Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 7 of 120
Found at i:1854607 original size:110 final size:113
Alignment explanation
Indices: 1854470--1854805 Score: 398
Period size: 110 Copynumber: 3.0 Consensus size: 113
1854460 AGGGTAAAAT
* * * *
1854470 AGTAATTTTTTGTGAAATCGAGGTTAAAAATGGGATTTTGGAAAGCTT-GAGGGTAAAACGGTAA
1 AGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAG-GGGTAAAATGGTAA
*
1854534 TTTTTGGTGAACTCGGGGTTAAAAATGGAATTTTGGAAAGTTTA-CCT-
65 TTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGCCTA
*
1854581 A-TAATTTTAGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAAT
1 AGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAAT
** * * * **
1854645 TTTTAATGAAATCGAGGTTAAAAAT-AAGATTTTAGAAAGTTTAGGGGTAAA
66 TTTTGGTGAAATCGGGGTTAAAAATGGA-ATTTTGGAAAGTTTA-GCCT--A
* * * *
1854696 ATGGTAATTTTTGGTAAAAT-TAGGGTTAAAAGTGGAATTTTGGAAAGTTTAGGGGTAAGATGGT
1 A--GTAATTTTTGGTGAAATCGA-GGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGT
1854760 AATTTTTGGTGAAATCGGGGTT-AAAATGGAATTTTGGAAAGTTTAG
63 AATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAG
1854806 GGGTAAAATG
Statistics
Matches: 190, Mismatches: 23, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
109 1 0.01
110 91 0.48
111 2 0.01
112 1 0.01
115 1 0.01
116 1 0.01
117 20 0.11
118 73 0.38
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (113 bp):
AGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAAT
TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGCCTA
Found at i:1854645 original size:29 final size:29
Alignment explanation
Indices: 1854606--1854865 Score: 179
Period size: 29 Copynumber: 8.9 Consensus size: 29
1854596 ATCGAGGTTA
1854606 AAAATGG-AATTTTGGAAAGTTTAGGGGT
1 AAAATGGTAATTTTGGAAAGTTTAGGGGT
* ** *
1854634 AAAATGGTAATTTTTAATGAAA-TCGA-GGTT
1 AAAATGGTAA-TTTT--GGAAAGTTTAGGGGT
* *
1854664 AAAAAT--AAGATTTTAGAAAGTTTAGGGGT
1 -AAAATGGTA-ATTTTGGAAAGTTTAGGGGT
* *
1854693 AAAATGGTAATTTTTGGTAAA-ATTAGGGTT
1 AAAATGGTAA-TTTTGG-AAAGTTTAGGGGT
1854723 AAAAGTGG-AATTTTGGAAAGTTTAGGGGT
1 AAAA-TGGTAATTTTGGAAAGTTTAGGGGT
* *
1854752 AAGATGGTAATTTTTGGTGAAA---TCGGGGTT
1 AAAATGGTAA-TTTT-G-GAAAGTTTAGGGG-T
1854782 AAAATGG-AATTTTGGAAAGTTTAGGGGT
1 AAAATGGTAATTTTGGAAAGTTTAGGGGT
1854810 AAAATGGTAATTTTTGG-AAGTTTA-GGGT
1 AAAATGGTAA-TTTTGGAAAGTTTAGGGGT
**
1854838 CAAAAT-GTAATTTTCTAAAGTTTTAGGG
1 -AAAATGGTAATTTTGGAAAG-TTTAGGG
1854866 TCAAAATATA
Statistics
Matches: 183, Mismatches: 21, Indels: 54
0.71 0.08 0.21
Matches are distributed among these distances:
26 4 0.02
27 9 0.05
28 43 0.23
29 59 0.32
30 46 0.25
31 14 0.08
32 8 0.04
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.35
Consensus pattern (29 bp):
AAAATGGTAATTTTGGAAAGTTTAGGGGT
Found at i:1854695 original size:169 final size:172
Alignment explanation
Indices: 1854432--1854824 Score: 503
Period size: 169 Copynumber: 2.3 Consensus size: 172
1854422 GAAAATTTAG
* * **
1854432 GGTTAAAAAT-GAGATTTT-GAAAGGTTTAAGGGTAAAATAGTAATTTTTTGTGAAATCGAGGTT
1 GGTTAAAAATGGA-ATTTTGGAAA-GTTTAGGGGTAAAATGGTAATTTTTAATGAAATCGAGGTT
** * * * *
1854495 AAAAATGGGATTTTGGAAAGCTTGAGGGTAAAACGGTAATTTTTGGTGAACTCGGGGTTAAAAAT
64 AAAAATAAGATTTTAGAAAGCTTGAGGGTAAAACGGTAATTTTTGGTAAAATCAGGGTTAAAAAT
1854560 GGAATTTTGGAAAGTTTA-CCT-A-TAATTTTAGGTGAAATCGA
129 GGAATTTTGGAAAGTTTAGCCTAAGTAATTTTAGGTGAAATCGA
1854601 GGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTAATGAAATCGAGGTTAA
1 GGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTAATGAAATCGAGGTTAA
* * * *
1854666 AAATAAGATTTTAGAAAG-TTTAGGGGTAAAATGGTAATTTTTGGTAAAATTAGGGTTAAAAGTG
66 AAATAAGATTTTAGAAAGCTTGA-GGGTAAAACGGTAATTTTTGGTAAAATCAGGGTTAAAAATG
** * *
1854730 GAATTTTGGAAAGTTTAGGGGTAAGATGGTAATTTTTGGTGAAATCGG
130 GAATTTTGGAAAGTTTA-GCCT-A-A--GTAATTTTAGGTGAAATCGA
1854778 GGTT-AAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTT
1 GGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTT
1854825 GGAAGTTTAG
Statistics
Matches: 195, Mismatches: 18, Indels: 15
0.86 0.08 0.07
Matches are distributed among these distances:
168 3 0.02
169 120 0.62
170 6 0.03
171 1 0.01
174 1 0.01
176 43 0.22
177 21 0.11
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.35
Consensus pattern (172 bp):
GGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTAATGAAATCGAGGTTAA
AAATAAGATTTTAGAAAGCTTGAGGGTAAAACGGTAATTTTTGGTAAAATCAGGGTTAAAAATGG
AATTTTGGAAAGTTTAGCCTAAGTAATTTTAGGTGAAATCGA
Found at i:1854878 original size:57 final size:58
Alignment explanation
Indices: 1854606--1854894 Score: 232
Period size: 59 Copynumber: 5.0 Consensus size: 58
1854596 ATCGAGGTTA
* * * ** * *
1854606 AAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTT-AATGAAATCGAGGTTA
1 AAAATGGAATTTTCGAAAGTTTAGGGGTAAAATGATAATTTTTGGAT-AGTTC-AGGGTC
* * * * * *
1854665 AAAAT-AAGATTTTAGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTAAAATT-AGGGTT
1 AAAATGGA-ATTTTCGAAAGTTTAGGGGTAAAATGATAATTTTTGG-ATAGTTCAGGGTC
* * * ** * *
1854723 AAAAGTGGAATTTTGGAAAGTTTAGGGGTAAGATGGTAATTTTTGG-TGAAATCGGGGTT
1 AAAA-TGGAATTTTCGAAAGTTTAGGGGTAAAATGATAATTTTTGGAT-AGTTCAGGGTC
* * *
1854782 AAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGA-AGTTTAGGGTC
1 AAAATGGAATTTTCGAAAGTTTAGGGGTAAAATGATAATTTTTGGATAGTTCAGGGTC
* *
1854839 AAAATGTAATTTTCTAAAGTTTTA-GGGTCAAAAT-ATAATTTTTGGATAGTTCAGGG
1 AAAATGGAATTTTCGAAAG-TTTAGGGGT-AAAATGATAATTTTTGGATAGTTCAGGG
1854895 ACCTTTAAAC
Statistics
Matches: 195, Mismatches: 24, Indels: 23
0.81 0.10 0.10
Matches are distributed among these distances:
57 37 0.19
58 69 0.35
59 84 0.43
60 4 0.02
61 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.36
Consensus pattern (58 bp):
AAAATGGAATTTTCGAAAGTTTAGGGGTAAAATGATAATTTTTGGATAGTTCAGGGTC
Found at i:1854894 original size:29 final size:29
Alignment explanation
Indices: 1854674--1854894 Score: 149
Period size: 29 Copynumber: 7.6 Consensus size: 29
1854664 AAAAATAAGA
*
1854674 TTTTAGAAAGTTTAGGGGT-AAAATGGTAAT
1 TTTTGGAAAGTTTA-GGGTCAAAAT-GTAAT
* * *
1854704 TTTTGGTAAA-ATTAGGGTTAAAAGTGGAA-
1 TTTTGG-AAAGTTTAGGGTCAAAA-TGTAAT
*
1854733 TTTTGGAAAGTTTAGGGGT-AAGATGGTAAT
1 TTTTGGAAAGTTTA-GGGTCAAAAT-GTAAT
** * *
1854763 TTTTGGTGAAA--TCGGGGTTAAAATGGAA-
1 TTTT-G-GAAAGTTTAGGGTCAAAATGTAAT
1854791 TTTTGGAAAGTTTAGGGGT-AAAATGGTAAT
1 TTTTGGAAAGTTTA-GGGTCAAAAT-GTAAT
1854821 TTTTGG-AAGTTTAGGGTCAAAATGTAAT
1 TTTTGGAAAGTTTAGGGTCAAAATGTAAT
*
1854849 TTTCT--AAAGTTTTAGGGTCAAAATATAAT
1 TTT-TGGAAAG-TTTAGGGTCAAAATGTAAT
* *
1854878 TTTTGGATAGTTCAGGG
1 TTTTGGAAAGTTTAGGG
1854895 ACCTTTAAAC
Statistics
Matches: 154, Mismatches: 16, Indels: 43
0.72 0.08 0.20
Matches are distributed among these distances:
26 4 0.03
27 1 0.01
28 30 0.19
29 73 0.47
30 37 0.24
31 5 0.03
32 4 0.03
ACGTcount: A:0.33, C:0.02, G:0.28, T:0.37
Consensus pattern (29 bp):
TTTTGGAAAGTTTAGGGTCAAAATGTAAT
Found at i:1856875 original size:17 final size:17
Alignment explanation
Indices: 1856848--1856931 Score: 87
Period size: 17 Copynumber: 4.8 Consensus size: 17
1856838 TTAAATTTTC
1856848 ATTTCAAAATAAATTTAA
1 ATTT-AAAATAAATTTAA
1856866 ATTTAAAATAAATTTAA
1 ATTTAAAATAAATTTAA
* ** * *
1856883 ACTCCAAACAAGTTTTAA
1 ATTTAAAATAA-ATTTAA
*
1856901 ATTTATAATAAATTTAA
1 ATTTAAAATAAATTTAA
*
1856918 ATTTAAAATGAATT
1 ATTTAAAATAAATT
1856932 AAAAATCTAA
Statistics
Matches: 52, Mismatches: 13, Indels: 3
0.76 0.19 0.04
Matches are distributed among these distances:
17 37 0.71
18 15 0.29
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.39
Consensus pattern (17 bp):
ATTTAAAATAAATTTAA
Found at i:1862351 original size:35 final size:37
Alignment explanation
Indices: 1862320--1862393 Score: 100
Period size: 37 Copynumber: 2.1 Consensus size: 37
1862310 CTAAGTTTGG
1862320 TTAA-ATTTAAATATA-A-TTTAATTTTTCAAGTTTAA
1 TTAATATTTAAA-ATAGATTTTAATTTTTCAAGTTTAA
* *
1862355 TTAATTTTTAAAATAGATTTTAATTTTTTAAGTTTAA
1 TTAATATTTAAAATAGATTTTAATTTTTCAAGTTTAA
1862392 TT
1 TT
1862394 TGAGTTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 7 0.21
36 7 0.21
37 20 0.59
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.55
Consensus pattern (37 bp):
TTAATATTTAAAATAGATTTTAATTTTTCAAGTTTAA
Found at i:1862377 original size:37 final size:40
Alignment explanation
Indices: 1862336--1862413 Score: 117
Period size: 37 Copynumber: 2.0 Consensus size: 40
1862326 TTAAATATAA
1862336 TTTAATTTTTCAAGTTTAA-TT-AATTTTTAAAA-TAGAT
1 TTTAATTTTTCAAGTTTAATTTGAATTTTTAAAATTAGAT
* *
1862373 TTTAATTTTTTAAGTTTAATTTGAGTTTTTAAAATTAGAT
1 TTTAATTTTTCAAGTTTAATTTGAATTTTTAAAATTAGAT
1862413 T
1 T
1862414 AAAGTTAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
37 18 0.50
38 2 0.06
39 10 0.28
40 6 0.17
ACGTcount: A:0.35, C:0.01, G:0.08, T:0.56
Consensus pattern (40 bp):
TTTAATTTTTCAAGTTTAATTTGAATTTTTAAAATTAGAT
Found at i:1863348 original size:23 final size:23
Alignment explanation
Indices: 1863308--1863390 Score: 125
Period size: 23 Copynumber: 3.7 Consensus size: 23
1863298 TTTAAATTAT
*
1863308 TTAATTAATT-AATTTGAATAAC
1 TTAAATAATTAAATTTGAATAAC
1863330 TTAAATAATTAAATTTGAATAAC
1 TTAAATAATTAAATTTGAATAAC
*
1863353 TTAAATAATTAAATTTGATTAAC
1 TTAAATAATTAAATTTGAATAAC
*
1863376 TTAAA-ATTTAAATTT
1 TTAAATAATTAAATTT
1863391 TTATTTTATT
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
22 18 0.32
23 39 0.68
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (23 bp):
TTAAATAATTAAATTTGAATAAC
Found at i:1864480 original size:21 final size:19
Alignment explanation
Indices: 1864456--1864503 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
1864446 TTAAATTTTC
* *
1864456 ATATATATATATTTTAAAA
1 ATATATAAAAATTTTAAAA
1864475 ATATATAAAAATTTTAAAA
1 ATATATAAAAATTTTAAAA
1864494 A-ATA-AAAAAT
1 ATATATAAAAAT
1864504 AAAAGAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 6 0.22
18 3 0.11
19 18 0.67
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
ATATATAAAAATTTTAAAA
Found at i:1864556 original size:2 final size:2
Alignment explanation
Indices: 1864551--1864583 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1864541 ATATAATTTT
1864551 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1864584 TCTAAAAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1866582 original size:509 final size:510
Alignment explanation
Indices: 1865624--1866604 Score: 1757
Period size: 509 Copynumber: 1.9 Consensus size: 510
1865614 CAATTTGGAG
*
1865624 GCCTACCAATCGATTTCAACTCATGGACATTGAGAATGACTACTATCTCGCAAAATTTGAATCTG
1 GCCTACCAATCAATTTCAACTCATGGACATTGAGAATGACTACTATCTCGCAAAATTTGAATCTG
* * *
1865689 CATTAGATTACAATATGGTACTTTCGAAGGGACTTTGGGTGGTTTATGGATATTATCTTACTGTT
66 CATTAGATTACAATATGGTACTTTCAAAGGGACCTTGGGTGGTTTATGGACATTATCTTACTGTT
*
1865754 CAACCTTGGTCATCGAATTTTTCGACGTTAGATGCCTTTCCTCAGAATGTTGTTGCGTGGATTAG
131 CAACCCTGGTCATCGAATTTTTCGACGTTAGATGCCTTTCCTCAGAATGTTGTTGCGTGGATTAG
* * *
1865819 GATACCTGGTCTTTCGGGTGCATTCTATAAAAGGAGTATGTTGCAAGAGATCGGAAGTTTGGTTG
196 GATACCTAGTCTTTCGGGTGCATTCTATAAAAGGAGTATGTTGCAAGACATCGGAAGTTAGGTTG
*
1865884 GAAAGGTTGTGAAAATTGACATGAATACTGATTCTGGTGAGAGGGGGTAGTTTGCACGATTTGCG
261 GAAAGGTTGTGAAAATTGACATGAATACTGATTCTGGTGAGAGGGGGCAGTTTGCACGATTTGCG
* * *
1865949 GTAAAGGTCAATCTTGCTGAACCACTTGTTTCGAAAATTTGTATTGCGAAAAGGATACATAGAGT
326 GTAAAGGTCAATCTTACTGAACCACTTATTTCGAAAATTCGTATTGCGAAAAGGATACATAGAGT
* *
1866014 GGAGTACGAATCTCTTCCATTTGTGTGTTTTGGTTGTGGTTGAGTTGGTCATATGAAGGATACCT
391 GGAGTACGAATCTCTTCCATCTGTGTGTTTTGGTTGTGGTCGAGTTGGTCATATGAAGGATACCT
1866079 GCCCGCTGGTATCGATGTGTGTTTTGGTTGTGGTCGGGTTGGTTATATGAAGGAT
456 GCCCGCTGGTATCGATGTGTGTTTTGGTTGTGGTCGGGTTGGTTATATGAAGGAT
*
1866134 GCCTACCAATCAATTTCAACTCATGGACATTGAGAATGACTACTTTCTCGCAAAATTTGAATCTG
1 GCCTACCAATCAATTTCAACTCATGGACATTGAGAATGACTACTATCTCGCAAAATTTGAATCTG
1866199 CATTAGA-TACAATATGGTACTTTCAAAGGGACCTTGGGTGGTTTATGGACATTATCTTACTGTT
66 CATTAGATTACAATATGGTACTTTCAAAGGGACCTTGGGTGGTTTATGGACATTATCTTACTGTT
*
1866263 CAACCCTGGTCATCGAATTTTTCGACGTTAGATGCTTTTCCTCAGAATGTTGTTGCGTGGATTAG
131 CAACCCTGGTCATCGAATTTTTCGACGTTAGATGCCTTTCCTCAGAATGTTGTTGCGTGGATTAG
1866328 GATACCTAGTCTTTCGGGTGCATTCTATAAAAGGAGTATGTTGCAAGACATCGGAAGTTAGGTTG
196 GATACCTAGTCTTTCGGGTGCATTCTATAAAAGGAGTATGTTGCAAGACATCGGAAGTTAGGTTG
* *
1866393 GAAAGGTTGTGAAAATTGACATGAATACTGATTCTGGTGCGAGGGGGCAGTTTGCACGGTTTGCG
261 GAAAGGTTGTGAAAATTGACATGAATACTGATTCTGGTGAGAGGGGGCAGTTTGCACGATTTGCG
*
1866458 GTACAGGTCAATCTTACTGAACCACTTATTTCGAAAATTCGTATTGCGAAAAGGATACATAGAGT
326 GTAAAGGTCAATCTTACTGAACCACTTATTTCGAAAATTCGTATTGCGAAAAGGATACATAGAGT
* **
1866523 GGAGTACGAATCTCTTCCATCTGTGTGTTTTGGTTGTGGTCGGGTTGGTCATATGAAGGATGTCT
391 GGAGTACGAATCTCTTCCATCTGTGTGTTTTGGTTGTGGTCGAGTTGGTCATATGAAGGATACCT
1866588 GCCCGCTGGTATCGATG
456 GCCCGCTGGTATCGATG
1866605 GAGAAATGTC
Statistics
Matches: 449, Mismatches: 22, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
509 379 0.84
510 70 0.16
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.34
Consensus pattern (510 bp):
GCCTACCAATCAATTTCAACTCATGGACATTGAGAATGACTACTATCTCGCAAAATTTGAATCTG
CATTAGATTACAATATGGTACTTTCAAAGGGACCTTGGGTGGTTTATGGACATTATCTTACTGTT
CAACCCTGGTCATCGAATTTTTCGACGTTAGATGCCTTTCCTCAGAATGTTGTTGCGTGGATTAG
GATACCTAGTCTTTCGGGTGCATTCTATAAAAGGAGTATGTTGCAAGACATCGGAAGTTAGGTTG
GAAAGGTTGTGAAAATTGACATGAATACTGATTCTGGTGAGAGGGGGCAGTTTGCACGATTTGCG
GTAAAGGTCAATCTTACTGAACCACTTATTTCGAAAATTCGTATTGCGAAAAGGATACATAGAGT
GGAGTACGAATCTCTTCCATCTGTGTGTTTTGGTTGTGGTCGAGTTGGTCATATGAAGGATACCT
GCCCGCTGGTATCGATGTGTGTTTTGGTTGTGGTCGGGTTGGTTATATGAAGGAT
Found at i:1873424 original size:6 final size:6
Alignment explanation
Indices: 1873399--1873443 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
1873389 ACAATTCATA
* * * *
1873399 TCACTT TCAATT CCAATT TCACTT TCAATT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
1873444 ATTTTGATCA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.24, C:0.29, G:0.00, T:0.47
Consensus pattern (6 bp):
TCACTT
Found at i:1873447 original size:18 final size:18
Alignment explanation
Indices: 1873399--1873447 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
1873389 ACAATTCATA
*
1873399 TCACTTTCAATTCCAATT
1 TCACTTTCAATTTCAATT
*
1873417 TCACTTTCAATTTCACTT
1 TCACTTTCAATTTCAATT
1873435 TCACTTTCAATTT
1 TCACTTTCAATTT
1873448 TGATCACAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTTCAATT
Found at i:1875359 original size:19 final size:19
Alignment explanation
Indices: 1875301--1875360 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
1875291 CCAAATCAGT
* *
1875301 AAATGATTTTAAATTTATTA
1 AAATTATTTTAAAATTA-TA
*
1875321 AATTTATTTTTTAAAA-TATA
1 AAATTA--TTTTAAAATTATA
1875341 AAATTATTTTAAAATTATA
1 AAATTATTTTAAAATTATA
1875360 A
1 A
1875361 TCATCATCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
18 8 0.24
19 5 0.15
20 11 0.33
21 2 0.06
22 7 0.21
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (19 bp):
AAATTATTTTAAAATTATA
Found at i:1876226 original size:8 final size:8
Alignment explanation
Indices: 1876213--1876237 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1876203 ACTTTAAAAA
1876213 ATAATTTT
1 ATAATTTT
1876221 ATAATTTT
1 ATAATTTT
1876229 ATAATTTT
1 ATAATTTT
1876237 A
1 A
1876238 AAAAATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
ATAATTTT
Found at i:1876228 original size:28 final size:30
Alignment explanation
Indices: 1876187--1876259 Score: 123
Period size: 29 Copynumber: 2.5 Consensus size: 30
1876177 GATGATGATG
1876187 ATTTTAATAATTTTAT-ACTTTAAAAAATA
1 ATTTTAATAATTTTATAACTTTAAAAAATA
*
1876216 ATTTT-ATAATTTTATAATTTTAAAAAATA
1 ATTTTAATAATTTTATAACTTTAAAAAATA
1876245 ATTTTAATAATTTTA
1 ATTTTAATAATTTTA
1876260 AAATCATTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
28 10 0.24
29 22 0.54
30 9 0.22
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (30 bp):
ATTTTAATAATTTTATAACTTTAAAAAATA
Found at i:1876245 original size:21 final size:22
Alignment explanation
Indices: 1876221--1876262 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1876211 AAATAATTTT
1876221 ATAATTTT-ATAATTTTAAAAA
1 ATAATTTTAATAATTTTAAAAA
1876242 ATAATTTTAATAATTTTAAAA
1 ATAATTTTAATAATTTTAAAA
1876263 TCATTTGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAATTTTAATAATTTTAAAAA
Found at i:1876852 original size:20 final size:19
Alignment explanation
Indices: 1876816--1876859 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
1876806 GACATATATT
* *
1876816 AATAATATTTATTAAATTA
1 AATAATATTTATCAAATAA
*
1876835 AATATATATTTCTCAAATAA
1 AATA-ATATTTATCAAATAA
1876855 AATAA
1 AATAA
1876860 GAGTTAATTG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
AATAATATTTATCAAATAA
Found at i:1890102 original size:25 final size:26
Alignment explanation
Indices: 1890073--1890121 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
1890063 ATTTTAAAAA
1890073 ATATTT-AGGGTTTAGATATTTTCCG
1 ATATTTAAGGGTTTAGATATTTTCCG
* *
1890098 ATATTTAAGGTTTTAGATCTTTTC
1 ATATTTAAGGGTTTAGATATTTTC
1890122 TCAGCTAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.51
Consensus pattern (26 bp):
ATATTTAAGGGTTTAGATATTTTCCG
Found at i:1890756 original size:16 final size:16
Alignment explanation
Indices: 1890735--1890768 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1890725 AATTCTAATA
* *
1890735 TATATTTTTAAAATTC
1 TATATTATTAAAAATC
1890751 TATATTATTAAAAATC
1 TATATTATTAAAAATC
1890767 TA
1 TA
1890769 CTAATATGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (16 bp):
TATATTATTAAAAATC
Found at i:1894626 original size:51 final size:51
Alignment explanation
Indices: 1894548--1894685 Score: 206
Period size: 51 Copynumber: 2.7 Consensus size: 51
1894538 TTCGGATCCA
* * *
1894548 TGTTCTCCGTACTCTGGTTTCCTGCCATACCCAGATCCGTACTCAGATTCT
1 TGTTCGCCATACTCTGGTTTCCGGCCATACCCAGATCCGTACTCAGATTCT
*
1894599 TGTTCGCCATACTCTGGTTTCCGGCCATACCCAGATCCGTACTCGGATTCT
1 TGTTCGCCATACTCTGGTTTCCGGCCATACCCAGATCCGTACTCAGATTCT
* *
1894650 TGTTCGCCATACT-TGGGTCTCCGACCATACCCAGAT
1 TGTTCGCCATACTCT-GGTTTCCGGCCATACCCAGAT
1894686 TCAAATTCAG
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
50 1 0.01
51 79 0.99
ACGTcount: A:0.17, C:0.33, G:0.18, T:0.32
Consensus pattern (51 bp):
TGTTCGCCATACTCTGGTTTCCGGCCATACCCAGATCCGTACTCAGATTCT
Found at i:1894732 original size:54 final size:54
Alignment explanation
Indices: 1894664--1894783 Score: 168
Period size: 54 Copynumber: 2.2 Consensus size: 54
1894654 CGCCATACTT
* * * *
1894664 GGGTCTCCGACCATACCCAGATTCAAATTCAGGAGGCGGAGGCTGCTCAAATTC
1 GGGTCTCCGTCCATACCCAGATCCAAACTCAGGAGGCGGAGACTGCTCAAATTC
* *
1894718 GGGTCTCCGTCCATACCCAGATCCAAACTCAGGCGGCGGAGACTGCTCATATTC
1 GGGTCTCCGTCCATACCCAGATCCAAACTCAGGAGGCGGAGACTGCTCAAATTC
* *
1894772 GGATTTCCGTCC
1 GGGTCTCCGTCC
1894784 GAAATCCGGT
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.23, C:0.31, G:0.25, T:0.22
Consensus pattern (54 bp):
GGGTCTCCGTCCATACCCAGATCCAAACTCAGGAGGCGGAGACTGCTCAAATTC
Found at i:1898618 original size:20 final size:20
Alignment explanation
Indices: 1898581--1898619 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1898571 TTTAATGAAA
*
1898581 TTATTAATATATTTTTTATT
1 TTATTAATATATATTTTATT
1898601 TTATT-ATATTATATTTTAT
1 TTATTAATA-TATATTTTAT
1898620 AATTTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TTATTAATATATATTTTATT
Found at i:1901737 original size:159 final size:158
Alignment explanation
Indices: 1901354--1901743 Score: 728
Period size: 158 Copynumber: 2.5 Consensus size: 158
1901344 GAAAAAAAAC
1901354 TGGAGATGCGGGGGATCGAACCCCGTGCCTCTCGCATGCAAAGCGAGCGCTCTACCATTTGAGCT
1 TGGAGATGCGGGGGATCGAACCCCGTGCCTCTCGCATGCAAAGCGAGCGCTCTACCATTTGAGCT
1901419 ACATCCCCTTCCAATTATTGCTTGTCAGAATTTTTATATACCCATTTTATTGGTTTGATTTTAAA
66 ACATCCCCTTCCAATTATTGCTTGTCAGAATTTTTATATACCCATTTTATTGGTTTGATTTTAAA
*
1901484 ATTTTGGAGTTGGAACTAAGGAATAATT
131 ATTTTAGAGTTGGAACTAAGGAATAATT
1901512 TGGAGATGCGGGGGATCGAACCCCGTGCCTCTCGCATGCAAAGCGAGCGCTCTACCATTTGAGCT
1 TGGAGATGCGGGGGATCGAACCCCGTGCCTCTCGCATGCAAAGCGAGCGCTCTACCATTTGAGCT
*
1901577 ACACCCCCTTCCAATTATTGCTTGTCAGAATTTTTATATACCCATTTTATTGGTTTGA-TTTAAA
66 ACATCCCCTTCCAATTATTGCTTGTCAGAATTTTTATATACCCATTTTATTGGTTTGATTTTAAA
1901641 ATTTTAGAGTTGGAACTAAGGAATAAAATT
131 ATTTTAGAGTTGGAACTAAGGAAT--AATT
*
1901671 TGGAGATGCGGGGGATCGAACCCCGTGCCTCTCGCATGCAAAGCGAGCGCTCTACCAGTTGAGCT
1 TGGAGATGCGGGGGATCGAACCCCGTGCCTCTCGCATGCAAAGCGAGCGCTCTACCATTTGAGCT
1901736 ACATCCCC
66 ACATCCCC
1901744 ATTTGTTAGC
Statistics
Matches: 226, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
157 29 0.13
158 122 0.54
159 75 0.33
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (158 bp):
TGGAGATGCGGGGGATCGAACCCCGTGCCTCTCGCATGCAAAGCGAGCGCTCTACCATTTGAGCT
ACATCCCCTTCCAATTATTGCTTGTCAGAATTTTTATATACCCATTTTATTGGTTTGATTTTAAA
ATTTTAGAGTTGGAACTAAGGAATAATT
Found at i:1908435 original size:4 final size:4
Alignment explanation
Indices: 1908426--1908487 Score: 63
Period size: 4 Copynumber: 15.2 Consensus size: 4
1908416 AAAAAAACGG
* * *
1908426 GAAA GAAA GAGAG GAAA GAAA GAAA GAAA GAAG GAGAG GAAA GAAA G-AA
1 GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA GAAA
*
1908475 GAAT GAAA GAAA G
1 GAAA GAAA GAAA G
1908488 GTAATGTGTT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
3 3 0.06
4 39 0.80
5 7 0.14
ACGTcount: A:0.65, C:0.00, G:0.34, T:0.02
Consensus pattern (4 bp):
GAAA
Found at i:1908448 original size:17 final size:17
Alignment explanation
Indices: 1908426--1908487 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 17
1908416 AAAAAAACGG
1908426 GAAAGAAAGAGAGGAAA
1 GAAAGAAAGAGAGGAAA
*
1908443 GAAAGAAAGAAAGAAGGAGAG
1 GAAAGAAAG--AG-AGGA-AA
*
1908464 GAAAGAAAGA-A-GAAT
1 GAAAGAAAGAGAGGAAA
1908479 GAAAGAAAG
1 GAAAGAAAG
1908488 GTAATGTGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
15 10 0.26
16 2 0.05
17 10 0.26
19 3 0.08
20 4 0.10
21 10 0.26
ACGTcount: A:0.65, C:0.00, G:0.34, T:0.02
Consensus pattern (17 bp):
GAAAGAAAGAGAGGAAA
Found at i:1908455 original size:25 final size:24
Alignment explanation
Indices: 1908426--1908484 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 24
1908416 AAAAAAACGG
1908426 GAAAGAAAGAGAGGAAAGAAAGAAA
1 GAAAGAAAGAGAGGAAAGAAAG-AA
*
1908451 GAAAGAAGGAGAGGAAAGAAAGAA
1 GAAAGAAAGAGAGGAAAGAAAGAA
*
1908475 GAATGAAAGA
1 GAAAGAAAGA
1908485 AAGGTAATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
24 10 0.32
25 21 0.68
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (24 bp):
GAAAGAAAGAGAGGAAAGAAAGAA
Found at i:1911790 original size:12 final size:12
Alignment explanation
Indices: 1911755--1911791 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
1911745 ATCCAATGCC
1911755 TCTTCCTCCTC-
1 TCTTCCTCCTCT
1911766 -C-TCCTCCTCT
1 TCTTCCTCCTCT
1911776 TCTTCCTCCTCT
1 TCTTCCTCCTCT
1911788 TCTT
1 TCTT
1911792 GTTGCTCTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
9 8 0.35
10 1 0.04
11 1 0.04
12 13 0.57
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (12 bp):
TCTTCCTCCTCT
Found at i:1913885 original size:94 final size:93
Alignment explanation
Indices: 1913775--1914132 Score: 490
Period size: 94 Copynumber: 3.8 Consensus size: 93
1913765 ATTATATTTT
* *
1913775 TTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTTACTAACAACACAATAAAAT
1 TTTTAAATCAAAAAATATGAACAATATTTTTTACTTACTACTAC-TACTAACAACAAAATAAAAT
* *
1913840 TACTAACTAATTTTTTAAATATTATTCAA
65 TACTAACTAATTTTTTAAACATTATTAAA
*
1913869 TTTTAAATCAAAAAATATGAACAATGTTTTTTACTAACTACTACTACTACTACTAACAACAAAAT
1 TTTTAAATCAAAAAATATGAACAAT-ATTTTT--T-ACT--TACTACTACTACTAACAACAAAAT
*
1913934 AAAATTAGTAACTAATTTTTTTAAACATTATTAAA
60 AAAATTACTAACTAA-TTTTTTAAACATTATTAAA
* *
1913969 TTTTAAATC-AATAATATAAACAATATTTTTTACTTACTACTACTACTAACAACAAAATAAAATT
1 TTTTAAATCAAAAAATATGAACAATATTTTTTACTTACTACTACTACTAACAACAAAATAAAATT
***
1914033 ACTAACTAGCAAAATTTAAACATTATTAAA
66 ACTAACTA--ATTTTTTAAACATTATTAAA
*
1914063 TTTTAAATCAATAAATATGAACAATATTTTTTAC-T--TACTACTACTAACAACAAAATAAAATT
1 TTTTAAATCAAAAAATATGAACAATATTTTTTACTTACTACTACTACTAACAACAAAATAAAATT
1914125 ACTAACTA
66 ACTAACTA
1914133 GCAAAATTAA
Statistics
Matches: 238, Mismatches: 16, Indels: 22
0.86 0.06 0.08
Matches are distributed among these distances:
92 35 0.15
93 37 0.16
94 50 0.21
95 30 0.13
96 1 0.00
97 1 0.00
98 8 0.03
99 41 0.17
100 35 0.15
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.37
Consensus pattern (93 bp):
TTTTAAATCAAAAAATATGAACAATATTTTTTACTTACTACTACTACTAACAACAAAATAAAATT
ACTAACTAATTTTTTAAACATTATTAAA
Found at i:1914129 original size:20 final size:21
Alignment explanation
Indices: 1914104--1914146 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1914094 TACTTACTAC
1914104 TACTAAC-AACAAAATAAAAT
1 TACTAACTAACAAAATAAAAT
* *
1914124 TACTAACTAGCAAAATTAAAT
1 TACTAACTAACAAAATAAAAT
1914145 TA
1 TA
1914147 AAGTAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (21 bp):
TACTAACTAACAAAATAAAAT
Found at i:1914495 original size:4 final size:4
Alignment explanation
Indices: 1914488--1914546 Score: 52
Period size: 4 Copynumber: 15.0 Consensus size: 4
1914478 TACCTTTTTT
* *
1914488 TTTC TTTC TCTTC -TTC -TTC TTTC TTTC TTTC ATTC TTTC TCTTT TTTC
1 TTTC TTTC T-TTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC T-TTC TTTC
*
1914536 TTGC TTT- TTTC
1 TTTC TTTC TTTC
1914547 ACTCAATTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
3 9 0.20
4 30 0.67
5 6 0.13
ACGTcount: A:0.02, C:0.25, G:0.02, T:0.71
Consensus pattern (4 bp):
TTTC
Found at i:1914512 original size:19 final size:19
Alignment explanation
Indices: 1914488--1914524 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1914478 TACCTTTTTT
1914488 TTTCTTTCTCTTC-TTCTTC
1 TTTCTTTCT-TTCATTCTTC
1914507 TTTCTTTCTTTCATTCTT
1 TTTCTTTCTTTCATTCTT
1914525 TCTCTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.03, C:0.27, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTCTTTCTTTCATTCTTC
Found at i:1914524 original size:25 final size:23
Alignment explanation
Indices: 1914488--1914542 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
1914478 TACCTTTTTT
1914488 TTTCTTTCTC-TTCTTCTTCTTTC
1 TTTCTTTCTCTTTC-TCTTCTTTC
*
1914511 TTTCTTTCATTCTTTCTCTTTTTTC
1 TTTCTTTC--TCTTTCTCTTCTTTC
*
1914536 TTGCTTT
1 TTTCTTT
1914543 TTTCACTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 8 0.30
25 16 0.59
26 3 0.11
ACGTcount: A:0.02, C:0.25, G:0.02, T:0.71
Consensus pattern (23 bp):
TTTCTTTCTCTTTCTCTTCTTTC
Found at i:1914763 original size:27 final size:27
Alignment explanation
Indices: 1914732--1914788 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
1914722 ACACCCCTTA
* *
1914732 GTGCCGCCATTTGATATTCCTCCATTG
1 GTGCCGCCACTTGATATTCCTCCACTG
* *
1914759 GTGCCGCCACTTGGTGTTCCTCCACTG
1 GTGCCGCCACTTGATATTCCTCCACTG
1914786 GTG
1 GTG
1914789 TCAGGTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.11, C:0.32, G:0.25, T:0.33
Consensus pattern (27 bp):
GTGCCGCCACTTGATATTCCTCCACTG
Found at i:1916065 original size:21 final size:19
Alignment explanation
Indices: 1916026--1916070 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 19
1916016 CCAGTTTCGA
1916026 AAATTTTAATAAAATATTT
1 AAATTTTAATAAAATATTT
*
1916045 AAATTTTGAATTAAATAATTT
1 AAATTTT-AATAAAAT-ATTT
1916066 AAATT
1 AAATT
1916071 ATTCAGATCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.30
20 7 0.30
21 9 0.39
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
AAATTTTAATAAAATATTT
Found at i:1923302 original size:29 final size:31
Alignment explanation
Indices: 1923236--1923302 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
1923226 AAAATTTGAG
*
1923236 GATTAAAATTGATCAATTTGAATAATAGAGA
1 GATTAAAATTAATCAATTTGAATAATAGAGA
* *
1923267 GACTAAAATTAATC-ATATT-AA-AATATAGA
1 GATTAAAATTAATCAAT-TTGAATAATAGAGA
1923296 GATTAAA
1 GATTAAA
1923303 TCTATAACTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
29 13 0.42
30 4 0.13
31 14 0.45
ACGTcount: A:0.52, C:0.04, G:0.12, T:0.31
Consensus pattern (31 bp):
GATTAAAATTAATCAATTTGAATAATAGAGA
Found at i:1925002 original size:21 final size:21
Alignment explanation
Indices: 1924973--1925013 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1924963 TTCTAAAGGT
*
1924973 ATCCTTTTTTATTTAATTTTG
1 ATCCATTTTTATTTAATTTTG
* *
1924994 ATCCATTTTTGTTTACTTTT
1 ATCCATTTTTATTTAATTTT
1925014 TCTGGGTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.12, G:0.05, T:0.66
Consensus pattern (21 bp):
ATCCATTTTTATTTAATTTTG
Found at i:1928685 original size:33 final size:33
Alignment explanation
Indices: 1928643--1928713 Score: 142
Period size: 33 Copynumber: 2.2 Consensus size: 33
1928633 CATGTCCTAA
1928643 TTCAGTTCATGCCCATGAACACATTCGTGGATC
1 TTCAGTTCATGCCCATGAACACATTCGTGGATC
1928676 TTCAGTTCATGCCCATGAACACATTCGTGGATC
1 TTCAGTTCATGCCCATGAACACATTCGTGGATC
1928709 TTCAG
1 TTCAG
1928714 AAGTGATTAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (33 bp):
TTCAGTTCATGCCCATGAACACATTCGTGGATC
Found at i:1929730 original size:22 final size:22
Alignment explanation
Indices: 1929689--1929751 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 22
1929679 AATTTTATAA
1929689 TTTAT-AATTTTTTTAA-TTTT
1 TTTATAAATTTTTTTAATTTTT
*
1929709 TTTATAAATTTTTATAATTTTT
1 TTTATAAATTTTTTTAATTTTT
** *
1929731 AATATATATTTTTTTAATTTT
1 TTTATAAATTTTTTTAATTTT
1929752 AAAAGGGTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
20 5 0.14
21 10 0.28
22 21 0.58
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTATAAATTTTTTTAATTTTT
Found at i:1929752 original size:21 final size:20
Alignment explanation
Indices: 1929691--1929753 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 20
1929681 TTTTATAATT
**
1929691 TATAATTTTTTTAATTTTTT
1 TATAATTTTTTTAATTTTAA
*
1929711 TATAAATTTTTATAATTTTTAA
1 TAT-AATTTTTTTAA-TTTTAA
1929733 TATATATTTTTTTAATTTTAA
1 TATA-ATTTTTTTAATTTTAA
1929754 AAGGGTTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 3 0.08
21 17 0.47
22 16 0.44
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TATAATTTTTTTAATTTTAA
Found at i:1931201 original size:23 final size:23
Alignment explanation
Indices: 1931175--1931220 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1931165 AAAAATAATA
1931175 TGCATTAAATTTGATGAATTTAT
1 TGCATTAAATTTGATGAATTTAT
1931198 TGCATTAAATTTGATGAATTTAT
1 TGCATTAAATTTGATGAATTTAT
1931221 CTTCACAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.48
Consensus pattern (23 bp):
TGCATTAAATTTGATGAATTTAT
Found at i:1937322 original size:21 final size:20
Alignment explanation
Indices: 1937293--1937337 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
1937283 TACTTAATTT
* *
1937293 AATACATTTTTAATTATTTAA
1 AATACATTTATAATT-TGTAA
*
1937314 AATATATTTATAATTTGTAA
1 AATACATTTATAATTTGTAA
1937334 AATA
1 AATA
1937338 AATAAATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (20 bp):
AATACATTTATAATTTGTAA
Found at i:1953363 original size:23 final size:24
Alignment explanation
Indices: 1953313--1953363 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
1953303 ATTTTTATTA
1953313 ATTAACATTTTTTATATAGTTATC
1 ATTAACATTTTTTATATAGTTATC
*
1953337 -TTAACATTATTTTA-ATATTTA-C
1 ATTAACATT-TTTTATATAGTTATC
1953359 ATTAA
1 ATTAA
1953364 AGTAGTATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
22 1 0.04
23 18 0.75
24 5 0.21
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (24 bp):
ATTAACATTTTTTATATAGTTATC
Found at i:1955142 original size:15 final size:15
Alignment explanation
Indices: 1955098--1955157 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 15
1955088 AAAAATATTT
1955098 ATATTATATTATTTTA
1 ATATT-TATTATTTTA
*
1955114 ATATTTAATAATTTTA
1 ATATTT-ATTATTTTA
1955130 TATATTT-TTATTTATTA
1 -ATATTTATTA-TT-TTA
*
1955147 ATATTTTTTAT
1 ATATTTATTAT
1955158 ATAGTTATCT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
15 3 0.08
16 22 0.59
17 12 0.32
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
ATATTTATTATTTTA
Found at i:1955147 original size:26 final size:26
Alignment explanation
Indices: 1955097--1955160 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
1955087 CAAAAATATT
*
1955097 TATATTATAT-TATTTTAATATTTAA
1 TATATTTTATATATTTTAATATTTAA
* *
1955122 TA-ATTTTATATATTTTTATTTATTAA
1 TATATTTTATATATTTTAATAT-TTAA
*
1955148 TATTTTTTATATA
1 TATATTTTATATA
1955161 GTTATCTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 6 0.19
25 11 0.34
26 6 0.19
27 9 0.28
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (26 bp):
TATATTTTATATATTTTAATATTTAA
Found at i:1958882 original size:18 final size:18
Alignment explanation
Indices: 1958852--1958898 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
1958842 AGTTGAACCA
1958852 AATTTTATAATTTTTTAAG
1 AATTTT-TAATTTTTTAAG
*
1958871 AATTTTTAATTTTTTATG
1 AATTTTTAATTTTTTAAG
1958889 AATTTTTAAT
1 AATTTTTAAT
1958899 AATTTATTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 21 0.78
19 6 0.22
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (18 bp):
AATTTTTAATTTTTTAAG
Found at i:1958904 original size:18 final size:18
Alignment explanation
Indices: 1958865--1958905 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1958855 TTTATAATTT
* **
1958865 TTTAAGAATTTTTAATTT
1 TTTATGAATTTTTAATAA
1958883 TTTATGAATTTTTAATAA
1 TTTATGAATTTTTAATAA
1958901 TTTAT
1 TTTAT
1958906 TTGATTTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (18 bp):
TTTATGAATTTTTAATAA
Found at i:1959935 original size:24 final size:25
Alignment explanation
Indices: 1959886--1959935 Score: 59
Period size: 24 Copynumber: 2.0 Consensus size: 25
1959876 TATCTCTGAA
* *
1959886 ATAATCAGAGTTTAATTGGGAAAAG
1 ATAATCAGAGTTTAACTGAGAAAAG
1959911 ATAA-CAGAGTTTAACT-AGAAGAAG
1 ATAATCAGAGTTTAACTGAGAA-AAG
1959935 A
1 A
1959936 ATACGAGGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 3 0.14
24 15 0.68
25 4 0.18
ACGTcount: A:0.48, C:0.06, G:0.22, T:0.24
Consensus pattern (25 bp):
ATAATCAGAGTTTAACTGAGAAAAG
Found at i:1960381 original size:20 final size:20
Alignment explanation
Indices: 1960358--1960426 Score: 93
Period size: 20 Copynumber: 3.2 Consensus size: 20
1960348 AAAATGCATA
*
1960358 AAAAATAACATCCAAACAAC
1 AAAAATAACATCAAAACAAC
1960378 AAAAATAACAATCAAAACAGCAGC
1 AAAAATAAC-ATCAAAACA--A-C
1960402 AAAAATAACATCAAAACAAC
1 AAAAATAACATCAAAACAAC
1960422 AAAAA
1 AAAAA
1960427 AATAGCAACA
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
20 15 0.34
21 9 0.20
23 10 0.23
24 10 0.23
ACGTcount: A:0.68, C:0.20, G:0.03, T:0.09
Consensus pattern (20 bp):
AAAAATAACATCAAAACAAC
Found at i:1970669 original size:21 final size:22
Alignment explanation
Indices: 1970631--1970671 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1970621 TTTTTTTAAA
**
1970631 AAATATTTATATTGTTTTATTT
1 AAATATTTATATAATTTTATTT
1970653 AAATATTTA-ATAATTTTAT
1 AAATATTTATATAATTTTAT
1970672 ACATTTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
AAATATTTATATAATTTTATTT
Found at i:1976886 original size:3 final size:3
Alignment explanation
Indices: 1976878--1976906 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1976868 ATTTAAATCT
1976878 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1976907 TCAAATTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1979130 original size:2 final size:2
Alignment explanation
Indices: 1979123--1979160 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1979113 ATCAGTTTTC
1979123 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1979161 TAACATGAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1979175 original size:3 final size:3
Alignment explanation
Indices: 1979167--1979200 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
1979157 ATATTAACAT
1979167 GAA GAA GAA GAA GAA GAA GAA GAA GAA G-A GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1979201 TATGTATGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1984534 original size:6 final size:6
Alignment explanation
Indices: 1984500--1984567 Score: 59
Period size: 6 Copynumber: 11.5 Consensus size: 6
1984490 TAATAGGGAT
* * * *
1984500 TTTCAA TTTACAA -TTC-A TATCAC TTTCAA TTTCAA TTTCAC TTTCAC
1 TTTCAA TTT-CAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
* *
1984547 TTTCAC TTTCAC TTTCAA TTT
1 TTTCAA TTTCAA TTTCAA TTT
1984568 TAATCACAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
4 1 0.02
5 3 0.06
6 46 0.87
7 3 0.06
ACGTcount: A:0.26, C:0.24, G:0.00, T:0.50
Consensus pattern (6 bp):
TTTCAA
Found at i:1984542 original size:18 final size:18
Alignment explanation
Indices: 1984519--1984567 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
1984509 ACAATTCATA
1984519 TCACTTTCAATTTCAATT
1 TCACTTTCAATTTCAATT
* *
1984537 TCACTTTCACTTTCACTT
1 TCACTTTCAATTTCAATT
1984555 TCACTTTCAATTT
1 TCACTTTCAATTT
1984568 TAATCACAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.22, C:0.27, G:0.00, T:0.51
Consensus pattern (18 bp):
TCACTTTCAATTTCAATT
Found at i:1984544 original size:12 final size:12
Alignment explanation
Indices: 1984519--1984567 Score: 71
Period size: 12 Copynumber: 4.1 Consensus size: 12
1984509 ACAATTCATA
1984519 TCACTTTCAATT
1 TCACTTTCAATT
* *
1984531 TCAATTTCACTT
1 TCACTTTCAATT
*
1984543 TCACTTTCACTT
1 TCACTTTCAATT
1984555 TCACTTTCAATT
1 TCACTTTCAATT
1984567 T
1 T
1984568 TAATCACAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.22, C:0.27, G:0.00, T:0.51
Consensus pattern (12 bp):
TCACTTTCAATT
Found at i:1986905 original size:75 final size:75
Alignment explanation
Indices: 1986813--1986962 Score: 264
Period size: 75 Copynumber: 2.0 Consensus size: 75
1986803 AATCCCAAGA
* *
1986813 AAACTTGATGTTCTACCTTTACTTGCTGACAAGTTGGGCACCTCGATACAAATTCAGTGATATCT
1 AAACTTGATGTTCTACCTTTACTTGCTGACAAGTTAGGCACCTCAATACAAATTCAGTGATATCT
1986878 TTTTTCATGT
66 TTTTTCATGT
* *
1986888 AAACTTGATGTTTTACCTTTACTTGCTGACAAGTTAGGCACCTCAATACAAATTTAGTGATATCT
1 AAACTTGATGTTCTACCTTTACTTGCTGACAAGTTAGGCACCTCAATACAAATTCAGTGATATCT
1986953 TTTTTCATGT
66 TTTTTCATGT
1986963 TGGACCAGGT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 71 1.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.40
Consensus pattern (75 bp):
AAACTTGATGTTCTACCTTTACTTGCTGACAAGTTAGGCACCTCAATACAAATTCAGTGATATCT
TTTTTCATGT
Found at i:1989117 original size:25 final size:24
Alignment explanation
Indices: 1989089--1989135 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
1989079 TAGATATAAG
1989089 ATATCA-AACATAAATATTAATAATT
1 ATATCATAA-ATAAATA-TAATAATT
*
1989114 ATATTATAAATAAATATAATAA
1 ATATCATAAATAAATATAATAA
1989136 ACATCTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 6 0.30
25 12 0.60
26 2 0.10
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (24 bp):
ATATCATAAATAAATATAATAATT
Found at i:1996826 original size:13 final size:13
Alignment explanation
Indices: 1996810--1996837 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1996800 GAACTTTCCA
1996810 GTAATCCTTTTCT
1 GTAATCCTTTTCT
1996823 GTAATCCTTTTCT
1 GTAATCCTTTTCT
1996836 GT
1 GT
1996838 TTGTTTACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.21, G:0.11, T:0.54
Consensus pattern (13 bp):
GTAATCCTTTTCT
Found at i:1998666 original size:26 final size:27
Alignment explanation
Indices: 1998618--1998685 Score: 66
Period size: 26 Copynumber: 2.5 Consensus size: 27
1998608 TTTTGTATTT
* * * *
1998618 ATTTATATTTAATAATTATAATTA-AG
1 ATTTATTTTTAAAAAATAAAATTATAG
*
1998644 ATTTATTTTTAAAAAATAAAATTATTTAT
1 ATTTATTTTTAAAAAATAAAATTA--TAG
1998673 ATTTATTTTTAAA
1 ATTTATTTTTAAA
1998686 CCGTTTAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 20 0.59
29 14 0.41
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (27 bp):
ATTTATTTTTAAAAAATAAAATTATAG
Found at i:1999427 original size:11 final size:11
Alignment explanation
Indices: 1999413--1999450 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
1999403 TGTTTTGCTG
1999413 TTATTTTGTTA
1 TTATTTTGTTA
*
1999424 TTATATTGTTA
1 TTATTTTGTTA
*
1999435 CTATTTTGTTA
1 TTATTTTGTTA
1999446 TTATT
1 TTATT
1999451 ATTTGAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.21, C:0.03, G:0.08, T:0.68
Consensus pattern (11 bp):
TTATTTTGTTA
Found at i:1999461 original size:22 final size:22
Alignment explanation
Indices: 1999414--1999461 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1999404 GTTTTGCTGT
* *
1999414 TATTTTGTTATTATATTGTTAC
1 TATTTTGTTATTATATTGTGAA
1999436 TATTTTGTTATTATTATT-TGAA
1 TATTTTGTTATTA-TATTGTGAA
1999458 TATT
1 TATT
1999462 ATATAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.25, C:0.02, G:0.08, T:0.65
Consensus pattern (22 bp):
TATTTTGTTATTATATTGTGAA
Found at i:2000260 original size:27 final size:27
Alignment explanation
Indices: 2000230--2000292 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
2000220 AGCAATTTAA
2000230 TTTTTTTTCTTTATATTCTTTTAACTT
1 TTTTTTTTCTTTATATTCTTTTAACTT
* * *
2000257 TTTTTTTCCTTTATGTTCTTTTCACTT
1 TTTTTTTTCTTTATATTCTTTTAACTT
2000284 TTTCTTTTT
1 TTT-TTTTT
2000293 TTTCCCTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 27 0.87
28 4 0.13
ACGTcount: A:0.10, C:0.14, G:0.02, T:0.75
Consensus pattern (27 bp):
TTTTTTTTCTTTATATTCTTTTAACTT
Found at i:2006347 original size:16 final size:18
Alignment explanation
Indices: 2006308--2006341 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2006298 TAAGTTTATA
2006308 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
2006325 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
2006342 AATTTAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:2008265 original size:31 final size:29
Alignment explanation
Indices: 2008230--2008303 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
2008220 ACAGCTCAGC
*
2008230 GACTAAAATGTTACAAAACGATAACATAAGT
1 GACTAAAATGTAACAAAAC-A-AACATAAGT
***
2008261 GACTAAAATGTAACATTTCAAACATAAGT
1 GACTAAAATGTAACAAAACAAACATAAGT
2008290 GACTAAAATGTAAC
1 GACTAAAATGTAAC
2008304 CTAAGTCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 23 0.59
30 1 0.03
31 15 0.38
ACGTcount: A:0.50, C:0.14, G:0.12, T:0.24
Consensus pattern (29 bp):
GACTAAAATGTAACAAAACAAACATAAGT
Found at i:2008321 original size:31 final size:29
Alignment explanation
Indices: 2008252--2008322 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
2008242 ACAAAACGAT
**
2008252 AACATAAGTGACTAAAATGTAACATTTCA
1 AACATAAGTGACTAAAATGTAACAAGTCA
2008281 AACATAAGTGACTAAAATGTAACCTAAGTCA
1 AACATAAGTGACTAAAATGTAA-C-AAGTCA
*
2008312 AACAAAAGTGA
1 AACATAAGTGA
2008323 TTATTTTTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 22 0.59
30 1 0.03
31 14 0.38
ACGTcount: A:0.51, C:0.14, G:0.13, T:0.23
Consensus pattern (29 bp):
AACATAAGTGACTAAAATGTAACAAGTCA
Found at i:2014521 original size:31 final size:31
Alignment explanation
Indices: 2014480--2014556 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
2014470 GATGGAATAC
*
2014480 AAATTCAGGGACCAACTAAATCCAAAAAAAAA
1 AAATT-AGGGACCAACTAAATACAAAAAAAAA
** *
2014512 AAATTAGGGACCAACTAAATACAAATGAATA
1 AAATTAGGGACCAACTAAATACAAAAAAAAA
*
2014543 AATTTAGGGACCAA
1 AAATTAGGGACCAA
2014557 ATTATATATT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 35 0.88
32 5 0.12
ACGTcount: A:0.55, C:0.16, G:0.13, T:0.17
Consensus pattern (31 bp):
AAATTAGGGACCAACTAAATACAAAAAAAAA
Found at i:2032971 original size:18 final size:18
Alignment explanation
Indices: 2032948--2032990 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
2032938 GCTCTTTTTT
*
2032948 TTTTTTTTTGCTCA-TCA
1 TTTTTTTTTCCTCATTCA
2032965 CTTTTTTTTTCCTCATTCA
1 -TTTTTTTTTCCTCATTCA
2032984 TTTTTTT
1 TTTTTTT
2032991 GTATTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTTTTTTTCCTCATTCA
Found at i:2035049 original size:15 final size:14
Alignment explanation
Indices: 2035016--2035054 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
2035006 CTTGTATTTG
2035016 GAATTTAATTTTCA
1 GAATTTAATTTTCA
* *
2035030 TAATTTTATTTTCAA
1 GAATTTAATTTTC-A
2035045 GAATTTAATT
1 GAATTTAATT
2035055 CCTCTATTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
14 11 0.55
15 9 0.45
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (14 bp):
GAATTTAATTTTCA
Found at i:2037860 original size:31 final size:31
Alignment explanation
Indices: 2037816--2037884 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
2037806 TTGATTATTA
**
2037816 AACTATTTGAAAGTTTTCATTAAAGTCACTG
1 AACTATTCAAAAGTTTTCATTAAAGTCACTG
* *
2037847 AACTATTCAAAAGTTTTTATTTAAGTCACTG
1 AACTATTCAAAAGTTTTCATTAAAGTCACTG
*
2037878 AGCTATT
1 AACTATT
2037885 GAGTTTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.41
Consensus pattern (31 bp):
AACTATTCAAAAGTTTTCATTAAAGTCACTG
Found at i:2038956 original size:11 final size:11
Alignment explanation
Indices: 2038940--2038967 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
2038930 GAGCAATCAT
2038940 AGCAAATTGAA
1 AGCAAATTGAA
2038951 AGCAAATTGAA
1 AGCAAATTGAA
2038962 AGCAAA
1 AGCAAA
2038968 GAGAGTGCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.11, G:0.18, T:0.14
Consensus pattern (11 bp):
AGCAAATTGAA
Found at i:2043333 original size:16 final size:15
Alignment explanation
Indices: 2043283--2043333 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
2043273 TCAGTCCAAT
*
2043283 ATTTTATTTA-TTAA
1 ATTTTATTTATTTTA
2043297 ATTTTA-TTATTTTA
1 ATTTTATTTATTTTA
*
2043311 TTATTTATTTATTTTGA
1 AT-TTTATTTATTTT-A
2043328 ATTTTA
1 ATTTTA
2043334 GATAAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 3 0.10
14 10 0.33
15 4 0.13
16 11 0.37
17 2 0.07
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (15 bp):
ATTTTATTTATTTTA
Found at i:2043880 original size:12 final size:12
Alignment explanation
Indices: 2043860--2043894 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2043850 AACATCCAAA
2043860 CAACAAAAATAC
1 CAACAAAAATAC
* *
2043872 CAACCAAAATAG
1 CAACAAAAATAC
2043884 CAACAAAAATA
1 CAACAAAAATA
2043895 ATATCAAACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.66, C:0.23, G:0.03, T:0.09
Consensus pattern (12 bp):
CAACAAAAATAC
Found at i:2054766 original size:2 final size:2
Alignment explanation
Indices: 2054759--2054785 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2054749 ATCTCTTGCT
2054759 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2054786 TCAAACCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2058934 original size:16 final size:18
Alignment explanation
Indices: 2058895--2058928 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2058885 TAAGTTTATA
2058895 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
2058912 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
2058929 AATTTAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:2062681 original size:2 final size:2
Alignment explanation
Indices: 2062674--2062723 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
2062664 TGAGTTAGGC
2062674 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2062716 TA TA TA TA
1 TA TA TA TA
2062724 AATAGATGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2064730 original size:26 final size:26
Alignment explanation
Indices: 2064687--2064757 Score: 74
Period size: 28 Copynumber: 2.7 Consensus size: 26
2064677 TAATTTATAT
*
2064687 TTTATATATTTTTATATTA-A-ATTA
1 TTTAAATATTTTTATATTATATATTA
*
2064711 TTTAAATATTATTTATTATTATATATTT
1 TTTAAATATT-TTTA-TATTATATATTA
2064739 TTTAAAATATTTTATATAT
1 TTT-AAATATTTT-TATAT
2064758 AATTAGTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
24 9 0.23
25 4 0.10
26 5 0.13
27 1 0.03
28 11 0.28
29 9 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (26 bp):
TTTAAATATTTTTATATTATATATTA
Found at i:2064733 original size:31 final size:32
Alignment explanation
Indices: 2064655--2064734 Score: 81
Period size: 31 Copynumber: 2.5 Consensus size: 32
2064645 TTATATTAAC
* * * *
2064655 TATTTAATATATATAATTAGATTAATTTATATTT
1 TATTTATTAT-TAT-ATTAAATTAATTTAAATAT
* *
2064689 TATATATTTTTATATTAAATT-ATTTAAATAT
1 TATTTATTATTATATTAAATTAATTTAAATAT
2064720 TATTTATTATTATAT
1 TATTTATTATTATAT
2064735 ATTTTTTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
31 21 0.55
32 7 0.18
33 3 0.08
34 7 0.18
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (32 bp):
TATTTATTATTATATTAAATTAATTTAAATAT
Found at i:2064787 original size:26 final size:26
Alignment explanation
Indices: 2064738--2064788 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
2064728 ATTATATATT
* *
2064738 TTTTAAAATATTTTATATATAATTAG
1 TTTTAAAATAATTTATATAGAATTAG
2064764 TTTTATAAATAATTTATAT-GAATTA
1 TTTTA-AAATAATTTATATAGAATTA
2064789 CTTAAAAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (26 bp):
TTTTAAAATAATTTATATAGAATTAG
Found at i:2065186 original size:51 final size:51
Alignment explanation
Indices: 2065113--2065247 Score: 177
Period size: 51 Copynumber: 2.6 Consensus size: 51
2065103 TTTCATTTAA
* * *
2065113 TACTCACGATGACATATT-GTCATCAGACCTTTAATTC-GTCATGGATTCATT
1 TACTCACGATGAC-TATTAGTCATCGGACCTTTAA-TCAGTAAAGGATTCATT
*
2065164 TACTCACGATGACTTTTAGTCATCGGACCTTTAATCAGTAAAGGATTCATT
1 TACTCACGATGACTATTAGTCATCGGACCTTTAATCAGTAAAGGATTCATT
2065215 TACTCACGATGAC-ACTTAGTCATCGGACTCTTT
1 TACTCACGATGACTA-TTAGTCATCGGAC-CTTT
2065248 CGTTTATAGC
Statistics
Matches: 75, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
50 5 0.07
51 66 0.88
52 4 0.05
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (51 bp):
TACTCACGATGACTATTAGTCATCGGACCTTTAATCAGTAAAGGATTCATT
Found at i:2068598 original size:25 final size:25
Alignment explanation
Indices: 2068569--2068703 Score: 131
Period size: 25 Copynumber: 5.7 Consensus size: 25
2068559 TCTAAACAGA
* *
2068569 GCCTTTGTGGTGTATTCGTTATGAT
1 GCCTTTGTGGCGTATTCATTATGAT
* *
2068594 ACCTTTGTGACGTATTCATTATGAT
1 GCCTTTGTGGCGTATTCATTATGAT
*
2068619 GCCTTTATGGCGTATTCATTATGAT
1 GCCTTTGTGGCGTATTCATTATGAT
*
2068644 GCC-TT-T---GT-TT-GTTATGAT
1 GCCTTTGTGGCGTATTCATTATGAT
* * *
2068662 GCTTTTCTGGCGTATTCGTTATGAT
1 GCCTTTGTGGCGTATTCATTATGAT
*
2068687 GTCTTTGTGGCGTATTC
1 GCCTTTGTGGCGTATTC
2068704 TATTTAGCCT
Statistics
Matches: 91, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
18 9 0.10
19 4 0.04
20 3 0.03
23 3 0.03
24 4 0.04
25 68 0.75
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.47
Consensus pattern (25 bp):
GCCTTTGTGGCGTATTCATTATGAT
Found at i:2068673 original size:43 final size:43
Alignment explanation
Indices: 2068612--2068694 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
2068602 GACGTATTCA
2068612 TTATGATGCCTTTATGGCGTATTCATTATGATGCCTTTGTTTG
1 TTATGATGCCTTTATGGCGTATTCATTATGATGCCTTTGTTTG
* * * *
2068655 TTATGATGCTTTTCTGGCGTATTCGTTATGATGTCTTTGT
1 TTATGATGCCTTTATGGCGTATTCATTATGATGCCTTTGT
2068695 GGCGTATTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.14, C:0.13, G:0.22, T:0.51
Consensus pattern (43 bp):
TTATGATGCCTTTATGGCGTATTCATTATGATGCCTTTGTTTG
Found at i:2071448 original size:90 final size:92
Alignment explanation
Indices: 2071294--2071476 Score: 334
Period size: 90 Copynumber: 2.0 Consensus size: 92
2071284 TAAGACCTCT
2071294 CTTTTTCCTTTTCCTCTATAGTTTATTTTTTTTCACGAAATAACTTTGAACATCATAAAATTGTG
1 CTTTTTCCTTTTCCTCTATAGTTTATTTTTTTTCACGAAATAACTTTGAACATCATAAAATTGTG
2071359 AACCAAAATTCAAAAAACATTCTTCTC
66 AACCAAAATTCAAAAAACATTCTTCTC
* *
2071386 CTTTTTCCTTTTCCTTTATAG-TT-TTTTTTTTCACGAAATAACTTTGAACATCATAAATTTGTG
1 CTTTTTCCTTTTCCTCTATAGTTTATTTTTTTTCACGAAATAACTTTGAACATCATAAAATTGTG
2071449 AACCAAAATTCAAAAAACATTCTTCTC
66 AACCAAAATTCAAAAAACATTCTTCTC
2071476 C
1 C
2071477 GATCTCCGAC
Statistics
Matches: 89, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
90 67 0.75
91 2 0.02
92 20 0.22
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (92 bp):
CTTTTTCCTTTTCCTCTATAGTTTATTTTTTTTCACGAAATAACTTTGAACATCATAAAATTGTG
AACCAAAATTCAAAAAACATTCTTCTC
Found at i:2072559 original size:5 final size:5
Alignment explanation
Indices: 2072551--2072578 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
2072541 GTTTCTTTCC
2072551 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
2072579 TCTTTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:2072588 original size:15 final size:16
Alignment explanation
Indices: 2072550--2072588 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
2072540 TGTTTCTTTC
2072550 CTTTATTTTATTTTAT
1 CTTTATTTTATTTTAT
2072566 -TTTATTTTATTTT-T
1 CTTTATTTTATTTTAT
*
2072580 CTTTCTTTT
1 CTTTATTTT
2072589 CATGTTTGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 20 0.95
ACGTcount: A:0.13, C:0.08, G:0.00, T:0.79
Consensus pattern (16 bp):
CTTTATTTTATTTTAT
Found at i:2080743 original size:19 final size:21
Alignment explanation
Indices: 2080700--2080746 Score: 64
Period size: 19 Copynumber: 2.3 Consensus size: 21
2080690 GACCCTCTAA
2080700 AAAAATTACAAAATAATTTTC
1 AAAAATTACAAAATAATTTTC
2080721 AAAAATT-CAAAAT-ATTTAT-
1 AAAAATTACAAAATAATTT-TC
2080740 AAAAATT
1 AAAAATT
2080747 TTAAAATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 11 0.44
20 7 0.28
21 7 0.28
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAAATTACAAAATAATTTTC
Found at i:2089461 original size:92 final size:87
Alignment explanation
Indices: 2089343--2089598 Score: 309
Period size: 92 Copynumber: 2.9 Consensus size: 87
2089333 CTTAAGGGTG
*
2089343 TAAAAA-ACCCTCAAATTTTTTCAAAAAAGGCAATTAAGCCCCTGCTTTCTTTTTACACTCAATT
1 TAAAAAGACCCTCAAACTTTTTCAAAAAA-GCAATTAAGCCCCTGCTTT-TTTTT-CACTCAATT
2089407 GGGTACTTGAA-TTGCCAAAAATGAAT
63 GGGTACTTGAACTT-CC-AAAATGAAT
* * * *
2089433 TCAAAAAGACCCTCAAACCTTTTCAAAAAAAGCAATTAAGCCCTTGCCATTTTTTTGCACTTAAT
1 T-AAAAAGACCCTCAAACTTTTTC-AAAAAAGCAATTAAGCCCCTG-C-TTTTTTTTCACTCAAT
* * *
2089498 TGGGTGCTTGAACTTTCAAAATGCAT
62 TGGGTACTTGAACTTCCAAAATGAAT
* * * *
2089524 TAAAAAGGCCCTCAAACTTTTTCAAAAAAGCAATTCAGCCCCTGATTTTTTTTCACTCAATTGAG
1 TAAAAAGACCCTCAAACTTTTTCAAAAAAGCAATTAAGCCCCTGCTTTTTTTTCACTCAATTGGG
2089589 TACTTGAACT
66 TACTTGAACT
2089599 GTTAAATGCA
Statistics
Matches: 143, Mismatches: 17, Indels: 15
0.82 0.10 0.09
Matches are distributed among these distances:
87 26 0.18
89 19 0.13
90 21 0.15
91 14 0.10
92 47 0.33
93 13 0.09
94 3 0.02
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.32
Consensus pattern (87 bp):
TAAAAAGACCCTCAAACTTTTTCAAAAAAGCAATTAAGCCCCTGCTTTTTTTTCACTCAATTGGG
TACTTGAACTTCCAAAATGAAT
Found at i:2089773 original size:21 final size:20
Alignment explanation
Indices: 2089726--2089832 Score: 71
Period size: 20 Copynumber: 5.5 Consensus size: 20
2089716 ACAAAAAACT
* *
2089726 ATAAAAAAA-ATAAAAATAA
1 ATAAAAAAATATAAAATTTA
* * *
2089745 AT-AAAAATTATTAATTTTA
1 ATAAAAAAATATAAAATTTA
2089764 ATAAAAAAATATAAAATTTA
1 ATAAAAAAATATAAAATTTA
* * *
2089784 TTAAAAATCAT-TAAAAATT-
1 ATAAAAA-AATATAAAATTTA
* *
2089803 ATAAAAAATTATAAACTTCT-
1 ATAAAAAAATATAAAATT-TA
2089823 ATAAAAAAAT
1 ATAAAAAAAT
2089833 TTATAAAATG
Statistics
Matches: 66, Mismatches: 17, Indels: 9
0.72 0.18 0.10
Matches are distributed among these distances:
18 6 0.09
19 21 0.32
20 37 0.56
21 2 0.03
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (20 bp):
ATAAAAAAATATAAAATTTA
Found at i:2089815 original size:10 final size:10
Alignment explanation
Indices: 2089764--2089817 Score: 56
Period size: 10 Copynumber: 5.5 Consensus size: 10
2089754 ATTAATTTTA
*
2089764 ATAAAAAAAT
1 ATAAAAAATT
*
2089774 AT-AAAATTT
1 ATAAAAAATT
* *
2089783 ATTAAAAATC
1 ATAAAAAATT
*
2089793 ATTAAAAATT
1 ATAAAAAATT
2089803 ATAAAAAATT
1 ATAAAAAATT
2089813 ATAAA
1 ATAAA
2089818 CTTCTATAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
9 7 0.19
10 30 0.81
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (10 bp):
ATAAAAAATT
Found at i:2090036 original size:10 final size:9
Alignment explanation
Indices: 2090001--2090208 Score: 59
Period size: 10 Copynumber: 21.7 Consensus size: 9
2089991 TATTGCGATA
2090001 ATTTTTTAT
1 ATTTTTTAT
*
2090010 ATTTTTTAGG
1 ATTTTTTA-T
*
2090020 A-ATTTTAT
1 ATTTTTTAT
*
2090028 ATTTCTTTAC
1 ATTT-TTTAT
2090038 ATTTTTTAT
1 ATTTTTTAT
2090047 AATTTTCTTAT
1 -ATTTT-TTAT
* *
2090058 GACTTTATA-
1 -ATTTTTTAT
**
2090067 AAATTTTAT
1 ATTTTTTAT
*
2090076 AATTTTTTTCT
1 -A-TTTTTTAT
*
2090087 ATATTTCTAT
1 AT-TTTTTAT
*
2090097 ATATTTTAT
1 ATTTTTTAT
2090106 AATTGTTTTAT
1 -ATT-TTTTAT
*
2090117 GATTTTATAT
1 -ATTTTTTAT
*
2090127 -TTTTTTCT
1 ATTTTTTAT
*
2090135 AATTTTTAATAA
1 -ATTTTT--TAT
* **
2090147 AATTTGAAT
1 ATTTTTTAT
2090156 ATTTTTTAT
1 ATTTTTTAT
2090165 AGTTTTTTATT
1 A-TTTTTTA-T
2090176 AATATTTTT-T
1 -AT-TTTTTAT
2090186 A-TTTTTAT
1 ATTTTTTAT
2090194 -TTTTTTAT
1 ATTTTTTAT
2090202 CATTTTT
1 -ATTTTT
2090209 GCCACATGTC
Statistics
Matches: 143, Mismatches: 33, Indels: 45
0.65 0.15 0.20
Matches are distributed among these distances:
7 5 0.03
8 20 0.14
9 33 0.23
10 50 0.35
11 28 0.20
12 7 0.05
ACGTcount: A:0.27, C:0.04, G:0.03, T:0.66
Consensus pattern (9 bp):
ATTTTTTAT
Found at i:2090423 original size:90 final size:88
Alignment explanation
Indices: 2090272--2090474 Score: 282
Period size: 90 Copynumber: 2.3 Consensus size: 88
2090262 GGGGTGGTTC
* ** * * *
2090272 AAGTACCAAATTGAGTGAAAAAAAATCAGGGGTTTAATTGCTTTTTTTGAAAAAGTTTGAGGGTC
1 AAGTACCCAATTGAGTGAAAAAAAATCAGGGCCTTAATAGCTTTTTTTGAAAAAATTTGAGGGCC
2090337 TTTTTGATGCATTTTGAAAGTTT
66 TTTTTGATGCATTTTGAAAGTTT
*
2090360 AAGTACCCAATTGAGT-ACAATAAAAATGTAGGGCCTTAATAGCTTTTTTTGAAAAAATTTGAGG
1 AAGTACCCAATTGAGTGA-AA-AAAAAT-CAGGGCCTTAATAGCTTTTTTTGAAAAAATTTGAGG
*
2090424 GCCTTTTTGATGCATTTTGATAGTTT
63 GCCTTTTTGATGCATTTTGAAAGTTT
* *
2090450 AAGTACCCAATTGAATAAAAAAAAA
1 AAGTACCCAATTGAGTGAAAAAAAA
2090475 GCAGAAACTT
Statistics
Matches: 102, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
87 1 0.01
88 17 0.17
89 11 0.11
90 72 0.71
91 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.35
Consensus pattern (88 bp):
AAGTACCCAATTGAGTGAAAAAAAATCAGGGCCTTAATAGCTTTTTTTGAAAAAATTTGAGGGCC
TTTTTGATGCATTTTGAAAGTTT
Found at i:2090499 original size:90 final size:90
Alignment explanation
Indices: 2090305--2090497 Score: 266
Period size: 90 Copynumber: 2.2 Consensus size: 90
2090295 AATCAGGGGT
* * *
2090305 TTAATTGCTTTTTTTGAAAAAGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTTAAGTACCCAA
1 TTAATAGCTTTTTTTGAAAAAATTTGAGGGCCTTTTTGATGCATTTTGAAAGTTTAAGTACCCAA
* * * ***
2090370 TTGAGTACAATAAAAATGTAGGGCC
66 TTGAATACAATAAAAAAGCAGAAAC
*
2090395 TTAATAGCTTTTTTTGAAAAAATTTGAGGGCCTTTTTGATGCATTTTGATAGTTTAAGTACCCAA
1 TTAATAGCTTTTTTTGAAAAAATTTGAGGGCCTTTTTGATGCATTTTGAAAGTTTAAGTACCCAA
2090460 TTGAATA-AA-AAAAAAGCAGAAAC
66 TTGAATACAATAAAAAAGCAGAAAC
2090483 TTAATTA-CTTTTTTT
1 TTAA-TAGCTTTTTTT
2090498 TTTAAATTGA
Statistics
Matches: 92, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
88 21 0.23
89 4 0.04
90 67 0.73
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.40
Consensus pattern (90 bp):
TTAATAGCTTTTTTTGAAAAAATTTGAGGGCCTTTTTGATGCATTTTGAAAGTTTAAGTACCCAA
TTGAATACAATAAAAAAGCAGAAAC
Found at i:2100575 original size:3 final size:3
Alignment explanation
Indices: 2100567--2100616 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
2100557 GTTACATGCA
2100567 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2100615 AA
1 AA
2100617 GCATGTCTAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2105590 original size:156 final size:156
Alignment explanation
Indices: 2105410--2105728 Score: 379
Period size: 156 Copynumber: 2.0 Consensus size: 156
2105400 GCATTGTGTC
* ** * * * *
2105410 AAAAAGATTGAGTATGTATATGTCGATTGAGTCTTAGTTCGATTGGTATGAGCATTATTATCAAT
1 AAAAAGATTGAGTATGAATATGTCGATTGAGTCTTAACTCGATTGGCATAAACATTATTACCAAT
* * * * * * *
2105475 ACAGGAGGACGTGAATTTGAATGTATTGGAGCGCATTATCCTTCTATTTATGGATTAGG-GAGGG
66 ACAGGAAGACGTGAATTCGAATGCATCGAAGCGCATTATCCTCCTATTTATGGATT-GGAGAGAG
* * *
2105539 ACTATGGGTACTTCTAGGCATTATATA
130 ACTATGAGTAATTCTAGACATTATATA
*
2105566 AAAAAGATTGAGTATGAATATGTCGATTGAGTCTTAACTCGATTGGCATAAACATTGTTACCAAT
1 AAAAAGATTGAGTATGAATATGTCGATTGAGTCTTAACTCGATTGGCATAAACATTATTACCAAT
* ** * * * *
2105631 GCAGGAAGACGTGGGTTCGAGTGCATCGAAGCGTATTATCCTCCTATTTATGGGTTGGATAGAGA
66 ACAGGAAGACGTGAATTCGAATGCATCGAAGCGCATTATCCTCCTATTTATGGATTGGAGAGAGA
* *
2105696 TTATGAGTAATTCTAGACATTATATC
131 CTATGAGTAATTCTAGACATTATATA
2105722 AAAAAGA
1 AAAAAGA
2105729 GCAGATATGA
Statistics
Matches: 135, Mismatches: 27, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
155 2 0.01
156 133 0.99
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.33
Consensus pattern (156 bp):
AAAAAGATTGAGTATGAATATGTCGATTGAGTCTTAACTCGATTGGCATAAACATTATTACCAAT
ACAGGAAGACGTGAATTCGAATGCATCGAAGCGCATTATCCTCCTATTTATGGATTGGAGAGAGA
CTATGAGTAATTCTAGACATTATATA
Found at i:2119766 original size:13 final size:13
Alignment explanation
Indices: 2119748--2119772 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2119738 TTTAGTATTG
2119748 AGCCTATTTAAAA
1 AGCCTATTTAAAA
2119761 AGCCTATTTAAA
1 AGCCTATTTAAA
2119773 GATGATAGCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (13 bp):
AGCCTATTTAAAA
Found at i:2123318 original size:26 final size:25
Alignment explanation
Indices: 2123289--2123353 Score: 82
Period size: 25 Copynumber: 2.6 Consensus size: 25
2123279 AATTTTAATA
*
2123289 AAAAATATATAATATTATTCAATA-TT
1 AAAAATA-ATAATAATATT-AATATTT
2123315 -AAAATAAT-ATAATATTAATATTT
1 AAAAATAATAATAATATTAATATTT
2123338 AAAAATAATAATAATA
1 AAAAATAATAATAATA
2123354 ATATGAACGA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
22 4 0.11
23 9 0.26
24 10 0.29
25 12 0.34
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (25 bp):
AAAAATAATAATAATATTAATATTT
Found at i:2123348 original size:22 final size:23
Alignment explanation
Indices: 2123290--2123357 Score: 77
Period size: 22 Copynumber: 3.0 Consensus size: 23
2123280 ATTTTAATAA
*
2123290 AAAATATATAATATTATTCAATATT
1 AAAATA-ATAATAATATT-AATATT
2123315 AAAATAAT-ATAATATTAATATT
1 AAAATAATAATAATATTAATATT
* *
2123337 TAAA-AATAATAATAATAATAT
1 AAAATAATAATAATATTAATAT
2123358 GAACGAACTA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
21 3 0.08
22 21 0.54
23 7 0.18
24 2 0.05
25 6 0.15
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (23 bp):
AAAATAATAATAATATTAATATT
Found at i:2129591 original size:49 final size:46
Alignment explanation
Indices: 2129519--2129625 Score: 142
Period size: 49 Copynumber: 2.3 Consensus size: 46
2129509 TTTGAATAAA
* * **
2129519 AAAAGACAAAACTACGTCATTTTGATAAATGTTTACCTTTTTAAAAGTT
1 AAAAGACAAAACTAAGTCATTTTGATAAAAGTTTACC-CATT--AAGTT
*
2129568 AAAAGACAAAACTAAGTCGTTTTGATAAAAGTTTACCCATTAAGTT
1 AAAAGACAAAACTAAGTCATTTTGATAAAAGTTTACCCATTAAGTT
2129614 AAAAGACAAAAC
1 AAAAGACAAAAC
2129626 CATTATATTG
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
46 17 0.32
48 2 0.04
49 34 0.64
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (46 bp):
AAAAGACAAAACTAAGTCATTTTGATAAAAGTTTACCCATTAAGTT
Found at i:2130557 original size:31 final size:30
Alignment explanation
Indices: 2130514--2130580 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
2130504 TTGAACTTTT
2130514 TTTTGTCCAATTTAGT-ACTCAAACTTGACAA
1 TTTT-TCCAATTTAGTAACT-AAACTTGACAA
* *
2130545 TTTTTCCTAATTTGGTAACTAAACTTGACAC
1 TTTTTCC-AATTTAGTAACTAAACTTGACAA
2130576 TTTTT
1 TTTTT
2130581 TTTTAAGTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 3 0.09
31 26 0.81
32 3 0.09
ACGTcount: A:0.28, C:0.18, G:0.09, T:0.45
Consensus pattern (30 bp):
TTTTTCCAATTTAGTAACTAAACTTGACAA
Found at i:2130592 original size:32 final size:31
Alignment explanation
Indices: 2130528--2130602 Score: 80
Period size: 32 Copynumber: 2.4 Consensus size: 31
2130518 GTCCAATTTA
* *
2130528 GTACTCAAACTTGACAATTTTTCCTAATTTG
1 GTACTTAAACTTGACAATTTTTCCTAAGTTG
* **
2130559 GTAAC-TAAACTTGACACTTTTTTTTTAAGTTG
1 GT-ACTTAAACTTGACA-ATTTTTCCTAAGTTG
2130591 GTACTTAAACTT
1 GTACTTAAACTT
2130603 TTTGAGATCC
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
31 14 0.39
32 22 0.61
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.44
Consensus pattern (31 bp):
GTACTTAAACTTGACAATTTTTCCTAAGTTG
Found at i:2130630 original size:91 final size:90
Alignment explanation
Indices: 2130464--2130649 Score: 223
Period size: 91 Copynumber: 2.1 Consensus size: 90
2130454 TTAATATAGT
* * * **
2130464 ATTTGGTACTTAAACTTGACATTTTTTCTTAATTTGATATTTGAACTTTTTTTTGTCCAATTTAG
1 ATTTGGTACTTAAACTTGACATTTTTTCTTAAGTTGATACTTAAACTTTTTTGAGTCCAATTTAG
2130529 TACTCAAACTTGACAATTTTTCCTA
66 TACTCAAACTTGACAATTTTTCCTA
* *
2130554 ATTTGGTAAC-TAAACTTGACACTTTTTTTTTAAGTTGGTACTTAAAC-TTTTTGAGATCCAATT
1 ATTTGGT-ACTTAAACTTGACA-TTTTTTCTTAAGTTGATACTTAAACTTTTTTGAG-TCCAATT
* ** **
2130617 TGGTACTTGAACTTGACTCTTTTTCCTA
63 TAGTACTCAAACTTGACAATTTTTCCTA
2130645 ATTTG
1 ATTTG
2130650 ATACCTAATT
Statistics
Matches: 81, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
90 24 0.30
91 57 0.70
ACGTcount: A:0.26, C:0.15, G:0.11, T:0.48
Consensus pattern (90 bp):
ATTTGGTACTTAAACTTGACATTTTTTCTTAAGTTGATACTTAAACTTTTTTGAGTCCAATTTAG
TACTCAAACTTGACAATTTTTCCTA
Found at i:2131994 original size:23 final size:25
Alignment explanation
Indices: 2131967--2132014 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2131957 TCAAGTAAGT
*
2131967 TGCGAA-C-AGTTTGCCAGTCAAAG
1 TGCGAATCGAGTTCGCCAGTCAAAG
*
2131990 TGCGAATCGGGTTCGCCAGTCAAAG
1 TGCGAATCGAGTTCGCCAGTCAAAG
2132015 ATACAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 6 0.29
24 1 0.05
25 14 0.67
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (25 bp):
TGCGAATCGAGTTCGCCAGTCAAAG
Found at i:2135976 original size:37 final size:36
Alignment explanation
Indices: 2135926--2136002 Score: 127
Period size: 37 Copynumber: 2.1 Consensus size: 36
2135916 ACCCACGTGA
* *
2135926 CCTTGTGCAGTGGTGATGGTTGCACCTGTGCAAGCAT
1 CCTTGTGCAGTGGTGATGATTGCACCTATGCAA-CAT
2135963 CCTTGTGCAGTGGTGATGATTGCACCTATGCAACAT
1 CCTTGTGCAGTGGTGATGATTGCACCTATGCAACAT
2135999 CCTT
1 CCTT
2136003 ATTAGTGGCT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
36 7 0.18
37 31 0.82
ACGTcount: A:0.18, C:0.23, G:0.27, T:0.31
Consensus pattern (36 bp):
CCTTGTGCAGTGGTGATGATTGCACCTATGCAACAT
Found at i:2136964 original size:23 final size:24
Alignment explanation
Indices: 2136908--2136973 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 24
2136898 TCATTAACAT
* *
2136908 TGTTCGTGAACATATTCAATTATA
1 TGTTCGTGAACATGTTCGATTATA
* * *
2136932 TGTTCATGAACACGTTCGTTTA-A
1 TGTTCGTGAACATGTTCGATTATA
2136955 TGTTCGTGAACATGTTCGA
1 TGTTCGTGAACATGTTCGA
2136974 ATAAGTTAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
23 17 0.50
24 17 0.50
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.39
Consensus pattern (24 bp):
TGTTCGTGAACATGTTCGATTATA
Found at i:2145620 original size:30 final size:29
Alignment explanation
Indices: 2145560--2145616 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
2145550 CGTTAATGAA
* *
2145560 TGATTAATTTATTTTTTTTGATAACATTAG
1 TGATCAATTTATTTTTTTT-ATAAAATTAG
2145590 TGATCAATTTATTATTTTTT-TAAAATT
1 TGATCAATTTATT-TTTTTTATAAAATT
2145617 TAGTAATTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 6 0.25
30 12 0.50
31 6 0.25
ACGTcount: A:0.32, C:0.04, G:0.07, T:0.58
Consensus pattern (29 bp):
TGATCAATTTATTTTTTTTATAAAATTAG
Found at i:2152372 original size:17 final size:17
Alignment explanation
Indices: 2152350--2152385 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
2152340 TTTTTATGTG
*
2152350 ATTGTTTAGAATGATAA
1 ATTGTTCAGAATGATAA
2152367 ATTGTTCAGAATGATAA
1 ATTGTTCAGAATGATAA
2152384 AT
1 AT
2152386 ACTTTCAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.17, T:0.39
Consensus pattern (17 bp):
ATTGTTCAGAATGATAA
Found at i:2155955 original size:27 final size:28
Alignment explanation
Indices: 2155919--2155973 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
2155909 TATTTTTAAA
2155919 TTTTTAAAT-ATTTATAAGTTAATATTT
1 TTTTTAAATAATTTATAAGTTAATATTT
* * *
2155946 TTTTTGAATAATTTATGAGTTATTATTT
1 TTTTTAAATAATTTATAAGTTAATATTT
2155974 GATATAATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (28 bp):
TTTTTAAATAATTTATAAGTTAATATTT
Found at i:2156811 original size:10 final size:9
Alignment explanation
Indices: 2156773--2156878 Score: 65
Period size: 10 Copynumber: 11.4 Consensus size: 9
2156763 ACACATGGCA
2156773 AAAAATTAT
1 AAAAATTAT
2156782 AAAAA--AT
1 AAAAATTAT
*
2156789 AAAAATAAAT
1 AAAAAT-TAT
2156799 AAAAATTAT
1 AAAAATTAT
* *
2156808 TAAATTCTCAT
1 AAAAAT-T-AT
*
2156819 AAAAATATAA
1 AAAAAT-TAT
2156829 AAAAATT-T
1 AAAAATTAT
** *
2156837 AAATTTTTT
1 AAAAATTAT
2156846 AAAAATATAT
1 AAAAAT-TAT
*
2156856 AAAAATCAT
1 AAAAATTAT
2156865 AAAAAATTAT
1 -AAAAATTAT
2156875 AAAA
1 AAAA
2156879 TGCATAAAAA
Statistics
Matches: 74, Mismatches: 15, Indels: 16
0.70 0.14 0.15
Matches are distributed among these distances:
7 7 0.09
8 5 0.07
9 23 0.31
10 32 0.43
11 7 0.09
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:2156848 original size:37 final size:37
Alignment explanation
Indices: 2156773--2156870 Score: 94
Period size: 37 Copynumber: 2.6 Consensus size: 37
2156763 ACACATGGCA
2156773 AAAAAT-TATAAAAA-ATAAAAATAAATAAAAATTATT
1 AAAAATATATAAAAATATAAAAA-AAATAAAAATTATT
* * * * * *
2156809 -AAATTCTCATAAAAATATAAAAAAATTTAAATTTTTT
1 AAAAATAT-ATAAAAATATAAAAAAAATAAAAATTATT
2156846 AAAAATATATAAAAATCATAAAAAA
1 AAAAATATATAAAAAT-ATAAAAAA
2156871 TTATAAAATG
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
35 4 0.08
36 1 0.02
37 25 0.50
38 20 0.40
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (37 bp):
AAAAATATATAAAAATATAAAAAAAATAAAAATTATT
Found at i:2156867 original size:19 final size:18
Alignment explanation
Indices: 2156773--2156891 Score: 66
Period size: 19 Copynumber: 6.4 Consensus size: 18
2156763 ACACATGGCA
2156773 AAAAAT-TATAAAAA-AT
1 AAAAATATATAAAAATAT
*
2156789 AAAAATAAATAAAAATTAT
1 AAAAATATATAAAAA-TAT
* * *
2156808 TAAATTCTCATAAAAATAT
1 AAAAATAT-ATAAAAATAT
* * ** *
2156827 AAAAAAATTTAAATTTTTT
1 AAAAATATATAAA-AATAT
2156846 AAAAATATATAAAAATCAT
1 AAAAATATATAAAAAT-AT
2156865 AAAAA-AT-TATAAAATGCAT
1 AAAAATATATA-AAAAT--AT
2156884 AAAAATAT
1 AAAAATAT
2156892 TATTTAACTG
Statistics
Matches: 76, Mismatches: 18, Indels: 14
0.70 0.17 0.13
Matches are distributed among these distances:
16 6 0.08
17 9 0.12
18 12 0.16
19 40 0.53
20 9 0.12
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (18 bp):
AAAAATATATAAAAATAT
Found at i:2156867 original size:28 final size:28
Alignment explanation
Indices: 2156787--2156867 Score: 83
Period size: 27 Copynumber: 2.8 Consensus size: 28
2156777 ATTATAAAAA
*
2156787 ATAAAAATAAATAAAAATTATTAAATTCTC
1 ATAAAAATATATAAAAA-TA-TAAATTCTC
* * *
2156817 ATAAAAATATAAAAAAATTTAAATT-TT
1 ATAAAAATATATAAAAATATAAATTCTC
*
2156844 TTAAAAATATATAAAAATCATAAA
1 ATAAAAATATATAAAAAT-ATAAA
2156868 AAATTATAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
27 17 0.40
28 10 0.23
29 1 0.02
30 15 0.35
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (28 bp):
ATAAAAATATATAAAAATATAAATTCTC
Found at i:2157570 original size:19 final size:19
Alignment explanation
Indices: 2157549--2157591 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 19
2157539 TAAATTTTTT
2157549 AAAAATATATAAAAAT-CATA
1 AAAAAT-TAT-AAAATGCATA
2157569 AAAAATTATAAAATGCATA
1 AAAAATTATAAAATGCATA
2157588 AAAA
1 AAAA
2157592 GTGTTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.23
19 11 0.50
20 6 0.27
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (19 bp):
AAAAATTATAAAATGCATA
Found at i:2160885 original size:59 final size:57
Alignment explanation
Indices: 2160736--2160922 Score: 160
Period size: 59 Copynumber: 3.2 Consensus size: 57
2160726 AATATTTAAT
* * * * *
2160736 AAATTTAGGTGTCAAATTGAATCTAAAAAAAGCTTAGGTACTAAATTAGGAAAAAAAATGTC
1 AAATTTAAGTGCCAAATTGAGTC-AAAAAAAGTTTAGGTACCAAATT----AAAAAAATGTC
* * * * * *
2160798 AAGTTCAAGTACCAAATTGGGTCCAAAAAAGTTTAGGTTCCAAATTAAGAAAAAGTGTC
1 AAATTTAAGTGCCAAATTGAGTCAAAAAAAGTTTAGGTACCAAATTAA-AAAAA-TGTC
* * ** *
2160857 AAATTTAAGTGCCGAATTGAGTCAAAAAAAATTTAAATACCAAATTAAAAAAA-ATC
1 AAATTTAAGTGCCAAATTGAGTCAAAAAAAGTTTAGGTACCAAATTAAAAAAATGTC
2160913 AAATTTAAGT
1 AAATTTAAGT
2160923 ATCAAATATT
Statistics
Matches: 101, Mismatches: 22, Indels: 10
0.76 0.17 0.08
Matches are distributed among these distances:
56 12 0.12
57 2 0.02
58 10 0.10
59 42 0.42
61 19 0.19
62 16 0.16
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.27
Consensus pattern (57 bp):
AAATTTAAGTGCCAAATTGAGTCAAAAAAAGTTTAGGTACCAAATTAAAAAAATGTC
Found at i:2161924 original size:33 final size:30
Alignment explanation
Indices: 2161882--2161949 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
2161872 AAAATTGATT
*
2161882 AAAACTTCTAGAAATTTATTATTAATT-TTTAA
1 AAAATTTCTA-AAATTT-TTA-TAATTATTTAA
*
2161914 ATAAATTTCTATAATTTTTATAATTATTTAA
1 A-AAATTTCTAAAATTTTTATAATTATTTAA
2161945 AAAAT
1 AAAAT
2161950 CACTATAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
30 9 0.28
31 9 0.28
32 6 0.19
33 8 0.25
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.49
Consensus pattern (30 bp):
AAAATTTCTAAAATTTTTATAATTATTTAA
Found at i:2161956 original size:30 final size:32
Alignment explanation
Indices: 2161894--2161956 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 32
2161884 AACTTCTAGA
**
2161894 AATTTATTATTAATTTTTAAATAAATTTCTAT
1 AATTTATTATTAATTTTTAAATAAATCACTAT
2161926 AATTT-TTA-TAATTATTTAAA-AAATCACTAT
1 AATTTATTATTAATT-TTTAAATAAATCACTAT
2161956 A
1 A
2161957 GAATGAACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 14 0.50
31 9 0.32
32 5 0.18
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (32 bp):
AATTTATTATTAATTTTTAAATAAATCACTAT
Found at i:2164674 original size:28 final size:28
Alignment explanation
Indices: 2164632--2164686 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
2164622 GAAAAAAATG
* * * *
2164632 CATTAATGCATTAAATGGATGGAAAAAC
1 CATTAAGGCACTAAATGCATCGAAAAAC
2164660 CATTAAGGCACTAAATGCATCGAAAAA
1 CATTAAGGCACTAAATGCATCGAAAAA
2164687 GCTATTGTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.47, C:0.15, G:0.16, T:0.22
Consensus pattern (28 bp):
CATTAAGGCACTAAATGCATCGAAAAAC
Found at i:2164872 original size:31 final size:32
Alignment explanation
Indices: 2164837--2164896 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
2164827 TTCATTTTCG
* *
2164837 TAATTAATTTATTTTTT-ATCTTATTTTTTTA
1 TAATTAATTAATTTTTTAATATTATTTTTTTA
2164868 TAATTAATTAATTTTTTAATATTATTTTT
1 TAATTAATTAATTTTTTAATATTATTTTT
2164897 ATAAAAAGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 16 0.62
32 10 0.38
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (32 bp):
TAATTAATTAATTTTTTAATATTATTTTTTTA
Found at i:2165032 original size:26 final size:28
Alignment explanation
Indices: 2164994--2165046 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 28
2164984 TATTTAATGA
*
2164994 AATTTTTTAAAAAAT-A-GGGATTAATT
1 AATTATTTAAAAAATAATGGGATTAATT
*
2165020 AATTATTTCAAAAATAATGGGATTAAT
1 AATTATTTAAAAAATAATGGGATTAAT
2165047 AAAAAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 13 0.57
27 1 0.04
28 9 0.39
ACGTcount: A:0.47, C:0.02, G:0.11, T:0.40
Consensus pattern (28 bp):
AATTATTTAAAAAATAATGGGATTAATT
Found at i:2189656 original size:189 final size:189
Alignment explanation
Indices: 2189345--2189695 Score: 548
Period size: 189 Copynumber: 1.9 Consensus size: 189
2189335 GTGCAATTTT
* * *
2189345 CAATAATGGATTCAGATTCACTTTTGCATATAGTTTTATTTGTTAAGTTTTATATCAAATCTTAT
1 CAATAATGAATTCAGATTCACTTCTGCATATAATTTTATTTGTTAAGTTTTATATCAAATCTTAT
* * *
2189410 TTTACAGTTCTAATAAATCTAACTTTTAATACAAGTAAAGACCTTTTTGAGTATGATT-AACCTA
66 TTTACAGTTCTAACAAATCTAAATTTTAATACAAGTAAAGACCTTTTTGAATATGATTGAA-CTA
* *
2189474 AATTTGAGTTAAAGGTTGGAAGGATACAAATTGAAAAATTTAAATATTCTGAATAATCTC
130 AATTTGAGTTAAAAGTTGGAAAGATACAAATTGAAAAATTTAAATATTCTGAATAATCTC
*
2189534 CAATAATGAATTCAGGTAT-ACTTCTGCATATAATTTTATTTGTTAAGTTTTATATCAAATCTTA
1 CAATAATGAATTCAGAT-TCACTTCTGCATATAATTTTATTTGTTAAGTTTTATATCAAATCTTA
*
2189598 TTTTAC-GCTTCTAACAAATCTAAATTTTAATACAAGTAAATA-CTCTTTTGAATATGATTGAAC
65 TTTTACAG-TTCTAACAAATCTAAATTTTAATACAAGTAAAGACCT-TTTTGAATATGATTGAAC
2189661 TAAATTTGAGTTAAAAGTTGGAAAGATACAAATTG
128 TAAATTTGAGTTAAAAGTTGGAAAGATACAAATTG
2189696 GTTTTACTTT
Statistics
Matches: 148, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
188 3 0.02
189 142 0.96
190 3 0.02
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.40
Consensus pattern (189 bp):
CAATAATGAATTCAGATTCACTTCTGCATATAATTTTATTTGTTAAGTTTTATATCAAATCTTAT
TTTACAGTTCTAACAAATCTAAATTTTAATACAAGTAAAGACCTTTTTGAATATGATTGAACTAA
ATTTGAGTTAAAAGTTGGAAAGATACAAATTGAAAAATTTAAATATTCTGAATAATCTC
Done.