Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 135 of 199
Found at i:40822147 original size:22 final size:22
Alignment explanation
Indices: 40822122--40822181 Score: 95
Period size: 22 Copynumber: 2.7 Consensus size: 22
40822112 AAATATATAG
40822122 CACTATCAATAATCAACCAATT
1 CACTATCAATAATCAACCAATT
40822144 CACTATCAATAATCAACCAATT
1 CACTATCAATAATCAACCAATT
*
40822166 CAC-ATTCAATTATCAA
1 CACTA-TCAATAATCAA
40822182 TTTATACAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
21 1 0.03
22 35 0.97
ACGTcount: A:0.45, C:0.27, G:0.00, T:0.28
Consensus pattern (22 bp):
CACTATCAATAATCAACCAATT
Found at i:40827956 original size:70 final size:70
Alignment explanation
Indices: 40827838--40827982 Score: 281
Period size: 70 Copynumber: 2.1 Consensus size: 70
40827828 ACTTAGTTGA
*
40827838 TTTGAAAGCTTAGAGAAACTATAATATAGGCCCATATCTACTTTGTTAGTGGGGTTGCTATTAGT
1 TTTGTAAGCTTAGAGAAACTATAATATAGGCCCATATCTACTTTGTTAGTGGGGTTGCTATTAGT
40827903 AAATC
66 AAATC
40827908 TTTGTAAGCTTAGAGAAACTATAATATAGGCCCATATCTACTTTGTTAGTGGGGTTGCTATTAGT
1 TTTGTAAGCTTAGAGAAACTATAATATAGGCCCATATCTACTTTGTTAGTGGGGTTGCTATTAGT
40827973 AAATC
66 AAATC
40827978 TTTGT
1 TTTGT
40827983 GTTATTCAAA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 74 1.00
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (70 bp):
TTTGTAAGCTTAGAGAAACTATAATATAGGCCCATATCTACTTTGTTAGTGGGGTTGCTATTAGT
AAATC
Found at i:40834649 original size:22 final size:22
Alignment explanation
Indices: 40834619--40834699 Score: 108
Period size: 22 Copynumber: 3.7 Consensus size: 22
40834609 CGGCATTCCC
*
40834619 GTTTCACGTACTAAGCTCTCAT
1 GTTTAACGTACTAAGCTCTCAT
40834641 GTTTAACGTACTAAGCTCTCAT
1 GTTTAACGTACTAAGCTCTCAT
* * *
40834663 GTTTAACGAACTAAACCCTCAT
1 GTTTAACGTACTAAGCTCTCAT
**
40834685 GGCTAACGTACTAAG
1 GTTTAACGTACTAAG
40834700 AAAAGATAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.31
Consensus pattern (22 bp):
GTTTAACGTACTAAGCTCTCAT
Found at i:40835104 original size:3 final size:3
Alignment explanation
Indices: 40835096--40835148 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
40835086 CTCTGGAGCT
*
40835096 TCA TCA TCA TCA TCA TCA TCA TCA CCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
40835144 TCA TC
1 TCA TC
40835149 TAAGTTCTCC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
TCA
Found at i:40841789 original size:13 final size:13
Alignment explanation
Indices: 40841762--40841798 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
40841752 TTATTTTTTA
40841762 AATT-TAAAT-TT
1 AATTATAAATATT
40841773 AATTATAAATATT
1 AATTATAAATATT
*
40841786 AATTAAAAATATT
1 AATTATAAATATT
40841799 TTTATTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 4 0.17
12 5 0.22
13 14 0.61
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTATAAATATT
Found at i:40844484 original size:16 final size:18
Alignment explanation
Indices: 40844463--40844500 Score: 62
Period size: 16 Copynumber: 2.2 Consensus size: 18
40844453 TATATATTCT
40844463 TAAAAAATA-TT-AAAAA
1 TAAAAAATATTTAAAAAA
40844479 TAAAAAATATTTAAAAAA
1 TAAAAAATATTTAAAAAA
40844497 TAAA
1 TAAA
40844501 GAAAACTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 9 0.45
17 2 0.10
18 9 0.45
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
TAAAAAATATTTAAAAAA
Found at i:40844804 original size:25 final size:25
Alignment explanation
Indices: 40844776--40844826 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
40844766 TAAAATAAGA
*
40844776 AGAAAGGAAA-AAAAAAAGAGCAAAT
1 AGAAAAGAAATAAAAAAAGAG-AAAT
*
40844801 AGAAAAGAAATAAAAAAGGAGAAAT
1 AGAAAAGAAATAAAAAAAGAGAAAT
40844826 A
1 A
40844827 ATGTAATAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.73, C:0.02, G:0.20, T:0.06
Consensus pattern (25 bp):
AGAAAAGAAATAAAAAAAGAGAAAT
Found at i:40863499 original size:26 final size:26
Alignment explanation
Indices: 40863433--40863506 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 26
40863423 AATATTTATA
* *
40863433 TTTACCCCCAGTAAAATTTTAACGAT
1 TTTACCCCTAGTAAAATTTTGACGAT
* *
40863459 TTTACCCCTAATAAAATTTTGATGAT
1 TTTACCCCTAGTAAAATTTTGACGAT
* * *
40863485 TTTTCTCCTGGTAAAATTTTGA
1 TTTACCCCTAGTAAAATTTTGA
40863507 GAAAATATGT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.31, C:0.18, G:0.09, T:0.42
Consensus pattern (26 bp):
TTTACCCCTAGTAAAATTTTGACGAT
Found at i:40870021 original size:23 final size:26
Alignment explanation
Indices: 40869960--40870022 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 26
40869950 TTTCAAATAT
40869960 AAAAATATTTAAATATGTATAAATCTA
1 AAAAAT-TTTAAATATGTATAAATCTA
*
40869987 AAAATTTCTTAAA-AT-TA-AAA-CTAA
1 AAAAATT-TTAAATATGTATAAATCT-A
40870011 AAAAATTTTAAA
1 AAAAATTTTAAA
40870023 CTAACATTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
23 7 0.22
24 10 0.31
25 2 0.06
26 3 0.09
27 10 0.31
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.35
Consensus pattern (26 bp):
AAAAATTTTAAATATGTATAAATCTA
Found at i:40886227 original size:21 final size:22
Alignment explanation
Indices: 40886178--40886218 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
40886168 ATTTAATTTT
40886178 AAAAAATATAATAATTAAATTG
1 AAAAAATATAATAATTAAATTG
*
40886200 AAAAAAT-TAATAGTTAAAT
1 AAAAAATATAATAATTAAAT
40886219 GATCAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (22 bp):
AAAAAATATAATAATTAAATTG
Found at i:40899680 original size:4 final size:4
Alignment explanation
Indices: 40899634--40899664 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
40899624 ATCTATCCTT
40899634 TTTA TTTA TTTA TTTA TTTA TTTA -TTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
40899665 ACTAATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:40901939 original size:16 final size:18
Alignment explanation
Indices: 40901912--40901944 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
40901902 TAGAATAAGG
40901912 TTGAGAAAATT-ATTTAA
1 TTGAGAAAATTAATTTAA
40901929 TTGAG-AAATTAATTTA
1 TTGAGAAAATTAATTTA
40901945 TGATGTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (18 bp):
TTGAGAAAATTAATTTAA
Found at i:40913943 original size:2 final size:2
Alignment explanation
Indices: 40913936--40913961 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40913926 GCAAATATGC
40913936 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
40913962 GTTCTGTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40914142 original size:2 final size:2
Alignment explanation
Indices: 40914135--40914169 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
40914125 TGTGTTAAGT
40914135 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40914170 GTTCGGATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:40914463 original size:41 final size:42
Alignment explanation
Indices: 40914339--40914482 Score: 202
Period size: 42 Copynumber: 3.5 Consensus size: 42
40914329 CAGTGCCTAT
* *
40914339 CAGGTTTATTGCCAGTGAAACAATATCAGACTTTACGTCTAG
1 CAGGCTTAATGCCAGTGAAACAATATCAGACTTTACGTCTAG
*
40914381 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
1 CAGGCTTAATGCCAGTGAAACAATATCAGACTTTACGTCTAG
* * * *
40914423 CAGGCTTAATGCCGGTGAAAC-ATTTCAGACTATATGTCTAG
1 CAGGCTTAATGCCAGTGAAACAATATCAGACTTTACGTCTAG
40914464 CAGGC-TAAGTGCCAGTGAA
1 CAGGCTTAA-TGCCAGTGAA
40914483 TCTGTTTAAA
Statistics
Matches: 94, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
40 3 0.03
41 31 0.33
42 60 0.64
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (42 bp):
CAGGCTTAATGCCAGTGAAACAATATCAGACTTTACGTCTAG
Found at i:40915705 original size:26 final size:26
Alignment explanation
Indices: 40915676--40915732 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
40915666 TCTCATCCTT
* * *
40915676 ATTTTACCCCTTACAAAATTTTGACG
1 ATTTTACCCCTGACAAAATTTTAACA
* *
40915702 ATTTTATCCCTGATAAAATTTTAACA
1 ATTTTACCCCTGACAAAATTTTAACA
40915728 ATTTT
1 ATTTT
40915733 GCCCTTGGTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.33, C:0.18, G:0.05, T:0.44
Consensus pattern (26 bp):
ATTTTACCCCTGACAAAATTTTAACA
Found at i:40918018 original size:26 final size:26
Alignment explanation
Indices: 40917986--40918049 Score: 101
Period size: 26 Copynumber: 2.5 Consensus size: 26
40917976 AATTTAAATG
40917986 AATTGAAAATTTGAATTGGGTCTGAA
1 AATTGAAAATTTGAATTGGGTCTGAA
*
40918012 AATTGAAATTTTGAATTGGGTCTGAA
1 AATTGAAAATTTGAATTGGGTCTGAA
**
40918038 AAAAGAAAATTT
1 AATTGAAAATTT
40918050 TGTGGTATAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.42, C:0.03, G:0.20, T:0.34
Consensus pattern (26 bp):
AATTGAAAATTTGAATTGGGTCTGAA
Found at i:40920130 original size:20 final size:19
Alignment explanation
Indices: 40920105--40920156 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
40920095 GAAAAAACAT
*
40920105 AAAAATTATTAAGAATTATA
1 AAAAATTATTAA-AAGTATA
*
40920125 AAAAA-T-TTAAAAGTATT
1 AAAAATTATTAAAAGTATA
40920142 AAAAATTATTTAAAA
1 AAAAATTA-TTAAAA
40920157 CAACAACCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
17 10 0.37
18 5 0.19
19 1 0.04
20 11 0.41
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (19 bp):
AAAAATTATTAAAAGTATA
Found at i:40920522 original size:19 final size:19
Alignment explanation
Indices: 40920500--40920550 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
40920490 TGAATAATTT
40920500 TAAAATTTTATATTTTTTA
1 TAAAATTTTATATTTTTTA
*
40920519 T-AAATTTTAATAGTTTTTA
1 TAAAATTTT-ATATTTTTTA
40920538 -AATAATTTTATAT
1 TAA-AATTTTATAT
40920551 AATTTTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
18 7 0.26
19 14 0.52
20 6 0.22
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (19 bp):
TAAAATTTTATATTTTTTA
Found at i:40920542 original size:21 final size:19
Alignment explanation
Indices: 40920502--40920557 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 19
40920492 AATAATTTTA
*
40920502 AAATTTT-ATATTTTTTAT
1 AAATTTTAATATTTTTAAT
40920520 AAATTTTAATAGTTTTTAA-
1 AAATTTTAATA-TTTTTAAT
40920539 ATAATTTTATATAATTTTT
1 A-AATTTTA-AT-ATTTTT
40920558 TTCACAATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
18 7 0.22
19 4 0.12
20 13 0.41
21 7 0.22
22 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
AAATTTTAATATTTTTAAT
Found at i:40922292 original size:4 final size:4
Alignment explanation
Indices: 40922276--40922353 Score: 50
Period size: 4 Copynumber: 18.0 Consensus size: 4
40922266 CAATGATAAG
* *
40922276 GAAA GAAA TAAA GAAA GAAAA GAAGGA GAAA -AAA CAAA GAAA GAAAA
1 GAAA GAAA GAAA GAAA G-AAA GAA--A GAAA GAAA GAAA GAAA G-AAA
* *
40922323 GAAAA GAAAA GAAAA GAAA AAAA GAGA GAAA
1 G-AAA G-AAA G-AAA GAAA GAAA GAAA GAAA
40922354 AGGAAATAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
3 3 0.05
4 32 0.52
5 23 0.37
6 4 0.06
ACGTcount: A:0.76, C:0.01, G:0.22, T:0.01
Consensus pattern (4 bp):
GAAA
Found at i:40922299 original size:5 final size:5
Alignment explanation
Indices: 40922285--40922342 Score: 66
Period size: 5 Copynumber: 11.6 Consensus size: 5
40922275 GGAAAGAAAT
* *
40922285 AAAG- AAAGA AAAGA AGGAGA AAAAA CAAAG- AAAGA AAAGA AAAGA AAAGA
1 AAAGA AAAGA AAAGA A-AAGA AAAGA -AAAGA AAAGA AAAGA AAAGA AAAGA
40922335 AAAGA AAA
1 AAAGA AAA
40922343 AAAGAGAGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
4 8 0.17
5 31 0.67
6 7 0.15
ACGTcount: A:0.78, C:0.02, G:0.21, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:40922320 original size:15 final size:15
Alignment explanation
Indices: 40922302--40922355 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
40922292 GAAAAGAAGG
*
40922302 AGAAAA-AACAAAGAA
1 AGAAAAGAA-AAAAAA
*
40922317 AGAAAAGAAAAGAAA
1 AGAAAAGAAAAAAAA
40922332 AGAAAAGAAAAAAAGA
1 AGAAAAGAAAAAAA-A
40922348 GAGAAAAG
1 -AGAAAAG
40922356 GAAATAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 23 0.70
16 3 0.09
17 7 0.21
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (15 bp):
AGAAAAGAAAAAAAA
Found at i:40922353 original size:36 final size:35
Alignment explanation
Indices: 40922277--40922344 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
40922267 AATGATAAGG
* *
40922277 AAAGAAA-TAAAGAAAGAAAAGAAGGAGAAAAAAC
1 AAAGAAAGAAAAGAAAGAAAAGAAGAAGAAAAAAC
40922311 AAAGAAAGAAAAGAAAAGAAAAGAA-AAGAAAAAA
1 AAAGAAAGAAAAG-AAAGAAAAGAAGAAGAAAAAA
40922345 AGAGAGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
34 7 0.23
35 12 0.40
36 11 0.37
ACGTcount: A:0.78, C:0.01, G:0.19, T:0.01
Consensus pattern (35 bp):
AAAGAAAGAAAAGAAAGAAAAGAAGAAGAAAAAAC
Found at i:40925570 original size:30 final size:31
Alignment explanation
Indices: 40925531--40925590 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
40925521 GGAGGTAGGA
*
40925531 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
40925562 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
40925591 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:40925817 original size:9 final size:9
Alignment explanation
Indices: 40925799--40925835 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
40925789 TATAGTTTGA
*
40925799 TATTCAAAT
1 TATTCGAAT
40925808 TATTCGAAT
1 TATTCGAAT
*
40925817 TATTCGAGT
1 TATTCGAAT
40925826 TATTCGAAT
1 TATTCGAAT
40925835 T
1 T
40925836 CAAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:40931221 original size:28 final size:27
Alignment explanation
Indices: 40931188--40931286 Score: 119
Period size: 28 Copynumber: 3.6 Consensus size: 27
40931178 TAATGAGATT
*
40931188 AGCACTAAGTGTGCGAGTTTAATTGAA
1 AGCACTAAGTGTGCGAGTATAATTGAA
*
40931215 ATGCACTAAGTGTGCGAGTATAATGGTAA
1 A-GCACTAAGTGTGCGAGTATAATTG-AA
* *
40931244 AGCACTAAGTGTGCGAGTGTGATT-ATTA
1 AGCACTAAGTGTGCGAGTATAATTGA--A
40931272 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
40931287 TACTTATTAA
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
26 1 0.02
27 1 0.02
28 58 0.92
29 3 0.05
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.28
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTATAATTGAA
Found at i:40936849 original size:108 final size:106
Alignment explanation
Indices: 40936656--40936859 Score: 284
Period size: 108 Copynumber: 1.9 Consensus size: 106
40936646 TGGATTAAGA
* * * * *
40936656 TTTAAGAGGTTATTTGGCTATTTGGTCAAATGAGAAATCGAAACCCAGCACATTAGGGCACATTT
1 TTTAAAAGGATATTTGGCTATTTGATCAAACGAGAAATCGAAACCCAGCACATTAAGGCACATTT
* *
40936721 TCTCGAATTTGCAAAAGCAAAACATTGCCTTACTTCGAAAT
66 TCTCGAATCTCCAAAAGCAAAACATTGCCTTACTTCGAAAT
* *
40936762 TTTAAAAGGATATTTGGCTATTTGAT-AGAACGAGAAAAATCGAAACTCAGCACATTAAGGCACG
1 TTTAAAAGGATATTTGGCTATTTGATCA-AACGAG--AAATCGAAACCCAGCACATTAAGGCACA
*
40936826 TTTTCTCGAATCTCCAAATGCAAAACATTGCCTT
63 TTTTCTCGAATCTCCAAAAGCAAAACATTGCCTT
40936860 TATTATTTTT
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
105 1 0.01
106 28 0.33
108 56 0.66
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.29
Consensus pattern (106 bp):
TTTAAAAGGATATTTGGCTATTTGATCAAACGAGAAATCGAAACCCAGCACATTAAGGCACATTT
TCTCGAATCTCCAAAAGCAAAACATTGCCTTACTTCGAAAT
Found at i:40937782 original size:3 final size:3
Alignment explanation
Indices: 40937690--40937762 Score: 119
Period size: 3 Copynumber: 24.3 Consensus size: 3
40937680 CAAGACATAG
* * *
40937690 ATA ATA ATA ATA TTA ATA ATA ATC ATA ATA ATA ATG ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
40937738 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
40937763 CTTATTAGTT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:40939650 original size:87 final size:87
Alignment explanation
Indices: 40939527--40940206 Score: 1074
Period size: 87 Copynumber: 7.8 Consensus size: 87
40939517 GCTAGTGCTT
* * *
40939527 AGGAAGGCAAGATCTGCTATCTTTAACCAGCACCACTGCAACTGATAGAGGCAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
40939592 CGATCTGCTTCGCTGTTAACGC
66 CGATCTGCTTCGCTGTTAACGC
* * *
40939614 AGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAAGCGATGGAGGCAAGGCTTTATTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
*
40939679 CGGTCTGCTTCGCTGTTAACGC
66 CGATCTGCTTCGCTGTTAACGC
* * *
40939701 AGGAAGGCAAGATCTGTTATCTTTAACCAGATCCACTGTAACCGATGGAGGCAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
*
40939766 CGATCTGCTTCACTGTTAACGC
66 CGATCTGCTTCGCTGTTAACGC
* * * *
40939788 AGGAAGACAAGATCTGTTATCTTTAACAAGCTCCACTGCAACC-ATTGGAGGCAATGCTTTGTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGA-TGGAGGCAAGGCTTTGTTT
*
40939852 TCGATCTGCTTCGCTGTTAACAC
65 TCGATCTGCTTCGCTGTTAACGC
* *
40939875 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCTACTGCAACCGATGGAGGAAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
*
40939940 CGTTCTGCTTCGCTGTTAACGC
66 CGATCTGCTTCGCTGTTAACGC
* * * * * *
40939962 AGAAAGGCAAGATCTACTATCTTTAATCAACTCCACTACAACCGATGGAGGCAAGGCTTTATTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
40940027 CGATCTGCTTCGCTGTTAACGC
66 CGATCTGCTTCGCTGTTAACGC
* *
40940049 AGGAAGGCAAGATCTACTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGACTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
* *
40940114 TGATCTGCTTCACTGTTAACGC
66 CGATCTGCTTCGCTGTTAACGC
*
40940136 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGTAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
40940201 CGATCT
66 CGATCT
40940207 TCACTGATCT
Statistics
Matches: 542, Mismatches: 49, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
86 1 0.00
87 540 1.00
88 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.29
Consensus pattern (87 bp):
AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
CGATCTGCTTCGCTGTTAACGC
Found at i:40941469 original size:13 final size:13
Alignment explanation
Indices: 40941437--40941470 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
40941427 TAGCCTCTCT
40941437 ATTTTTACTCTTTC
1 ATTTTT-CTCTTTC
*
40941451 ATTTTTCTTTTTC
1 ATTTTTCTCTTTC
40941464 ATTTTTC
1 ATTTTTC
40941471 ATCATCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.71
Consensus pattern (13 bp):
ATTTTTCTCTTTC
Found at i:40941902 original size:6 final size:6
Alignment explanation
Indices: 40941886--40941919 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
40941876 TGATTTCTCT
* *
40941886 TTTTGC TTTTGA CTTTGA TTTTGA TTTTGA TTTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTT
40941920 TTTTTTCTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.12, C:0.06, G:0.15, T:0.68
Consensus pattern (6 bp):
TTTTGA
Found at i:40946131 original size:108 final size:106
Alignment explanation
Indices: 40945944--40946147 Score: 320
Period size: 108 Copynumber: 1.9 Consensus size: 106
40945934 TGGATTAAGA
* * *
40945944 TTTAAGAGGATATTTGGCTATTTGGTCAAACAAGAAATCGAAACCCAACACATTAGGGCACATTT
1 TTTAAAAGGATATTTGGCTATTTGATCAAACAAAAAATCGAAACCCAACACATTAGGGCACATTT
*
40946009 TCTCGAATTTCCAAACGCAAAACATTGCCTTACTTCGAAAT
66 TCTCGAATCTCCAAACGCAAAACATTGCCTTACTTCGAAAT
* *
40946050 TTTAAAAGGATATTTGGCTATTTGAT-AGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACG
1 TTTAAAAGGATATTTGGCTATTTGATCA-AAC-A-AAAAATCGAAACCCAACACATTAGGGCACA
40946114 TTTTCTCGAATCTCCAAACGCAAAACATTGCCTT
63 TTTTCTCGAATCTCCAAACGCAAAACATTGCCTT
40946148 TATTATTTTT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
105 1 0.01
106 27 0.30
107 1 0.01
108 60 0.67
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (106 bp):
TTTAAAAGGATATTTGGCTATTTGATCAAACAAAAAATCGAAACCCAACACATTAGGGCACATTT
TCTCGAATCTCCAAACGCAAAACATTGCCTTACTTCGAAAT
Found at i:40947071 original size:3 final size:3
Alignment explanation
Indices: 40946985--40947051 Score: 98
Period size: 3 Copynumber: 22.3 Consensus size: 3
40946975 CAAGACATAG
* * **
40946985 ATA ATA ATA ATA ATA TTA ATA ATA ATC ATA ATA ATA AGG ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
40947033 ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA A
40947052 CTTATTAGTT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:40954788 original size:20 final size:20
Alignment explanation
Indices: 40954765--40954828 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 20
40954755 ATGTACGTAT
* *
40954765 ATATATTATACTTTCTATAC
1 ATATATTATAATTTATATAC
* *
40954785 ATATTTTATAATTTATATAT
1 ATATATTATAATTTATATAC
* *
40954805 ATATA-TAT-ATATATATAT
1 ATATATTATAATTTATATAC
40954823 ATATAT
1 ATATAT
40954829 ACACATATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
18 14 0.38
19 3 0.08
20 20 0.54
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATATTATAATTTATATAC
Found at i:40954838 original size:2 final size:2
Alignment explanation
Indices: 40954798--40954829 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
40954788 TTTTATAATT
40954798 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40954830 CACATATATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40955588 original size:98 final size:98
Alignment explanation
Indices: 40955468--40955664 Score: 376
Period size: 98 Copynumber: 2.0 Consensus size: 98
40955458 TTAAAAATAA
*
40955468 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
40955533 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
*
40955566 TAAAGGAAATATTCCGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
40955631 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
40955664 T
1 T
40955665 TTTATTGCAC
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 97 1.00
ACGTcount: A:0.28, C:0.10, G:0.25, T:0.38
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:40970372 original size:31 final size:29
Alignment explanation
Indices: 40970304--40970372 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
40970294 CTTAGGTTAG
* * *
40970304 ATTTTAGTCACTTATGTTTGAAATGTTAC
1 ATTTTAGTCACTTACGTTTCAAATGTAAC
*
40970333 GTTTTAGTCACTTACGTTATCAAATTGTAAC
1 ATTTTAGTCACTTACGTT-TCAAA-TGTAAC
40970364 ATTTTAGTC
1 ATTTTAGTC
40970373 CTTGAGCAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 16 0.48
30 4 0.12
31 13 0.39
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (29 bp):
ATTTTAGTCACTTACGTTTCAAATGTAAC
Found at i:40976774 original size:30 final size:30
Alignment explanation
Indices: 40976739--40976912 Score: 222
Period size: 30 Copynumber: 5.7 Consensus size: 30
40976729 GTACATGTTT
40976739 TATATATTGCCGAATTGATTTGTATATGGATA
1 TATATATTGCCGAATTGATTTGTATATGG--A
* * * *
40976771 TATATATTTCCGAATTTATTTATATATAGA
1 TATATATTGCCGAATTGATTTGTATATGGA
* *
40976801 TATATATAGCTGAATTGATTTGTATATGGA
1 TATATATTGCCGAATTGATTTGTATATGGA
* *
40976831 TATACATTGCCGAATTGATTTGTATATAGA
1 TATATATTGCCGAATTGATTTGTATATGGA
* * *
40976861 TATACATTGCTGAATTGATTTGTATATGTA
1 TATATATTGCCGAATTGATTTGTATATGGA
*
40976891 TATATATTACCGAATTGATTTG
1 TATATATTGCCGAATTGATTTG
40976913 AGCATTGGAT
Statistics
Matches: 122, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
30 97 0.80
32 25 0.20
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.45
Consensus pattern (30 bp):
TATATATTGCCGAATTGATTTGTATATGGA
Found at i:40976857 original size:60 final size:60
Alignment explanation
Indices: 40976739--40976912 Score: 249
Period size: 60 Copynumber: 2.9 Consensus size: 60
40976729 GTACATGTTT
* * * *
40976739 TATATATTGCCGAATTGATTTGTATATGGATATATATATTTCCGAATTTATTTATATATAGA
1 TATATATTGCTGAATTGATTTGTATATGG--ATATATATTACCGAATTGATTTGTATATAGA
* * *
40976801 TATATATAGCTGAATTGATTTGTATATGGATATACATTGCCGAATTGATTTGTATATAGA
1 TATATATTGCTGAATTGATTTGTATATGGATATATATTACCGAATTGATTTGTATATAGA
* *
40976861 TATACATTGCTGAATTGATTTGTATATGTATATATATTACCGAATTGATTTG
1 TATATATTGCTGAATTGATTTGTATATGGATATATATTACCGAATTGATTTG
40976913 AGCATTGGAT
Statistics
Matches: 101, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
60 74 0.73
62 27 0.27
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.45
Consensus pattern (60 bp):
TATATATTGCTGAATTGATTTGTATATGGATATATATTACCGAATTGATTTGTATATAGA
Found at i:40976896 original size:92 final size:89
Alignment explanation
Indices: 40976739--40976912 Score: 215
Period size: 92 Copynumber: 1.9 Consensus size: 89
40976729 GTACATGTTT
* * * * *
40976739 TATATATTGCCGAATTGATTTGTATATGGATATATATATTTCCGAATTTATTTATATATAGATAT
1 TATACATTGCCGAATTGATTTGTATAT-GAGATATACATTGCCGAATTGATTTATATATAGATAT
*
40976804 ATATAGCTGAATTGATTTGTATATGGA
65 AT-TA-CCGAATTGATTTGTATATGGA
* * *
40976831 TATACATTGCCGAATTGATTTGTATAT-AGATATACATTGCTGAATTGATTTGTATATGTATATA
1 TATACATTGCCGAATTGATTTGTATATGAGATATACATTGCCGAATTGA-TT-TATATATAGATA
40976895 TATTACCGAATTGATTTG
64 TATTACCGAATTGATTTG
40976913 AGCATTGGAT
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
90 28 0.39
91 4 0.06
92 39 0.55
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.45
Consensus pattern (89 bp):
TATACATTGCCGAATTGATTTGTATATGAGATATACATTGCCGAATTGATTTATATATAGATATA
TTACCGAATTGATTTGTATATGGA
Found at i:40981713 original size:124 final size:124
Alignment explanation
Indices: 40981481--40981717 Score: 341
Period size: 124 Copynumber: 1.9 Consensus size: 124
40981471 GCCAAACAAT
* * **
40981481 AACTACTGTAGAAAAAGAGCATCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATTT
1 AACTACTGTAGAAAAAGAACATCCACGTGGGAGATTTTTTCAGTAATTTTGCTGACAGTGCATCC
* * **
40981546 TGCTTGAAGCGTTTTTGACACTAATTTTTTAGATTCGTCTTCTCAAAAATTTTTTTAGG
66 TGCTTGAAGCATTTTTGACACTAATTTTTCAGAACCGTCTTCTCAAAAATTTTTTTAGG
**
40981605 AACTACTGTAGAAAAAGAATTTCCACGTGGGAGATTTTTTCAGTAATTTTGCTGACAGTGCATCC
1 AACTACTGTAGAAAAAGAACATCCACGTGGGAGATTTTTTCAGTAATTTTGCTGACAGTGCATCC
* * *
40981670 TGCTTGAAGCATTTTTTACA-TTATCTTTTCAGAACCGTTTTCTCAAAA
66 TGCTTGAAGCATTTTTGACACTAAT-TTTTCAGAACCGTCTTCTCAAAA
40981718 TTAATTTTTC
Statistics
Matches: 99, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
123 3 0.03
124 96 0.97
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.38
Consensus pattern (124 bp):
AACTACTGTAGAAAAAGAACATCCACGTGGGAGATTTTTTCAGTAATTTTGCTGACAGTGCATCC
TGCTTGAAGCATTTTTGACACTAATTTTTCAGAACCGTCTTCTCAAAAATTTTTTTAGG
Found at i:40981875 original size:34 final size:33
Alignment explanation
Indices: 40981830--40981962 Score: 124
Period size: 33 Copynumber: 3.9 Consensus size: 33
40981820 CTAAACACAA
40981830 AATTATTTTAAAAAAACTAAACCCTAATTTAATT
1 AATT-TTTTAAAAAAACTAAACCCTAATTTAATT
**
40981864 AATTTTCTT-AAAACTCTAAACCCTAATTTAATT
1 AATTTT-TTAAAAAAACTAAACCCTAATTTAATT
* * * ***
40981897 TATTTATTTAAAACACCTAAAATGTAATTTAATT
1 AATTT-TTTAAAAAAACTAAACCCTAATTTAATT
* *
40981931 AATTTTTAAAAAAAACTCTAAACCTTAATTTA
1 AATTTTTTAAAAAAA--CTAAACCCTAATTTA
40981963 TTTTTTAAAA
Statistics
Matches: 78, Mismatches: 16, Indels: 9
0.76 0.16 0.09
Matches are distributed among these distances:
33 37 0.47
34 29 0.37
35 12 0.15
ACGTcount: A:0.46, C:0.13, G:0.01, T:0.41
Consensus pattern (33 bp):
AATTTTTTAAAAAAACTAAACCCTAATTTAATT
Found at i:40981917 original size:67 final size:65
Alignment explanation
Indices: 40981836--40981969 Score: 153
Period size: 67 Copynumber: 2.0 Consensus size: 65
40981826 ACAAAATTAT
* *
40981836 TTTAAAAAAACTAAACCCTAATTTAATTAATTTTCT-TAAAACTCTAAACCCTAATTTAATTTAT
1 TTTAAAAAAACTAAAACCTAATTTAATTAATTTT-TAAAAAACTCTAAACCCTAATTT-ATTT-T
40981900 TTA
63 TTA
* * ** *
40981903 TTTAAAACACCTAAAATGTAATTTAATTAATTTTTAAAAAAAACTCTAAACCTTAATTTATTTTT
1 TTTAAAAAAACTAAAACCTAATTTAATTAATTTTT--AAAAAACTCTAAACCCTAATTTATTTTT
40981968 TA
64 TA
40981970 AAATTTTTAA
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
66 1 0.02
67 33 0.58
68 4 0.07
69 19 0.33
ACGTcount: A:0.44, C:0.13, G:0.01, T:0.43
Consensus pattern (65 bp):
TTTAAAAAAACTAAAACCTAATTTAATTAATTTTTAAAAAACTCTAAACCCTAATTTATTTTTTA
Found at i:40993403 original size:16 final size:16
Alignment explanation
Indices: 40993378--40993422 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
40993368 GTATTGGAAC
40993378 AGAGGCGTAATAGAAT
1 AGAGGCGTAATAGAAT
* *
40993394 AGAGGTGTAATGGAAT
1 AGAGGCGTAATAGAAT
40993410 AGAGGCGTAATAG
1 AGAGGCGTAATAG
40993423 TATTCTTGTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.40, C:0.04, G:0.36, T:0.20
Consensus pattern (16 bp):
AGAGGCGTAATAGAAT
Found at i:40993629 original size:18 final size:17
Alignment explanation
Indices: 40993608--40993642 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40993598 TTATTATTAA
*
40993608 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
40993626 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
40993643 TCTTAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:40993730 original size:26 final size:25
Alignment explanation
Indices: 40993689--40993857 Score: 76
Period size: 26 Copynumber: 6.9 Consensus size: 25
40993679 ATCATAATAT
* *
40993689 ATAATACTATAAAATATAATTTAAA
1 ATAATATTATTAAATATAATTTAAA
40993714 ATAATTATTATTAAATATAATTTATTAA
1 ATAA-TATTATTAAATATAATTTA--AA
*
40993742 A-AATA-TA-T-AATTTAA--TAAA
1 ATAATATTATTAAATATAATTTAAA
* * *
40993761 ATTATTAATATTAAATAT--TCTT-AT
1 A-TAATATTATTAAATATAAT-TTAAA
* *
40993785 ATGAAT-TTACTAAAATCATAA--T-AT
1 AT-AATATTA-TTAAAT-ATAATTTAAA
* *
40993809 ATAATACTATAAAATATAATTTAAA
1 ATAATATTATTAAATATAATTTAAA
40993834 ATAATTATTATTAAATATAATTTA
1 ATAA-TATTATTAAATATAATTTA
40993858 TTAAAAATAT
Statistics
Matches: 110, Mismatches: 13, Indels: 41
0.67 0.08 0.25
Matches are distributed among these distances:
19 3 0.03
21 5 0.05
22 6 0.05
23 19 0.17
24 22 0.20
25 14 0.13
26 36 0.33
27 2 0.02
28 3 0.03
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (25 bp):
ATAATATTATTAAATATAATTTAAA
Found at i:40993774 original size:18 final size:18
Alignment explanation
Indices: 40993728--40993774 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
40993718 TTATTATTAA
*
40993728 ATATAATTTATTAAAAAT
1 ATATAATTTAATAAAAAT
*
40993746 ATATAATTTAATAAAATT
1 ATATAATTTAATAAAAAT
40993764 AT-TAATATTAA
1 ATATAAT-TTAA
40993775 ATATTCTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 4 0.15
18 22 0.85
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:40993801 original size:120 final size:120
Alignment explanation
Indices: 40993588--40993993 Score: 760
Period size: 120 Copynumber: 3.4 Consensus size: 120
40993578 TTAATCATAT
* *
40993588 TTTAACATAATTATTATTAAATATATTTTAATT-AAAATATATAATTTAATAAAATTCTTAATAT
1 TTTAAAATAATTATTATTAAATATAATTT-ATTAAAAATATATAATTTAATAAAATTCTTAATAT
40993652 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
65 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
*
40993708 TTTAAAATAATTATTATTAAATATAATTTATTAAAAATATATAATTTAATAAAATTATTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTATTAAAAATATATAATTTAATAAAATTCTTAATATT
40993773 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
40993828 TTTAAAATAATTATTATTAAATATAATTTATTAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTATTAAAAATATATAATTTAATAAAATTCTTAATATT
40993893 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
*
40993948 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATT
1 TTTAAAATAATTATTATTAAATATAATTTATTAAAAATATATAATT
40993994 CCCCCCACTT
Statistics
Matches: 280, Mismatches: 5, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
119 3 0.01
120 277 0.99
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.44
Consensus pattern (120 bp):
TTTAAAATAATTATTATTAAATATAATTTATTAAAAATATATAATTTAATAAAATTCTTAATATT
AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
Found at i:40998106 original size:20 final size:20
Alignment explanation
Indices: 40998081--40998122 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
40998071 ACTTGTAGAG
40998081 GATGATGACATAGAGACTAT
1 GATGATGACATAGAGACTAT
40998101 GATGATGACATAGAGACTAT
1 GATGATGACATAGAGACTAT
40998121 GA
1 GA
40998123 CCGCATTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.10, G:0.26, T:0.24
Consensus pattern (20 bp):
GATGATGACATAGAGACTAT
Found at i:40999804 original size:12 final size:11
Alignment explanation
Indices: 40999789--40999894 Score: 56
Period size: 11 Copynumber: 10.4 Consensus size: 11
40999779 ACAAAAATTA
40999789 AAAAAGTATTTT
1 AAAAA-TATTTT
40999801 AAAAATATTTT
1 AAAAATATTTT
40999812 --AAA-A--TT
1 AAAAATATTTT
*
40999818 AAAAA-AATTT
1 AAAAATATTTT
40999828 AAAAAGTATTTT
1 AAAAA-TATTTT
*
40999840 AAAAA-A-ATT
1 AAAAATATTTT
40999849 -AAAA-A-TTT
1 AAAAATATTTT
*
40999857 AAAAA-ATTTAA
1 AAAAATATTT-T
40999868 AAAAAGTATTTT
1 AAAAA-TATTTT
*
40999880 AAAAGTATTTT
1 AAAAATATTTT
40999891 AAAA
1 AAAA
40999895 TTTAAAAATT
Statistics
Matches: 77, Mismatches: 6, Indels: 23
0.73 0.06 0.22
Matches are distributed among these distances:
6 2 0.03
8 12 0.16
9 10 0.13
10 10 0.13
11 21 0.27
12 18 0.23
13 4 0.05
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:40999809 original size:11 final size:10
Alignment explanation
Indices: 40999796--40999871 Score: 51
Period size: 9 Copynumber: 8.1 Consensus size: 10
40999786 TTAAAAAAGT
40999796 ATTTTAAAAA
1 ATTTTAAAAA
40999806 TATTTT--AAA
1 -ATTTTAAAAA
40999815 A--TTAAAAA
1 ATTTTAAAAA
*
40999823 AATTTAAAAA
1 ATTTTAAAAA
40999833 GTATTTTAAAAA
1 --ATTTTAAAAA
*
40999845 A-ATT-AAAA
1 ATTTTAAAAA
40999853 A-TTTAAAAA
1 ATTTTAAAAA
40999862 A-TTTAAAAA
1 ATTTTAAAAA
40999871 A
1 A
40999872 AGTATTTTAA
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
6 2 0.04
8 12 0.22
9 19 0.35
10 8 0.15
11 5 0.09
12 9 0.16
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (10 bp):
ATTTTAAAAA
Found at i:40999821 original size:17 final size:16
Alignment explanation
Indices: 40999799--40999869 Score: 52
Period size: 16 Copynumber: 4.0 Consensus size: 16
40999789 AAAAAGTATT
*
40999799 TTAAAAATATTTTAAAA
1 TTAAAAA-AATTTAAAA
40999816 TTAAAAAAATTTAAAAAGTA
1 TTAAAAAAATTT--AAA--A
*
40999836 TTTTAAAAAAATTAAAAA
1 --TTAAAAAAATTTAAAA
*
40999854 TTTAAAAAATTTAAAA
1 TTAAAAAAATTTAAAA
40999870 AAAGTATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
16 18 0.41
17 7 0.16
18 4 0.09
20 4 0.09
22 11 0.25
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (16 bp):
TTAAAAAAATTTAAAA
Found at i:40999826 original size:9 final size:9
Alignment explanation
Indices: 40999812--40999872 Score: 52
Period size: 9 Copynumber: 6.4 Consensus size: 9
40999802 AAAATATTTT
40999812 AAAATTAAA
1 AAAATTAAA
40999821 AAAATTTAAA
1 AAAA-TTAAA
*
40999831 AAGTATTTTAAA
1 AA--A-ATTAAA
40999843 AAAATT-AA
1 AAAATTAAA
*
40999851 AAATTTAAA
1 AAAATTAAA
*
40999860 AAATTTAAA
1 AAAATTAAA
40999869 AAAA
1 AAAA
40999873 GTATTTTAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
8 7 0.16
9 20 0.47
10 8 0.19
12 8 0.19
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.30
Consensus pattern (9 bp):
AAAATTAAA
Found at i:40999845 original size:40 final size:39
Alignment explanation
Indices: 40999763--40999910 Score: 174
Period size: 40 Copynumber: 3.7 Consensus size: 39
40999753 ACCAAAAATT
*
40999763 TATTTTAAAAATTAAAACAAAAATTAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATT--AA-AAAAATTTAAAAAGTATTTTAAAAA
40999806 TATTTTAAAATTAAAAAAATTTAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAATTTAAAAAGTATTTTAAAAA
* * * *
40999845 -AATTAAAAATTTAAAAAATTTAAAAAAAGTATTTTAAAAG
1 TATTTTAAAATTAAAAAAATTT--AAAAAGTATTTTAAAAA
*
40999885 TATTTTAAAATT-TAAAAATTTAAAAA
1 TATTTTAAAATTAAAAAAATTTAAAAA
40999911 ATAAAAAAAT
Statistics
Matches: 94, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
38 23 0.24
39 24 0.26
40 26 0.28
41 9 0.10
42 6 0.06
43 6 0.06
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.36
Consensus pattern (39 bp):
TATTTTAAAATTAAAAAAATTTAAAAAGTATTTTAAAAA
Found at i:41001160 original size:155 final size:155
Alignment explanation
Indices: 41000871--41001168 Score: 384
Period size: 155 Copynumber: 1.9 Consensus size: 155
41000861 TTTTTTTGTC
* * * * *
41000871 TTGGCTGTTGAAATTTTGGGGGGGAAAGTATGTTTGTATTGAAGTTTTACAGATAAAGTGTGATA
1 TTGGCTGTTGAAATTTTGGGAGGAAAAATATGTTTGTATTGAAGTTTTACAGAGAAAGTGTAATA
* * * * * * * *
41000936 TTTTTAAGGTCTGTTTTTATTATTTGTTATAATAATTTGTATATTATATATGTTTATATTTCAAT
66 GTTTTAAGATATGTTTATATTATTTGTAATAATAATTTGTATATTATATATATTTAGATTTCAAA
41001001 TTATTGTTAATTTCTTTTATTGTAG
131 TTATTGTTAATTTCTTTTATTGTAG
* * * * **
41001026 TTGGTTGTTGGAATTTTGGGAGGAAAAATTTGTTTGTGTT-AGAGTTTTAGGGAGAAAGTGTAAT
1 TTGGCTGTTGAAATTTTGGGAGGAAAAATATGTTTGTATTGA-AGTTTTACAGAGAAAGTGTAAT
*
41001090 AGTTTTAAGATATGTTTATATTGTTTGTAATAATAATTTGTATATTATATATATTTAGACTTT-A
65 AGTTTTAAGATATGTTTATATTATTTGTAATAATAATTTGTATATTATATATATTTAGA-TTTCA
41001154 AATTATTGTTAATTT
129 AATTATTGTTAATTT
41001169 TTAGGTTTAA
Statistics
Matches: 121, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
154 1 0.01
155 117 0.97
156 3 0.02
ACGTcount: A:0.29, C:0.02, G:0.19, T:0.50
Consensus pattern (155 bp):
TTGGCTGTTGAAATTTTGGGAGGAAAAATATGTTTGTATTGAAGTTTTACAGAGAAAGTGTAATA
GTTTTAAGATATGTTTATATTATTTGTAATAATAATTTGTATATTATATATATTTAGATTTCAAA
TTATTGTTAATTTCTTTTATTGTAG
Found at i:41001208 original size:21 final size:21
Alignment explanation
Indices: 41001184--41001223 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
41001174 TTTAATATCT
*
41001184 AAGATTATATTTTTATTTGTA
1 AAGATTATATTTGTATTTGTA
41001205 AAGATTATATTTGTATTTG
1 AAGATTATATTTGTATTTG
41001224 AGTTTTAGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (21 bp):
AAGATTATATTTGTATTTGTA
Found at i:41005443 original size:26 final size:26
Alignment explanation
Indices: 41005412--41005463 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
41005402 AATGCCGACC
* *
41005412 CACAGCTCATGTGAGCAGGCCCATTT
1 CACAGCTCATGTCAGCAGGCACATTT
*
41005438 CACAGCTCGTGTCAGCAGGCACATTT
1 CACAGCTCATGTCAGCAGGCACATTT
41005464 TACCAAGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.23, C:0.31, G:0.23, T:0.23
Consensus pattern (26 bp):
CACAGCTCATGTCAGCAGGCACATTT
Found at i:41012094 original size:2 final size:2
Alignment explanation
Indices: 41012087--41012151 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
41012077 TTTCTCCCTT
41012087 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
41012129 AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC A
41012152 TATATATATA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:41013716 original size:17 final size:19
Alignment explanation
Indices: 41013680--41013717 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
41013670 TATTATATAC
*
41013680 ATGTTTTATGTATATTTAA
1 ATGTTTAATGTATATTTAA
41013699 ATGTTTAAT-TAT-TTTAA
1 ATGTTTAATGTATATTTAA
41013716 AT
1 AT
41013718 CGAATATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 3 0.17
19 8 0.44
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (19 bp):
ATGTTTAATGTATATTTAA
Found at i:41014308 original size:30 final size:29
Alignment explanation
Indices: 41014257--41014314 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
41014247 GCTAAAACAT
*
41014257 AAAAACAATTATTTATCAAAATAGTATTA
1 AAAAACAATTAATTATCAAAATAGTATTA
*
41014286 AAAAACTAATTAATTA-CGAAAATGGTATT
1 AAAAAC-AATTAATTATC-AAAATAGTATT
41014315 GGATCTAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (29 bp):
AAAAACAATTAATTATCAAAATAGTATTA
Found at i:41016967 original size:44 final size:45
Alignment explanation
Indices: 41016902--41016986 Score: 120
Period size: 44 Copynumber: 1.9 Consensus size: 45
41016892 TTCATATGAT
*
41016902 GCCATAGTGTCTTTCAGCTATG-GTCTTACACA-TTTTATCATGGC
1 GCCATAGTGTCTTTCAACTATGAG-CTTACACATTTTTATCATGGC
* *
41016946 GCCATAGTTTCTTTCAACTATGAGCTTACTCATTTTTATCA
1 GCCATAGTGTCTTTCAACTATGAGCTTACACATTTTTATCA
41016987 CGATGCCATA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
44 27 0.75
45 9 0.25
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.41
Consensus pattern (45 bp):
GCCATAGTGTCTTTCAACTATGAGCTTACACATTTTTATCATGGC
Found at i:41017012 original size:45 final size:45
Alignment explanation
Indices: 41016970--41017073 Score: 136
Period size: 45 Copynumber: 2.3 Consensus size: 45
41016960 CAACTATGAG
* ** *
41016970 CTTACTCATTTTTATCACGATGCCATAACATATTTTAGCTATGGT
1 CTTACTCATTTTTATCACAACACCATAACATATTTAAGCTATGGT
* * *
41017015 CTTACTTATTTTTATCATAACACCATAACATCTTTAAGCTATGGT
1 CTTACTCATTTTTATCACAACACCATAACATATTTAAGCTATGGT
*
41017060 CTTATTCATTTTTA
1 CTTACTCATTTTTA
41017074 GGCATATAGC
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.28, C:0.19, G:0.08, T:0.45
Consensus pattern (45 bp):
CTTACTCATTTTTATCACAACACCATAACATATTTAAGCTATGGT
Found at i:41024040 original size:15 final size:15
Alignment explanation
Indices: 41024017--41024068 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
41024007 CTAACTGAGC
* *
41024017 TTAAATTTTTATTAA
1 TTAAGTTTTAATTAA
*
41024032 TTAAGTTTTAACTAA
1 TTAAGTTTTAATTAA
* *
41024047 TTAA-ATTTGATTAA
1 TTAAGTTTTAATTAA
41024061 TTAAGTTT
1 TTAAGTTT
41024069 CTGTATATGT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
14 11 0.38
15 18 0.62
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (15 bp):
TTAAGTTTTAATTAA
Found at i:41024704 original size:28 final size:29
Alignment explanation
Indices: 41024636--41024712 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
41024626 CCTCGATACG
*
41024636 ATGTTAACTTGTGTGAACAAATTCATAAA
1 ATGTTAACTTGTGTGAGCAAATTCATAAA
* *
41024665 ATGTCAATTTGTGTGAGCAAATTCAT-AA
1 ATGTTAACTTGTGTGAGCAAATTCATAAA
* *
41024693 ATGTTAGCTTGTGTAAGCAA
1 ATGTTAACTTGTGTGAGCAA
41024713 CCCTAATCAT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
28 18 0.44
29 23 0.56
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.35
Consensus pattern (29 bp):
ATGTTAACTTGTGTGAGCAAATTCATAAA
Found at i:41025904 original size:36 final size:36
Alignment explanation
Indices: 41025855--41025928 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
41025845 GTGGCCTAAC
*
41025855 GTCGTGACATGACAAACTATTTTGCGACGTCATGAT
1 GTCGTGACATGACAAACTACTTTGCGACGTCATGAT
* *
41025891 GTCGTGACGTGACAAACTACTTTGCGATGTCATGAT
1 GTCGTGACATGACAAACTACTTTGCGACGTCATGAT
41025927 GT
1 GT
41025929 GGAAATGATG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (36 bp):
GTCGTGACATGACAAACTACTTTGCGACGTCATGAT
Found at i:41026890 original size:19 final size:19
Alignment explanation
Indices: 41026855--41026896 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
41026845 TATGTTAATT
*
41026855 TAAAGTTAAATTAATAATAA
1 TAAAGTTAAA-TAATAAAAA
41026875 TAAAGTTAAA-ACATAAAAA
1 TAAAGTTAAATA-ATAAAAA
41026894 TAA
1 TAA
41026897 TGGTCATCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 9 0.45
20 10 0.50
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (19 bp):
TAAAGTTAAATAATAAAAA
Found at i:41036062 original size:40 final size:43
Alignment explanation
Indices: 41036018--41036097 Score: 96
Period size: 42 Copynumber: 1.9 Consensus size: 43
41036008 GGTAAAAACA
41036018 TAACT-ACTATTATCAA-T-AAAATCAAATACAAA-ATGAATAT
1 TAACTCAC-ATTATCAACTCAAAATCAAATACAAAGATGAATAT
* * *
41036058 TAACTCACATTATTAACTCAAACTCAAATTCAAAGATGAA
1 TAACTCACATTATCAACTCAAAATCAAATACAAAGATGAA
41036098 AATAGCATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
40 12 0.36
41 3 0.09
42 13 0.39
43 5 0.15
ACGTcount: A:0.51, C:0.16, G:0.04, T:0.29
Consensus pattern (43 bp):
TAACTCACATTATCAACTCAAAATCAAATACAAAGATGAATAT
Found at i:41040409 original size:17 final size:16
Alignment explanation
Indices: 41040387--41040420 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
41040377 GAGTATAGTA
41040387 AAATATTAAAAATAAAT
1 AAATATTAAAAA-AAAT
*
41040404 AAATATTTAAAAAAAT
1 AAATATTAAAAAAAAT
41040420 A
1 A
41040421 TATCTACTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATATTAAAAAAAAT
Found at i:41040722 original size:13 final size:13
Alignment explanation
Indices: 41040704--41040728 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41040694 ATTTAGTATT
41040704 TATATAATAAATG
1 TATATAATAAATG
41040717 TATATAATAAAT
1 TATATAATAAAT
41040729 ATATTTTTTA
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:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (13 bp):
TATATAATAAATG
Found at i:41040783 original size:20 final size:21
Alignment explanation
Indices: 41040754--41040792 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
41040744 TATTGTAAAG
41040754 TATTTGTAAAATAC-TTTTTT
1 TATTTGTAAAATACATTTTTT
*
41040774 TATTTTTAAAATACATTTT
1 TATTTGTAAAATACATTTT
41040793 CGGATATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (21 bp):
TATTTGTAAAATACATTTTTT
Found at i:41046297 original size:9 final size:9
Alignment explanation
Indices: 41046285--41046318 Score: 68
Period size: 9 Copynumber: 3.8 Consensus size: 9
41046275 ACAAAATTTA
41046285 CAATTTATT
1 CAATTTATT
41046294 CAATTTATT
1 CAATTTATT
41046303 CAATTTATT
1 CAATTTATT
41046312 CAATTTA
1 CAATTTA
41046319 GTCCCTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (9 bp):
CAATTTATT
Found at i:41047731 original size:17 final size:18
Alignment explanation
Indices: 41047694--41047732 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
41047684 TAAATTAATT
*
41047694 ATTTTATAAATACTTATA
1 ATTTTATAAATACTTAGA
*
41047712 ATTTTAT-AATTCTTAGA
1 ATTTTATAAATACTTAGA
41047729 ATTT
1 ATTT
41047733 CACTTCCGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (18 bp):
ATTTTATAAATACTTAGA
Found at i:41058180 original size:42 final size:42
Alignment explanation
Indices: 41058070--41058159 Score: 153
Period size: 42 Copynumber: 2.1 Consensus size: 42
41058060 TCTTAGGCCA
* *
41058070 TGTAACATTCGAAATAGGGACACACGGCCGTGTCCCAGCTCG
1 TGTAACATTCGAAATAGGGACACACGGCCGTCTCCCAGCCCG
*
41058112 TGTAACATTCGAAATAGGGACACACGGTCGTCTCCCAGCCCG
1 TGTAACATTCGAAATAGGGACACACGGCCGTCTCCCAGCCCG
41058154 TGTAAC
1 TGTAAC
41058160 TCTCTGAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (42 bp):
TGTAACATTCGAAATAGGGACACACGGCCGTCTCCCAGCCCG
Found at i:41060255 original size:138 final size:137
Alignment explanation
Indices: 41060008--41060267 Score: 387
Period size: 138 Copynumber: 1.9 Consensus size: 137
41059998 ATGGGTATGT
* * * * *
41060008 TCACACAAGTTGACGGTCGGAATGTAGCTACACGATGCTGCTCACACAAGTTGATGAGTATCCGC
1 TCACACAAGCTGACGGTCGGAATGTAGCTACACGATGCTGCTCACACAAGCTAATAAGTATCCAC
* * * * *
41060073 AACAAATGTTGAAACTCAGCTATCGGTAGGACATTCAGGACCAGCACCCTAAACATGGTAACCTC
66 AAAAAATGTTCAAACTCAGCCATCGGTAGAACATTCAGGACCAGCACCCAAAACATGGTAACCTC
41060138 GGTCTAC
131 GGTCTAC
*
41060145 TCACACAAGCTGACGGTCGGAATGTAAGCTACACGATGTTGCTCACACAAGCTAATAAGTATCCA
1 TCACACAAGCTGACGGTCGGAATGT-AGCTACACGATGCTGCTCACACAAGCTAATAAGTATCCA
*
41060210 CAAAAAATG-TCAAACCTCAGCCATCGGTAGAACATTTAGGACCAGCACCCAAAACATG
65 CAAAAAATGTTCAAA-CTCAGCCATCGGTAGAACATTCAGGACCAGCACCCAAAACATG
41060268 AAAACCCTAA
Statistics
Matches: 109, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
137 28 0.26
138 81 0.74
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (137 bp):
TCACACAAGCTGACGGTCGGAATGTAGCTACACGATGCTGCTCACACAAGCTAATAAGTATCCAC
AAAAAATGTTCAAACTCAGCCATCGGTAGAACATTCAGGACCAGCACCCAAAACATGGTAACCTC
GGTCTAC
Found at i:41065354 original size:22 final size:20
Alignment explanation
Indices: 41065306--41065355 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
41065296 TTAAACACCT
41065306 TTTAAAAATAAAATAATCAA
1 TTTAAAAATAAAATAATCAA
* * *
41065326 ATGAAAAATTAAACATAATCAG
1 TTTAAAAA-TAAA-ATAATCAA
41065348 TTTAAAAA
1 TTTAAAAA
41065356 AATATTAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
20 6 0.26
21 4 0.17
22 13 0.57
ACGTcount: A:0.62, C:0.06, G:0.04, T:0.28
Consensus pattern (20 bp):
TTTAAAAATAAAATAATCAA
Found at i:41068416 original size:17 final size:15
Alignment explanation
Indices: 41068386--41068437 Score: 50
Period size: 17 Copynumber: 3.2 Consensus size: 15
41068376 ACTACAAAAC
*
41068386 ATTTATTATTAATAT
1 ATTTATTTTTAATAT
41068401 ATTTATAATTTTAATAAAT
1 ATTTAT--TTTTAAT--AT
*
41068420 ATTTATTTTTAAAAT
1 ATTTATTTTTAATAT
41068435 ATT
1 ATT
41068438 AATATTGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
15 11 0.35
17 12 0.39
19 8 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTTATTTTTAATAT
Found at i:41068436 original size:15 final size:15
Alignment explanation
Indices: 41068381--41068437 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
41068371 TTTATACTAC
* *
41068381 AAAACATTTATTATT
1 AAAATATTTATTTTT
*
41068396 AATATATTTATAATTTT
1 AAAATATTTAT--TTTT
41068413 AATAAATATTTATTTTT
1 -A-AAATATTTATTTTT
41068430 AAAATATT
1 AAAATATT
41068438 AATATTGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 16 0.47
16 1 0.03
17 7 0.21
18 1 0.03
19 9 0.26
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (15 bp):
AAAATATTTATTTTT
Found at i:41070896 original size:22 final size:22
Alignment explanation
Indices: 41070866--41070919 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
41070856 ATAAGGTCCA
*
41070866 TCTCAAGACAAAGAGTTCCTCG
1 TCTCGAGACAAAGAGTTCCTCG
**
41070888 TCTCGAGACAAAGAGTTCCTTT
1 TCTCGAGACAAAGAGTTCCTCG
41070910 TCTCGAGACA
1 TCTCGAGACA
41070920 CAACATTGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (22 bp):
TCTCGAGACAAAGAGTTCCTCG
Found at i:41072251 original size:27 final size:27
Alignment explanation
Indices: 41072220--41072288 Score: 138
Period size: 27 Copynumber: 2.6 Consensus size: 27
41072210 TATTTTTCCT
41072220 ATATAATATTTGAAACTAGGGTACTAG
1 ATATAATATTTGAAACTAGGGTACTAG
41072247 ATATAATATTTGAAACTAGGGTACTAG
1 ATATAATATTTGAAACTAGGGTACTAG
41072274 ATATAATATTTGAAA
1 ATATAATATTTGAAA
41072289 TTTTGTTAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (27 bp):
ATATAATATTTGAAACTAGGGTACTAG
Found at i:41072523 original size:6 final size:6
Alignment explanation
Indices: 41072517--41072557 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
41072507 ATTTTCCATA
* * *
41072517 AAAATA AAAACG AAAACG AAAATG AAAATG AAAATG AAAAT
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAAT
41072558 AACCTATGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.71, C:0.05, G:0.12, T:0.12
Consensus pattern (6 bp):
AAAATG
Found at i:41073061 original size:23 final size:23
Alignment explanation
Indices: 41073035--41073079 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
41073025 AGAAAATGTC
* *
41073035 ACAATAAAATTAACCAAAACGTT
1 ACAAAAAAATGAACCAAAACGTT
*
41073058 ACAAAAAAATGAACTAAAACGT
1 ACAAAAAAATGAACCAAAACGT
41073080 CAAAAAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.60, C:0.16, G:0.07, T:0.18
Consensus pattern (23 bp):
ACAAAAAAATGAACCAAAACGTT
Found at i:41087076 original size:2 final size:2
Alignment explanation
Indices: 41087069--41087115 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
41087059 AATTATGGTG
41087069 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41087111 TA TA T
1 TA TA T
41087116 GACTTACTGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:41091293 original size:15 final size:14
Alignment explanation
Indices: 41091272--41091307 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
41091262 ATAATCATTA
*
41091272 ATAATTATCTTAAT
1 ATAATTATCCTAAT
41091286 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
41091301 ATAATTA
1 ATAATTA
41091308 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:41093054 original size:22 final size:21
Alignment explanation
Indices: 41093029--41093088 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
41093019 GCTGAGGGGT
* *
41093029 GGTGCTTGGATGCAGGGATAAG
1 GGTGCTTGGCTGCAGGAAT-AG
*
41093051 GGTGGTTGGCTGCAGGAATAG
1 GGTGCTTGGCTGCAGGAATAG
*
41093072 GGTAGTTTGGCTGCAGG
1 GGT-GCTTGGCTGCAGG
41093089 CATTCTGAGC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.15
22 28 0.85
ACGTcount: A:0.18, C:0.10, G:0.47, T:0.25
Consensus pattern (21 bp):
GGTGCTTGGCTGCAGGAATAG
Found at i:41093274 original size:36 final size:33
Alignment explanation
Indices: 41093234--41093317 Score: 98
Period size: 36 Copynumber: 2.4 Consensus size: 33
41093224 ATTCATATCC
*
41093234 AAATAAGTAATAAATAATAAAATAAATTAAAGTAAT
1 AAATAA-TAA-AAATAATAAAATAAAATAAA-TAAT
41093270 AAATAAATTAAAGAA-AATAAAATAAAATAAATAAT
1 AAAT-AA-TAAA-AATAATAAAATAAAATAAATAAT
41093305 AAATAATAAAAAT
1 AAATAATAAAAAT
41093318 TGGGTTGCCT
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
32 2 0.05
33 4 0.09
34 2 0.05
35 8 0.19
36 20 0.47
37 7 0.16
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (33 bp):
AAATAATAAAAATAATAAAATAAAATAAATAAT
Found at i:41100509 original size:16 final size:18
Alignment explanation
Indices: 41100485--41100527 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
41100475 AAACCTTACT
*
41100485 AAGATAAAAACCCT-GTG
1 AAGAAAAAAACCCTAGTG
*
41100502 -AGAAAAAAATCCTAGTG
1 AAGAAAAAAACCCTAGTG
41100519 AAGAAAAAA
1 AAGAAAAAA
41100528 GATTACACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 11 0.50
17 3 0.14
18 8 0.36
ACGTcount: A:0.58, C:0.12, G:0.16, T:0.14
Consensus pattern (18 bp):
AAGAAAAAAACCCTAGTG
Found at i:41101320 original size:2 final size:2
Alignment explanation
Indices: 41101313--41101337 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41101303 CAATTTATTC
41101313 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
41101338 TTCTCAATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41120284 original size:56 final size:51
Alignment explanation
Indices: 41120218--41120409 Score: 163
Period size: 50 Copynumber: 3.7 Consensus size: 51
41120208 GGAATGAGAC
* **
41120218 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGGTTATGAGAGGT
1 CCCACGTAAGACCATGTCTGGGACATGGCATTGGCA--ACCGA-G--ATGAGAGGT
* * * *
41120274 CCTACGTAAGATCATGTATGGGACAAGGCATTGGC-ACCGAGATGAGAGGT
1 CCCACGTAAGACCATGTCTGGGACATGGCATTGGCAACCGAGATGAGAGGT
* * * * **
41120324 CCCCCGTAAGACCATGTCCGGGACATGGCATGGGC-ACCGATATGAGAACT
1 CCCACGTAAGACCATGTCTGGGACATGGCATTGGCAACCGAGATGAGAGGT
* * * * *
41120374 CCTATGTAAGACCATATCTGGGATATGACATTGGCA
1 CCCACGTAAGACCATGTCTGGGACATGGCATTGGCA
41120410 GTATAGGAAA
Statistics
Matches: 110, Mismatches: 25, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
50 76 0.69
52 1 0.01
53 3 0.03
56 30 0.27
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.23
Consensus pattern (51 bp):
CCCACGTAAGACCATGTCTGGGACATGGCATTGGCAACCGAGATGAGAGGT
Found at i:41120685 original size:20 final size:20
Alignment explanation
Indices: 41120660--41120698 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
41120650 TGAGTTATTT
41120660 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
41120680 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
41120699 GAAAAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:41125742 original size:20 final size:20
Alignment explanation
Indices: 41125717--41125755 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
41125707 TACTTTCTTC
41125717 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
41125737 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
41125756 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:41126074 original size:50 final size:50
Alignment explanation
Indices: 41126006--41126151 Score: 179
Period size: 50 Copynumber: 2.9 Consensus size: 50
41125996 TTTCCTGTAC
* * * **
41126006 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGG
* *
41126056 TGTCC-ATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TG-CCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGG
**
41126106 TGCCAATGCCATGTCCCAGACATTATCTTAC-GTGGGACCTCTCATA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAG-GGGACCTCTCATA
41126152 ACCTCAATAA
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
49 3 0.04
50 78 0.94
51 2 0.02
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGG
Found at i:41126168 original size:56 final size:50
Alignment explanation
Indices: 41126006--41126192 Score: 142
Period size: 50 Copynumber: 3.6 Consensus size: 50
41125996 TTTCCTGTAC
* * * ** ** * **
41126006 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGATCTTACGGGGGACCTCTCATCTCAA
* **
41126056 TGTCC-ATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TG-CCAATGCCATGTCCCAGACATGATCTTACGGGGGACCTCTCATCTCAA
* *
41126106 TGCCAATGCCATGTCCCAGACATTATCTTACGTGGGACCTCTCATAACCTCAATAA
1 TGCCAATGCCATGTCCCAGACATGATCTTACGGGGGACCTCTCAT---CTC---AA
* * *
41126162 TGCCAATTCCATGTCCCAAACATGGTCTTAC
1 TGCCAATGCCATGTCCCAGACATGATCTTAC
41126193 TGTAACACCC
Statistics
Matches: 113, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
49 2 0.02
50 79 0.70
51 2 0.02
53 3 0.03
56 27 0.24
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGATCTTACGGGGGACCTCTCATCTCAA
Found at i:41128181 original size:45 final size:45
Alignment explanation
Indices: 41128100--41128231 Score: 196
Period size: 45 Copynumber: 3.0 Consensus size: 45
41128090 AATCGTTACA
* * **
41128100 CGGTGG-ATCAGCACATAGC-ACCACCCTTATAATCAATTATATT
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATACC
* *
41128143 CGGTGGAATCAGCACATAGCAACCACCTTTATAGTCAATGGTACC
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATACC
41128188 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATAC
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATAC
41128232 TCAGTACACG
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
43 6 0.08
44 13 0.16
45 60 0.76
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATACC
Found at i:41141625 original size:22 final size:22
Alignment explanation
Indices: 41141590--41141633 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
41141580 CATAGTCATG
41141590 AGTTATGTCTCTTG-TTACTAAA
1 AGTTATGTCTCTTGATTA-TAAA
41141612 AGTTATGT-TACTTGATTATAAA
1 AGTTATGTCT-CTTGATTATAAA
41141634 CAAATAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 1 0.05
22 16 0.80
23 3 0.15
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (22 bp):
AGTTATGTCTCTTGATTATAAA
Found at i:41150734 original size:44 final size:44
Alignment explanation
Indices: 41150685--41150773 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
41150675 CTCCCATGAA
*
41150685 TGCAATATTGTACATTATAAGGAGATAAGAAAGACCTTTAAAAC
1 TGCAATATTGAACATTATAAGGAGATAAGAAAGACCTTTAAAAC
41150729 TGCAATATTGAACATTATAAGGAGATAAGAAAGACCTTTAAAAC
1 TGCAATATTGAACATTATAAGGAGATAAGAAAGACCTTTAAAAC
41150773 T
1 T
41150774 AAATAAAGAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.46, C:0.11, G:0.16, T:0.27
Consensus pattern (44 bp):
TGCAATATTGAACATTATAAGGAGATAAGAAAGACCTTTAAAAC
Found at i:41154134 original size:25 final size:23
Alignment explanation
Indices: 41154106--41154151 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
41154096 AATATAATAC
41154106 AAATACACAAATTCTTCTTCTTTTT
1 AAATACAC--ATTCTTCTTCTTTTT
*
41154131 AAATACACATTCTTTTTCTTT
1 AAATACACATTCTTCTTCTTT
41154152 CTTTCTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 12 0.60
25 8 0.40
ACGTcount: A:0.30, C:0.20, G:0.00, T:0.50
Consensus pattern (23 bp):
AAATACACATTCTTCTTCTTTTT
Found at i:41155375 original size:5 final size:5
Alignment explanation
Indices: 41155367--41155399 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
41155357 TATATTATAT
41155367 AAATA AAATA AAATA AAATA AAA-A AATATA AAA
1 AAATA AAATA AAATA AAATA AAATA AA-ATA AAA
41155400 GAATAGTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 3 0.12
5 20 0.77
6 3 0.12
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:41155387 original size:15 final size:15
Alignment explanation
Indices: 41155362--41155399 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
41155352 ATATATATAT
41155362 TATATAAATAAAATAAA
1 TATA-AAATAAAA-AAA
41155379 -ATAAAATAAAAAAA
1 TATAAAATAAAAAAA
41155393 TATAAAA
1 TATAAAA
41155400 GAATAGTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 3 0.15
15 14 0.70
16 3 0.15
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
TATAAAATAAAAAAA
Found at i:41155631 original size:3 final size:3
Alignment explanation
Indices: 41155623--41155661 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
41155613 ATGCGTAAAT
*
41155623 ATA ATA ATA ATA ATA ACA ATAA ATA ATA AT- ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA
41155662 GTGAAAAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:41157470 original size:17 final size:17
Alignment explanation
Indices: 41157448--41157486 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
41157438 CTGACTCTAT
*
41157448 TTTTAT-TTTCTAGTTTA
1 TTTTATATTT-TAGTATA
41157465 TTTTATATTTTAGTATA
1 TTTTATATTTTAGTATA
41157482 TTTTA
1 TTTTA
41157487 CATCTAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (17 bp):
TTTTATATTTTAGTATA
Found at i:41157972 original size:2 final size:2
Alignment explanation
Indices: 41157965--41158008 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
41157955 GAAGCAATAA
*
41157965 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41158007 AT
1 AT
41158009 TTTGTTTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:41159378 original size:74 final size:73
Alignment explanation
Indices: 41159236--41159377 Score: 171
Period size: 74 Copynumber: 1.9 Consensus size: 73
41159226 ATTGTCACAA
* * * * * *
41159236 TAAAATCTTAAGCAATTGTGACAAATTTAAATGATCATAATTATTTAATTTGTTTGTGATAAAAT
1 TAAAATCATAAGCAATTGTGACAAAATTAAATGATAATAATAATTT-ATTTATTTGTGACAAAAT
41159301 TTTTGGTAT
65 TTTTGGTAT
* *
41159310 TAAAATCATAAGTAATTGTGACAAAATTAAATGGTAATAATAATTT-TTCTATTT-TGACAAATA
1 TAAAATCATAAGCAATTGTGACAAAATTAAATGATAATAATAATTTATT-TATTTGTGACAAA-A
41159373 TTTTT
64 TTTTT
41159378 TACTCTAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
72 8 0.14
73 10 0.17
74 40 0.69
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.44
Consensus pattern (73 bp):
TAAAATCATAAGCAATTGTGACAAAATTAAATGATAATAATAATTTATTTATTTGTGACAAAATT
TTTGGTAT
Found at i:41159766 original size:3 final size:3
Alignment explanation
Indices: 41159758--41159783 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
41159748 CTATGTGCTT
41159758 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
41159784 TATATAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:41162050 original size:21 final size:21
Alignment explanation
Indices: 41162024--41162066 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
41162014 ATAAGAATAA
41162024 ACTATGGATAAATGAGTGTAT
1 ACTATGGATAAATGAGTGTAT
*
41162045 ACTATGGATAAATGGGTGTAT
1 ACTATGGATAAATGAGTGTAT
41162066 A
1 A
41162067 TGTCATATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.33
Consensus pattern (21 bp):
ACTATGGATAAATGAGTGTAT
Found at i:41174527 original size:22 final size:21
Alignment explanation
Indices: 41174502--41174545 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
41174492 TGATAAAATT
41174502 TAATATATA-ATTATATTATTTA
1 TAATATATATATTA-ATT-TTTA
*
41174524 TAATTTATATATTAATTTTTA
1 TAATATATATATTAATTTTTA
41174545 T
1 T
41174546 CAACTTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATATATATATTAATTTTTA
Found at i:41175052 original size:44 final size:45
Alignment explanation
Indices: 41174934--41175079 Score: 260
Period size: 45 Copynumber: 3.3 Consensus size: 45
41174924 AAAGTTTGAT
41174934 TATTTC-AATAAATTGTTATATTAGCTTAATAATGACATGAAATG
1 TATTTCTAATAAATTGTTATATTAGCTTAATAATGACATGAAATG
41174978 TATTTCTAATAAATTGTTATATTAGCTTAATAATGACATGAAATG
1 TATTTCTAATAAATTGTTATATTAGCTTAATAATGACATGAAATG
* *
41175023 CATTTC-AATAAATTGTTATATTAGTTTAATAATGACATGAAATG
1 TATTTCTAATAAATTGTTATATTAGCTTAATAATGACATGAAATG
41175067 TATTTCTAATAAA
1 TATTTCTAATAAA
41175080 CCATGCGAAT
Statistics
Matches: 97, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
44 48 0.49
45 49 0.51
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (45 bp):
TATTTCTAATAAATTGTTATATTAGCTTAATAATGACATGAAATG
Found at i:41187959 original size:16 final size:16
Alignment explanation
Indices: 41187928--41188006 Score: 117
Period size: 16 Copynumber: 5.1 Consensus size: 16
41187918 TTCGCTGTAT
41187928 TGGAATAGAG--GTAA
1 TGGAATAGAGACGTAA
41187942 TGGAATAGAGACGTAA
1 TGGAATAGAGACGTAA
*
41187958 TGGAATAAAGACGTAA
1 TGGAATAGAGACGTAA
*
41187974 TGGAATAAAGACGTAA
1 TGGAATAGAGACGTAA
*
41187990 TGGAATAGAGGCGTAA
1 TGGAATAGAGACGTAA
41188006 T
1 T
41188007 AGCAATTCAA
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
14 10 0.17
16 50 0.83
ACGTcount: A:0.44, C:0.05, G:0.30, T:0.20
Consensus pattern (16 bp):
TGGAATAGAGACGTAA
Found at i:41188047 original size:45 final size:44
Alignment explanation
Indices: 41187986--41188094 Score: 131
Period size: 45 Copynumber: 2.5 Consensus size: 44
41187976 GAATAAAGAC
41187986 GTAATGGAATAGAGGCGTAATAGCAATTCAAT-TGTTTGGTTGAAT
1 GTAAT-GAATAGAGGCGTAATAGCAATTC-ATGTGTTTGGTTGAAT
* *
41188031 GTAATGAAATAGAGGCGTAATAG-TATTCTTGTGTTTGGTTGAAT
1 GTAATG-AATAGAGGCGTAATAGCAATTCATGTGTTTGGTTGAAT
41188075 G----GAATAGAGGCGTAATAGCA
1 GTAATGAATAGAGGCGTAATAGCA
41188095 TAAGGAAAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
43 1 0.02
44 19 0.33
45 21 0.36
ACGTcount: A:0.33, C:0.06, G:0.28, T:0.32
Consensus pattern (44 bp):
GTAATGAATAGAGGCGTAATAGCAATTCATGTGTTTGGTTGAAT
Found at i:41188092 original size:39 final size:40
Alignment explanation
Indices: 41187988--41188094 Score: 128
Period size: 44 Copynumber: 2.6 Consensus size: 40
41187978 ATAAAGACGT
41187988 AATGGAATAGAGGCGTAATAGCAATTCAATTGTTTGGTTG
1 AATGGAATAGAGGCGTAATAGCAATTCAATTGTTTGGTTG
* *
41188028 AATGTAATGAAATAGAGGCGTAATAG-TATTC-TTGTGTTTGGTTG
1 AATG----G-AATAGAGGCGTAATAGCAATTCAAT-TGTTTGGTTG
41188072 AATGGAATAGAGGCGTAATAGCA
1 AATGGAATAGAGGCGTAATAGCA
41188095 TAAGGAAAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
39 16 0.28
40 5 0.09
43 1 0.02
44 19 0.33
45 16 0.28
ACGTcount: A:0.34, C:0.07, G:0.28, T:0.32
Consensus pattern (40 bp):
AATGGAATAGAGGCGTAATAGCAATTCAATTGTTTGGTTG
Found at i:41188217 original size:11 final size:11
Alignment explanation
Indices: 41188198--41188230 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
41188188 TTAATATAAA
41188198 TAATAAATAATT
1 TAAT-AATAATT
41188210 TAATAATAATT
1 TAATAATAATT
41188221 TAA-AATAATT
1 TAATAATAATT
41188231 ATTATTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 7 0.33
11 10 0.48
12 4 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TAATAATAATT
Found at i:41188245 original size:26 final size:26
Alignment explanation
Indices: 41188215--41188303 Score: 72
Period size: 28 Copynumber: 3.3 Consensus size: 26
41188205 TAATTTAATA
41188215 ATAATTTAAAATAATTATTATTAAAT
1 ATAATTTAAAATAATTATTATTAAAT
* * *
41188241 ATAATTTAATAAAAATATATAATTTAAT
1 ATAATTTAA-AATAAT-TATTATTAAAT
* * * *
41188269 AAAATTCTGAATATAATTATTCTTATAT
1 ATAATT-T-AAAATAATTATTATTAAAT
41188297 -TAATTTA
1 ATAATTTA
41188304 CTAAAATCAT
Statistics
Matches: 48, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
25 1 0.02
26 10 0.21
27 9 0.19
28 21 0.44
29 5 0.10
30 2 0.04
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (26 bp):
ATAATTTAAAATAATTATTATTAAAT
Found at i:41188251 original size:24 final size:21
Alignment explanation
Indices: 41188175--41188286 Score: 70
Period size: 22 Copynumber: 5.1 Consensus size: 21
41188165 GTTATTAAGT
41188175 TTTAATAAGATTATTAATATAA
1 TTTAATAA-ATTATTAATATAA
* *
41188197 -ATAATAAATAATTTAATAATAA
1 TTTAATAAATTA-TTAAT-ATAA
41188219 TTTAAAATAATTATTATTAAATATAA
1 TTT--AATAA--ATTATT-AATATAA
*
41188245 TTTAATAAA--AAT-ATATAA
1 TTTAATAAATTATTAATATAA
* *
41188263 TTTAATAAAATTCTGAATATAA
1 TTTAAT-AAATTATTAATATAA
41188285 TT
1 TT
41188287 ATTCTTATAT
Statistics
Matches: 70, Mismatches: 8, Indels: 24
0.69 0.08 0.24
Matches are distributed among these distances:
18 12 0.17
19 3 0.04
20 5 0.07
21 11 0.16
22 13 0.19
23 1 0.01
24 5 0.07
25 5 0.07
26 9 0.13
27 6 0.09
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (21 bp):
TTTAATAAATTATTAATATAA
Found at i:41188264 original size:55 final size:55
Alignment explanation
Indices: 41188193--41188309 Score: 148
Period size: 55 Copynumber: 2.1 Consensus size: 55
41188183 GATTATTAAT
41188193 ATAAATAATAAATAATTTAATAATAATT-T-AAAATAATTATTATTAAATATAATTTA
1 ATAAA-AATAAATAATTTAATAA-AATTCTGAAAATAATTATTATTAAAT-TAATTTA
* * * *
41188249 ATAAAAATATATAATTTAATAAAATTCTGAATATAATTATTCTTATATTAATTTA
1 ATAAAAATAAATAATTTAATAAAATTCTGAAAATAATTATTATTAAATTAATTTA
*
41188304 CTAAAA
1 ATAAAA
41188310 TCATAATATA
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
54 4 0.07
55 29 0.54
56 21 0.39
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.43
Consensus pattern (55 bp):
ATAAAAATAAATAATTTAATAAAATTCTGAAAATAATTATTATTAAATTAATTTA
Found at i:41200469 original size:15 final size:16
Alignment explanation
Indices: 41200438--41200471 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
41200428 ATTGGATTTA
*
41200438 ATTAAATATGAGTTAT
1 ATTAAATATGAGCTAT
41200454 ATTAAAT-TGAGCTAT
1 ATTAAATATGAGCTAT
41200469 ATT
1 ATT
41200472 TACTCATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.41, C:0.03, G:0.12, T:0.44
Consensus pattern (16 bp):
ATTAAATATGAGCTAT
Found at i:41201023 original size:24 final size:25
Alignment explanation
Indices: 41200944--41201033 Score: 74
Period size: 27 Copynumber: 3.6 Consensus size: 25
41200934 TGGCACTCTG
* * *
41200944 GAGCTTCCTGATTAAAGGCTCTTTCAT
1 GAGCTTCCTAATTAATGGCTC--GCAT
* **
41200971 GAGCTTCCTAATTAATGGCTCTCCG
1 GAGCTTCCTAATTAATGGCTCGCAT
* *
41200996 GAGCTTCCTGA-TATTGGCTCGCAT
1 GAGCTTCCTAATTAATGGCTCGCAT
*
41201020 GAGCTTCCCAATTA
1 GAGCTTCCTAATTA
41201034 TCGCTCTTAT
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
24 18 0.35
25 14 0.27
27 19 0.37
ACGTcount: A:0.21, C:0.26, G:0.20, T:0.33
Consensus pattern (25 bp):
GAGCTTCCTAATTAATGGCTCGCAT
Found at i:41205069 original size:50 final size:50
Alignment explanation
Indices: 41204966--41205155 Score: 191
Period size: 50 Copynumber: 3.7 Consensus size: 50
41204956 AAAGAGATCT
*
41204966 CATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGGTCC
* *
41205022 CATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
** * * * * **
41205072 CCCGTAAGACCATGTCTGGGACATGCCATGGGCACCTATATGAGAACTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
* * * *
41205122 CATGTAAGACCATATTTGGGATATGGCACTGGCA
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCA
41205156 GTACAAGAAA
Statistics
Matches: 113, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
50 77 0.68
53 3 0.03
55 1 0.01
56 32 0.28
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (50 bp):
CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
Found at i:41205155 original size:100 final size:104
Alignment explanation
Indices: 41204969--41205155 Score: 247
Period size: 100 Copynumber: 1.8 Consensus size: 104
41204959 GAGATCTCAT
* * * **
41204969 GTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCCCATGTAAGACCA
1 GTAAGACCATGTCTGGGACATGCCATGGGCATCACT--GATTATGAGAACTCCCATGTAAGACCA
* **
41205034 TGTTTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCC
64 TATTTGGGACATGGCACTGGCACCGAGATGAGAGGTCCCCC
41205075 GTAAGACCATGTCTGGGACATGCCATGGGCA-C-CT-A-TATGAGAACTCCCATGTAAGACCATA
1 GTAAGACCATGTCTGGGACATGCCATGGGCATCACTGATTATGAGAACTCCCATGTAAGACCATA
*
41205136 TTTGGGATATGGCACTGGCA
66 TTTGGGACATGGCACTGGCA
41205156 GTACAAGAAA
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
100 40 0.56
101 1 0.01
104 1 0.01
105 1 0.01
106 29 0.40
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (104 bp):
GTAAGACCATGTCTGGGACATGCCATGGGCATCACTGATTATGAGAACTCCCATGTAAGACCATA
TTTGGGACATGGCACTGGCACCGAGATGAGAGGTCCCCC
Found at i:41206802 original size:20 final size:20
Alignment explanation
Indices: 41206777--41206823 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
41206767 GATTTTGTTT
41206777 GTTAAGAAGAAAGATGGATC
1 GTTAAGAAGAAAGATGGATC
41206797 GTTAAGAAGAAAGATGGATC
1 GTTAAGAAGAAAGATGGATC
41206817 GTTAAGA
1 GTTAAGA
41206824 TTGTGTATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.45, C:0.04, G:0.30, T:0.21
Consensus pattern (20 bp):
GTTAAGAAGAAAGATGGATC
Found at i:41212213 original size:39 final size:39
Alignment explanation
Indices: 41212141--41212362 Score: 108
Period size: 39 Copynumber: 5.6 Consensus size: 39
41212131 TTGTATGATT
* *
41212141 GCACATATGTGCCCCTATTTGTACTTCAGTACCCTTAAAC
1 GCACATACGTG-CCCTATTTGTACTTCAGTACCCCTAAAC
* * * *
41212181 GCACATACGTGCCCTGTTTGTACTT-TGATACCCCTGAAT
1 GCACATACGTGCCCTATTTGTACTTCAG-TACCCCTAAAC
* * * **
41212220 GCACACACGTGCCCTATCTT-TACTTC-GACACCCCTGATT
1 GCACATACGTGCCCTAT-TTGTACTTCAG-TACCCCTAAAC
*** * * * * * **
41212259 GCACACGTGTGCCCATGTTTGTACTTCGGTACACTTGATT
1 GCACATACGTGCCC-TATTTGTACTTCAGTACCCCTAAAC
* * *
41212299 GCACATACGTGCCCCTATATGTACTTCGGTACCCCTGAAC
1 GCACATACGTG-CCCTATTTGTACTTCAGTACCCCTAAAC
* ** * *
41212339 ACATTTACGTGCCTTAATTGTACT
1 GCACATACGTGCCCTATTTGTACT
41212363 CTGGTAACCC
Statistics
Matches: 144, Mismatches: 31, Indels: 15
0.76 0.16 0.08
Matches are distributed among these distances:
38 1 0.01
39 76 0.53
40 63 0.44
41 4 0.03
ACGTcount: A:0.22, C:0.30, G:0.16, T:0.32
Consensus pattern (39 bp):
GCACATACGTGCCCTATTTGTACTTCAGTACCCCTAAAC
Done.