Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008653.1 Hibiscus syriacus cultivar Beakdansim tig00111644_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1778368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 9
Found at i:257499 original size:45 final size:43
Alignment explanation
Indices: 257289--257499 Score: 164
Period size: 40 Copynumber: 5.1 Consensus size: 43
257279 CATTTTGAAA
* *
257289 ATATATAATATATAGTTTTTAAAACATTTTGAAAACAT-T--T
1 ATATATAATATATATTTTTTAAAACATTTTGAAAATATATAAT
* * * *
257329 ATATATTATATA-ATTTGTTTAAAACGTTTT-TACA-A-A-AA-
1 ATATATAATATATATTT-TTTAAAACATTTTGAAAATATATAAT
* * *
257367 A-ATATAATATATAGTTTTCAAAACATTTTTGAATATATATATAT
1 ATATATAATATATATTTTTTAAAACA-TTTTGAAAATATATA-AT
* *
257411 ATATATATTATATAGTTTTTTTAAACATTTTG--AA-A-ATAA-
1 ATATATAATATATA-TTTTTTAAAACATTTTGAAAATATATAAT
257450 ATATATAATATATATTTTTTGAAAAACATTTTGAAAATATATAAT
1 ATATATAATATATATTTTTT--AAAACATTTTGAAAATATATAAT
257495 ATATA
1 ATATA
257500 ATTTTTAAAA
Statistics
Matches: 132, Mismatches: 18, Indels: 37
0.71 0.10 0.20
Matches are distributed among these distances:
37 16 0.12
38 15 0.11
39 20 0.15
40 35 0.27
41 4 0.03
42 4 0.03
43 3 0.02
44 5 0.04
45 21 0.16
46 9 0.07
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (43 bp):
ATATATAATATATATTTTTTAAAACATTTTGAAAATATATAAT
Found at i:257515 original size:34 final size:36
Alignment explanation
Indices: 257448--257527 Score: 110
Period size: 36 Copynumber: 2.2 Consensus size: 36
257438 TTTTGAAAAT
*
257448 AAATATATAATATATATTTTTTGAAAAACA-TTTTGA
1 AAATATATAATATATAATTTTT-AAAAACATTTTTGA
*
257484 AAATATATAATATATAATTTTT-AAAATATTTTTGA
1 AAATATATAATATATAATTTTTAAAAACATTTTTGA
257519 AAATTATAT
1 AAA-TATAT
257528 GGTTTTTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
34 5 0.12
35 9 0.22
36 26 0.65
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (36 bp):
AAATATATAATATATAATTTTTAAAAACATTTTTGA
Found at i:257516 original size:84 final size:80
Alignment explanation
Indices: 257260--257521 Score: 240
Period size: 84 Copynumber: 3.2 Consensus size: 80
257250 TTATTTATTT
*
257260 ATTTATAT-ATTTTTGAAAACATTTTG----AAAATATATAATATATAGTTTTTAAAACATTTTG
1 ATTTATATAATTTTTTAAAACATTTTGACAAAAAATATATAATATATA-TTTTTAAAACATTTTG
*
257320 AAAACAT-T-TATAT-
65 AAAATATATATATATA
* * *
257333 A-TTATATAATTTGTTTAAAACGTTTTTACAAAAAA-ATATAATATATAGTTTTCAAAACATTTT
1 ATTTATATAATTT-TTTAAAACATTTTGACAAAAAATATATAATATATA-TTTTTAAAACA-TTT
*
257396 TGAATATATATATATATA
63 TGAAAATATATATATATA
* *
257414 TATATTATATAGTTTTTTTAAACATTTTGA-AAATAAATATATAATATATATTTTTTGAAAAACA
1 -AT-TTATATAATTTTTTAAAACATTTTGACAAA-AAATATATAATATATA-TTTTT--AAAACA
257478 TTTTGAAAATATATAATATATA
60 TTTTGAAAATATAT-ATATATA
* *
257500 ATTTTTAAAATATTTTTGAAAA
1 ATTTATATAAT-TTTTT-AAAA
257522 TTATATGGTT
Statistics
Matches: 152, Mismatches: 17, Indels: 27
0.78 0.09 0.14
Matches are distributed among these distances:
72 6 0.04
73 5 0.03
74 11 0.07
77 23 0.15
78 14 0.09
79 1 0.01
80 5 0.03
82 4 0.03
83 15 0.10
84 32 0.21
85 20 0.13
86 16 0.11
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.46
Consensus pattern (80 bp):
ATTTATATAATTTTTTAAAACATTTTGACAAAAAATATATAATATATATTTTTAAAACATTTTGA
AAATATATATATATA
Found at i:257538 original size:17 final size:15
Alignment explanation
Indices: 257509--257593 Score: 66
Period size: 17 Copynumber: 5.5 Consensus size: 15
257499 AATTTTTAAA
*
257509 ATATTTTTGAAAATT
1 ATATTTTTTAAAATT
**
257524 ATATGGTTTTTAAAAAA
1 ATAT--TTTTTAAAATT
*
257541 ATATTTTTGAAAATTAT
1 ATATTTTTTAAAA-T-T
*
257558 ATATTTTTTAAAAAT
1 ATATTTTTTAAAATT
*
257573 AT-TTTTTTAAAA-A
1 ATATTTTTTAAAATT
257586 ATATTTTT
1 ATATTTTT
257594 GGAAATTTAT
Statistics
Matches: 56, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
13 2 0.04
14 15 0.27
15 15 0.27
17 24 0.43
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (15 bp):
ATATTTTTTAAAATT
Found at i:257547 original size:32 final size:32
Alignment explanation
Indices: 257506--257585 Score: 115
Period size: 32 Copynumber: 2.5 Consensus size: 32
257496 TATAATTTTT
*
257506 AAAATATTTTTGAAAATTATATGGTTTTTAAA
1 AAAATATTTTTGAAAATTATATAGTTTTTAAA
*
257538 AAAATATTTTTGAAAATTATATATTTTTTAAA
1 AAAATATTTTTGAAAATTATATAGTTTTTAAA
* * *
257570 AATATTTTTTTAAAAA
1 AAAATATTTTTGAAAA
257586 ATATTTTTGG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (32 bp):
AAAATATTTTTGAAAATTATATAGTTTTTAAA
Found at i:257553 original size:15 final size:15
Alignment explanation
Indices: 257506--257594 Score: 65
Period size: 15 Copynumber: 5.8 Consensus size: 15
257496 TATAATTTTT
257506 AAAATATTTTTGAAA
1 AAAATATTTTTGAAA
** *
257521 ATTATATGGTTTTTAAA
1 AAAATAT--TTTTGAAA
257538 AAAATATTTTTGAAA
1 AAAATATTTTTGAAA
* *
257553 ATTATATATTTTT--TA
1 A--AAATATTTTTGAAA
**
257568 AAAATATTTTTTTAA
1 AAAATATTTTTGAAA
257583 AAAATATTTTTG
1 AAAATATTTTTG
257595 GAAATTTATA
Statistics
Matches: 57, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
13 9 0.16
15 27 0.47
17 21 0.37
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.51
Consensus pattern (15 bp):
AAAATATTTTTGAAA
Found at i:257672 original size:3 final size:3
Alignment explanation
Indices: 257664--257725 Score: 56
Period size: 3 Copynumber: 20.7 Consensus size: 3
257654 GTTTTTATAT
** * *
257664 TTA TTA TTA TTA TTA TTA TTTA TTA GCA CTA TTA TTA TTA ATA TT-
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
257709 TTA TTA CTTA TT- TTA TT
1 TTA TTA -TTA TTA TTA TT
257726 TTAATTTTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
2 4 0.08
3 38 0.79
4 6 0.12
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:257685 original size:19 final size:19
Alignment explanation
Indices: 257661--257721 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
257651 ATAGTTTTTA
257661 TATTTATTATTATTATTAT
1 TATTTATTATTATTATTAT
** *
257680 TATTTATTAGCACTATTAT
1 TATTTATTATTATTATTAT
*
257699 TA-TTAATATT-TTATTACT
1 TATTTATTATTATTATTA-T
257717 TATTT
1 TATTT
257722 TATTTTAATT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
17 5 0.15
18 8 0.24
19 20 0.61
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (19 bp):
TATTTATTATTATTATTAT
Found at i:258968 original size:4 final size:4
Alignment explanation
Indices: 258959--258994 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
258949 TTTGGTCCCT
* *
258959 TTTA TTTA TTTA TTTA TTTA ATTA TTTA TTCA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
258995 CCTATACATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (4 bp):
TTTA
Found at i:259353 original size:8 final size:8
Alignment explanation
Indices: 259342--259378 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
259332 AGGGATAGCC
259342 ATTTTTTT
1 ATTTTTTT
*
259350 ATTTTATT
1 ATTTTTTT
259358 ATTTTTTT
1 ATTTTTTT
259366 ATTATTTTT
1 ATT-TTTTT
259375 ATTT
1 ATTT
259379 ACAATATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
8 18 0.69
9 8 0.31
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (8 bp):
ATTTTTTT
Found at i:259478 original size:24 final size:22
Alignment explanation
Indices: 259425--259478 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 22
259415 ATTATTATTA
259425 GTATTA-TTAATTTTCTTTTTT
1 GTATTATTTAATTTTCTTTTTT
*
259446 GGATGTATTTAATTTTCATTTTTT
1 GTAT-TATTTAATTTTC-TTTTTT
259470 GTTATTATT
1 G-TATTATT
259479 ATTTTTAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 3 0.11
22 2 0.07
23 9 0.33
24 11 0.41
25 2 0.07
ACGTcount: A:0.20, C:0.04, G:0.09, T:0.67
Consensus pattern (22 bp):
GTATTATTTAATTTTCTTTTTT
Found at i:259484 original size:23 final size:21
Alignment explanation
Indices: 259425--259484 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 21
259415 ATTATTATTA
259425 GTATTATTAATTTTCTTTTTT
1 GTATTATTAATTTTCTTTTTT
*
259446 GGATGTATTTAATTTTCATTTTTT
1 GTAT-TA-TTAATTTTC-TTTTTT
*
259470 GTTATTATTATTTTT
1 G-TATTATTAATTTT
259485 AACATTTTCG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
21 3 0.09
22 2 0.06
23 16 0.50
24 9 0.28
25 2 0.06
ACGTcount: A:0.20, C:0.03, G:0.08, T:0.68
Consensus pattern (21 bp):
GTATTATTAATTTTCTTTTTT
Found at i:262677 original size:20 final size:20
Alignment explanation
Indices: 262667--262707 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
262657 AATGTACCTA
262667 TTATGATTTTAAGGTAATAT
1 TTATGATTTTAAGGTAATAT
262687 TTATGATTTTAAGGTAATAT
1 TTATGATTTTAAGGTAATAT
262707 T
1 T
262708 GGGACACACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (20 bp):
TTATGATTTTAAGGTAATAT
Found at i:268866 original size:5 final size:5
Alignment explanation
Indices: 268848--268890 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
268838 TGATCGGCCT
* * *
268848 GACCC GACCT GACTC GACTC GA-CC GACCC GACCC GACCC GACC
1 GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACC
268891 GTTAACTGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
4 3 0.09
5 30 0.91
ACGTcount: A:0.21, C:0.51, G:0.21, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:268875 original size:19 final size:19
Alignment explanation
Indices: 268851--268891 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
268841 TCGGCCTGAC
* * *
268851 CCGACCTGACTCGACTCGA
1 CCGACCCGACCCGACCCGA
268870 CCGACCCGACCCGACCCGA
1 CCGACCCGACCCGACCCGA
268889 CCG
1 CCG
268892 TTAACTGTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.20, C:0.51, G:0.22, T:0.07
Consensus pattern (19 bp):
CCGACCCGACCCGACCCGA
Found at i:268918 original size:6 final size:7
Alignment explanation
Indices: 268887--268924 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
268877 GACCCGACCC
268887 GACCGTT
1 GACCGTT
* *
268894 AACTGTT
1 GACCGTT
268901 GACCGTT
1 GACCGTT
268908 GACCG-T
1 GACCGTT
268914 GACCGTT
1 GACCGTT
268921 GACC
1 GACC
268925 TCCTTTGACC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.18, C:0.29, G:0.26, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:268918 original size:13 final size:13
Alignment explanation
Indices: 268900--268924 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
268890 CGTTAACTGT
268900 TGACCGTTGACCG
1 TGACCGTTGACCG
268913 TGACCGTTGACC
1 TGACCGTTGACC
268925 TCCTTTGACC
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:0.16, C:0.32, G:0.28, T:0.24
Consensus pattern (13 bp):
TGACCGTTGACCG
Found at i:272850 original size:81 final size:80
Alignment explanation
Indices: 272752--272913 Score: 245
Period size: 81 Copynumber: 2.0 Consensus size: 80
272742 AAAGATAACG
* * *
272752 AGATATAATAATGAGTGATAAATAATTACTTTCATCACGTTAT-TTTTTAAATTAAATTATCTTA
1 AGATATAATAATGAGTGATAAATAATTAATTTCATCACGTTATCTTTAT-AA-TAAATTATCTCA
272816 TAAAATCATCATATAAA
64 TAAAATCATCATATAAA
* **
272833 AGATATAATAATGAGTGATAAATGATTAATTTCATCACGTTATCTTTATAATGGATTATCTCATA
1 AGATATAATAATGAGTGATAAATAATTAATTTCATCACGTTATCTTTATAATAAATTATCTCATA
272898 AAATCATCATATAAA
66 AAATCATCATATAAA
272913 A
1 A
272914 ATAAGAGCTA
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
80 27 0.36
81 43 0.58
82 4 0.05
ACGTcount: A:0.44, C:0.09, G:0.08, T:0.39
Consensus pattern (80 bp):
AGATATAATAATGAGTGATAAATAATTAATTTCATCACGTTATCTTTATAATAAATTATCTCATA
AAATCATCATATAAA
Found at i:273200 original size:20 final size:20
Alignment explanation
Indices: 273156--273453 Score: 129
Period size: 20 Copynumber: 14.6 Consensus size: 20
273146 AATGACCAAT
273156 AAAATCGCAACGCGA--TAG
1 AAAATCGCAACGCGATTTAG
273174 AAAAATCGCAACGCGATTTAG
1 -AAAATCGCAACGCGATTTAG
** ***
273195 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
273215 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
273235 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
273256 AAGCTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* *
273279 AAAATCGCAATGCGATTCA-
1 AAAATCGCAACGCGATTTAG
* * *
273298 ATCAATCGCAATGCGATTGAG
1 A-AAATCGCAACGCGATTTAG
* * *
273319 AGAGTTGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
* * *
273339 AAGAGAATCGCAATGCGACTGAG
1 -A-A-AATCGCAACGCGATTTAG
* * * * *
273362 AGATTCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * * *
273382 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * * *
273402 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
*
273422 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
273442 AAAATCGCAACG
1 AAAATCGCAACG
273454 TTAAAAAGAA
Statistics
Matches: 223, Mismatches: 41, Indels: 29
0.76 0.14 0.10
Matches are distributed among these distances:
19 16 0.07
20 160 0.72
21 19 0.09
22 1 0.00
23 27 0.12
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:273419 original size:60 final size:63
Alignment explanation
Indices: 273260--273453 Score: 225
Period size: 63 Copynumber: 3.1 Consensus size: 63
273250 GCTTCCAAGC
* * * * * *
273260 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTCA-ATCAATCGCAATGCGATTGAGAGAG
1 TCGCAACGCGATCTAGAAGAGAATCGCAATGCGACTGAGA-GAATCGCAATGCGATTGAGAGAA
* * * *
273323 TTGCAACGCGATTTAGAAGAGAATCGCAATGCGACTGAGAGATTCGCAATGCGACTGAGAGAA
1 TCGCAACGCGATCTAGAAGAGAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAA
* * * *
273386 TCGCAATGCGA-CT-G-AGAGAATCGCAATGCGACTGAGAGAATCGCAACGCGATTTAGAAAA
1 TCGCAACGCGATCTAGAAGAGAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAA
273446 TCGCAACG
1 TCGCAACG
273454 TTAAAAAGAA
Statistics
Matches: 113, Mismatches: 17, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
60 48 0.42
61 1 0.01
62 1 0.01
63 62 0.55
64 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.26, T:0.19
Consensus pattern (63 bp):
TCGCAACGCGATCTAGAAGAGAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAA
Found at i:273448 original size:40 final size:40
Alignment explanation
Indices: 273301--273451 Score: 185
Period size: 40 Copynumber: 3.7 Consensus size: 40
273291 CGATTCAATC
* * * *
273301 AATCGCAATGCGATTGAGAGAGTTGCAACGCGATTTAGAAGAG
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGA-CT-G-AGAG
* *
273344 AATCGCAATGCGACTGAGAGATTCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGACTGAGAG
*
273384 AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGACTGAGAG
* * *
273424 AATCGCAACGCGATTTAGAAAATCGCAA
1 AATCGCAATGCGATTGAGAGAATCGCAA
273452 CGTTAAAAAG
Statistics
Matches: 98, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
40 67 0.68
41 1 0.01
42 1 0.01
43 29 0.30
ACGTcount: A:0.36, C:0.19, G:0.28, T:0.18
Consensus pattern (40 bp):
AATCGCAATGCGATTGAGAGAATCGCAATGCGACTGAGAG
Found at i:273463 original size:20 final size:20
Alignment explanation
Indices: 273440--273483 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
273430 AACGCGATTT
*
273440 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGATAAAA
*
273460 AGAAAATCGCAACGATCAAA
1 AGAAAATCGCAACGATAAAA
273480 AGAA
1 AGAA
273484 TAGTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.57, C:0.16, G:0.16, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGATAAAA
Found at i:273468 original size:60 final size:60
Alignment explanation
Indices: 273156--273471 Score: 181
Period size: 60 Copynumber: 5.2 Consensus size: 60
273146 AATGACCAAT
*
273156 AAAATCGCAACGCGA-T-AGAAAAATCGCAACGCGATTTAGAAAATCGCAACGTTAAAAAG
1 AAAATCGCAATGCGACTGAG-AAAATCGCAACGCGATTTAGAAAATCGCAACGTTAAAAAG
* * ** * ** ** * *
273215 AAAATCGCAACG-GTCAAAAGAAAATCGCAACGCGAGCTTCCAAGCTCGCAACGCGATTTAGAAG
1 AAAATCGCAATGCGAC-TGAGAAAATCGCAACGCGA-TTTAGAAAATCGCAA--CG-TTAAAAAG
* * * * * * * * * *
273279 AAAATCGCAATGCGATTCA-ATCAATCGCAATGCGATTGAGAGAGTTGCAACGCGATTTAGAAG
1 AAAATCGCAATGCGACTGAGA-AAATCGCAACGCGATTTAGAAAATCGCAA--CG-TTAAAAAG
* * * * * * * * ** ***
273342 AGAATCGCAATGCGACTGAGAGATTCGCAATGCGACTGAGAGAATCGCAATGCGACTGAG
1 AAAATCGCAATGCGACTGAGAAAATCGCAACGCGATTTAGAAAATCGCAACGTTAAAAAG
* *
273402 AGAATCGCAATGCGACTGAGAGAATCGCAACGCGATTTAGAAAATCGCAACGTTAAAAAG
1 AAAATCGCAATGCGACTGAGAAAATCGCAACGCGATTTAGAAAATCGCAACGTTAAAAAG
273462 AAAATCGCAA
1 AAAATCGCAA
273472 CGATCAAAAG
Statistics
Matches: 196, Mismatches: 51, Indels: 19
0.74 0.19 0.07
Matches are distributed among these distances:
58 1 0.01
59 12 0.06
60 75 0.38
61 13 0.07
63 63 0.32
64 31 0.16
65 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.23, T:0.17
Consensus pattern (60 bp):
AAAATCGCAATGCGACTGAGAAAATCGCAACGCGATTTAGAAAATCGCAACGTTAAAAAG
Found at i:273572 original size:6 final size:5
Alignment explanation
Indices: 273565--273647 Score: 105
Period size: 5 Copynumber: 15.6 Consensus size: 5
273555 CGTATTACCA
273565 CGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGA-C CGACC CGACC
1 CGACC -CGACC -CGACC -CGACC -CGACC -CGACC -CGACC CGACC CGACC
273615 CGACC CGACC CGACC CGACC CGACC CGACC CGA
1 CGACC CGACC CGACC CGACC CGACC CGACC CGA
273648 GACGGCGGCG
Statistics
Matches: 76, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
4 3 0.04
5 40 0.53
6 33 0.43
ACGTcount: A:0.27, C:0.54, G:0.19, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:274344 original size:6 final size:6
Alignment explanation
Indices: 274328--274383 Score: 105
Period size: 6 Copynumber: 9.5 Consensus size: 6
274318 TCTCGTCTCG
274328 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
274375 GGTCGT GGT
1 GGTCGT GGT
274384 AATACGTGTC
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.10
6 45 0.90
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:274486 original size:20 final size:20
Alignment explanation
Indices: 274461--274504 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
274451 TTTTTAACTA
*
274461 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
274481 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
274501 TTCT
1 TTCT
274505 AAATCGCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:274514 original size:20 final size:20
Alignment explanation
Indices: 274491--274788 Score: 152
Period size: 20 Copynumber: 14.6 Consensus size: 20
274481 TTCTTTTTAA
274491 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
274511 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
274531 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
274551 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
274571 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
* * *
274594 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * **
274614 CATTGCGATTCTAAAAATCG
1 CGTTGCGATTTTCTAAATCG
* *** *
274634 CATTGCGATTCAATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
274654 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
274677 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
274698 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
274716 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
274738 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
274758 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
274777 CGTTGCGATTTT
1 CGTTGCGATTTT
274789 ATTGGTCATT
Statistics
Matches: 223, Mismatches: 44, Indels: 23
0.77 0.15 0.08
Matches are distributed among these distances:
18 2 0.01
19 17 0.08
20 157 0.70
21 14 0.06
22 6 0.03
23 27 0.12
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:274537 original size:40 final size:40
Alignment explanation
Indices: 274493--274684 Score: 222
Period size: 40 Copynumber: 4.7 Consensus size: 40
274483 CTTTTTAACG
274493 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
* * * * *
274533 TTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
*
274573 TTGCGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCA
1 TTGCGA--TT-TTCTAAATCGCGTTGCGATTCTCTCAATCGCA
* ** * **
274616 TTGCGATTCTAAAAATCGCATTGCGATTCAATCAATCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
274656 TTGCGATTTTCTTCTAAATCGCGTTGCGA
1 TTGCGA--TT-TTCTAAATCGCGTTGCGA
274685 ACTTGGAAGC
Statistics
Matches: 124, Mismatches: 22, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
40 72 0.58
41 2 0.02
42 4 0.03
43 46 0.37
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.36
Consensus pattern (40 bp):
TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
Found at i:274609 original size:83 final size:83
Alignment explanation
Indices: 274501--274684 Score: 296
Period size: 83 Copynumber: 2.2 Consensus size: 83
274491 CGTTGCGATT
* *** * **
274501 TTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTC
1 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTAAAAATCGCATTGCGATTCAATC
*
274566 AGTCGCATTGCGATTTTC
66 AATCGCATTGCGATTTTC
274584 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTAAAAATCGCATTGCGATTCAATC
1 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTAAAAATCGCATTGCGATTCAATC
274649 AATCGCATTGCGATTTTC
66 AATCGCATTGCGATTTTC
274667 TTCTAAATCGCGTTGCGA
1 TTCTAAATCGCGTTGCGA
274685 ACTTGGAAGC
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
83 93 1.00
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.35
Consensus pattern (83 bp):
TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTAAAAATCGCATTGCGATTCAATC
AATCGCATTGCGATTTTC
Found at i:274677 original size:63 final size:59
Alignment explanation
Indices: 274505--274663 Score: 174
Period size: 63 Copynumber: 2.6 Consensus size: 59
274495 GCGATTTTCT
* * * **
274505 AAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCT
1 AAATCGCATTGCGATTC-ATCAATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTAA
* * * * *
274565 CAGTCGCATTGCGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTAA
1 AAATCGCATTGCGA--TTCATC--AATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTAA
274628 AAATCGCATTGCGATTCAATCAATCGCATTGCGATT
1 AAATCGCATTGCGATTC-ATCAATCGCATTGCGATT
274664 TTCTTCTAAA
Statistics
Matches: 80, Mismatches: 14, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
60 24 0.30
61 5 0.06
62 5 0.06
63 46 0.57
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.34
Consensus pattern (59 bp):
AAATCGCATTGCGATTCATCAATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTAA
Found at i:274778 original size:19 final size:20
Alignment explanation
Indices: 274738--274788 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
274728 TTCTTTTTAA
*
274738 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
274758 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
274777 CGTTGCGATTTT
1 CGTTGCGATTTT
274789 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:275341 original size:19 final size:19
Alignment explanation
Indices: 275317--275389 Score: 85
Period size: 19 Copynumber: 3.6 Consensus size: 19
275307 GATGGTAATT
*
275317 TTTATTTATTTATTTTGGA
1 TTTATTTATTTATTTTGAA
275336 TTTATTTATTTATTTTGAA
1 TTTATTTATTTATTTTGAA
275355 TTTATGTATCCATTTATTTAT-AA
1 TTTAT-T-T--ATTTATTT-TGAA
275378 TTTATTTATTTA
1 TTTATTTATTTA
275390 GTTATTTTGG
Statistics
Matches: 48, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
19 28 0.58
20 1 0.02
21 2 0.04
22 1 0.02
23 15 0.31
24 1 0.02
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (19 bp):
TTTATTTATTTATTTTGAA
Found at i:275394 original size:23 final size:23
Alignment explanation
Indices: 275335--275417 Score: 89
Period size: 23 Copynumber: 3.7 Consensus size: 23
275325 TTTATTTTGG
275335 ATTTATTTATTTATTTTGAATTT
1 ATTTATTTATTTATTTTGAATTT
* **
275358 ATGTATCCATTTATTTAT-AATTT
1 ATTTATTTATTTATTT-TGAATTT
* *
275381 ATTTATTTAGTTATTTTGGATTT
1 ATTTATTTATTTATTTTGAATTT
*
275404 ATTT-CTTATTTATT
1 ATTTATTTATTTATT
275418 CCACTCGAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
22 9 0.19
23 38 0.79
24 1 0.02
ACGTcount: A:0.25, C:0.04, G:0.06, T:0.65
Consensus pattern (23 bp):
ATTTATTTATTTATTTTGAATTT
Found at i:275437 original size:4 final size:4
Alignment explanation
Indices: 275317--275417 Score: 59
Period size: 4 Copynumber: 26.5 Consensus size: 4
275307 GATGGTAATT
** ** *
275317 TTTA TTTA TTTA TTT- TGGA TTTA TTTA TTTA TTT- TGAA TTTA TGTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
** * * **
275363 TCCA TTTA TTTA -TAA TTTA TTTA TTTA GTTA TTT- TGGA TTTA TTT-
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
*
275408 CTTA TTTA TT
1 TTTA TTTA TT
275418 CCACTCGAAT
Statistics
Matches: 69, Mismatches: 23, Indels: 10
0.68 0.23 0.10
Matches are distributed among these distances:
3 7 0.10
4 62 0.90
ACGTcount: A:0.24, C:0.03, G:0.07, T:0.66
Consensus pattern (4 bp):
TTTA
Found at i:275452 original size:23 final size:23
Alignment explanation
Indices: 275426--275483 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 23
275416 TTCCACTCGA
275426 ATTTATTTATTTCA-AATTTATTT
1 ATTTATTTATTT-ATAATTTATTT
* *
275449 ATTTATTTGTTTCA-AAATTATTT
1 ATTTATTTATTT-ATAATTTATTT
*
275472 ATTTATTCATTT
1 ATTTATTTATTT
275484 GAAGGGATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (23 bp):
ATTTATTTATTTATAATTTATTT
Found at i:277700 original size:17 final size:18
Alignment explanation
Indices: 277654--277706 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
277644 TCAATTTTTA
*
277654 AATTTTGTTTAAATTATT
1 AATTTTCTTTAAATTATT
***
277672 AATCAACTTTAAATTATT
1 AATTTTCTTTAAATTATT
*
277690 -ATTTTCTTTAAGTTATT
1 AATTTTCTTTAAATTATT
277707 TTTGAACAAT
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.57
Consensus pattern (18 bp):
AATTTTCTTTAAATTATT
Found at i:281418 original size:19 final size:19
Alignment explanation
Indices: 281394--281481 Score: 60
Period size: 19 Copynumber: 4.8 Consensus size: 19
281384 TCGAAATGGA
281394 GTGCATGGATGCACT-CAGG
1 GTGCATGGATGCACTGCA-G
**
281413 GTGCATCAATGCA---CA-
1 GTGCATGGATGCACTGCAG
* *
281428 GTGCATGGATGCAATGTAG
1 GTGCATGGATGCACTGCAG
* *
281447 GTGCATGGATGCATTGCGGG
1 GTGCATGGATGCACTGC-AG
*
281467 GTGCATGGATTCACT
1 GTGCATGGATGCACT
281482 TTGATACCCT
Statistics
Matches: 54, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
15 11 0.20
17 2 0.04
18 1 0.02
19 26 0.48
20 14 0.26
ACGTcount: A:0.23, C:0.18, G:0.34, T:0.25
Consensus pattern (19 bp):
GTGCATGGATGCACTGCAG
Found at i:281471 original size:20 final size:19
Alignment explanation
Indices: 281428--281476 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
281418 TCAATGCACA
*
281428 GTGCATGGATGCAATGTAG
1 GTGCATGGATGCAATGGAG
* *
281447 GTGCATGGATGCATTGCGGG
1 GTGCATGGATGCAATG-GAG
281467 GTGCATGGAT
1 GTGCATGGAT
281477 TCACTTTGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.20, C:0.12, G:0.41, T:0.27
Consensus pattern (19 bp):
GTGCATGGATGCAATGGAG
Found at i:283539 original size:19 final size:18
Alignment explanation
Indices: 283507--283553 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
283497 AATTGCATGC
*
283507 ATATC-AAAACTCAGTAT
1 ATATCAAAAAATCAGTAT
*
283524 ATATACAAAAAATCAGTGT
1 ATAT-CAAAAAATCAGTAT
*
283543 ATCTCAAAAAA
1 ATATCAAAAAA
283554 ATTTCCCAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 4 0.16
18 8 0.32
19 13 0.52
ACGTcount: A:0.53, C:0.15, G:0.06, T:0.26
Consensus pattern (18 bp):
ATATCAAAAAATCAGTAT
Found at i:284802 original size:21 final size:22
Alignment explanation
Indices: 284757--284810 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
284747 TGTATGAACA
284757 GTATCGATACCATATGGAAGAG
1 GTATCGATACCATATGGAAGAG
*
284779 GTATCGATACC-TATGTGGAG-G
1 GTATCGATACCATATG-GAAGAG
284800 GTATCGATACC
1 GTATCGATACC
284811 CGGGGGAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 16 0.53
22 14 0.47
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.26
Consensus pattern (22 bp):
GTATCGATACCATATGGAAGAG
Found at i:285914 original size:2 final size:2
Alignment explanation
Indices: 285907--286012 Score: 212
Period size: 2 Copynumber: 53.0 Consensus size: 2
285897 AGATAAAATG
285907 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
285949 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
285991 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
286013 GACTATGGGT
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 104 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:286458 original size:18 final size:18
Alignment explanation
Indices: 286435--286471 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
286425 GTTCTTAAGG
286435 AGTGGTCATTCGGGACAT
1 AGTGGTCATTCGGGACAT
286453 AGTGGTCATTCGGGACAT
1 AGTGGTCATTCGGGACAT
286471 A
1 A
286472 TGTGTTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.27
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:289880 original size:21 final size:21
Alignment explanation
Indices: 289854--289896 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
289844 GGCAAGGGGC
289854 ATCGGTACCTGTTGAGTGGGT
1 ATCGGTACCTGTTGAGTGGGT
289875 ATCGGTACCTGTTGAGTGGGT
1 ATCGGTACCTGTTGAGTGGGT
289896 A
1 A
289897 CCGATACTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.14, G:0.37, T:0.33
Consensus pattern (21 bp):
ATCGGTACCTGTTGAGTGGGT
Found at i:290081 original size:22 final size:22
Alignment explanation
Indices: 290055--290110 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
290045 ACCTAGGAAG
*
290055 GGTATCGGTACCCTATAGTAGA
1 GGTATCAGTACCCTATAGTAGA
290077 GGTATCAGTACCCTATAGTAGA
1 GGTATCAGTACCCTATAGTAGA
*
290099 GGTATCAATACC
1 GGTATCAGTACC
290111 TTGAGGTTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (22 bp):
GGTATCAGTACCCTATAGTAGA
Found at i:291611 original size:18 final size:18
Alignment explanation
Indices: 291588--291660 Score: 110
Period size: 18 Copynumber: 4.1 Consensus size: 18
291578 GTTCTTAAGG
*
291588 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGAACAT
*
291606 AGTGGTCCTTCGGAACGT
1 AGTGGTCCTTCGGAACAT
*
291624 AGTGATCCTTCGGAACAT
1 AGTGGTCCTTCGGAACAT
*
291642 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGAACAT
291660 A
1 A
291661 TGTGTTATAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 49 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTCGGAACAT
Found at i:298970 original size:32 final size:31
Alignment explanation
Indices: 298922--298999 Score: 95
Period size: 32 Copynumber: 2.5 Consensus size: 31
298912 CTTGGGGCCT
* *
298922 GAGAGCATACCCAAGAAAGTTCTCGAGGCCACG
1 GAGAGCCTACCCAAGAAAGATCTCG-GGCC-CG
*
298955 GAG-GCCTACCCAAGAAAGATCTCGGGGCCG
1 GAGAGCCTACCCAAGAAAGATCTCGGGCCCG
*
298985 TAGAGCCTACCCAAG
1 GAGAGCCTACCCAAG
299000 GGTCACATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
30 4 0.10
31 14 0.35
32 19 0.47
33 3 0.08
ACGTcount: A:0.31, C:0.29, G:0.28, T:0.12
Consensus pattern (31 bp):
GAGAGCCTACCCAAGAAAGATCTCGGGCCCG
Found at i:305708 original size:23 final size:23
Alignment explanation
Indices: 305678--305744 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
305668 CGATACCCCC
305678 TTGAAGGGGAACCGATTCCCCTT
1 TTGAAGGGGAACCGATTCCCCTT
305701 TTGAAGGGGAACCGATTCCCC-T
1 TTGAAGGGGAACCGATTCCCCTT
* * * *
305723 ATGTAGGGGAATCGATACCCCT
1 TTGAAGGGGAACCGATTCCCCT
305745 GGGGGTTCTG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
22 18 0.46
23 21 0.54
ACGTcount: A:0.24, C:0.25, G:0.27, T:0.24
Consensus pattern (23 bp):
TTGAAGGGGAACCGATTCCCCTT
Found at i:305744 original size:22 final size:21
Alignment explanation
Indices: 305662--305744 Score: 85
Period size: 22 Copynumber: 3.8 Consensus size: 21
305652 TTGGTGCAGA
*
305662 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATA-CCCCTTGAAG
*
305684 GGGAACCGATTCCCCTTTTGAAG
1 GGGAACCGATACCCC--TTGAAG
* *
305707 GGGAACCGATTCCCCTATGTAG
1 GGGAACCGATACCCCT-TGAAG
*
305729 GGGAATCGATACCCCT
1 GGGAACCGATACCCCT
305745 GGGGGTTCTG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
21 5 0.09
22 27 0.51
23 21 0.40
ACGTcount: A:0.24, C:0.28, G:0.27, T:0.22
Consensus pattern (21 bp):
GGGAACCGATACCCCTTGAAG
Found at i:308119 original size:31 final size:31
Alignment explanation
Indices: 308077--308144 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
308067 AAACATTTTG
*
308077 ATATTTCGATATAACAAATTAAGTTAAATAA
1 ATATTTAGATATAACAAATTAAGTTAAATAA
*
308108 ATATTTAGATATAACAAATTAAGTTAAATGA
1 ATATTTAGATATAACAAATTAAGTTAAATAA
308139 AT-TTTA
1 ATATTTA
308145 AGATTTTCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 4 0.11
31 31 0.89
ACGTcount: A:0.50, C:0.04, G:0.07, T:0.38
Consensus pattern (31 bp):
ATATTTAGATATAACAAATTAAGTTAAATAA
Found at i:308177 original size:13 final size:13
Alignment explanation
Indices: 308159--308191 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
308149 TTTCTAAGTA
308159 TATTCGATATAAT
1 TATTCGATATAAT
308172 TATTCGATATAAT
1 TATTCGATATAAT
308185 TATTCGA
1 TATTCGA
308192 ATATCAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.45
Consensus pattern (13 bp):
TATTCGATATAAT
Found at i:309501 original size:18 final size:18
Alignment explanation
Indices: 309478--309522 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
309468 TCGGATACCA
* *
309478 AGAAACCAAATTTACTTC
1 AGAAACCAAACTTAATTC
* *
309496 AGAAACTAAACTTAATTT
1 AGAAACCAAACTTAATTC
309514 AGAAACCAA
1 AGAAACCAA
309523 CTTGAATATG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.51, C:0.18, G:0.07, T:0.24
Consensus pattern (18 bp):
AGAAACCAAACTTAATTC
Found at i:309689 original size:30 final size:30
Alignment explanation
Indices: 309655--309744 Score: 162
Period size: 30 Copynumber: 3.0 Consensus size: 30
309645 TTTGGTCAAA
* *
309655 GTCAACGGTTTGACTCGGTCAAAGTCAACG
1 GTCAATGGGTTGACTCGGTCAAAGTCAACG
309685 GTCAATGGGTTGACTCGGTCAAAGTCAACG
1 GTCAATGGGTTGACTCGGTCAAAGTCAACG
309715 GTCAATGGGTTGACTCGGTCAAAGTCAACG
1 GTCAATGGGTTGACTCGGTCAAAGTCAACG
309745 AGTTGACCCA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 58 1.00
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (30 bp):
GTCAATGGGTTGACTCGGTCAAAGTCAACG
Found at i:309705 original size:17 final size:17
Alignment explanation
Indices: 309683--309736 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
309673 TCAAAGTCAA
309683 CGGTCAATGGGTTGACT
1 CGGTCAATGGGTTGACT
* * *
309700 CGGTCAA--AG-TCA-A
1 CGGTCAATGGGTTGACT
309713 CGGTCAATGGGTTGACT
1 CGGTCAATGGGTTGACT
309730 CGGTCAA
1 CGGTCAA
309737 AGTCAACGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 8
0.66 0.15 0.20
Matches are distributed among these distances:
13 7 0.26
14 2 0.07
15 2 0.07
16 2 0.07
17 14 0.52
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.24
Consensus pattern (17 bp):
CGGTCAATGGGTTGACT
Found at i:309762 original size:13 final size:14
Alignment explanation
Indices: 309744--309781 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
309734 CAAAGTCAAC
*
309744 GAGTTGAC-CCAGT
1 GAGTTGACTCAAGT
*
309757 GAGTTGACTCAATT
1 GAGTTGACTCAAGT
309771 GAGTTGACTCA
1 GAGTTGACTCA
309782 GAGATAGGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (14 bp):
GAGTTGACTCAAGT
Found at i:311407 original size:26 final size:26
Alignment explanation
Indices: 311350--311401 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
311340 AATAATTTCC
*
311350 CATAGTTTTGTGGTAATCTAAAAGTT
1 CATAGTTTTGTGGTAATCCAAAAGTT
311376 CATAGTTTTGTGGTAATCCAAAAGTT
1 CATAGTTTTGTGGTAATCCAAAAGTT
311402 TTTAGTATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (26 bp):
CATAGTTTTGTGGTAATCCAAAAGTT
Found at i:314902 original size:19 final size:20
Alignment explanation
Indices: 314855--314908 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
314845 AAACTTCAAT
* *
314855 GAAAGTTTCGAAACTCTTGA
1 GAAAGTTTCAAAACTATTGA
*
314875 GATAGTTTCAAAACTATTG-
1 GAAAGTTTCAAAACTATTGA
314894 GAAAGTTTCAAAACT
1 GAAAGTTTCAAAACT
314909 TTTTGGGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (20 bp):
GAAAGTTTCAAAACTATTGA
Found at i:318086 original size:19 final size:18
Alignment explanation
Indices: 318016--318088 Score: 51
Period size: 19 Copynumber: 3.9 Consensus size: 18
318006 CATTGGATCC
318016 AAAGTATC-AAACTTTAA
1 AAAGTATCGAAACTTTAA
* *
318033 TGAAAGTTTCGAAACTCTTGAG
1 --AAAGTATCGAAACT-TT-AA
* *
318055 ATAGTTTCG-AACTATTAA
1 AAAGTATCGAAACT-TTAA
318073 AAAGTATCGAAACTTT
1 AAAGTATCGAAACTTT
318089 TTAGGAAACT
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
18 10 0.23
19 17 0.40
20 13 0.30
21 2 0.05
22 1 0.02
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (18 bp):
AAAGTATCGAAACTTTAA
Found at i:322346 original size:4 final size:4
Alignment explanation
Indices: 322337--322362 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
322327 GATTTGACAC
322337 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
322363 ATAGTTTATT
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):
AATA
Found at i:326768 original size:11 final size:11
Alignment explanation
Indices: 326752--326777 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
326742 ACCCGTGACA
326752 CAAATCAACCT
1 CAAATCAACCT
326763 CAAATCAACCT
1 CAAATCAACCT
326774 CAAA
1 CAAA
326778 CTCATGCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (11 bp):
CAAATCAACCT
Found at i:329189 original size:28 final size:28
Alignment explanation
Indices: 329126--329189 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
329116 TGATTTTATG
* *
329126 TCAAGGATGAACTTAAACTTATAAAAAT
1 TCAAGGACGAACCTAAACTTATAAAAAT
*
329154 TTAGAGGACGAACCTAAACTTAT-AAAAT
1 TCA-AGGACGAACCTAAACTTATAAAAAT
329182 TCCAAGGA
1 T-CAAGGA
329190 GACAAAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
28 12 0.40
29 18 0.60
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.25
Consensus pattern (28 bp):
TCAAGGACGAACCTAAACTTATAAAAAT
Found at i:343463 original size:91 final size:92
Alignment explanation
Indices: 343355--343547 Score: 300
Period size: 91 Copynumber: 2.1 Consensus size: 92
343345 AATCTTCCTT
* *
343355 GAGTGACAGCGGAATGGATCAACT-CCTCCAGATCTGATATTTCCTTCAGAAAAAGTGGAATAGG
1 GAGTGACAGCGGAATGGATCAACTCCCT-CAGATCTGATATTCCCTTCAGAAAAAGTGGAACAGG
343419 TCCCTCTTT-CAAGATTTGATATTCCCC
65 TCCCTCTTTCCAAGATTTGATATTCCCC
* *
343446 GAGTGACAGCGGAATGGATCAACTCCCTCAGATCTGATATTCCCTTCAGAAGAAGTGGAACATGT
1 GAGTGACAGCGGAATGGATCAACTCCCTCAGATCTGATATTCCCTTCAGAAAAAGTGGAACAGGT
* * *
343511 CCTTTTTTCCAAGATTTGATATTCCCT
66 CCCTCTTTCCAAGATTTGATATTCCCC
343538 GAGTGACAGC
1 GAGTGACAGC
343548 AGAACAAGTC
Statistics
Matches: 93, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
91 63 0.68
92 30 0.32
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (92 bp):
GAGTGACAGCGGAATGGATCAACTCCCTCAGATCTGATATTCCCTTCAGAAAAAGTGGAACAGGT
CCCTCTTTCCAAGATTTGATATTCCCC
Found at i:343484 original size:45 final size:45
Alignment explanation
Indices: 343355--343489 Score: 116
Period size: 45 Copynumber: 3.0 Consensus size: 45
343345 AATCTTCCTT
*
343355 GAGTGACAGCGGAATGGATCAACT-CCTCCAGATCTGATATTTCCTTC
1 GAGTGACAGCGGAATGGATCAACTCCCT-CAGATCTGATA-TTCC-CC
** * * * ** *
343402 -AGAAAAAGTGGAATAGG-TC-CCTCTTTCAAGATTTGATATTCCCC
1 GAGTGACAGCGGAAT-GGATCAACTCCCTC-AGATCTGATATTCCCC
343446 GAGTGACAGCGGAATGGATCAACTCCCTCAGATCTGATATTCCC
1 GAGTGACAGCGGAATGGATCAACTCCCTCAGATCTGATATTCCC
343490 TTCAGAAGAA
Statistics
Matches: 65, Mismatches: 17, Indels: 14
0.68 0.18 0.15
Matches are distributed among these distances:
44 3 0.05
45 33 0.51
46 27 0.42
47 2 0.03
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (45 bp):
GAGTGACAGCGGAATGGATCAACTCCCTCAGATCTGATATTCCCC
Found at i:343648 original size:224 final size:227
Alignment explanation
Indices: 343249--343669 Score: 634
Period size: 224 Copynumber: 1.9 Consensus size: 227
343239 GTTTAATTTG
*
343249 CAGATCTGATATTCCCTTCAGAATAAGCAAAACATGTCTCTCTTTTCCAAGATTTGATATTCCCT
1 CAGATCTGATATTCCCTTCAGAAGAAGCAAAACATGTCTCTCTTTTCCAAGATTTGATATTCCCT
** * *
343314 AAGTGACAGTGGAATAAGTCTGCCCCAATTCAATCTTCCTTGAGTGACAGCGGAATGGATCAACT
66 AAGTGACAGCAGAACAAGTCTGCCCCAATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACT
* * *
343379 CCTCCAGATCTGATATTTCCTTCAGAAAAAGTGGAATAGGTCCCTC-TTT-CAAGATTTGATATT
131 CCTCCAGATCTGATATTCCCTTCAGAAAAAGCGAAATAGGTCCCTCTTTTCCAAGATTTGATATT
343442 CCCCGAGTGACAGCGGAATGGATCAACTCCCT
196 CCCCGAGTGACAGCGGAATGGATCAACTCCCT
*** *
343474 CAGATCTGATATTCCCTTCAGAAGAAGTGGAACATGTC-CTTTTTTCCAAGATTTGATATTCCCT
1 CAGATCTGATATTCCCTTCAGAAGAAGCAAAACATGTCTCTCTTTTCCAAGATTTGATATTCCCT
* * *
343538 GAGTGACAGCAGAACAAGTCTGCCTCGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACT
66 AAGTGACAGCAGAACAAGTCTGCCCCAATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACT
* * * *
343603 CC-CTCATATCTGATATTCCCTTCAGAAGAAGCGAAATATGTCCCTCTTTTCCAATATTTGATAT
131 CCTC-CAGATCTGATATTCCCTTCAGAAAAAGCGAAATAGGTCCCTCTTTTCCAAGATTTGATAT
343667 TCC
195 TCC
343670 TTTTAGAAGA
Statistics
Matches: 174, Mismatches: 19, Indels: 5
0.88 0.10 0.03
Matches are distributed among these distances:
223 1 0.01
224 121 0.70
225 37 0.21
226 15 0.09
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.30
Consensus pattern (227 bp):
CAGATCTGATATTCCCTTCAGAAGAAGCAAAACATGTCTCTCTTTTCCAAGATTTGATATTCCCT
AAGTGACAGCAGAACAAGTCTGCCCCAATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACT
CCTCCAGATCTGATATTCCCTTCAGAAAAAGCGAAATAGGTCCCTCTTTTCCAAGATTTGATATT
CCCCGAGTGACAGCGGAATGGATCAACTCCCT
Found at i:343712 original size:181 final size:181
Alignment explanation
Indices: 343480--343849 Score: 571
Period size: 181 Copynumber: 2.0 Consensus size: 181
343470 CCCTCAGATC
* * * * * *
343480 TGATATTCCCTTCAGAAGAAGTGGAACATGTCCTTTTTTCCAAGATTTGATATTCCCTGAGTGAC
1 TGATATTCCCTTCAGAAGAAGCGAAACAAGTCATTCTTTCCAAGATTTGATATTCCCTAAGTGAC
* * *
343545 AGCAGAACAAGTCTGCCTCGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACTCCCTCAT
66 AGCAGAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACTCCCCCAG
*
343610 ATCTGATATTCCCTTCAGAAGAAGCGAAATATGTCCCTCTTTTCCAATATT
131 ATCTGATATTCCCTTCAGAAGAAGCGAAACATGTCCCTCTTTTCCAATATT
* *
343661 TGATATTCCTTTTAGAAGAAGCGAAACAAGTCATATCTTT-CAAGATTTGATATTCCCTAAGTGA
1 TGATATTCCCTTCAGAAGAAGCGAAACAAGTCAT-TCTTTCCAAGATTTGATATTCCCTAAGTGA
* *
343725 CAGCGGAACAAGTCTGCCCCGATTCAATCTTCCTTGAGTGACAGCGGAATGGATCAACTCCCCCA
65 CAGCAGAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACTCCCCCA
* * *
343790 GATCTGATATTCCCTTCAGAAGAAGTGGAACATGTCCCTCTTTTTCAATATT
130 GATCTGATATTCCCTTCAGAAGAAGCGAAACATGTCCCTCTTTTCCAATATT
343842 TGATATTC
1 TGATATTC
343850 ACTAAGTGAC
Statistics
Matches: 171, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
181 167 0.98
182 4 0.02
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (181 bp):
TGATATTCCCTTCAGAAGAAGCGAAACAAGTCATTCTTTCCAAGATTTGATATTCCCTAAGTGAC
AGCAGAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACTCCCCCAG
ATCTGATATTCCCTTCAGAAGAAGCGAAACATGTCCCTCTTTTCCAATATT
Found at i:344059 original size:133 final size:134
Alignment explanation
Indices: 343661--344595 Score: 1062
Period size: 133 Copynumber: 7.1 Consensus size: 134
343651 TTCCAATATT
* * * * * *
343661 TGATATTCCTTTTAGAAGAAGCGAAACAAGT-CATATCTTT-CAAGATTTGATATTCCCTAAGTG
1 TGATATTCCCTTCAGAAGAAGCGAAACATGTCCCTCT-TTTCCAAGATTTGATATTCCCTGAGTG
* *
343724 ACAGCGGAACAAGTCTGCCCCGATTCAATCTTCCTTGAGTGACAGCGGAATGGATCAACTCCCCC
65 ACAGCGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACTCCTCC
343789 AGATC
130 AGATC
* * * * * *
343794 TGATATTCCCTTCAGAAGAAGTGGAACATGTCCCTCTTTTTCAATATTTGATATTCACTAAGTGA
1 TGATATTCCCTTCAGAAGAAGCGAAACATGTCCCTCTTTTCCAAGATTTGATATTCCCTGAGTGA
* * * * * * * *
343859 CAGC---AGAA-----CCCCTATTCAATCTTCCATGATTGAAAACAGAATGGATCAATTCC-CCA
66 CAGCGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACTCCTCC-
343915 AGATC
130 AGATC
* * * * * * *
343920 TTATATTCCCTTCAGAAGAAGCAAAATAGGTCACTCTTTTCCAAGATTTGATATTTCATGAGTG-
1 TGATATTCCCTTCAGAAGAAGCGAAACATGTCCCTCTTTTCCAAGATTTGATATTCCCTGAGTGA
* * *
343984 CAGCGGAGCAAGTCTGCCCCGATTCAATCTTCCCTGAGTGATAGCGGAATGGATCAAATCCTCCA
66 CAGCGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACTCCTCCA
344049 GATC
131 GATC
* * * *
344053 TGATATTCCCTTCAGAAGAAGTGGAACATGTCCCTCTTTT--AAGGTTTGATATTACCTGAGTGA
1 TGATATTCCCTTCAGAAGAAGCGAAACATGTCCCTCTTTTCCAAGATTTGATATTCCCTGAGTGA
* * * * * *
344116 CATCGGAACAAGTATGCCCCGATTTAATCTTCTCTAAGTGACAGCGGAATGGATCAACTCCGCCA
66 CAGCGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACTCCTCCA
* *
344181 TATA
131 GATC
* *** * * *
344185 TGATATTCCCTTCAAAAGAAAATAAACATGTCTCTTTTTTCCAAGATTTGATATTCCCTAAGTGA
1 TGATATTCCCTTCAGAAGAAGCGAAACATGTCCCTCTTTTCCAAGATTTGATATTCCCTGAGTGA
* * ** *
344250 CAGCAGAACAAGTCTGCCCCGATTCAATCTTCTCTGAGTGACAATGAAATGGATCAACTCCTCCA
66 CAGCGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACTCCTCCA
344315 GATC
131 GATC
* * * *
344319 TGATATTCCCTTCATAAGAAGCGGAATATGTCCCTCTTTTCCAAGATTTGATATTTCCTGAGTGA
1 TGATATTCCCTTCAGAAGAAGCGAAACATGTCCCTCTTTTCCAAGATTTGATATTCCCTGAGTGA
* *
344384 CAGC-GAACAAGTCTGCCCCGATTCAATCTTCCCTAAGTGACAGCGAAATGGATCAACT-CTCCC
66 CAGCGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACTCCT-CC
344447 AGATC
130 AGATC
* * * * *
344452 TGATATTCTCTTTAGAAGAAGC-AAAAATGTCCCT-TTGTTCCAAGATTTGATATTCCTTGAATG
1 TGATATTCCCTTCAGAAGAAGCGAAACATGTCCCTCTT-TTCCAAGATTTGATATTCCCTGAGTG
* *
344515 ACAGCGGAACAAGTCTGCCCTGATTCAATCTTCCCTGAGTGACAGCGAAATGGATCAACATCC-C
65 ACAGCGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAAC-TCCTC
*
344579 CAGATT
129 CAGATC
344585 TGATATTCCCT
1 TGATATTCCCT
344596 GAGTGACAGC
Statistics
Matches: 675, Mismatches: 107, Indels: 40
0.82 0.13 0.05
Matches are distributed among these distances:
125 6 0.01
126 94 0.14
128 2 0.00
131 24 0.04
132 131 0.19
133 248 0.37
134 169 0.25
135 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (134 bp):
TGATATTCCCTTCAGAAGAAGCGAAACATGTCCCTCTTTTCCAAGATTTGATATTCCCTGAGTGA
CAGCGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACTCCTCCA
GATC
Found at i:347704 original size:5 final size:5
Alignment explanation
Indices: 347694--347761 Score: 63
Period size: 5 Copynumber: 13.8 Consensus size: 5
347684 GGATACCTGA
* *
347694 AAAAT AAAAT AAAAT AAAAT AAAAT -AAAT -ACAT GATAAAT TAAA- AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -A-AAAT AAAAT AAAAT
347743 AAAAT AAACA- AAAAT AAAA
1 AAAAT AAA-AT AAAAT AAAA
347762 ATAGGTTGCC
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
4 11 0.21
5 38 0.72
6 1 0.02
7 3 0.06
ACGTcount: A:0.76, C:0.03, G:0.01, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:350830 original size:18 final size:18
Alignment explanation
Indices: 350807--350843 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
350797 AGTTAAACTA
*
350807 TGTACTCAATGATTTTTC
1 TGTACTCAATGATCTTTC
*
350825 TGTACTCGATGATCTTTC
1 TGTACTCAATGATCTTTC
350843 T
1 T
350844 TAGTGAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.19, G:0.14, T:0.49
Consensus pattern (18 bp):
TGTACTCAATGATCTTTC
Found at i:352087 original size:14 final size:14
Alignment explanation
Indices: 352068--352103 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
352058 TGTTTCTTCC
352068 AGTTCAGGAGAGAG
1 AGTTCAGGAGAGAG
352082 AGTTCAGGAGAGAG
1 AGTTCAGGAGAGAG
352096 AGTTCAGG
1 AGTTCAGG
352104 GTTTCCAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.08, G:0.42, T:0.17
Consensus pattern (14 bp):
AGTTCAGGAGAGAG
Found at i:353341 original size:23 final size:23
Alignment explanation
Indices: 353286--353343 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
353276 ATGACGTTGC
* * *
353286 ACCCAATCAACAGCTTCTAGAAG
1 ACCCAATCAGCAACTTCTAGAAA
* *
353309 GCCCAGTCAGCAACTTCTAGAAA
1 ACCCAATCAGCAACTTCTAGAAA
*
353332 ATCCAATCAGCA
1 ACCCAATCAGCA
353344 GATTGCGTGG
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.38, C:0.31, G:0.14, T:0.17
Consensus pattern (23 bp):
ACCCAATCAGCAACTTCTAGAAA
Found at i:353554 original size:23 final size:22
Alignment explanation
Indices: 353520--353575 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
353510 CTCTTTGTTC
*
353520 TTTTTTTC--TTCTTTTAT-AAT
1 TTTTTTTCTTTTCTTTT-TCAAG
353540 TTTTTTTACTTTTCTTTTTCAAG
1 TTTTTTT-CTTTTCTTTTTCAAG
353563 TTTTTTTCTTTTC
1 TTTTTTTCTTTTC
353576 AAGTTTACTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 7 0.23
21 1 0.03
22 7 0.23
23 16 0.52
ACGTcount: A:0.11, C:0.12, G:0.02, T:0.75
Consensus pattern (22 bp):
TTTTTTTCTTTTCTTTTTCAAG
Found at i:353571 original size:17 final size:16
Alignment explanation
Indices: 353549--353581 Score: 57
Period size: 16 Copynumber: 2.0 Consensus size: 16
353539 TTTTTTTTAC
353549 TTTTCTTTTTCAAGTTT
1 TTTTC-TTTTCAAGTTT
353566 TTTTCTTTTCAAGTTT
1 TTTTCTTTTCAAGTTT
353582 ACTTTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.12, C:0.12, G:0.06, T:0.70
Consensus pattern (16 bp):
TTTTCTTTTCAAGTTT
Found at i:356087 original size:10 final size:10
Alignment explanation
Indices: 356048--356097 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
356038 TTCATCACAC
356048 CAAATTCTCT
1 CAAATTCTCT
*
356058 CAATTTCTCT
1 CAAATTCTCT
*
356068 CAACTTCTCT
1 CAAATTCTCT
*
356078 CAAATACTCT
1 CAAATTCTCT
* *
356088 TATATTCTCT
1 CAAATTCTCT
356098 GTTTAAGGTA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.26, C:0.30, G:0.00, T:0.44
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:356161 original size:23 final size:22
Alignment explanation
Indices: 356122--356166 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
356112 TTATTATATT
*
356122 TTTAATATTTTGTATTTAATTTA
1 TTTAATATTTTGAATTT-ATTTA
356145 TTTAAGTATTTT-AATTTATTTA
1 TTTAA-TATTTTGAATTTATTTA
356167 ATATTTTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 9 0.45
24 6 0.30
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (22 bp):
TTTAATATTTTGAATTTATTTA
Found at i:356173 original size:17 final size:18
Alignment explanation
Indices: 356136--356174 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
356126 ATATTTTGTA
356136 TTTAATTTATTTAAGTAT
1 TTTAATTTATTTAAGTAT
356154 TTTAATTTATTTAA-TAT
1 TTTAATTTATTTAAGTAT
356171 TTTA
1 TTTA
356175 CTTATATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTAATTTATTTAAGTAT
Found at i:361865 original size:30 final size:30
Alignment explanation
Indices: 361831--361889 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
361821 CCTTTGTAGG
* *
361831 CTCATATACAATATTGTTATCTTTTATAAT
1 CTCATATACAATACTGATATCTTTTATAAT
* **
361861 CTCATGTACCGTACTGATATCTTTTATAA
1 CTCATATACAATACTGATATCTTTTATAA
361890 GACCATGTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.17, G:0.07, T:0.46
Consensus pattern (30 bp):
CTCATATACAATACTGATATCTTTTATAAT
Found at i:361909 original size:12 final size:12
Alignment explanation
Indices: 361892--361957 Score: 62
Period size: 12 Copynumber: 5.6 Consensus size: 12
361882 TTTTATAAGA
*
361892 CCATGTATTAAC
1 CCATGTATTAGC
*
361904 CCATGTATTAGT
1 CCATGTATTAGC
*
361916 CAATGTATTAGC
1 CCATGTATTAGC
* *
361928 CCATTTATTA-T
1 CCATGTATTAGC
* *
361939 CTATGCATTAGC
1 CCATGTATTAGC
361951 CCATGTA
1 CCATGTA
361958 CAGTACTGAG
Statistics
Matches: 40, Mismatches: 13, Indels: 2
0.73 0.24 0.04
Matches are distributed among these distances:
11 7 0.17
12 33 0.82
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (12 bp):
CCATGTATTAGC
Found at i:361930 original size:24 final size:23
Alignment explanation
Indices: 361894--361957 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 23
361884 TTATAAGACC
*
361894 ATGTATTAACCCATGTATTAGTCA
1 ATGTATTAGCCCATGTATTA-TCA
* *
361918 ATGTATTAGCCCATTTATTATCT
1 ATGTATTAGCCCATGTATTATCA
*
361941 ATGCATTAGCCCATGTA
1 ATGTATTAGCCCATGTA
361958 CAGTACTGAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
23 17 0.49
24 18 0.51
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (23 bp):
ATGTATTAGCCCATGTATTATCA
Found at i:361952 original size:23 final size:24
Alignment explanation
Indices: 361898--361957 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
361888 AAGACCATGT
* *
361898 ATTAACCCATGTATTAGTCAATGT
1 ATTAGCCCATGTATTAGTCAATGC
* *
361922 ATTAGCCCATTTATTA-TCTATGC
1 ATTAGCCCATGTATTAGTCAATGC
361945 ATTAGCCCATGTA
1 ATTAGCCCATGTA
361958 CAGTACTGAG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
23 17 0.55
24 14 0.45
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (24 bp):
ATTAGCCCATGTATTAGTCAATGC
Found at i:363829 original size:12 final size:12
Alignment explanation
Indices: 363812--363877 Score: 80
Period size: 12 Copynumber: 5.6 Consensus size: 12
363802 TTTTATAAGA
*
363812 CCATGTATTAAC
1 CCATGTATTAGC
*
363824 CCATGTATTAGT
1 CCATGTATTAGC
*
363836 CAATGTATTAGC
1 CCATGTATTAGC
363848 CCATGTATTAG-
1 CCATGTATTAGC
* *
363859 CTATGCATTAGC
1 CCATGTATTAGC
363871 CCATGTA
1 CCATGTA
363878 AAATACTGAT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
11 9 0.20
12 35 0.80
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (12 bp):
CCATGTATTAGC
Found at i:363850 original size:24 final size:23
Alignment explanation
Indices: 363814--363877 Score: 92
Period size: 24 Copynumber: 2.7 Consensus size: 23
363804 TTATAAGACC
*
363814 ATGTATTAACCCATGTATTAGTCA
1 ATGTATTAGCCCATGTATTAG-CA
*
363838 ATGTATTAGCCCATGTATTAGCT
1 ATGTATTAGCCCATGTATTAGCA
*
363861 ATGCATTAGCCCATGTA
1 ATGTATTAGCCCATGTA
363878 AAATACTGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
23 17 0.46
24 20 0.54
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.36
Consensus pattern (23 bp):
ATGTATTAGCCCATGTATTAGCA
Found at i:363872 original size:23 final size:24
Alignment explanation
Indices: 363818--363877 Score: 86
Period size: 23 Copynumber: 2.5 Consensus size: 24
363808 AAGACCATGT
* *
363818 ATTAACCCATGTATTAGTCAATGT
1 ATTAGCCCATGTATTAGTCAATGC
*
363842 ATTAGCCCATGTATTAG-CTATGC
1 ATTAGCCCATGTATTAGTCAATGC
363865 ATTAGCCCATGTA
1 ATTAGCCCATGTA
363878 AAATACTGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
23 17 0.52
24 16 0.48
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (24 bp):
ATTAGCCCATGTATTAGTCAATGC
Found at i:364021 original size:38 final size:38
Alignment explanation
Indices: 363955--364050 Score: 147
Period size: 38 Copynumber: 2.5 Consensus size: 38
363945 GTATAAATTG
* * *
363955 TGTCTCGAATGACCTATCATCCCAAAGGATGTCATCTA
1 TGTCCCGAAGGACCTATCATCCCAAAGGATGTAATCTA
* *
363993 TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTG
1 TGTCCCGAAGGACCTATCATCCCAAAGGATGTAATCTA
364031 TGTCCCGAAGGACCTATCAT
1 TGTCCCGAAGGACCTATCAT
364051 ATGTCTCGTA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 53 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (38 bp):
TGTCCCGAAGGACCTATCATCCCAAAGGATGTAATCTA
Found at i:364055 original size:21 final size:20
Alignment explanation
Indices: 363988--364055 Score: 70
Period size: 21 Copynumber: 3.5 Consensus size: 20
363978 AAAGGATGTC
363988 ATCTATGTCCCGAAGGACCT
1 ATCTATGTCCCGAAGGACCT
**
364008 ATC-A--TCCCGAAGGATGT
1 ATCTATGTCCCGAAGGACCT
*
364025 AATCTGTGTCCCGAAGGACCT
1 -ATCTATGTCCCGAAGGACCT
364046 ATCATATGTC
1 ATC-TATGTC
364056 TCGTAGGACA
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
17 11 0.30
18 3 0.08
19 1 0.03
20 6 0.16
21 16 0.43
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (20 bp):
ATCTATGTCCCGAAGGACCT
Found at i:366854 original size:11 final size:12
Alignment explanation
Indices: 366832--366856 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
366822 GCATCTCTCA
366832 TTTCATTTTTTT
1 TTTCATTTTTTT
366844 TTTCATTTTTTT
1 TTTCATTTTTTT
366856 T
1 T
366857 CTGTTTTTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTCATTTTTTT
Found at i:368877 original size:17 final size:17
Alignment explanation
Indices: 368855--368888 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
368845 TCAGATGTCT
*
368855 ATCATTTCTCTTCCGAC
1 ATCATTGCTCTTCCGAC
368872 ATCATTGCTCTTCCGAC
1 ATCATTGCTCTTCCGAC
368889 TTTTTTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.35, G:0.09, T:0.38
Consensus pattern (17 bp):
ATCATTGCTCTTCCGAC
Found at i:369362 original size:24 final size:23
Alignment explanation
Indices: 369326--369389 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
369316 TTATAAGACC
* *
369326 ATGTGTTAACCCATGTATTAGTCA
1 ATGTATTAGCCCATGTATTA-TCA
* *
369350 ATGTATTAGCCCATTTATTATCT
1 ATGTATTAGCCCATGTATTATCA
*
369373 ATGCATTAGCCCATGTA
1 ATGTATTAGCCCATGTA
369390 CAGTACTGAG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 17 0.50
24 17 0.50
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (23 bp):
ATGTATTAGCCCATGTATTATCA
Found at i:369384 original size:23 final size:24
Alignment explanation
Indices: 369335--369389 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
369325 CATGTGTTAA
*
369335 CCCATGTATTAGTCAATGTATTAG
1 CCCATGTATTAGTCAATGCATTAG
* *
369359 CCCATTTATTA-TCTATGCATTAG
1 CCCATGTATTAGTCAATGCATTAG
369382 CCCATGTA
1 CCCATGTA
369390 CAGTACTGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 17 0.63
24 10 0.37
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (24 bp):
CCCATGTATTAGTCAATGCATTAG
Found at i:369491 original size:17 final size:17
Alignment explanation
Indices: 369469--369533 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
369459 ATAAATTGTG
369469 TCCCAAAGGACCTATCA
1 TCCCAAAGGACCTATCA
**
369486 TCCCAAAGGATGTCATCCA
1 TCCCAAAGGACCT-AT-CA
* *
369505 TGTCCCGAATGACCTATCA
1 --TCCCAAAGGACCTATCA
369524 TCCCAAAGGA
1 TCCCAAAGGA
369534 TGTAATCTGT
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
17 19 0.53
18 2 0.06
19 4 0.11
20 2 0.06
21 9 0.25
ACGTcount: A:0.32, C:0.32, G:0.15, T:0.20
Consensus pattern (17 bp):
TCCCAAAGGACCTATCA
Found at i:369519 original size:38 final size:38
Alignment explanation
Indices: 369467--369562 Score: 147
Period size: 38 Copynumber: 2.5 Consensus size: 38
369457 GTATAAATTG
* *
369467 TGTCCCAAAGGACCTATCATCCCAAAGGATGTCATCCA
1 TGTCCCGAAGGACCTATCATCCCAAAGGATGTAATCCA
* **
369505 TGTCCCGAATGACCTATCATCCCAAAGGATGTAATCTG
1 TGTCCCGAAGGACCTATCATCCCAAAGGATGTAATCCA
369543 TGTCCCGAAGGACCTATCAT
1 TGTCCCGAAGGACCTATCAT
369563 ATGTCTCGTA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (38 bp):
TGTCCCGAAGGACCTATCATCCCAAAGGATGTAATCCA
Found at i:372381 original size:15 final size:15
Alignment explanation
Indices: 372354--372389 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
372344 TTTAGGCCTC
372354 TCATTTCATTTTTTT
1 TCATTTCATTTTTTT
372369 TCATTCTCA-TTTTTT
1 TCATT-TCATTTTTTT
372384 TCATTT
1 TCATTT
372390 TTTTTGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 1 0.05
15 16 0.80
16 3 0.15
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (15 bp):
TCATTTCATTTTTTT
Found at i:374845 original size:24 final size:23
Alignment explanation
Indices: 374809--374872 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 23
374799 TTATAAGACC
374809 ATGTATTAACCCATGTATTAGTCA
1 ATGTATTAACCCATGTATTA-TCA
* * *
374833 ATGTATTATCCCATTTATTATCT
1 ATGTATTAACCCATGTATTATCA
* *
374856 ATGCATTAGCCCATGTA
1 ATGTATTAACCCATGTA
374873 CAGTACTGAT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 16 0.47
24 18 0.53
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.41
Consensus pattern (23 bp):
ATGTATTAACCCATGTATTATCA
Found at i:374868 original size:23 final size:24
Alignment explanation
Indices: 374813--374872 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
374803 AAGACCATGT
*
374813 ATTAACCCATGTATTAGTCAATGT
1 ATTAACCCATGTATTAGTCAATGC
* * *
374837 ATTATCCCATTTATTA-TCTATGC
1 ATTAACCCATGTATTAGTCAATGC
*
374860 ATTAGCCCATGTA
1 ATTAACCCATGTA
374873 CAGTACTGAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 16 0.53
24 14 0.47
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (24 bp):
ATTAACCCATGTATTAGTCAATGC
Found at i:375002 original size:38 final size:38
Alignment explanation
Indices: 374948--375045 Score: 151
Period size: 38 Copynumber: 2.6 Consensus size: 38
374938 TCGTATAAAT
* *
374948 TGTGTCCCAAAGGACCTATCATCCCAAAGGATGTCATA
1 TGTGTCCCGAAGGACCTATCATCCCAAAGGATGTAATA
* * *
374986 TGTGTCCCGAATGACCTATCATCCCGAAGGATGTAATC
1 TGTGTCCCGAAGGACCTATCATCCCAAAGGATGTAATA
375024 TGTGTCCCGAAGGACCTATCAT
1 TGTGTCCCGAAGGACCTATCAT
375046 ATGTCTCGTA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.26
Consensus pattern (38 bp):
TGTGTCCCGAAGGACCTATCATCCCAAAGGATGTAATA
Found at i:377892 original size:11 final size:10
Alignment explanation
Indices: 377878--377935 Score: 71
Period size: 10 Copynumber: 5.6 Consensus size: 10
377868 CACTTTTTTA
*
377878 AAAAATAAAT
1 AAAAATGAAT
377888 AAAAATGCAAT
1 AAAAATG-AAT
377899 AAAAATGAATT
1 AAAAATGAA-T
377910 AAAAATGAAT
1 AAAAATGAAT
* *
377920 AAAATTCAAT
1 AAAAATGAAT
377930 AAAAAT
1 AAAAAT
377936 ATAATGTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
10 22 0.52
11 20 0.48
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.22
Consensus pattern (10 bp):
AAAAATGAAT
Found at i:377903 original size:21 final size:20
Alignment explanation
Indices: 377878--377935 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
377868 CACTTTTTTA
377878 AAAAATAAATAAAAATGCAAT
1 AAAAATAAATAAAAATG-AAT
*
377899 AAAAATGAATTAAAAATGAAT
1 AAAAAT-AAATAAAAATGAAT
* *
377920 AAAATTCAATAAAAAT
1 AAAAATAAATAAAAAT
377936 ATAATGTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 8 0.25
21 14 0.44
22 10 0.31
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.22
Consensus pattern (20 bp):
AAAAATAAATAAAAATGAAT
Found at i:378014 original size:11 final size:11
Alignment explanation
Indices: 377998--378022 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
377988 ATTAATTTTA
377998 AAAAAAATATT
1 AAAAAAATATT
378009 AAAAAAATATT
1 AAAAAAATATT
378020 AAA
1 AAA
378023 TTTTTATTTT
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAAAAATATT
Found at i:378328 original size:22 final size:22
Alignment explanation
Indices: 378291--378339 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
378281 TTGTCTCGTC
*
378291 ATTAATTATTATTTTTAACAACA
1 ATTAATTAATATTTTTAACAA-A
*
378314 ATTAA-TAATATTTTTAATAAA
1 ATTAATTAATATTTTTAACAAA
378335 ATTAA
1 ATTAA
378340 AATTTAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 6 0.25
22 13 0.54
23 5 0.21
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (22 bp):
ATTAATTAATATTTTTAACAAA
Found at i:378739 original size:10 final size:11
Alignment explanation
Indices: 378713--378737 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
378703 TAAAATTAAA
378713 TTTTAATATTT
1 TTTTAATATTT
378724 TTTTAATATTT
1 TTTTAATATTT
378735 TTT
1 TTT
378738 AAAATTAATA
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTAATATTT
Found at i:378843 original size:11 final size:10
Alignment explanation
Indices: 378797--378856 Score: 57
Period size: 10 Copynumber: 5.8 Consensus size: 10
378787 CTTTACATTA
378797 TATTTTTATT
1 TATTTTTATT
* *
378807 GAATTTTATT
1 TATTTTTATT
*
378817 CATTTTTAATT
1 TATTTTT-ATT
*
378828 CATTTTTATT
1 TATTTTTATT
*
378838 GTATTTTTCTT
1 -TATTTTTATT
378849 TATTTTTA
1 TATTTTTA
378857 AAAAAAGTGA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
10 23 0.56
11 18 0.44
ACGTcount: A:0.22, C:0.05, G:0.03, T:0.70
Consensus pattern (10 bp):
TATTTTTATT
Found at i:380443 original size:20 final size:20
Alignment explanation
Indices: 380388--380444 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
380378 AAAAAAACCC
*
380388 CAGTGCATTTTGGTTC-AAA
1 CAGTGCAGTTTGGTTCAAAA
*****
380407 CAGTGCAGAAAAATTCAAAA
1 CAGTGCAGTTTGGTTCAAAA
380427 CAGTGCAGTTTGGTTCAA
1 CAGTGCAGTTTGGTTCAA
380445 GCGAAAAAAC
Statistics
Matches: 26, Mismatches: 11, Indels: 1
0.68 0.29 0.03
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (20 bp):
CAGTGCAGTTTGGTTCAAAA
Found at i:381860 original size:120 final size:120
Alignment explanation
Indices: 381647--381885 Score: 442
Period size: 120 Copynumber: 2.0 Consensus size: 120
381637 TTCTAGAAAC
* *
381647 TAGATTGACAAATTGTCTTTCTTAAAATCAAAAACACTTTCACTTCAAAAATAGATTTTGGCTTG
1 TAGATTGACAAATTGCCTTTCTTAAAATCAAAAACACTTTCAATTCAAAAATAGATTTTGGCTTG
*
381712 GATAATGTTATGGTTTACCGTTGGGATAGAATCAATTCGAATAACTTAGCGAATA
66 GACAATGTTATGGTTTACCGTTGGGATAGAATCAATTCGAATAACTTAGCGAATA
*
381767 TAGATTGACGAATTGCCTTTCTTAAAATCAAAAACACTTTCAATTCAAAAATAGATTTTGGCTTG
1 TAGATTGACAAATTGCCTTTCTTAAAATCAAAAACACTTTCAATTCAAAAATAGATTTTGGCTTG
381832 GACAATGTTATGGTTTACCGTTGGGATAGAATCAATTCGAATAACTTAGCGAAT
66 GACAATGTTATGGTTTACCGTTGGGATAGAATCAATTCGAATAACTTAGCGAAT
381886 GGTAAGCTAA
Statistics
Matches: 115, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 115 1.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (120 bp):
TAGATTGACAAATTGCCTTTCTTAAAATCAAAAACACTTTCAATTCAAAAATAGATTTTGGCTTG
GACAATGTTATGGTTTACCGTTGGGATAGAATCAATTCGAATAACTTAGCGAATA
Found at i:383845 original size:21 final size:21
Alignment explanation
Indices: 383811--383857 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
383801 CTTTACCTTG
383811 TTTT-ATTAATTTTTATT-TA
1 TTTTAATTAATTTTTATTATA
*
383830 CTTTTAATTCATTTTTATTATA
1 -TTTTAATTAATTTTTATTATA
383852 TTTTAA
1 TTTTAA
383858 ATATATGAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 4 0.17
21 18 0.75
22 2 0.08
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTAATTAATTTTTATTATA
Found at i:384160 original size:11 final size:10
Alignment explanation
Indices: 384139--384195 Score: 62
Period size: 10 Copynumber: 5.6 Consensus size: 10
384129 CTCATATATT
384139 TAAAAATCAA
1 TAAAAATCAA
384149 TAAAAATACAA
1 TAAAAAT-CAA
*
384160 TAATAAT-AA
1 TAAAAATCAA
*
384169 TTAAAAATGAA
1 -TAAAAATCAA
*
384180 TAAAATTCAA
1 TAAAAATCAA
384190 TAAAAA
1 TAAAAA
384196 AAAAGATAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
9 2 0.05
10 26 0.67
11 11 0.28
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (10 bp):
TAAAAATCAA
Found at i:384281 original size:27 final size:26
Alignment explanation
Indices: 384245--384295 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
384235 TATTCTTTCT
*
384245 AATATTAATTTTAATAATATTAAATA
1 AATATTAATTCTAATAATATTAAATA
**
384271 AATATTAAATTCTAATTTTATTAAA
1 AATATT-AATTCTAATAATATTAAA
384296 AATGAATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (26 bp):
AATATTAATTCTAATAATATTAAATA
Found at i:384967 original size:2 final size:2
Alignment explanation
Indices: 384962--384992 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
384952 ATATATATAT
384962 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
384993 AGGGTCTGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:387505 original size:38 final size:37
Alignment explanation
Indices: 387435--387536 Score: 125
Period size: 37 Copynumber: 2.7 Consensus size: 37
387425 TTTTTACCCT
* * *
387435 AAATCCGAACCC-AATCTGACCTGAATATCACACTTAAAA
1 AAATCCG-ACCCGACTC-GACCCGAATAGCACACTT-AAA
387474 AAATCCGACCCGACTCGACCCGAATAGCACACTTAAA
1 AAATCCGACCCGACTCGACCCGAATAGCACACTTAAA
* *
387511 AAACCCGACCCGACCCGACCCGAATA
1 AAATCCGACCCGACTCGACCCGAATA
387537 TATGAATTAG
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
37 27 0.47
38 20 0.35
39 10 0.18
ACGTcount: A:0.39, C:0.35, G:0.12, T:0.14
Consensus pattern (37 bp):
AAATCCGACCCGACTCGACCCGAATAGCACACTTAAA
Found at i:387521 original size:37 final size:38
Alignment explanation
Indices: 387452--387536 Score: 127
Period size: 37 Copynumber: 2.3 Consensus size: 38
387442 AACCCAATCT
* * * *
387452 GACCTGAATATCACACTTAAAAAAATCCGACCCGACTC
1 GACCCGAATAGCACACTTAAAAAAACCCGACCCGACCC
387490 GACCCGAATAGCACACTT-AAAAAACCCGACCCGACCC
1 GACCCGAATAGCACACTTAAAAAAACCCGACCCGACCC
387527 GACCCGAATA
1 GACCCGAATA
387537 TATGAATTAG
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
37 27 0.63
38 16 0.37
ACGTcount: A:0.39, C:0.35, G:0.13, T:0.13
Consensus pattern (38 bp):
GACCCGAATAGCACACTTAAAAAAACCCGACCCGACCC
Found at i:390641 original size:2 final size:2
Alignment explanation
Indices: 390634--390772 Score: 208
Period size: 2 Copynumber: 70.0 Consensus size: 2
390624 TCGGAATGTT
* * * * * * *
390634 TC TC TC TC TC TC TC TC TC TC TC TC TC AC AC AC GC AC GC GC T-
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
390675 TC 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 TC
390717 TC 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 TC
390759 TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC
390773 ACGCGCGCAC
Statistics
Matches: 131, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
1 1 0.01
2 130 0.99
ACGTcount: A:0.03, C:0.50, G:0.02, T:0.45
Consensus pattern (2 bp):
TC
Found at i:394591 original size:36 final size:36
Alignment explanation
Indices: 394543--394615 Score: 121
Period size: 36 Copynumber: 2.0 Consensus size: 36
394533 TTACCTTCTA
*
394543 TTTCAGATGCAACAGGA-TCCGAATCTGGTTCTTGGC
1 TTTCAGAGGCAACAGGACT-CGAATCTGGTTCTTGGC
394579 TTTCAGAGGCAACAGGACTCGAATCTGGTTCTTGGC
1 TTTCAGAGGCAACAGGACTCGAATCTGGTTCTTGGC
394615 T
1 T
394616 AATGCTAGGC
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 34 0.97
37 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (36 bp):
TTTCAGAGGCAACAGGACTCGAATCTGGTTCTTGGC
Found at i:401894 original size:23 final size:20
Alignment explanation
Indices: 401867--401919 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
401857 GTATCGGTAT
401867 TGTTCATACAATATCGATACTAC
1 TGTTCATACAATATC---ACTAC
* *
401890 TGTTCATACAGTATCAGTAC
1 TGTTCATACAATATCACTAC
401910 TGTTCATACA
1 TGTTCATACA
401920 GTATTTCGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 14 0.50
23 14 0.50
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (20 bp):
TGTTCATACAATATCACTAC
Found at i:402459 original size:19 final size:19
Alignment explanation
Indices: 402435--402473 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
402425 AGCTTACCCG
*
402435 ATCCCCTTTCATGATCACA
1 ATCCCCTTTCATGACCACA
402454 ATCCCCTTTCATGACCACA
1 ATCCCCTTTCATGACCACA
402473 A
1 A
402474 AACCCTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.38, G:0.05, T:0.28
Consensus pattern (19 bp):
ATCCCCTTTCATGACCACA
Found at i:402479 original size:19 final size:19
Alignment explanation
Indices: 402438--402479 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
402428 TTACCCGATC
* **
402438 CCCTTTCATGATCACAATC
1 CCCTTTCATGACCACAAAA
402457 CCCTTTCATGACCACAAAA
1 CCCTTTCATGACCACAAAA
402476 CCCT
1 CCCT
402480 AATTCAACTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.29, C:0.40, G:0.05, T:0.26
Consensus pattern (19 bp):
CCCTTTCATGACCACAAAA
Found at i:410439 original size:45 final size:45
Alignment explanation
Indices: 410383--410519 Score: 229
Period size: 45 Copynumber: 3.0 Consensus size: 45
410373 TCGAGAAAAT
*
410383 GCATGCGAACTAGATATCATGCGGTTAGGTTTATTTTTTGAATAA
1 GCATGCAAACTAGATATCATGCGGTTAGGTTTATTTTTTGAATAA
*
410428 GCATGCAAACTAGATATCACGCGGTTAGGTTTATTTTTTGAATAA
1 GCATGCAAACTAGATATCATGCGGTTAGGTTTATTTTTTGAATAA
*
410473 GCATGCAAATTAGATATCATGCGGTTAGGATTTATTTTTGTGAATAA
1 GCATGCAAACTAGATATCATGCGGTTAGG-TTTATTTTT-TGAATAA
410520 CAAAGCATGG
Statistics
Matches: 86, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
45 70 0.81
46 9 0.10
47 7 0.08
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.37
Consensus pattern (45 bp):
GCATGCAAACTAGATATCATGCGGTTAGGTTTATTTTTTGAATAA
Found at i:420188 original size:9 final size:9
Alignment explanation
Indices: 420168--420207 Score: 73
Period size: 9 Copynumber: 4.6 Consensus size: 9
420158 AATAAAAGAT
420168 AAAATG-AA
1 AAAATGAAA
420176 AAAATGAAA
1 AAAATGAAA
420185 AAAATGAAA
1 AAAATGAAA
420194 AAAATGAAA
1 AAAATGAAA
420203 AAAAT
1 AAAAT
420208 AATAATAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 6 0.19
9 25 0.81
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (9 bp):
AAAATGAAA
Found at i:420220 original size:30 final size:29
Alignment explanation
Indices: 420184--420263 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 29
420174 AAAAAATGAA
*
420184 AAAAATGAAAAAAATGAAAAA-AATAATAAT
1 AAAAATGAAAAAAA-GAAAAAGAATAA-AAG
* *
420214 AAAAATGAGAAGAAGAAAAAGAATAAAAG
1 AAAAATGAAAAAAAGAAAAAGAATAAAAG
420243 AAAAATGAGAAAAAAGAAAAA
1 AAAAATGA-AAAAAAGAAAAA
420264 TGATGGAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
29 16 0.37
30 27 0.63
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (29 bp):
AAAAATGAAAAAAAGAAAAAGAATAAAAG
Found at i:420263 original size:8 final size:8
Alignment explanation
Indices: 420154--420299 Score: 64
Period size: 9 Copynumber: 17.1 Consensus size: 8
420144 TCGCTTGAAG
420154 AAGAAATAA
1 AAGAAA-AA
*
420163 AAGATAAA
1 AAGAAAAA
*
420171 ATGAAAAA
1 AAGAAAAA
*
420179 ATGAAAAA
1 AAGAAAAA
420187 AATGAAAAA
1 AA-GAAAAA
420196 AATGAAAAA
1 AA-GAAAAA
*
420205 AATAATAATA
1 AAGAA-AA-A
* *
420215 AA-AATGAG
1 AAGAA-AAA
420223 AAGAAGAAA
1 AAGAA-AAA
*
420232 AAGAATAA
1 AAGAAAAA
420240 AAG-AAAA
1 AAGAAAAA
*
420247 ATGAGAAAA
1 AAGA-AAAA
420256 AAGAAAAA
1 AAGAAAAA
*
420264 TGATGGAAAAA
1 --A-AGAAAAA
*
420275 ACGAAAAGA
1 AAGAAAA-A
*
420284 AA-AAAAG
1 AAGAAAAA
420291 AAGAAAAA
1 AAGAAAAA
420299 A
1 A
420300 TGGAAAATGG
Statistics
Matches: 107, Mismatches: 19, Indels: 23
0.72 0.13 0.15
Matches are distributed among these distances:
7 7 0.07
8 44 0.41
9 46 0.43
10 4 0.04
11 6 0.06
ACGTcount: A:0.75, C:0.01, G:0.15, T:0.10
Consensus pattern (8 bp):
AAGAAAAA
Found at i:420273 original size:16 final size:16
Alignment explanation
Indices: 420214--420292 Score: 71
Period size: 14 Copynumber: 5.1 Consensus size: 16
420204 AAATAATAAT
*
420214 AAAAATGAG-AAGAAG
1 AAAAATGAGAAAAAAG
*
420229 AAAAA-GA-ATAAAAG
1 AAAAATGAGAAAAAAG
420243 AAAAATGAGAAAAAAG
1 AAAAATGAGAAAAAAG
420259 AAAAATGATGGAAAAAACG
1 AAAAATGA--GAAAAAA-G
420278 -AAAA-GA-AAAAAAG
1 AAAAATGAGAAAAAAG
420291 AA
1 AA
420293 GAAAAAATGG
Statistics
Matches: 54, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
13 1 0.02
14 18 0.33
15 7 0.13
16 14 0.26
17 2 0.04
18 11 0.20
19 1 0.02
ACGTcount: A:0.73, C:0.01, G:0.19, T:0.06
Consensus pattern (16 bp):
AAAAATGAGAAAAAAG
Found at i:420287 original size:69 final size:70
Alignment explanation
Indices: 420150--420299 Score: 159
Period size: 68 Copynumber: 2.2 Consensus size: 70
420140 TATTTCGCTT
* *
420150 GAAGAAGAAATAAAAGATAAAATGAAAAAATGAAAAAAATGAAAAAAATGAAAAAAATAATAATA
1 GAAGAAGAAA-AAAAGATAAAATGAAAAAATGAAAAAAATGAAAAAAATGAAAAAAAGAATAAGA
*
420215 AAAATGA
65 AAAA-AA
* * *
420222 GAAGAAGAAAAAGA-ATAAAA-G-AAAAATGAGAAAAAA-GAAAAATGATGGAAAAAACGAA-AA
1 GAAGAAGAAAAAAAGATAAAATGAAAAAATGA-AAAAAATGAAAAA-AAT-GAAAAAAAGAATAA
420282 GAAAAAAA
63 GAAAAAAA
420290 GAAGAA-AAAA
1 GAAGAAGAAAA
420300 TGGAAAATGG
Statistics
Matches: 69, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
67 4 0.06
68 21 0.30
69 16 0.23
70 15 0.22
71 3 0.04
72 10 0.14
ACGTcount: A:0.74, C:0.01, G:0.16, T:0.09
Consensus pattern (70 bp):
GAAGAAGAAAAAAAGATAAAATGAAAAAATGAAAAAAATGAAAAAAATGAAAAAAAGAATAAGAA
AAAAA
Found at i:420296 original size:42 final size:42
Alignment explanation
Indices: 420214--420349 Score: 116
Period size: 43 Copynumber: 3.1 Consensus size: 42
420204 AAATAATAAT
* *
420214 AAAAATGAGAAGAAGAAAAAGAATAAAAGAAAAATG-AGAAAAAAG
1 AAAAATG-GAAGAA-AAAACGAA-AAGA-AAAAATGAAGAAAAAAG
* *
420259 AAAAAT-GATGGAAAAAACGAAAAGAAAAAAAGAAGAAAAAATG
1 AAAAATGGA-AGAAAAAACGAAAAGAAAAAATGAAGAAAAAA-G
* * *
420302 GAAAATGGAAGAAAAAATG-AAAGAGAAAAATGAAAAAAAAAG
1 AAAAATGGAAGAAAAAACGAAAAGA-AAAAATGAAGAAAAAAG
*
420344 AGAAAT
1 AAAAAT
420350 AAAAGGAGGG
Statistics
Matches: 75, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
41 6 0.08
42 21 0.28
43 37 0.49
44 5 0.07
45 6 0.08
ACGTcount: A:0.72, C:0.01, G:0.20, T:0.07
Consensus pattern (42 bp):
AAAAATGGAAGAAAAAACGAAAAGAAAAAATGAAGAAAAAAG
Found at i:420330 original size:14 final size:13
Alignment explanation
Indices: 420303--420336 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
420293 GAAAAAATGG
*
420303 AAAATGGAAGA-A
1 AAAATGAAAGAGA
420315 AAAATGAAAGAGA
1 AAAATGAAAGAGA
420328 AAAATGAAA
1 AAAATGAAA
420337 AAAAAAGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.09
Consensus pattern (13 bp):
AAAATGAAAGAGA
Done.