAAAAATGAAATTTTTAGA
34676 CAATTTAGGG
Statistics
Matches: 156, Mismatches: 16, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
145 23 0.15
146 108 0.69
147 25 0.16
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.34
Consensus pattern (146 bp):
GGAAGTTCGAGGGTAAAAATGAAATTTTTAGATATTCGAGAGTAAAAATGGAATTTTTGGAGTTT
CGAGGTCGAAAATAGAATTTTTGGAAGTTCGGGGGTAAAAATGAAATTTTTAGAAATTTCGGGGT
CAAAAATGAAGTTTTT
Found at i:34685 original size:29 final size:27
Alignment explanation
Indices: 34595--34685 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 27
34585 GGAAGTTCGG
*
34595 GGGTAAAAATGAAATTTTTAGAAATTTTG
1 GGGTAAAAATG-AATTTTTAGAAA-TTTA
* * *
34624 GGGTCAAAAATGAAGTTTTTGGAAGTTCGA
1 GGGT-AAAAATGAA-TTTTTAGAAATT-TA
34654 GGGTAAAAATGTAATTTTTAGACAATTTA
1 GGGTAAAAATG-AATTTTTAGA-AATTTA
34683 GGG
1 GGG
34686 ACCTCCAGGG
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
29 26 0.52
30 24 0.48
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.34
Consensus pattern (27 bp):
GGGTAAAAATGAATTTTTAGAAATTTA
Found at i:35477 original size:45 final size:45
Alignment explanation
Indices: 35413--35508 Score: 192
Period size: 45 Copynumber: 2.1 Consensus size: 45
35403 TAAAGCATCC
35413 TCTTTTCTTTCATTTTTTCCTTTTTACTATTTAAAAACATTTTAA
1 TCTTTTCTTTCATTTTTTCCTTTTTACTATTTAAAAACATTTTAA
35458 TCTTTTCTTTCATTTTTTCCTTTTTACTATTTAAAAACATTTTAA
1 TCTTTTCTTTCATTTTTTCCTTTTTACTATTTAAAAACATTTTAA
35503 TCTTTT
1 TCTTTT
35509 GAAAAACGTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (45 bp):
TCTTTTCTTTCATTTTTTCCTTTTTACTATTTAAAAACATTTTAA
Found at i:35525 original size:45 final size:45
Alignment explanation
Indices: 35431--35528 Score: 124
Period size: 45 Copynumber: 2.2 Consensus size: 45
35421 TTCATTTTTT
**** ** *
35431 CCTTTTTACTATTTAAAAACATTTTAATCTTTTCTTTCATTTTTT
1 CCTTTTTACTATTTAAAAACATTTTAATCTTTTCAAAAACGTTTC
*
35476 CCTTTTTACTATTTAAAAACATTTTAATCTTTTGAAAAACGTTTC
1 CCTTTTTACTATTTAAAAACATTTTAATCTTTTCAAAAACGTTTC
35521 CCTTTTTA
1 CCTTTTTA
35529 TACCTTTAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.28, C:0.16, G:0.02, T:0.54
Consensus pattern (45 bp):
CCTTTTTACTATTTAAAAACATTTTAATCTTTTCAAAAACGTTTC
Found at i:36563 original size:17 final size:17
Alignment explanation
Indices: 36538--36617 Score: 97
Period size: 17 Copynumber: 4.7 Consensus size: 17
36528 TAAATAGATT
* * *
36538 TAAACTTAAATTTATAG
1 TAAATTTAAATTTAAAA
* *
36555 TAAATTTAAATTTTAAG
1 TAAATTTAAATTTAAAA
*
36572 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
*
36589 TAAATTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
36606 TAAATTTAAATT
1 TAAATTTAAATT
36618 CTGTTGGGCC
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 54 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:36563 original size:23 final size:22
Alignment explanation
Indices: 36524--36587 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 22
36514 TTTGGACATT
* *
36524 AATTTAAATAGATTTAAACTTA
1 AATTTAAGTAAATTTAAACTTA
36546 AATTTATAGTAAATTTAAA--T-
1 AATTTA-AGTAAATTTAAACTTA
36566 --TTTAAGTAAATTTAAACTTA
1 AATTTAAGTAAATTTAAACTTA
36586 AA
1 AA
36588 ATAAATTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
17 12 0.35
18 4 0.12
19 1 0.03
21 1 0.03
22 6 0.18
23 10 0.29
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (22 bp):
AATTTAAGTAAATTTAAACTTA
Found at i:36564 original size:6 final size:6
Alignment explanation
Indices: 36535--36617 Score: 57
Period size: 6 Copynumber: 14.5 Consensus size: 6
36525 ATTTAAATAG
* * * * *
36535 ATTTAA ACTTAA ATTTAT A-GTAA ATTTAA ATTTTA A-GTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* * * *
36581 ACTTAA A-ATAA ATTTAA TTTTAA A-ATAA ATTTAA ATT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATT
36618 CTGTTGGGCC
Statistics
Matches: 56, Mismatches: 17, Indels: 8
0.69 0.21 0.10
Matches are distributed among these distances:
5 14 0.25
6 42 0.75
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (6 bp):
ATTTAA
Found at i:36604 original size:12 final size:12
Alignment explanation
Indices: 36535--36617 Score: 57
Period size: 11 Copynumber: 7.2 Consensus size: 12
36525 ATTTAAATAG
*
36535 ATTTAAACTTAA
1 ATTTAAATTTAA
* *
36547 ATTTATA-GTAA
1 ATTTAAATTTAA
*
36558 ATTTAAATTTTA
1 ATTTAAATTTAA
*
36570 A-GTAAATTTAA
1 ATTTAAATTTAA
* *
36581 ACTTAAA-ATAA
1 ATTTAAATTTAA
*
36592 ATTTAATTTTAA
1 ATTTAAATTTAA
*
36604 A-ATAAATTTAA
1 ATTTAAATTTAA
36615 ATT
1 ATT
36618 CTGTTGGGCC
Statistics
Matches: 52, Mismatches: 15, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
11 35 0.67
12 17 0.33
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (12 bp):
ATTTAAATTTAA
Found at i:37098 original size:31 final size:29
Alignment explanation
Indices: 37060--37134 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
37050 AATGGCTCAA
*
37060 TGACTAAAATATTACAACACGATAACGTAAG
1 TGACTAAAATATAACAACAC-A-AACGTAAG
* ***
37091 TGACTAAAATGTAACATTTCAAACGTAAG
1 TGACTAAAATATAACAACACAAACGTAAG
37120 TGACTAAAATATAAC
1 TGACTAAAATATAAC
37135 TTGAGACAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 22 0.58
30 1 0.03
31 15 0.39
ACGTcount: A:0.48, C:0.15, G:0.12, T:0.25
Consensus pattern (29 bp):
TGACTAAAATATAACAACACAAACGTAAG
Found at i:37173 original size:2 final size:2
Alignment explanation
Indices: 37168--37217 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
37158 ATATACACAC
* * *
37168 AT AT AT AT AT AT AT AT AC AC AC 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 AT AT
37210 AT AT AT AT
1 AT AT AT AT
37218 GTGTGTGTCA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:37180 original size:20 final size:20
Alignment explanation
Indices: 37155--37204 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
37145 CAAAAGTGAC
* *
37155 TATATATACACACATATATA
1 TATATATATACACACATATA
37175 TATATATATACACACATATA
1 TATATATATACACACATATA
37195 TATATATATA
1 TATATATATA
37205 TATATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (20 bp):
TATATATATACACACATATA
Found at i:37183 original size:22 final size:22
Alignment explanation
Indices: 37155--37206 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
37145 CAAAAGTGAC
37155 TATATATACACACATATATATA
1 TATATATACACACATATATATA
37177 TATATATACACACATATATATA
1 TATATATACACACATATATATA
37199 TATATATA
1 TATATATA
37207 TATATATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (22 bp):
TATATATACACACATATATATA
Found at i:40059 original size:12 final size:12
Alignment explanation
Indices: 40044--40069 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40034 AATTTTTGCG
40044 TTCTTTTTTTCT
1 TTCTTTTTTTCT
40056 TTCTTTTTTTCT
1 TTCTTTTTTTCT
40068 TT
1 TT
40070 ACAATCTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTCTTTTTTTCT
Found at i:46532 original size:32 final size:32
Alignment explanation
Indices: 46463--46536 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 32
46453 ATATTTCTTG
* *
46463 AAATTAATGTTTTTTGCCTAATTTCCTCATTG
1 AAATTAATGCTTTTTGCCTAATTTCCTCATTA
* * *
46495 GAATTAATGCTTTTTGCCTAATTTCTTCTTTA
1 AAATTAATGCTTTTTGCCTAATTTCCTCATTA
46527 AAATTAATGC
1 AAATTAATGC
46537 CTTTATGGAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.27, C:0.15, G:0.09, T:0.49
Consensus pattern (32 bp):
AAATTAATGCTTTTTGCCTAATTTCCTCATTA
Found at i:59594 original size:15 final size:16
Alignment explanation
Indices: 59576--59613 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
59566 AATAAAAAAT
*
59576 ATATAAAATTATTA-A
1 ATATAAAATTAATATA
*
59591 ATATTAAATTAATATA
1 ATATAAAATTAATATA
59607 ATATAAA
1 ATATAAA
59614 TATATTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATATAAAATTAATATA
Found at i:76095 original size:31 final size:31
Alignment explanation
Indices: 76058--76130 Score: 128
Period size: 31 Copynumber: 2.4 Consensus size: 31
76048 AAATGTTACG
*
76058 TTTTAGTCACTTATGTTAGCGTGTTATAACA
1 TTTTAGTCACTTATGTTAACGTGTTATAACA
*
76089 TTTTAGTCACTTATGTTAACTTGTTATAACA
1 TTTTAGTCACTTATGTTAACGTGTTATAACA
76120 TTTTAGTCACT
1 TTTTAGTCACT
76131 AAGTCATTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.26, C:0.14, G:0.12, T:0.48
Consensus pattern (31 bp):
TTTTAGTCACTTATGTTAACGTGTTATAACA
Found at i:78856 original size:67 final size:67
Alignment explanation
Indices: 78748--78888 Score: 273
Period size: 67 Copynumber: 2.1 Consensus size: 67
78738 GTTTGACATA
*
78748 TGTGGATTCATCTTTTATTTGTTTAAATATTATCCTGAAGTTTGTAAGATTTATCTTTCATAGCC
1 TGTGGATTCATCTTTTATTTGTTTAAATATTATCCTGAAGTTTGTAAGATTTATCTTTCATAACC
78813 AT
66 AT
78815 TGTGGATTCATCTTTTATTTGTTTAAATATTATCCTGAAGTTTGTAAGATTTATCTTTCATAACC
1 TGTGGATTCATCTTTTATTTGTTTAAATATTATCCTGAAGTTTGTAAGATTTATCTTTCATAACC
78880 AT
66 AT
78882 TGTGGAT
1 TGTGGAT
78889 ATGTGCTTAG
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 73 1.00
ACGTcount: A:0.26, C:0.11, G:0.14, T:0.49
Consensus pattern (67 bp):
TGTGGATTCATCTTTTATTTGTTTAAATATTATCCTGAAGTTTGTAAGATTTATCTTTCATAACC
AT
Found at i:83995 original size:19 final size:19
Alignment explanation
Indices: 83951--83995 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
83941 ATTCTTTGAA
83951 TTAAAAAATATTTTTTTAT
1 TTAAAAAATATTTTTTTAT
* * * *
83970 ATCAAAAATGTTTTTTTTT
1 TTAAAAAATATTTTTTTAT
83989 TTAAAAA
1 TTAAAAA
83996 CACTACTAAA
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (19 bp):
TTAAAAAATATTTTTTTAT
Found at i:84289 original size:31 final size:27
Alignment explanation
Indices: 84245--84329 Score: 71
Period size: 33 Copynumber: 2.8 Consensus size: 27
84235 TTTTTTTAAA
84245 TTAATAAATATAAATTTATATTTTAATATTTT
1 TTAA-AAATATAAATTTA-A-TTT-A-ATTTT
*
84277 TTAAAATAATAAAAATTTAATTTAATTTT
1 TT-AAA-AATATAAATTTAATTTAATTTT
84306 TTAAAAATTATAAAAATTTAATTT
1 TTAAAAA-TAT--AAATTTAATTT
84330 CGATTCCTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
27 2 0.04
28 5 0.11
29 7 0.15
30 12 0.26
31 3 0.07
32 4 0.09
33 13 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
TTAAAAATATAAATTTAATTTAATTTT
Found at i:84305 original size:37 final size:36
Alignment explanation
Indices: 84226--84305 Score: 97
Period size: 37 Copynumber: 2.2 Consensus size: 36
84216 TGGTTTTTTA
* * * *
84226 AATTTAAATTTTTTTTAAATTAATAAATATAAATTT
1 AATTTTAATATTTTTTAAAATAATAAAAATAAATTT
*
84262 ATATTTTAATATTTTTTAAAATAATAAAAATTTAATTT
1 A-ATTTTAATATTTTTTAAAATAATAAAAA-TAAATTT
84300 AATTTT
1 AATTTT
84306 TTAAAAATTA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
36 1 0.03
37 29 0.78
38 7 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (36 bp):
AATTTTAATATTTTTTAAAATAATAAAAATAAATTT
Found at i:84307 original size:30 final size:31
Alignment explanation
Indices: 84237--84329 Score: 107
Period size: 30 Copynumber: 2.9 Consensus size: 31
84227 ATTTAAATTT
*
84237 TTTTTAAATTAATAAATATAAATTTATATTTTAATA
1 TTTTTAAA--AAT-AATAAAAATTTA-A-TTTAATA
*
84273 TTTTTTAAAATAATAAAAATTTAATTTAAT-
1 TTTTTAAAAATAATAAAAATTTAATTTAATA
*
84303 TTTTTAAAAATTATAAAAATTTAATTT
1 TTTTTAAAAATAATAAAAATTTAATTT
84330 CGATTCCTTA
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
30 25 0.47
31 6 0.11
32 1 0.02
33 11 0.21
34 3 0.06
36 7 0.13
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (31 bp):
TTTTTAAAAATAATAAAAATTTAATTTAATA
Found at i:84343 original size:30 final size:29
Alignment explanation
Indices: 84277--84344 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
84267 TTAATATTTT
* **
84277 TTAAAATAATAAAAATTTAATTTAATTTT
1 TTAAAATTATAAAAATTTAATTTAATTCC
*
84306 TTAAAAATTATAAAAATTTAATTTCGATTCC
1 TT-AAAATTATAAAAATTTAATTT-AATTCC
84337 TTAAAATT
1 TTAAAATT
84345 TTCGCCCTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 2 0.06
30 26 0.79
31 5 0.15
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (29 bp):
TTAAAATTATAAAAATTTAATTTAATTCC
Found at i:87616 original size:352 final size:352
Alignment explanation
Indices: 86965--87666 Score: 1359
Period size: 352 Copynumber: 2.0 Consensus size: 352
86955 TGGCTGTGGC
86965 TCCAATAGGACATGTGTATACCTTTGATTTCCATGAACAGAGGTCTGCCTCAGCTAAGTAAGCCT
1 TCCAATAGGACATGTGTATACCTTTGATTTCCATGAACAGAGGTCTGCCTCAGCTAAGTAAGCCT
87030 TAATGTTTATCGTTTGCGAAAGTGCATTGTGATGAAATATGATAGAGTAAATGCTCAGGTTGAAC
66 TAATGTTTATCGTTTGCGAAAGTGCATTGTGATGAAATATGATAGAGTAAATGCTCAGGTTGAAC
87095 TTAAATTCTGGGTCATCTCGAATTGATGTCTTCATAGATCTATATTTTGTTTCTGTGATACTTTA
131 TTAAATTCTGGGTCATCTCGAATTGATGTCTTCATAGATCTATATTTTGTTTCTGTGATACTTTA
87160 TTGTATCTAATTGTCTCAGTTTACAGATCTTTATTAGTTTCATTAGTGAGTGCATTATTATGAAA
196 TTGTATCTAATTGTCTCAGTTTACAGATCTTTATTAGTTTCATTAGTGAGTGCATTATTATGAAA
87225 TTTTGGTTTCAAAGATTCAAGTTATGAAATATGATTTTAGTAACTGCTAGGTTGAGCTTGAATTC
261 TTTTGGTTTCAAAGATTCAAGTTATGAAATATGATTTTAGTAACTGCTAGGTTGAGCTTGAATTC
87290 TAGGTAGATTTCAGAAGTCTGTTCATG
326 TAGGTAGATTTCAGAAGTCTGTTCATG
*
87317 TCCAATAGGACATGTGTATACCTTTGATTTCCATGAACAGAGGTCTGTCTCAGCTAAGTAAGCCT
1 TCCAATAGGACATGTGTATACCTTTGATTTCCATGAACAGAGGTCTGCCTCAGCTAAGTAAGCCT
87382 TAATGTTTATCGTTTGCGAAAGTGCATTGTGATGAAATATGATAGAGTAAATGCTCAGGTTGAAC
66 TAATGTTTATCGTTTGCGAAAGTGCATTGTGATGAAATATGATAGAGTAAATGCTCAGGTTGAAC
*
87447 TTAAATTCTGGGTCATCTCGAGTTGATGTCTTCATAGATCTATATTTTGTTTCTGTGATACTTTA
131 TTAAATTCTGGGTCATCTCGAATTGATGTCTTCATAGATCTATATTTTGTTTCTGTGATACTTTA
* *
87512 TTGTATCTAATTGTCTCAGTTTACAGATTTTTATTAGTTTCATTAGTGAGTGCATTGTTATGAAA
196 TTGTATCTAATTGTCTCAGTTTACAGATCTTTATTAGTTTCATTAGTGAGTGCATTATTATGAAA
*
87577 TTTTGGTTTCAAAGATTCAAGTTATGAAATATTATTTTAGTAACTGCTAGGTTGAGCTTGAATTC
261 TTTTGGTTTCAAAGATTCAAGTTATGAAATATGATTTTAGTAACTGCTAGGTTGAGCTTGAATTC
87642 TAGGTAGATTTCAGAAGTCTGTTCA
326 TAGGTAGATTTCAGAAGTCTGTTCA
87667 GGTGGATGTA
Statistics
Matches: 345, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
352 345 1.00
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.40
Consensus pattern (352 bp):
TCCAATAGGACATGTGTATACCTTTGATTTCCATGAACAGAGGTCTGCCTCAGCTAAGTAAGCCT
TAATGTTTATCGTTTGCGAAAGTGCATTGTGATGAAATATGATAGAGTAAATGCTCAGGTTGAAC
TTAAATTCTGGGTCATCTCGAATTGATGTCTTCATAGATCTATATTTTGTTTCTGTGATACTTTA
TTGTATCTAATTGTCTCAGTTTACAGATCTTTATTAGTTTCATTAGTGAGTGCATTATTATGAAA
TTTTGGTTTCAAAGATTCAAGTTATGAAATATGATTTTAGTAACTGCTAGGTTGAGCTTGAATTC
TAGGTAGATTTCAGAAGTCTGTTCATG
Found at i:90188 original size:7 final size:7
Alignment explanation
Indices: 90176--90202 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
90166 TATAGAAGAT
90176 AAAAATA
1 AAAAATA
90183 AAAAATA
1 AAAAATA
90190 AAAAATA
1 AAAAATA
90197 AAAAAT
1 AAAAAT
90203 CGAATCTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAAATA
Found at i:93921 original size:34 final size:34
Alignment explanation
Indices: 93878--93944 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
93868 GAAGAATAAA
93878 TGTTGTGTTTTGGTCTTATAATGATTGATTCATC
1 TGTTGTGTTTTGGTCTTATAATGATTGATTCATC
93912 TGTTGTGTTTTGGTCTTATAATGATTGATTCAT
1 TGTTGTGTTTTGGTCTTATAATGATTGATTCAT
93945 TTCTTAACTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.18, C:0.07, G:0.21, T:0.54
Consensus pattern (34 bp):
TGTTGTGTTTTGGTCTTATAATGATTGATTCATC
Found at i:95081 original size:23 final size:23
Alignment explanation
Indices: 95062--95147 Score: 79
Period size: 23 Copynumber: 3.7 Consensus size: 23
95052 TTGTTTAATG
95062 TTAAT-GAACATGTTCATTTAAC
1 TTAATCGAACATGTTCATTTAAC
**
95084 TTAATCGAACATGTTCA-CGAAC
1 TTAATCGAACATGTTCATTTAAC
* *
95106 ATTAAACGAACATGTTCA-TGAAC
1 -TTAATCGAACATGTTCATTTAAC
*
95129 ATATAATTGAACATGTTCA
1 -T-TAATCGAACATGTTCA
95148 CGAACAATGT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
22 8 0.15
23 33 0.60
24 14 0.25
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.33
Consensus pattern (23 bp):
TTAATCGAACATGTTCATTTAAC
Found at i:95106 original size:12 final size:12
Alignment explanation
Indices: 95089--95158 Score: 54
Period size: 12 Copynumber: 5.8 Consensus size: 12
95079 TTAACTTAAT
95089 CGAACATGTTCA
1 CGAACATGTTCA
**
95101 CGAACAT-TAAA
1 CGAACATGTTCA
95112 CGAACATGTTCA
1 CGAACATGTTCA
* * *
95124 TGAACAT-ATAA
1 CGAACATGTTCA
*
95135 TTGAACATGTTCA
1 -CGAACATGTTCA
95148 CGAACAATGTT
1 CGAAC-ATGTT
95159 AATGAATAAT
Statistics
Matches: 44, Mismatches: 10, Indels: 7
0.72 0.16 0.11
Matches are distributed among these distances:
11 11 0.25
12 26 0.59
13 7 0.16
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (12 bp):
CGAACATGTTCA
Found at i:98576 original size:16 final size:15
Alignment explanation
Indices: 98555--98608 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 15
98545 TTTGATTCGC
98555 TGTAATAGAATAGAGT
1 TGTAATAGAATAGA-T
*
98571 TGTAATGGAATAGAAT
1 TGTAATAGAATAG-AT
* *
98587 TATAATAAAATATGAT
1 TGTAATAGAATA-GAT
98603 TGTAAT
1 TGTAAT
98609 CAATAATTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
16 29 0.94
17 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.19, T:0.35
Consensus pattern (15 bp):
TGTAATAGAATAGAT
Found at i:98787 original size:58 final size:57
Alignment explanation
Indices: 98723--98885 Score: 197
Period size: 58 Copynumber: 2.8 Consensus size: 57
98713 TATTGTTATA
98723 AAATTTTAATA-AGATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATT
1 AAATTTTAATATA-ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAA-T
* * * *
98781 ATATTTTAACATAATTATTATTAAATATAATTAAAT-AAAA-AATATATAATTTAAT
1 AAATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAAT
* * *
98836 AAAGTTTTTAATATAATTATTATTAAAATATAAATTAGTAAAAATTATAA
1 AAA--TTTTAATATAATTATTATT-AAATATAATTTAATAAAAATAATAA
98886 TATATAATAT
Statistics
Matches: 88, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
55 3 0.03
56 13 0.15
57 22 0.25
58 42 0.48
59 5 0.06
60 3 0.03
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.43
Consensus pattern (57 bp):
AAATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAAT
Done.