Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold283
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: 2945114
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 15
Found at i:1466919 original size:20 final size:19
Alignment explanation
Indices: 1466887--1466924 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1466877 TCATAAATCG
1466887 ATTAATAAATATTTTTAAT
1 ATTAATAAATATTTTTAAT
*
1466906 ATTATATAATTATTTTTAA
1 ATTA-ATAAATATTTTTAA
1466925 AAAATATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTAATAAATATTTTTAAT
Found at i:1466975 original size:23 final size:23
Alignment explanation
Indices: 1466932--1466974 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
1466922 TAAAAAATAT
1466932 TATTTAATAAATTTAAATTTTAA
1 TATTTAATAAATTTAAATTTTAA
1466955 TATTT-AT-AATTTATAATTTT
1 TATTTAATAAATTTA-AATTTT
1466975 TTATTACTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 8 0.42
23 5 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TATTTAATAAATTTAAATTTTAA
Found at i:1467467 original size:29 final size:28
Alignment explanation
Indices: 1467434--1467501 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 28
1467424 ATTATTTAAA
*
1467434 TTATAATTATTAATATATTAATA-ATTTAT
1 TTAT-ATT-TTAAAATATTAATATATTTAT
*
1467463 TTATATTTTAAAATATTTATATATTTAT
1 TTATATTTTAAAATATTAATATATTTAT
*
1467491 ATATTATTTTA
1 TTA-TATTTTA
1467502 TTTTATTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 12 0.35
28 11 0.32
29 11 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
TTATATTTTAAAATATTAATATATTTAT
Found at i:1467498 original size:35 final size:35
Alignment explanation
Indices: 1467404--1467506 Score: 95
Period size: 35 Copynumber: 2.9 Consensus size: 35
1467394 AGATTCAATA
* * *
1467404 ATTTATATATTTTTATTATAATTATTTAAATTAT-AATT
1 ATTTATATA--TTTA-TAT-ATTATTTATATTTTAAAAT
* *
1467442 ATTAATATATTAATA-ATTTATTTATATTTTAAAAT
1 ATTTATATATTTATATA-TTATTTATATTTTAAAAT
1467477 ATTTATATATTTATATATTATTT-TATTTTA
1 ATTTATATATTTATATATTATTTATATTTTA
1467507 TTTAAATTTA
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
33 1 0.02
34 18 0.33
35 24 0.44
36 4 0.07
38 8 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (35 bp):
ATTTATATATTTATATATTATTTATATTTTAAAAT
Found at i:1467538 original size:45 final size:45
Alignment explanation
Indices: 1467458--1467545 Score: 106
Period size: 45 Copynumber: 2.0 Consensus size: 45
1467448 ATATTAATAA
* * *** *
1467458 TTTATTTATATTTTAAAATATTTATATATTTATATATTATTTTAT
1 TTTATTTATAATTTAAAATAATTATATAAAAATATATCATTTTAT
1467503 TTTATTTA-AATTTAATAATAATTATATAAAAATATATCATTTT
1 TTTATTTATAATTTAA-AATAATTATATAAAAATATATCATTTT
1467546 CAAGTTACTA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
44 6 0.17
45 30 0.83
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (45 bp):
TTTATTTATAATTTAAAATAATTATATAAAAATATATCATTTTAT
Found at i:1468109 original size:19 final size:17
Alignment explanation
Indices: 1468072--1468109 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
1468062 AATAAATTTT
1468072 TATATTTTTATCATATA
1 TATATTTTTATCATATA
*
1468089 TATATATTTTATTATAT-
1 TATAT-TTTTATCATATA
1468106 TATA
1 TATA
1468110 ATCATATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (17 bp):
TATATTTTTATCATATA
Found at i:1468130 original size:27 final size:28
Alignment explanation
Indices: 1468063--1468133 Score: 76
Period size: 27 Copynumber: 2.6 Consensus size: 28
1468053 TAATAAAAAA
* *
1468063 ATAAA-TTTTTATATTTTTATCATATAT
1 ATAAATTTTTTATATTATAATCATATAT
*
1468090 ATATATTTTATTATATTATAATCATAT-T
1 ATAAATTTT-TTATATTATAATCATATAT
1468118 A-AAATTATTTTATATT
1 ATAAATT-TTTTATATT
1468134 TATATAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
27 15 0.41
28 7 0.19
29 15 0.41
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (28 bp):
ATAAATTTTTTATATTATAATCATATAT
Found at i:1468428 original size:9 final size:9
Alignment explanation
Indices: 1468408--1468470 Score: 51
Period size: 9 Copynumber: 7.0 Consensus size: 9
1468398 CTTGTTGATA
1468408 TAAATTAAT
1 TAAATTAAT
1468417 T-AATTAAAT
1 TAAATT-AAT
1468426 TAATATT-A-
1 TAA-ATTAAT
*
1468434 TAAATTAAA
1 TAAATTAAT
1468443 TAATATTAAT
1 TAA-ATTAAT
*
1468453 TTAATTAAT
1 TAAATTAAT
*
1468462 AAAATTAAT
1 TAAATTAAT
1468471 ATGGATCAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
7 3 0.07
8 8 0.18
9 22 0.50
10 8 0.18
11 3 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TAAATTAAT
Found at i:1475023 original size:26 final size:27
Alignment explanation
Indices: 1474985--1475039 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
1474975 TATATGATTT
*
1474985 TAATGTATTTATAAATAAATTAAA-AAA
1 TAATGTATATAT-AATAAATTAAATAAA
*
1475012 TAAT-TATATATAATATATTAAATAAA
1 TAATGTATATATAATAAATTAAATAAA
1475038 TA
1 TA
1475040 TATGATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 10 0.40
26 11 0.44
27 4 0.16
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (27 bp):
TAATGTATATATAATAAATTAAATAAA
Found at i:1478829 original size:23 final size:21
Alignment explanation
Indices: 1478785--1478873 Score: 81
Period size: 23 Copynumber: 4.0 Consensus size: 21
1478775 TTTTTTAATT
* *
1478785 TAATTATAAATATTAATATAAAA
1 TAATTAT-AATATT-ATTTTAAA
1478808 TAATTTATAATATTATTTTAAA
1 TAA-TTATAATATTATTTTAAA
* **
1478830 TAA-TAAAATAAAATTTTAAA
1 TAATTATAATATTATTTTAAA
1478850 TCAACTTATAATATTATTTTAAA
1 T-AA-TTATAATATTATTTTAAA
1478873 T
1 T
1478874 TAAAATCCTT
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
20 15 0.28
21 2 0.04
22 9 0.17
23 24 0.44
24 4 0.07
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
TAATTATAATATTATTTTAAA
Found at i:1484052 original size:29 final size:28
Alignment explanation
Indices: 1484006--1484081 Score: 91
Period size: 29 Copynumber: 2.7 Consensus size: 28
1483996 TAAAATAATG
* *
1484006 AAAAAATTCTTAATTTTTTTAT-TTTTTA
1 AAAAAACTCTTAATTTTTTT-TGTATTTA
*
1484034 AAAAAACTCTTATTCTTTTTTTGTATTTA
1 AAAAAACTCTTAAT-TTTTTTTGTATTTA
*
1484063 AATAAACTCTTAATTTTTT
1 AAAAAACTCTTAATTTTTT
1484082 AATTTGTAAC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 18 0.44
29 23 0.56
ACGTcount: A:0.34, C:0.08, G:0.01, T:0.57
Consensus pattern (28 bp):
AAAAAACTCTTAATTTTTTTTGTATTTA
Found at i:1484055 original size:30 final size:29
Alignment explanation
Indices: 1484006--1484074 Score: 81
Period size: 28 Copynumber: 2.4 Consensus size: 29
1483996 TAAAATAATG
*
1484006 AAAAAATTCTTAATT-TTTTTATT-T-TTTA
1 AAAAAACTCTT-ATTCTTTTT-TTGTATTTA
1484034 AAAAAACTCTTATTCTTTTTTTGTATTTA
1 AAAAAACTCTTATTCTTTTTTTGTATTTA
*
1484063 AATAAACTCTTA
1 AAAAAACTCTTA
1484075 ATTTTTTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
27 5 0.14
28 16 0.44
29 15 0.42
ACGTcount: A:0.36, C:0.09, G:0.01, T:0.54
Consensus pattern (29 bp):
AAAAAACTCTTATTCTTTTTTTGTATTTA
Found at i:1484096 original size:31 final size:30
Alignment explanation
Indices: 1484032--1484107 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 30
1484022 TTTTATTTTT
* **
1484032 TAAAAAAACTCTT-ATTCTTTTTTTGTATT
1 TAAATAAACTCTTAATTCTTTTTTTGTAAC
1484061 TAAATAAACTCTTAATT-TTTTAATTTGTAAC
1 TAAATAAACTCTTAATTCTTTT--TTTGTAAC
*
1484092 TAAATAAGCTCTTAAT
1 TAAATAAACTCTTAAT
1484108 CTATAAAAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
29 16 0.40
30 3 0.08
31 21 0.52
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.49
Consensus pattern (30 bp):
TAAATAAACTCTTAATTCTTTTTTTGTAAC
Found at i:1485009 original size:28 final size:29
Alignment explanation
Indices: 1484948--1485012 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
1484938 AATTTTTAAT
* * *
1484948 TTATAAATACTTATTTGAATGCAAATAAAA
1 TTATAAA-ATTTATTTAAATACAAATAAAA
1484978 --ATAAAATTTATTTAAATAC-AATAAAA
1 TTATAAAATTTATTTAAATACAAATAAAA
1485004 TTATAAAAT
1 TTATAAAAT
1485013 CTCACTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
26 7 0.23
27 11 0.37
28 12 0.40
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (29 bp):
TTATAAAATTTATTTAAATACAAATAAAA
Found at i:1491686 original size:36 final size:36
Alignment explanation
Indices: 1491646--1491775 Score: 143
Period size: 36 Copynumber: 3.6 Consensus size: 36
1491636 TTACTCTATT
*
1491646 CCTGAATCCAAACTCTAAACAACCTCAAAATCCACC
1 CCTGAATCCAAACTCTGAACAACCTCAAAATCCACC
* * *
1491682 CCTGAAACCAAACTCTGAACAACCTCATAATCTACC
1 CCTGAATCCAAACTCTGAACAACCTCAAAATCCACC
* * * * * * *
1491718 CATTAATCCAAACTCGGAGCAGCCTGAAAATCCAAC
1 CCTGAATCCAAACTCTGAACAACCTCAAAATCCACC
* *
1491754 CCAGAACCCAAACTCTGAACAA
1 CCTGAATCCAAACTCTGAACAA
1491776 TTTCAGCCGA
Statistics
Matches: 73, Mismatches: 21, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
36 73 1.00
ACGTcount: A:0.41, C:0.35, G:0.08, T:0.16
Consensus pattern (36 bp):
CCTGAATCCAAACTCTGAACAACCTCAAAATCCACC
Found at i:1492550 original size:13 final size:13
Alignment explanation
Indices: 1492532--1492556 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1492522 TTTATTGTTA
1492532 AATATTTATAATT
1 AATATTTATAATT
1492545 AATATTTATAAT
1 AATATTTATAAT
1492557 AATTGATTGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATATTTATAATT
Found at i:1492795 original size:13 final size:14
Alignment explanation
Indices: 1492764--1492801 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
1492754 GGAGAGATAC
*
1492764 ATATATATATATAT
1 ATATATATTTATAT
1492778 ATATAT-TTTATAT
1 ATATATATTTATAT
*
1492791 GTATATATTTA
1 ATATATATTTA
1492802 ATTATTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (14 bp):
ATATATATTTATAT
Found at i:1492795 original size:15 final size:15
Alignment explanation
Indices: 1492771--1492800 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1492761 TACATATATA
1492771 TATATATATATATTT
1 TATATATATATATTT
*
1492786 TATATGTATATATTT
1 TATATATATATATTT
1492801 AATTATTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (15 bp):
TATATATATATATTT
Found at i:1492795 original size:23 final size:23
Alignment explanation
Indices: 1492764--1492815 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
1492754 GGAGAGATAC
1492764 ATATATATATATAT-ATATATTTT
1 ATATATATATATATAAT-TATTTT
* *
1492787 ATATGTATATATTTAATTATTTT
1 ATATATATATATATAATTATTTT
1492810 ATATAT
1 ATATAT
1492816 TTAAAAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 23 0.92
24 2 0.08
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
ATATATATATATATAATTATTTT
Found at i:1498135 original size:32 final size:32
Alignment explanation
Indices: 1498099--1498163 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
1498089 AGCTGACCCG
*
1498099 ATGTATCAAGAACTCTGGCATAAGCTCCTACT
1 ATGTATCAAGAACTCTAGCATAAGCTCCTACT
*
1498131 ATGTATCAAGAACTCTAGCATGAGCTCCTACT
1 ATGTATCAAGAACTCTAGCATAAGCTCCTACT
1498163 A
1 A
1498164 AAGAGTCAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (32 bp):
ATGTATCAAGAACTCTAGCATAAGCTCCTACT
Found at i:1498799 original size:37 final size:37
Alignment explanation
Indices: 1498718--1498802 Score: 93
Period size: 37 Copynumber: 2.3 Consensus size: 37
1498708 GACGTTGCCG
*
1498718 CCCAAAT-TATAACAATCATAGTGAATTGACACTACCA
1 CCCAAATAT-TAACAATCATAGTGAATTGACACAACCA
* * * *
1498755 CCTAAATATTAACAGTCATAGTGGATTGAC-CAAATCA
1 CCCAAATATTAACAATCATAGTGAATTGACAC-AACCA
1498792 CCCAAATATTA
1 CCCAAATATTA
1498803 CTTGTCGTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
36 1 0.03
37 38 0.95
38 1 0.03
ACGTcount: A:0.42, C:0.22, G:0.09, T:0.26
Consensus pattern (37 bp):
CCCAAATATTAACAATCATAGTGAATTGACACAACCA
Found at i:1506439 original size:58 final size:58
Alignment explanation
Indices: 1506349--1506465 Score: 216
Period size: 58 Copynumber: 2.0 Consensus size: 58
1506339 CTCATTTTAA
*
1506349 TTTCAAAAATAGTGGCAAAGGGCAATATAGCTTCTTACAACAACTTAGTGAACACAGT
1 TTTCAAAAATAGTGGCAAAGGGCAATATAGCTTCTTACAACAACTTAGCGAACACAGT
*
1506407 TTTCAAAAATAGTGGCAAAGGGCAATATAGCTTCTTACAACTACTTAGCGAACACAGT
1 TTTCAAAAATAGTGGCAAAGGGCAATATAGCTTCTTACAACAACTTAGCGAACACAGT
1506465 T
1 T
1506466 GAATGTACTT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.26
Consensus pattern (58 bp):
TTTCAAAAATAGTGGCAAAGGGCAATATAGCTTCTTACAACAACTTAGCGAACACAGT
Found at i:1514071 original size:30 final size:30
Alignment explanation
Indices: 1514035--1514114 Score: 124
Period size: 30 Copynumber: 2.7 Consensus size: 30
1514025 AGTGGTGTAG
*
1514035 TAGTCCTTAATTTAAAGGATAATGATGCAC
1 TAGTCCTTAATTTAAGGGATAATGATGCAC
* * *
1514065 TAGTCCTTAATCTAAGGGATAGTGGTGCAC
1 TAGTCCTTAATTTAAGGGATAATGATGCAC
1514095 TAGTCCTTAATTTAAGGGAT
1 TAGTCCTTAATTTAAGGGAT
1514115 TTAAATTAGT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (30 bp):
TAGTCCTTAATTTAAGGGATAATGATGCAC
Found at i:1514685 original size:3 final size:3
Alignment explanation
Indices: 1514677--1514703 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1514667 AATCAAATAC
1514677 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1514704 TCCAAGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1519349 original size:2 final size:2
Alignment explanation
Indices: 1519344--1519375 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1519334 AATATCTCTC
1519344 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
1519376 TAAGTCTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1519427 original size:7 final size:7
Alignment explanation
Indices: 1519412--1519469 Score: 66
Period size: 7 Copynumber: 8.6 Consensus size: 7
1519402 TTTAACTTTA
*
1519412 ATTTTTT
1 ATTTATT
1519419 ATTTATT
1 ATTTATT
**
1519426 ATCAATT
1 ATTTATT
*
1519433 AATT-TT
1 ATTTATT
1519439 A-TTATT
1 ATTTATT
1519445 ATTTATT
1 ATTTATT
1519452 ATTTATT
1 ATTTATT
1519459 ATTTATT
1 ATTTATT
1519466 ATTT
1 ATTT
1519470 TTTTAAATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
5 2 0.05
6 6 0.14
7 35 0.81
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (7 bp):
ATTTATT
Found at i:1523080 original size:20 final size:21
Alignment explanation
Indices: 1523024--1523080 Score: 53
Period size: 23 Copynumber: 2.6 Consensus size: 21
1523014 TTAAAAATTT
**
1523024 ATATAAATATAAAATACTTTAA
1 ATATAAATATAAAATAC-AAAA
1523046 ATATAATTATAATAAAATA-AAAA
1 ATATAA--AT-ATAAAATACAAAA
1523069 ATATAAATATAA
1 ATATAAATATAA
1523081 TACGAATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
20 4 0.13
21 2 0.07
22 6 0.20
23 8 0.27
24 2 0.07
25 8 0.27
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
ATATAAATATAAAATACAAAA
Found at i:1524318 original size:64 final size:63
Alignment explanation
Indices: 1524217--1524343 Score: 245
Period size: 64 Copynumber: 2.0 Consensus size: 63
1524207 AAAGGGTGAG
1524217 AGTAATTAGGGCTAAAAAGCAAAGAAAGCCTAACAGTTCAGATTTCTTTCTGCAACTCTATGAA
1 AGTAATTAGGGCTAAAAAGCAAAGAAAGCCTAACAGTTCAGA-TTCTTTCTGCAACTCTATGAA
1524281 AGTAATTAGGGCTAAAAAGCAAAGAAAGCCTAACAGTTCAGATTCTTTCTGCAACTCTATGAA
1 AGTAATTAGGGCTAAAAAGCAAAGAAAGCCTAACAGTTCAGATTCTTTCTGCAACTCTATGAA
1524344 TACTCTCCTT
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
63 21 0.33
64 42 0.67
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.26
Consensus pattern (63 bp):
AGTAATTAGGGCTAAAAAGCAAAGAAAGCCTAACAGTTCAGATTCTTTCTGCAACTCTATGAA
Found at i:1537146 original size:10 final size:10
Alignment explanation
Indices: 1537131--1537169 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
1537121 ATATAAAATA
*
1537131 ATTTATGTAT
1 ATTTATATAT
1537141 ATTTATATAT
1 ATTTATATAT
1537151 ATTTATATTAT
1 ATTTATA-TAT
*
1537162 AATTATAT
1 ATTTATAT
1537170 TTTGAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (10 bp):
ATTTATATAT
Found at i:1537490 original size:22 final size:22
Alignment explanation
Indices: 1537462--1537503 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1537452 ATTAAAATAT
1537462 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
1537484 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
1537504 AATAAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:1537833 original size:26 final size:27
Alignment explanation
Indices: 1537778--1537857 Score: 90
Period size: 27 Copynumber: 2.9 Consensus size: 27
1537768 ATATTTATTT
1537778 AAATTTAATTATAAAATATAATTTTAA
1 AAATTTAATTATAAAATATAATTTTAA
*
1537805 AAATTTATTTAT-AAATAATAATTTTAA
1 AAATTTAATTATAAAAT-ATAATTTTAA
* * *
1537832 AATTTTAAATTAATTAAATTTAATTT
1 AAATTT-AATT-ATAAAATATAATTT
1537858 AAATTTAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
26 4 0.09
27 26 0.58
28 3 0.07
29 8 0.18
30 4 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
AAATTTAATTATAAAATATAATTTTAA
Found at i:1537853 original size:23 final size:22
Alignment explanation
Indices: 1537811--1537854 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
1537801 TTAAAAATTT
*
1537811 ATTTATAAATAATAATTTTAAA
1 ATTTATAAATAATAAATTTAAA
1537833 ATTT-TAAATTAATTAAATTTAA
1 ATTTATAAA-TAA-TAAATTTAA
1537855 TTTAAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 4 0.21
22 7 0.37
23 8 0.42
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTTATAAATAATAAATTTAAA
Found at i:1541222 original size:8 final size:7
Alignment explanation
Indices: 1541197--1541265 Score: 52
Period size: 7 Copynumber: 9.7 Consensus size: 7
1541187 TTATTTTAAA
1541197 AAATTTT
1 AAATTTT
1541204 AAATTTT
1 AAATTTT
1541211 AAATTATT
1 AAATT-TT
*
1541219 AAATATT
1 AAATTTT
* *
1541226 ATATTTAAA
1 AAATTT--T
1541235 AAATTTT
1 AAATTTT
**
1541242 AAAAATT
1 AAATTTT
1541249 AAA--TT
1 AAATTTT
1541254 AAATTTT
1 AAATTTT
1541261 AAATT
1 AAATT
1541266 CTTGATAAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
5 5 0.10
7 33 0.67
8 6 0.12
9 5 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (7 bp):
AAATTTT
Found at i:1556443 original size:14 final size:13
Alignment explanation
Indices: 1556408--1556449 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
1556398 ATTTTAAATA
1556408 TTAATTT-ATTTT
1 TTAATTTAATTTT
1556420 TATAAGTTTAATTTAT
1 T-TAA-TTTAATTT-T
1556436 TTAATTTAATTTT
1 TTAATTTAATTTT
1556449 T
1 T
1556450 ATTACGCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
12 1 0.04
13 5 0.19
14 11 0.42
15 7 0.27
16 2 0.08
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (13 bp):
TTAATTTAATTTT
Found at i:1557619 original size:11 final size:11
Alignment explanation
Indices: 1557583--1557625 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
1557573 AAATAAAAAA
1557583 TTAATTTTAAT
1 TTAATTTTAAT
*
1557594 TGTAATATATAAT
1 T-TAAT-TTTAAT
*
1557607 TTAGTTTTAAT
1 TTAATTTTAAT
1557618 TTAATTTT
1 TTAATTTT
1557626 TTTATTGAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 13 0.50
12 7 0.27
13 6 0.23
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (11 bp):
TTAATTTTAAT
Found at i:1557750 original size:17 final size:18
Alignment explanation
Indices: 1557728--1557763 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1557718 ATTAAAATCG
1557728 AATTAAATTTT-ATTTTT
1 AATTAAATTTTAATTTTT
*
1557745 AATTAATTTTTAATTTTT
1 AATTAAATTTTAATTTTT
1557763 A
1 A
1557764 TAAAATAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
AATTAAATTTTAATTTTT
Found at i:1559308 original size:5 final size:5
Alignment explanation
Indices: 1559298--1559410 Score: 71
Period size: 5 Copynumber: 23.2 Consensus size: 5
1559288 TGGTTTAAAA
* * *
1559298 AATAT AATAT -ATAT AAAAT AATTAA AATAT AATAT ATTAT AATAT AA-AT
1 AATAT AATAT AATAT AATAT AA-TAT AATAT AATAT AATAT AATAT AATAT
* *
1559347 AA-AT -ATCAT AATATT TATAT AATAT AA-AT TAT-T AATAT -ATCAT
1 AATAT AAT-AT AATA-T AATAT AATAT AATAT AATAT AATAT AAT-AT
*
1559390 AAT-T TATAT AAATAT AATAT A
1 AATAT AATAT -AATAT AATAT A
1559411 TCTTAAATAT
Statistics
Matches: 84, Mismatches: 12, Indels: 24
0.70 0.10 0.20
Matches are distributed among these distances:
3 1 0.01
4 21 0.25
5 47 0.56
6 15 0.18
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
AATAT
Found at i:1559382 original size:24 final size:23
Alignment explanation
Indices: 1559322--1559384 Score: 58
Period size: 24 Copynumber: 2.6 Consensus size: 23
1559312 AAAATAATTA
1559322 AAATATA-ATATATTATAATATAAAT
1 AAATATATA-ATATT-T-ATATAAAT
1559347 AAATATCATAATATTTATATAATAT
1 AAATAT-ATAATATTTATATAA-AT
1559372 AAAT-TATTAATAT
1 AAATATA-TAATAT
1559385 ATCATAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
23 1 0.03
24 13 0.38
25 13 0.38
26 6 0.18
27 1 0.03
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
AAATATATAATATTTATATAAAT
Found at i:1559404 original size:18 final size:18
Alignment explanation
Indices: 1559324--1559404 Score: 64
Period size: 18 Copynumber: 4.6 Consensus size: 18
1559314 AATAATTAAA
* *
1559324 ATATAATATATTATAATAT
1 ATATAA-ATATCATAATTT
*
1559343 AAATAAATATCATAATATT
1 ATATAAATATCATAAT-TT
1559362 -TATATAATAT-A-AA-TT
1 ATATA-AATATCATAATTT
1559377 AT-TAATATATCATAATTT
1 ATATAA-ATATCATAATTT
1559395 ATATAAATAT
1 ATATAAATAT
1559405 AATATATCTT
Statistics
Matches: 50, Mismatches: 4, Indels: 17
0.70 0.06 0.24
Matches are distributed among these distances:
14 1 0.02
15 8 0.16
16 2 0.04
17 4 0.08
18 21 0.42
19 14 0.28
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATAAATATCATAATTT
Found at i:1559412 original size:25 final size:24
Alignment explanation
Indices: 1559297--1559411 Score: 99
Period size: 25 Copynumber: 4.5 Consensus size: 24
1559287 ATGGTTTAAA
*
1559297 AAATATAATATATATAAAATA-ATT
1 AAATATAATATATATAATATATA-T
*
1559321 AAAATATAATATATTATAATATAAAT
1 -AAATATAATATA-TATAATATATAT
* *
1559347 AAATATCATA-ATATTTATATAATAT
1 AAATATAATATATA-TAATAT-ATAT
*
1559372 AAATTATTAATATATCATAATTTATAT
1 AAA-TA-TAATATAT-ATAATATATAT
1559399 AAATATAATATAT
1 AAATATAATATAT
1559412 CTTAAATATA
Statistics
Matches: 75, Mismatches: 7, Indels: 16
0.77 0.07 0.16
Matches are distributed among these distances:
23 2 0.03
24 6 0.08
25 35 0.47
26 13 0.17
27 12 0.16
28 6 0.08
29 1 0.01
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
AAATATAATATATATAATATATAT
Found at i:1566566 original size:2 final size:2
Alignment explanation
Indices: 1566559--1566595 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1566549 GCTTAACATT
1566559 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1566596 AAATATTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1568909 original size:2 final size:2
Alignment explanation
Indices: 1568902--1568941 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1568892 CTCTCCTTCA
1568902 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1568942 ATTCTGTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1572077 original size:30 final size:30
Alignment explanation
Indices: 1572042--1572098 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1572032 ATATAACTTA
**
1572042 TAAATTTTTAATT-TTATTAAATTATATTAT
1 TAAATTTTT-ATTATTAAAAAATTATATTAT
1572072 TAAATTTTTATTATTAAAAAATTATAT
1 TAAATTTTTATTATTAAAAAATTATAT
1572099 CATTTAAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 21 0.88
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
TAAATTTTTATTATTAAAAAATTATATTAT
Found at i:1572085 original size:14 final size:13
Alignment explanation
Indices: 1572055--1572089 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
1572045 ATTTTTAATT
1572055 TTATTAAATTATA
1 TTATTAAATTATA
*
1572068 TTATTAAATTTTTA
1 TTATTAAA-TTATA
1572082 TTATTAAA
1 TTATTAAA
1572090 AAATTATATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTATTAAATTATA
Found at i:1573016 original size:14 final size:14
Alignment explanation
Indices: 1572973--1573019 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
1572963 ATATAATTTG
1572973 ATTTATTAA-TAAA
1 ATTTATTAATTAAA
** *
1572986 ATATTAAAAATTTAA
1 AT-TTATTAATTAAA
1573001 ATTTATTAATTAAA
1 ATTTATTAATTAAA
1573015 ATTTA
1 ATTTA
1573020 ATTTCCCTCA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
13 2 0.08
14 19 0.73
15 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATTTATTAATTAAA
Found at i:1573240 original size:20 final size:18
Alignment explanation
Indices: 1573215--1573251 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
1573205 ATAAAAAGCA
1573215 TTGTTAATCAAAAATAATTT
1 TTGTTAA-CAAAAA-AATTT
1573235 TTGTTAACAAAAAAATT
1 TTGTTAACAAAAAAATT
1573252 AATTTTTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 6 0.35
20 7 0.41
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (18 bp):
TTGTTAACAAAAAAATTT
Found at i:1579012 original size:14 final size:14
Alignment explanation
Indices: 1578993--1579020 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1578983 TAAAAATTAA
1578993 AAAAATTTAAATAT
1 AAAAATTTAAATAT
1579007 AAAAATTTAAATAT
1 AAAAATTTAAATAT
1579021 CAAATCTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AAAAATTTAAATAT
Found at i:1585347 original size:14 final size:13
Alignment explanation
Indices: 1585337--1585379 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
1585327 GAATTTTGTA
1585337 TTTTAAATTTTAT
1 TTTTAAATTTTAT
1585350 TTTTAAA-TTTA-
1 TTTTAAATTTTAT
*
1585361 ATTT-AATTTTAT
1 TTTTAAATTTTAT
1585373 TTTTAAA
1 TTTTAAA
1585380 ATTAATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 2 0.08
11 7 0.28
12 7 0.28
13 9 0.36
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TTTTAAATTTTAT
Found at i:1585372 original size:23 final size:25
Alignment explanation
Indices: 1585342--1585394 Score: 83
Period size: 23 Copynumber: 2.2 Consensus size: 25
1585332 TTGTATTTTA
*
1585342 AATTTTATTTTT-AAATTTA-ATTT
1 AATTTTATTTTTAAAATTAATATTT
1585365 AATTTTATTTTTAAAATTAATATTT
1 AATTTTATTTTTAAAATTAATATTT
1585390 AATTT
1 AATTT
1585395 AAAATAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 12 0.44
24 6 0.22
25 9 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
AATTTTATTTTTAAAATTAATATTT
Found at i:1589807 original size:21 final size:20
Alignment explanation
Indices: 1589759--1589807 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
1589749 TAAATTCATA
1589759 TTAAATTTAAATACAATATT
1 TTAAATTTAAATACAATATT
* **
1589779 TAATAATTTAAATTGATATATT
1 TTA-AATTTAAATACA-ATATT
1589801 TTAAATT
1 TTAAATT
1589808 ATTATTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 2 0.09
21 14 0.61
22 7 0.30
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (20 bp):
TTAAATTTAAATACAATATT
Found at i:1589845 original size:18 final size:21
Alignment explanation
Indices: 1589803--1589844 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1589793 GATATATTTT
*
1589803 AAATTATTATTTATTTAATAA
1 AAATTATTATTTAATTAATAA
1589824 AAATTATT-TTTAATT-ATAA
1 AAATTATTATTTAATTAATAA
1589843 AA
1 AA
1589845 TATAAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 6 0.30
21 8 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AAATTATTATTTAATTAATAA
Found at i:1596049 original size:14 final size:15
Alignment explanation
Indices: 1596027--1596069 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
1596017 TTTAATATTT
1596027 TTATAATAATTTAAA
1 TTATAATAATTTAAA
1596042 TTAT-ATAATTTAAA
1 TTATAATAATTTAAA
* *
1596056 -TAAAATATTTTAAA
1 TTATAATAATTTAAA
1596070 AATTTTCGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 2 0.08
14 19 0.76
15 4 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTATAATAATTTAAA
Found at i:1597078 original size:8 final size:8
Alignment explanation
Indices: 1597061--1597112 Score: 51
Period size: 8 Copynumber: 7.1 Consensus size: 8
1597051 ATATTAATAA
1597061 AAAATT-T
1 AAAATTAT
1597068 AAAATTAT
1 AAAATTAT
1597076 AAAA-T-T
1 AAAATTAT
1597082 AAAATTAT
1 AAAATTAT
1597090 AAAA-TA-
1 AAAATTAT
*
1597096 ATAATTAT
1 AAAATTAT
*
1597104 AACATTAT
1 AAAATTAT
1597112 A
1 A
1597113 TTAAAATTAC
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
6 8 0.22
7 12 0.32
8 17 0.46
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (8 bp):
AAAATTAT
Found at i:1597085 original size:14 final size:14
Alignment explanation
Indices: 1597061--1597110 Score: 66
Period size: 14 Copynumber: 3.5 Consensus size: 14
1597051 ATATTAATAA
1597061 AAAATTTAAAATTAT
1 AAAA-TTAAAATTAT
1597076 AAAATTAAAATTAT
1 AAAATTAAAATTAT
1597090 AAAA-TAATAATTAT
1 AAAATTAA-AATTAT
*
1597104 AACATTA
1 AAAATTA
1597111 TATTAAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 3 0.09
14 23 0.72
15 6 0.19
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (14 bp):
AAAATTAAAATTAT
Found at i:1599097 original size:2 final size:2
Alignment explanation
Indices: 1599090--1599142 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
1599080 AACTCAAGTT
1599090 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
1599132 TA TA TA TA TA T
1 TA TA TA TA TA T
1599143 TTAAAAAAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1602075 original size:2 final size:2
Alignment explanation
Indices: 1602068--1602115 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1602058 TGAGAAGGGG
1602068 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1602110 GA GA GA
1 GA GA GA
1602116 AGGGTTGCAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1602843 original size:22 final size:23
Alignment explanation
Indices: 1602812--1602854 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1602802 TATAATTATA
*
1602812 TAATTTAAATA-TAAATAAAAAT
1 TAATTAAAATATTAAATAAAAAT
*
1602834 TAATTAAAATATTATATAAAA
1 TAATTAAAATATTAAATAAAA
1602855 TATATAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
TAATTAAAATATTAAATAAAAAT
Found at i:1602875 original size:17 final size:17
Alignment explanation
Indices: 1602811--1602881 Score: 60
Period size: 17 Copynumber: 4.2 Consensus size: 17
1602801 ATATAATTAT
1602811 ATAAT-TTAA-ATATAA
1 ATAATATTAATATATAA
*
1602826 ATAAAAATTAAT-TA-AA
1 AT-AATATTAATATATAA
*
1602842 ATATTATATAAAATATATAA
1 ATA--ATAT-TAATATATAA
1602862 ATAATATTAATATATAA
1 ATAATATTAATATATAA
1602879 ATA
1 ATA
1602882 TTTTAAAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
15 3 0.07
16 6 0.14
17 21 0.48
18 7 0.16
19 2 0.05
20 5 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAATATTAATATATAA
Found at i:1602889 original size:35 final size:36
Alignment explanation
Indices: 1602820--1602915 Score: 101
Period size: 37 Copynumber: 2.6 Consensus size: 36
1602810 TATAATTTAA
1602820 ATATAAATAAAAATTAAT-TAAAATATTATATAAAA-T
1 ATATAAAT--AAATTAATATAAAATATTATATAAAATT
1602856 ATATAAATAATATTAATATATAAATATT-T-TAAAATTT
1 ATATAAATAA-ATTAATATA-AAATATTATATAAAA-TT
*
1602893 ATATAATATAAATTAGTATAAAA
1 ATATAA-ATAAATTAATATAAAA
1602916 ATAATATTTT
Statistics
Matches: 53, Mismatches: 1, Indels: 12
0.80 0.02 0.18
Matches are distributed among these distances:
34 2 0.04
35 11 0.21
36 14 0.26
37 22 0.42
38 4 0.08
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (36 bp):
ATATAAATAAATTAATATAAAATATTATATAAAATT
Found at i:1606776 original size:20 final size:21
Alignment explanation
Indices: 1606738--1606778 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1606728 CACATTAATG
1606738 AAATTAATTAATATTTTTTAA
1 AAATTAATTAATATTTTTTAA
*
1606759 AAATTATTTAAT-TTTTTTAA
1 AAATTAATTAATATTTTTTAA
1606779 TTTTTACAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
AAATTAATTAATATTTTTTAA
Found at i:1610833 original size:2 final size:2
Alignment explanation
Indices: 1610826--1610882 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
1610816 CTTTTGGTTT
1610826 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
1610868 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
1610883 CTTAGGTGTA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1611907 original size:17 final size:17
Alignment explanation
Indices: 1611857--1611910 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
1611847 TAAATATTTC
1611857 AAAATTTATATAA-TAT
1 AAAATTTATATAAGTAT
1611873 -AAA-TTAT-TAATGTAAT
1 AAAATTTATATAA-GT-AT
1611889 AAAATTTATATAAGTAT
1 AAAATTTATATAAGTAT
1611906 AAAAT
1 AAAAT
1611911 GGGATTATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
13 3 0.09
14 4 0.12
15 4 0.12
16 2 0.06
17 10 0.31
18 6 0.19
19 3 0.09
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.41
Consensus pattern (17 bp):
AAAATTTATATAAGTAT
Found at i:1619638 original size:14 final size:15
Alignment explanation
Indices: 1619619--1619660 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
1619609 CAGATCAAAA
1619619 TATTAAATTTATA-T
1 TATTAAATTTATATT
*
1619633 TATTAAAATTTAAATT
1 TATT-AAATTTATATT
1619649 TATT-AATTTATA
1 TATTAAATTTATA
1619661 AATAAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 11 0.46
15 8 0.33
16 5 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTAAATTTATATT
Found at i:1619755 original size:24 final size:25
Alignment explanation
Indices: 1619713--1619773 Score: 88
Period size: 24 Copynumber: 2.4 Consensus size: 25
1619703 TTAAAAAAAG
*
1619713 TTTTAAATATTTTATTTTTATTTAA
1 TTTTAAATATTTTATTTTTATTAAA
*
1619738 TTTTAATTA-TTTATTTTTATTAAA
1 TTTTAAATATTTTATTTTTATTAAA
1619762 TTTTAAAATATT
1 TTTT-AAATATT
1619774 AAAGTTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 18 0.58
25 12 0.39
26 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (25 bp):
TTTTAAATATTTTATTTTTATTAAA
Found at i:1619773 original size:15 final size:16
Alignment explanation
Indices: 1619755--1619789 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1619745 TATTTATTTT
1619755 TATTAAA-TTTTAAAA
1 TATTAAAGTTTTAAAA
*
1619770 TATTAAAGTTTTAATA
1 TATTAAAGTTTTAAAA
1619786 TATT
1 TATT
1619790 TTTAATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (16 bp):
TATTAAAGTTTTAAAA
Found at i:1619979 original size:18 final size:19
Alignment explanation
Indices: 1619953--1620001 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
1619943 TAGACTCAAC
1619953 TTTTT-TATTTAA-ATTAT
1 TTTTTATATTTAATATTAT
*
1619970 TTTTTATATTTAATATTTT
1 TTTTTATATTTAATATTAT
1619989 TATTTTAGTATTT
1 T-TTTTA-TATTT
1620002 TCATATATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 5 0.19
18 7 0.26
19 5 0.19
20 5 0.19
21 5 0.19
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTTTATATTTAATATTAT
Found at i:1620002 original size:13 final size:15
Alignment explanation
Indices: 1619970--1620007 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1619960 TTTAAATTAT
1619970 TTTTTATATTTAATA
1 TTTTTATATTTAATA
*
1619985 TTTTTAT-TTTAGTA
1 TTTTTATATTTAATA
*
1619999 TTTTCATAT
1 TTTTTATAT
1620008 ATCAAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (15 bp):
TTTTTATATTTAATA
Found at i:1621208 original size:16 final size:16
Alignment explanation
Indices: 1621187--1621223 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
1621177 TTTTTATTTA
1621187 AATTTAAT-TAAAAATT
1 AATTTAATAT-AAAATT
1621203 AATTTAATATAAAATT
1 AATTTAATATAAAATT
1621219 AATTT
1 AATTT
1621224 TTTAAATCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 19 0.95
17 1 0.05
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AATTTAATATAAAATT
Found at i:1621491 original size:20 final size:20
Alignment explanation
Indices: 1621468--1621536 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
1621458 AAATTTTAAT
1621468 TTTTATATTATATTTATATA
1 TTTTATATTATATTTATATA
* *
1621488 TTTTATGTTATAATTATAT-
1 TTTTATATTATATTTATATA
*
1621507 TTTT-TAATATA-TTA-ATA
1 TTTTATATTATATTTATATA
*
1621524 ATTTATATTATAT
1 TTTTATATTATAT
1621537 AAAATTTAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
16 2 0.05
17 6 0.15
18 11 0.28
19 4 0.10
20 17 0.43
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (20 bp):
TTTTATATTATATTTATATA
Found at i:1623735 original size:17 final size:17
Alignment explanation
Indices: 1623709--1623742 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1623699 TTTAATTGTA
* *
1623709 ATTAATTTTTTATATTT
1 ATTAAATTTTTAAATTT
1623726 ATTAAATTTTTAAATTT
1 ATTAAATTTTTAAATTT
1623743 TAATTATTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTAAATTTTTAAATTT
Found at i:1624462 original size:5 final size:5
Alignment explanation
Indices: 1624452--1624479 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1624442 AATTGATGTA
1624452 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1624480 TCATTTATTA
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:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:1625980 original size:7 final size:7
Alignment explanation
Indices: 1625970--1625995 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1625960 CACAGCAACT
1625970 CAAATCA
1 CAAATCA
1625977 CAAATCA
1 CAAATCA
1625984 CAAATCA
1 CAAATCA
1625991 CAAAT
1 CAAAT
1625996 ACTTTGTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.27, G:0.00, T:0.15
Consensus pattern (7 bp):
CAAATCA
Found at i:1626981 original size:71 final size:69
Alignment explanation
Indices: 1626822--1627041 Score: 388
Period size: 71 Copynumber: 3.2 Consensus size: 69
1626812 GTAAAATAGA
1626822 GCAAATTTTGGCTTAGGACGTGGGTAACAAGTCTCAATGATGC-TTTTTTTTTTTTAATAATTGA
1 GCAAATTTTGGCTTAGGACGTGGGTAACAAGTCTCAATGATGCTTTTTTTTTTTTTAATAATTGA
1626886 TTAT
66 TTAT
1626890 GCAAATTTTGGCTTAGGACGTGGGTAACAAGTCTCAATGATGCTTTTTTTTTTTTTTTAATAATT
1 GCAAATTTTGGCTTAGGACGTGGGTAACAAGTCTCAATGATGC--TTTTTTTTTTTTTAATAATT
1626955 GATTAT
64 GATTAT
* *
1626961 GCAAATTTTGGCTTAGGACGTGGGTAGCAAGTCTCAGTGATGCTTTTTTTTTTTTTAATAATTGA
1 GCAAATTTTGGCTTAGGACGTGGGTAACAAGTCTCAATGATGCTTTTTTTTTTTTTAATAATTGA
1627026 TTACT
66 TTA-T
1627031 GCAAATTTTGG
1 GCAAATTTTGG
1627042 TAAATGCCCA
Statistics
Matches: 146, Mismatches: 2, Indels: 6
0.95 0.01 0.04
Matches are distributed among these distances:
68 43 0.29
69 25 0.17
70 12 0.08
71 66 0.45
ACGTcount: A:0.25, C:0.10, G:0.20, T:0.45
Consensus pattern (69 bp):
GCAAATTTTGGCTTAGGACGTGGGTAACAAGTCTCAATGATGCTTTTTTTTTTTTTAATAATTGA
TTAT
Found at i:1630388 original size:2 final size:2
Alignment explanation
Indices: 1630383--1630421 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1630373 ATAAACTAAA
1630383 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1630422 AAATCTTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1631910 original size:16 final size:17
Alignment explanation
Indices: 1631889--1631931 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
1631879 AGCTCAATAT
*
1631889 AATAATTTTAAAT-AAA
1 AATAATTTAAAATAAAA
1631905 AATAA-TTAAAATAAAA
1 AATAATTTAAAATAAAA
*
1631921 AATAATATAAA
1 AATAATTTAAA
1631932 TATATAATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 6 0.26
16 13 0.57
17 4 0.17
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AATAATTTAAAATAAAA
Found at i:1631966 original size:31 final size:32
Alignment explanation
Indices: 1631919--1631998 Score: 78
Period size: 32 Copynumber: 2.6 Consensus size: 32
1631909 ATTAAAATAA
* * *
1631919 AAAATAATAT-AA-ATATATAATT-GTTTTTT
1 AAAATTATATAAATATATATAATTAATATTTT
*
1631948 AAAATT-TATAAAATATATATTATTAATATTTT
1 AAAATTATAT-AAATATATATAATTAATATTTT
*
1631980 AACATTATATAAATATATA
1 AAAATTATATAAATATATA
1631999 ACATCTTAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
28 3 0.07
29 5 0.12
30 2 0.05
31 9 0.22
32 19 0.46
33 3 0.07
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (32 bp):
AAAATTATATAAATATATATAATTAATATTTT
Found at i:1637142 original size:25 final size:26
Alignment explanation
Indices: 1637114--1637165 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 26
1637104 TCATAAAAAT
* *
1637114 TAAAAAAATTATTTTATA-ATATTTA
1 TAAAAAAATTATTGTAAATATATTTA
*
1637139 T-AAATAATTATTGTAAATATATTTA
1 TAAAAAAATTATTGTAAATATATTTA
1637164 TA
1 TA
1637166 TGTATTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (26 bp):
TAAAAAAATTATTGTAAATATATTTA
Found at i:1640154 original size:21 final size:21
Alignment explanation
Indices: 1640128--1640186 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
1640118 AAAGATATAT
* *
1640128 TTGGATGAAATGATGTATTGA
1 TTGGATGAAATAATATATTGA
**
1640149 TTGGATGAAATAATATATTTT
1 TTGGATGAAATAATATATTGA
*
1640170 TTGGATGAAAAAATATA
1 TTGGATGAAATAATATA
1640187 ATTTTTATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.41, C:0.00, G:0.20, T:0.39
Consensus pattern (21 bp):
TTGGATGAAATAATATATTGA
Found at i:1640191 original size:21 final size:21
Alignment explanation
Indices: 1640149--1640192 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1640139 GATGTATTGA
* *
1640149 TTGGATGAAATAATATATTTT
1 TTGGATGAAAAAATATAATTT
1640170 TTGGATGAAAAAATATAATTT
1 TTGGATGAAAAAATATAATTT
1640191 TT
1 TT
1640193 ATGACCAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (21 bp):
TTGGATGAAAAAATATAATTT
Found at i:1643944 original size:184 final size:184
Alignment explanation
Indices: 1643624--1643992 Score: 720
Period size: 184 Copynumber: 2.0 Consensus size: 184
1643614 TGCTGTTCTT
1643624 CAAGAACCCAGATTCGGTTGAGTACCTTGAGCAACTCTGTCGATGTCTTAAGACCATAACCTGAT
1 CAAGAACCCAGATTCGGTTGAGTACCTTGAGCAACTCTGTCGATGTCTTAAGACCATAACCTGAT
1643689 CCCCCAAACCTTTCTTTAAAATCCAAAGAACTAGATGGCGTGATTGCAGGGTTATAAGGTGCCAC
66 CCCCCAAACCTTTCTTTAAAATCCAAAGAACTAGATGGCGTGATTGCAGGGTTATAAGGTGCCAC
1643754 CTGCAAAGAACACAAATATAAATCTATGTAACCGATATAGTAGCAGCATAATAG
131 CTGCAAAGAACACAAATATAAATCTATGTAACCGATATAGTAGCAGCATAATAG
* *
1643808 CAAGAGCCCATATTCGGTTGAGTACCTTGAGCAACTCTGTCGATGTCTTAAGACCATAACCTGAT
1 CAAGAACCCAGATTCGGTTGAGTACCTTGAGCAACTCTGTCGATGTCTTAAGACCATAACCTGAT
1643873 CCCCCAAACCTTTCTTTAAAATCCAAAGAACTAGATGGCGTGATTGCAGGGTTATAAGGTGCCAC
66 CCCCCAAACCTTTCTTTAAAATCCAAAGAACTAGATGGCGTGATTGCAGGGTTATAAGGTGCCAC
1643938 CTGCAAAGAACACAAATATAAATCTATGTAACCGATATAGTAGCAGCATAATAG
131 CTGCAAAGAACACAAATATAAATCTATGTAACCGATATAGTAGCAGCATAATAG
1643992 C
1 C
1643993 TTTTCTGCGA
Statistics
Matches: 183, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
184 183 1.00
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.25
Consensus pattern (184 bp):
CAAGAACCCAGATTCGGTTGAGTACCTTGAGCAACTCTGTCGATGTCTTAAGACCATAACCTGAT
CCCCCAAACCTTTCTTTAAAATCCAAAGAACTAGATGGCGTGATTGCAGGGTTATAAGGTGCCAC
CTGCAAAGAACACAAATATAAATCTATGTAACCGATATAGTAGCAGCATAATAG
Found at i:1645736 original size:15 final size:16
Alignment explanation
Indices: 1645718--1645751 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1645708 AATCAAAATT
*
1645718 TAATAAATTTTTAA-A
1 TAATAAAATTTTAATA
1645733 TAATAAAATTTTAATA
1 TAATAAAATTTTAATA
1645749 TAA
1 TAA
1645752 AAGAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATAAAATTTTAATA
Found at i:1646634 original size:128 final size:124
Alignment explanation
Indices: 1646493--1646761 Score: 337
Period size: 128 Copynumber: 2.1 Consensus size: 124
1646483 AATTATTTTT
* * *
1646493 TAAAAATAAAAAATTAAATTGAAAAAAGTTTATTATTAT-TTTTTAATAAAATTAAAAATAATAT
1 TAAAAATTAAAAATTAAAATAAAAAAAGTTTATTATTATATTTTTAATAAAA-T-AAAA-AATAT
* * *
1646557 TTAATTAAATTTTAA-AAAATTATATTAACAAATTAAAATATTAATTA-TATGTTTTTATAAAAA
63 TTAATT-AAGTTTAAGAAAATTACATTAACAAATTAAAATATTAATTATTATATTTTT-T-AAAA
* * * *
1646620 TAAAAAATTTAAAATAAAAAATAAAAAAAGTTTTTTATTATAATTTTTAATTAAATAAAAAATAT
1 T-AAAAATTAAAAAT-TAAAATAAAAAAAGTTTATTATTAT-ATTTTTAATAAAATAAAAAATAT
*
1646685 TTAATTAAGTTTAAGAAATTTACATTAACAAATTAAAATATTAATTATTATATTTTTTAAAA
63 TTAATTAAGTTTAAGAAAATTACATTAACAAATTAAAATATTAATTATTATATTTTTTAAAA
1646747 TAAAAATTAAAAATT
1 TAAAAATTAAAAATT
1646762 TATTAATTTT
Statistics
Matches: 123, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
126 12 0.10
127 13 0.11
128 53 0.43
129 33 0.27
130 1 0.01
131 11 0.09
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.41
Consensus pattern (124 bp):
TAAAAATTAAAAATTAAAATAAAAAAAGTTTATTATTATATTTTTAATAAAATAAAAAATATTTA
ATTAAGTTTAAGAAAATTACATTAACAAATTAAAATATTAATTATTATATTTTTTAAAA
Found at i:1650510 original size:23 final size:25
Alignment explanation
Indices: 1650484--1650535 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 25
1650474 TATAATAAAA
*
1650484 TAAAAAAT-AAATTAAATTA-ATTT
1 TAAAAAATAAAAATAAATTAGATTT
1650507 T-AAAAATAAAAATAAATTAGATTT
1 TAAAAAATAAAAATAAATTAGATTT
1650531 TAAAA
1 TAAAA
1650536 TTTTTTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 6 0.24
23 11 0.44
24 5 0.20
25 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (25 bp):
TAAAAAATAAAAATAAATTAGATTT
Found at i:1651050 original size:14 final size:14
Alignment explanation
Indices: 1651031--1651071 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 14
1651021 ATATTCGTAA
1651031 AAAAAAATTATTTT
1 AAAAAAATTATTTT
1651045 -AAAAAA-TATTTT
1 AAAAAAATTATTTT
1651057 ATAAAAAATTTATTT
1 A-AAAAAA-TTATTT
1651072 ATGAAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 6 0.26
13 6 0.26
14 6 0.26
16 5 0.22
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AAAAAAATTATTTT
Found at i:1651072 original size:15 final size:15
Alignment explanation
Indices: 1651031--1651073 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
1651021 ATATTCGTAA
*
1651031 AAAAAAATTATTT-T
1 AAAAAATTTATTTAT
*
1651045 AAAAAATAT-TTTAT
1 AAAAAATTTATTTAT
1651059 AAAAAATTTATTTAT
1 AAAAAATTTATTTAT
1651074 GAAATTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 3 0.12
14 16 0.67
15 5 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AAAAAATTTATTTAT
Found at i:1651307 original size:9 final size:9
Alignment explanation
Indices: 1651292--1651339 Score: 53
Period size: 10 Copynumber: 5.0 Consensus size: 9
1651282 TAAATTTTTA
1651292 TAAAAAAA-
1 TAAAAAAAT
1651300 TAAAAAAATT
1 TAAAAAAA-T
1651310 TAAAAAAAT
1 TAAAAAAAT
1651319 TAAAAAATAT
1 TAAAAAA-AT
1651329 GTAGAAAAAAT
1 -TA-AAAAAAT
1651340 ATATAATTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
8 8 0.23
9 8 0.23
10 10 0.29
11 4 0.11
12 5 0.14
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (9 bp):
TAAAAAAAT
Found at i:1651313 original size:18 final size:19
Alignment explanation
Indices: 1651292--1651340 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 19
1651282 TAAATTTTTA
*
1651292 TAAAAAAATAAAAAA-ATT
1 TAAAAAAATAAAAAATATG
1651310 TAAAAAAATTAAAAAATATG
1 TAAAAAAA-TAAAAAATATG
1651330 TAGAAAAAATA
1 TA-AAAAAATA
1651341 TATAATTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 8 0.30
19 7 0.26
20 6 0.22
21 6 0.22
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.22
Consensus pattern (19 bp):
TAAAAAAATAAAAAATATG
Found at i:1659455 original size:2 final size:2
Alignment explanation
Indices: 1659392--1659442 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1659382 AAATCGATTC
1659392 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
1659434 TA TA TA TA T
1 TA TA TA TA T
1659443 CATTCTCATA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1660513 original size:16 final size:17
Alignment explanation
Indices: 1660470--1660516 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 17
1660460 ATTTAATTTG
*
1660470 AATTATTTTATTATTATT
1 AATTAATTT-TTATTATT
1660488 AATATAAATTTTTATTA-T
1 AAT-T-AATTTTTATTATT
1660506 AATTAATTTTT
1 AATTAATTTTT
1660517 TATATAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 7 0.27
17 1 0.04
18 7 0.27
19 7 0.27
20 4 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
AATTAATTTTTATTATT
Found at i:1660522 original size:16 final size:17
Alignment explanation
Indices: 1660483--1660523 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1660473 TATTTTATTA
1660483 TTAT-TAATATAAATTT
1 TTATATAATATAAATTT
*
1660499 TTATTATAAT-TAATTTT
1 TTA-TATAATATAAATTT
1660516 TTATATAA
1 TTATATAA
1660524 AATTATTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 8 0.36
17 10 0.45
18 4 0.18
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATATAATATAAATTT
Found at i:1660933 original size:18 final size:18
Alignment explanation
Indices: 1660901--1660944 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
1660891 AACTTTATTC
*
1660901 ATTTTAATTTTTTAAATT
1 ATTTTTATTTTTTAAATT
*
1660919 -TTTTTATTTTATTAATTT
1 ATTTTTATTTT-TTAAATT
1660937 ATTTTTAT
1 ATTTTTAT
1660945 AAATAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 9 0.41
18 6 0.27
19 7 0.32
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (18 bp):
ATTTTTATTTTTTAAATT
Found at i:1666492 original size:16 final size:17
Alignment explanation
Indices: 1666460--1666494 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1666450 TAAATAATTT
*
1666460 ATATAATTATTTTAAAA
1 ATATAATTATTTAAAAA
1666477 ATATAA-TATTTAAAAA
1 ATATAATTATTTAAAAA
1666493 AT
1 AT
1666495 TTGATATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATAATTATTTAAAAA
Found at i:1666993 original size:19 final size:19
Alignment explanation
Indices: 1666966--1667002 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1666956 AATAAGGTTT
*
1666966 ATTTATTTAACAAATAATG
1 ATTTATTTAAAAAATAATG
*
1666985 ATTTTTTTAAAAAATAAT
1 ATTTATTTAAAAAATAAT
1667003 TTTTAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (19 bp):
ATTTATTTAAAAAATAATG
Found at i:1667010 original size:13 final size:14
Alignment explanation
Indices: 1666988--1667017 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1666978 AATAATGATT
1666988 TTTTTAAAAAATAA
1 TTTTTAAAAAATAA
1667002 TTTTT-AAAAATAA
1 TTTTTAAAAAATAA
1667015 TTT
1 TTT
1667018 ATTTTTTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTTTAAAAAATAA
Found at i:1667030 original size:19 final size:19
Alignment explanation
Indices: 1667002--1667038 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1666992 TAAAAAATAA
1667002 TTTTTAAAAATAATTTATT
1 TTTTTAAAAATAATTTATT
* *
1667021 TTTTTGAAAATATTTTAT
1 TTTTTAAAAATAATTTAT
1667039 GAAAAAATGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
TTTTTAAAAATAATTTATT
Found at i:1667031 original size:32 final size:32
Alignment explanation
Indices: 1666971--1667036 Score: 82
Period size: 33 Copynumber: 2.1 Consensus size: 32
1666961 GGTTTATTTA
1666971 TTTAACAAATAATGATTTTTTTAAAAAATAATT
1 TTTAACAAATAATGATTTTTTTAAAAAAT-ATT
* *
1667004 TTTAA-AAATAATTTATTTTTTT-GAAAATATT
1 TTTAACAAATAA-TGATTTTTTTAAAAAATATT
1667035 TT
1 TT
1667037 ATGAAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 5 0.17
32 11 0.37
33 14 0.47
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (32 bp):
TTTAACAAATAATGATTTTTTTAAAAAATATT
Found at i:1667541 original size:22 final size:21
Alignment explanation
Indices: 1667507--1667562 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
1667497 TTTTGTAAAT
* *
1667507 ATTAAAAAATAATATAAAATTA
1 ATTAAATATTAAT-TAAAATTA
* *
1667529 ATTAAATATTAATTAACATTT
1 ATTAAATATTAATTAAAATTA
1667550 ATATAAATATTAA
1 AT-TAAATATTAA
1667563 ATTTTATCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 8 0.28
22 21 0.72
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
ATTAAATATTAATTAAAATTA
Found at i:1668263 original size:2 final size:2
Alignment explanation
Indices: 1668256--1668285 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1668246 AGTTTTCAAC
1668256 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1668286 CGTAAATCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1668476 original size:2 final size:2
Alignment explanation
Indices: 1668469--1668495 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1668459 AGTGATAGAT
1668469 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1668496 CGAACAGAAC
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1678268 original size:23 final size:23
Alignment explanation
Indices: 1678238--1678285 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
1678228 CTAAGAAAGG
1678238 AAAAAAAGGGTGGATAAATCAAT
1 AAAAAAAGGGTGGATAAATCAAT
1678261 AAAAAAAGGGTGGATAAATCAAT
1 AAAAAAAGGGTGGATAAATCAAT
1678284 AA
1 AA
1678286 CTATGAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.58, C:0.04, G:0.21, T:0.17
Consensus pattern (23 bp):
AAAAAAAGGGTGGATAAATCAAT
Found at i:1681385 original size:28 final size:29
Alignment explanation
Indices: 1681349--1681414 Score: 91
Period size: 28 Copynumber: 2.3 Consensus size: 29
1681339 TAATATTTTT
* *
1681349 AATTTATTTAAAT-ATATTAAAAATTAAAA
1 AATTTATTTAAATAAAAATAAAAA-TAAAA
1681378 AA-TTATTTAAATAAAAATAAAAATAAAA
1 AATTTATTTAAATAAAAATAAAAATAAAA
1681406 AATTTATTT
1 AATTTATTT
1681415 TGATGAAAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 17 0.52
29 16 0.48
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (29 bp):
AATTTATTTAAATAAAAATAAAAATAAAA
Found at i:1681900 original size:16 final size:16
Alignment explanation
Indices: 1681875--1681908 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
1681865 AAATAATAAA
1681875 AAAATTTATTT-ATTT
1 AAAATTTATTTAATTT
1681890 AAAATTATATTTAATTT
1 AAAATT-TATTTAATTT
1681907 AA
1 AA
1681909 TTCAGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 5 0.29
17 6 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AAAATTTATTTAATTT
Found at i:1681979 original size:3 final size:3
Alignment explanation
Indices: 1681971--1682000 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1681961 ATAAAAATAA
1681971 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1682001 TAATTAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1682066 original size:18 final size:17
Alignment explanation
Indices: 1682028--1682075 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
1682018 AATTTTAATT
*
1682028 TAAAAATTATGTTATTTA
1 TAAAAATTAT-TTTTTTA
1682046 TAAAAATTATTTTTTTCA
1 TAAAAATTATTTTTTT-A
1682064 T--AAATTATTTTT
1 TAAAAATTATTTTT
1682076 AAAAAAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 11 0.39
17 5 0.18
18 12 0.43
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (17 bp):
TAAAAATTATTTTTTTA
Found at i:1684658 original size:18 final size:17
Alignment explanation
Indices: 1684637--1684696 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
1684627 TTTAAAATTT
1684637 ATATAATATAAATTATTA
1 ATATAATATAAATT-TTA
*
1684655 ATAT-AT-TAAAATTTA
1 ATATAATATAAATTTTA
*
1684670 ATATAAATATCATATTTTA
1 ATAT-AATAT-AAATTTTA
1684689 A-ATAATAT
1 ATATAATAT
1684697 TTTGATATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
15 7 0.20
16 5 0.14
17 9 0.26
18 7 0.20
19 7 0.20
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATAATATAAATTTTA
Found at i:1684660 original size:15 final size:15
Alignment explanation
Indices: 1684628--1684674 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
1684618 TAAGTAATTT
1684628 TTAAAATTT-ATATAA
1 TTAAAATTTAATAT-A
*
1684643 TATAAATTATTAATATA
1 T-TAAAAT-TTAATATA
1684660 TTAAAATTTAATATA
1 TTAAAATTTAATATA
1684675 AATATCATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 9 0.33
16 10 0.37
17 4 0.15
18 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTAAAATTTAATATA
Found at i:1685764 original size:4 final size:4
Alignment explanation
Indices: 1685755--1685780 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1685745 ATGAAAGCAA
1685755 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
1685781 CTAGCTACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1685952 original size:30 final size:30
Alignment explanation
Indices: 1685873--1685952 Score: 74
Period size: 30 Copynumber: 2.6 Consensus size: 30
1685863 TATATTAAAT
* *
1685873 TAAATTTAAATAGTAA-ACAAATTTATTTATT
1 TAAA-TTAAATA-TAATAAAAATTTATTTATA
*
1685904 TAAATTAAATCTAATAAAAATTTATTT-TA
1 TAAATTAAATATAATAAAAATTTATTTATA
* *
1685933 TAATTTAAAATATATTAAAA
1 TAAATT-AAATATAATAAAA
1685953 TATTAAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
29 9 0.22
30 28 0.68
31 4 0.10
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.44
Consensus pattern (30 bp):
TAAATTAAATATAATAAAAATTTATTTATA
Found at i:1693317 original size:6 final size:7
Alignment explanation
Indices: 1693295--1693319 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1693285 TTCATAAATA
1693295 TTTAATT
1 TTTAATT
1693302 TTTAATT
1 TTTAATT
1693309 TTTAATT
1 TTTAATT
1693316 TTTA
1 TTTA
1693320 TTGATAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTAATT
Found at i:1715223 original size:2 final size:2
Alignment explanation
Indices: 1715216--1715254 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1715206 GCAACTCCAT
1715216 TA TA TA 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 TA TA TA T
1715255 TCATTCATTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1717816 original size:16 final size:15
Alignment explanation
Indices: 1717778--1717819 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
1717768 GATTTAAATC
1717778 TATTTAAATTATTTT
1 TATTTAAATTATTTT
*
1717793 TAAATTAAATTAATTTT
1 T-ATTTAAATT-ATTTT
1717810 TATTTAAATT
1 TATTTAAATT
1717820 TTAACAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 1 0.04
16 16 0.70
17 6 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TATTTAAATTATTTT
Found at i:1717899 original size:3 final size:3
Alignment explanation
Indices: 1717891--1717917 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1717881 TAGAATTAGT
1717891 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1717918 CACTTTTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1719340 original size:6 final size:6
Alignment explanation
Indices: 1719329--1719358 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
1719319 CCACTTTTTC
1719329 ATACTA ATACTA ATACTA ATACTA ATACTA
1 ATACTA ATACTA ATACTA ATACTA ATACTA
1719359 CTATTATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
ATACTA
Found at i:1719366 original size:3 final size:3
Alignment explanation
Indices: 1719360--1719384 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1719350 CTAATACTAC
1719360 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
1719385 CAGTTAAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1722094 original size:24 final size:25
Alignment explanation
Indices: 1722021--1722099 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 25
1722011 TAACATGATA
1722021 ATTATTTTATTATTTAAAATATATTAAAT
1 ATTATTTTATTATTT-AAATA-A--AAAT
*
1722050 ATTAATTTTAAT-TTTAAATAAAAAT
1 ATT-ATTTTATTATTTAAATAAAAAT
*
1722075 ATT-TTTTATTATTTAAATAATAAT
1 ATTATTTTATTATTTAAATAAAAAT
1722099 A
1 A
1722100 CAAATTAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
23 6 0.13
24 13 0.29
25 7 0.16
27 1 0.02
28 5 0.11
29 6 0.13
30 7 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
ATTATTTTATTATTTAAATAAAAAT
Found at i:1722424 original size:27 final size:26
Alignment explanation
Indices: 1722394--1722511 Score: 76
Period size: 23 Copynumber: 4.8 Consensus size: 26
1722384 AATATATTTT
1722394 TAAAATTTATATAATATAAATTATTAA
1 TAAAATTTATATAATATAAATTA-TAA
1722421 T-AAA-TTATAATTAATATAAA-TATAA
1 TAAAATTTAT-A-TAATATAAATTATAA
*
1722446 -AATATTT-TA-AATAT-AATTATAA
1 TAAAATTTATATAATATAAATTATAA
* *
1722468 TAAAA-TAAAAT-ATATAAA-TATAA
1 TAAAATTTATATAATATAAATTATAA
* * *
1722491 TATAAATATACATATTATAAA
1 TA-AAATTTATATAATATAAA
1722512 ATTTAATGTT
Statistics
Matches: 71, Mismatches: 8, Indels: 25
0.68 0.08 0.24
Matches are distributed among these distances:
21 2 0.03
22 11 0.15
23 15 0.21
24 6 0.08
25 13 0.18
26 14 0.20
27 10 0.14
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (26 bp):
TAAAATTTATATAATATAAATTATAA
Found at i:1722442 original size:6 final size:6
Alignment explanation
Indices: 1722433--1722505 Score: 57
Period size: 6 Copynumber: 12.8 Consensus size: 6
1722423 AATTATAATT
* * * *
1722433 AATATA AATATA AA-AT- ATTTTA AATATA ATTAT- AATA-A AATAAA
1 AATATA AATATA AATATA AATATA AATATA AATATA AATATA AATATA
*
1722477 ATATATA AATAT- AATATA AATATA CATAT
1 A-ATATA AATATA AATATA AATATA AATAT
1722506 TATAAAATTT
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
4 1 0.02
5 15 0.28
6 32 0.60
7 5 0.09
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (6 bp):
AATATA
Found at i:1722495 original size:11 final size:11
Alignment explanation
Indices: 1722402--1722505 Score: 73
Period size: 11 Copynumber: 9.8 Consensus size: 11
1722392 TTTAAAATTT
1722402 ATATAATATAA
1 ATATAATATAA
1722413 ATTATTAATA-AA
1 A-TA-TAATATAA
*
1722425 TTATAAT-T-A
1 ATATAATATAA
1722434 ATATAAATATAA
1 ATAT-AATATAA
* *
1722446 A-ATATTTTAA
1 ATATAATATAA
1722456 ATATAAT-TATA
1 ATATAATATA-A
1722467 ATA-AA-ATAA
1 ATATAATATAA
1722476 A-AT-ATATAA
1 ATATAATATAA
1722485 ATATAATATAA
1 ATATAATATAA
1722496 ATATACATAT
1 ATATA-ATAT
1722506 TATAAAATTT
Statistics
Matches: 74, Mismatches: 5, Indels: 27
0.70 0.05 0.25
Matches are distributed among these distances:
8 2 0.03
9 11 0.15
10 21 0.28
11 25 0.34
12 10 0.14
13 5 0.07
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (11 bp):
ATATAATATAA
Found at i:1722511 original size:40 final size:39
Alignment explanation
Indices: 1722402--1722513 Score: 104
Period size: 40 Copynumber: 2.7 Consensus size: 39
1722392 TTTAAAATTT
1722402 ATATAATATAAATTATTAATAAATTATAATTAATATAAATATAAA
1 ATATAATATAAA-TA-TAAT--ATTATAA--AATATAAATATAAA
* *
1722447 ATAT--TTTAAATATAATTATAATAAAATA-AAATATATAA
1 ATATAATATAAATATAA-TATTATAAAATATAAATATA-AA
1722485 ATATAATATAAATATACATATTATAAAAT
1 ATATAATATAAATATA-ATATTATAAAAT
1722514 TTAATGTTGC
Statistics
Matches: 58, Mismatches: 4, Indels: 15
0.75 0.05 0.19
Matches are distributed among these distances:
37 7 0.12
38 10 0.17
40 25 0.43
41 4 0.07
42 3 0.05
43 5 0.09
45 4 0.07
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (39 bp):
ATATAATATAAATATAATATTATAAAATATAAATATAAA
Found at i:1724531 original size:16 final size:18
Alignment explanation
Indices: 1724510--1724546 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
1724500 TTTATAATAA
*
1724510 ATAAATTTA-AAATAT-T
1 ATAAATTGATAAATATAT
1724526 ATAAATTGATAAATATAT
1 ATAAATTGATAAATATAT
1724544 ATA
1 ATA
1724547 TTTTTATTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 8 0.44
17 6 0.33
18 4 0.22
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
ATAAATTGATAAATATAT
Done.