Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 6 of 202
Found at i:1867681 original size:29 final size:29
Alignment explanation
Indices: 1867648--1867704 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
1867638 TATTGTATGT
1867648 TTTTA-AAGGATT-AAATCAAAATTTTATCA
1 TTTTAGAAGG-TTAAAAT-AAAATTTTATCA
*
1867677 TTTTAGAAGGTTAAAATATAATTTTATC
1 TTTTAGAAGGTTAAAATAAAATTTTATC
1867705 TTTATTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (29 bp):
TTTTAGAAGGTTAAAATAAAATTTTATCA
Found at i:1877550 original size:57 final size:57
Alignment explanation
Indices: 1877462--1877709 Score: 313
Period size: 57 Copynumber: 4.4 Consensus size: 57
1877452 TTAATGTCCC
* * *
1877462 TTGCCACCAGAACTTGGACCTGAATTGG-GGTTGACAGCATCAGTAAATGCATGACCT
1 TTGCCTCCTGAACTTGGACCTGAATTGGTGG-TGACAGCATCACTAAATGCATGACCT
**
1877519 TTGCCTCCTTCACTTGGACCTGAATTGG-GGTTGACAGCATCAGC-AAATGCATGACCT
1 TTGCCTCCTGAACTTGGACCTGAATTGGTGG-TGACAGCATCA-CTAAATGCATGACCT
* * **
1877576 TTGCCTCCTGGACTTGGACCTGAGTTGGTGGTGACAGCATCACTATGTGCATGACCT
1 TTGCCTCCTGAACTTGGACCTGAATTGGTGGTGACAGCATCACTAAATGCATGACCT
* * * *
1877633 TTGCCACCAGAACTTGGCCCTGAATTGGTGGTGACAGAATCACTAAATGCATGACCT
1 TTGCCTCCTGAACTTGGACCTGAATTGGTGGTGACAGCATCACTAAATGCATGACCT
* *
1877690 TTGCCTCCTGGACTAGGACC
1 TTGCCTCCTGAACTTGGACC
1877710 ACTGGTCTTG
Statistics
Matches: 165, Mismatches: 23, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
56 1 0.01
57 162 0.98
58 2 0.01
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.27
Consensus pattern (57 bp):
TTGCCTCCTGAACTTGGACCTGAATTGGTGGTGACAGCATCACTAAATGCATGACCT
Found at i:1883633 original size:44 final size:42
Alignment explanation
Indices: 1883531--1883661 Score: 142
Period size: 43 Copynumber: 3.0 Consensus size: 42
1883521 AGCTCGTACA
*
1883531 ATGCCTACGTCCCAGACGAGGTCTTACATGT-AATCAAATATCG
1 ATGCC-ACGTCCCAGACGA-GTCTTACACGTAAATCAAATATCG
*
1883574 ATGCCACTGTCCCAGACAGAGTCTTACACGTAAATCTCAAT-TCG
1 ATGCCAC-GTCCCAGAC-GAGTCTTACACGTAAATC-AAATATCG
* *
1883618 ATGCCGACGTCCCAGACGTGGTCTTACACG-AAATCACATATCG
1 ATGCC-ACGTCCCAGACG-AGTCTTACACGTAAATCAAATATCG
1883661 A
1 A
1883662 AATCCTATGT
Statistics
Matches: 76, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
42 4 0.05
43 34 0.45
44 33 0.43
45 5 0.07
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (42 bp):
ATGCCACGTCCCAGACGAGTCTTACACGTAAATCAAATATCG
Found at i:1889674 original size:14 final size:14
Alignment explanation
Indices: 1889655--1889684 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1889645 ATGAGTTTGA
1889655 GTATGTTAAAACAC
1 GTATGTTAAAACAC
1889669 GTATGTTAAAACAC
1 GTATGTTAAAACAC
1889683 GT
1 GT
1889685 TTATCCTCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (14 bp):
GTATGTTAAAACAC
Found at i:1902162 original size:3 final size:3
Alignment explanation
Indices: 1902154--1902198 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
1902144 AAACAAACCT
1902154 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1902199 AAAAGTTAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1903034 original size:23 final size:24
Alignment explanation
Indices: 1903008--1903054 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1902998 CCCTTCTCCT
1903008 CTCTGTTCTTTT-TTTTCTTTTTG
1 CTCTGTTCTTTTGTTTTCTTTTTG
* *
1903031 CTCTTTTTTTTTGTTTTCTTTTTG
1 CTCTGTTCTTTTGTTTTCTTTTTG
1903055 TTGTTGGTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.00, C:0.15, G:0.09, T:0.77
Consensus pattern (24 bp):
CTCTGTTCTTTTGTTTTCTTTTTG
Found at i:1912136 original size:38 final size:36
Alignment explanation
Indices: 1912094--1912183 Score: 99
Period size: 38 Copynumber: 2.3 Consensus size: 36
1912084 TTAAAAAGTA
*
1912094 TTTATATTAAAAAACACTACCATAAATATAATAAATATTT
1 TTTATATTAAAAAA-A-TA-AATAAATATAATAAATA-TT
1912134 TATTATATTAAAAAAATAAATAAATATAATAAATATAT
1 T-TTATATTAAAAAAATAAATAAATATAATAAATAT-T
*
1912172 TATTGTATTAAA
1 T-TTATATTAAA
1912184 TATAATTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
37 1 0.02
38 28 0.61
39 2 0.04
40 2 0.04
41 13 0.28
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (36 bp):
TTTATATTAAAAAAATAAATAAATATAATAAATATT
Found at i:1919725 original size:3 final size:3
Alignment explanation
Indices: 1919717--1919746 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1919707 CGCTTTTATA
1919717 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT
1919747 TTCGAGTATC
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:0.00, C:0.33, G:0.33, T:0.33
Consensus pattern (3 bp):
GCT
Found at i:1921428 original size:51 final size:52
Alignment explanation
Indices: 1921373--1921489 Score: 134
Period size: 51 Copynumber: 2.3 Consensus size: 52
1921363 TATAAAACTT
* *
1921373 ATATATATATATAAAATACA-TAATGCATTTATGAAAACAAGGAAA-ATATAA
1 ATATATATATATAAAATACATTAATGCATTTA-CAAAAAAAGGAAATATATAA
* * * *
1921424 ATATATACATATAAAATATATTCATGCATTTACAAAAAAATGAAATATATAA
1 ATATATATATATAAAATACATTAATGCATTTACAAAAAAAGGAAATATATAA
*
1921476 GTATA-ATATA-AAAA
1 ATATATATATATAAAA
1921490 CGTGGAAAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
50 4 0.07
51 32 0.57
52 20 0.36
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (52 bp):
ATATATATATATAAAATACATTAATGCATTTACAAAAAAAGGAAATATATAA
Found at i:1922251 original size:23 final size:22
Alignment explanation
Indices: 1922208--1922265 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
1922198 AAAGGGTATC
* *
1922208 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
1922229 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
1922252 TACATATCATATCT
1 TACAAATCATATCT
1922266 AAGATTACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 18 0.56
23 11 0.34
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:1922259 original size:17 final size:17
Alignment explanation
Indices: 1922237--1922289 Score: 70
Period size: 19 Copynumber: 3.0 Consensus size: 17
1922227 ATTACAAAAT
1922237 CATATCTTCTAAGATTA
1 CATATCTTCTAAGATTA
1922254 CATATCATATCTAAGATTA
1 CATATC-T-TCTAAGATTA
* *
1922273 CATATCCTCGAAGATTA
1 CATATCTTCTAAGATTA
1922290 TGTTTCCATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 15 0.47
18 1 0.03
19 16 0.50
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.36
Consensus pattern (17 bp):
CATATCTTCTAAGATTA
Found at i:1922268 original size:19 final size:20
Alignment explanation
Indices: 1922221--1922278 Score: 73
Period size: 19 Copynumber: 2.8 Consensus size: 20
1922211 AAATTAAATC
*
1922221 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTAC-ATATCATA--T
1922244 TCTAAGATTACATATCATA-
1 TCTAAGATTACATATCATAT
1922263 TCTAAGATTACATATC
1 TCTAAGATTACATATC
1922279 CTCGAAGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 16 0.47
22 7 0.21
23 11 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (20 bp):
TCTAAGATTACATATCATAT
Found at i:1930005 original size:26 final size:26
Alignment explanation
Indices: 1929975--1930032 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
1929965 GAAATTAAAT
*
1929975 ATTTATT-TTACTTTAAAATAATATAA
1 ATTTATTATTA-TTTAAAATAAGATAA
*
1930001 ATTTAATTATTATTTAAATTAAGATAA
1 ATTT-ATTATTATTTAAAATAAGATAA
*
1930028 TTTTA
1 ATTTA
1930033 ACATGTAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
26 5 0.19
27 19 0.70
28 3 0.11
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (26 bp):
ATTTATTATTATTTAAAATAAGATAA
Found at i:1930176 original size:16 final size:17
Alignment explanation
Indices: 1930155--1930188 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1930145 TGGTATAATA
1930155 TTAA-TTTTACTAAAAT
1 TTAATTTTTACTAAAAT
*
1930171 TTAATTTTTACTATAAT
1 TTAATTTTTACTAAAAT
1930188 T
1 T
1930189 ATGCACATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAATTTTTACTAAAAT
Found at i:1933825 original size:59 final size:59
Alignment explanation
Indices: 1933762--1933931 Score: 304
Period size: 59 Copynumber: 2.9 Consensus size: 59
1933752 TCAAGTTTGT
*
1933762 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
*
1933821 TTTACTAATTAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
* *
1933880 TTTATTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATT
1933932 AATAATTTGA
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 106 1.00
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (59 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
Found at i:1933965 original size:16 final size:16
Alignment explanation
Indices: 1933944--1933975 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1933934 TAATTTGATT
*
1933944 ATTTTACTAACAATTA
1 ATTTTAATAACAATTA
1933960 ATTTTAATAACAATTA
1 ATTTTAATAACAATTA
1933976 GTTCTAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTTTAATAACAATTA
Found at i:1935783 original size:57 final size:57
Alignment explanation
Indices: 1935637--1935751 Score: 212
Period size: 57 Copynumber: 2.0 Consensus size: 57
1935627 ATTAATTATT
* *
1935637 ATAATTTAAATACTTTTATTATACATATATTATTAAATTAATTTATTTTATTGTTAA
1 ATAATTTAAATAATTTTATTATACATATATTATTAAATTAATTTATTTTAATGTTAA
1935694 ATAATTTAAATAATTTTATTATACATATATTATTAAATTAATTTATTTTAATGTTAA
1 ATAATTTAAATAATTTTATTATACATATATTATTAAATTAATTTATTTTAATGTTAA
1935751 A
1 A
1935752 ATTGTTAATA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.53
Consensus pattern (57 bp):
ATAATTTAAATAATTTTATTATACATATATTATTAAATTAATTTATTTTAATGTTAA
Found at i:1937644 original size:20 final size:20
Alignment explanation
Indices: 1937619--1937658 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1937609 AATATTTTCC
*
1937619 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
1937639 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
1937659 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:1937664 original size:34 final size:34
Alignment explanation
Indices: 1937607--1937672 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 34
1937597 CAAACACCAG
*
1937607 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTAC-GAAAAGT
1937642 AAAACATTTTCCAG-AAATCATTTTACGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACGAAAA
1937673 ATATTTTACT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 5 0.17
34 12 0.40
35 13 0.43
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.32
Consensus pattern (34 bp):
AAAACATTTTCCAGTAAATCATTTTACGAAAAGT
Found at i:1945041 original size:17 final size:17
Alignment explanation
Indices: 1945019--1945058 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1945009 AAAAACTTAC
*
1945019 ATTAACCCGAACATAAA
1 ATTAACCCAAACATAAA
*
1945036 ATTAACCCAAACTTAAA
1 ATTAACCCAAACATAAA
1945053 A-TAACC
1 ATTAACC
1945059 GAATTTCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.53, C:0.25, G:0.03, T:0.20
Consensus pattern (17 bp):
ATTAACCCAAACATAAA
Found at i:1959476 original size:16 final size:16
Alignment explanation
Indices: 1959457--1959508 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
1959447 GGCATTTTTG
* *
1959457 GTTTGAATTATTTCGA
1 GTTTAAATTATTTCAA
*
1959473 GTTTAAATTGTTTCAA
1 GTTTAAATTATTTCAA
*
1959489 GTTTAAA-CATTTCAA
1 GTTTAAATTATTTCAA
*
1959504 ATTTA
1 GTTTA
1959509 TATTCTAGAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
15 10 0.33
16 20 0.67
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.48
Consensus pattern (16 bp):
GTTTAAATTATTTCAA
Found at i:1962918 original size:18 final size:18
Alignment explanation
Indices: 1962895--1962940 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
1962885 TTTGTTCACA
* * *
1962895 GGTTTTGGTGTTGGGTGT
1 GGTTTTGGAGTTGGATGG
1962913 GGTTTTGGAGTTGGATGG
1 GGTTTTGGAGTTGGATGG
1962931 GGTTTTGGAG
1 GGTTTTGGAG
1962941 GTCTGTTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.07, C:0.00, G:0.50, T:0.43
Consensus pattern (18 bp):
GGTTTTGGAGTTGGATGG
Found at i:1973645 original size:60 final size:63
Alignment explanation
Indices: 1973513--1973654 Score: 175
Period size: 60 Copynumber: 2.3 Consensus size: 63
1973503 TTTAGACAAA
* * *
1973513 AAAGCCAAGTTTAGGTACCTAATTGGACCAAGAAAAAAATCTTTAGGTACTAAATTAAACCTT
1 AAAGCCAAGTTCAGGTACCTAATTAGACCAAGAAAAAAATCTTTAGGTACCAAATTAAACCTT
* * * *
1973576 AAAGTCAAGTTCAAGTACCTAATTAGACCAA-AAAAGAA-C-TT-GGATACCAAATTGAACCTT
1 AAAGCCAAGTTCAGGTACCTAATTAGACCAAGAAAAAAATCTTTAGG-TACCAAATTAAACCTT
*
1973636 CAAGCCAAGTTCAGGTACC
1 AAAGCCAAGTTCAGGTACC
1973655 AAAATGTATA
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
59 2 0.03
60 32 0.47
61 1 0.01
62 6 0.09
63 27 0.40
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (63 bp):
AAAGCCAAGTTCAGGTACCTAATTAGACCAAGAAAAAAATCTTTAGGTACCAAATTAAACCTT
Found at i:1982166 original size:22 final size:22
Alignment explanation
Indices: 1982141--1982190 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
1982131 TTGATTTCAC
* *
1982141 ATTATTTTGCTACCATTTTGTT
1 ATTATTTTACTACCATTTTATT
* *
1982163 ATTATATTACTACTATTTTATT
1 ATTATTTTACTACCATTTTATT
*
1982185 GTTATT
1 ATTATT
1982191 GTTTGGATAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.10, G:0.06, T:0.60
Consensus pattern (22 bp):
ATTATTTTACTACCATTTTATT
Found at i:1983814 original size:23 final size:25
Alignment explanation
Indices: 1983778--1983833 Score: 71
Period size: 23 Copynumber: 2.3 Consensus size: 25
1983768 TTAATATTTA
*
1983778 TAATTTTTTTATT-AATTTGGTT-T
1 TAATTTTTTAATTAAATTTGGTTAT
* *
1983801 TCATTTTTTAATTAAATTTTGTTAT
1 TAATTTTTTAATTAAATTTGGTTAT
1983826 TAATTTTT
1 TAATTTTT
1983834 CAAAAGAGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 11 0.41
24 8 0.30
25 8 0.30
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (25 bp):
TAATTTTTTAATTAAATTTGGTTAT
Found at i:1983833 original size:13 final size:12
Alignment explanation
Indices: 1983774--1983833 Score: 52
Period size: 12 Copynumber: 5.1 Consensus size: 12
1983764 GTCTTTAATA
1983774 TTTA-TAATTTT
1 TTTATTAATTTT
*
1983785 TTTATTAATTTG
1 TTTATTAATTTT
* *
1983797 GTT-TTCATTTT
1 TTTATTAATTTT
*
1983808 TTAATTAAATTTT
1 TTTATT-AATTTT
*
1983821 GTTATTAATTTT
1 TTTATTAATTTT
1983833 T
1 T
1983834 CAAAAGAGTA
Statistics
Matches: 36, Mismatches: 10, Indels: 5
0.71 0.20 0.10
Matches are distributed among these distances:
11 11 0.31
12 16 0.44
13 9 0.25
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (12 bp):
TTTATTAATTTT
Found at i:1986512 original size:12 final size:13
Alignment explanation
Indices: 1986483--1986520 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
1986473 TAAAAAACAT
*
1986483 TAATTTGTTTATA
1 TAATTTTTTTATA
1986496 TAATTTTTTTA-A
1 TAATTTTTTTATA
*
1986508 TAATTTTATTATA
1 TAATTTTTTTATA
1986521 CATTTTGTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (13 bp):
TAATTTTTTTATA
Found at i:1989217 original size:20 final size:19
Alignment explanation
Indices: 1989192--1989239 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
1989182 TCAAAACACG
*
1989192 TTTATAATAATATAACTAAT
1 TTTATAATAAAATAA-TAAT
1989212 TTTATATATAAAATAATAAT
1 TTTATA-ATAAAATAATAAT
*
1989232 TTAATAAT
1 TTTATAAT
1989240 TTTTGAACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 15 0.60
21 8 0.32
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTATAATAAAATAATAAT
Found at i:1990691 original size:6 final size:6
Alignment explanation
Indices: 1990680--1990706 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1990670 CAAAGCTAAA
1990680 CCATCT CCATCT CCATCT CCATCT CCA
1 CCATCT CCATCT CCATCT CCATCT CCA
1990707 ACCGCTACGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.52, G:0.00, T:0.30
Consensus pattern (6 bp):
CCATCT
Found at i:1996744 original size:23 final size:22
Alignment explanation
Indices: 1996712--1996773 Score: 88
Period size: 22 Copynumber: 2.7 Consensus size: 22
1996702 GCCCGGCCCG
*
1996712 TTTTTAATTAAAATTAAAATTATA
1 TTTTT-ATTAAAATTAAAACTA-A
1996736 TTTTTATTAAAATTAAAACTAA
1 TTTTTATTAAAATTAAAACTAA
*
1996758 TTGTTATTAAAATTAA
1 TTTTTATTAAAATTAA
1996774 TTGTTATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 16 0.44
23 15 0.42
24 5 0.14
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTTTATTAAAATTAAAACTAA
Found at i:1996786 original size:16 final size:16
Alignment explanation
Indices: 1996747--1996787 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
1996737 TTTTATTAAA
*
1996747 ATTAAAACTAATTGTT
1 ATTAAAATTAATTGTT
1996763 ATTAAAATTAATTGTT
1 ATTAAAATTAATTGTT
1996779 ATTAAAATT
1 ATTAAAATT
1996788 GTATCAGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (16 bp):
ATTAAAATTAATTGTT
Found at i:1996909 original size:34 final size:37
Alignment explanation
Indices: 1996870--1996955 Score: 115
Period size: 40 Copynumber: 2.3 Consensus size: 37
1996860 TTGTTAATTG
1996870 TATTAATTGTTACTAA-A-ATT-ATCAAATTATTAAT
1 TATTAATTGTTACTAACATATTAATCAAATTATTAAT
*
1996904 TATTAATTGTTACTAACATTTTGTTAATCAAATTATTAAT
1 TATTAATTGTTACTAACA---TATTAATCAAATTATTAAT
1996944 TATTAATTGTTA
1 TATTAATTGTTA
1996956 ATTGTATTAA
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
34 16 0.36
35 1 0.02
39 2 0.04
40 26 0.58
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.50
Consensus pattern (37 bp):
TATTAATTGTTACTAACATATTAATCAAATTATTAAT
Found at i:2002902 original size:31 final size:31
Alignment explanation
Indices: 2002862--2002922 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
2002852 TTGGACAAAA
*
2002862 AAGCTAAGTTCAAGTA-ATAATTTGAATCAAG
1 AAGCCAAGTTCAAGTACATAATTTG-ATCAAG
* *
2002893 AAGCCAAGTTCAGGTACTTAATTTGATCAA
1 AAGCCAAGTTCAAGTACATAATTTGATCAA
2002923 AATAAACTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 19 0.73
32 7 0.27
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (31 bp):
AAGCCAAGTTCAAGTACATAATTTGATCAAG
Found at i:2007697 original size:2 final size:2
Alignment explanation
Indices: 2007690--2007722 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2007680 TAAAGTTGAC
2007690 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 A
2007723 ATGGATACTG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2012101 original size:18 final size:18
Alignment explanation
Indices: 2012078--2012113 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2012068 CAATTAAACC
2012078 ATTTGATTGATATATTTA
1 ATTTGATTGATATATTTA
* *
2012096 ATTTGATTTATTTATTTA
1 ATTTGATTGATATATTTA
2012114 TAAATAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (18 bp):
ATTTGATTGATATATTTA
Found at i:2012176 original size:20 final size:20
Alignment explanation
Indices: 2012153--2012191 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2012143 CAATTTAAAA
2012153 TATAAAAAATTATTAATATG
1 TATAAAAAATTATTAATATG
* **
2012173 TATATAATTTTATTAATAT
1 TATAAAAAATTATTAATAT
2012192 ATGTAAAAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAAATTATTAATATG
Found at i:2023081 original size:4 final size:4
Alignment explanation
Indices: 2023074--2023099 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2023064 TTACAGTTGG
2023074 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
2023100 TTATTATTTG
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:2027670 original size:22 final size:22
Alignment explanation
Indices: 2027638--2027681 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2027628 TATATAAAAA
2027638 GAGCTTAAATACAAATGAGTTT
1 GAGCTTAAATACAAATGAGTTT
* *
2027660 GAGCTTGAATACTAATGAGTTT
1 GAGCTTAAATACAAATGAGTTT
2027682 AATTGAGCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.34
Consensus pattern (22 bp):
GAGCTTAAATACAAATGAGTTT
Found at i:2039877 original size:2 final size:2
Alignment explanation
Indices: 2039829--2039858 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2039819 AGCAATAATG
2039829 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
2039859 AAGGTATTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2044462 original size:29 final size:29
Alignment explanation
Indices: 2044423--2044499 Score: 109
Period size: 30 Copynumber: 2.6 Consensus size: 29
2044413 AAATTGTGGA
* *
2044423 TTTAATTTTTATACTTTTAATTGATCAAT
1 TTTAATCTTTATACTTTTAAATGATCAAT
*
2044452 TTTAATCTTTATATTTTTTAAATGATCAAT
1 TTTAATCTTTATA-CTTTTAAATGATCAAT
*
2044482 TTTAGTCTTTATACTTTT
1 TTTAATCTTTATACTTTT
2044500 TGAATTATGA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 16 0.38
30 26 0.62
ACGTcount: A:0.29, C:0.08, G:0.04, T:0.60
Consensus pattern (29 bp):
TTTAATCTTTATACTTTTAAATGATCAAT
Found at i:2051525 original size:20 final size:20
Alignment explanation
Indices: 2051502--2051540 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2051492 CATTAAATAA
2051502 ATTATTAAAAATTTAAAAAT
1 ATTATTAAAAATTTAAAAAT
*
2051522 ATTATTACAAATTTAAAAA
1 ATTATTAAAAATTTAAAAA
2051541 AATAGTTCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
ATTATTAAAAATTTAAAAAT
Found at i:2051567 original size:21 final size:20
Alignment explanation
Indices: 2051543--2051600 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
2051533 TTTAAAAAAA
2051543 TAGTTCGATCAATTCAACTAT
1 TAGTTCGATCAATTCAACT-T
* * *
2051564 TAGTTCAATCGATTTTAACTT
1 TAGTTCGATC-AATTCAACTT
2051585 TA-TTCGTATCAATTCA
1 TAGTTCG-ATCAATTCA
2051601 CAAATCAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
20 7 0.24
21 15 0.52
22 7 0.24
ACGTcount: A:0.31, C:0.17, G:0.09, T:0.43
Consensus pattern (20 bp):
TAGTTCGATCAATTCAACTT
Found at i:2063405 original size:14 final size:14
Alignment explanation
Indices: 2063380--2063416 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2063370 TTCTCATTTT
2063380 TCATTTTCTTTCTC
1 TCATTTTCTTTCTC
* *
2063394 TCGTTTTTTTTCTC
1 TCATTTTCTTTCTC
2063408 TCATTTTCT
1 TCATTTTCT
2063417 CCTATTACCG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.05, C:0.24, G:0.03, T:0.68
Consensus pattern (14 bp):
TCATTTTCTTTCTC
Found at i:2063735 original size:21 final size:24
Alignment explanation
Indices: 2063685--2063740 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 24
2063675 GGATAATTAA
2063685 CTTAATTAA-TTTAAACTAATCATG
1 CTTAATTAACTTTAAACTAA-CATG
2063709 CTTTAATTAACTTTAAACT-A-AT-
1 C-TTAATTAACTTTAAACTAACATG
2063731 CTTAATTAAC
1 CTTAATTAAC
2063741 ATAAGTAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
21 9 0.30
22 1 0.03
23 2 0.07
24 1 0.03
25 9 0.30
26 8 0.27
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.43
Consensus pattern (24 bp):
CTTAATTAACTTTAAACTAACATG
Found at i:2063739 original size:25 final size:25
Alignment explanation
Indices: 2063680--2063739 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
2063670 ATTAGGGATA
2063680 ATTAACTTAATTAATTTAAACTAATC
1 ATTAA-TTAATTAATTTAAACTAATC
***
2063706 ATGCTTTAATTAACTTTAAACTAATC
1 ATTAATTAATTAA-TTTAAACTAATC
2063732 -TTAATTAA
1 ATTAATTAA
2063740 CATAAGTAAG
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
25 13 0.48
26 14 0.52
ACGTcount: A:0.43, C:0.12, G:0.02, T:0.43
Consensus pattern (25 bp):
ATTAATTAATTAATTTAAACTAATC
Found at i:2065657 original size:41 final size:42
Alignment explanation
Indices: 2065517--2065667 Score: 151
Period size: 42 Copynumber: 3.6 Consensus size: 42
2065507 AAGGCTTAAT
* * *
2065517 AGAACCTCATGAGAGCTAAACAGAAACCCATAAGGGTTGAAC
1 AGAAGCTCATGAGAGCTGAACAGAAACCCATAAGGGTTAAAC
* * * * *
2065559 GGAAGCTCGTAAAAGCTGAACGGAAACCCATAAGGGTTAAAC
1 AGAAGCTCATGAGAGCTGAACAGAAACCCATAAGGGTTAAAC
* * * * *
2065601 AGAAGCACATTAGAGCTGAAC-GAAACTCATATGAGTTAAAC
1 AGAAGCTCATGAGAGCTGAACAGAAACCCATAAGGGTTAAAC
* * *
2065642 AGAAGCTCGTGAGAGCTAAATAGAAA
1 AGAAGCTCATGAGAGCTGAACAGAAA
2065668 GAAACACAAA
Statistics
Matches: 87, Mismatches: 21, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
41 33 0.38
42 54 0.62
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.16
Consensus pattern (42 bp):
AGAAGCTCATGAGAGCTGAACAGAAACCCATAAGGGTTAAAC
Found at i:2076111 original size:2 final size:2
Alignment explanation
Indices: 2076106--2076130 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2076096 GAAGCATCTA
2076106 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 A
2076131 GTTAATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2076738 original size:31 final size:31
Alignment explanation
Indices: 2076700--2076768 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
2076690 ATACCGATTA
*
2076700 TTGAATAGTCTAGTGACTTAAATAAAAACTT
1 TTGAATAGTCTAGTGACTTAAACAAAAACTT
* *
2076731 TTGAATAGTTTAGTGACTTAAACAAAATCTT
1 TTGAATAGTCTAGTGACTTAAACAAAAACTT
*
2076762 TCGAATA
1 TTGAATA
2076769 ATTCAGTGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (31 bp):
TTGAATAGTCTAGTGACTTAAACAAAAACTT
Found at i:2076777 original size:31 final size:31
Alignment explanation
Indices: 2076711--2076777 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
2076701 TGAATAGTCT
* * * *
2076711 AGTGACTTAAATAAAAACTTTTGAATAGTTT
1 AGTGACTTAAACAAAAACTTTCGAATAATTC
*
2076742 AGTGACTTAAACAAAATCTTTCGAATAATTC
1 AGTGACTTAAACAAAAACTTTCGAATAATTC
2076773 AGTGA
1 AGTGA
2076778 TCATTCTATA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.34
Consensus pattern (31 bp):
AGTGACTTAAACAAAAACTTTCGAATAATTC
Found at i:2078074 original size:17 final size:18
Alignment explanation
Indices: 2078043--2078076 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2078033 GTCTCACATC
*
2078043 ATTTTCATATCAAGATAG
1 ATTTTCATATAAAGATAG
2078061 ATTTT-ATATAAAGATA
1 ATTTTCATATAAAGATA
2078077 TTTACATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (18 bp):
ATTTTCATATAAAGATAG
Found at i:2078752 original size:22 final size:21
Alignment explanation
Indices: 2078726--2078782 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 21
2078716 GCTATGCGAG
2078726 TAAAAATGAAAATAATATATT-T
1 TAAAAA-GAAAATAATA-ATTAT
*
2078748 T-AAAAGAAACTAATAATTAT
1 TAAAAAGAAAATAATAATTAT
2078768 TAATAAAGAAAATAA
1 TAA-AAAGAAAATAA
2078783 AAAATACATG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 3 0.10
20 11 0.37
21 5 0.17
22 11 0.37
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (21 bp):
TAAAAAGAAAATAATAATTAT
Found at i:2078863 original size:34 final size:31
Alignment explanation
Indices: 2078800--2078877 Score: 106
Period size: 34 Copynumber: 2.5 Consensus size: 31
2078790 ATGAATGGTT
*
2078800 ATTGATAAAAG-A-TTTTTTTTTGACGATTA
1 ATTGATAAAAGAATTTTTTTTTTGACAATTA
2078829 ATTGATAAAAGAATTTTTTTTTTGAACCAAATTA
1 ATTGATAAAAGAATTTTTTTTTTG-A-C-AATTA
2078863 ATTGATAAAAGAATT
1 ATTGATAAAAGAATT
2078878 GTATGAGAGA
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
29 11 0.26
30 1 0.02
31 10 0.23
32 1 0.02
33 1 0.02
34 19 0.44
ACGTcount: A:0.41, C:0.04, G:0.12, T:0.44
Consensus pattern (31 bp):
ATTGATAAAAGAATTTTTTTTTTGACAATTA
Found at i:2089234 original size:5 final size:5
Alignment explanation
Indices: 2089224--2089251 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
2089214 TATTTAAAAA
2089224 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
2089252 TAAGGTTAAA
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:2089990 original size:30 final size:29
Alignment explanation
Indices: 2089937--2089993 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
2089927 ATGTTAAAAA
*
2089937 TAATTTTTAGTTATTTTTATATTTTTTGG
1 TAATTTTTAATTATTTTTATATTTTTTGG
* *
2089966 TAATTTTATAATTGTTTTTCTATTTTTT
1 TAATTTT-TAATTATTTTTATATTTTTT
2089994 AAATAATGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 7 0.29
30 17 0.71
ACGTcount: A:0.21, C:0.02, G:0.07, T:0.70
Consensus pattern (29 bp):
TAATTTTTAATTATTTTTATATTTTTTGG
Found at i:2090785 original size:27 final size:27
Alignment explanation
Indices: 2090747--2090801 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
2090737 AGGATGGAGT
2090747 TATTTTTGGTAAAAGTATCATAAAGGC
1 TATTTTTGGTAAAAGTATCATAAAGGC
2090774 TATTTTTGGTAAAAGTATCATAAAGGC
1 TATTTTTGGTAAAAGTATCATAAAGGC
2090801 T
1 T
2090802 CTTATATTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.38
Consensus pattern (27 bp):
TATTTTTGGTAAAAGTATCATAAAGGC
Found at i:2092579 original size:30 final size:29
Alignment explanation
Indices: 2092513--2092584 Score: 76
Period size: 30 Copynumber: 2.5 Consensus size: 29
2092503 GTACTCTCTA
2092513 TATATTT-AGAATTTAATCCTCAATTTTT
1 TATATTTAAGAATTTAATCCTCAATTTTT
* * *
2092541 TATTTTTAAGAATTTAGTCTCTCTATTTTT
1 TATATTTAAGAATTTAATC-CTCAATTTTT
*
2092571 TGA-ATTTAAAAATT
1 T-ATATTTAAGAATT
2092585 CGGGTCTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 6 0.17
29 10 0.28
30 19 0.53
31 1 0.03
ACGTcount: A:0.32, C:0.08, G:0.06, T:0.54
Consensus pattern (29 bp):
TATATTTAAGAATTTAATCCTCAATTTTT
Found at i:2097937 original size:16 final size:16
Alignment explanation
Indices: 2097918--2097959 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
2097908 TCTCATGTTA
*
2097918 TTTTTT-ATTCATAAT
1 TTTTTTAATTAATAAT
2097933 TTTTTTAATTAATAAT
1 TTTTTTAATTAATAAT
**
2097949 TACTTTAATTA
1 TTTTTTAATTA
2097960 TATTCATACT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTTTAATTAATAAT
Found at i:2105765 original size:184 final size:184
Alignment explanation
Indices: 2105351--2105871 Score: 714
Period size: 184 Copynumber: 2.8 Consensus size: 184
2105341 AGACAAGACC
* * *
2105351 TGATTGTACATAAAAAATATACATTAGATACCATACGACAATCGAACCGGAACTAGAGACATAAC
1 TGATTGCACATGAAAAATATACATTAGATACCATACGACAATCGAACCGGAACTAGAGCCATAAC
* *
2105416 GACCATAAACACAAATTATATGCACTTTTGTATCCCAAAACAAACCAGCAGATACCGCATTAAGT
66 GACCATAAACACAATTTATATGCACTTTTGTATCCCACAACAAACCAGCAGATACCG-ATTAAGT
2105481 GCATCATCACTAAGATATTTAGGAAATATTCAACAGAACCGGAATCTAAGGTTCT
130 GCATCATCACTAAGATATTTAGGAAATATTCAACAGAACCGGAATCTAAGGTTCT
* *
2105536 TGATTGCACATGAAAAATATACATTAGATACCATATGACAATCGAACCGGAACTCGAGCCATAAC
1 TGATTGCACATGAAAAATATACATTAGATACCATACGACAATCGAACCGGAACTAGAGCCATAAC
* * *
2105601 GACCATAAACACAATTTATATGCACTTTTGTATCCCACAACGATCCAGCAGATACTG-TGTAAGT
66 GACCATAAACACAATTTATATGCACTTTTGTATCCCACAACAAACCAGCAGATACCGAT-TAAGT
* * *
2105665 GCAT-AGTCACTAAGA-ACTTTAGGAAATATTTAA-AGGAACTGGCATCTAAGGTTCT
130 GCATCA-TCACTAAGATA-TTTAGGAAATATTCAACA-GAACCGGAATCTAAGGTTCT
*
2105720 TGATTGCACATGAAAAATATACATTAGATACCATAGGGA-AATCGAACCGGAACTAGAGCCATAA
1 TGATTGCACATGAAAAATATACATTAGATACCATA-CGACAATCGAACCGGAACTAGAGCCATAA
* * * * * * *
2105784 CAACCATTAGCACAATTTATATGCAATTTTGTATCCCACAATAAACCAGCAAATACC-ACATAAG
65 CGACCATAAACACAATTTATATGCACTTTTGTATCCCACAACAAACCAGCAGATACCGA-TTAAG
* *
2105848 TGCAT-AGTCATTAACATATTTAGG
129 TGCATCA-TCACTAAGATATTTAGG
2105872 CCACTTATAC
Statistics
Matches: 301, Mismatches: 27, Indels: 17
0.87 0.08 0.05
Matches are distributed among these distances:
183 4 0.01
184 182 0.60
185 115 0.38
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (184 bp):
TGATTGCACATGAAAAATATACATTAGATACCATACGACAATCGAACCGGAACTAGAGCCATAAC
GACCATAAACACAATTTATATGCACTTTTGTATCCCACAACAAACCAGCAGATACCGATTAAGTG
CATCATCACTAAGATATTTAGGAAATATTCAACAGAACCGGAATCTAAGGTTCT
Found at i:2109250 original size:13 final size:13
Alignment explanation
Indices: 2109232--2109256 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2109222 ATTTTTAATA
2109232 TTATTTTGTGTGT
1 TTATTTTGTGTGT
2109245 TTATTTTGTGTG
1 TTATTTTGTGTG
2109257 CATTTGATTG
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:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:2110487 original size:2 final size:2
Alignment explanation
Indices: 2110480--2110519 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2110470 ATGTTATAAT
2110480 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
2110520 GATTCGAATA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2110666 original size:2 final size:2
Alignment explanation
Indices: 2110659--2110690 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2110649 TGAGTTCAAT
*
2110659 TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2110691 AGTATAGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2111074 original size:41 final size:40
Alignment explanation
Indices: 2111044--2111189 Score: 120
Period size: 41 Copynumber: 3.6 Consensus size: 40
2111034 GGTTATGTAC
*
2111044 CTAGCAGGCTTAATGCTGGTGAAGTAATTCAGACTTTACG
1 CTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTTTACG
* *
2111084 TCTAGCAGGCTTAATGCCGGTG-A-TACATTTCAGACTATATG
1 -CTAGCAGGCTTAATGCCGGTGAAGTA-A-TTCAGACTTTACG
* * * *
2111125 TCTAGCAGGC-TAAGTGCCGGTGTACTGAA-TCAGGCTTTAAG
1 -CTAGCAGGCTTAA-TGCCGGTGAAGT-AATTCAGACTTTACG
* *
2111166 CCTAGCAGGCTAAATGCCAGTGAA
1 -CTAGCAGGCTTAATGCCGGTGAA
2111190 TCTGTTTAAA
Statistics
Matches: 88, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
39 2 0.02
40 5 0.06
41 75 0.85
42 3 0.03
43 2 0.02
44 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (40 bp):
CTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTTTACG
Found at i:2111490 original size:2 final size:2
Alignment explanation
Indices: 2111483--2111534 Score: 50
Period size: 2 Copynumber: 25.0 Consensus size: 2
2111473 TGCATTTGAG
* * * *
2111483 AT AT AT AT AT AT AT AT AT AT AC AT GT ACT CAT TT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T -AT AT AT AT AT AT AT
2111527 AT AT AT AT
1 AT AT AT AT
2111535 TCGAATGTAT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
2 37 0.93
3 2 0.05
4 1 0.03
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2117813 original size:10 final size:9
Alignment explanation
Indices: 2117760--2117825 Score: 51
Period size: 10 Copynumber: 6.7 Consensus size: 9
2117750 AGGTTACAAA
*
2117760 AAAAAATTC
1 AAAAAATTT
2117769 AAAATAATTTT
1 AAAA-AA-TTT
*
2117780 AAAATATTT
1 AAAAAATTT
2117789 ATAAAAATTT
1 A-AAAAATTT
*
2117799 TAAAAATTCT
1 AAAAAATT-T
2117809 AAAAAATATAT
1 AAAAAAT-T-T
2117820 AAAAAA
1 AAAAAA
2117826 AGTTAAGATT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
9 15 0.33
10 17 0.37
11 14 0.30
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (9 bp):
AAAAAATTT
Found at i:2117824 original size:20 final size:19
Alignment explanation
Indices: 2117761--2117815 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 19
2117751 GGTTACAAAA
2117761 AAAAATTC-AAAATAATTTT
1 AAAAATTCTAAAA-AATTTT
2117780 AAAATATT-TATAAAAATTTT
1 AAAA-ATTCTA-AAAAATTTT
2117800 AAAAATTCTAAAAAAT
1 AAAAATTCTAAAAAAT
2117816 ATATAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
19 13 0.41
20 16 0.50
21 3 0.09
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAAATTCTAAAAAATTTT
Found at i:2119989 original size:2 final size:2
Alignment explanation
Indices: 2119982--2120018 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2119972 GGGTTTCTTC
2119982 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 T
2120019 TCAAATAGAT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2124367 original size:38 final size:38
Alignment explanation
Indices: 2124312--2124391 Score: 126
Period size: 38 Copynumber: 2.1 Consensus size: 38
2124302 TCTAATGATG
*
2124312 ATTA-GTGTTCACCTTCTATACTATGTCGTGGATTCGA
1 ATTATGTGTTCACCTTCTAGACTATGTCGTGGATTCGA
* *
2124349 GTTATGTGTTCACCTTCTAGACTATGTTGTGGATTCGA
1 ATTATGTGTTCACCTTCTAGACTATGTCGTGGATTCGA
2124387 ATTAT
1 ATTAT
2124392 AGTACCAGTG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
37 3 0.08
38 35 0.92
ACGTcount: A:0.21, C:0.16, G:0.20, T:0.42
Consensus pattern (38 bp):
ATTATGTGTTCACCTTCTAGACTATGTCGTGGATTCGA
Found at i:2133487 original size:17 final size:16
Alignment explanation
Indices: 2133465--2133503 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
2133455 AATGCAGGTG
2133465 AAAAATAAATTTATATA
1 AAAAATAAATTTATA-A
*
2133482 AAAAATATATTTATAA
1 AAAAATAAATTTATAA
2133498 AAAAAT
1 AAAAAT
2133504 TGGTATTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAAATAAATTTATAA
Found at i:2135733 original size:14 final size:15
Alignment explanation
Indices: 2135710--2135752 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 15
2135700 ATTTTAGAAG
*
2135710 TTTTTATATATTCTA
1 TTTTTATATATTATA
2135725 TTTTT-TATATTATA
1 TTTTTATATATTATA
2135739 TTTTATGATATATT
1 TTTT-T-ATATATT
2135753 TCAATTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 12 0.50
15 6 0.25
17 6 0.25
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (15 bp):
TTTTTATATATTATA
Found at i:2138920 original size:28 final size:28
Alignment explanation
Indices: 2138876--2138943 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
2138866 TAAATTTTTA
* *
2138876 ATTTTAAAATTTCAAAA-TATATAAAAAT
1 ATTTTAAAAATTAAAAATTAT-TAAAAAT
* **
2138904 GTTTTAAAAATTAAAAATTATTAAATTT
1 ATTTTAAAAATTAAAAATTATTAAAAAT
2138932 ATTTTAAAAATT
1 ATTTTAAAAATT
2138944 TTAATATATA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
28 30 0.91
29 3 0.09
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (28 bp):
ATTTTAAAAATTAAAAATTATTAAAAAT
Found at i:2138940 original size:21 final size:21
Alignment explanation
Indices: 2138914--2138982 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
2138904 GTTTTAAAAA
*
2138914 TTAAAAATTATTAA-ATTTATT
1 TTAAAAATT-TTAATATATATT
2138935 TTAAAAATTTTAATATATATT
1 TTAAAAATTTTAATATATATT
* * *
2138956 TTTAATATTTT-AT-GAT-TT
1 TTAAAAATTTTAATATATATT
2138974 TTAAAAATT
1 TTAAAAATT
2138983 AATTAAATGT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
18 9 0.22
19 2 0.05
20 6 0.15
21 24 0.59
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (21 bp):
TTAAAAATTTTAATATATATT
Found at i:2141772 original size:3 final size:3
Alignment explanation
Indices: 2141764--2141803 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
2141754 TGGTGTTTTA
*
2141764 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT TGT GGT G
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT G
2141804 TAGTAGCCAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.65, T:0.35
Consensus pattern (3 bp):
GGT
Found at i:2145251 original size:7 final size:7
Alignment explanation
Indices: 2145239--2145263 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2145229 ATATATTTTT
2145239 TTTATAA
1 TTTATAA
2145246 TTTATAA
1 TTTATAA
2145253 TTTATAA
1 TTTATAA
2145260 TTTA
1 TTTA
2145264 ACAAATATTA
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TTTATAA
Found at i:2153406 original size:22 final size:22
Alignment explanation
Indices: 2153373--2153433 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
2153363 GCCCGGGCCG
* *
2153373 TTTTTAATTAAAATTAAAATTAT
1 TTTTTAA-TAAAATTAAAACTAA
2153396 TTTTTAATAAAATTAAAACTAA
1 TTTTTAATAAAATTAAAACTAA
* *
2153418 TTGTTATTAAAATTAA
1 TTTTTAATAAAATTAA
2153434 TTGTTAGTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 27 0.79
23 7 0.21
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTTTAATAAAATTAAAACTAA
Found at i:2153446 original size:16 final size:16
Alignment explanation
Indices: 2153409--2153448 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
2153399 TTAATAAAAT
* *
2153409 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
2153425 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
2153441 TAAAATTA
1 TAAAATTA
2153449 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:2153527 original size:59 final size:59
Alignment explanation
Indices: 2153459--2153628 Score: 304
Period size: 59 Copynumber: 2.9 Consensus size: 59
2153449 TCAAATTATT
*
2153459 AATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
*
2153518 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAATAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
* *
2153577 AATCATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAA
2153629 ATAAACTTGA
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 106 1.00
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (59 bp):
AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
Found at i:2153733 original size:22 final size:22
Alignment explanation
Indices: 2153695--2153736 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2153685 AAATAAACTT
*
2153695 AAAATAAAACTATTATATTTTA
1 AAAATAAAAATATTATATTTTA
2153717 AAAATAAAAA-ATATATATTT
1 AAAATAAAAATAT-TATATTT
2153737 AATATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
AAAATAAAAATATTATATTTTA
Found at i:2160223 original size:15 final size:17
Alignment explanation
Indices: 2160187--2160223 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
2160177 CTTTTTAAAT
2160187 TTAATTTTATATAAAAA
1 TTAATTTTATATAAAAA
*
2160204 ATAATTTTA-A-AAAAA
1 TTAATTTTATATAAAAA
2160219 TTAAT
1 TTAAT
2160224 ACAGATAGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
15 9 0.50
16 1 0.06
17 8 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAATTTTATATAAAAA
Found at i:2161763 original size:2 final size:2
Alignment explanation
Indices: 2161756--2161803 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2161746 ATAAACATAA
2161756 AT AT 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 AT AT
2161798 AT AT AT
1 AT AT AT
2161804 CAGCATCAAC
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2167591 original size:8 final size:8
Alignment explanation
Indices: 2167547--2167575 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
2167537 TTTAAAATAT
2167547 TTTTTTTA
1 TTTTTTTA
2167555 TTTTTTTA
1 TTTTTTTA
2167563 TTTTTTTA
1 TTTTTTTA
2167571 TTTTT
1 TTTTT
2167576 AAAATAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTTA
Found at i:2167601 original size:47 final size:46
Alignment explanation
Indices: 2167496--2167601 Score: 108
Period size: 47 Copynumber: 2.3 Consensus size: 46
2167486 CGAATATAAT
* *
2167496 AAATATATATTTT-TTATTTTTATTTTTAATTGTAAAATACTTTTA
1 AAATATTTATTTTATTATTTTTATTTTTAATTGTAAAATAATTTTA
* * * *
2167541 AAATATTTTTTTTATT-TTTTTATTTTTTTATTTTTAAAATAATTTTT
1 AAATATTTATTTTATTATTTTTA--TTTTTAATTGTAAAATAATTTTA
* *
2167588 TAATGTTTATTTTA
1 AAATATTTATTTTA
2167602 AAAATGGGCC
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
45 17 0.35
46 2 0.04
47 30 0.61
ACGTcount: A:0.31, C:0.01, G:0.02, T:0.66
Consensus pattern (46 bp):
AAATATTTATTTTATTATTTTTATTTTTAATTGTAAAATAATTTTA
Found at i:2172835 original size:30 final size:31
Alignment explanation
Indices: 2172801--2172864 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
2172791 CCTTTGGGGC
*
2172801 AATATAATTGAAAAAT-ACGTAATTAATTTG
1 AATATAATTAAAAAATGACGTAATTAATTTG
2172831 AATATAATTAAAAAATGACGTAATTAATTTG
1 AATATAATTAAAAAATGACGTAATTAATTTG
2172862 AAT
1 AAT
2172865 TTAGTAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 15 0.47
31 17 0.53
ACGTcount: A:0.52, C:0.03, G:0.09, T:0.36
Consensus pattern (31 bp):
AATATAATTAAAAAATGACGTAATTAATTTG
Found at i:2172873 original size:30 final size:30
Alignment explanation
Indices: 2172801--2172873 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 30
2172791 CCTTTGGGGC
* *
2172801 AATATAATTGAAAAATACGTAATTAATTTG
1 AATATAAGTAAAAAATACGTAATTAATTTG
*
2172831 AATATAATTAAAAAATGACGTAATTAATTTG
1 AATATAAGTAAAAAAT-ACGTAATTAATTTG
*
2172862 AAT-TTAGTAAAA
1 AATATAAGTAAAA
2172874 TAATTTTAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
30 22 0.56
31 17 0.44
ACGTcount: A:0.52, C:0.03, G:0.10, T:0.36
Consensus pattern (30 bp):
AATATAAGTAAAAAATACGTAATTAATTTG
Found at i:2186887 original size:15 final size:14
Alignment explanation
Indices: 2186867--2186896 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
2186857 CCGTTCTCTT
2186867 TCCTTCTCCTTTCTC
1 TCCTTCTCC-TTCTC
2186882 TCCTTCTCCTTCTC
1 TCCTTCTCCTTCTC
2186896 T
1 T
2186897 TTCCGTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (14 bp):
TCCTTCTCCTTCTC
Found at i:2194976 original size:127 final size:127
Alignment explanation
Indices: 2194750--2195004 Score: 474
Period size: 127 Copynumber: 2.0 Consensus size: 127
2194740 TGATCAGCAT
*
2194750 AACAAATAAACACTGAAGAGAGTATATAACATTTGAATTAAACAACGAAAATTAGACATGGCATA
1 AACAAATAAACACTGAAGAGAGTATATAACATTTGAATTAAACAACGAAAATTAGACAAGGCATA
*
2194815 ACCTCGTTATATTTCTGTTTAGCATACTATTTTATATCCTAGGAATGAGGACTTACTGTATC
66 ACCTCGTTATATTTCTGTTTAGCATACTATTTTATATCCCAGGAATGAGGACTTACTGTATC
2194877 AACAAATAAACACTGAAGAGAGTATATAACATTTGAATTAAACAACGAAAATTAGACAAGGCATA
1 AACAAATAAACACTGAAGAGAGTATATAACATTTGAATTAAACAACGAAAATTAGACAAGGCATA
* *
2194942 ACCTTGTTATATTTCTGTTTAGCATACTATTTTATATCCCAGGGATGAGGACTTACTGTATC
66 ACCTCGTTATATTTCTGTTTAGCATACTATTTTATATCCCAGGAATGAGGACTTACTGTATC
2195004 A
1 A
2195005 GCAGAAGAAG
Statistics
Matches: 124, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
127 124 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (127 bp):
AACAAATAAACACTGAAGAGAGTATATAACATTTGAATTAAACAACGAAAATTAGACAAGGCATA
ACCTCGTTATATTTCTGTTTAGCATACTATTTTATATCCCAGGAATGAGGACTTACTGTATC
Found at i:2201523 original size:78 final size:78
Alignment explanation
Indices: 2201394--2201550 Score: 314
Period size: 78 Copynumber: 2.0 Consensus size: 78
2201384 GGGTTGTTAA
2201394 GTTTTTATTCTTTTTAAAGTTTGGTTAACGAGCTCCAAGTGATAATTTGACGATTGGTGCGATGA
1 GTTTTTATTCTTTTTAAAGTTTGGTTAACGAGCTCCAAGTGATAATTTGACGATTGGTGCGATGA
2201459 ATCAATATCTATC
66 ATCAATATCTATC
2201472 GTTTTTATTCTTTTTAAAGTTTGGTTAACGAGCTCCAAGTGATAATTTGACGATTGGTGCGATGA
1 GTTTTTATTCTTTTTAAAGTTTGGTTAACGAGCTCCAAGTGATAATTTGACGATTGGTGCGATGA
2201537 ATCAATATCTATC
66 ATCAATATCTATC
2201550 G
1 G
2201551 ATGAGTAAAA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.41
Consensus pattern (78 bp):
GTTTTTATTCTTTTTAAAGTTTGGTTAACGAGCTCCAAGTGATAATTTGACGATTGGTGCGATGA
ATCAATATCTATC
Found at i:2202144 original size:13 final size:12
Alignment explanation
Indices: 2202118--2202151 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
2202108 TGTTTTTAAG
*
2202118 TTTTTTATTTTA
1 TTTTTAATTTTA
2202130 TTTTTAATTTATA
1 TTTTTAATTT-TA
2202143 TTTTTAATT
1 TTTTTAATT
2202152 AATAACTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTAATTTTA
Found at i:2202313 original size:22 final size:24
Alignment explanation
Indices: 2202288--2202337 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
2202278 ACTTTTCTTT
2202288 ATATATAATTTTT-A-TATGTTAA
1 ATATATAATTTTTCATTATGTTAA
* *
2202310 ATATTTATTTTTTCATTATGTTAA
1 ATATATAATTTTTCATTATGTTAA
2202334 ATAT
1 ATAT
2202338 CATATATGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 11 0.46
23 1 0.04
24 12 0.50
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (24 bp):
ATATATAATTTTTCATTATGTTAA
Found at i:2202471 original size:71 final size:70
Alignment explanation
Indices: 2202346--2202494 Score: 158
Period size: 71 Copynumber: 2.1 Consensus size: 70
2202336 ATCATATATG
** * * * *
2202346 ATATTTGAAATAATTAATTGATTGTTTATATTATAATTTATCATATTCACAATGTACGTGAAAGA
1 ATATTTGAAATAATTAATCAATTGTTTATATTAAAACTTATCATATGCACAATGTACAT-AAA-A
*
2202411 ATAAT-A
64 AAAATAA
* * * *
2202417 ATATTTGAAATAATTAATCAATTTTTTATTTTAAAACTTA-CGGTATGCATAATGTACATAAAAA
1 ATATTTGAAATAATTAATCAATTGTTTATATTAAAACTTATC-ATATGCACAATGTACATAAAAA
2202481 AAATAA
65 AAATAA
2202487 ATATTTGA
1 ATATTTGA
2202495 CATATAAAAA
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
69 5 0.08
70 13 0.20
71 47 0.72
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (70 bp):
ATATTTGAAATAATTAATCAATTGTTTATATTAAAACTTATCATATGCACAATGTACATAAAAAA
AATAA
Found at i:2203655 original size:2 final size:2
Alignment explanation
Indices: 2203648--2203696 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
2203638 TTTACCCTAT
* *
2203648 TA TA TA TA TG CA 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
2203690 TA TA TA T
1 TA TA TA T
2203697 GCCAATTTGC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2212630 original size:139 final size:139
Alignment explanation
Indices: 2212371--2212644 Score: 392
Period size: 139 Copynumber: 2.0 Consensus size: 139
2212361 GTCCTATAAA
* * * *
2212371 GGAAATGGCTCCTATGACTAAGAAGGGAAAGAAAGCTAAATCTGTGAAGAAGGCTCGGAAAGTGA
1 GGAAATGCCTCCTATGACTAAGAAGGGAAAGAAAACTAAATCTGGGAAGAAGGCTCAGAAAGTGA
* * * * *
2212436 TAAAGAGTATGTATCCTCTAGTCAAACGCACAAAGAAATTGAAATCTACTTCCTCTTAGCAGAGT
66 AAAAGAATATGTATCCTCTAGTCAAACGAACAAAGAAATTGAAATCCACTCCCTCTTAGCAGAGT
2212501 CTGCTCAAG
131 CTGCTCAAG
*
2212510 GGAAATGCCTCCTATGTA-TAAGATGGTG-AAGAAAACTAAATCTGGGAAGAAGGCTCAGAAAGT
1 GGAAATGCCTCCTATG-ACTAAGAAGG-GAAAGAAAACTAAATCTGGGAAGAAGGCTCAGAAAGT
* *
2212573 GAAAAAGAATGTGTATCCTCTAGTCAAACGAACGAAGAAATTGAAATCCA-TGCCCTCTTAGCAG
64 GAAAAAGAATATGTATCCTCTAGTCAAACGAACAAAGAAATTGAAATCCACT-CCCTCTTAGCAG
2212637 AGTCTGCT
128 AGTCTGCT
2212645 TTGTGAGTTT
Statistics
Matches: 120, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
138 1 0.01
139 117 0.98
140 2 0.02
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (139 bp):
GGAAATGCCTCCTATGACTAAGAAGGGAAAGAAAACTAAATCTGGGAAGAAGGCTCAGAAAGTGA
AAAAGAATATGTATCCTCTAGTCAAACGAACAAAGAAATTGAAATCCACTCCCTCTTAGCAGAGT
CTGCTCAAG
Found at i:2225303 original size:30 final size:29
Alignment explanation
Indices: 2225269--2225327 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
2225259 TTATGGGATC
*
2225269 TGGATCAAATTAGTCCTTTTTATAATTAAA
1 TGGATCAAATTAGT-CTTTATATAATTAAA
* * *
2225299 TGGATGAATTTAGTCTTTATATTATTAAA
1 TGGATCAAATTAGTCTTTATATAATTAAA
2225328 AAGGATGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.46
Consensus pattern (29 bp):
TGGATCAAATTAGTCTTTATATAATTAAA
Found at i:2225334 original size:30 final size:30
Alignment explanation
Indices: 2225278--2225336 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
2225268 CTGGATCAAA
* *
2225278 TTAGTCCTTTTTATAATTAAATGGATGAAT
1 TTAGTCCTTTATATAATTAAAAGGATGAAT
*
2225308 TTAGT-CTTTATATTATTAAAAAGGATGAA
1 TTAGTCCTTTATATAATT-AAAAGGATGAA
2225337 ATAAGTTTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.37, C:0.05, G:0.14, T:0.44
Consensus pattern (30 bp):
TTAGTCCTTTATATAATTAAAAGGATGAAT
Found at i:2226380 original size:30 final size:30
Alignment explanation
Indices: 2226336--2226396 Score: 72
Period size: 29 Copynumber: 2.0 Consensus size: 30
2226326 TAGACCTGAA
*
2226336 TTTTGAAATCTAAAAAGTA-AAGAGACTAAAT
1 TTTTGAAATAT-AAAAGTATAAGAG-CTAAAT
*
2226367 TTTTGAAA-ATAAAAGTATATGAGCTAAAT
1 TTTTGAAATATAAAAGTATAAGAGCTAAAT
2226396 T
1 T
2226397 CTAAAGTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 14 0.52
30 5 0.19
31 8 0.30
ACGTcount: A:0.49, C:0.05, G:0.13, T:0.33
Consensus pattern (30 bp):
TTTTGAAATATAAAAGTATAAGAGCTAAAT
Found at i:2229125 original size:21 final size:21
Alignment explanation
Indices: 2229096--2229137 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2229086 TTCAAGTTTT
2229096 TGTTCTTGAGGTCTAGAGACA
1 TGTTCTTGAGGTCTAGAGACA
* * *
2229117 TGTTTTTGATGTCTCGAGACA
1 TGTTCTTGAGGTCTAGAGACA
2229138 CATGTCCGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.14, G:0.26, T:0.38
Consensus pattern (21 bp):
TGTTCTTGAGGTCTAGAGACA
Found at i:2241298 original size:16 final size:16
Alignment explanation
Indices: 2241258--2241290 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2241248 TATATATCAT
2241258 TATTAAATTATATTTAA
1 TATT-AATTATATTTAA
2241275 TATTAATTAT-TTTAA
1 TATTAATTATATTTAA
2241290 T
1 T
2241291 GTATAATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 6 0.38
17 4 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTAATTATATTTAA
Found at i:2241341 original size:81 final size:82
Alignment explanation
Indices: 2241250--2241401 Score: 227
Period size: 81 Copynumber: 1.8 Consensus size: 82
2241240 TATGAAATTA
* *
2241250 TATATCATTATTAAATTATATTTAATATTAATTATTTT-AATGTAT-AATTCATATAAGAGAATT
1 TATATCATTATTAAATTATATGTAATAATAATTATTTTAAAT-TATAAATTCATATAAGAGAATT
2241313 TATTATCAAGAATTTTAT
65 TATTATCAAGAATTTTAT
* *
2241331 TATATTATTATTAAATTATATGTAATAATAATTATTTTAAATTATACAAATTCATATAAGATAAT
1 TATATCATTATTAAATTATATGTAATAATAATTATTTTAAATTAT--AAATTCATATAAGAGAAT
2241396 TTATTA
64 TTATTA
2241402 GTTATAATTA
Statistics
Matches: 63, Mismatches: 4, Indels: 5
0.88 0.06 0.07
Matches are distributed among these distances:
81 38 0.60
82 3 0.05
84 22 0.35
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (82 bp):
TATATCATTATTAAATTATATGTAATAATAATTATTTTAAATTATAAATTCATATAAGAGAATTT
ATTATCAAGAATTTTAT
Found at i:2241464 original size:54 final size:55
Alignment explanation
Indices: 2241406--2241715 Score: 144
Period size: 54 Copynumber: 5.3 Consensus size: 55
2241396 TTATTAGTTA
*
2241406 TAATTATTTTAAATTT-TATTAAACCATATATTTTAATTAAAATATATTTAATAT
1 TAATTATTTTAAATTTATATTAAATCATATATTTTAATTAAAATATATTTAATAT
* * * * * **
2241460 TAATTATTTCAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATA
1 TAATTATTTTAAATT-TATATTA-A--ATCATATATT-TTAATT-A--AAA-T-ATAT-TTAATA
2241525 T
55 T
* * * * *
2241526 TAATTATTATGAATTT-TATTAAATTATATATTTTAATTATAATATATTTAATAA
1 TAATTATTTTAAATTTATATTAAATCATATATTTTAATTAAAATATATTTAATAT
* * * **
2241580 TAATTATGTT-AATTTATATTTTATAGTATCATATATTATGATTTCAGTAAATTCATATAAGAAT
1 TAATTATTTTAAATTTATA--TTA-A--ATCATATATT-TTAATT-A--AAA-T-ATAT-TTAAT
2241644 AT
54 AT
* * * * *
2241646 TGATTA-TTAAGAATTT-TATTATAATTATATATTTTAATTATAATATATTTAATAA
1 TAATTATTTTA-AATTTATATTA-AATCATATATTTTAATTAAAATATATTTAATAT
2241701 TAATTATGTTTAAAT
1 TAATTAT-TTTAAAT
2241716 ATGATTAAAT
Statistics
Matches: 188, Mismatches: 39, Indels: 56
0.66 0.14 0.20
Matches are distributed among these distances:
53 5 0.03
54 28 0.15
55 14 0.07
56 15 0.08
57 8 0.04
58 2 0.01
59 19 0.10
60 13 0.07
61 15 0.08
62 9 0.05
63 6 0.03
64 11 0.06
65 10 0.05
66 28 0.15
67 5 0.03
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.51
Consensus pattern (55 bp):
TAATTATTTTAAATTTATATTAAATCATATATTTTAATTAAAATATATTTAATAT
Found at i:2241496 original size:59 final size:57
Alignment explanation
Indices: 2241430--2241616 Score: 148
Period size: 59 Copynumber: 3.1 Consensus size: 57
2241420 TTTATTAAAC
2241430 CATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATCTTTTATAGTAT
1 CATATATTTTAATTAAAATATATTTAATATTAATTATTT-AAATTAT-TTTTATAGTAT
* * ** * *
2241489 CATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTATGAATT-TTATTA-A--AT
1 CATATATT-TTAATT-A--AAA-T-ATAT-TTAATATTAATTATT-TAAATTATTTTTATAGTAT
* * * *
2241550 TATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTAT
1 CATATATTTTAATTAAAATATATTTAATATTAATTAT-TTAAATTAT-TTTTATAGTAT
2241609 CATATATT
1 CATATATT
2241617 ATGATTTCAG
Statistics
Matches: 97, Mismatches: 17, Indels: 28
0.68 0.12 0.20
Matches are distributed among these distances:
54 15 0.15
55 6 0.06
56 5 0.05
57 3 0.03
59 18 0.19
60 8 0.08
61 10 0.10
63 4 0.04
64 5 0.05
65 5 0.05
66 17 0.18
67 1 0.01
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.51
Consensus pattern (57 bp):
CATATATTTTAATTAAAATATATTTAATATTAATTATTTAAATTATTTTTATAGTAT
Found at i:2241525 original size:66 final size:63
Alignment explanation
Indices: 2241455--2241653 Score: 175
Period size: 66 Copynumber: 3.2 Consensus size: 63
2241445 AAATATATTT
2241455 AATATTAATTATTTCAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTAT-TTTTATAGTATCATATATTATGATTT-AGTAAATTCATATAA
2241520 G
63 G
* * * * * **
2241521 AATATTAATTATTATGAATT-TTATTA-A--ATTATATATT-TTAATTA-T-AA-T-ATAT-TT
1 AATATTAATTATT-TAAATTATTTTTATAGTATCATATATTATGATTTAGTAAATTCATATAAG
* *
2241575 AATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATGATTTCAGTAAATTCATATAA
1 AATATTAATTAT-TTAAATTAT-TTTTATAGTATCATATATTATGATTT-AGTAAATTCATATAA
2241640 G
63 G
*
2241641 AATATTGATTATT
1 AATATTAATTATT
2241654 AAGAATTTTA
Statistics
Matches: 101, Mismatches: 18, Indels: 29
0.68 0.12 0.20
Matches are distributed among these distances:
54 15 0.15
55 6 0.06
56 5 0.05
57 3 0.03
58 1 0.01
59 10 0.10
60 8 0.08
61 10 0.10
62 1 0.01
63 3 0.03
64 5 0.05
65 6 0.06
66 27 0.27
67 1 0.01
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.50
Consensus pattern (63 bp):
AATATTAATTATTTAAATTATTTTTATAGTATCATATATTATGATTTAGTAAATTCATATAAG
Found at i:2241541 original size:120 final size:120
Alignment explanation
Indices: 2241406--2241715 Score: 487
Period size: 120 Copynumber: 2.6 Consensus size: 120
2241396 TTATTAGTTA
* * ** * *
2241406 TAATTATTTTAAATTTTATTAAACCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTC
1 TAATTATTATGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-
* *
2241470 AAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATAT
65 AAATTATATTTTATAGTATCATATATTATGATTTCAGTAAATTCATATAAGAATAT
2241526 TAATTATTATGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTA
1 TAATTATTATGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTA
*
2241591 ATTTATATTTTATAGTATCATATATTATGATTTCAGTAAATTCATATAAGAATAT
66 AATTATATTTTATAGTATCATATATTATGATTTCAGTAAATTCATATAAGAATAT
* *
2241646 TGATTATTAAGAATTTTATTATAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 TAATTATTATGAATTTTATTA-AATTATATATTTTAATTATAATATATTTAATAATAATTATG-T
2241711 TAAAT
64 TAAAT
2241716 ATGATTAAAT
Statistics
Matches: 175, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
120 127 0.73
121 43 0.25
122 5 0.03
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.51
Consensus pattern (120 bp):
TAATTATTATGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTA
AATTATATTTTATAGTATCATATATTATGATTTCAGTAAATTCATATAAGAATAT
Found at i:2241577 original size:15 final size:15
Alignment explanation
Indices: 2241542--2241593 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
2241532 TTATGAATTT
*
2241542 TATTAAATTAT-ATA
1 TATTTAATTATAATA
2241556 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
2241570 TATTTAATAATAAT-
1 TATTTAATTATAATA
2241584 TATGTTAATT
1 TAT-TTAATT
2241594 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:2241679 original size:18 final size:18
Alignment explanation
Indices: 2241658--2241693 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
2241648 ATTATTAAGA
2241658 ATTTT-ATTATAATTATAT
1 ATTTTAATTATAA-TATAT
2241676 ATTTTAATTATAATATAT
1 ATTTTAATTATAATATAT
2241694 TTAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTTAATTATAATATAT
Found at i:2241683 original size:13 final size:14
Alignment explanation
Indices: 2241662--2241704 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
2241652 TTAAGAATTT
*
2241662 TATTATAATTAT-A
1 TATTTTAATTATAA
2241675 TATTTTAATTATAA
1 TATTTTAATTATAA
*
2241689 TATATTTAATAATAA
1 TAT-TTTAATTATAA
2241704 T
1 T
2241705 TATGTTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 11 0.42
14 4 0.15
15 11 0.42
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TATTTTAATTATAA
Found at i:2241693 original size:16 final size:16
Alignment explanation
Indices: 2241666--2241713 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
2241656 GAATTTTATT
*
2241666 ATAATTATATATTTTA
1 ATAATAATATATTTTA
*
2241682 ATTATAATATA-TTTA
1 ATAATAATATATTTTA
2241697 ATAATAAT-TATGTTTA
1 ATAATAATATAT-TTTA
2241713 A
1 A
2241714 ATATGATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 2 0.07
15 11 0.41
16 14 0.52
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATAATAATATATTTTA
Found at i:2241698 original size:15 final size:15
Alignment explanation
Indices: 2241662--2241704 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
2241652 TTAAGAATTT
2241662 TATTATAATTAT-ATA
1 TATT-TAATTATAATA
2241677 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
2241691 TATTTAATAATAAT
1 TATTTAATTATAAT
2241705 TATGTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 7 0.28
14 6 0.24
15 12 0.48
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:2242568 original size:112 final size:113
Alignment explanation
Indices: 2242370--2242593 Score: 344
Period size: 112 Copynumber: 2.0 Consensus size: 113
2242360 TATTCTGTTA
* * * *
2242370 AATTAGGGTTACATGTGACTCTGGATTTGGGGGATTTTTTTTAATTTCTGCTGGGTTTAAGGTTT
1 AATTAGGGTTACAGGTGACTCTCGATTTGGGGAATTTTTTTTAATTTCTGCTAGGTTTAAGGTTT
2242435 CTAAGTCTCTTTATTTTCAATTCCAGTGGTATAATATTTCTAGGGTTG
66 CTAAGTCTCTTTATTTTCAATTCCAGTGGTATAATATTTCTAGGGTTG
* * * *
2242483 AATTAGGGTTACAGGTGACTGTCGATTT-GGGAATTTTTTTTACTTTCTGTTAGGTTTAGGGTTT
1 AATTAGGGTTACAGGTGACTCTCGATTTGGGGAATTTTTTTTAATTTCTGCTAGGTTTAAGGTTT
*
2242547 CTAAG-CTTCTTTGTTTTCAATTCCAGTGGTATAATATTTCTAGGGTT
66 CTAAGTC-TCTTTATTTTCAATTCCAGTGGTATAATATTTCTAGGGTT
2242594 TTAGAGCTGT
Statistics
Matches: 101, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
111 1 0.01
112 75 0.74
113 25 0.25
ACGTcount: A:0.20, C:0.11, G:0.23, T:0.46
Consensus pattern (113 bp):
AATTAGGGTTACAGGTGACTCTCGATTTGGGGAATTTTTTTTAATTTCTGCTAGGTTTAAGGTTT
CTAAGTCTCTTTATTTTCAATTCCAGTGGTATAATATTTCTAGGGTTG
Found at i:2247620 original size:161 final size:159
Alignment explanation
Indices: 2247385--2247983 Score: 620
Period size: 160 Copynumber: 3.7 Consensus size: 159
2247375 TGTTCTTTGG
* * * ** * *
2247385 CTTGCTGCTCTAGTGATCCTCATATAATATTTTATGTTAGCCAT-GATTGTAAATCATAATTCTT
1 CTTGCTGGTCTAGTGAACCTCATATAATTTTTTATCATAGCC-TGGATTGTTAATCAT-ACTCTT
* * * * * *
2247449 CATCAAAGTATACCCAGTGAAGCTTCTTCTTTATCGTCTCCTTTCAAAGCTTTTTTTTATTGCTT
64 CATCAAAGTATACCTATTGAAGCTTTTTCTTTATTGTCTCCTTTCAAAGCTTTTCTTTATTGCCT
* *
2247514 TAGAATTTTTATGTT-TGTCATGTTATTTATGA
129 TAGAATTTATATGTTCTATCAT-TT-TTTATGA
*
2247546 CTTTCTGGTCTAGTGAACCTCATATAATTTTTTATCATAGCCTGGATTGTTAATCATACTCCTTC
1 CTTGCTGGTCTAGTGAACCTCATATAATTTTTTATCATAGCCTGGATTGTTAATCATACT-CTTC
* * * * *
2247611 ATTAAAGTATACTTTTTGAAGCTTTTTCTTTATTGCCTCCGTTT-GAAGCTTTTCTTTATTGCCT
65 ATCAAAGTATACCTATTGAAGCTTTTTCTTTATTGTCTCC-TTTCAAAGCTTTTCTTTATTGCCT
2247675 TAGAATTTATATGTTCTATCATTTTGTT-TGA
129 TAGAATTTATATGTTCTATCATTTT-TTATGA
* * * * * *
2247706 CTTGCTGATCTAGTGTACCTCAGATAATTTTTTATCATAGCCAGGATTTTTAGTCATACTCTGTC
1 CTTGCTGGTCTAGTGAACCTCATATAATTTTTTATCATAGCCTGGATTGTTAATCATACTCT-TC
* * * *
2247771 ATCAAAGTATACCTTTTGAAGCTTTTTCTTTATTGACTCCTTTCGAAGCGTTTCTTTATTGCCTT
65 ATCAAAGTATACCTATTGAAGCTTTTTCTTTATTGTCTCCTTTCAAAGCTTTTCTTTATTGCCTT
*
2247836 AGAATTTATATTTTCTATCATATTGTTTATGA
130 AGAATTTATATGTTCTATCAT-TT-TTTATGA
* * * * *
2247868 CTTGCTTGTCTAGCGAACCACATATATATATTTATCTTAATTCTTAG-CTGGGATTGTTGATCAT
1 CTTGCTGGTCTAGTGAACCTC--ATATA-ATTT-T-TT-A-TCATAGCCT-GGATTGTTAATCAT
* * *
2247932 A--CTTCATCAAAGTATGCCTAATGGAGC-TTTTCTTTATTGTCTCCTTTCAAAG
58 ACTCTTCATCAAAGTATACCTATTGAAGCTTTTTCTTTATTGTCTCCTTTCAAAG
2247984 TTAACTATAG
Statistics
Matches: 370, Mismatches: 50, Indels: 32
0.82 0.11 0.07
Matches are distributed among these distances:
159 5 0.01
160 139 0.38
161 123 0.33
162 28 0.08
164 4 0.01
165 27 0.07
166 21 0.06
167 4 0.01
168 2 0.01
169 17 0.05
ACGTcount: A:0.24, C:0.17, G:0.13, T:0.46
Consensus pattern (159 bp):
CTTGCTGGTCTAGTGAACCTCATATAATTTTTTATCATAGCCTGGATTGTTAATCATACTCTTCA
TCAAAGTATACCTATTGAAGCTTTTTCTTTATTGTCTCCTTTCAAAGCTTTTCTTTATTGCCTTA
GAATTTATATGTTCTATCATTTTTTATGA
Found at i:2251611 original size:6 final size:6
Alignment explanation
Indices: 2251593--2251632 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
2251583 GCCCCACACC
*
2251593 CCCCAT CCTCAT CCCCAT CCCCAT CCCCAT CCCCAT CCCC
1 CCCCAT CCCCAT CCCCAT CCCCAT CCCCAT CCCCAT CCCC
2251633 CATTCTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.15, C:0.68, G:0.00, T:0.17
Consensus pattern (6 bp):
CCCCAT
Found at i:2257586 original size:20 final size:20
Alignment explanation
Indices: 2257561--2257605 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
2257551 TAATTTTGAA
2257561 AATTTTT-TATAATTTTTTG
1 AATTTTTATATAATTTTTTG
** *
2257580 AATTTTTATATGTTTTTTTT
1 AATTTTTATATAATTTTTTG
2257600 AATTTT
1 AATTTT
2257606 AAGAGCTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (20 bp):
AATTTTTATATAATTTTTTG
Found at i:2257953 original size:23 final size:23
Alignment explanation
Indices: 2257923--2257968 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
2257913 CTGTAGAATG
2257923 ACCAAAATGCAAT-TCGAAGTATA
1 ACCAAAATGCAATCT-GAAGTATA
2257946 ACCAAAATGCAATCTGAAGTATA
1 ACCAAAATGCAATCTGAAGTATA
2257969 GTTTAGGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.22
Consensus pattern (23 bp):
ACCAAAATGCAATCTGAAGTATA
Found at i:2269507 original size:18 final size:18
Alignment explanation
Indices: 2269470--2269519 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
2269460 GAGGTAACTA
* * *
2269470 ATGATCCTCATCACCGTC
1 ATGATCATCATCATCATC
2269488 ATGATCATCATCATCATC
1 ATGATCATCATCATCATC
**
2269506 ATTTTCATCATCAT
1 ATGATCATCATCAT
2269520 AGTCAAGCTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.28, C:0.30, G:0.06, T:0.36
Consensus pattern (18 bp):
ATGATCATCATCATCATC
Found at i:2278443 original size:8 final size:7
Alignment explanation
Indices: 2278413--2278439 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2278403 CAATCAACGC
2278413 AAAAAAG
1 AAAAAAG
2278420 AAAAAAG
1 AAAAAAG
2278427 AAAAAAG
1 AAAAAAG
2278434 AAAAAA
1 AAAAAA
2278440 AGAATTGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:2288555 original size:22 final size:24
Alignment explanation
Indices: 2288520--2288568 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
2288510 ATGATGAAAT
2288520 AAATAATAATATAT-TAGATTTAA
1 AAATAATAATATATATAGATTTAA
2288543 AAATAA-AATATATAATAGATTTAA
1 AAATAATAATATAT-ATAGATTTAA
2288567 AA
1 AA
2288569 CATCAACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 7 0.29
23 6 0.25
24 11 0.46
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATAATAATATATATAGATTTAA
Found at i:2294366 original size:42 final size:42
Alignment explanation
Indices: 2294313--2294408 Score: 129
Period size: 42 Copynumber: 2.3 Consensus size: 42
2294303 CTATATGAAT
* * *
2294313 GGCACTAAGTGTGTAAAATTAAAATGATGATGTTGAATAATA
1 GGCACTAAGTGTGCAAAATTAAAATAATGATGTTGAATAACA
** * *
2294355 GGCACTAAGTGTGCGGAATTATAATAATGATGTTGAATAACG
1 GGCACTAAGTGTGCAAAATTAAAATAATGATGTTGAATAACA
2294397 GGCACTAAGTGT
1 GGCACTAAGTGT
2294409 ACGATACCGA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.29
Consensus pattern (42 bp):
GGCACTAAGTGTGCAAAATTAAAATAATGATGTTGAATAACA
Found at i:2301018 original size:18 final size:17
Alignment explanation
Indices: 2300964--2301031 Score: 73
Period size: 18 Copynumber: 3.8 Consensus size: 17
2300954 GTATTTAATT
*
2300964 AATTTTTAAAAATTTAA
1 AATTTTTAAAAAATTAA
**
2300981 AATTTCAAAAAATTATTAA
1 AATTTTTAAAAA--ATTAA
2301000 AACTTTTTAAAAAATTAA
1 AA-TTTTTAAAAAATTAA
2301018 AATTATTTAAAAAA
1 AATT-TTTAAAAAA
2301032 AATATATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
17 12 0.29
18 16 0.38
19 6 0.14
20 8 0.19
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
AATTTTTAAAAAATTAA
Found at i:2314054 original size:44 final size:44
Alignment explanation
Indices: 2313991--2314109 Score: 175
Period size: 44 Copynumber: 2.7 Consensus size: 44
2313981 AAACTCATTG
* * *
2313991 TTATCTGATCAGTGACAAGTGATGAGTGATTGTTTTAGTTACAC
1 TTATCTGATCAGTGACAAGTGATGAGTGATAGCTTTAGCTACAC
*
2314035 TTATCTGATCAGTGACAAGTGATGAGTGGTAGCTTTAGCTACAC
1 TTATCTGATCAGTGACAAGTGATGAGTGATAGCTTTAGCTACAC
* **
2314079 TTATCTGATCAGGGACAAGTGACAAGTGATA
1 TTATCTGATCAGTGACAAGTGATGAGTGATA
2314110 AATGTGACCC
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 67 1.00
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.33
Consensus pattern (44 bp):
TTATCTGATCAGTGACAAGTGATGAGTGATAGCTTTAGCTACAC
Found at i:2316988 original size:11 final size:11
Alignment explanation
Indices: 2316972--2316996 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2316962 TCTATCTTGG
2316972 TACCTCTATGT
1 TACCTCTATGT
2316983 TACCTCTATGT
1 TACCTCTATGT
2316994 TAC
1 TAC
2316997 GTTCACCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.28, G:0.08, T:0.44
Consensus pattern (11 bp):
TACCTCTATGT
Found at i:2323779 original size:20 final size:21
Alignment explanation
Indices: 2323756--2323798 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2323746 TCAATTCGAT
2323756 TTAAAAAAAT-AAATTTTAAA
1 TTAAAAAAATCAAATTTTAAA
** *
2323776 TTAACTAAATCGAATTTTAAA
1 TTAAAAAAATCAAATTTTAAA
2323797 TT
1 TT
2323799 TATTTGATGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (21 bp):
TTAAAAAAATCAAATTTTAAA
Found at i:2325962 original size:21 final size:21
Alignment explanation
Indices: 2325936--2325979 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
2325926 GAAATTTTGA
2325936 ATCGATTTAATATATTAT-TAT
1 ATCGATTTAA-ATATTATATAT
2325957 ATCGATTTAAATATTATATAT
1 ATCGATTTAAATATTATATAT
2325978 AT
1 AT
2325980 TAATATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.50
Consensus pattern (21 bp):
ATCGATTTAAATATTATATAT
Done.