Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013949.1 Kokia drynarioides strain JFW-HI SEQ_128979, 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: 179745
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 22 characters in sequence are not A, C, G, or T
Found at i:4050 original size:204 final size:204
Alignment explanation
Indices: 3450--4417 Score: 1504
Period size: 204 Copynumber: 4.8 Consensus size: 204
3440 ACGTGACCAT
* *
3450 CTTCCGGATGAGACACTGAGAAGCAGGTCGAAGCGATGAAAGGTTAGCTTCCTGATGAGATACTG
1 CTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCGATAAAAGGTTAGCTTCCTGATGAGATACTG
** * * * * *
3515 AGAAGTGAACCAAATTCGNGTTCCTGATGAGATACAGAGAAGCGAGTTG-AA-ATA-AGCGACGC
66 AGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGGAGCGAATTGAAACAAACAGCGATGT
* * * * *
3577 GGTCATATTCCTGATAAAACACTGAGAAGAAGACCCAAACGAGGCTCGATA-TGAGCAAAATCTT
131 GATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTC-AAAGTGAGCAAAATCTT
***
3641 CGAACCTTGG
195 CGAACCCCAG
*
3651 CTTCTTGATGAGACACTGAGAAGCAGGTCGAAGC-A-AGAAAGGTTAGCTTCCTGATGAGATACT
1 CTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCGATA-AAAGGTTAGCTTCCTGATGAGATACT
* * ** * *
3714 GAGAAGTGAACCAAATTCGCCTTCCTTATGAGATACAGAAAAGCGAGTTGAAAC--A-AGCGAAG
65 GAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGGAGCGAATTGAAACAAACAGCGATG
* * * *
3776 CGGTCATCTTCCTGATGAGACACTAAGAAGAAGACCCAAACGAGGCTCAAAGTCAGCAAAATCTT
130 TGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCAAAGTGAGCAAAATCTT
*
3841 CGAACCCCAA
195 CGAACCCCAG
*
3851 CTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCGATAAAAGGTTAGCTTCCTGATGAAATACTG
1 CTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCGATAAAAGGTTAGCTTCCTGATGAGATACTG
3916 AGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGGAGCGAATTGAAACAAACAGCGATGT
66 AGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGGAGCGAATTGAAACAAACAGCGATGT
* *
3981 GTTCATCTTCCTAATGAGACACTGAGAAGAAGACCCAAACGAGGCTCAAAGTGAGCAAAATCTTC
131 GATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCAAAGTGAGCAAAATCTTC
4046 GAACCCCAG
196 GAACCCCAG
* *
4055 CTTCCTGATGAGACACTGAGAAGCAAGTTGAAGCGATAAAAGGTTAGCTTCCTGATGAGATACTG
1 CTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCGATAAAAGGTTAGCTTCCTGATGAGATACTG
*
4120 AGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGGAGCGAATTGAAACAAACAGTGATGT
66 AGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGGAGCGAATTGAAACAAACAGCGATGT
4185 GATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCAAAGTGAGCAAAATCTTC
131 GATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCAAAGTGAGCAAAATCTTC
*
4250 GAACCACAG
196 GAACCCCAG
*
4259 CTTCCTGATGAGACACTGAGAAGTAGGTCGAAGCGATAAAAGGTTAGCTTCCTGATGAGATACTG
1 CTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCGATAAAAGGTTAGCTTCCTGATGAGATACTG
*
4324 AGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGGAGCGAATTGAAACAAACAGCGATGT
66 AGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGGAGCGAATTGAAACAAACAGCGATGT
*
4389 GATCATCTTCTTGATGAGACACTGAGAAG
131 GATCATCTTCCTGATGAGACACTGAGAAG
4418 CAAGTCGAAG
Statistics
Matches: 713, Mismatches: 45, Indels: 15
0.92 0.06 0.02
Matches are distributed among these distances:
199 2 0.00
200 175 0.25
201 109 0.15
202 1 0.00
203 1 0.00
204 425 0.60
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.20
Consensus pattern (204 bp):
CTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCGATAAAAGGTTAGCTTCCTGATGAGATACTG
AGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGGAGCGAATTGAAACAAACAGCGATGT
GATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCAAAGTGAGCAAAATCTTC
GAACCCCAG
Found at i:4508 original size:136 final size:136
Alignment explanation
Indices: 4259--4553 Score: 482
Period size: 136 Copynumber: 2.2 Consensus size: 136
4249 CGAACCACAG
* * * *
4259 CTTCCTGATGAGACACTGAGAAGTAGGTCGAAGCGATAAAAGGTTAGCTTCCTGATGAGATACTG
1 CTTCCTGATGAGACACTGAGAAGCAAGTCGAAGCGATAAAAGGTTAGCTTCCTAATAAGATACTG
* *
4324 AGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGGAGCGAATTGAAACAAACAGCGATGT
66 AGAAGTGAACCAAATTCATCTTCCTGATGAGATACAAAGGAGCAAATTGAAACAAACAGCGATGT
4389 GATCAT
131 GATCAT
* *
4395 CTTCTTGATGAGACACTGAGAAGCAAGTCGAAGCGATAAAAGGTTAGCTTCCTAATAAGATATTG
1 CTTCCTGATGAGACACTGAGAAGCAAGTCGAAGCGATAAAAGGTTAGCTTCCTAATAAGATACTG
*
4460 AGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAAAGGAGCAAATTGAAACAAACAGCGATGT
66 AGAAGTGAACCAAATTCATCTTCCTGATGAGATACAAAGGAGCAAATTGAAACAAACAGCGATGT
4525 GATCAT
131 GATCAT
* * *
4531 CTTCCTGACGAGGCACGGAGAAG
1 CTTCCTGATGAGACACTGAGAAG
4554 AAGGCCCAAA
Statistics
Matches: 146, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
136 146 1.00
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.22
Consensus pattern (136 bp):
CTTCCTGATGAGACACTGAGAAGCAAGTCGAAGCGATAAAAGGTTAGCTTCCTAATAAGATACTG
AGAAGTGAACCAAATTCATCTTCCTGATGAGATACAAAGGAGCAAATTGAAACAAACAGCGATGT
GATCAT
Found at i:4510 original size:340 final size:334
Alignment explanation
Indices: 4055--4705 Score: 946
Period size: 340 Copynumber: 1.9 Consensus size: 334
4045 CGAACCCCAG
* * *
4055 CTTCCTGATGAGACACTGAGAAGCAAGTTGAAGCGATAAAAGGTTAGCTTCCTGATGAGATACTG
1 CTTCCTGATGAGACACTGAGAAGCAAGTCGAAGCGATAAAAGGTTAGCTTCCTAATAAGATACTG
* * *
4120 AGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGGAGCGAATTGAAACAAACAGTGATGT
66 AGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAAAGGAGCAAATTGAAACAAACAGCGATGT
* * ** *
4185 GATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCAAAGTGAGCAAAATCTTC
131 GATCATCTTCCTGACGAGACACGGAGAAGAAGACCCAAACGAGGCTCAAAACGAGCAAAATATTC
* * *
4250 GAACCACAGCTTCCTGA-TGAGACACTGAGAAGTAGGTCGAAGCGATAAAA-GGTTAGCTTCCTG
196 GAACCACAACTTCCTGATTGAG--A--G-GAAG--GAT-GAAGCAATAAAATGGTTAGCTTCCTG
* * * * *
4313 ATGAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGGAGCGAATTGAAACA
253 ATGAGATACTAAGAAGCGAACCAAATTCATCTTCCTAATGAGATACAAAGAAGCGAATTGAAACA
4378 AACAGCGATGTGATCAT
318 AACAGCGATGTGATCAT
* *
4395 CTTCTTGATGAGACACTGAGAAGCAAGTCGAAGCGATAAAAGGTTAGCTTCCTAATAAGATATTG
1 CTTCCTGATGAGACACTGAGAAGCAAGTCGAAGCGATAAAAGGTTAGCTTCCTAATAAGATACTG
4460 AGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAAAGGAGCAAATTGAAACAAACAGCGATGT
66 AGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAAAGGAGCAAATTGAAACAAACAGCGATGT
* * *
4525 GATCATCTTCCTGACGAGGCACGGAGAAGAAGGCCCAAACGAGGCTCAAAACGAGCAAAATATTT
131 GATCATCTTCCTGACGAGACACGGAGAAGAAGACCCAAACGAGGCTCAAAACGAGCAAAATATTC
* * * *
4590 GAACCCCAACTTCTTGATTGAGAGGCAGGATGAAGCAATAAAATGGTTAGCTTCTTGATGAGATA
196 GAACCACAACTTCCTGATTGAGAGGAAGGATGAAGCAATAAAATGGTTAGCTTCCTGATGAGATA
* *
4655 CTAAGAAGCGGACCAAATTCGTCTTCCTAATGAGATACAAAGAAGCGAATT
261 CTAAGAAGCGAACCAAATTCATCTTCCTAATGAGATACAAAGAAGCGAATT
4706 AAAATAAGCG
Statistics
Matches: 279, Mismatches: 30, Indels: 10
0.87 0.09 0.03
Matches are distributed among these distances:
333 11 0.04
334 66 0.24
336 3 0.01
337 1 0.00
339 1 0.00
340 193 0.69
341 4 0.01
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.22
Consensus pattern (334 bp):
CTTCCTGATGAGACACTGAGAAGCAAGTCGAAGCGATAAAAGGTTAGCTTCCTAATAAGATACTG
AGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAAAGGAGCAAATTGAAACAAACAGCGATGT
GATCATCTTCCTGACGAGACACGGAGAAGAAGACCCAAACGAGGCTCAAAACGAGCAAAATATTC
GAACCACAACTTCCTGATTGAGAGGAAGGATGAAGCAATAAAATGGTTAGCTTCCTGATGAGATA
CTAAGAAGCGAACCAAATTCATCTTCCTAATGAGATACAAAGAAGCGAATTGAAACAAACAGCGA
TGTGATCAT
Found at i:5126 original size:6 final size:6
Alignment explanation
Indices: 5112--5191 Score: 64
Period size: 6 Copynumber: 14.0 Consensus size: 6
5102 GGCCTTTTAT
* * *
5112 TTTAAA TTTAGA TTT-AT TTTAAT TTTAAA -TT--A TCTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
*
5157 TTT-AA TTTAAA TTTAAA TTT-AA TTTCAAA GTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
5192 AAGTCCAAAG
Statistics
Matches: 61, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
3 1 0.02
5 17 0.28
6 37 0.61
7 6 0.10
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:5129 original size:17 final size:17
Alignment explanation
Indices: 5107--5191 Score: 100
Period size: 17 Copynumber: 5.0 Consensus size: 17
5097 GACGGGGCCT
*
5107 TTTATTTTAAATTTAGA
1 TTTATTTTAAATTTAAA
*
5124 TTTATTTTAATTTTAAA
1 TTTATTTTAAATTTAAA
*
5141 -TTATCTTAAATTTAAA
1 TTTATTTTAAATTTAAA
*
5157 TTTAATTTAAATTTAAA
1 TTTATTTTAAATTTAAA
* *
5174 TTTAATTTCAAAGTTAAA
1 TTT-ATTTTAAATTTAAA
5192 AAGTCCAAAG
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
16 14 0.25
17 32 0.56
18 11 0.19
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (17 bp):
TTTATTTTAAATTTAAA
Found at i:5150 original size:33 final size:33
Alignment explanation
Indices: 5108--5175 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
5098 ACGGGGCCTT
* * * *
5108 TTATTTTAAATTTAGATTTATTTTAATTTTAAA
1 TTATCTTAAATTTAAATTTAATTTAAATTTAAA
5141 TTATCTTAAATTTAAATTTAATTTAAATTTAAA
1 TTATCTTAAATTTAAATTTAATTTAAATTTAAA
5174 TT
1 TT
5176 TAATTTCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (33 bp):
TTATCTTAAATTTAAATTTAATTTAAATTTAAA
Found at i:5165 original size:11 final size:11
Alignment explanation
Indices: 5107--5181 Score: 59
Period size: 11 Copynumber: 6.7 Consensus size: 11
5097 GACGGGGCCT
*
5107 TTTATTTTAAA
1 TTTAATTTAAA
*
5118 TTTAGATTT-AT
1 TTTA-ATTTAAA
5129 TTTAATTTTAAA
1 TTTAA-TTTAAA
5141 -TT-ATCTTAAA
1 TTTAAT-TTAAA
5151 TTTAAATTT-AA
1 TTT-AATTTAAA
5162 TTTAAATTTAAA
1 TTT-AATTTAAA
5174 TTTAATTT
1 TTTAATTT
5182 CAAAGTTAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
9 1 0.02
10 7 0.13
11 32 0.60
12 11 0.21
13 2 0.04
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:5885 original size:13 final size:13
Alignment explanation
Indices: 5866--5904 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
5856 ATTGATAACT
5866 GTATTAATAATTA
1 GTATTAATAATTA
* *
5879 TTATTAATAATCA
1 GTATTAATAATTA
*
5892 GTATTAATTATTA
1 GTATTAATAATTA
5905 AAAATAAAAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (13 bp):
GTATTAATAATTA
Found at i:6935 original size:30 final size:30
Alignment explanation
Indices: 6868--7186 Score: 248
Period size: 30 Copynumber: 10.8 Consensus size: 30
6858 GGAGGTCCCT
*
6868 AAACTGTCCAAAAATTACTA-TTTTACCCTC-
1 AAACT-TCCAAAAATTACCATTTTTACCC-CA
*
6898 GAACTTCCAAAAATT-CCATTTTTATCCCCA
1 AAACTTCCAAAAATTACCATTTTTA-CCCCA
*
6928 AAACTTCCTAAAATTACCA-TTTTACCCTC-
1 AAACTTCCAAAAATTACCATTTTTACCC-CA
* * * * *
6957 GAACATCCAAAAA-TCCCATTTTTAACCTCG
1 AAACTTCCAAAAATTACCATTTTT-ACCCCA
* *
6987 AACCTTCCAAAAATTACCA-TTTTACCCCC
1 AAACTTCCAAAAATTACCATTTTTACCCCA
* *
7016 GAACTTCCAAAAA-TATCATTTTTAACCCCA
1 AAACTTCCAAAAATTACCATTTTT-ACCCCA
** *
7046 AAACTTCTTAAAATTACCA-TTTTACCCCT
1 AAACTTCCAAAAATTACCATTTTTACCCCA
** ** *
7075 AAACTT-TTAAAGGTCCCATTTTTAACCCCA
1 AAACTTCCAAAAATTACCATTTTT-ACCCCA
**
7105 AAACTTCCAAAAATTACCA-TTTTACCCTT
1 AAACTTCCAAAAATTACCATTTTTACCCCA
* * *
7134 GAACTTCCAAAAA-TCCCATTTTTAACCCCG
1 AAACTTCCAAAAATTACCATTTTT-ACCCCA
*
7164 AAACTTCCTAAAATTACCATTTT
1 AAACTTCCAAAAATTACCATTTT
7187 ACTCCCGGAT
Statistics
Matches: 229, Mismatches: 42, Indels: 35
0.75 0.14 0.11
Matches are distributed among these distances:
28 23 0.10
29 88 0.38
30 92 0.40
31 26 0.11
ACGTcount: A:0.36, C:0.29, G:0.03, T:0.32
Consensus pattern (30 bp):
AAACTTCCAAAAATTACCATTTTTACCCCA
Found at i:6970 original size:59 final size:59
Alignment explanation
Indices: 6868--7188 Score: 428
Period size: 59 Copynumber: 5.4 Consensus size: 59
6858 GGAGGTCCCT
* * *
6868 AAACTGTCCAAAAATTACTATTTTACCCTCGAACTTCCAAAAATTCCATTTTTATCCCCA
1 AAACT-TCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCA
* * * *
6928 AAACTTCCTAAAATTACCATTTTACCCTCGAACATCCAAAAATCCCATTTTTAACCTCG
1 AAACTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCA
* * **
6987 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATATCATTTTTAACCCCA
1 AAACTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCA
** * ** **
7046 AAACTTCTTAAAATTACCATTTTACCC-CTAAACTTTTAAAGGTCCCATTTTTAACCCCA
1 AAACTTCCAAAAATTACCATTTTACCCTC-GAACTTCCAAAAATCCCATTTTTAACCCCA
* *
7105 AAACTTCCAAAAATTACCATTTTACCCTTGAACTTCCAAAAATCCCATTTTTAACCCCG
1 AAACTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCA
*
7164 AAACTTCCTAAAATTACCATTTTAC
1 AAACTTCCAAAAATTACCATTTTAC
7189 TCCCGGATCT
Statistics
Matches: 224, Mismatches: 35, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
58 1 0.00
59 218 0.97
60 5 0.02
ACGTcount: A:0.36, C:0.29, G:0.03, T:0.32
Consensus pattern (59 bp):
AAACTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCA
Found at i:18395 original size:9 final size:9
Alignment explanation
Indices: 18381--18406 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
18371 GGACTGGATT
18381 GTGAAAATG
1 GTGAAAATG
18390 GTGAAAATG
1 GTGAAAATG
18399 GTGAAAAT
1 GTGAAAAT
18407 ACATGTCCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (9 bp):
GTGAAAATG
Found at i:20421 original size:18 final size:19
Alignment explanation
Indices: 20393--20442 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
20383 GGTTTGACCG
* *
20393 GTTAGGTGTTTGGTTTAGGT
1 GTTAGG-GTTTGGGTTAAGT
20413 -TTAGGGTTTGGGTTAAGT
1 GTTAGGGTTTGGGTTAAGT
20431 GTT-GGGTTTGGG
1 GTTAGGGTTTGGG
20443 CTAACAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 20 0.74
19 7 0.26
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (19 bp):
GTTAGGGTTTGGGTTAAGT
Found at i:28093 original size:43 final size:43
Alignment explanation
Indices: 28045--28187 Score: 191
Period size: 43 Copynumber: 3.3 Consensus size: 43
28035 ATGTCTCGAG
28045 ATGAGCATGAGATTATGTTAAAAAGGAAGACTCGTGACTCGGA
1 ATGAGCATGAGATTATGTTAAAAAGGAAGACTCGTGACTCGGA
* *
28088 ATGAGCATAAGATTATGTTAAAAAGGAAGACTCGTGACTTGGAA
1 ATGAGCATGAGATTATGTTAAAAAGGAAGACTCGTGACTCGG-A
* * ** * *
28132 AT-AGCATGATATTTTGTTTTAAA-GAAGACTCATGACTCGGG
1 ATGAGCATGAGATTATGTTAAAAAGGAAGACTCGTGACTCGGA
28173 ATGAGCATGAGATTA
1 ATGAGCATGAGATTA
28188 CATGTAAAGA
Statistics
Matches: 86, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
41 2 0.02
42 25 0.29
43 56 0.65
44 3 0.03
ACGTcount: A:0.37, C:0.10, G:0.25, T:0.27
Consensus pattern (43 bp):
ATGAGCATGAGATTATGTTAAAAAGGAAGACTCGTGACTCGGA
Found at i:32347 original size:44 final size:44
Alignment explanation
Indices: 32284--32372 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
32274 ACATGTTATG
32284 ACTGAATTGGTCTTTGTCCCATCTTCAGTTCCTTGGGGTCTTGA
1 ACTGAATTGGTCTTTGTCCCATCTTCAGTTCCTTGGGGTCTTGA
32328 ACTGAATTGGTCTTTGTCCCATCTTCAGTTCCTTGGGGTCTTGA
1 ACTGAATTGGTCTTTGTCCCATCTTCAGTTCCTTGGGGTCTTGA
32372 A
1 A
32373 TTCAAAGAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.40
Consensus pattern (44 bp):
ACTGAATTGGTCTTTGTCCCATCTTCAGTTCCTTGGGGTCTTGA
Found at i:37123 original size:18 final size:18
Alignment explanation
Indices: 37102--37136 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
37092 AGTATAATAA
* *
37102 AAAAATAAAAGGAAACAT
1 AAAAACAAAAGAAAACAT
37120 AAAAACAAAAGAAAACA
1 AAAAACAAAAGAAAACA
37137 ACCATTCCAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.77, C:0.09, G:0.09, T:0.06
Consensus pattern (18 bp):
AAAAACAAAAGAAAACAT
Found at i:38074 original size:25 final size:25
Alignment explanation
Indices: 38038--38088 Score: 86
Period size: 25 Copynumber: 2.0 Consensus size: 25
38028 ATCCTACTTG
38038 AAATGGTAGTTACGATTTCATATGT
1 AAATGGTAGTTACGATTTCATATGT
38063 AAATAGGT-GTTACGATTTCATATGT
1 AAAT-GGTAGTTACGATTTCATATGT
38088 A
1 A
38089 TATATGCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 22 0.88
26 3 0.12
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AAATGGTAGTTACGATTTCATATGT
Found at i:46815 original size:14 final size:15
Alignment explanation
Indices: 46790--46827 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
46780 GAATTAAAAG
46790 AGAAAGTCATGAGTA
1 AGAAAGTCATGAGTA
*
46805 AGAAA-TCATGAGTG
1 AGAAAGTCATGAGTA
*
46819 ATAAAGTCA
1 AGAAAGTCA
46828 CAAGGTTACC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.47, C:0.08, G:0.24, T:0.21
Consensus pattern (15 bp):
AGAAAGTCATGAGTA
Found at i:51096 original size:17 final size:19
Alignment explanation
Indices: 51074--51110 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
51064 CGGTCGATTT
51074 CAGATA-TTA-ATCATTGA
1 CAGATACTTACATCATTGA
*
51091 CAGATACTTACATGATTGA
1 CAGATACTTACATCATTGA
51110 C
1 C
51111 TACCATCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 3 0.18
19 8 0.47
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (19 bp):
CAGATACTTACATCATTGA
Found at i:54556 original size:16 final size:16
Alignment explanation
Indices: 54535--54567 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
54525 CAGTTCACAT
54535 ACCCAAACTGTAACTC
1 ACCCAAACTGTAACTC
*
54551 ACCCAATCTGTAACTC
1 ACCCAAACTGTAACTC
54567 A
1 A
54568 AAGCTCCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.36, G:0.06, T:0.21
Consensus pattern (16 bp):
ACCCAAACTGTAACTC
Found at i:59043 original size:33 final size:33
Alignment explanation
Indices: 59006--59080 Score: 105
Period size: 33 Copynumber: 2.3 Consensus size: 33
58996 TATGGCATCC
* *
59006 ACAGAGATAGTCTGTTAAGACAATAAACATAGA
1 ACAGAGATAGTCTGCTAAGACAATAAACATAAA
** *
59039 ACAGAGATAGTCTGCTGGGACAGTAAACATAAA
1 ACAGAGATAGTCTGCTAAGACAATAAACATAAA
59072 ACAGAGATA
1 ACAGAGATA
59081 ATTCGCTTGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.47, C:0.13, G:0.21, T:0.19
Consensus pattern (33 bp):
ACAGAGATAGTCTGCTAAGACAATAAACATAAA
Found at i:61820 original size:10 final size:10
Alignment explanation
Indices: 61805--61847 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
61795 TAATAATTTT
61805 TTTTAAAATA
1 TTTTAAAATA
61815 TTTTAAAATTAA
1 TTTTAAAA-T-A
*
61827 TTTAAAAATA
1 TTTTAAAATA
*
61837 TTTTTAAATA
1 TTTTAAAATA
61847 T
1 T
61848 AAAATTATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
10 18 0.64
11 2 0.07
12 8 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
TTTTAAAATA
Found at i:61916 original size:6 final size:6
Alignment explanation
Indices: 61899--61942 Score: 52
Period size: 7 Copynumber: 6.8 Consensus size: 6
61889 TTTCTGCTTT
*
61899 CCTTCT CCTTCC CCTTCCC CCTTCCC CCTTCCC CCTTCC CCTTC
1 CCTTCC CCTTCC CCTT-CC CCTT-CC CCTT-CC CCTTCC CCTTC
61943 TCCATTTTCC
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
6 16 0.44
7 20 0.56
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (6 bp):
CCTTCC
Found at i:61921 original size:7 final size:7
Alignment explanation
Indices: 61905--61939 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
61895 CTTTCCTTCT
61905 CCTT-CC
1 CCTTCCC
61911 CCTTCCC
1 CCTTCCC
61918 CCTTCCC
1 CCTTCCC
61925 CCTTCCC
1 CCTTCCC
61932 CCTTCCC
1 CCTTCCC
61939 C
1 C
61940 TTCTCCATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 4 0.14
7 24 0.86
ACGTcount: A:0.00, C:0.71, G:0.00, T:0.29
Consensus pattern (7 bp):
CCTTCCC
Found at i:62637 original size:6 final size:6
Alignment explanation
Indices: 62626--62687 Score: 52
Period size: 6 Copynumber: 9.8 Consensus size: 6
62616 CCGTAAGGAT
* * * * *
62626 GGAGAA GGAGAA GGAGAA GGGGAA GGGGGAA GGGGGAA GGGGGAA GGGGAA
1 GGAGAA GGAGAA GGAGAA GGAGAA -GGAGAA -GGAGAA -GGAGAA GGAGAA
62677 GGAGAA GGAGA
1 GGAGAA GGAGA
62688 GTAGAAAAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
6 33 0.62
7 20 0.38
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (6 bp):
GGAGAA
Found at i:62656 original size:7 final size:7
Alignment explanation
Indices: 62644--62678 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
62634 AGAAGGAGAA
62644 GGGGAAG
1 GGGGAAG
62651 GGGGAAG
1 GGGGAAG
62658 GGGGAAG
1 GGGGAAG
62665 GGGGAA-
1 GGGGAAG
62671 GGGGAAG
1 GGGGAAG
62678 G
1 G
62679 AGAAGGAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.29, C:0.00, G:0.71, T:0.00
Consensus pattern (7 bp):
GGGGAAG
Found at i:62779 original size:11 final size:11
Alignment explanation
Indices: 62738--62778 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
62728 ATAATTTTAT
*
62738 ATTTAAAAATA
1 ATTTTAAAATA
*
62749 ATTTTAAATTA
1 ATTTTAAAATA
62760 ATTTTAAAAT-
1 ATTTTAAAATA
62770 ATTTTAAAA
1 ATTTTAAAA
62779 AATAATTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATTTTAAAATA
Found at i:64402 original size:48 final size:48
Alignment explanation
Indices: 64364--64455 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
64354 CCATGATATG
* * *
64364 ACTATGTGGTTG-TTATCGGTATTTATGTGGTGGCTTATCCACAATGT
1 ACTATGTGGTCGTTTATAGGCATTTATGTGGTGGCTTATCCACAATGT
* *
64411 ATTATGTGGTCGTTTATAGGCATTTATGTGGTGGCTTGTCCACAA
1 ACTATGTGGTCGTTTATAGGCATTTATGTGGTGGCTTATCCACAA
64456 ATGGTGTGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
47 10 0.26
48 29 0.74
ACGTcount: A:0.20, C:0.13, G:0.26, T:0.41
Consensus pattern (48 bp):
ACTATGTGGTCGTTTATAGGCATTTATGTGGTGGCTTATCCACAATGT
Found at i:65590 original size:16 final size:16
Alignment explanation
Indices: 65569--65606 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
65559 TTATGTCAAT
65569 TTTTATTATTAGATAG
1 TTTTATTATTAGATAG
* *
65585 TTTTATTTTTAGATTG
1 TTTTATTATTAGATAG
65601 TTTTAT
1 TTTTAT
65607 AGCAACTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.11, T:0.66
Consensus pattern (16 bp):
TTTTATTATTAGATAG
Found at i:65632 original size:38 final size:38
Alignment explanation
Indices: 65581--65657 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
65571 TTATTATTAG
*
65581 ATAGTTTTATTTTTAGATTGTTTTATAGCAACTAAGTT
1 ATAGTTTTATTTTTAGATTGCTTTATAGCAACTAAGTT
65619 ATAGTTTTATTTTTAGATTGCTTTATAGCAACTAAGTT
1 ATAGTTTTATTTTTAGATTGCTTTATAGCAACTAAGTT
65657 A
1 A
65658 GCAAAATTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.30, C:0.06, G:0.13, T:0.51
Consensus pattern (38 bp):
ATAGTTTTATTTTTAGATTGCTTTATAGCAACTAAGTT
Found at i:66080 original size:6 final size:6
Alignment explanation
Indices: 66069--66094 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
66059 ATTATTTAAT
66069 AATTTC AATTTC AATTTC AATTTC AA
1 AATTTC AATTTC AATTTC AATTTC AA
66095 AATTCAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (6 bp):
AATTTC
Found at i:66108 original size:14 final size:14
Alignment explanation
Indices: 66091--66117 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
66081 AATTTCAATT
66091 TCAAAATTCAAAAG
1 TCAAAATTCAAAAG
66105 TCAAAATTCAAAA
1 TCAAAATTCAAAA
66118 TATACATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.15, G:0.04, T:0.22
Consensus pattern (14 bp):
TCAAAATTCAAAAG
Found at i:66493 original size:23 final size:24
Alignment explanation
Indices: 66467--66525 Score: 59
Period size: 26 Copynumber: 2.4 Consensus size: 24
66457 TAAATACATA
66467 TAAATTATTATTT-ATTT-TATAAT
1 TAAA-TATTATTTAATTTATATAAT
*
66490 TAAAATATTTTTTAAATTTATATAAT
1 T-AAATATTATTT-AATTTATATAAT
66516 TATAATATTA
1 TA-AATATTA
66526 ATTACATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
23 8 0.28
24 3 0.10
25 5 0.17
26 13 0.45
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TAAATATTATTTAATTTATATAAT
Found at i:66560 original size:31 final size:31
Alignment explanation
Indices: 66501--66560 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
66491 AAAATATTTT
* * *
66501 TTAAATTTATATAATTATAATATTAATTACA
1 TTAAATTTATAAAAATATAATATAAATTACA
* *
66532 TTAATTTTATAAAAATATAATCTAAATTA
1 TTAAATTTATAAAAATATAATATAAATTA
66561 ATATTTTAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (31 bp):
TTAAATTTATAAAAATATAATATAAATTACA
Found at i:68463 original size:18 final size:18
Alignment explanation
Indices: 68414--68466 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
68404 GGAAAACACT
*
68414 TCATGCATTCCATACAAC
1 TCATGCATTCCATGCAAC
* *
68432 TCGTCCACTT-CATGCAAC
1 TCATGCA-TTCCATGCAAC
68450 TCATGCATTCCATGCAA
1 TCATGCATTCCATGCAA
68467 TGTGCTGCAC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
17 2 0.07
18 24 0.86
19 2 0.07
ACGTcount: A:0.28, C:0.34, G:0.09, T:0.28
Consensus pattern (18 bp):
TCATGCATTCCATGCAAC
Found at i:85417 original size:10 final size:11
Alignment explanation
Indices: 85387--85420 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
85377 TAAAATAATA
85387 AATATTATTTT
1 AATATTATTTT
85398 AATATTATTTT
1 AATATTATTTT
*
85409 TAT-TTATTTT
1 AATATTATTTT
85419 AA
1 AA
85421 ATAAAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 8 0.38
11 13 0.62
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
AATATTATTTT
Found at i:85537 original size:647 final size:650
Alignment explanation
Indices: 84221--86261 Score: 1766
Period size: 697 Copynumber: 3.0 Consensus size: 650
84211 AGTATATAAT
* *
84221 AATT-TTATTGGTAATATTGTCAATTGAATTAATATTATAAGTCAACTTGATACCAACTCAAGAA
1 AATTCTTATTGATAATATTGTCAATTGAATTAATATCATAAGTCAACTTGATACCAACTCAAGAA
* * * *
84285 AAATAATAATGATATGATAAATAATTTGAGTGCATTTAATATTTTACTTTTACTCACAATTTAAA
66 AAATAACAATGATATAATAAACAATTTGAGTGCATTTAACATTTTACTTTTACTCACAATTTAAA
*
84350 TTATTTTTATTTTAATTCCATATATATTGTTATTAGTTTCAAATCTCTTTCAGCAGATCGAGTTG
131 TTATTTTTATTTTAATTCCATATATATTGTTATTACTTTCAAATCTCTTTCAGCAGATCGAGTTG
** * ** *
84415 ATCTTACATGGATTGATTTAGATTAGATTAATAAGATTTCAATTTCGTATTTGAGTCATTTTTAT
196 ATCTTACATGGATCAATTTAGATTAGATTAATAAGATTTCAATTTCGCATTCAAGTCATTTTTAA
* * * *** *
84480 TTTATGTTCGTTTTGCGATAAATGATTTTGGATTTGAGTCATTTTATATTTGAAGATTGAATTTT
261 TTTATGTCCGCTTTGCGATAAATGATTTTGAAACCGAGTCATTTTATATTTGAAGATTAAATTTT
*
84545 TCAGAAAAATTTGTTTTGGGTTAGTCATTCATATTTAACTATTTAGGATTAAATTAATATATTGA
326 TCAGAAAAATTTATTTTGGGTTAGTCATTCATATTTAACTATTTAGGATTAAATTAATATATTGA
* * * * * *
84610 TTATTTTATTTTGAATTTCATTCTTTTCGATTTATTTGTATTGTACATAAAGATTCTGATTGAGT
391 -GA-TTTATTTTGAATTTCATTCTTTTAGATTTATCTATATTATACATAAAGATTCAGATTGAGT
* *
84675 TGGTCTTACCCATAATAGGGTTTTAGTTATTAAAATATTAAAATGCTCTTATTTTAACGAAGTAA
454 TGGACTTACCCATAATAGGGTCTTAG---TT---ATATTAAAA-----TTA-TTTAAC-AAGTAA
*
84740 TAAATGTTAATTTAAGAGTATTTTTATTTTTAAAATAAAATCTAGAAAAAAAAATCCATGCTTAC
506 TAAATATTAATTTAAGAGTATTTTTATTTTTAAAATAAAATCTAGAAAAAAAAATCCATGCTTAC
* *
84805 GATGGGTTGAACCCAAAACACCGAACATATACTCTTACAATTTTGTCATTTCAATTAATATAACA
571 GATGGGTTAAACCCAAAACACCGAACATATACTCTTACAATTTTGTCATTTCAACTAATATAACA
84870 TTTGGTTGTTAAGTG
636 TTTGGTTGTTAAGTG
* * *
84885 AATTCTTATTGATAATATTGTCAATTGAGTTAATATCATAAGTCAATTTGATACCAACTTAAGAA
1 AATTCTTATTGATAATATTGTCAATTGAATTAATATCATAAGTCAACTTGATACCAACTCAAGAA
* *
84950 AAATAACAATGCTATAATAAACAA-TTGAAGTGCATTTAACATTATTATTTTTACTCACAATTTA
66 AAATAACAATGATATAATAAACAATTTG-AGTGCATTTAACATT-TTACTTTTACTCACAATTTA
* * * *
85014 AATTATTTTTTATTTTAATTCCGTATTTATTGTTATTACTTTCAAATCTCTTTCGGGAGATCGAG
129 AATTA-TTTTTATTTTAATTCCATATATATTGTTATTACTTTCAAATCTCTTTCAGCAGATCGAG
* * * *
85079 TTGTTCTTACATGGATCAATTTAGATTGGATTAATACGATTTCAATTTTGCATTCAAGTCATTTT
193 TTGATCTTACATGGATCAATTTAGATTAGATTAATAAGATTTCAATTTCGCATTCAAGTCATTTT
* ** * *
85144 TAATTTATGTCCGCTTTGGGATCGATGATTTTGAAACCGAGTCATTTTATCTTTGAGGATTAAAT
258 TAATTTATGTCCGCTTTGCGATAAATGATTTTGAAACCGAGTCATTTTATATTTGAAGATTAAAT
** * * * * *
85209 TTTTTGGATAAGTTTATTTTGGGTTATGGTCATTTATGTTTAACTATTTAGGATTAATTTTAATA
323 TTTTCAGAAAAATTTATTTTGGGTTA--GTCATTCATATTTAACTATTTAGGATTAA-ATTAATA
* *
85274 TA-TG-GA-TTATTTTGAATTTCATTCTTTTATATTTATCTATATTATATA-AAAGATTCAGATT
385 TATTGAGATTTATTTTGAATTTCATTCTTTTAGATTTATCTATATTATACATAAAGATTCAGATT
* *
85335 GAGTTGGAGTTACCCATAATCGGGTCTTAG-T-TATTAAAA-TA-TTAA-AA-TAATAAATATTA
450 GAGTTGGACTTACCCATAATAGGGTCTTAGTTATATTAAAATTATTTAACAAGTAATAAATATTA
* * * * * * *
85394 TTTTAATATTATTTTTATTTATTTTAAATAAAATTTAGAAAAAAAAATTCATGCTTATGATGGGT
515 ATTTAAGAGTATTTTTA-TT-TTTAAAATAAAATCTAGAAAAAAAAATCCATGCTTACGATGGGT
** * * * * * * * *
85459 TAAACTGAAAACACTGAACATGTATTTTTTCATTTTTGTCATTTCAACTAATATGATATTTGGTT
578 TAAACCCAAAACACCGAACATATACTCTTACAATTTTGTCATTTCAACTAATATAACATTTGGTT
85524 GTTAAGTG
643 GTTAAGTG
* * *
85532 AATTCTTAATAAATATATATAATTATTTTCACTCACATCGTGAATATGTCATAATCTTATTGGTA
1 AATTC-T--T--AT-T-GATAA-TA--TT--GTCA-AT--TG-A-AT-TAAT-ATC--A----TA
* * * **
85597 ATGTTGTCAA-TTAAGTTAATATCATAAGTTAACTCGATAACAACTCAA-AAAAATAATAATGCT
41 A----GTCAACTT--G---ATA-C-CAACTCAA---GA-AA-AA-T-AACAATGAT-ATAA---T
* * * * *
85660 ATTATAAACAATTTGAGTGCATTAAATATTATTACTTTTACTCACAATTTAAATTATTTTTTATT
84 A--A-ACA-ATTTG-AGTGCATTTAACATT-TTACTTTTACTCACAATTTAAATTA-TTTTTATT
* ** * * *
85725 TTAATTCCGTATATATTGTTATTGGTTTCAAATCTCATTC-GATAGATCGGGTTGATCTTACATG
142 TTAATTCCATATATATTGTTATTACTTTCAAATCTCTTTCAG-CAGATCGAGTTGATCTTACATG
* * * *
85789 GATCAATTTAGA-TCGAATTAATAAGATTTCAATTTTGTATT-AGAGTCATTTTTAATTTATGTT
206 GATCAATTTAGATTAG-ATTAATAAGATTTCAATTTCGCATTCA-AGTCATTTTTAATTTATGTC
* * * * * * ** ** * *
85852 CGTTTTGGGGTCATTGATTTTGGATTCGAGTCATTAAATATTTGAGGATTGAATTTTTC-GAATA
269 CGCTTTGCGATAAATGATTTTGAAACCGAGTCATTTTATATTTGAAGATTAAATTTTTCAGAA-A
* * * * * *
85916 AATTTGTTTTGGGTTATAGTCATTCATATTTAACTATTTTGGATTAATTTTATATATGGATTATT
333 AATTTATTTTGGG-T-TAGTCATTCATATTTAACTATTTAGGATTAAATTAATATATTGA-GA-T
* * * * **
85981 TTATTTTGAATTTCATTCTTTTAGATTTATTTATATTGTATATAAATATTTTGATTGAGTT-GAC
394 TTATTTTGAATTTCATTCTTTTAGATTTATCTATATTATACATAAAGATTCAGATTGAGTTGGA-
* * *
86045 CTTACCCAAAATCGGAAT-TTAGTTATTAAAATATTAAAATGCTCTTATTTTAACAAAGTAATAA
458 CTTACCCATAATAGG-GTCTTAG---TT---ATATTAAAA-----TTA-TTTAAC-AAGTAATAA
* * * * *
86109 ATGTTAATTTAAGTA-TATTTTTATCATTTTTTAAATAAAATCTTGAAAAAAGAATTCATGCTTA
509 ATATTAATTTAAG-AGTA-TTTT-T-ATTTTTAAAATAAAATCTAGAAAAAAAAATCCATGCTTA
* * * *
86173 CTATGGGTTGAACCCAAAACACCGAACATATACTCTTCCAACTTTGTCATTTCAACTAATATAAC
570 CGATGGGTTAAACCCAAAACACCGAACATATACTCTTACAATTTTGTCATTTCAACTAATATAAC
86238 ATTTGGTTGTTAAGTG
635 ATTTGGTTGTTAAGTG
86254 AATTCTTA
1 AATTCTTA
86262 GTAAATATTA
Statistics
Matches: 1125, Mismatches: 154, Indels: 143
0.79 0.11 0.10
Matches are distributed among these distances:
645 25 0.02
646 4 0.00
647 106 0.09
648 5 0.00
650 3 0.00
652 2 0.00
653 1 0.00
654 4 0.00
655 2 0.00
656 8 0.01
657 2 0.00
659 3 0.00
660 3 0.00
662 2 0.00
663 1 0.00
664 46 0.04
665 128 0.11
666 27 0.02
667 184 0.16
668 1 0.00
669 29 0.03
670 8 0.01
672 3 0.00
675 2 0.00
676 5 0.00
677 1 0.00
680 3 0.00
681 1 0.00
682 6 0.01
685 2 0.00
686 2 0.00
687 2 0.00
688 4 0.00
689 6 0.01
692 2 0.00
694 1 0.00
695 2 0.00
696 15 0.01
697 244 0.22
698 1 0.00
699 3 0.00
701 41 0.04
702 32 0.03
703 1 0.00
706 1 0.00
710 8 0.01
716 2 0.00
717 1 0.00
718 4 0.00
719 1 0.00
720 2 0.00
721 19 0.02
722 110 0.10
723 3 0.00
724 1 0.00
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (650 bp):
AATTCTTATTGATAATATTGTCAATTGAATTAATATCATAAGTCAACTTGATACCAACTCAAGAA
AAATAACAATGATATAATAAACAATTTGAGTGCATTTAACATTTTACTTTTACTCACAATTTAAA
TTATTTTTATTTTAATTCCATATATATTGTTATTACTTTCAAATCTCTTTCAGCAGATCGAGTTG
ATCTTACATGGATCAATTTAGATTAGATTAATAAGATTTCAATTTCGCATTCAAGTCATTTTTAA
TTTATGTCCGCTTTGCGATAAATGATTTTGAAACCGAGTCATTTTATATTTGAAGATTAAATTTT
TCAGAAAAATTTATTTTGGGTTAGTCATTCATATTTAACTATTTAGGATTAAATTAATATATTGA
GATTTATTTTGAATTTCATTCTTTTAGATTTATCTATATTATACATAAAGATTCAGATTGAGTTG
GACTTACCCATAATAGGGTCTTAGTTATATTAAAATTATTTAACAAGTAATAAATATTAATTTAA
GAGTATTTTTATTTTTAAAATAAAATCTAGAAAAAAAAATCCATGCTTACGATGGGTTAAACCCA
AAACACCGAACATATACTCTTACAATTTTGTCATTTCAACTAATATAACATTTGGTTGTTAAGTG
Found at i:87425 original size:27 final size:25
Alignment explanation
Indices: 87383--87432 Score: 73
Period size: 27 Copynumber: 1.9 Consensus size: 25
87373 ATTTAAACTA
*
87383 TTTTTTATTTTAATTTCATATATAT
1 TTTTTTATTTTAATTTCAAATATAT
87408 TTTTATTATTATTAATTTCAAATAT
1 TTTT-TTATT-TTAATTTCAAATAT
87433 TACATTTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 4 0.18
26 5 0.23
27 13 0.59
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (25 bp):
TTTTTTATTTTAATTTCAAATATAT
Found at i:87444 original size:29 final size:26
Alignment explanation
Indices: 87387--87447 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 26
87377 AAACTATTTT
* * *
87387 TTATTTTAATTTCATATATATTTTTA
1 TTATTTTAATTTCAAATATAATTTGA
87413 TTATTATTAATTTCAAATATTACATTTGA
1 TTATT-TTAATTTCAAATA-TA-ATTTGA
87442 TTATTT
1 TTATTT
87448 ATTGTATGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 5 0.17
27 12 0.41
28 3 0.10
29 9 0.31
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.61
Consensus pattern (26 bp):
TTATTTTAATTTCAAATATAATTTGA
Found at i:88904 original size:147 final size:147
Alignment explanation
Indices: 88637--88930 Score: 579
Period size: 147 Copynumber: 2.0 Consensus size: 147
88627 TTATAGTTTA
88637 ACTTAAATAATATATGTTATATGAAAGAGAAAACAAATAATATTAAAAAAATATCAATTCAAAAA
1 ACTTAAATAATATATGTTATATGAAAGAGAAAACAAATAATATTAAAAAAATATCAATTCAAAAA
88702 TAACTCAAAACCTTCATCAACTTAAATGATGGTAATTCTAATATAATTCTTACCTCGATGTGTTT
66 TAACTCAAAACCTTCATCAACTTAAATGATGGTAATTCTAATATAATTCTTACCTCGATGTGTTT
88767 ATGCAATGCAATTAATG
131 ATGCAATGCAATTAATG
88784 ACTTAAATAATATATGTTATATGAAAGAGAAAACAAATAATATTAAAAAAATATCAATTCAAAAA
1 ACTTAAATAATATATGTTATATGAAAGAGAAAACAAATAATATTAAAAAAATATCAATTCAAAAA
*
88849 TAACTCAAAACTTTCATCAACTTAAATGATGGTAATTCTAATATAATTCTTACCTCGATGTGTTT
66 TAACTCAAAACCTTCATCAACTTAAATGATGGTAATTCTAATATAATTCTTACCTCGATGTGTTT
88914 ATGCAATGCAATTAATG
131 ATGCAATGCAATTAATG
88931 GTGGTGATTC
Statistics
Matches: 146, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
147 146 1.00
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (147 bp):
ACTTAAATAATATATGTTATATGAAAGAGAAAACAAATAATATTAAAAAAATATCAATTCAAAAA
TAACTCAAAACCTTCATCAACTTAAATGATGGTAATTCTAATATAATTCTTACCTCGATGTGTTT
ATGCAATGCAATTAATG
Found at i:91418 original size:50 final size:51
Alignment explanation
Indices: 91233--91410 Score: 225
Period size: 51 Copynumber: 3.5 Consensus size: 51
91223 CTGTATAGGA
* * * * *
91233 ATTCATATACTCACGATGACACTAAGTTATCGGACCTTTAATTCGTCATGG
1 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATTCCTCAAGG
* * *
91284 ATTCATTTACTCAAGATGACACATAGTCATCGGACCTTTAA-TCCGCAAGG
1 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATTCCTCAAGG
* * *
91334 ATTCATTTACTCACGATGACATTTAGTCATCGGACCTTTAATTCTTAAAGG
1 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATTCCTCAAGG
* *
91385 ATCCATTTACTTACGATGAC-CTTAGT
1 ATTCATTTACTCACGATGACACTTAGT
91411 TTTCGGACTC
Statistics
Matches: 109, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
50 49 0.45
51 60 0.55
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.34
Consensus pattern (51 bp):
ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATTCCTCAAGG
Found at i:98573 original size:51 final size:51
Alignment explanation
Indices: 98452--98691 Score: 302
Period size: 51 Copynumber: 4.6 Consensus size: 51
98442 TTTCATTTAA
* ** * *
98452 TACTCACGATGACA-TATAGTCATCGAACCCCTTTGTTCCGTATAGGAATTCATA
1 TACTCACGATGACACT-TAGTCATCGGA--CCTTTAATCCGTAAAGG-ATTCATT
* * *
98506 TACTCACGATGACACTTAGTCATTGGACCTTTAATCTGTAAAAGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
** * *
98557 TACTCATTATGTCACTTAGTCATCCGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* *
98608 TACTCACGATGACACTTAGTCATTGGACCTTTAATCCGTAAGGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
98659 TACTCACGATGACACTTAGTCATCGGACTCTTT
1 TACTCACGATGACACTTAGTCATCGGAC-CTTT
98692 TGTTTATAGC
Statistics
Matches: 162, Mismatches: 22, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
51 122 0.75
52 16 0.10
54 23 0.14
55 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
Found at i:101055 original size:16 final size:14
Alignment explanation
Indices: 101043--101073 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
101033 ATATTCTCTA
101043 TTCTTTTTTTTCTT
1 TTCTTTTTTTTCTT
101057 TTCTTTTTTTT-TT
1 TTCTTTTTTTTCTT
101070 TTCT
1 TTCT
101074 GAGCATCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (14 bp):
TTCTTTTTTTTCTT
Found at i:102397 original size:30 final size:30
Alignment explanation
Indices: 102363--102427 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
102353 CACCGAAAGA
* *
102363 TCTTCTTCAATTTCCACAGGATCTTCTTCT
1 TCTTCTTCAACTTCCACAGGATCTTCGTCT
* **
102393 TCTTCTTCTACTTCTTCAGGATCTTCGTCT
1 TCTTCTTCAACTTCCACAGGATCTTCGTCT
102423 TCTTC
1 TCTTC
102428 AGCTTGCTGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.12, C:0.31, G:0.08, T:0.49
Consensus pattern (30 bp):
TCTTCTTCAACTTCCACAGGATCTTCGTCT
Found at i:103338 original size:8 final size:7
Alignment explanation
Indices: 103324--103374 Score: 50
Period size: 7 Copynumber: 6.7 Consensus size: 7
103314 AATTTAAAAT
103324 AAATTAA
1 AAATTAA
103331 AAAGTTAA
1 AAA-TTAA
103339 TAAATTAAA
1 -AAATT-AA
103348 TAAATTAA
1 -AAATTAA
103356 AAATTAGA
1 AAATTA-A
103364 AAA-TAA
1 AAATTAA
103370 AAATT
1 AAATT
103375 CTTACCACCT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
6 4 0.10
7 12 0.31
8 12 0.31
9 11 0.28
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (7 bp):
AAATTAA
Found at i:103338 original size:26 final size:25
Alignment explanation
Indices: 103309--103358 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
103299 GTATAAAATA
*
103309 TTAACAATTTAAAATAAATTAAAAAG
1 TTAACAAATT-AAATAAATTAAAAAG
*
103335 TTAATAAATTAAATAAATTAAAAA
1 TTAACAAATTAAATAAATTAAAAA
103359 TTAGAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (25 bp):
TTAACAAATTAAATAAATTAAAAAG
Found at i:103340 original size:16 final size:16
Alignment explanation
Indices: 103321--103367 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
103311 AACAATTTAA
*
103321 AATAAATTAAAAAGTT
1 AATAAATTAAAAAATT
103337 AATAAATTAAATAAATT
1 AATAAATTAAA-AAATT
*
103354 AA-AAATTAGAAAAT
1 AATAAATTAAAAAAT
103368 AAAAATTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 4 0.14
16 18 0.64
17 6 0.21
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (16 bp):
AATAAATTAAAAAATT
Found at i:103351 original size:9 final size:9
Alignment explanation
Indices: 103320--103356 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
103310 TAACAATTTA
103320 AAATAAATT
1 AAATAAATT
*
103329 AAA-AAGTT
1 AAATAAATT
103337 -AATAAATT
1 AAATAAATT
103345 AAATAAATT
1 AAATAAATT
103354 AAA
1 AAA
103357 AATTAGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
7 2 0.08
8 8 0.33
9 14 0.58
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (9 bp):
AAATAAATT
Found at i:103373 original size:25 final size:25
Alignment explanation
Indices: 103318--103371 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
103308 ATTAACAATT
103318 TAAAATAAATTAAAAAGTTAATAAA
1 TAAAATAAATTAAAAAGTTAATAAA
*
103343 TTAAATAAATTAAAAA-TTAGA-AAA
1 TAAAATAAATTAAAAAGTTA-ATAAA
103367 TAAAA
1 TAAAA
103372 ATTCTTACCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 10 0.38
25 16 0.62
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.28
Consensus pattern (25 bp):
TAAAATAAATTAAAAAGTTAATAAA
Found at i:110273 original size:5 final size:5
Alignment explanation
Indices: 110263--110352 Score: 123
Period size: 5 Copynumber: 18.4 Consensus size: 5
110253 TGCTATTTGG
*
110263 AAGAA AAGAA ACA-AA AAGAA AA-AA AAGAA AA-AA AAGAA ATGAA AAGAA
1 AAGAA AAGAA A-AGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA
* *
110311 ACGAA ACGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AA
110353 ATATCATATT
Statistics
Matches: 77, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
4 9 0.12
5 67 0.87
6 1 0.01
ACGTcount: A:0.79, C:0.03, G:0.17, T:0.01
Consensus pattern (5 bp):
AAGAA
Found at i:123732 original size:108 final size:111
Alignment explanation
Indices: 123610--123815 Score: 337
Period size: 108 Copynumber: 1.9 Consensus size: 111
123600 CGAAAACAAA
* *
123610 GAACATTTATCGATTTTAAATAGGATATTCAATTATTTAGGTTC-AAG-AAAAAAA-CATACCCA
1 GAACATTCATCGATTTTAAATAGGATACTCAATTATTTAGGTTCAAAGAAAAAAAATCATACCCA
* *
123672 ACACGTTAGGGCACAATTTCTCGAGTTCCCTAAGCAACAGAACATC
66 ACACGTTAGAGCACAATTTCTCGAATTCCCTAAGCAACAGAACATC
123718 GAACATTCATCGATTTTAAATAGGATACTCAATTATTTAGGTTCAAAGAAAAAAAATCATACCCA
1 GAACATTCATCGATTTTAAATAGGATACTCAATTATTTAGGTTCAAAGAAAAAAAATCATACCCA
* *
123783 ACACGTTAGAGCATAATTTCTTGAATTCCCTAA
66 ACACGTTAGAGCACAATTTCTCGAATTCCCTAA
123816 ATAAAATAGC
Statistics
Matches: 89, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
108 42 0.47
109 3 0.03
110 7 0.08
111 37 0.42
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (111 bp):
GAACATTCATCGATTTTAAATAGGATACTCAATTATTTAGGTTCAAAGAAAAAAAATCATACCCA
ACACGTTAGAGCACAATTTCTCGAATTCCCTAAGCAACAGAACATC
Found at i:124074 original size:3 final size:3
Alignment explanation
Indices: 124060--124089 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
124050 ACGTTGGTAT
*
124060 TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
124090 CACAAAATGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:126546 original size:45 final size:45
Alignment explanation
Indices: 126090--126536 Score: 520
Period size: 45 Copynumber: 9.9 Consensus size: 45
126080 GCTTCTATGA
* * *
126090 GATGGTAGCTTTAATCTGCCCCTCTTGATTTAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGA-CTAGGGGTAAAAGATTG
* * * * * *
126136 GATAGTTGCTT-AATTTGCCCTTCTTGATTAAGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGACTAGGGGTAAAAGATTG
* * * ** *
126180 GATGATAGCTTCAATCCGCCCCTCTTGGTTAGAGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGACTAGGGGTAAAAGATTG
* *
126225 GATGGTGGCTTCAATTTGCCCCTCTTGACTAAGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGACTAGGGGTAAAAGATTG
* * * *
126270 GATGGTGTCATCAATTTGCCCCTCTT-AGTTAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGA-CTAGGGGTAAAAGATTG
** * * *
126315 GATGGTATCTTCAATCTACCCTTCTTGACTAGGGATAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGACTAGGGGTAAAAGATTG
* * *
126360 GATGATGACTTTAATCTGCCCCTCTTGACTAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGACTAGGGGTAAAAGATTG
* * *
126405 GACGGTGGTTTCAATCTGCCCCTCTTGACTAGGGGTAAATGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGACTAGGGGTAAAAGATTG
* * *
126450 GACGGTGGCTTCAATCTGCTCCACTTGACTAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGACTAGGGGTAAAAGATTG
* * *
126495 GACGGTGGCTTCAGTCTGCCCCTCTTGACTATGGGTAAAAGA
1 GATGGTGGCTTCAATCTGCCCCTCTTGACTAGGGGTAAAAGA
126537 CTGAACGGTG
Statistics
Matches: 344, Mismatches: 54, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
44 25 0.07
45 309 0.90
46 10 0.03
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.32
Consensus pattern (45 bp):
GATGGTGGCTTCAATCTGCCCCTCTTGACTAGGGGTAAAAGATTG
Found at i:127627 original size:7 final size:7
Alignment explanation
Indices: 127615--127668 Score: 54
Period size: 7 Copynumber: 7.4 Consensus size: 7
127605 CGACCACTCC
127615 TTTTTCT
1 TTTTTCT
127622 TTTTTCT
1 TTTTTCT
127629 TTTTTCT
1 TTTTTCT
* *
127636 TTATTAT
1 TTTTTCT
*
127643 TATTTTTT
1 T-TTTTCT
127651 TCTTTTCT
1 T-TTTTCT
*
127659 TCTTTCT
1 TTTTTCT
127666 TTT
1 TTT
127669 CTTTTAGGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
7 27 0.71
8 11 0.29
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTTCT
Found at i:133281 original size:18 final size:19
Alignment explanation
Indices: 133240--133289 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
133230 GTAGTAACGT
133240 AAAATGATAAA-TAAAATAC
1 AAAA-GATAAAGTAAAATAC
* *
133259 GAAAGCTAAAGTAAAA-AC
1 AAAAGATAAAGTAAAATAC
133277 AAAAGATAAAGTA
1 AAAAGATAAAGTA
133290 CTAAAATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 18 0.69
19 8 0.31
ACGTcount: A:0.66, C:0.06, G:0.12, T:0.16
Consensus pattern (19 bp):
AAAAGATAAAGTAAAATAC
Found at i:138795 original size:22 final size:22
Alignment explanation
Indices: 138757--138804 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 22
138747 TTTCTTACTC
138757 TTTCTTTTTAAGTTTTT-ACTCAT
1 TTTCTTTTT-AGTTTTTCACT-AT
138780 TTTCTTTTT-GTATTTTCACTAT
1 TTTCTTTTTAGT-TTTTCACTAT
138802 TTT
1 TTT
138805 TCTCTTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
21 2 0.09
22 9 0.39
23 12 0.52
ACGTcount: A:0.15, C:0.12, G:0.04, T:0.69
Consensus pattern (22 bp):
TTTCTTTTTAGTTTTTCACTAT
Found at i:139706 original size:18 final size:16
Alignment explanation
Indices: 139685--139723 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
139675 CCAAAAATTA
139685 AAAGTCTTCAAATAAATC
1 AAAGTCTT-AAA-AAATC
*
139703 AAAGTCTTAAAAAATT
1 AAAGTCTTAAAAAATC
139719 AAAGT
1 AAAGT
139724 TCAATCTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
17 3 0.15
18 8 0.40
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (16 bp):
AAAGTCTTAAAAAATC
Found at i:150152 original size:31 final size:30
Alignment explanation
Indices: 150085--150153 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 30
150075 ACGATAACGC
*
150085 AAGTGACTAAAACGTAACATTTCAAACTTA
1 AAGTGACTAAAACGTAACATTTCAAACTAA
*
150115 AA-TGACTAAAATGTAAC-TTGAGTCAAAC-AA
1 AAGTGACTAAAACGTAACATT---TCAAACTAA
150145 AAGTGACTA
1 AAGTGACTA
150154 TTTTAATAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
28 2 0.06
29 14 0.42
30 5 0.15
31 12 0.36
ACGTcount: A:0.48, C:0.14, G:0.13, T:0.25
Consensus pattern (30 bp):
AAGTGACTAAAACGTAACATTTCAAACTAA
Found at i:150428 original size:12 final size:13
Alignment explanation
Indices: 150392--150434 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
150382 TAAATATTAG
150392 TTTTTCATTTTACA
1 TTTTT-ATTTTACA
* *
150406 TTTCTAATTTA-A
1 TTTTTATTTTACA
150418 TTTTTATTTTACA
1 TTTTTATTTTACA
150431 TTTT
1 TTTT
150435 ACATATAGAC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
12 10 0.42
13 10 0.42
14 4 0.17
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTTTATTTTACA
Found at i:152446 original size:39 final size:39
Alignment explanation
Indices: 152392--152652 Score: 290
Period size: 39 Copynumber: 6.7 Consensus size: 39
152382 AATCTGAACA
* * * * *
152392 TAAACTGGTAGTGACAGTGTAAACACTGAAATACTATAC
1 TAAATTGGCAGTGACACTGTAAACACTGCAATGCTATAC
* * * *
152431 TAAACTGGCAATGACACTGTAAATACTGCAATGCTATAT
1 TAAATTGGCAGTGACACTGTAAACACTGCAATGCTATAC
* * *
152470 TGAATTGGCAGTGACATTGTAAAAACTGCAATGCTATAC
1 TAAATTGGCAGTGACACTGTAAACACTGCAATGCTATAC
* * *
152509 TGAATTGACAGTGACACTGTAAACACTGCAATGCTATAT
1 TAAATTGGCAGTGACACTGTAAACACTGCAATGCTATAC
*
152548 TAAATTGGCAGTGACACTGTAAACACTACAATGCTATAC
1 TAAATTGGCAGTGACACTGTAAACACTGCAATGCTATAC
* * * *
152587 TGAATTAGC-GATGACACTGTAAACACTTCAAAGCTATAC
1 TAAATTGGCAG-TGACACTGTAAACACTGCAATGCTATAC
* * * *
152626 TGAAGTGGTAGTGGCACTGTAAACACT
1 TAAATTGGCAGTGACACTGTAAACACT
152653 ACTAGGTTAT
Statistics
Matches: 191, Mismatches: 29, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
38 1 0.01
39 189 0.99
40 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (39 bp):
TAAATTGGCAGTGACACTGTAAACACTGCAATGCTATAC
Found at i:152608 original size:117 final size:117
Alignment explanation
Indices: 152401--152652 Score: 326
Period size: 117 Copynumber: 2.2 Consensus size: 117
152391 ATAAACTGGT
* * *
152401 AGTGACAGTGTAAACACTGAAATACTATACTAAACTGGCAATGACACTGTAAATACTGCAATGCT
1 AGTGACACTGTAAACACTGAAATACTATACTAAACTGGCAATGACACTGTAAACACTACAATGCT
* * * * *
152466 ATATTGAATTGGCAGTGACATTGTAAAAACTGCAATGCTATACTGAATTGAC
66 ATACTGAATTAGCAGTGACACTGTAAAAACTGCAAAGCTATACTGAAGTGAC
* * * * *
152518 AGTGACACTGTAAACACTGCAATGCTATATTAAATTGGCAGTGACACTGTAAACACTACAATGCT
1 AGTGACACTGTAAACACTGAAATACTATACTAAACTGGCAATGACACTGTAAACACTACAATGCT
* * **
152583 ATACTGAATTAGC-GATGACACTGTAAACACTTCAAAGCTATACTGAAGTGGT
66 ATACTGAATTAGCAG-TGACACTGTAAAAACTGCAAAGCTATACTGAAGTGAC
*
152635 AGTGGCACTGTAAACACT
1 AGTGACACTGTAAACACT
152653 ACTAGGTTAT
Statistics
Matches: 116, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
116 1 0.01
117 115 0.99
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (117 bp):
AGTGACACTGTAAACACTGAAATACTATACTAAACTGGCAATGACACTGTAAACACTACAATGCT
ATACTGAATTAGCAGTGACACTGTAAAAACTGCAAAGCTATACTGAAGTGAC
Found at i:155524 original size:47 final size:47
Alignment explanation
Indices: 155472--155568 Score: 133
Period size: 47 Copynumber: 2.1 Consensus size: 47
155462 ACCTCTCCAC
* * *
155472 TATGTTGGTGTGC-AGGTGGTTAGGTGCTTTGCATTATGCTTGTGTTG
1 TATGTTAGTGTGCTA-GTGATTAGGTGCATTGCATTATGCTTGTGTTG
* *
155519 TATGTTAGTGTGCTAGTGATTGGGTGCATTGCTTTATGCTTGTGTTG
1 TATGTTAGTGTGCTAGTGATTAGGTGCATTGCATTATGCTTGTGTTG
155566 TAT
1 TAT
155569 TGCATTAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
47 43 0.98
48 1 0.02
ACGTcount: A:0.12, C:0.08, G:0.33, T:0.46
Consensus pattern (47 bp):
TATGTTAGTGTGCTAGTGATTAGGTGCATTGCATTATGCTTGTGTTG
Found at i:168914 original size:46 final size:46
Alignment explanation
Indices: 168847--168941 Score: 181
Period size: 46 Copynumber: 2.1 Consensus size: 46
168837 GAAAAAAGTC
168847 AAGAAGGGTGAAGGAGGGATGGGAAATTCATTAGAGGTGGTTTAGG
1 AAGAAGGGTGAAGGAGGGATGGGAAATTCATTAGAGGTGGTTTAGG
*
168893 AAGAAGGGTGAAGGAGTGATGGGAAATTCATTAGAGGTGGTTTAGG
1 AAGAAGGGTGAAGGAGGGATGGGAAATTCATTAGAGGTGGTTTAGG
168939 AAG
1 AAG
168942 CACTTTCTCA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.34, C:0.02, G:0.42, T:0.22
Consensus pattern (46 bp):
AAGAAGGGTGAAGGAGGGATGGGAAATTCATTAGAGGTGGTTTAGG
Found at i:175422 original size:3 final size:3
Alignment explanation
Indices: 175366--175409 Score: 79
Period size: 3 Copynumber: 14.3 Consensus size: 3
175356 CCTTTTTTTA
175366 ATT ATTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
175410 AAACAATATT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:176001 original size:22 final size:22
Alignment explanation
Indices: 175973--176017 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
175963 TTATTGTTTA
* *
175973 TAAGTTAAGTTATTTGCTTGTT
1 TAAGTTAAATTATTTACTTGTT
175995 TAAGTTAAATTATTTACTTGTT
1 TAAGTTAAATTATTTACTTGTT
176017 T
1 T
176018 TACATGGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.04, G:0.13, T:0.56
Consensus pattern (22 bp):
TAAGTTAAATTATTTACTTGTT
Done.