Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006023.1 Hibiscus syriacus cultivar Beakdansim tig00014213_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: 1315283
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 8
Found at i:668486 original size:32 final size:32
Alignment explanation
Indices: 668450--668511 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
668440 ATTAAAAATG
668450 ACACAAACAAAAGAAAAGAAA-TAAGTTAGTGT
1 ACACAAACAAAAGAAAAGAAATTAA-TTAGTGT
*
668482 ACACAAACAAAAGAAAATAAATTAATTAGT
1 ACACAAACAAAAGAAAAGAAATTAATTAGT
668512 ACATGTAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 25 0.89
33 3 0.11
ACGTcount: A:0.61, C:0.10, G:0.11, T:0.18
Consensus pattern (32 bp):
ACACAAACAAAAGAAAAGAAATTAATTAGTGT
Found at i:672654 original size:9 final size:9
Alignment explanation
Indices: 672631--672675 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
672621 TTTCAAATTT
672631 TAAAAAATCA
1 TAAAAAAT-A
*
672641 GAAAAAATA
1 TAAAAAATA
672650 TAAAAAATA
1 TAAAAAATA
*
672659 TACAAAATA
1 TAAAAAATA
*
672668 AAAAAAAT
1 TAAAAAAT
672676 TACAAAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
9 23 0.77
10 7 0.23
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (9 bp):
TAAAAAATA
Found at i:672670 original size:16 final size:17
Alignment explanation
Indices: 672644--672682 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
672634 AAAATCAGAA
*
672644 AAAATATAAAAAATATAC
1 AAAATAAAAAAAAT-TAC
672662 AAAATAAAAAAAATTAC
1 AAAATAAAAAAAATTAC
672679 AAAA
1 AAAA
672683 AAATTAGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (17 bp):
AAAATAAAAAAAATTAC
Found at i:674569 original size:5 final size:5
Alignment explanation
Indices: 674553--674583 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
674543 CATTCAATGG
674553 TTAAT ATTAAT TTAAT TTAAT TTAAT TTAAT
1 TTAAT -TTAAT TTAAT TTAAT TTAAT TTAAT
674584 CATAGTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TTAAT
Found at i:682234 original size:3 final size:3
Alignment explanation
Indices: 682226--682268 Score: 59
Period size: 3 Copynumber: 13.7 Consensus size: 3
682216 AGTATTTTTA
*
682226 AAT AAT AAT AAT AAT ACT AAT AAT AAT AAT AACTT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA--T AAT AAT AA
682269 CGAGTTGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
3 33 0.92
5 3 0.08
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:682507 original size:41 final size:41
Alignment explanation
Indices: 682453--682549 Score: 158
Period size: 41 Copynumber: 2.4 Consensus size: 41
682443 GATCCATTCT
**
682453 GCTGTCACTCAGGGAAGATTGAATCATTGCAGACTTGTTCC
1 GCTGTCACTCAGGGAAGATTGAATCAGGGCAGACTTGTTCC
682494 GCTGTCACTCAGGGAAGATTGAATCAGGGCAGACTTGTTCC
1 GCTGTCACTCAGGGAAGATTGAATCAGGGCAGACTTGTTCC
* *
682535 GTTGTCACTAAGGGA
1 GCTGTCACTCAGGGA
682550 CTATCAAATA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (41 bp):
GCTGTCACTCAGGGAAGATTGAATCAGGGCAGACTTGTTCC
Found at i:686404 original size:16 final size:16
Alignment explanation
Indices: 686385--686427 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
686375 ATTAATGAAT
*
686385 AAAATGCAATGCGAAA-
1 AAAATGCAATG-AAAAG
686401 AAAATGCAATGAAAAG
1 AAAATGCAATGAAAAG
686417 AAAATGCAATG
1 AAAATGCAATG
686428 TGGATGCAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 3 0.12
16 22 0.88
ACGTcount: A:0.58, C:0.09, G:0.19, T:0.14
Consensus pattern (16 bp):
AAAATGCAATGAAAAG
Found at i:690686 original size:3 final size:3
Alignment explanation
Indices: 690678--690782 Score: 126
Period size: 3 Copynumber: 35.7 Consensus size: 3
690668 GTGGGCTGTA
690678 AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
** * * **
690724 GTT AGT ATT TTT AAAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
690769 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
690783 AATGTTAGTA
Statistics
Matches: 90, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
2 6 0.07
3 83 0.92
4 1 0.01
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:690775 original size:62 final size:62
Alignment explanation
Indices: 690678--690815 Score: 276
Period size: 62 Copynumber: 2.2 Consensus size: 62
690668 GTGGGCTGTA
690678 AATAATAATAATAATAATAATATAATAATAATAATAATAATAAAATGTTAGTATTTTTAAAT
1 AATAATAATAATAATAATAATATAATAATAATAATAATAATAAAATGTTAGTATTTTTAAAT
690740 AATAATAATAATAATAATAATATAATAATAATAATAATAATAAAATGTTAGTATTTTTAAAT
1 AATAATAATAATAATAATAATATAATAATAATAATAATAATAAAATGTTAGTATTTTTAAAT
690802 AATAATAATAATAA
1 AATAATAATAATAA
690816 CTTAATAAGA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 76 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (62 bp):
AATAATAATAATAATAATAATATAATAATAATAATAATAATAAAATGTTAGTATTTTTAAAT
Found at i:692660 original size:21 final size:21
Alignment explanation
Indices: 692609--692681 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
692599 TTTTCCCAAT
** *
692609 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTGGGAAAA
* *
692629 TCGCAACGCGAATTGGGAAAT
1 TCGCAATGCGAATTGGGAAAA
*
692650 TCGCATTGCGAATTGGGAAAA
1 TCGCAATGCGAATTGGGAAAA
692671 TCGCAATGCGA
1 TCGCAATGCGA
692682 TACTGACTAT
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
20 11 0.26
21 32 0.74
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTGGGAAAA
Found at i:692695 original size:20 final size:20
Alignment explanation
Indices: 692670--692764 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
692660 AATTGGGAAA
*
692670 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
692690 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
692711 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
692731 TTCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
*
692751 TTCGCAACGCGATA
1 ATCGCAACGCGATA
692765 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:692980 original size:22 final size:22
Alignment explanation
Indices: 692952--692995 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
692942 CACTCTCTCA
692952 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
692974 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
692996 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:693284 original size:20 final size:20
Alignment explanation
Indices: 693259--693296 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
693249 CGATTCTCTC
693259 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
693279 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
693297 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:694635 original size:18 final size:18
Alignment explanation
Indices: 694614--694658 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
694604 TCCACTGCGG
*
694614 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
694632 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
694650 GAGCCATCA
1 GAGCCATCA
694659 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:695149 original size:20 final size:20
Alignment explanation
Indices: 695124--695169 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
695114 TAGTTTACTT
695124 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
695144 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
695164 TCGCAA
1 TCGCAA
695170 TGCGAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:695198 original size:14 final size:14
Alignment explanation
Indices: 695179--695236 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
695169 ATGCGAAATA
695179 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
695193 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
695209 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
695225 AAAATCGCAACG
1 AAAATCGCAACG
695237 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:695221 original size:32 final size:32
Alignment explanation
Indices: 695163--695253 Score: 146
Period size: 32 Copynumber: 2.8 Consensus size: 32
695153 GGAAATGGCT
*
695163 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
1 ATCGCAATGCGAAAT-GAAATCGCAACGACAAA
695196 ATCGCAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAATCGCAACGACAAA
*
695228 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATG-AAATCGCAA
695254 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAATCGCAACGACAAA
Found at i:695289 original size:14 final size:14
Alignment explanation
Indices: 695270--695327 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
695260 TTGTGTTTCG
695270 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
695284 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
695300 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
695316 CGTTGCGATTTT
1 CGTTGCGATTTT
695328 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:695304 original size:32 final size:33
Alignment explanation
Indices: 695265--695343 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
695255 GCGATTTGTG
695265 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
695297 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
695330 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
695344 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:695342 original size:19 final size:19
Alignment explanation
Indices: 695286--695385 Score: 77
Period size: 19 Copynumber: 5.5 Consensus size: 19
695276 GATTTTGTCG
*
695286 TTGCGA-TTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
*
695304 TTGCGA-TTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
695318 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
***
695337 TTGCGATAGCCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
** *
695357 TTGCGATAGTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
695376 TTGCGATTTT
1 TTGCGATTTT
695386 AAGTTTCGTG
Statistics
Matches: 67, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
14 6 0.09
15 3 0.04
16 4 0.06
17 4 0.06
18 9 0.13
19 23 0.34
20 18 0.27
ACGTcount: A:0.14, C:0.21, G:0.22, T:0.43
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:695358 original size:20 final size:19
Alignment explanation
Indices: 695328--695382 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
695318 TTGCGATTTT
695328 CATTTCGCATTGCGATAGC
1 CATTTCGCATTGCGATAGC
*
695347 CATTTCCGCATTGCGATAGT
1 CATTT-CGCATTGCGATAGC
*
695367 CATTTCGCGTTGCGAT
1 CATTTCGCATTGCGAT
695383 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.35
Consensus pattern (19 bp):
CATTTCGCATTGCGATAGC
Found at i:697261 original size:14 final size:14
Alignment explanation
Indices: 697242--697277 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
697232 ATTGTTTAAT
697242 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
697256 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
697270 TGATTTGT
1 TGATTTGT
697278 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:697504 original size:20 final size:20
Alignment explanation
Indices: 697447--697504 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
697437 TCGCATTGTG
* *
697447 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
*
697467 ATTTTTGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
697487 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
697505 TCAAATGATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.40
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:698008 original size:19 final size:19
Alignment explanation
Indices: 697986--698116 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
697976 GGAAATTACT
697986 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
698005 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
698019 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
698038 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
698052 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
698071 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
698085 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
698104 ATCGCAACGCGAA
1 ATCGCAATGCGAA
698117 TTTAATTTCA
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 27 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.46
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:698023 original size:33 final size:33
Alignment explanation
Indices: 697986--698112 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
697976 GGAAATTACT
697986 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
698019 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
698051 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
698085 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
698113 CGAATTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:698063 original size:66 final size:66
Alignment explanation
Indices: 697987--698119 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
697977 GAAATTACTA
*
697987 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
698052 T
66 T
*
698053 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
698118 T
66 T
698119 T
1 T
698120 AATTTCACAT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:698314 original size:14 final size:14
Alignment explanation
Indices: 698295--698331 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
698285 CATCAATTAA
698295 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
698309 ACAAATCACCTTTT
1 ACAAATCAACTTTT
698323 ACAAATCAA
1 ACAAATCAA
698332 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:699753 original size:21 final size:21
Alignment explanation
Indices: 699687--699753 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
699677 GTGAATCGGG
*
699687 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
699707 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
699729 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
699750 CTCT
1 CTCT
699754 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:699772 original size:42 final size:41
Alignment explanation
Indices: 699687--699809 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
699677 GTGAATCGGG
* * * * *
699687 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
699729 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
699771 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
699810 CGAGTCGGCT
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:700955 original size:21 final size:22
Alignment explanation
Indices: 700913--700955 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
700903 AATAACAAAC
*
700913 ATTAGTAATTGTTAAATAATTA
1 ATTAGTAATTGTTAAAAAATTA
700935 ATTA-TAATT-TTAAAAACATTA
1 ATTAGTAATTGTTAAAAA-ATTA
700956 TATAGAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 9 0.47
22 4 0.21
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (22 bp):
ATTAGTAATTGTTAAAAAATTA
Found at i:701890 original size:33 final size:33
Alignment explanation
Indices: 701833--701931 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
701823 ACGAGATAAT
* *
701833 GAGAATCGCAATGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
701867 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
701900 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
701932 GCGAAATAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 45 0.78
34 13 0.22
ACGTcount: A:0.39, C:0.25, G:0.23, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:701925 original size:19 final size:19
Alignment explanation
Indices: 701808--701992 Score: 165
Period size: 19 Copynumber: 10.1 Consensus size: 19
701798 TCTTTTGGTT
*
701808 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
* *
701827 GATAATGAGAATCGCAATGC
1 GA-AATGAAAATCGCAACGC
**
701847 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
701865 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
701881 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
701899 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
701914 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
701934 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
701953 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
701972 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
701991 GA
1 GA
701993 TTTTGGTTTC
Statistics
Matches: 137, Mismatches: 16, Indels: 26
0.77 0.09 0.15
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 62 0.45
20 44 0.32
21 2 0.01
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:701946 original size:39 final size:38
Alignment explanation
Indices: 701903--701992 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 38
701893 GCGACCAGAC
701903 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAA-CGCGAAATAAA
*
701942 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
*
701980 AATCGCAATGCGA
1 AATCGCAACGCGA
701993 TTTTGGTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 22 0.45
39 27 0.55
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
Found at i:702021 original size:19 final size:19
Alignment explanation
Indices: 701988--702028 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
701978 AAAATCGCAA
*
701988 TGCGATTTTGGTTTCACGT
1 TGCGATTTTGATTTCACGT
* *
702007 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCACGT
702026 TGC
1 TGC
702029 AATTATCTCG
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:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCACGT
Found at i:702648 original size:20 final size:20
Alignment explanation
Indices: 702623--702676 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
702613 GATTTTGTAT
702623 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
702643 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
702663 TATCGCATTGCGAT
1 TATCGCATTGCGAT
702677 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:702695 original size:61 final size:61
Alignment explanation
Indices: 702583--702697 Score: 142
Period size: 61 Copynumber: 1.9 Consensus size: 61
702573 CGCTATGTAA
* * * ** *
702583 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCGCATTGCGATAGTAAGT
* *
702644 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAATATCGCATTGCGAT
702698 TTACTTATTC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
61 43 0.96
62 2 0.04
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCGCATTGCGATAGTAAGT
Found at i:703629 original size:2 final size:2
Alignment explanation
Indices: 703624--703668 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
703614 TAAAAAATAC
*
703624 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
703665 AT AT
1 AT AT
703669 TAAAATATTA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:703672 original size:12 final size:13
Alignment explanation
Indices: 703617--703676 Score: 68
Period size: 14 Copynumber: 4.5 Consensus size: 13
703607 AAAATATTAA
*
703617 AAAATACATATAT
1 AAAATATATATAT
*
703630 ATATATATATATAT
1 A-AAATATATATAT
*
703644 ATATATATATATAT
1 A-AAATATATATAT
703658 AAAATATATAT-T
1 AAAATATATATAT
703670 AAAATAT
1 AAAATAT
703677 TAAATTTAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
12 8 0.19
13 10 0.23
14 25 0.58
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (13 bp):
AAAATATATATAT
Found at i:703676 original size:19 final size:21
Alignment explanation
Indices: 703617--703681 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 21
703607 AAAATATTAA
* *
703617 AAAATACATATATATATATAT
1 AAAATATATATATATAAATAT
* *
703638 -ATATATATATATATATATAT
1 AAAATATATATATATAAATAT
703658 AAAATATATAT-TA-AAATAT
1 AAAATATATATATATAAATAT
*
703677 TAAAT
1 AAAAT
703682 TTAACCCCCT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
19 9 0.24
20 20 0.53
21 9 0.24
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
AAAATATATATATATAAATAT
Found at i:705489 original size:28 final size:28
Alignment explanation
Indices: 705440--705539 Score: 121
Period size: 28 Copynumber: 3.6 Consensus size: 28
705430 TGATAAGGTT
* *
705440 TAGGGTTTAGGGTTTAGAGTTTATATGA
1 TAGGATTTAGGGTTTAGGGTTTATATGA
* *
705468 TATGATTTAGGGTTTAGGGTTTATATGG
1 TAGGATTTAGGGTTTAGGGTTTATATGA
* *
705496 TAGGATTTAAGGTTTAGGGTTTACAT-A
1 TAGGATTTAGGGTTTAGGGTTTATATGA
*
705523 TTAGGGTTTAGGGTTTA
1 -TAGGATTTAGGGTTTA
705540 AGTTATGCAC
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
28 61 1.00
ACGTcount: A:0.24, C:0.01, G:0.31, T:0.44
Consensus pattern (28 bp):
TAGGATTTAGGGTTTAGGGTTTATATGA
Found at i:707746 original size:11 final size:11
Alignment explanation
Indices: 707731--707774 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
707721 AGCTTGAGTT
707731 GAGCTTCAATC
1 GAGCTTCAATC
* *
707742 AAGCTTCAATT
1 GAGCTTCAATC
*
707753 GAGCTTAAAATC
1 GAGCTT-CAATC
707765 GAGCTTCAAT
1 GAGCTTCAAT
707775 TGAATTCGAG
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
11 17 0.65
12 9 0.35
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (11 bp):
GAGCTTCAATC
Found at i:707769 original size:23 final size:22
Alignment explanation
Indices: 707720--707777 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 22
707710 GCTAACAATT
* * *
707720 GAGCTTGAGTTGAGCTTCAATC
1 GAGCTTCAATTGAGCTTAAATC
*
707742 AAGCTTCAATTGAGCTTAAAATC
1 GAGCTTCAATTGAGCTT-AAATC
707765 GAGCTTCAATTGA
1 GAGCTTCAATTGA
707778 ATTCGAGTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 14 0.47
23 16 0.53
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (22 bp):
GAGCTTCAATTGAGCTTAAATC
Found at i:707813 original size:24 final size:24
Alignment explanation
Indices: 707746--707843 Score: 73
Period size: 24 Copynumber: 4.2 Consensus size: 24
707736 TCAATCAAGC
* ** *
707746 TTCAATTGAGCTT-AAAATCGAGC
1 TTCAATTGAGCTTCGAGTTCGAGT
*
707769 TTCAATTGA-ATTCGAGTTTCGAGT
1 TTCAATTGAGCTTCGAG-TTCGAGT
*
707793 TTCAATTGAGCTTTGAGTTCGAGCT
1 TTCAATTGAGCTTCGAGTTCGAG-T
*
707818 TT--TTTGAG-TTCGAGTT-GAGT
1 TTCAATTGAGCTTCGAGTTCGAGT
707838 TTCAAT
1 TTCAAT
707844 ACTATATTTC
Statistics
Matches: 59, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
20 3 0.05
21 3 0.05
22 10 0.17
23 15 0.25
24 20 0.34
25 8 0.14
ACGTcount: A:0.24, C:0.13, G:0.21, T:0.41
Consensus pattern (24 bp):
TTCAATTGAGCTTCGAGTTCGAGT
Found at i:709768 original size:3 final size:3
Alignment explanation
Indices: 709754--709801 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
709744 TTAAAATGAT
* *
709754 TAA TAA -AA TAA TAA TAA TAA TAA TAG TAG TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
709800 TA
1 TA
709802 TTTTTGGTAG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 4 0.10
3 37 0.90
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:710188 original size:40 final size:42
Alignment explanation
Indices: 710092--710328 Score: 184
Period size: 40 Copynumber: 5.5 Consensus size: 42
710082 AAGGGTGATA
* *
710092 ACACGGTTCCTACGCGATGAGGAAGG-CTGGTTATCTAGGGG-TG
1 ACACGGTTCCTACGTGATGAGG-AGGTCTGG-T-TCTGGGGGATG
*
710135 ACACGGCTCCTACGTGATGAGGAGGTCTGG-TC-GGGGGATG
1 ACACGGTTCCTACGTGATGAGGAGGTCTGGTTCTGGGGGATG
* * ** *
710175 ACATGGTTCCTACGTGATGAGGATGG-CAGGTCATCTTTAGGAATGATT
1 ACACGGTTCCTACGTGATGAGGA-GGTCTGGT--TC--T-GG-GGGATG
* *
710223 ACACGGTTCCTATGTGATGAGGACGTCTGGTTATCTGGGGG-TG
1 ACACGGTTCCTACGTGATGAGGAGGTCTGG-T-TCTGGGGGATG
* * *
710266 ACACGGCTCCTACGTAATGAGGAGGTCT-GATC-GGGGGATG
1 ACACGGTTCCTACGTGATGAGGAGGTCTGGTTCTGGGGGATG
*
710306 ACACGGTTCCTACGCGATGAGGA
1 ACACGGTTCCTACGTGATGAGGA
710329 CGGCATGCCA
Statistics
Matches: 156, Mismatches: 24, Indels: 31
0.74 0.11 0.15
Matches are distributed among these distances:
39 9 0.06
40 52 0.33
41 2 0.01
42 4 0.03
43 51 0.33
44 1 0.01
45 2 0.01
46 1 0.01
47 3 0.02
48 30 0.19
49 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.36, T:0.24
Consensus pattern (42 bp):
ACACGGTTCCTACGTGATGAGGAGGTCTGGTTCTGGGGGATG
Found at i:710278 original size:131 final size:132
Alignment explanation
Indices: 709991--710346 Score: 455
Period size: 131 Copynumber: 2.7 Consensus size: 132
709981 GGTTTGGTCG
* * * * * * * *
709991 TCTAAGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTCGGTGAATGATACGGCTCATACGT
1 TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGTTCCTACGT
* **
710056 GATGAAG-TGTTATGGCCATCTTTAGGAAGGGTGATAACACGGTTCCTACGCGATGAGGAAGGCT
66 GATGAGGATGGCA-GGCCATCTTTAGGAA--GTGATAACACGGTTCCTACGCGATGAGGAAGGCT
710120 GGTTA
128 GGTTA
*
710125 TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACATGGTTCCTACGT
1 TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGTTCCTACGT
* * * * * *
710190 GATGAGGATGGCAGGTCATCTTTAGGAA-TGATTACACGGTTCCTATGTGATGAGGACGTCTGGT
66 GATGAGGATGGCAGGCCATCTTTAGGAAGTGATAACACGGTTCCTACGCGATGAGGAAGGCTGGT
710254 TA
131 TA
* * * *
710256 TCTGGGGGTGACACGGCTCCTACGTAATGAGGAGGTCTGATCGGGGGATGACACGGTTCCTACGC
1 TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGTTCCTACGT
* *
710321 GATGAGGACGGCATGCCATCTTTAGG
66 GATGAGGATGGCAGGCCATCTTTAGG
710347 GATAATGTAT
Statistics
Matches: 195, Mismatches: 26, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
131 116 0.59
134 76 0.39
135 3 0.02
ACGTcount: A:0.22, C:0.18, G:0.34, T:0.25
Consensus pattern (132 bp):
TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGTTCCTACGT
GATGAGGATGGCAGGCCATCTTTAGGAAGTGATAACACGGTTCCTACGCGATGAGGAAGGCTGGT
TA
Found at i:710519 original size:66 final size:64
Alignment explanation
Indices: 710449--710594 Score: 202
Period size: 66 Copynumber: 2.2 Consensus size: 64
710439 GTTTCAGGAC
* * * * *
710449 AAACAGACTCAAAGATTTTCCTTCAAAAGATATTGTCTCAAGAGAGATAATATTTTGTTTCTAAA
1 AAACAGACTCAAAGATTTTCCTTCAAAAGAAACTGTCTCAAGACACA-AA-ATTTTGTTTCCAAA
710514 G
64 G
* * *
710515 AAACATACTCAAAGATTTTTCTTCAAAAGAAACTGTCTCAAGACACAAAATTTTGTTTCCAAAT
1 AAACAGACTCAAAGATTTTCCTTCAAAAGAAACTGTCTCAAGACACAAAATTTTGTTTCCAAAG
710579 AAACAGACTCAAAGAT
1 AAACAGACTCAAAGAT
710595 GGGTTATGTC
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
64 28 0.39
65 2 0.03
66 41 0.58
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.30
Consensus pattern (64 bp):
AAACAGACTCAAAGATTTTCCTTCAAAAGAAACTGTCTCAAGACACAAAATTTTGTTTCCAAAG
Found at i:710802 original size:32 final size:32
Alignment explanation
Indices: 710754--710817 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
710744 TTCACATCAG
* *
710754 GATGTTGACTCCCCAAATACGCCCCAACATTC
1 GATGTTGAATCCCCAAAGACGCCCCAACATTC
* * *
710786 GATGTTGAATCTCCAAAGATGCCCCATCATTC
1 GATGTTGAATCCCCAAAGACGCCCCAACATTC
710818 ATTATTTCTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.28, C:0.33, G:0.14, T:0.25
Consensus pattern (32 bp):
GATGTTGAATCCCCAAAGACGCCCCAACATTC
Found at i:711903 original size:13 final size:14
Alignment explanation
Indices: 711867--711915 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
711857 TCTTGTCTTC
*
711867 TTTTTT-TCTTCAT
1 TTTTTTCTCTTTAT
711880 TTGTTTT-TCTTT-T
1 TT-TTTTCTCTTTAT
711893 TTTTTTCTCTTTGAT
1 TTTTTTCTCTTT-AT
711908 TTTTTTCT
1 TTTTTTCT
711916 TTTCATTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
12 4 0.13
13 10 0.32
14 8 0.26
15 9 0.29
ACGTcount: A:0.04, C:0.12, G:0.04, T:0.80
Consensus pattern (14 bp):
TTTTTTCTCTTTAT
Found at i:711911 original size:25 final size:26
Alignment explanation
Indices: 711862--711918 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 26
711852 GTGCTTCTTG
*
711862 TCTTCTTTTTTTCTTCATTTG-TTTT
1 TCTTTTTTTTTTCTTCATTTGTTTTT
711887 TCTTTTTTTTTTC-TC-TTTGATTTTTT
1 TCTTTTTTTTTTCTTCATTTG--TTTTT
711913 TCTTTT
1 TCTTTT
711919 CATTTATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 4 0.14
24 2 0.07
25 12 0.43
26 10 0.36
ACGTcount: A:0.04, C:0.14, G:0.04, T:0.79
Consensus pattern (26 bp):
TCTTTTTTTTTTCTTCATTTGTTTTT
Found at i:711923 original size:14 final size:15
Alignment explanation
Indices: 711867--711923 Score: 54
Period size: 14 Copynumber: 4.1 Consensus size: 15
711857 TCTTGTCTTC
711867 TTTTTT-TC-TTCAT
1 TTTTTTCTCTTTCAT
711880 TTGTTTT-TCTTT--T
1 TT-TTTTCTCTTTCAT
*
711893 TTTTTTCTCTTTGAT
1 TTTTTTCTCTTTCAT
711908 TTTTTTCT-TTTCAT
1 TTTTTTCTCTTTCAT
711922 TT
1 TT
711924 ATTTATTTGC
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
12 4 0.11
13 10 0.26
14 13 0.34
15 11 0.29
ACGTcount: A:0.05, C:0.12, G:0.04, T:0.79
Consensus pattern (15 bp):
TTTTTTCTCTTTCAT
Found at i:715901 original size:29 final size:30
Alignment explanation
Indices: 715773--716026 Score: 153
Period size: 30 Copynumber: 8.6 Consensus size: 30
715763 CAGTAAATAA
* *
715773 AGAAACTTAAAGGACTAAAATAACTAAAAT
1 AGAAACTTAAAGGACTAAAATAGCTAAAAC
* * * * * *
715803 AAAAAGTTAAAAGACCAAAATAGCAAAAAT
1 AGAAACTTAAAGGACTAAAATAGCTAAAAC
*
715833 AAAAACTTAAAGGACTAAAATAGCTAAAAC
1 AGAAACTTAAAGGACTAAAATAGCTAAAAC
* * *
715863 AGAAAGTTAAAGGACTAAAGT-GGTAAAAC
1 AGAAACTTAAAGGACTAAAATAGCTAAAAC
* ** *
715892 ATAAACTTAAAGGGTTAAAACAG-T--AAC
1 AGAAACTTAAAGGACTAAAATAGCTAAAAC
** * *
715919 CTAAACTTAAGGGTCT-AAATAGC-AAATAC
1 AGAAACTTAAAGGACTAAAATAGCTAAA-AC
* * * * * *
715948 AGACATTTAAAGAACTAAAATAACAAAAAT
1 AGAAACTTAAAGGACTAAAATAGCTAAAAC
* * * *
715978 AAAAACTTAAGGGACTAAAAT-GGTATTAAC
1 AGAAACTTAAAGGACTAAAATAGCTA-AAAC
* *
716008 AGAAACTAAAAGGGCTAAA
1 AGAAACTTAAAGGACTAAA
716027 CATTAATTAC
Statistics
Matches: 167, Mismatches: 49, Indels: 16
0.72 0.21 0.07
Matches are distributed among these distances:
26 5 0.03
27 15 0.09
28 1 0.01
29 35 0.21
30 108 0.65
31 3 0.02
ACGTcount: A:0.56, C:0.11, G:0.14, T:0.19
Consensus pattern (30 bp):
AGAAACTTAAAGGACTAAAATAGCTAAAAC
Found at i:715923 original size:21 final size:21
Alignment explanation
Indices: 715877--715923 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
715867 AGTTAAAGGA
715877 CTAAAGTGGTAAAACATAAAC
1 CTAAAGTGGTAAAACATAAAC
*
715898 TTAAAG-GGTTAAAACAGT-AAC
1 CTAAAGTGG-TAAAACA-TAAAC
715919 CTAAA
1 CTAAA
715924 CTTAAGGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 2 0.09
21 19 0.86
22 1 0.05
ACGTcount: A:0.51, C:0.13, G:0.15, T:0.21
Consensus pattern (21 bp):
CTAAAGTGGTAAAACATAAAC
Found at i:716269 original size:76 final size:76
Alignment explanation
Indices: 716178--716318 Score: 198
Period size: 76 Copynumber: 1.9 Consensus size: 76
716168 ACTACCAAGG
* *
716178 AGTGACTAAAAT-AAAATATTTACGAATA-ACATGACCCAAATTCAAATATCCAACAAAAT-ACA
1 AGTGACTAAAATAAAAATAATTACGAATATA-ATGA-CCAAAGTCAAAT-TCCAACAAAATAACA
716240 AAATACATGAAATA
63 AAATACATGAAATA
* *
716254 AGTGACTAAAATAAAAATAATTACGAATATAATGACCAAAGTCGAATTCTAACAAAATAACAAAA
1 AGTGACTAAAATAAAAATAATTACGAATATAATGACCAAAGTCAAATTCCAACAAAATAACAAAA
716319 AAGTAAGAAC
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
75 10 0.17
76 28 0.48
77 19 0.33
78 1 0.02
ACGTcount: A:0.56, C:0.14, G:0.08, T:0.22
Consensus pattern (76 bp):
AGTGACTAAAATAAAAATAATTACGAATATAATGACCAAAGTCAAATTCCAACAAAATAACAAAA
TACATGAAATA
Found at i:716813 original size:15 final size:15
Alignment explanation
Indices: 716793--716824 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
716783 AGAACCCTTT
716793 GGTTTCTTCGACTCC
1 GGTTTCTTCGACTCC
716808 GGTTTCTTCGACTCC
1 GGTTTCTTCGACTCC
716823 GG
1 GG
716825 CGACCCTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.31, G:0.25, T:0.38
Consensus pattern (15 bp):
GGTTTCTTCGACTCC
Found at i:717553 original size:3 final size:3
Alignment explanation
Indices: 717539--717573 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
717529 TTAAAATGAT
717539 TAA TAA -AA TAA TAA TAA TAA TAA TAAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TA
717574 TTTTTCGTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.83
4 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:719322 original size:282 final size:282
Alignment explanation
Indices: 718808--719367 Score: 883
Period size: 282 Copynumber: 2.0 Consensus size: 282
718798 GTATTTATGT
**
718808 AGATGACATAGTTCTTGCAGGAAAGAACTTGGAGCTATTAAATGAGATTCAGACTTTTCTTCAGC
1 AGATGACATAGTTCTTGCAGGAAAGAACTTGGAGCTATTAAAAAAGATTCAGACTTTTCTTCAGC
* *
718873 AACATTTTAAACTAAAAATCCCAGATCCTTTGAAATATTTTCTTGGTTTTGAGATTGCTCGAAAT
66 AACATTTTAAACTAAAAATCCCAGATCCTTTGAAATATTTTCTTGGTTTTGAGACTGCTCAAAAT
* *
718938 GCTACTGGGATCTCTTTGTCCAAAGACATCATACATTACAACTTTCGGAAGACACCGATACTCTT
131 GCTACTGGGATCACTTTGTCCAAAGACATCATACATTACAACTTTCGGAAGACACCGATACTCAT
* *
719003 GGTAAGAAACCTGTTGATCTATCAATTTTTCCCTCTCATAAATTGAGTTTTCATGAAGGTGAGTT
196 GGTAAGAAACCTGCTGATCTATCAATTTTTCCCTCTCATAAATTGAGTATTCATGAAGGTGAGTT
* *
719068 ATTGTTTGATCCTTAACTGTGG
261 ATTGTCTGATCCTCAACTGTGG
*
719090 AGATGACATAGTTCTTGCAGGAAAGAACTTGGAGCTATTAAAAAAGGTTCAGACTTTTCTTCAGC
1 AGATGACATAGTTCTTGCAGGAAAGAACTTGGAGCTATTAAAAAAGATTCAGACTTTTCTTCAGC
* * *
719155 AACA-TTTAAGCTAAAAATCCTAGGTCCTTTGAAATATTTTCTTGGTTTTGAGACTGCTCAAAAT
66 AACATTTTAAACTAAAAATCCCAGATCCTTTGAAATATTTTCTTGGTTTTGAGACTGCTCAAAAT
* * * * ** *
719219 TCTACTGGGATCACTTTGTCACAAAGACATTATGCATTATAACTTTTC-GAAGACATTGATGCTC
131 GCTACTGGGATCACTTTGTC-CAAAGACATCATACATTACAAC-TTTCGGAAGACACCGATACTC
719283 ATGGTAAGAAACCTGCTGATCTATCAATTGTTT-CCTCTCATAAATTGAGTATTCATGAAGGTGA
194 ATGGTAAGAAACCTGCTGATCTATCAATT-TTTCCCTCTCATAAATTGAGTATTCATGAAGGTGA
719347 GTTATTGTCTGATCCTCAACT
258 GTTATTGTCTGATCCTCAACT
719368 ATATTGAAGG
Statistics
Matches: 254, Mismatches: 21, Indels: 6
0.90 0.07 0.02
Matches are distributed among these distances:
281 73 0.29
282 174 0.69
283 7 0.03
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (282 bp):
AGATGACATAGTTCTTGCAGGAAAGAACTTGGAGCTATTAAAAAAGATTCAGACTTTTCTTCAGC
AACATTTTAAACTAAAAATCCCAGATCCTTTGAAATATTTTCTTGGTTTTGAGACTGCTCAAAAT
GCTACTGGGATCACTTTGTCCAAAGACATCATACATTACAACTTTCGGAAGACACCGATACTCAT
GGTAAGAAACCTGCTGATCTATCAATTTTTCCCTCTCATAAATTGAGTATTCATGAAGGTGAGTT
ATTGTCTGATCCTCAACTGTGG
Found at i:719648 original size:3 final size:3
Alignment explanation
Indices: 719635--719673 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
719625 TTGTCCAGTT
719635 TTA TT- TTA TTA TTA TTA TTA TTA -TA TTA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
719674 AATAAATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 6 0.18
3 27 0.82
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:719661 original size:8 final size:8
Alignment explanation
Indices: 719635--719673 Score: 60
Period size: 8 Copynumber: 4.8 Consensus size: 8
719625 TTGTCCAGTT
*
719635 TTATTTTA
1 TTATTATA
719643 TTATTATTA
1 TTATTA-TA
719652 TTATTATA
1 TTATTATA
719660 TTATTATA
1 TTATTATA
719668 TTATTA
1 TTATTA
719674 AATAAATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 21 0.72
9 8 0.28
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TTATTATA
Found at i:719784 original size:14 final size:14
Alignment explanation
Indices: 719765--719794 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
719755 AGCCCAAAAA
719765 ACAACCCGGTCCAG
1 ACAACCCGGTCCAG
*
719779 ACAACCCGGTCTAG
1 ACAACCCGGTCCAG
719793 AC
1 AC
719795 CCGATCCGGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.40, G:0.20, T:0.10
Consensus pattern (14 bp):
ACAACCCGGTCCAG
Found at i:721734 original size:29 final size:29
Alignment explanation
Indices: 721700--721758 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
721690 CTTAAATTAA
721700 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
721729 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
721758 T
1 T
721759 AGGTGAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:725580 original size:21 final size:20
Alignment explanation
Indices: 725554--725695 Score: 162
Period size: 21 Copynumber: 6.8 Consensus size: 20
725544 AGGGTGTCAA
*
725554 AGTGCATTCATGCACCCCTGC
1 AGTGCATCCATGCA-CCCTGC
725575 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCA-CCCTGC
725596 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCA-CCCTGC
725617 AGTGCATCCATGCA-CCTGCAC
1 AGTGCATCCATGCACCCTG--C
* *
725638 TAGTGCATCGATGCACCATGC
1 -AGTGCATCCATGCACCCTGC
725659 AGTGCATCCATGCA-CCTGCAC
1 AGTGCATCCATGCACCCTG--C
725680 TAGTGCATCCATGCAC
1 -AGTGCATCCATGCAC
725696 TCAAACACCG
Statistics
Matches: 107, Mismatches: 6, Indels: 14
0.84 0.05 0.11
Matches are distributed among these distances:
19 7 0.07
20 13 0.12
21 57 0.53
22 27 0.25
23 3 0.03
ACGTcount: A:0.22, C:0.36, G:0.20, T:0.23
Consensus pattern (20 bp):
AGTGCATCCATGCACCCTGC
Found at i:725588 original size:13 final size:13
Alignment explanation
Indices: 725585--725672 Score: 55
Period size: 13 Copynumber: 6.9 Consensus size: 13
725575 AGTGCATCCA
*
725585 TGCATCCCTGCAG
1 TGCATCCATGCAG
725598 TGCATCCATGCA-
1 TGCATCCATGCAG
725610 T-C--CC-TGCAG
1 TGCATCCATGCAG
*
725619 TGCATCCATGCACC
1 TGCATCCATGCA-G
*
725633 TGCA-CTAGTGCATCG
1 TGCATCCA-TGCA--G
725648 ATGCA-CCATGCAG
1 -TGCATCCATGCAG
725661 TGCATCCATGCA
1 TGCATCCATGCA
725673 CCTGCACTAG
Statistics
Matches: 60, Mismatches: 5, Indels: 20
0.71 0.06 0.24
Matches are distributed among these distances:
8 4 0.07
9 3 0.05
10 1 0.02
11 1 0.02
12 7 0.12
13 25 0.42
14 8 0.13
15 5 0.08
16 6 0.10
ACGTcount: A:0.22, C:0.35, G:0.20, T:0.23
Consensus pattern (13 bp):
TGCATCCATGCAG
Found at i:725615 original size:42 final size:41
Alignment explanation
Indices: 725554--725695 Score: 189
Period size: 42 Copynumber: 3.4 Consensus size: 41
725544 AGGGTGTCAA
*
725554 AGTGCATTCATGCACCCCTGCAGTGCATCCATGCATCCCTG-C-
1 AGTGCATCCATGCA-CCCTGCAGTGCATCCATGCA--CCTGACT
725596 AGTGCATCCATGCATCCCTGCAGTGCATCCATGCACCTGCACT
1 AGTGCATCCATGCA-CCCTGCAGTGCATCCATGCACCTG-ACT
* *
725639 AGTGCATCGATGCACCATGCAGTGCATCCATGCACCTGCACT
1 AGTGCATCCATGCACCCTGCAGTGCATCCATGCACCTG-ACT
725681 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
725696 TCAAACACCG
Statistics
Matches: 92, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
40 4 0.04
42 75 0.82
43 13 0.14
ACGTcount: A:0.22, C:0.36, G:0.20, T:0.23
Consensus pattern (41 bp):
AGTGCATCCATGCACCCTGCAGTGCATCCATGCACCTGACT
Found at i:725741 original size:20 final size:20
Alignment explanation
Indices: 725716--725790 Score: 105
Period size: 20 Copynumber: 3.7 Consensus size: 20
725706 AATGCAATTA
*
725716 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTGCT
**
725736 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATC-CTGCT
725757 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
*
725777 GTGCATCCATGCAT
1 GTGCATCGATGCAT
725791 GAAGGCTGCA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 31 0.65
21 17 0.35
ACGTcount: A:0.19, C:0.28, G:0.24, T:0.29
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGCT
Found at i:725763 original size:41 final size:41
Alignment explanation
Indices: 725716--725798 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
725706 AATGCAATTA
* *
725716 GTGCATCGATGCATCCTTCTGTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATCCTGCTGTGCATCCATGCATCAAGGCT
*
725757 GTGCATCGATGCATCCTGCTGTGCATCCATGCATGAAGGCT
1 GTGCATCGATGCATCCTGCTGTGCATCCATGCATCAAGGCT
725798 G
1 G
725799 CAACGGCTAG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.28
Consensus pattern (41 bp):
GTGCATCGATGCATCCTGCTGTGCATCCATGCATCAAGGCT
Found at i:725931 original size:21 final size:21
Alignment explanation
Indices: 725902--725941 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
725892 TTTTAGTAGA
725902 AAAATCATCTCCAAACGGCTCC
1 AAAATCATC-CCAAACGGCTCC
*
725924 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCAAACGGCT
725942 ATATACGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 4 0.24
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCAAACGGCTCC
Found at i:727071 original size:19 final size:20
Alignment explanation
Indices: 727047--727094 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
727037 AACGATTTTC
*
727047 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
727066 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
727086 TTTTGAAAA
1 TTTTGAAAA
727095 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:728396 original size:29 final size:30
Alignment explanation
Indices: 728327--728385 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
728317 CAATTTAAGG
728327 CAAAATGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
*
728357 CAAAATATTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
728386 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.44
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:728514 original size:22 final size:20
Alignment explanation
Indices: 728466--728543 Score: 79
Period size: 21 Copynumber: 3.8 Consensus size: 20
728456 AGGGTGTCAA
*
728466 AGTGCATCCATGCACCCCTG-T
1 AGTGCATCCATGCA--CATGCT
728487 AGTGCATCCATGCACATGCACT
1 AGTGCATCCATGCACATG--CT
*
728509 AGTGCATCGATGCACCATGC-
1 AGTGCATCCATGCA-CATGCT
728529 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
728544 TCAAACACCG
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
19 4 0.08
20 13 0.26
21 15 0.30
22 14 0.28
23 4 0.08
ACGTcount: A:0.24, C:0.33, G:0.21, T:0.22
Consensus pattern (20 bp):
AGTGCATCCATGCACATGCT
Found at i:728589 original size:20 final size:20
Alignment explanation
Indices: 728564--728638 Score: 96
Period size: 20 Copynumber: 3.7 Consensus size: 20
728554 AATGCAATTA
*
728564 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTGCT
* **
728584 GTGCATAGATGCATCAAGGCT
1 GTGCATCGATGCATC-CTGCT
728605 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
*
728625 GTGCATCCATGCAT
1 GTGCATCGATGCAT
728639 GAAGGCTGCA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 30 0.65
21 16 0.35
ACGTcount: A:0.20, C:0.27, G:0.24, T:0.29
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGCT
Found at i:728611 original size:41 final size:41
Alignment explanation
Indices: 728564--728646 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 41
728554 AATGCAATTA
* *
728564 GTGCATCGATGCATCCTTCTGTGCATAGATGCATCAAGGCT
1 GTGCATCGATGCATCCTGCTGTGCATACATGCATCAAGGCT
* *
728605 GTGCATCGATGCATCCTGCTGTGCATCCATGCATGAAGGCT
1 GTGCATCGATGCATCCTGCTGTGCATACATGCATCAAGGCT
728646 G
1 G
728647 CAACGGCTAG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.20, C:0.25, G:0.27, T:0.28
Consensus pattern (41 bp):
GTGCATCGATGCATCCTGCTGTGCATACATGCATCAAGGCT
Found at i:729043 original size:34 final size:32
Alignment explanation
Indices: 729004--729073 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
728994 TTTTGTAAAG
* *
729004 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
729038 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
729070 GGGA
1 GGGA
729074 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:730348 original size:29 final size:29
Alignment explanation
Indices: 730314--730372 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
730304 CCTAAATTAA
730314 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
730343 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
730372 T
1 T
730373 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:735011 original size:17 final size:16
Alignment explanation
Indices: 734974--735026 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 16
734964 TATCACAATA
734974 ATTTAATATTTTAT-T
1 ATTTAATATTTTATAT
734989 GAATTTAATATTTTATCAT
1 --ATTTAATATTTTAT-AT
*
735008 ATTTAATAATTTATAT
1 ATTTAATATTTTATAT
735024 ATT
1 ATT
735027 AATGTAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
16 5 0.15
17 27 0.82
19 1 0.03
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (16 bp):
ATTTAATATTTTATAT
Found at i:741447 original size:22 final size:21
Alignment explanation
Indices: 741394--741439 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
741384 AAAAGAAAAA
* *
741394 ACTA-ATTATTTTCTACAACT
1 ACTACATTATTTTCCAAAACT
741414 ACTACACTTATTTTCCAAAACT
1 ACTACA-TTATTTTCCAAAACT
741436 ACTA
1 ACTA
741440 TGATTATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 4 0.18
21 1 0.05
22 17 0.77
ACGTcount: A:0.37, C:0.24, G:0.00, T:0.39
Consensus pattern (21 bp):
ACTACATTATTTTCCAAAACT
Found at i:742796 original size:20 final size:20
Alignment explanation
Indices: 742771--742844 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
742761 CGATCTTCCA
742771 AGAATCGCAACACGATTCAG
1 AGAATCGCAACACGATTCAG
*
742791 AGAATCGC-A-ACGTCTTCCA-
1 AGAATCGCAACACG-ATT-CAG
*
742810 AGAATCGCAACGCGATTCAG
1 AGAATCGCAACACGATTCAG
* *
742830 AAAATCGCAAAACGA
1 AGAATCGCAACACGA
742845 CCACGGCCCC
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
18 3 0.07
19 13 0.30
20 25 0.58
21 2 0.05
ACGTcount: A:0.41, C:0.26, G:0.19, T:0.15
Consensus pattern (20 bp):
AGAATCGCAACACGATTCAG
Found at i:742813 original size:39 final size:39
Alignment explanation
Indices: 742764--742839 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
742754 CACAACGCGA
*
742764 TCTTCCAAGAATCGCAACACGATTCAGAGAATCGCAACG
1 TCTTCCAAGAATCGCAACACGATTCAGAAAATCGCAACG
*
742803 TCTTCCAAGAATCGCAACGCGATTCAGAAAATCGCAA
1 TCTTCCAAGAATCGCAACACGATTCAGAAAATCGCAA
742840 AACGACCACG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.37, C:0.28, G:0.17, T:0.18
Consensus pattern (39 bp):
TCTTCCAAGAATCGCAACACGATTCAGAAAATCGCAACG
Found at i:742815 original size:19 final size:19
Alignment explanation
Indices: 742764--742821 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 19
742754 CACAACGCGA
742764 TCTTCCAAGAATCGCAACACG
1 TCTTCCAAGAATCGC-A-ACG
*
742785 -ATT-CAGAGAATCGCAACG
1 TCTTCCA-AGAATCGCAACG
742803 TCTTCCAAGAATCGCAACG
1 TCTTCCAAGAATCGCAACG
742822 CGATTCAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 3 0.09
19 17 0.53
20 12 0.38
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.19
Consensus pattern (19 bp):
TCTTCCAAGAATCGCAACG
Found at i:744066 original size:36 final size:36
Alignment explanation
Indices: 744014--744087 Score: 112
Period size: 36 Copynumber: 2.1 Consensus size: 36
744004 ATCGAATTAA
* * *
744014 ACGGGGACATGAAAAAATCGTTTATGCTAAACGGGG
1 ACGGGGACAGGAAAAAACCGTTTATGCTAAACGAGG
*
744050 ACGGGGACAGGGAAAAACCGTTTATGCTAAACGAGG
1 ACGGGGACAGGAAAAAACCGTTTATGCTAAACGAGG
744086 AC
1 AC
744088 AGGTTTGGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.36, C:0.16, G:0.31, T:0.16
Consensus pattern (36 bp):
ACGGGGACAGGAAAAAACCGTTTATGCTAAACGAGG
Found at i:744129 original size:12 final size:12
Alignment explanation
Indices: 744101--744137 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
744091 TTTGGTAATC
744101 CCCGCCCCGATTA
1 CCCGCCCCGA-TA
744114 CCCGCCCCGATA
1 CCCGCCCCGATA
*
744126 CCCGACCCGATA
1 CCCGCCCCGATA
744138 AATATTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.19, C:0.54, G:0.16, T:0.11
Consensus pattern (12 bp):
CCCGCCCCGATA
Found at i:744205 original size:32 final size:30
Alignment explanation
Indices: 744165--744237 Score: 101
Period size: 32 Copynumber: 2.3 Consensus size: 30
744155 TTATTATATT
744165 ATATATATATAATATTAATAAATTTAATTTAA
1 ATATATATATAATATT--TAAATTTAATTTAA
*
744197 ATTAATATATATAATATTTATATTTAATTTAA
1 A-T-ATATATATAATATTTAAATTTAATTTAA
744229 ATATATATA
1 ATATATATA
744238 CCCGGCCCGA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
30 7 0.18
31 1 0.03
32 15 0.39
33 1 0.03
34 14 0.37
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
ATATATATATAATATTTAAATTTAATTTAA
Found at i:746155 original size:2 final size:2
Alignment explanation
Indices: 746150--746189 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
746140 AAATACATAC
* *
746150 AT AT AT AT AT AT AC AT AT AC 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
746190 TAAAATATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:746664 original size:64 final size:64
Alignment explanation
Indices: 746586--746724 Score: 154
Period size: 64 Copynumber: 2.2 Consensus size: 64
746576 GGATCTTGAT
* * * *
746586 AGGTCGGGTAAAATCGGGTACAGGTCA-ACTCAGGTTGATTTGACACTAAATCTAGATCGGGTTC
1 AGGTCGGGTCAAATC-AGTACAGGTCATACTCAGGTTGATTTGACACCAAATCCAGATCGGGTTC
* * * * ** *
746650 AGGTCAGGTCAAATCAGTTCGGGTTATTTTCAGGTTGATTTGACACCAGATCCAGATCGGGTTC
1 AGGTCGGGTCAAATCAGTACAGGTCATACTCAGGTTGATTTGACACCAAATCCAGATCGGGTTC
*
746714 AAGTCGGGTCA
1 AGGTCGGGTCA
746725 TTTTCAGTTC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
63 7 0.11
64 54 0.89
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (64 bp):
AGGTCGGGTCAAATCAGTACAGGTCATACTCAGGTTGATTTGACACCAAATCCAGATCGGGTTC
Found at i:747441 original size:24 final size:23
Alignment explanation
Indices: 747400--747533 Score: 81
Period size: 26 Copynumber: 6.0 Consensus size: 23
747390 AAAAAAATAT
747400 AATATATATAA-TA-A--TATAA
1 AATATATATAACTATATTTATAA
747419 AATTATATATAACTATATTTATATTA
1 AA-TATATATAACTATATTTATA--A
*
747445 AA-CTATATAA-T-TA-TTATAA
1 AATATATATAACTATATTTATAA
* *
747464 AATATATATAAATTATATTTATGTGA
1 AATATATAT-AACTATATTTA--TAA
* * *
747490 ACTATATATAAACTATGTATATAA
1 AATATATAT-AACTATATTTATAA
747514 AAT-TATA-AACTATATTTATA
1 AATATATATAACTATATTTATA
747534 TTATAAACTA
Statistics
Matches: 90, Mismatches: 11, Indels: 26
0.71 0.09 0.20
Matches are distributed among these distances:
19 5 0.06
20 14 0.16
21 20 0.22
22 4 0.04
23 7 0.08
24 18 0.20
26 22 0.24
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (23 bp):
AATATATATAACTATATTTATAA
Found at i:747464 original size:18 final size:18
Alignment explanation
Indices: 747396--747556 Score: 61
Period size: 18 Copynumber: 8.8 Consensus size: 18
747386 TTTGAAAAAA
*
747396 ATATAA-TATATATAATAAT
1 ATATAATTAT-TATAA-ACT
*
747415 ATAAAATTA-TATATAACT
1 ATATAATTATTATA-AACT
747433 ATAT--TTA-TATTAAACT
1 ATATAATTATTA-TAAACT
*
747449 ATATAATTATTATAAAAT
1 ATATAATTATTATAAACT
* **
747467 ATAT-ATAAATTAT-ATTT
1 ATATAAT-TATTATAAACT
* *
747484 ATGTGAACTATATATAAACT
1 ATAT-AATTAT-TATAAACT
**
747504 ATGTATATAAAATTATAAACT
1 A--TATA-ATTATTATAAACT
*
747525 ATAT-TTATATTATAAACT
1 ATATAAT-TATTATAAACT
747543 ATAT-ATTATTATAA
1 ATATAATTATTATAA
747557 GTTATATATA
Statistics
Matches: 108, Mismatches: 19, Indels: 32
0.68 0.12 0.20
Matches are distributed among these distances:
16 13 0.12
17 17 0.16
18 43 0.40
19 15 0.14
20 5 0.05
21 10 0.09
22 5 0.05
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (18 bp):
ATATAATTATTATAAACT
Found at i:747533 original size:21 final size:18
Alignment explanation
Indices: 747515--747556 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
747505 TGTATATAAA
747515 ATTATAAACTATATTTAT
1 ATTATAAACTATATTTAT
*
747533 ATTATAAACTATATAT-T
1 ATTATAAACTATATTTAT
747550 ATTATAA
1 ATTATAA
747557 GTTATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (18 bp):
ATTATAAACTATATTTAT
Found at i:747571 original size:93 final size:93
Alignment explanation
Indices: 747413--747614 Score: 293
Period size: 93 Copynumber: 2.2 Consensus size: 93
747403 ATATATAATA
747413 ATATAAAATTATATATAACTATATTTATATTAAACTATATAATTATTATAAAATATATATAAATT
1 ATATAAAA-T-TATATAACTATATTTATATTAAACTATATAATTATTATAAAATATATATAAATT
* *
747478 ATATTTATGTGAACTATATATAAACTATGT
64 ATATTTATGTGAACTATATATAAACAATGC
**
747508 ATATAAAATTATA-AACTATATTTATATTATAAACTATAT-ATTATTATAAGTTATATATAAATT
1 ATATAAAATTATATAACTATATTTATA-T-TAAACTATATAATTATTATAAAATATATATAAATT
* *
747571 ATGTTTATGTGAACTATATATAAGCAATGC
64 ATATTTATGTGAACTATATATAAACAATGC
747601 ATAT-AAATTATATA
1 ATATAAAATTATATA
747615 TGTATAAACT
Statistics
Matches: 98, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
92 21 0.21
93 58 0.59
94 11 0.11
95 8 0.08
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (93 bp):
ATATAAAATTATATAACTATATTTATATTAAACTATATAATTATTATAAAATATATATAAATTAT
ATTTATGTGAACTATATATAAACAATGC
Found at i:747674 original size:69 final size:69
Alignment explanation
Indices: 747611--747744 Score: 207
Period size: 69 Copynumber: 1.9 Consensus size: 69
747601 ATATAAATTA
* *
747611 TATATGTATAAACTATA-AAAAGTATATAGTTTATAAAATATTATTTATATTAATATAGTATATA
1 TATATGTATAAACTATATAAAA-TATATAATTTATAAAATATAATTTATATTAATATAGTATATA
747675 TAAAC
65 TAAAC
***
747680 TATATGTATAAACTATATAAAATATATAATTTATATGTTATAATTTATATTAATATAGTATATAT
1 TATATGTATAAACTATATAAAATATATAATTTATAAAATATAATTTATATTAATATAGTATATAT
747745 GTATGCATTA
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
69 55 0.93
70 4 0.07
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (69 bp):
TATATGTATAAACTATATAAAATATATAATTTATAAAATATAATTTATATTAATATAGTATATAT
AAAC
Found at i:747689 original size:13 final size:13
Alignment explanation
Indices: 747673--747697 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
747663 ATATAGTATA
747673 TATAAACTATATG
1 TATAAACTATATG
747686 TATAAACTATAT
1 TATAAACTATAT
747698 AAAATATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (13 bp):
TATAAACTATATG
Found at i:747816 original size:2 final size:2
Alignment explanation
Indices: 747811--747866 Score: 87
Period size: 2 Copynumber: 28.0 Consensus size: 2
747801 TTATATAGTT
*
747811 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
747854 TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA
747867 CATGGTTTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
1 1 0.02
2 48 0.96
3 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:748253 original size:2 final size:2
Alignment explanation
Indices: 748246--748287 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
748236 CACTTGAATA
*
748246 AT AT AT AT TT AT AT -T 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
748287 A
1 A
748288 AACATAAGTG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:749328 original size:23 final size:24
Alignment explanation
Indices: 749302--749351 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
749292 TTATTTTTTC
*
749302 TTTATATGAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
749325 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
749349 TTT
1 TTT
749352 CCTTGCATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:749662 original size:16 final size:16
Alignment explanation
Indices: 749595--749665 Score: 115
Period size: 16 Copynumber: 4.4 Consensus size: 16
749585 CGGGTCATTT
749595 ACAGGTCAGGTTAAAA
1 ACAGGTCAGGTTAAAA
*
749611 ACAAGTCAGGTTAAAA
1 ACAGGTCAGGTTAAAA
*
749627 ACATGTCAGGTTAAAA
1 ACAGGTCAGGTTAAAA
*
749643 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTAAAA
749659 ACAGGTC
1 ACAGGTC
749666 GGGTAATACC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (16 bp):
ACAGGTCAGGTTAAAA
Found at i:751682 original size:21 final size:21
Alignment explanation
Indices: 751664--751714 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
751654 TTTCTTTTCT
*
751664 TTATTTTT-ATTTATTTTTTA
1 TTATTTTTCATCTATTTTTTA
751684 TTATTTTTCATCTATTTTCTT-
1 TTATTTTTCATCTATTTT-TTA
751705 TTCATTTTTC
1 TT-ATTTTTC
751715 TTTTCATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 8 0.30
21 10 0.37
22 9 0.33
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.75
Consensus pattern (21 bp):
TTATTTTTCATCTATTTTTTA
Found at i:751715 original size:12 final size:12
Alignment explanation
Indices: 751698--751724 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
751688 TTTTCATCTA
751698 TTTTCTTTTCAT
1 TTTTCTTTTCAT
751710 TTTTCTTTTCAT
1 TTTTCTTTTCAT
751722 TTT
1 TTT
751725 GTTTTAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTCTTTTCAT
Found at i:761472 original size:20 final size:21
Alignment explanation
Indices: 761449--761489 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
761439 TCACTCATTA
*
761449 TACTT-TTAATTTTTTCAATT
1 TACTTATTAAATTTTTCAATT
*
761469 TACTTATTAAATTTTTGAATT
1 TACTTATTAAATTTTTCAATT
761490 GCTCACTCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (21 bp):
TACTTATTAAATTTTTCAATT
Found at i:761568 original size:16 final size:17
Alignment explanation
Indices: 761547--761580 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
761537 TTTTATTATT
*
761547 ATTTAATATA-AAAATA
1 ATTTAAAATATAAAATA
761563 ATTTAAAATATAAAATA
1 ATTTAAAATATAAAATA
761580 A
1 A
761581 AAAACATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTTAAAATATAAAATA
Found at i:763641 original size:17 final size:19
Alignment explanation
Indices: 763607--763643 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
763597 ATAAGTATAT
763607 AAAATATAAATATATTTAA
1 AAAATATAAATATATTTAA
763626 AAAATATAAA-AT-TTTAA
1 AAAATATAAATATATTTAA
763643 A
1 A
763644 CTCATTTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 2 0.11
19 10 0.56
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAATATAAATATATTTAA
Found at i:763687 original size:2 final size:2
Alignment explanation
Indices: 763680--763721 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
763670 GTATTGTTTA
763680 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
763722 TCAACCATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:769337 original size:18 final size:18
Alignment explanation
Indices: 769311--769356 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 18
769301 TATTATTTTA
* *
769311 AAATATTTTATGATATTT
1 AAATTTTTTATGATATTC
769329 AAATTTTTTTATGATATTC
1 AAA-TTTTTTATGATATTC
769348 AAATTTTTT
1 AAATTTTTT
769357 TTAACACATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (18 bp):
AAATTTTTTATGATATTC
Found at i:769359 original size:20 final size:19
Alignment explanation
Indices: 769316--769357 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
769306 TTTTAAAATA
*
769316 TTTTATGATATTTAAATTT
1 TTTTATGATATTCAAATTT
769335 TTTTATGATATTCAAATTT
1 TTTTATGATATTCAAATTT
769354 TTTT
1 TTTT
769358 TAACACATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (19 bp):
TTTTATGATATTCAAATTT
Found at i:770512 original size:16 final size:17
Alignment explanation
Indices: 770491--770524 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
770481 TTCTATTATT
*
770491 ATTTAATATA-AAAATA
1 ATTTAAAATATAAAATA
770507 ATTTAAAATATAAAATA
1 ATTTAAAATATAAAATA
770524 A
1 A
770525 AAACATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTTAAAATATAAAATA
Found at i:777217 original size:14 final size:12
Alignment explanation
Indices: 777200--777273 Score: 62
Period size: 14 Copynumber: 5.8 Consensus size: 12
777190 GATTTAGGAT
777200 TTTTAGTTTGATTA
1 TTTTA-TTT-ATTA
777214 TTTTA-TTATTA
1 TTTTATTTATTA
*
777225 CTTTTTATTTAGTA
1 --TTTTATTTATTA
777239 TTTTTAGTTTGATTA
1 -TTTTA-TTT-ATTA
777254 TTTTA-TTATTA
1 TTTTATTTATTA
777265 TTTTATTTA
1 TTTTATTTA
777274 GGAATTAATT
Statistics
Matches: 52, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
11 13 0.25
12 7 0.13
13 11 0.21
14 18 0.35
15 3 0.06
ACGTcount: A:0.23, C:0.01, G:0.07, T:0.69
Consensus pattern (12 bp):
TTTTATTTATTA
Found at i:777242 original size:40 final size:38
Alignment explanation
Indices: 777191--777276 Score: 145
Period size: 40 Copynumber: 2.2 Consensus size: 38
777181 AACCTTTTAG
777191 ATTTAGGATTTTTAGTTTGATTATTTTATTATTACTTTTT
1 ATTTAGGATTTTTAGTTTGATTATTTTATTATTA--TTTT
*
777231 ATTTAGTATTTTTAGTTTGATTATTTTATTATTATTTT
1 ATTTAGGATTTTTAGTTTGATTATTTTATTATTATTTT
777269 ATTTAGGA
1 ATTTAGGA
777277 ATTAATTATT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
38 11 0.25
40 33 0.75
ACGTcount: A:0.24, C:0.01, G:0.10, T:0.64
Consensus pattern (38 bp):
ATTTAGGATTTTTAGTTTGATTATTTTATTATTATTTT
Found at i:777266 original size:11 final size:11
Alignment explanation
Indices: 777210--777271 Score: 52
Period size: 11 Copynumber: 5.0 Consensus size: 11
777200 TTTTAGTTTG
777210 ATTATTTTATT
1 ATTATTTTATT
777221 ATTACTTTTTATTT
1 ATTA--TTTTA-TT
*
777235 AGTATTTTTAGTTT
1 ATTA-TTTTA--TT
777249 GATTATTTTATT
1 -ATTATTTTATT
777261 ATTATTTTATT
1 ATTATTTTATT
777272 TAGGAATTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
11 15 0.34
12 2 0.05
13 11 0.25
14 13 0.30
15 3 0.07
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.69
Consensus pattern (11 bp):
ATTATTTTATT
Found at i:786570 original size:21 final size:21
Alignment explanation
Indices: 786546--786606 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
786536 TTCAAAGAAA
786546 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
786567 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
786581 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
786602 CATTT
1 CATTT
786607 TTCAAAGTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:786580 original size:35 final size:36
Alignment explanation
Indices: 786495--786613 Score: 188
Period size: 35 Copynumber: 3.3 Consensus size: 36
786485 ATCCCATTAT
* *
786495 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
786531 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
786567 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
786602 CATTTTTCAAAG
1 CATTTTTCAAAG
786614 TTGGTTACCA
Statistics
Matches: 77, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
35 35 0.45
36 22 0.29
37 20 0.26
ACGTcount: A:0.44, C:0.20, G:0.05, T:0.31
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:786627 original size:34 final size:36
Alignment explanation
Indices: 786495--786641 Score: 171
Period size: 35 Copynumber: 4.2 Consensus size: 36
786485 ATCCCATTAT
*
786495 CATTTTTCAACA-AACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAA-AGAACATTTACCAAACTTTGAAAAAC
*
786531 TATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
1 CATTTTTCAAAG-AACATTTACCAAACTTTGAAAAAC
786567 CA-TTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
1 CATTTTTCAAAG-AACATTTACCAAACTTTGAAAAAC
****
786602 CATTTTTCAAAG-TTGGTTACCAAAC-TTGAAAAAC
1 CATTTTTCAAAGAACATTTACCAAACTTTGAAAAAC
786636 CATTTT
1 CATTTT
786642 AATACTTTCA
Statistics
Matches: 100, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
33 3 0.03
34 20 0.20
35 36 0.36
36 24 0.24
37 17 0.17
ACGTcount: A:0.42, C:0.20, G:0.06, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAACATTTACCAAACTTTGAAAAAC
Found at i:791177 original size:37 final size:36
Alignment explanation
Indices: 791118--791237 Score: 181
Period size: 35 Copynumber: 3.3 Consensus size: 36
791108 ATCCCATTAT
* *
791118 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
791154 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
791190 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
791225 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
791238 TTGGTTACCA
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
35 35 0.45
36 13 0.17
37 29 0.38
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:791193 original size:21 final size:21
Alignment explanation
Indices: 791169--791229 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
791159 TTCAAAGAAA
791169 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
791190 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
791204 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
791225 CATTT
1 CATTT
791230 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:791246 original size:35 final size:36
Alignment explanation
Indices: 791120--791265 Score: 135
Period size: 35 Copynumber: 4.1 Consensus size: 36
791110 CCCATTATCA
*
791120 TTTTTCAACA-AACA-TCTACCAAACTTTGAAAAAC-T
1 TTTTTCAA-AGAACAGT-TACCAAACTTTGAAAACCAT
*
791155 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA-
1 -TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
*
791192 -TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
1 TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
***
791228 TTTTTCAAAG-TTGGTTACCAAAC-TTGAAAAACCAT
1 TTTTTCAAAGAACAGTTACCAAACTTTG-AAAACCAT
791263 TTT
1 TTT
791266 AATACTTTCA
Statistics
Matches: 98, Mismatches: 5, Indels: 15
0.83 0.04 0.13
Matches are distributed among these distances:
34 3 0.03
35 56 0.57
36 8 0.08
37 30 0.31
38 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.33
Consensus pattern (36 bp):
TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
Found at i:791422 original size:27 final size:28
Alignment explanation
Indices: 791391--791450 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
791381 GGTACAGTGC
*
791391 CCTTTCCAAT-TCTAACATTTTAAATCT
1 CCTTTCCAATATCTAACATTCTAAATCT
*
791418 CCTTTCCACTATCTAACATTCTAAATCT
1 CCTTTCCAATATCTAACATTCTAAATCT
791446 CCTTT
1 CCTTT
791451 TGAAATGTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 9 0.30
28 21 0.70
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (28 bp):
CCTTTCCAATATCTAACATTCTAAATCT
Found at i:794969 original size:30 final size:30
Alignment explanation
Indices: 794901--794976 Score: 84
Period size: 29 Copynumber: 2.5 Consensus size: 30
794891 TAAGAATATG
*
794901 CTCATAATAAAAAAATATTGAAAAAATGGAC
1 CTCATAAT-AAAAAATATTGAAAAAATGGAA
* *
794932 CTC-TAATAAAAAGTATTGAAAAAAT-TATA
1 CTCATAATAAAAAATATTGAAAAAATGGA-A
*
794961 CTCATAATAACAAATA
1 CTCATAATAAAAAATA
794977 AATTATAGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
28 1 0.03
29 20 0.53
30 14 0.37
31 3 0.08
ACGTcount: A:0.57, C:0.11, G:0.07, T:0.26
Consensus pattern (30 bp):
CTCATAATAAAAAATATTGAAAAAATGGAA
Found at i:798812 original size:7 final size:7
Alignment explanation
Indices: 798800--798826 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
798790 AACTTTCAAA
798800 TTAATTT
1 TTAATTT
798807 TTAATTT
1 TTAATTT
798814 TTAATTT
1 TTAATTT
798821 TTAATT
1 TTAATT
798827 ATATATCAAT
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
TTAATTT
Found at i:799707 original size:31 final size:31
Alignment explanation
Indices: 799660--799724 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
799650 AAGGGAAATG
* *
799660 GTCTTTAACGTTATCGATTCTTTCAATTTTA
1 GTCTCTAACGTTATCGATTCATTCAATTTTA
* *
799691 GTCTCTAATGTTATCGATTCATTCGATTTTA
1 GTCTCTAACGTTATCGATTCATTCAATTTTA
799722 GTC
1 GTC
799725 CATCGGCTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.22, C:0.17, G:0.12, T:0.49
Consensus pattern (31 bp):
GTCTCTAACGTTATCGATTCATTCAATTTTA
Found at i:806078 original size:38 final size:37
Alignment explanation
Indices: 806001--806248 Score: 322
Period size: 38 Copynumber: 6.6 Consensus size: 37
805991 ACATATAACG
* *
806001 TATATAATATATAGTTTTAAAAAAATATTTTT--TAA-A
1 TATATAATATATAGTTTT--GAAAATATTTTTGAAAATA
*
806037 TATATAATATATAGTTTTAAAAATATTTTTAGAAAATA
1 TATATAATATATAGTTTTGAAAATATTTTT-GAAAATA
* * * *
806075 TATATAATATATAATTTTGAAAACAATTTTCAAATATA
1 TATATAATATATAGTTTTGAAAATATTTTTGAAA-ATA
*
806113 TATATAATATATAGTTTTGAAAATATTTTTCGAGAATA
1 TATATAATATATAGTTTTGAAAATATTTTT-GAAAATA
806151 TATATAATATATAGTTTTGAAAATATTTTTGAAAATA
1 TATATAATATATAGTTTTGAAAATATTTTTGAAAATA
* *
806188 TATATAATATATAGTTTTGAAAACATTTTTCGAATATA
1 TATATAATATATAGTTTTGAAAATATTTTT-GAAAATA
*
806226 TATATAATATATTGTTTTGAAAA
1 TATATAATATATAGTTTTGAAAA
806249 GCATATATAA
Statistics
Matches: 190, Mismatches: 15, Indels: 12
0.88 0.07 0.06
Matches are distributed among these distances:
34 12 0.06
36 18 0.09
37 40 0.21
38 118 0.62
39 2 0.01
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.45
Consensus pattern (37 bp):
TATATAATATATAGTTTTGAAAATATTTTTGAAAATA
Found at i:806271 original size:28 final size:26
Alignment explanation
Indices: 806225--806276 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
806215 TTTCGAATAT
*
806225 ATATATAATATATTGTTTTGAAAAGC
1 ATATATAATATATTGTTTTAAAAAGC
*
806251 ATATATAATATTAGTTTTTTTAAAAA
1 ATATATAATA-TA-TTGTTTTAAAAA
806277 AATATTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 10 0.45
27 2 0.09
28 10 0.45
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (26 bp):
ATATATAATATATTGTTTTAAAAAGC
Found at i:806344 original size:15 final size:15
Alignment explanation
Indices: 806324--806353 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
806314 ATTTACATTA
*
806324 TTATTTATTTCTTTT
1 TTATTTATTTATTTT
806339 TTATTTATTTATTTT
1 TTATTTATTTATTTT
806354 GTTTACATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (15 bp):
TTATTTATTTATTTT
Found at i:806957 original size:83 final size:83
Alignment explanation
Indices: 806813--806974 Score: 243
Period size: 83 Copynumber: 2.0 Consensus size: 83
806803 CACTGCAAGA
* *
806813 AACGAGAACCCCGGAATACGGAAGGTCAATAGGTAAAAATCGAACATTTCACCTTAGATTTATGT
1 AACGAGAACCCCGAAATACGGAAGGTCAATAGGTAAAAATCGAACATTTCACCTTAAATTTATGT
*
806878 CATTTATGGGATTTGGGG
66 CATTTAGGGGATTTGGGG
* * * *
806896 AACGAGAACGCCGAAATACTGAAGGTCAATGGGTAAAAATCGAACCTTTCACCTTAAATTTATGT
1 AACGAGAACCCCGAAATACGGAAGGTCAATAGGTAAAAATCGAACATTTCACCTTAAATTTATGT
**
806961 TGTTTAGGGGATTT
66 CATTTAGGGGATTT
806975 AGGGTTCTAT
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
83 70 1.00
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (83 bp):
AACGAGAACCCCGAAATACGGAAGGTCAATAGGTAAAAATCGAACATTTCACCTTAAATTTATGT
CATTTAGGGGATTTGGGG
Done.