Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168040.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_292, 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: 38372
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Found at i:3473 original size:19 final size:20
Alignment explanation
Indices: 3449--3506 Score: 75
Period size: 19 Copynumber: 2.9 Consensus size: 20
3439 CATCATATTG
3449 TGCAATAAATATAA-AATCA
1 TGCAATAAATATAATAATCA
3468 TGCAAT-AATAATAATAATCA
1 TGCAATAAAT-ATAATAATCA
*
3488 TGCAAATAAATATATTAAT
1 TGC-AATAAATATAATAAT
3507 AATCATACAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
18 3 0.09
19 10 0.29
20 8 0.24
21 10 0.29
22 3 0.09
ACGTcount: A:0.55, C:0.09, G:0.05, T:0.31
Consensus pattern (20 bp):
TGCAATAAATATAATAATCA
Found at i:3506 original size:24 final size:20
Alignment explanation
Indices: 3449--3517 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 20
3439 CATCATATTG
3449 TGCAATAA-ATATAA-AATCA
1 TGCAATAATA-ATAATAATCA
3468 TGCAATAATAATAATAATCA
1 TGCAATAATAATAATAATCA
3488 TGCAAATAAATATATTAATAATCA
1 TGC-AAT-AATA-A-TAATAATCA
*
3512 TACAAT
1 TGCAAT
3518 CACACAAATA
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
19 12 0.28
20 9 0.21
21 3 0.07
22 4 0.09
23 4 0.09
24 11 0.26
ACGTcount: A:0.55, C:0.10, G:0.04, T:0.30
Consensus pattern (20 bp):
TGCAATAATAATAATAATCA
Found at i:3659 original size:39 final size:39
Alignment explanation
Indices: 3568--3760 Score: 228
Period size: 39 Copynumber: 4.9 Consensus size: 39
3558 CAATTAAATG
* * *
3568 TATAATCATGAAATTAACAATA-AAAATCA-CCAAATAAATA
1 TATAATAATGCAATTAACAATATAAAA-CATGCAAAT--ATA
*
3608 TATAATAATGCAATTAACAATATAAATCATGCAAATATA
1 TATAATAATGCAATTAACAATATAAAACATGCAAATATA
*
3647 TATAATCATGCAATTAACAATATAAAACATGCAAATATA
1 TATAATAATGCAATTAACAATATAAAACATGCAAATATA
* ** * *
3686 TTTTTTAATGCAATTAACAATATAAAACTTGCAATTAAATA
1 TATAATAATGCAATTAACAATATAAAACATGCAA--ATATA
*
3727 TATAATGATGCAATTAACAATATAAAACATGCAA
1 TATAATAATGCAATTAACAATATAAAACATGCAA
3761 TCACACAAAT
Statistics
Matches: 132, Mismatches: 17, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
39 69 0.52
40 22 0.17
41 41 0.31
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.30
Consensus pattern (39 bp):
TATAATAATGCAATTAACAATATAAAACATGCAAATATA
Found at i:3747 original size:80 final size:81
Alignment explanation
Indices: 3553--3760 Score: 273
Period size: 80 Copynumber: 2.6 Consensus size: 81
3543 ATGCAAATAG
* * *
3553 ACATGCAATTAAATGTATAATCATGAAATTAACAATA-AAAATCA-CCAAATAAATATATAATAA
1 ACATGCAATTAAATATATAATCATGCAATTAACAATATAAAA-CATGCAAAT-AATATATAATAA
3616 TGCAATTAACAATATAAA
64 TGCAATTAACAATATAAA
* * * **
3634 TCATGCAA--ATATATATAATCATGCAATTAACAATATAAAACATGCAAAT-ATATTTTTTAATG
1 ACATGCAATTAAATATATAATCATGCAATTAACAATATAAAACATGCAAATAATATATAATAATG
3696 CAATTAACAATATAAA
66 CAATTAACAATATAAA
* *
3712 ACTTGCAATTAAATATATAATGATGCAATTAACAATATAAAACATGCAA
1 ACATGCAATTAAATATATAATCATGCAATTAACAATATAAAACATGCAA
3761 TCACACAAAT
Statistics
Matches: 111, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
78 32 0.29
79 26 0.23
80 46 0.41
81 7 0.06
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.30
Consensus pattern (81 bp):
ACATGCAATTAAATATATAATCATGCAATTAACAATATAAAACATGCAAATAATATATAATAATG
CAATTAACAATATAAA
Found at i:3796 original size:20 final size:20
Alignment explanation
Indices: 3771--3863 Score: 114
Period size: 20 Copynumber: 4.6 Consensus size: 20
3761 TCACACAAAT
*
3771 AAATAAATTGATAATCATGC
1 AAATAAATTAATAATCATGC
* *
3791 AAATAAATTGATAATCATGT
1 AAATAAATTAATAATCATGC
* *
3811 AAATAAATTAATAGTCACGC
1 AAATAAATTAATAATCATGC
*
3831 AAATATATTAATAAATCATGC
1 AAATAAATTAAT-AATCATGC
*
3852 AAATATATTAAT
1 AAATAAATTAAT
3864 CATACAAATA
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
20 46 0.72
21 18 0.28
ACGTcount: A:0.52, C:0.09, G:0.08, T:0.32
Consensus pattern (20 bp):
AAATAAATTAATAATCATGC
Found at i:3904 original size:32 final size:33
Alignment explanation
Indices: 3850--3913 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 33
3840 AATAAATCAT
*
3850 GCAAATATATTAATCATACAAATAAAATATTAA
1 GCAAATAAATTAATCATACAAATAAAATATTAA
* **
3883 GCAAATAAATT-ATCATGCAAATTTAATATTA
1 GCAAATAAATTAATCATACAAATAAAATATTA
3914 GTCATGCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 17 0.63
33 10 0.37
ACGTcount: A:0.53, C:0.09, G:0.05, T:0.33
Consensus pattern (33 bp):
GCAAATAAATTAATCATACAAATAAAATATTAA
Found at i:3920 original size:20 final size:20
Alignment explanation
Indices: 3887--3943 Score: 91
Period size: 20 Copynumber: 3.0 Consensus size: 20
3877 TATTAAGCAA
3887 ATAA-ATTA-TCATGCAAAT
1 ATAATATTAGTCATGCAAAT
*
3905 TTAATATTAGTCATGCAAAT
1 ATAATATTAGTCATGCAAAT
3925 ATAATATTAGTCATGCAAA
1 ATAATATTAGTCATGCAAA
3944 ATCATGCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
18 3 0.09
19 4 0.11
20 28 0.80
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.35
Consensus pattern (20 bp):
ATAATATTAGTCATGCAAAT
Found at i:6343 original size:16 final size:17
Alignment explanation
Indices: 6319--6351 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6309 ATCAAATTTT
6319 TATAAAC-AATTAAAAA
1 TATAAACAAATTAAAAA
*
6335 TATATACAAATTAAAAA
1 TATAAACAAATTAAAAA
6352 AAATTTAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (17 bp):
TATAAACAAATTAAAAA
Found at i:16167 original size:44 final size:43
Alignment explanation
Indices: 16104--16441 Score: 370
Period size: 44 Copynumber: 7.9 Consensus size: 43
16094 GAGCATTTAC
* *
16104 TTTCAAAGTTG-TGATGCCTCTATTTAGATGAGCTTTGTTTATT
1 TTTCAAAGTCGTTGA-GCCTCTATTTAGAGGAGCTTTGTTTATT
*
16147 TTTCAAAAGTCATTGAGCCTCTATTTAGAGGAGCTTTGTTTATT
1 TTTC-AAAGTCGTTGAGCCTCTATTTAGAGGAGCTTTGTTTATT
* * *
16191 GTTT--AAGTTGTTGAACCTCTATTTAGATGAGCTTTGTTTATT
1 -TTTCAAAGTCGTTGAGCCTCTATTTAGAGGAGCTTTGTTTATT
* *
16233 GTTT--AAGTCGTTGAGTCTCTGTTTAGAGGAGCTTTGTTTATT
1 -TTTCAAAGTCGTTGAGCCTCTATTTAGAGGAGCTTTGTTTATT
* *
16275 TTTCAAAAGTCGTCGAGCCTCTATTTAGAGGAGCTTAGTTTATT
1 TTTC-AAAGTCGTTGAGCCTCTATTTAGAGGAGCTTTGTTTATT
* * * **
16319 TTTTAGAAGTCGTTAAGCCTCTAATTAGAGGAGC--CATTTA-T
1 TTTCA-AAGTCGTTGAGCCTCTATTTAGAGGAGCTTTGTTTATT
*
16360 TTTCAAGGTCG-TGAAGCCTCTATTTAGAGGAGCTTTGTTTATTTT
1 TTTCAAAGTCGTTG-AGCCTCTATTTAGAGGAGCTTTGTTTA--TT
* *
16405 TTTCAAAGTCATTGAGCCTCTACTTAGAGGAGCTTTG
1 TTTCAAAGTCGTTGAGCCTCTATTTAGAGGAGCTTTG
16442 ATCAAAATTT
Statistics
Matches: 250, Mismatches: 31, Indels: 26
0.81 0.10 0.08
Matches are distributed among these distances:
39 1 0.00
40 23 0.09
41 8 0.03
42 79 0.32
43 5 0.02
44 94 0.38
45 38 0.15
46 2 0.01
ACGTcount: A:0.23, C:0.13, G:0.21, T:0.43
Consensus pattern (43 bp):
TTTCAAAGTCGTTGAGCCTCTATTTAGAGGAGCTTTGTTTATT
Found at i:16293 original size:128 final size:127
Alignment explanation
Indices: 16097--16441 Score: 421
Period size: 128 Copynumber: 2.7 Consensus size: 127
16087 TGTCAATGAG
* * * * *
16097 CATTTACTTTCAAAGTTGTGATGCCTCTATTTAGATGAGCTTTGTTTATTTTTCAAAAGTCATTG
1 CATTTATTTTCAAGGTCGTGAAGCCTCTATTTAGAGGAGCTTTGTTTATTTTTCAAAAGTCATTG
* * *
16162 AGCCTCTATTTAGAGGAGCTTTGTTTATTGTTT-AAGTTGTTGAA-CCTCTATTTAGATGAGC
66 AGCCTCTATTTAGAGGAGCTTTGTTTATTGTTTAAAGTCGTT-AAGCCTCTAATTAGAGGAGC
** * * *
16223 TTTGTTTATTGTTTAA-GTCGTTG-AGTCTCTGTTTAGAGGAGCTTTGTTTATTTTTCAAAAGTC
1 --CATTTATT-TTCAAGGTCG-TGAAGCCTCTATTTAGAGGAGCTTTGTTTATTTTTCAAAAGTC
* * * *
16286 GTCGAGCCTCTATTTAGAGGAGCTTAGTTTATTTTTTAGAAGTCGTTAAGCCTCTAATTAGAGGA
62 ATTGAGCCTCTATTTAGAGGAGCTTTGTTTATTGTTTA-AAGTCGTTAAGCCTCTAATTAGAGGA
16351 GC
126 GC
16353 CATTTATTTTCAAGGTCGTGAAGCCTCTATTTAGAGGAGCTTTGTTTATTTTTTTC-AAAGTCAT
1 CATTTATTTTCAAGGTCGTGAAGCCTCTATTTAGAGGAGCTTTGTTTA--TTTTTCAAAAGTCAT
*
16417 TGAGCCTCTACTTAGAGGAGCTTTG
64 TGAGCCTCTATTTAGAGGAGCTTTG
16442 ATCAAAATTT
Statistics
Matches: 183, Mismatches: 25, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
127 6 0.03
128 112 0.61
129 37 0.20
130 28 0.15
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.43
Consensus pattern (127 bp):
CATTTATTTTCAAGGTCGTGAAGCCTCTATTTAGAGGAGCTTTGTTTATTTTTCAAAAGTCATTG
AGCCTCTATTTAGAGGAGCTTTGTTTATTGTTTAAAGTCGTTAAGCCTCTAATTAGAGGAGC
Found at i:16663 original size:10 final size:10
Alignment explanation
Indices: 16637--16780 Score: 71
Period size: 10 Copynumber: 14.2 Consensus size: 10
16627 TGTATCTTAT
16637 TTATTTATTA
1 TTATTTATTA
*
16647 CTA-TTATTA
1 TTATTTATTA
16656 TTATTTATTAA
1 TTATTTATT-A
* *
16667 TATATATATTT
1 T-TATTTATTA
*
16678 TTATTTGTTA
1 TTATTTATTA
* *
16688 ATATATATTA
1 TTATTTATTA
16698 TTATTTATCTA
1 TTATTTAT-TA
*
16709 TTAATGTA-TA
1 TT-ATTTATTA
*
16719 TAAATTT-TTA
1 T-TATTTATTA
* *
16729 TTATTAACTA
1 TTATTTATTA
*
16739 TTATCTATTA
1 TTATTTATTA
*
16749 TTTATCTATTA
1 -TTATTTATTA
* *
16760 GTATATA-TA
1 TTATTTATTA
*
16769 TTTTTTATTA
1 TTATTTATTA
16779 TT
1 TT
16781 TATCTTTTTT
Statistics
Matches: 98, Mismatches: 26, Indels: 20
0.68 0.18 0.14
Matches are distributed among these distances:
9 17 0.17
10 53 0.54
11 17 0.17
12 11 0.11
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.61
Consensus pattern (10 bp):
TTATTTATTA
Found at i:16726 original size:48 final size:46
Alignment explanation
Indices: 16648--16780 Score: 166
Period size: 48 Copynumber: 2.9 Consensus size: 46
16638 TATTTATTAC
* *
16648 TATTATTA-TTATTTATTAA-TATATATATTTTTATTTGTTAA-TAT
1 TATTATTATTTATCTATTAAGTATATATATTTTTA-TTATTAACTAT
*
16692 ATATTATTATTTATCTATTAATGTATATAAATTTTTATTATTAACTAT
1 -TATTATTATTTATCTATTAA-GTATATATATTTTTATTATTAACTAT
16740 TATCTATTATTTATCTATT-AGTATATATATTTTTTATTATT
1 TAT-TATTATTTATCTATTAAGTATATATA-TTTTTATTATT
16781 TATCTTTTTT
Statistics
Matches: 78, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
45 8 0.10
46 18 0.23
47 21 0.27
48 31 0.40
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (46 bp):
TATTATTATTTATCTATTAAGTATATATATTTTTATTATTAACTAT
Found at i:17051 original size:21 final size:21
Alignment explanation
Indices: 17022--17071 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
17012 TAGATACAGC
17022 TTTATGAATTTGTGAAAATTTT
1 TTTATGAATTTGTG-AAATTTT
* *
17044 TTTA-GAATTTTTGAAGTTTT
1 TTTATGAATTTGTGAAATTTT
*
17064 TTTCTGAA
1 TTTATGAA
17072 AAATTTTTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 9 0.38
21 11 0.46
22 4 0.17
ACGTcount: A:0.28, C:0.02, G:0.14, T:0.56
Consensus pattern (21 bp):
TTTATGAATTTGTGAAATTTT
Found at i:17807 original size:60 final size:59
Alignment explanation
Indices: 17646--17807 Score: 209
Period size: 59 Copynumber: 2.7 Consensus size: 59
17636 AAATAAAATT
* * *
17646 CTAAAAAATAAATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTT
1 CTAAAAAA-ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTC
* * *
17706 CTAAAAAAATATTTTTGAGGAAAAGTTAAAAGTATCAATTTTCTTTGAAAATAA-TTTC
1 CTAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTC
* * *
17764 CTAAAAAAGGTTTTTTTTTAGGAAAAGTTGAAAGTATCAATTTT
1 CTAAAAAA--ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTT
17808 TCTTGTACAA
Statistics
Matches: 90, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
58 11 0.12
59 41 0.46
60 38 0.42
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (59 bp):
CTAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTC
Found at i:17907 original size:23 final size:22
Alignment explanation
Indices: 17870--17912 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
17860 TGAATCATTA
**
17870 TTCTTTTTTTCATTTTATTTTTT
1 TTCTTTTTTAAATTTT-TTTTTT
17893 TTCTTTTTTAAATTTTTTTT
1 TTCTTTTTTAAATTTTTTTT
17913 AATGTTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.12, C:0.07, G:0.00, T:0.81
Consensus pattern (22 bp):
TTCTTTTTTAAATTTTTTTTTT
Found at i:25121 original size:57 final size:57
Alignment explanation
Indices: 25052--25239 Score: 207
Period size: 63 Copynumber: 3.2 Consensus size: 57
25042 TTGTACATGG
*
25052 AAAATTGATACTTTCAACTTTTCCCTAAAATATTTTTCAGAAACTTTAATTTCGAGA
1 AAAATTGATACTTTCAACTTTTCCCTAAAATATTTTTTAGAAACTTTAATTTCGAGA
* * * * * **
25109 AAAATTGATACTTTCAACTTTTCCTCAAAAAAAAACTTTTTTTTTGAAAATTTATTCTTAAAG-
1 AAAATTGATACTTTCAACTTTTCC-C----TAAAA-TATTTTTTAGAAACTTTAAT-TTCGAGA
* *
25172 AAAATTGATACTTTTAACTTTTCCCTAAAAATATTTTTTGGAAACTTTAATTTCGAGA
1 AAAATTGATACTTTCAACTTTTCCCT-AAAATATTTTTTAGAAACTTTAATTTCGAGA
25230 AAAATTGATA
1 AAAATTGATA
25240 ATATTTTTTG
Statistics
Matches: 106, Mismatches: 16, Indels: 17
0.76 0.12 0.12
Matches are distributed among these distances:
57 28 0.26
58 27 0.25
59 4 0.04
62 5 0.05
63 38 0.36
64 4 0.04
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.41
Consensus pattern (57 bp):
AAAATTGATACTTTCAACTTTTCCCTAAAATATTTTTTAGAAACTTTAATTTCGAGA
Found at i:25243 original size:38 final size:38
Alignment explanation
Indices: 25201--25277 Score: 138
Period size: 38 Copynumber: 2.0 Consensus size: 38
25191 TTTCCCTAAA
25201 AATATTTTTTGGAAACTTTAATTTCG-AGAAAAATTGAT
1 AATATTTTTTGGAAACTTTAATTTCGAAG-AAAATTGAT
25239 AATATTTTTTGGAAACTTTAATTTCGAAGAAAATTGAT
1 AATATTTTTTGGAAACTTTAATTTCGAAGAAAATTGAT
25277 A
1 A
25278 CTTTCAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
38 36 0.95
39 2 0.05
ACGTcount: A:0.40, C:0.05, G:0.13, T:0.42
Consensus pattern (38 bp):
AATATTTTTTGGAAACTTTAATTTCGAAGAAAATTGAT
Found at i:25313 original size:58 final size:59
Alignment explanation
Indices: 25239--25365 Score: 193
Period size: 58 Copynumber: 2.2 Consensus size: 59
25229 AAAAATTGAT
* * * * *
25239 AATATTTTTTGGAAACTTTAATTTCGAAGAAAATTGATACTTTCAATTTTTCC-CTAAA
1 AATATTTTTTGAAAACTTTAATTTCGAAAAAAATTGATACTATCAACTTTTCCTCAAAA
25297 AATATTTTTTGAAAACTTTAATTTCGAAAAAAATTGATACTATCAACTTTTCCTCAAAA
1 AATATTTTTTGAAAACTTTAATTTCGAAAAAAATTGATACTATCAACTTTTCCTCAAAA
*
25356 AAAATTTTTT
1 AATATTTTTT
25366 TTTAATTTTA
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
58 49 0.79
59 13 0.21
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.43
Consensus pattern (59 bp):
AATATTTTTTGAAAACTTTAATTTCGAAAAAAATTGATACTATCAACTTTTCCTCAAAA
Found at i:25413 original size:14 final size:14
Alignment explanation
Indices: 25378--25441 Score: 55
Period size: 14 Copynumber: 4.7 Consensus size: 14
25368 TAATTTTATT
25378 TAAAGAAAAT-AAAA
1 TAAA-AAAATAAAAA
*
25392 TAATAAAATAAAAA
1 TAAAAAAATAAAAA
*
25406 TAAAAAAAGT-CAAA
1 TAAAAAAA-TAAAAA
*
25420 T--AAAGATAAAAA
1 TAAAAAAATAAAAA
25432 TAAAAAAATA
1 TAAAAAAATA
25442 TTAGACAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
11 1 0.03
12 8 0.21
13 5 0.13
14 24 0.62
15 1 0.03
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.17
Consensus pattern (14 bp):
TAAAAAAATAAAAA
Found at i:25420 original size:20 final size:19
Alignment explanation
Indices: 25383--25441 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 19
25373 TTATTTAAAG
*
25383 AAAATAAAATAATAAAATA
1 AAAATAAAAAAATAAAATA
*
25402 AAAATAAAAAAAGTCAAATA
1 AAAATAAAAAAA-TAAAATA
* *
25422 AAGATAAAAATAAAAAAATA
1 AAAATAAAAA-AATAAAATA
25442 TTAGACAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
19 11 0.33
20 20 0.61
21 2 0.06
ACGTcount: A:0.78, C:0.02, G:0.03, T:0.17
Consensus pattern (19 bp):
AAAATAAAAAAATAAAATA
Found at i:25864 original size:44 final size:43
Alignment explanation
Indices: 25811--25901 Score: 103
Period size: 44 Copynumber: 2.1 Consensus size: 43
25801 ATCTTAACCG
* * * *
25811 AAAATTAATTAAAATAAA-AAGATAAATATATTAATAGATAACAA
1 AAAAATAATT-AAATAAATAAAATAAATAGATAAATA-ATAACAA
* *
25855 AAAAATAATTAGATAAATAAAATAAATAGATAAATAATAATAA
1 AAAAATAATTAAATAAATAAAATAAATAGATAAATAATAACAA
25898 AAAA
1 AAAA
25902 TAAAAGCAGA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
43 16 0.40
44 24 0.60
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.25
Consensus pattern (43 bp):
AAAAATAATTAAATAAATAAAATAAATAGATAAATAATAACAA
Found at i:25896 original size:23 final size:23
Alignment explanation
Indices: 25870--25938 Score: 68
Period size: 27 Copynumber: 2.8 Consensus size: 23
25860 TAATTAGATA
25870 AATAAAATAAATAGATAAATAAT
1 AATAAAATAAATAGATAAATAAT
*
25893 AATAAAAAATAAAAGCAGATAAATAAT
1 AAT--AAAAT-AAA-TAGATAAATAAT
*
25920 AA-AAATATTAATAGATAAA
1 AATAAA-ATAAATAGATAAA
25939 ATATATATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
23 10 0.26
24 5 0.13
25 7 0.18
26 3 0.08
27 13 0.34
ACGTcount: A:0.70, C:0.01, G:0.06, T:0.23
Consensus pattern (23 bp):
AATAAAATAAATAGATAAATAAT
Found at i:25897 original size:27 final size:29
Alignment explanation
Indices: 25857--25926 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 29
25847 GATAACAAAA
*
25857 AAATAATTAGATAAATAAAAT-AAA-TAGAT
1 AAATAA-TA-ATAAATAAAATAAAAGCAGAT
25886 AAATAATAAT-AA-AAAATAAAAGCAGAT
1 AAATAATAATAAATAAAATAAAAGCAGAT
25913 AAATAATAA-AAATA
1 AAATAATAATAAATA
25927 TTAATAGATA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
25 5 0.14
26 5 0.14
27 17 0.47
28 3 0.08
29 6 0.17
ACGTcount: A:0.70, C:0.01, G:0.06, T:0.23
Consensus pattern (29 bp):
AAATAATAATAAATAAAATAAAAGCAGAT
Found at i:25900 original size:24 final size:24
Alignment explanation
Indices: 25867--25938 Score: 74
Period size: 25 Copynumber: 2.9 Consensus size: 24
25857 AAATAATTAG
*
25867 ATAAATAAAATAAATAGATAAATA
1 ATAAAAAAAATAAATAGATAAATA
*
25891 ATAATAAAAAATAAAAGCAGATAAATA
1 ATAA-AAAAAAT-AAA-TAGATAAATA
* *
25918 AT-AAAAATATTAATAGATAAA
1 ATAAAAAAAATAAATAGATAAA
25939 ATATATATTA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
23 7 0.17
24 6 0.15
25 12 0.30
26 4 0.10
27 11 0.28
ACGTcount: A:0.69, C:0.01, G:0.06, T:0.24
Consensus pattern (24 bp):
ATAAAAAAAATAAATAGATAAATA
Found at i:25904 original size:17 final size:17
Alignment explanation
Indices: 25856--25905 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
25846 AGATAACAAA
* *
25856 AAAATAATTAGATAAAT
1 AAAATAAATAAATAAAT
*
25873 AAAATAAATAGATAAAT
1 AAAATAAATAAATAAAT
25890 AATAATAAA-AAATAAA
1 AA-AATAAATAAATAAA
25906 AGCAGATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 24 0.80
18 6 0.20
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (17 bp):
AAAATAAATAAATAAAT
Found at i:27704 original size:22 final size:21
Alignment explanation
Indices: 27673--27736 Score: 69
Period size: 20 Copynumber: 3.0 Consensus size: 21
27663 TACTATGCTT
*
27673 AAAAGGAAAAAAAGTAAAGAAA
1 AAAAGAAAAAAAAGTAAA-AAA
27695 AAAAGAAAAAAAAAAG-AAAAAA
1 AAAAG--AAAAAAAAGTAAAAAA
*
27717 GAAAGAAAAAAAA-TAAAAAA
1 AAAAGAAAAAAAAGTAAAAAA
27737 GGGGAATGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
20 14 0.38
22 12 0.32
23 3 0.08
24 8 0.22
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.03
Consensus pattern (21 bp):
AAAAGAAAAAAAAGTAAAAAA
Found at i:27722 original size:30 final size:30
Alignment explanation
Indices: 27680--27736 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
27670 CTTAAAAGGA
27680 AAAAAAGTAAAGAAAAAAAGAAAAAAAAAAG
1 AAAAAAGTAAAGAAAAAAA-AAAAAAAAAAG
*
27711 AAAAAAG-AAAGAAAAAAAATAAAAAA
1 AAAAAAGTAAAGAAAAAAAAAAAAAAA
27737 GGGGAATGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 7 0.28
30 11 0.44
31 7 0.28
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.04
Consensus pattern (30 bp):
AAAAAAGTAAAGAAAAAAAAAAAAAAAAAG
Found at i:27734 original size:18 final size:18
Alignment explanation
Indices: 27673--27728 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 18
27663 TACTATGCTT
*
27673 AAAAGGAAAAAAAGTAAAGAA
1 AAAAAGAAAAAAA--AAAG-A
27694 AAAAAGAAAAAAAAAAGA
1 AAAAAGAAAAAAAAAAGA
27712 AAAAAGAAAGAAAAAAA
1 AAAAAGAAA-AAAAAAA
27729 ATAAAAAAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
18 10 0.30
19 11 0.33
21 12 0.36
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (18 bp):
AAAAAGAAAAAAAAAAGA
Found at i:27736 original size:11 final size:11
Alignment explanation
Indices: 27679--27729 Score: 75
Period size: 11 Copynumber: 4.5 Consensus size: 11
27669 GCTTAAAAGG
27679 AAAAAAAGTAAA
1 AAAAAAAG-AAA
27691 GAAAAAAAGAAA
1 -AAAAAAAGAAA
27703 AAAAAAAGAAA
1 AAAAAAAGAAA
*
27714 AAAGAAAGAAA
1 AAAAAAAGAAA
27725 AAAAA
1 AAAAA
27730 TAAAAAAGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
11 25 0.69
12 3 0.08
13 8 0.22
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:28824 original size:44 final size:43
Alignment explanation
Indices: 28762--29230 Score: 415
Period size: 42 Copynumber: 10.9 Consensus size: 43
28752 GAGCATTTAC
* *
28762 TTTCAAAGTTG-TGAAGCCTCTGTTTAGAGGAGCTTTATTTATT
1 TTTCAAAGTCGTTG-AGCCTCTGTTTAGAGGAGCTTTGTTTATT
28805 TTTCAAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTGTTTATT
1 TTTC-AAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTGTTTATT
* * * *
28849 GTTT--AAGTCGTTAAGCTTTTATTTAGAGGAGCTTTGTTTATT
1 -TTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTGTTTATT
** * * *
28891 TTTCAAAAGTCGTCAAGCATCTATTTAGTGGAGCTTTGTTTATT
1 TTTC-AAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTGTTTATT
* * * * *
28935 GTTT--AAGTCGTTGAGCTTCTATTTAGAGAAACTGTGTTTATT
1 -TTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTGTTTATT
* * *
28977 GTTT--AAGTCATTGAGCCTCTGTTTAAAGGAACTTTGTTTACTTT
1 -TTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTGTTTA--TT
* *
29021 TTTCAAAAGTCGTCGAGCTTCTGTTTAGAGGAGCTTTGTTTATT
1 TTTC-AAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTGTTTATT
*
29065 TGTT-TAAGTCGTTGAGCCTCTGTTTAGAGGAGC-TTGATTTATTT
1 T-TTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTG-TTTA-TT
* * * *
29109 TTTAAAAGTCGTTGAACCTCTGATTAGAGGAGC--TATTTA-T
1 TTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTGTTTATT
* * * *
29149 TTTCAAGGTTGTAGAGCCTTTGTTTAGAAGG-GCTTTGTTTATTTT
1 TTTCAAAGTCGTTGAGCCTCTGTTTAG-AGGAGCTTTGTTTA--TT
** *
29194 TTTCAAAGTCGTTGAGCCTCTACTTAGAGAAGCTTTG
1 TTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTG
29231 ATCAAAATTT
Statistics
Matches: 353, Mismatches: 50, Indels: 44
0.79 0.11 0.10
Matches are distributed among these distances:
40 23 0.07
41 6 0.02
42 111 0.31
43 40 0.11
44 104 0.29
45 38 0.11
46 31 0.09
ACGTcount: A:0.22, C:0.12, G:0.22, T:0.44
Consensus pattern (43 bp):
TTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTGTTTATT
Found at i:29048 original size:88 final size:87
Alignment explanation
Indices: 28939--29120 Score: 251
Period size: 88 Copynumber: 2.1 Consensus size: 87
28929 TTTATTGTTT
*
28939 AAGTCGTTGAGCTTCTATTTAGAGAAACTGTGTTTA-TTGTTTAAGTCATTGAGCCTCTGTTTAA
1 AAGTCGTCGAGCTTCTATTTAGAGAAACTGTGTTTATTTGTTTAAGTCATTGAGCCTCTGTTTAA
29003 AGGAACTTTG-TTTACTTTTTTCAA
66 AGGAAC-TTGATTTA-TTTTTT-AA
* * * * * *
29027 AAGTCGTCGAGCTTCTGTTTAGAGGAGCTTTGTTTATTTGTTTAAGTCGTTGAGCCTCTGTTTAG
1 AAGTCGTCGAGCTTCTATTTAGAGAAACTGTGTTTATTTGTTTAAGTCATTGAGCCTCTGTTTAA
*
29092 AGGAGCTTGATTTATTTTTTAA
66 AGGAACTTGATTTATTTTTTAA
29114 AAGTCGT
1 AAGTCGT
29121 TGAACCTCTG
Statistics
Matches: 84, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
87 9 0.11
88 40 0.48
89 35 0.42
ACGTcount: A:0.23, C:0.12, G:0.21, T:0.44
Consensus pattern (87 bp):
AAGTCGTCGAGCTTCTATTTAGAGAAACTGTGTTTATTTGTTTAAGTCATTGAGCCTCTGTTTAA
AGGAACTTGATTTATTTTTTAA
Found at i:29208 original size:85 final size:86
Alignment explanation
Indices: 28762--29227 Score: 315
Period size: 86 Copynumber: 5.4 Consensus size: 86
28752 GAGCATTTAC
* * *
28762 TTTCAAAGTTG-TGAAGCCTCTGTTTAGAGGAGCTTTATTTATTT-TTCAAAAGTCGTTGAGCCT
1 TTTCAAAGTCGTTG-AGCCTCTGATTAGAGGAGC--TATTTATTTGTTC--AAGTCGTAGAGCCT
*
28825 CTGTTTAG-AGGAGCTTTGTTTATTG
61 CTGTTTAGAAGGAGCTTTGTTTATTT
* * * * *
28850 TTT--AAGTCGTTAAG-CTTTTATTTAGAGGAGCTTTGTTTATTT-TTCAAAAGTCGTCA-AGCA
1 TTTCAAAGTCGTTGAGCCTCTGA-TTAGAGGAGC--TATTTATTTGTTC--AAGTCGT-AGAGCC
* * *
28910 TCTATTTAG-TGGAGCTTTGTTTATTG
60 TCTGTTTAGAAGGAGCTTTGTTTATTT
* * * * * * *
28936 TTT--AAGTCGTTGAGCTTCT-ATTTAGAGAAACTGTGTT-TATTGTTTAAGTCATTGAGCCTCT
1 TTTCAAAGTCGTTGAGCCTCTGA-TTAGAGGAGCTAT-TTAT-TTGTTCAAGTCGTAGAGCCTCT
*
28997 GTTTA-AAGGAACTTTGTTTACTTT
63 GTTTAGAAGGAGCTTTGTTTA-TTT
* * * * * *
29021 TTTCAAAAGTCGTCGAGCTTCTGTTTAGAGGAGCTTTGTTTATTTGTTTAAGTCGTTGAGCCTCT
1 TTTC-AAAGTCGTTGAGCCTCTGATTAGAGGAGC--TATTTATTTGTTCAAGTCGTAGAGCCTCT
29086 GTTTAG-AGGAGC-TTGATTTATTT
63 GTTTAGAAGGAGCTTTG-TTTATTT
* * * *
29109 TTTAAAAGTCGTTGAACCTCTGATTAGAGGAGCTATTTA-TT-TTCAAGGTTGTAGAGCCTTTGT
1 TTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTATTTATTTGTTCAA-GTCGTAGAGCCTCTGT
29172 TTAGAAGG-GCTTTGTTTATTTT
65 TTAGAAGGAGCTTTGTTTA-TTT
*
29194 TTTCAAAGTCGTTGAGCCTCT-ACTTAGAGAAGCT
1 TTTCAAAGTCGTTGAGCCTCTGA-TTAGAGGAGCT
29228 TTGATCAAAA
Statistics
Matches: 312, Mismatches: 42, Indels: 51
0.77 0.10 0.13
Matches are distributed among these distances:
83 4 0.01
84 58 0.19
85 55 0.18
86 91 0.29
87 28 0.09
88 35 0.11
89 37 0.12
90 4 0.01
ACGTcount: A:0.23, C:0.12, G:0.21, T:0.44
Consensus pattern (86 bp):
TTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTATTTATTTGTTCAAGTCGTAGAGCCTCTGTT
TAGAAGGAGCTTTGTTTATTT
Found at i:29463 original size:4 final size:4
Alignment explanation
Indices: 29404--29444 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
29394 ATTTTGTATT
*
29404 TTTA TTT- TGTA TCTTA TTTA TTTA TTTA TTTA -TTA TTTA TT
1 TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TT
29445 GCTATTATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
3 5 0.16
4 24 0.75
5 3 0.09
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:29472 original size:38 final size:38
Alignment explanation
Indices: 29417--29574 Score: 98
Period size: 38 Copynumber: 4.3 Consensus size: 38
29407 ATTTTGTATC
* * * **
29417 TTATTTATTTATTTATTTATTATTTATTGCTAT-TATTA
1 TTATTTATTAATATATTT-TTATCTATTAATATATATTA
29455 TTATTTATTAATATATTTTTATCTATTAATATATATTA
1 TTATTTATTAATATATTTTTATCTATTAATATATATTA
* * * * * *
29493 TTTTTTATCT-AT-TA-ATGTA--TATAAATTTTTATTA
1 TTATTTAT-TAATATATTTTTATCTATTAATATATATTA
** *
29527 TTAACTATTAA-ATATTATTTATCTATTAGTATATA-TA
1 TTATTTATTAATATATT-TTTATCTATTAATATATATTA
29564 TTTATTTATTA
1 -TTATTTATTA
29575 TTTATCTATT
Statistics
Matches: 89, Mismatches: 22, Indels: 18
0.69 0.17 0.14
Matches are distributed among these distances:
33 1 0.01
34 20 0.22
36 6 0.07
37 15 0.17
38 46 0.52
39 1 0.01
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (38 bp):
TTATTTATTAATATATTTTTATCTATTAATATATATTA
Found at i:29476 original size:24 final size:25
Alignment explanation
Indices: 29449--29566 Score: 85
Period size: 24 Copynumber: 5.0 Consensus size: 25
29439 TTTATTGCTA
*
29449 TTAT-TATTATTTATTAATATATTT
1 TTATCTATTATGTATTAATATATTT
* *
29473 TTATCTATTA-ATATATATTAT-TTT
1 TTATCTATTATGTAT-TAATATATTT
*
29497 TTATCTATTAATGTA-T-ATAAATTT
1 TTATCTATT-ATGTATTAATATATTT
**
29521 TTAT-TATTAACTATTAA-ATATTAT
1 TTATCTATTATGTATTAATATATT-T
29545 TTATCTATTA-GTA-T-ATATATTT
1 TTATCTATTATGTATTAATATATTT
29567 ATTTATTATT
Statistics
Matches: 75, Mismatches: 9, Indels: 22
0.71 0.08 0.21
Matches are distributed among these distances:
22 5 0.07
23 17 0.23
24 35 0.47
25 16 0.21
26 2 0.03
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (25 bp):
TTATCTATTATGTATTAATATATTT
Found at i:29481 original size:31 final size:34
Alignment explanation
Indices: 29421--29491 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
29411 TGTATCTTAT
* * *
29421 TTATTTATTTATTTATTATTTATTGCTATTATTA
1 TTATTTATTAATATATTATTTATTGCTATTAATA
29455 TTATTTATTAATATATT-TTTA-T-CTATTAATA
1 TTATTTATTAATATATTATTTATTGCTATTAATA
29486 TATATT
1 T-TATT
29492 ATTTTTTATC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 9 0.27
32 5 0.15
33 4 0.12
34 15 0.45
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (34 bp):
TTATTTATTAATATATTATTTATTGCTATTAATA
Found at i:29568 original size:24 final size:24
Alignment explanation
Indices: 29465--29576 Score: 110
Period size: 24 Copynumber: 4.8 Consensus size: 24
29455 TTATTTATTA
29465 ATATA-TTTTTATCTATTAA-TAT
1 ATATATTTTTTATCTATTAAGTAT
29487 ATATTATTTTTTATCTATTAATGTAT
1 ATA-TATTTTTTATCTATTAA-GTAT
* *
29513 ATA-AATTTTTAT-TATTAACTATT
1 ATATATTTTTTATCTATTAAGTA-T
* *
29536 AAATATTATTTATCTATT-AGTAT
1 ATATATTTTTTATCTATTAAGTAT
29559 ATATATTTATTTAT-TATT
1 ATATATTT-TTTATCTATT
29577 TATCTATTTT
Statistics
Matches: 74, Mismatches: 8, Indels: 15
0.76 0.08 0.15
Matches are distributed among these distances:
22 5 0.07
23 22 0.30
24 37 0.50
25 4 0.05
26 6 0.08
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.59
Consensus pattern (24 bp):
ATATATTTTTTATCTATTAAGTAT
Found at i:29590 original size:17 final size:17
Alignment explanation
Indices: 29517--29602 Score: 58
Period size: 17 Copynumber: 5.4 Consensus size: 17
29507 ATGTATATAA
*
29517 ATTTTTATTA-TTAACT
1 ATTTTTATTATTTATCT
**
29533 ATTAAATATTATTTATCT
1 ATT-TTTATTATTTATCT
** *
29551 ATTAGTA-TATATAT-T
1 ATTTTTATTATTTATCT
*
29566 -TATTTATTATTTATCT
1 ATTTTTATTATTTATCT
29582 ATTTTTATTATTT-T-T
1 ATTTTTATTATTTATCT
29597 ATTTTT
1 ATTTTT
29603 CACTGGGATT
Statistics
Matches: 55, Mismatches: 10, Indels: 11
0.72 0.13 0.14
Matches are distributed among these distances:
14 3 0.05
15 14 0.25
16 11 0.20
17 19 0.35
18 8 0.15
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.65
Consensus pattern (17 bp):
ATTTTTATTATTTATCT
Found at i:29591 original size:48 final size:47
Alignment explanation
Indices: 29426--29594 Score: 135
Period size: 48 Copynumber: 3.7 Consensus size: 47
29416 CTTATTTATT
29426 TATTTATTTATTATTTATTGCTATTATTATTATTTAT-TA--A-TATAT-
1 TATTTATTTATTA-TTA-T-CTATTATTATTATTTATCTATTAGTATATA
* * *
29471 T-TTTATCTATTA--ATATA-TATTATTTTTTATCTATTAATGTATATA
1 TATTTATTTATTATTATCTATTATTATTATTTATCTATT-A-GTATATA
* * *
29516 -AATT-TTTATTATTAACTATTAAATATTATTTATCTATTAGTATATA
1 TATTTATTTATTATTATCTATT-ATTATTATTTATCTATTAGTATATA
*
29562 TATTTATTTATTATTTATCTATTTTTATTATTT
1 TATTTATTTATTA-TTATCTATTATTATTATTT
29595 TTATTTTTCA
Statistics
Matches: 96, Mismatches: 13, Indels: 27
0.71 0.10 0.20
Matches are distributed among these distances:
38 12 0.12
39 4 0.04
40 1 0.01
41 1 0.01
42 1 0.01
44 21 0.22
45 3 0.03
46 10 0.10
47 5 0.05
48 30 0.31
49 8 0.08
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (47 bp):
TATTTATTTATTATTATCTATTATTATTATTTATCTATTAGTATATA
Found at i:30320 original size:3 final size:3
Alignment explanation
Indices: 30314--30375 Score: 88
Period size: 3 Copynumber: 19.7 Consensus size: 3
30304 TTTTTCTTAT
*
30314 TTA TTA TTA TTA TTA TTTC TTA TTTA TTTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA
30362 TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
30376 TATTGATTAG
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
3 46 0.84
4 9 0.16
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:30340 original size:27 final size:25
Alignment explanation
Indices: 30310--30384 Score: 98
Period size: 27 Copynumber: 2.9 Consensus size: 25
30300 TTTTTTTTTC
*
30310 TTATTTATTATTATTATTATTTCTTA
1 TTATTTATTATTATTATTA-TTATTA
30336 TTTATTTATTATTATTATTATTATTA
1 -TTATTTATTATTATTATTATTATTA
30362 TTA-TTATTATTATTTATTGATTA
1 TTATTTATTATTA-TTATT-ATTA
30385 GATTAGAATT
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
24 9 0.20
25 8 0.18
26 9 0.20
27 19 0.42
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (25 bp):
TTATTTATTATTATTATTATTATTA
Found at i:30571 original size:58 final size:57
Alignment explanation
Indices: 30431--30571 Score: 173
Period size: 58 Copynumber: 2.5 Consensus size: 57
30421 AAAAAATAAT
* *
30431 TTTCTTT-AAATAAAATTCC-AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAA
1 TTTCTTTGAAAT-AATTTCCTAAAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAA
* *
30487 TTTTTCTTGAAAATAAGTTT--TCAAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAA
1 TTTCT-TTG-AAATAA-TTTCCTAAAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAA
30545 TTGTCTTTGAAATAATTTCCTAAAAAA
1 TT-TCTTTGAAATAATTTCCTAAAAAA
30572 GGTTTTTTTT
Statistics
Matches: 71, Mismatches: 6, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
56 7 0.10
57 8 0.11
58 48 0.68
59 8 0.11
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.37
Consensus pattern (57 bp):
TTTCTTTGAAATAATTTCCTAAAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAA
Found at i:30580 original size:58 final size:58
Alignment explanation
Indices: 30446--30571 Score: 177
Period size: 58 Copynumber: 2.2 Consensus size: 58
30436 TTAAATAAAA
* *
30446 TTCCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGT
1 TTCC-AAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTCTCTTGAAAATAAGT
*
30505 TTTCAAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTGTCT-TTG-AAATAA-T
1 TTCCAAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATT-TCTCTTGAAAATAAGT
*
30561 TTCCTAAAAAA
1 TTCCAAAAAAA
30572 GGTTTTTTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
56 10 0.16
57 6 0.10
58 40 0.66
59 5 0.08
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (58 bp):
TTCCAAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTCTCTTGAAAATAAGT
Found at i:33163 original size:16 final size:16
Alignment explanation
Indices: 33142--33172 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
33132 TCCTACCTTT
*
33142 TATTATTGTGTCATAA
1 TATTATTATGTCATAA
33158 TATTATTATGTCATA
1 TATTATTATGTCATA
33173 GACTGATCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.06, G:0.10, T:0.52
Consensus pattern (16 bp):
TATTATTATGTCATAA
Found at i:35809 original size:22 final size:21
Alignment explanation
Indices: 35784--35833 Score: 57
Period size: 24 Copynumber: 2.3 Consensus size: 21
35774 ACAAATTTAA
*
35784 CTTAATTA-AATTAATTTGGAC
1 CTTAATAATAATTAATTT-GAC
35805 TCTTAAATAATAATTAATTTGAC
1 -CTT-AATAATAATTAATTTGAC
35828 CTTAAT
1 CTTAAT
35834 CCCTTCCCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 3 0.12
22 6 0.24
23 7 0.28
24 9 0.36
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (21 bp):
CTTAATAATAATTAATTTGAC
Found at i:37515 original size:41 final size:40
Alignment explanation
Indices: 37470--37698 Score: 275
Period size: 41 Copynumber: 5.7 Consensus size: 40
37460 GCAAATAGAC
*
37470 ATGCAATGAAATATATAATCATGCAATTAACAATGTAAAAT
1 ATGCAAT-AAATATATAATCATGCAATTAACAATATAAAAT
37511 ATGCAAATAAATATATAATCATGCAATTAACAATA-AAAAT
1 ATGC-AATAAATATATAATCATGCAATTAACAATATAAAAT
*
37551 CATGCAAATAAATATATAATAATGCAATTAACAATAT-AAAT
1 -ATGC-AATAAATATATAATCATGCAATTAACAATATAAAAT
* * * *
37592 CATGCAA-ATATATATAATTAAGCAATTAACAATATAAAAC
1 -ATGCAATAAATATATAATCATGCAATTAACAATATAAAAT
* * *
37632 ATGCACTAAATATATAATCAAGCAATTAACAATATAAAAC
1 ATGCAATAAATATATAATCATGCAATTAACAATATAAAAT
* * *
37672 ATGCCATTGAATATAAAATCATGCAAT
1 ATG-CAATAAATATATAATCATGCAAT
37699 CACACAAATA
Statistics
Matches: 169, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
39 30 0.18
40 44 0.26
41 92 0.54
42 3 0.02
ACGTcount: A:0.54, C:0.12, G:0.07, T:0.28
Consensus pattern (40 bp):
ATGCAATAAATATATAATCATGCAATTAACAATATAAAAT
Found at i:37516 original size:21 final size:22
Alignment explanation
Indices: 37479--37698 Score: 170
Period size: 21 Copynumber: 10.8 Consensus size: 22
37469 CATGCAATGA
*
37479 AATATATAATCATGCAATTAAC
1 AATATAAAATCATGCAATTAAC
* *
37501 AATGTAAAAT-ATGCAAAT-A-
1 AATATAAAATCATGCAATTAAC
*
37520 AATATATAATCATGCAATTAAC
1 AATATAAAATCATGCAATTAAC
*
37542 AATA-AAAATCATGCAAAT-A-
1 AATATAAAATCATGCAATTAAC
* *
37561 AATATATAATAATGCAATTAAC
1 AATATAAAATCATGCAATTAAC
37583 AATAT-AAATCATGC-A--AA-
1 AATATAAAATCATGCAATTAAC
* * * *
37600 TATATATAATTAAGCAATTAAC
1 AATATAAAATCATGCAATTAAC
*
37622 AATATAAAA-CATGC-ACT-A-
1 AATATAAAATCATGCAATTAAC
* *
37640 AATATATAATCAAGCAATTAAC
1 AATATAAAATCATGCAATTAAC
* *
37662 AATATAAAA-CATGCCATT--G
1 AATATAAAATCATGCAATTAAC
37681 AATATAAAATCATGCAAT
1 AATATAAAATCATGCAAT
37699 CACACAAATA
Statistics
Matches: 152, Mismatches: 30, Indels: 34
0.70 0.14 0.16
Matches are distributed among these distances:
17 4 0.03
18 16 0.11
19 27 0.18
20 32 0.21
21 41 0.27
22 32 0.21
ACGTcount: A:0.54, C:0.12, G:0.06, T:0.28
Consensus pattern (22 bp):
AATATAAAATCATGCAATTAAC
Found at i:37675 original size:120 final size:121
Alignment explanation
Indices: 37480--37711 Score: 317
Period size: 120 Copynumber: 1.9 Consensus size: 121
37470 ATGCAATGAA
* * * *
37480 ATATATAATCATGCAATTAACAATGTAAAATATGCAAATAAATATATAATCATGCAATTAACAAT
1 ATATATAATCAAGCAATTAACAATATAAAACATGCAAATAAATATATAATCAAGCAATTAACAAT
* *
37545 AAAAATCATGCAAATAAATATATAATAATGCAATTA-ACAATATAAATCATGCAAAT
66 AAAAATCATGCAAATAAATATAAAATAATGCAATCACACAA-ATAAATCATGCAAAT
* *
37601 ATATATAATTAAGCAATTAACAATATAAAACATGC-ACTAAATATATAATCAAGCAATTAACAAT
1 ATATATAATCAAGCAATTAACAATATAAAACATGCAAATAAATATATAATCAAGCAATTAACAAT
* * * *
37665 ATAAAA-CATGCCATTGAATATAAAATCATGCAATCACACAAATAAAT
66 A-AAAATCATGCAAATAAATATAAAATAATGCAATCACACAAATAAAT
37712 AAATTGATAA
Statistics
Matches: 97, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
120 58 0.60
121 39 0.40
ACGTcount: A:0.54, C:0.12, G:0.06, T:0.28
Consensus pattern (121 bp):
ATATATAATCAAGCAATTAACAATATAAAACATGCAAATAAATATATAATCAAGCAATTAACAAT
AAAAATCATGCAAATAAATATAAAATAATGCAATCACACAAATAAATCATGCAAAT
Found at i:37803 original size:16 final size:16
Alignment explanation
Indices: 37784--37829 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
37774 ATTAATTATA
37784 CAAATAAAATATTAAG
1 CAAATAAAATATTAAG
* * *
37800 CAAATAAATTATCATG
1 CAAATAAAATATTAAG
*
37816 CAAATATAATATTA
1 CAAATAAAATATTA
37830 GTCATGCAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.57, C:0.09, G:0.04, T:0.30
Consensus pattern (16 bp):
CAAATAAAATATTAAG
Found at i:37836 original size:20 final size:18
Alignment explanation
Indices: 37803--37840 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 18
37793 TATTAAGCAA
37803 ATAAATTATCATGCAAAT
1 ATAAATTATCATGCAAAT
37821 ATAATATTAGTCATGCAAAT
1 ATAA-ATTA-TCATGCAAAT
37841 TCATGCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
19 4 0.22
20 10 0.56
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.34
Consensus pattern (18 bp):
ATAAATTATCATGCAAAT
Done.