Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167895.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_161, 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: 62012
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:2490 original size:17 final size:17
Alignment explanation
Indices: 2465--2511 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
2455 CACAAACTCA
*
2465 ATTTCATTACACTTTAT
1 ATTTCATTACAATTTAT
*
2482 ATTTTATTACAATTTAT
1 ATTTCATTACAATTTAT
*
2499 -TTTACTTTACAAT
1 ATTT-CATTACAAT
2512 GCATTTAGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 3 0.12
17 22 0.88
ACGTcount: A:0.32, C:0.13, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTCATTACAATTTAT
Found at i:5283 original size:24 final size:24
Alignment explanation
Indices: 5256--5304 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
5246 GGTTTTTATA
5256 GAACCAGATTTCTGATAGGAGCAT
1 GAACCAGATTTCTGATAGGAGCAT
5280 GAACCAGATTTCTGATAGGAGCAT
1 GAACCAGATTTCTGATAGGAGCAT
5304 G
1 G
5305 GGAATTGGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (24 bp):
GAACCAGATTTCTGATAGGAGCAT
Found at i:6910 original size:65 final size:65
Alignment explanation
Indices: 6784--6913 Score: 156
Period size: 65 Copynumber: 2.0 Consensus size: 65
6774 TGGGTTCAAA
* ** *
6784 ATCTTAGTGCCAACTAGATTGGACTTAAAATTTCATCTAACGTGAACTCAGATAGGTTTAAAAAG
1 ATCTCAGTGCCAACTAGATTGGACTTAAAATTTCATCTAACGCCAACTCAGATAGGCTTAAAAAG
* * * *
6849 ATCTCAGTGCCAACTAGGTT-GAGCTTAAAATTTCATCTAATGCCAACTTA-ATTGGACTTAAAA
1 ATCTCAGTGCCAACTAGATTGGA-CTTAAAATTTCATCTAACGCCAACTCAGATAGG-CTTAAAA
6912 AG
64 AG
6914 TTTTGATGCC
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
64 6 0.11
65 49 0.89
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (65 bp):
ATCTCAGTGCCAACTAGATTGGACTTAAAATTTCATCTAACGCCAACTCAGATAGGCTTAAAAAG
Found at i:7125 original size:20 final size:20
Alignment explanation
Indices: 7097--7135 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
7087 ATCTCATCCT
*
7097 AAAAGTCTCATCATTTTTTC
1 AAAAGTCTCAACATTTTTTC
*
7117 AAAATTCTCAACATTTTTT
1 AAAAGTCTCAACATTTTTT
7136 TTTTAGAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.18, G:0.03, T:0.46
Consensus pattern (20 bp):
AAAAGTCTCAACATTTTTTC
Found at i:7271 original size:16 final size:16
Alignment explanation
Indices: 7252--7293 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
7242 ATATTGGTAT
7252 TTTTTTCTTTCTTTTC
1 TTTTTTCTTTCTTTTC
* *
7268 TTTTTTTTTTCTTTTG
1 TTTTTTCTTTCTTTTC
7284 TTTTTCTCTT
1 TTTTT-TCTT
7294 GATAGACTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 19 0.86
17 3 0.14
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.83
Consensus pattern (16 bp):
TTTTTTCTTTCTTTTC
Found at i:7282 original size:9 final size:9
Alignment explanation
Indices: 7222--7275 Score: 54
Period size: 9 Copynumber: 5.9 Consensus size: 9
7212 TTGGACTAAT
7222 TTTTTTTTC
1 TTTTTTTTC
7231 TTTTTTTTC
1 TTTTTTTTC
* * **
7240 TTATATTGG
1 TTTTTTTTC
7249 TATTTTTTTC
1 T-TTTTTTTC
*
7259 TTTCTTTTC
1 TTTTTTTTC
7268 TTTTTTTT
1 TTTTTTTT
7276 TTCTTTTGTT
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
9 29 0.85
10 5 0.15
ACGTcount: A:0.06, C:0.09, G:0.04, T:0.81
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:7293 original size:13 final size:11
Alignment explanation
Indices: 7221--7290 Score: 52
Period size: 11 Copynumber: 6.0 Consensus size: 11
7211 TTTGGACTAA
7221 TTTTTTTTTCT
1 TTTTTTTTTCT
*
7232 TTTTTTTCTTAT
1 TTTTTTT-TTCT
7244 ATTGGTATTTTTT-T
1 -TT--T-TTTTTTCT
* *
7258 CTTTCTTTTCT
1 TTTTTTTTTCT
7269 TTTTTTTTTCT
1 TTTTTTTTTCT
*
7280 TTTGTTTTTCT
1 TTTTTTTTTCT
7291 CTTGATAGAC
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
10 5 0.11
11 28 0.60
12 3 0.06
13 3 0.06
14 1 0.02
15 3 0.06
16 4 0.09
ACGTcount: A:0.04, C:0.10, G:0.04, T:0.81
Consensus pattern (11 bp):
TTTTTTTTTCT
Found at i:14342 original size:3 final size:3
Alignment explanation
Indices: 14334--14375 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
14324 GCTAAGTGAT
* *
14334 TTA TTA TTA TTA TTA TTA ATA TTA ATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
14376 CTGTTGTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:14914 original size:20 final size:21
Alignment explanation
Indices: 14886--14928 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
14876 TTAGTTTTTT
*
14886 TTTCATTTTCTT-TGTAAAAA
1 TTTCATTTTCTTCTATAAAAA
* *
14906 TTTCTTTTTTTTCTATAAAAA
1 TTTCATTTTCTTCTATAAAAA
14927 TT
1 TT
14929 ATTATTTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.28, C:0.09, G:0.02, T:0.60
Consensus pattern (21 bp):
TTTCATTTTCTTCTATAAAAA
Found at i:22153 original size:17 final size:18
Alignment explanation
Indices: 22126--22160 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
22116 TTTATTAAAA
*
22126 TTTCTTATTTTTTTATTT
1 TTTCTTATTTTTTGATTT
22144 TTTC-TATTTTTTGATTT
1 TTTCTTATTTTTTGATTT
22161 GAAAATAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.11, C:0.06, G:0.03, T:0.80
Consensus pattern (18 bp):
TTTCTTATTTTTTGATTT
Found at i:22378 original size:4 final size:4
Alignment explanation
Indices: 22369--22406 Score: 58
Period size: 4 Copynumber: 9.2 Consensus size: 4
22359 AATACTTTGA
*
22369 AAAT AAAT AAAC AAAT AACAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT A
22407 CTAAAATAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 27 0.87
5 4 0.13
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:22393 original size:17 final size:17
Alignment explanation
Indices: 22371--22403 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
22361 TACTTTGAAA
22371 ATAAATAAACAAATAAC
1 ATAAATAAACAAATAAC
*
22388 ATAAATAAATAAATAA
1 ATAAATAAACAAATAA
22404 ATACTAAAAT
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:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (17 bp):
ATAAATAAACAAATAAC
Found at i:22506 original size:17 final size:17
Alignment explanation
Indices: 22481--22523 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
22471 ATTGGAATAG
* *
22481 CTCGGCTTGCAATTTAA
1 CTCGGCTTGCAACTGAA
*
22498 CTTGGCTTGCAACTGAA
1 CTCGGCTTGCAACTGAA
22515 CTCGGCTTG
1 CTCGGCTTG
22524 GCTCGAGCCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.19, C:0.26, G:0.23, T:0.33
Consensus pattern (17 bp):
CTCGGCTTGCAACTGAA
Found at i:25114 original size:11 final size:11
Alignment explanation
Indices: 25094--25149 Score: 64
Period size: 10 Copynumber: 5.1 Consensus size: 11
25084 AAAATCTTAC
25094 TCAA-CTTTTT
1 TCAAGCTTTTT
25104 TCAAGC-TTTT
1 TCAAGCTTTTT
25114 TCTAAGCTTTTTT
1 TC-AAGC-TTTTT
25127 TCAAGC-TTTT
1 TCAAGCTTTTT
25137 TCTAAGCTTTTT
1 TC-AAGCTTTTT
25149 T
1 T
25150 TATCTTCTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
10 16 0.40
11 9 0.22
12 9 0.22
13 6 0.15
ACGTcount: A:0.18, C:0.18, G:0.07, T:0.57
Consensus pattern (11 bp):
TCAAGCTTTTT
Found at i:25114 original size:12 final size:11
Alignment explanation
Indices: 25098--25151 Score: 72
Period size: 11 Copynumber: 4.8 Consensus size: 11
25088 TCTTACTCAA
*
25098 CTTTTTTCAAG
1 CTTTTTTTAAG
*
25109 CTTTTTCTAAG
1 CTTTTTTTAAG
25120 CTTTTTTTCAAG
1 CTTTTTTT-AAG
*
25132 CTTTTTCTAAG
1 CTTTTTTTAAG
25143 CTTTTTTTA
1 CTTTTTTTA
25152 TCTTCTCAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
11 27 0.73
12 10 0.27
ACGTcount: A:0.17, C:0.17, G:0.07, T:0.59
Consensus pattern (11 bp):
CTTTTTTTAAG
Found at i:25129 original size:23 final size:23
Alignment explanation
Indices: 25099--25150 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
25089 CTTACTCAAC
25099 TTTTTTCAAGCTTTTTCTAAGCT
1 TTTTTTCAAGCTTTTTCTAAGCT
25122 TTTTTTCAAGCTTTTTCTAAGCT
1 TTTTTTCAAGCTTTTTCTAAGCT
25145 TTTTTT
1 TTTTTT
25151 ATCTTCTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.15, C:0.15, G:0.08, T:0.62
Consensus pattern (23 bp):
TTTTTTCAAGCTTTTTCTAAGCT
Found at i:28311 original size:42 final size:41
Alignment explanation
Indices: 28233--28323 Score: 112
Period size: 42 Copynumber: 2.2 Consensus size: 41
28223 ATTTTACAAG
* * *
28233 TTTTATTTCTAAATTTTTCACCATTTGGGCCAATTTAAAATT
1 TTTTATTTTTAAATTTTCCACCAGTTGGGCCAATTT-AAATT
***
28275 TTTTATTTTTAAATTTTCCACCAGTTGGGTTTATTTAAATT
1 TTTTATTTTTAAATTTTCCACCAGTTGGGCCAATTTAAATT
28316 TTTT-TTTT
1 TTTTATTTT
28324 ATCGTTGGAA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
40 4 0.09
41 9 0.21
42 30 0.70
ACGTcount: A:0.24, C:0.11, G:0.08, T:0.57
Consensus pattern (41 bp):
TTTTATTTTTAAATTTTCCACCAGTTGGGCCAATTTAAATT
Found at i:28957 original size:17 final size:18
Alignment explanation
Indices: 28937--28976 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
28927 TACTTTGAAC
*
28937 ATAAATTAACAAAAT-AA
1 ATAAATAAACAAAATAAA
*
28954 ATAAATAAATAAAATAAA
1 ATAAATAAACAAAATAAA
28972 ATAAA
1 ATAAA
28977 ATACCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.23
Consensus pattern (18 bp):
ATAAATAAACAAAATAAA
Found at i:35478 original size:70 final size:70
Alignment explanation
Indices: 35393--35529 Score: 265
Period size: 70 Copynumber: 2.0 Consensus size: 70
35383 GACTTTCGAT
*
35393 GTATTTTCTTTATAATAATGTTTTGTCCTTATCAAAGTTAATATTGAGAAGGACTAATCATTAAT
1 GTATTTTCTTTATAATAACGTTTTGTCCTTATCAAAGTTAATATTGAGAAGGACTAATCATTAAT
35458 TTGAC
66 TTGAC
35463 GTATTTTCTTTATAATAACGTTTTGTCCTTATCAAAGTTAATATTGAGAAGGACTAATCATTAAT
1 GTATTTTCTTTATAATAACGTTTTGTCCTTATCAAAGTTAATATTGAGAAGGACTAATCATTAAT
35528 TT
66 TT
35530 CTTGCAAACA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 66 1.00
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (70 bp):
GTATTTTCTTTATAATAACGTTTTGTCCTTATCAAAGTTAATATTGAGAAGGACTAATCATTAAT
TTGAC
Found at i:38466 original size:18 final size:17
Alignment explanation
Indices: 38443--38479 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
38433 AACCAATATT
*
38443 ATTATTATTTTTTAAAAA
1 ATTATTA-TTATTAAAAA
38461 ATTATTATTATTAAAAA
1 ATTATTATTATTAAAAA
38478 AT
1 AT
38480 GTAGACTCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTATTATTATTAAAAA
Found at i:38778 original size:24 final size:24
Alignment explanation
Indices: 38746--38798 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
38736 ACCATGAATC
38746 GAAATCATGCCCGAAGGTCTTACA
1 GAAATCATGCCCGAAGGTCTTACA
* *
38770 GAAATCATGCCTGGAGGTCTTACA
1 GAAATCATGCCCGAAGGTCTTACA
38794 -AAATC
1 GAAATC
38799 GACTGGGACA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 5 0.19
24 22 0.81
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.23
Consensus pattern (24 bp):
GAAATCATGCCCGAAGGTCTTACA
Found at i:39054 original size:109 final size:109
Alignment explanation
Indices: 38858--39058 Score: 244
Period size: 109 Copynumber: 1.8 Consensus size: 109
38848 ATCGTGAATC
* ** * * *
38858 AAAATTATGCTCGAAGGTCTTACAGAATCGACCAGGACAACACCGCAAGTTGAGAATAATGAATC
1 AAAATCATGCTCGAAAATCTTACAGAATCGACCAGGACAACACCGCAAGTTCAAAATAAAGAATC
*
38923 AATAAGGATAATACCGCCAATCGAAATTTTGCCCAAAGGTCTTA
66 AATAAGGATAACACCGCCAATCGAAATTTTGCCCAAAGGTCTTA
* **
38967 AAAATCATGCTCGAAAATCTTACAGAATTGACTGGGACAACACCGCAAG-TCAAAATTAAAGAAT
1 AAAATCATGCTCGAAAATCTTACAGAATCGACCAGGACAACACCGCAAGTTCAAAA-TAAAGAAT
* * * *
39031 CGAT-CGAGATAACACTGCGAATCGAAAT
65 CAATAAG-GATAACACCGCCAATCGAAAT
39059 CATGCTCGAA
Statistics
Matches: 76, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
108 5 0.07
109 71 0.93
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (109 bp):
AAAATCATGCTCGAAAATCTTACAGAATCGACCAGGACAACACCGCAAGTTCAAAATAAAGAATC
AATAAGGATAACACCGCCAATCGAAATTTTGCCCAAAGGTCTTA
Found at i:39087 original size:87 final size:87
Alignment explanation
Indices: 38968--39247 Score: 368
Period size: 87 Copynumber: 3.2 Consensus size: 87
38958 AAGGTCTTAA
* ** * * *
38968 AAATCATGCTCGAAAATCTTACAGAATTGACTGGGACAACACCGCAAGTC-AAAATTAAAGAATC
1 AAATCATACTCGAAGGTCTTACAGAATCGACTGGGACAACACCGCAAGTCGAGAA-TAATGAATC
* *
39032 GATCGAGATAACACTGCGAATCG
65 GATCGGGATAACACCGCGAATCG
* * *
39055 AAATCATGCTCGAAGGTTTTACAGAATCGACTGGGATAACACCGCAAGTCGAGAATAATGAATCG
1 AAATCATACTCGAAGGTCTTACAGAATCGACTGGGACAACACCGCAAGTCGAGAATAATGAATCG
*
39120 ATCGGGATAACACCGCGAATCA
66 ATCGGGATAACACCGCGAATCG
* * * *
39142 AAATTATACCCAAAGGTCTT--AGAATCGACTGGGACAACACCGTAAGTCGAGAATAATGAATCG
1 AAATCATACTCGAAGGTCTTACAGAATCGACTGGGACAACACCGCAAGTCGAGAATAATGAATCG
*
39205 ATCGGGATAACACCGTGAATCG
66 ATCGGGATAACACCGCGAATCG
*
39227 AAATTATACTCGAAGGTCTTA
1 AAATCATACTCGAAGGTCTTA
39248 GAAATCAATA
Statistics
Matches: 170, Mismatches: 21, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
85 79 0.46
87 88 0.52
88 3 0.02
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.21
Consensus pattern (87 bp):
AAATCATACTCGAAGGTCTTACAGAATCGACTGGGACAACACCGCAAGTCGAGAATAATGAATCG
ATCGGGATAACACCGCGAATCG
Found at i:39100 original size:196 final size:199
Alignment explanation
Indices: 38742--39162 Score: 521
Period size: 196 Copynumber: 2.1 Consensus size: 199
38732 CAACACCATG
* * * **
38742 AATCGAAATCATGCCCGAAGGTCTTACAGAAATCATGCCTGGAGGTCTTACAAAATCGACTGGGA
1 AATCGAAATTATGCCCAAAGGTCTTACAGAAATCATGCCTGAAAATCTTACAAAATCGACTGGGA
* * * * * *
38807 CAACACCACAAGTTGAGAATAATGAATCGATCGGGGATAACATCGTGAATCAAAATTATGCTCGA
66 CAACACCACAAGTTCAAAATAAAGAATCGATCGGAGATAACATCGCGAATCAAAATCATGCTCGA
* *
38872 AGGTCTTACAGAATCGACCAGGACAACACCGCAAGTTGAGAATAATGAATCAATAAGGATAATAC
131 AGGTCTTACAGAATCGACCAGGACAACACCGCAAGTCGAGAATAATGAATCAATAAGGATAACAC
38937 CGCC
196 CGCC
* * *
38941 AATCGAAATTTTGCCCAAAGGTCTTA-A-AAATCATG-CTCGAAAATCTTACAGAATTGACTGGG
1 AATCGAAATTATGCCCAAAGGTCTTACAGAAATCATGCCT-GAAAATCTTACAAAATCGACTGGG
* *
39003 ACAACACCGCAAG-TCAAAATTAAAGAATCGATC-GAGATAACA-CTGCGAATCGAAATCATGCT
65 ACAACACCACAAGTTCAAAA-TAAAGAATCGATCGGAGATAACATC-GCGAATCAAAATCATGCT
* ** * * **
39065 CGAAGGTTTTACAGAATCGACTGGGATAACACCGCAAGTCGAGAATAATGAATCGATCGGGATAA
128 CGAAGGTCTTACAGAATCGACCAGGACAACACCGCAAGTCGAGAATAATGAATCAATAAGGATAA
*
39130 CACCGCG
193 CACCGCC
* *
39137 AATCAAAATTATACCCAAAGGTCTTA
1 AATCGAAATTATGCCCAAAGGTCTTA
39163 GAATCGACTG
Statistics
Matches: 190, Mismatches: 29, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
195 1 0.01
196 114 0.60
197 51 0.27
198 1 0.01
199 23 0.12
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (199 bp):
AATCGAAATTATGCCCAAAGGTCTTACAGAAATCATGCCTGAAAATCTTACAAAATCGACTGGGA
CAACACCACAAGTTCAAAATAAAGAATCGATCGGAGATAACATCGCGAATCAAAATCATGCTCGA
AGGTCTTACAGAATCGACCAGGACAACACCGCAAGTCGAGAATAATGAATCAATAAGGATAACAC
CGCC
Found at i:39193 original size:85 final size:85
Alignment explanation
Indices: 38990--39250 Score: 362
Period size: 85 Copynumber: 3.0 Consensus size: 85
38980 AAAATCTTAC
* * * * *
38990 AGAATTGACTGGGACAACACCGCAAGTC-AAAATTAAAGAATCGATCGAGATAACACTGCGAATC
1 AGAATCGACTGGGACAACACCGCAAGTCGAGAA-TAATGAATCGATCGGGATAACACCGCGAATC
* * *
39054 GAAATCATGCTCGAAGGTTTT
65 GAAATTATACTCGAAGGTCTT
*
39075 ACAGAATCGACTGGGATAACACCGCAAGTCGAGAATAATGAATCGATCGGGATAACACCGCGAAT
1 --AGAATCGACTGGGACAACACCGCAAGTCGAGAATAATGAATCGATCGGGATAACACCGCGAAT
* * *
39140 CAAAATTATACCCAAAGGTCTT
64 CGAAATTATACTCGAAGGTCTT
* *
39162 AGAATCGACTGGGACAACACCGTAAGTCGAGAATAATGAATCGATCGGGATAACACCGTGAATCG
1 AGAATCGACTGGGACAACACCGCAAGTCGAGAATAATGAATCGATCGGGATAACACCGCGAATCG
39227 AAATTATACTCGAAGGTCTT
66 AAATTATACTCGAAGGTCTT
39247 AGAA
1 AGAA
39251 ATCAATATCT
Statistics
Matches: 155, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
85 83 0.54
87 69 0.45
88 3 0.02
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.20
Consensus pattern (85 bp):
AGAATCGACTGGGACAACACCGCAAGTCGAGAATAATGAATCGATCGGGATAACACCGCGAATCG
AAATTATACTCGAAGGTCTT
Found at i:39993 original size:33 final size:32
Alignment explanation
Indices: 39824--40339 Score: 483
Period size: 33 Copynumber: 15.9 Consensus size: 32
39814 ATTCTTTTGG
* * *
39824 GGCCAAATAAACTGGGCTTAAATTTTATTGAA
1 GGCCAGATAAACTGGGCTTAAAGTTTATTGAT
* * * **
39856 GGTCAGCTAAACTAGGCTTAAAACCTTATTTGA-
1 GGCCAGATAAACTGGGCTT-AAAGTTTA-TTGAT
*
39889 GGCCAGAT-AACTGGGCTTAAA-TGTCATTGAT
1 GGCCAGATAAACTGGGCTTAAAGT-TTATTGAT
*
39920 GGCCAGATAAAGT-GGCTTAAAGTTTCATTGAT
1 GGCCAGATAAACTGGGCTTAAAGTTT-ATTGAT
* * *
39952 GGCTAGATAAACTAGGCTTAAAACTTTATTTGA-
1 GGCCAGATAAACTGGGCTT-AAAGTTTA-TTGAT
*
39985 GGCCAGATAAACTGGGCTTAAATTTTCATTGAT
1 GGCCAGATAAACTGGGCTTAAAGTTT-ATTGAT
* *
40018 GGCTAGATAAACTGGGCTTAAA-TGTCATTGAT
1 GGCCAGATAAACTGGGCTTAAAGT-TTATTGAT
40050 GGCCAGATAAACTGGGCTTAAAGTTTCATTGAT
1 GGCCAGATAAACTGGGCTTAAAGTTT-ATTGAT
* * * * * *
40083 AGCCATATAAACTAGGTTTAAAACTTCATTTGA-
1 GGCCAGATAAACTGGGCTT-AAAGTTTA-TTGAT
* *
40116 GGCCAGATAAACTGGGCTT-AAGTGTCATTAAT
1 GGCCAGATAAACTGGGCTTAAAGT-TTATTGAT
*
40148 GGCCAGATAAATTGGGCTTAAAGTTTCATTGAT
1 GGCCAGATAAACTGGGCTTAAAGTTT-ATTGAT
* * *
40181 GGCTAGATAAACTGGGCTTAAAACTTCATTTGA-
1 GGCCAGATAAACTGGGCTT-AAAGTTTA-TTGAT
* * *
40214 GGCCAGATAAACTGGCCTTAAAGGTCATTGAT
1 GGCCAGATAAACTGGGCTTAAAGTTTATTGAT
40246 GGCCAGATAAACTGGGCTTAAAGTTTTATTGAT
1 GGCCAGATAAACTGGGCTTAAAG-TTTATTGAT
* * * *
40279 GGGCAGATAAACTGGACTTAAAGGTCATTGAT
1 GGCCAGATAAACTGGGCTTAAAGTTTATTGAT
* * *
40311 GACTAGATAAACTGGGCTTAAATTTTATT
1 GGCCAGATAAACTGGGCTTAAAGTTTATT
40340 TCTTTTGTTT
Statistics
Matches: 399, Mismatches: 60, Indels: 50
0.78 0.12 0.10
Matches are distributed among these distances:
30 4 0.01
31 32 0.08
32 163 0.41
33 168 0.42
34 32 0.08
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (32 bp):
GGCCAGATAAACTGGGCTTAAAGTTTATTGAT
Found at i:40059 original size:98 final size:97
Alignment explanation
Indices: 39824--40333 Score: 552
Period size: 98 Copynumber: 5.2 Consensus size: 97
39814 ATTCTTTTGG
* * * * * * * *
39824 GGCCAAATAAACTGGGCTTAAATTTTATTGAAGGTCAGCTAAACTAGGCTTAAAACCTTATTTGA
1 GGCCAGATAAACTGGGCTTAAATGTCATTGATGGCCAGATAAACTGGGCTTAAAACTTTA-TTGA
39889 -GGCCAGAT-AACTGGGCTTAAA-TGTCATTGAT
65 TGGCCAGATAAACTGGGCTTAAACT-TCATTGAT
* * * *
39920 GGCCAGATAAAGT-GGCTTAAAGTTTCATTGATGGCTAGATAAACTAGGCTTAAAACTTTATTTG
1 GGCCAGATAAACTGGGCTTAAA-TGTCATTGATGGCCAGATAAACTGGGCTTAAAACTTTA-TTG
*
39984 A-GGCCAGATAAACTGGGCTTAAATTTTCATTGAT
64 ATGGCCAGATAAACTGGGCTTAAA-CTTCATTGAT
* *
40018 GGCTAGATAAACTGGGCTTAAATGTCATTGATGGCCAGATAAACTGGGCTT-AAAGTTTCATTGA
1 GGCCAGATAAACTGGGCTTAAATGTCATTGATGGCCAGATAAACTGGGCTTAAAACTTT-ATTGA
* * * *
40082 TAGCCATATAAACTAGGTTTAAAACTTCATTTGA-
65 TGGCCAGATAAACTGGGCTT-AAACTTCA-TTGAT
* * * *
40116 GGCCAGATAAACTGGGCTTAAGTGTCATTAATGGCCAGATAAATTGGGCTT-AAAGTTTCATTGA
1 GGCCAGATAAACTGGGCTTAAATGTCATTGATGGCCAGATAAACTGGGCTTAAAACTTT-ATTGA
*
40180 TGGCTAGATAAACTGGGCTTAAAACTTCATTTGA-
65 TGGCCAGATAAACTGGGCTT-AAACTTCA-TTGAT
* * **
40214 GGCCAGATAAACTGGCCTTAAAGGTCATTGATGGCCAGATAAACTGGGCTTAAAGTTTTATTGAT
1 GGCCAGATAAACTGGGCTTAAATGTCATTGATGGCCAGATAAACTGGGCTTAAAACTTTATTGAT
* * **
40279 GGGCAGATAAACTGGACTTAAAGGTCATTGAT
66 GGCCAGATAAACTGGGCTTAAACTTCATTGAT
* *
40311 GACTAGATAAACTGGGCTTAAAT
1 GGCCAGATAAACTGGGCTTAAAT
40334 TTTATTTCTT
Statistics
Matches: 359, Mismatches: 44, Indels: 21
0.85 0.10 0.05
Matches are distributed among these distances:
95 8 0.02
96 60 0.17
97 48 0.13
98 222 0.62
99 21 0.06
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.30
Consensus pattern (97 bp):
GGCCAGATAAACTGGGCTTAAATGTCATTGATGGCCAGATAAACTGGGCTTAAAACTTTATTGAT
GGCCAGATAAACTGGGCTTAAACTTCATTGAT
Found at i:40081 original size:65 final size:65
Alignment explanation
Indices: 39824--40332 Score: 552
Period size: 65 Copynumber: 7.8 Consensus size: 65
39814 ATTCTTTTGG
* * * * * * * **
39824 GGCCAAATAAACTGGGCTTAAATTTTATTGAAGGTCAGCTAAACTAGGCTTAAAACCTT-ATTTG
1 GGCCAGATAAACTGGGCTTAAATGTCATTGATGGCCAGATAAACTGGGCTT-AAAGTTTCA-TTG
39888 A-
64 AT
*
39889 GGCCAGAT-AACTGGGCTTAAATGTCATTGATGGCCAGATAAAGT-GGCTTAAAGTTTCATTGAT
1 GGCCAGATAAACTGGGCTTAAATGTCATTGATGGCCAGATAAACTGGGCTTAAAGTTTCATTGAT
* * * *
39952 GGCTAGATAAACTAGGCTTAAAACT-TTATTTGA-GGCCAGATAAACTGGGCTTAAATTTTCATT
1 GGCCAGATAAACTGGGCTT-AAA-TGTCA-TTGATGGCCAGATAAACTGGGCTTAAAGTTTCATT
40015 GAT
63 GAT
*
40018 GGCTAGATAAACTGGGCTTAAATGTCATTGATGGCCAGATAAACTGGGCTTAAAGTTTCATTGAT
1 GGCCAGATAAACTGGGCTTAAATGTCATTGATGGCCAGATAAACTGGGCTTAAAGTTTCATTGAT
* * * * *
40083 AGCCATATAAACTAGGTTTAAAACT-TCATTTGA-GGCCAGATAAACTGGGCTT-AAGTGTCATT
1 GGCCAGATAAACTGGGCTT-AAA-TGTCA-TTGATGGCCAGATAAACTGGGCTTAAAGTTTCATT
*
40145 AAT
63 GAT
* * * **
40148 GGCCAGATAAATTGGGCTTAAAGTTTCATTGATGGCTAGATAAACTGGGCTTAAAACTTCATTTG
1 GGCCAGATAAACTGGGCTTAAA-TGTCATTGATGGCCAGATAAACTGGGCTTAAAGTTTCA-TTG
40213 A-
64 AT
* * *
40214 GGCCAGATAAACTGGCCTTAAAGGTCATTGATGGCCAGATAAACTGGGCTTAAAGTTTTATTGAT
1 GGCCAGATAAACTGGGCTTAAATGTCATTGATGGCCAGATAAACTGGGCTTAAAGTTTCATTGAT
* * * * *
40279 GGGCAGATAAACTGGACTTAAAGGTCATTGATGACTAGATAAACTGGGCTTAAA
1 GGCCAGATAAACTGGGCTTAAATGTCATTGATGGCCAGATAAACTGGGCTTAAA
40333 TTTTATTTCT
Statistics
Matches: 380, Mismatches: 47, Indels: 34
0.82 0.10 0.07
Matches are distributed among these distances:
62 9 0.02
63 13 0.03
64 56 0.15
65 203 0.53
66 91 0.24
67 8 0.02
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.30
Consensus pattern (65 bp):
GGCCAGATAAACTGGGCTTAAATGTCATTGATGGCCAGATAAACTGGGCTTAAAGTTTCATTGAT
Found at i:41538 original size:18 final size:17
Alignment explanation
Indices: 41517--41550 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
41507 TCTAAAAAAA
41517 TCTTTTGGGTTTTTTTTG
1 TCTTTT-GGTTTTTTTTG
*
41535 TCTTTTTGTTTTTTTT
1 TCTTTTGGTTTTTTTT
41551 TTCAAAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.00, C:0.06, G:0.15, T:0.79
Consensus pattern (17 bp):
TCTTTTGGTTTTTTTTG
Found at i:41637 original size:9 final size:9
Alignment explanation
Indices: 41623--41657 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
41613 CATAACCAAT
*
41623 TTTTTTTTC
1 TTTTTTTTG
41632 TTTTTTTTG
1 TTTTTTTTG
*
41641 TTGTTTTTG
1 TTTTTTTTG
41650 TTTTTTTT
1 TTTTTTTT
41658 TTATGTCCCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.00, C:0.03, G:0.09, T:0.89
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:48168 original size:15 final size:15
Alignment explanation
Indices: 48150--48445 Score: 109
Period size: 16 Copynumber: 19.5 Consensus size: 15
48140 TTGAAGATTC
48150 GGATTTTAAGGGTTT
1 GGATTTTAAGGGTTT
*
48165 GGA-TTTAAGAGTTT
1 GGATTTTAAGGGTTT
*
48179 AAGGGTTTT-AGGGTTT
1 --GGATTTTAAGGGTTT
*
48195 -GATTTTAA-GGTAT
1 GGATTTTAAGGGTTT
*
48208 GGAAGGTTT-AGGGTTT
1 GG-A-TTTTAAGGGTTT
* *
48224 TGATTTT-AGAGTTT
1 GGATTTTAAGGGTTT
*
48238 AAAGATTTT-AGGGTTT
1 --GGATTTTAAGGGTTT
* **
48254 CGATTTTAA-AATTT
1 GGATTTTAAGGGTTT
*
48268 -GAGGTTT-AGGGTTT
1 GGA-TTTTAAGGGTTT
*
48282 TGA-TTTAAGGGTTT
1 GGATTTTAAGGGTTT
48296 GGATTTT-AGGAGTTTT
1 GGATTTTAAGG-G-TTT
*
48312 GGATTTTAGGGGTTT
1 GGATTTTAAGGGTTT
*
48327 GGATTTTAGGGGGTTTT
1 GGATTTTA-AGGG-TTT
* *
48344 GAATTTT-TGGGATTT
1 GGATTTTAAGGG-TTT
*
48359 GGA-TTTAAGAGATTTT
1 GGATTTTAAG-G-GTTT
* *
48375 AGATTTTGA-GGTTT
1 GGATTTTAAGGGTTT
* *
48389 GTATTTTAGGGGTTT
1 GGATTTTAAGGGTTT
* **
48404 CGAATTTTAAGATTTT
1 -GGATTTTAAGGGTTT
48420 GGATTTTAAGGGGATTTT
1 GGATTTTAA-GGG--TTT
48438 GGATTTTA
1 GGATTTTA
48446 GGGGGCTTTA
Statistics
Matches: 211, Mismatches: 40, Indels: 57
0.69 0.13 0.19
Matches are distributed among these distances:
13 15 0.07
14 59 0.28
15 47 0.22
16 61 0.29
17 18 0.09
18 11 0.05
ACGTcount: A:0.22, C:0.01, G:0.30, T:0.47
Consensus pattern (15 bp):
GGATTTTAAGGGTTT
Found at i:48173 original size:14 final size:14
Alignment explanation
Indices: 48154--48337 Score: 63
Period size: 14 Copynumber: 12.6 Consensus size: 14
48144 AGATTCGGAT
48154 TTTAAGGGTTTGGA
1 TTTAAGGGTTTGGA
* *
48168 TTTAAGAGTTTAAGGG
1 TTTAAGGGTTT--GGA
*
48184 TTTTAGGGTTT-GA
1 TTTAAGGGTTTGGA
*
48197 TTTTAA-GGTATGGAA
1 -TTTAAGGGTTTGG-A
*
48212 GGTTT-AGGGTTTTGA
1 --TTTAAGGGTTTGGA
* * *
48227 TTTTAGAGTTTAAAGA
1 TTTAAGGGTTT--GGA
* *
48243 TTTTAGGGTTTCGA
1 TTTAAGGGTTTGGA
** *
48257 TTTTAA-AATTTGAGG
1 -TTTAAGGGTTTG-GA
*
48272 TTTA-GGGTTTTGA
1 TTTAAGGGTTTGGA
48285 TTTAAGGGTTTGGA
1 TTTAAGGGTTTGGA
*
48299 TTTTAGGAGTTTTGGA
1 TTTAAGG-G-TTTGGA
*
48315 TTTTAGGGGTTTGGA
1 -TTTAAGGGTTTGGA
*
48330 TTTTAGGG
1 TTTAAGGG
48338 GGTTTTGAAT
Statistics
Matches: 124, Mismatches: 29, Indels: 34
0.66 0.16 0.18
Matches are distributed among these distances:
13 13 0.10
14 53 0.43
15 15 0.12
16 38 0.31
17 5 0.04
ACGTcount: A:0.22, C:0.01, G:0.31, T:0.46
Consensus pattern (14 bp):
TTTAAGGGTTTGGA
Found at i:48192 original size:30 final size:29
Alignment explanation
Indices: 48153--48317 Score: 110
Period size: 30 Copynumber: 5.6 Consensus size: 29
48143 AAGATTCGGA
48153 TTTTAAGGGTTTGGATTTAAGAGTTTAAGGG
1 TTTT-AGGGTTTGGATTTAAGAGTTTAA-GG
*
48184 TTTTAGGGTTT-GATTTTAAG-GTATGGAAGG
1 TTTTAGGGTTTGGA-TTTAAGAGT-T-TAAGG
* * *
48214 -TTTAGGGTTTTGATTTTAGAGTTTAAAGA
1 TTTTAGGGTTTGGATTTAAGAGTTT-AAGG
* * *
48243 TTTTAGGGTTTCGATTTTAA-AATTTGAGG
1 TTTTAGGGTTTGGA-TTTAAGAGTTTAAGG
* *
48272 -TTTAGGGTTTTGATTTAAGGGTTT--GG
1 TTTTAGGGTTTGGATTTAAGAGTTTAAGG
48298 ATTTTAGGAGTTTTGGATTT
1 -TTTTAGG-G-TTTGGATTT
48318 TAGGGGTTTG
Statistics
Matches: 108, Mismatches: 13, Indels: 27
0.73 0.09 0.18
Matches are distributed among these distances:
26 2 0.02
27 5 0.05
28 21 0.19
29 26 0.24
30 44 0.41
31 10 0.09
ACGTcount: A:0.23, C:0.01, G:0.29, T:0.47
Consensus pattern (29 bp):
TTTTAGGGTTTGGATTTAAGAGTTTAAGG
Found at i:48199 original size:59 final size:60
Alignment explanation
Indices: 48158--48295 Score: 174
Period size: 59 Copynumber: 2.4 Consensus size: 60
48148 TCGGATTTTA
* * *
48158 AGGGTTTGGATTTAAGAGTTTAAGGGTTTTAGGGTTT-GATTTTAAGGTATGGAAGGTTT
1 AGGGTTTGGATTTAAGAGTTTAAAGATTTTAGGGTTTCGATTTTAAGATATGGAAGGTTT
* * * *
48217 AGGGTTTTGATTTTAGAGTTTAAAGATTTTAGGGTTTCGATTTTAAAAT-TTG-AGGTTT
1 AGGGTTTGGATTTAAGAGTTTAAAGATTTTAGGGTTTCGATTTTAAGATATGGAAGGTTT
* *
48275 AGGGTTTTGATTTAAGGGTTT
1 AGGGTTTGGATTTAAGAGTTT
48296 GGATTTTAGG
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
58 25 0.36
59 35 0.51
60 9 0.13
ACGTcount: A:0.24, C:0.01, G:0.30, T:0.46
Consensus pattern (60 bp):
AGGGTTTGGATTTAAGAGTTTAAAGATTTTAGGGTTTCGATTTTAAGATATGGAAGGTTT
Found at i:48201 original size:22 final size:21
Alignment explanation
Indices: 48151--48204 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
48141 TGAAGATTCG
48151 GATTTTAAGGGTTTGGATTTAA
1 GATTTTAAGGGTTTGGATTT-A
* *
48173 GAGTTTAAGGGTTTTAGGGTTT-
1 GATTTTAAGGG-TTT-GGATTTA
48195 GATTTTAAGG
1 GATTTTAAGG
48205 TATGGAAGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 19 0.70
23 3 0.11
24 5 0.19
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.44
Consensus pattern (21 bp):
GATTTTAAGGGTTTGGATTTA
Found at i:48296 original size:13 final size:15
Alignment explanation
Indices: 48275--48367 Score: 73
Period size: 15 Copynumber: 6.1 Consensus size: 15
48265 TTTGAGGTTT
48275 AGGGTTTT-GATTTA
1 AGGGTTTTGGATTTA
*
48289 AGGG-TTTGGATTTT
1 AGGGTTTTGGATTTA
*
48303 AGGAGTTTTGGATTTT
1 AGG-GTTTTGGATTTA
*
48319 AGGGGTTTGGATTTTA
1 AGGGTTTTGGA-TTTA
* * *
48335 GGGGGTTTTGAATTTT
1 -AGGGTTTTGGATTTA
* *
48351 TGGGATTTGGATTTA
1 AGGGTTTTGGATTTA
48366 AG
1 AG
48368 AGATTTTAGA
Statistics
Matches: 62, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
13 3 0.05
14 12 0.19
15 20 0.32
16 19 0.31
17 8 0.13
ACGTcount: A:0.18, C:0.00, G:0.34, T:0.47
Consensus pattern (15 bp):
AGGGTTTTGGATTTA
Found at i:48326 original size:31 final size:31
Alignment explanation
Indices: 48272--48449 Score: 157
Period size: 31 Copynumber: 5.8 Consensus size: 31
48262 AAATTTGAGG
*
48272 TTTA-GGGTTTT-GA-TTTAAGGGTTTGGAT
1 TTTAGGGGTTTTGGATTTTAGGGGTTTGGAT
*
48300 TTTAGGAGTTTTGGATTTTAGGGGTTTGGAT
1 TTTAGGGGTTTTGGATTTTAGGGGTTTGGAT
* * *
48331 TTTAGGGGGTTTTGAATTTTTGGGATTTGGAT
1 TTTA-GGGGTTTTGGATTTTAGGGGTTTGGAT
* * * * * *
48363 TTAAGAGATTTTAGATTTT-GAGGTTTGTAT
1 TTTAGGGGTTTTGGATTTTAGGGGTTTGGAT
* * * **
48393 TTTAGGGGTTTCGAATTTTAAGATTTTGGAT
1 TTTAGGGGTTTTGGATTTTAGGGGTTTGGAT
48424 TTTAAGGGGATTTTGGATTTTAGGGG
1 TTT-AGGGG-TTTTGGATTTTAGGGG
48450 GCTTTAGAAA
Statistics
Matches: 113, Mismatches: 30, Indels: 9
0.74 0.20 0.06
Matches are distributed among these distances:
28 4 0.04
29 6 0.05
30 23 0.20
31 38 0.34
32 31 0.27
33 11 0.10
ACGTcount: A:0.20, C:0.01, G:0.31, T:0.48
Consensus pattern (31 bp):
TTTAGGGGTTTTGGATTTTAGGGGTTTGGAT
Found at i:50040 original size:17 final size:18
Alignment explanation
Indices: 50018--50051 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
50008 TATTATTATT
50018 ATTATTATT-TTAAAAAC
1 ATTATTATTATTAAAAAC
50035 ATTATTATTATTAAAAA
1 ATTATTATTATTAAAAA
50052 ATGTAAACCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTATTATTATTAAAAAC
Found at i:50052 original size:20 final size:20
Alignment explanation
Indices: 50015--50052 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
50005 CAATATTATT
**
50015 ATTATTATTATTTTAAAAAC
1 ATTATTATTATTAAAAAAAC
50035 ATTATTATTATTAAAAAA
1 ATTATTATTATTAAAAAA
50053 TGTAAACCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTATTATTATTAAAAAAAC
Found at i:52347 original size:28 final size:27
Alignment explanation
Indices: 52304--52356 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
52294 ATAGTTTTCT
52304 TATTTGTGAGGAATAATCTTCTTATATA
1 TATTTGTGAGGAATAATCTT-TTATATA
* *
52332 TATTTGTGAGGTATAATGTTTTATA
1 TATTTGTGAGGAATAATCTTTTATA
52357 ATAAAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.30, C:0.04, G:0.17, T:0.49
Consensus pattern (27 bp):
TATTTGTGAGGAATAATCTTTTATATA
Found at i:54091 original size:30 final size:30
Alignment explanation
Indices: 54031--54106 Score: 73
Period size: 30 Copynumber: 2.5 Consensus size: 30
54021 TTCCAAATTT
** *
54031 TTTAATTGTTTGGTATTTTTTTTCTCTTTA
1 TTTAATTGTTTATTATTTGTTTTCTCTTTA
*
54061 TTTAATTGTTTATTCATTTGTTTTGT-TTTA
1 TTTAATTGTTTATT-ATTTGTTTTCTCTTTA
*
54091 TGCATAATTGTTTATT
1 T--TTAATTGTTTATT
54107 TATTCACTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
30 17 0.45
31 9 0.24
32 12 0.32
ACGTcount: A:0.17, C:0.05, G:0.11, T:0.67
Consensus pattern (30 bp):
TTTAATTGTTTATTATTTGTTTTCTCTTTA
Found at i:54101 original size:32 final size:32
Alignment explanation
Indices: 54063--54124 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
54053 TCTCTTTATT
***
54063 TAATTGTTTATTCATTTGTTTTGTTTTATGCA
1 TAATTGTTTATTCATTCACTTTGTTTTATGCA
*
54095 TAATTGTTTATTTATTCACTTTGTTTTATG
1 TAATTGTTTATTCATTCACTTTGTTTTATG
54125 GTTTTCATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.19, C:0.06, G:0.11, T:0.63
Consensus pattern (32 bp):
TAATTGTTTATTCATTCACTTTGTTTTATGCA
Found at i:54347 original size:8 final size:8
Alignment explanation
Indices: 54332--54378 Score: 58
Period size: 8 Copynumber: 5.6 Consensus size: 8
54322 ATTTATTTTT
54332 TAAAAAAA
1 TAAAAAAA
*
54340 TTAAAAAAT
1 -TAAAAAAA
54349 TAAAAATAA
1 TAAAAA-AA
*
54358 TAAAAACA
1 TAAAAAAA
54366 TAAAAAAA
1 TAAAAAAA
54374 TAAAA
1 TAAAA
54379 TTTTTGGAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
8 19 0.58
9 14 0.42
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (8 bp):
TAAAAAAA
Found at i:54353 original size:17 final size:17
Alignment explanation
Indices: 54331--54378 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
54321 TATTTATTTT
54331 TTAAAAAAATTAAAAA-A
1 TTAAAAAAA-TAAAAACA
54348 TTAAAAATAATAAAAACA
1 TTAAAAA-AATAAAAACA
54366 -TAAAAAAATAAAA
1 TTAAAAAAATAAAA
54379 TTTTTGGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 7 0.24
17 19 0.66
18 3 0.10
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (17 bp):
TTAAAAAAATAAAAACA
Found at i:55843 original size:21 final size:21
Alignment explanation
Indices: 55817--55885 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
55807 ATCTATATGT
55817 CATTTCATTCTCATGTTCTAG
1 CATTTCATTCTCATGTTCTAG
* *
55838 CATTTCATTCT-GTGTATC-AT
1 CATTTCATTCTCATGT-TCTAG
55858 C-TTT-ATTCTCATGTTCTAG
1 CATTTCATTCTCATGTTCTAG
55877 CATTATCAT
1 CATT-TCAT
55886 ATCATGATCA
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
18 7 0.18
19 8 0.21
20 7 0.18
21 14 0.37
22 2 0.05
ACGTcount: A:0.20, C:0.22, G:0.09, T:0.49
Consensus pattern (21 bp):
CATTTCATTCTCATGTTCTAG
Found at i:60906 original size:11 final size:11
Alignment explanation
Indices: 60816--60906 Score: 51
Period size: 11 Copynumber: 7.9 Consensus size: 11
60806 ACAATGGATG
60816 AAAGATGAAAA
1 AAAGATGAAAA
*
60827 AAAGGA-AAAAA
1 AAA-GATGAAAA
*
60838 AAATAGTGAAAA
1 AAAGA-TGAAAA
*
60850 GTTAAAGATAAAAA
1 ---AAAGATGAAAA
*
60864 AAAGAGGAAAA
1 AAAGATGAAAA
*
60875 TAAA-AAGAAAA
1 -AAAGATGAAAA
* *
60886 AAAAAGGAAAA
1 AAAGATGAAAA
60897 AAAGATGAAA
1 AAAGATGAAA
60907 TGAGGAAAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 16
0.69 0.12 0.18
Matches are distributed among these distances:
10 4 0.07
11 39 0.64
12 9 0.15
14 5 0.08
15 4 0.07
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.09
Consensus pattern (11 bp):
AAAGATGAAAA
Found at i:60906 original size:22 final size:24
Alignment explanation
Indices: 60833--60906 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 24
60823 AAAAAAAGGA
*
60833 AAAAAAAATAGTGAAAAGTTAAAGAT-
1 AAAAAAAAGAG-GAAAA--TAAAGATG
*
60859 AAAAAAAAGAGGAAAATAAA-AAG
1 AAAAAAAAGAGGAAAATAAAGATG
60882 AAAAAAAA-AGGAAAA-AAAGATG
1 AAAAAAAAGAGGAAAATAAAGATG
60904 AAA
1 AAA
60907 TGAGGAAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
21 3 0.07
22 13 0.30
23 12 0.28
25 5 0.12
26 10 0.23
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.09
Consensus pattern (24 bp):
AAAAAAAAGAGGAAAATAAAGATG
Done.