Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 137 of 226
Found at i:42614951 original size:25 final size:25
Alignment explanation
Indices: 42614917--42614968 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
42614907 ATTTTTTAGG
42614917 GTTAGATTAATAAATTATGGTCAAT
1 GTTAGATTAATAAATTATGGTCAAT
42614942 GTTAGATTAATAAATTATGGTCAAT
1 GTTAGATTAATAAATTATGGTCAAT
42614967 GT
1 GT
42614969 GGATTTCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.38, C:0.04, G:0.17, T:0.40
Consensus pattern (25 bp):
GTTAGATTAATAAATTATGGTCAAT
Found at i:42615443 original size:20 final size:20
Alignment explanation
Indices: 42615418--42615456 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
42615408 ATTTCGCTAC
* *
42615418 TACATTAAATAATTTTTAAG
1 TACATTAAAAAAATTTTAAG
42615438 TACATTAAAAAAATTTTAA
1 TACATTAAAAAAATTTTAA
42615457 CTATTATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (20 bp):
TACATTAAAAAAATTTTAAG
Found at i:42617378 original size:19 final size:21
Alignment explanation
Indices: 42617354--42617396 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
42617344 TTTCCTCTAG
42617354 TTTGCA-CA-AGGTATCGATA
1 TTTGCATCATAGGTATCGATA
*
42617373 TTTGCATTATAGGTATCGATA
1 TTTGCATCATAGGTATCGATA
42617394 TTT
1 TTT
42617397 TTATAATCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.29
20 1 0.05
21 14 0.67
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.42
Consensus pattern (21 bp):
TTTGCATCATAGGTATCGATA
Found at i:42618744 original size:58 final size:58
Alignment explanation
Indices: 42618674--42618792 Score: 229
Period size: 58 Copynumber: 2.1 Consensus size: 58
42618664 AATGAAAAGT
*
42618674 GAAATCAGTAAATAAACCTTGACCCACTATCTAACGAGATAGGAACCAAAGGTATAGC
1 GAAATCAATAAATAAACCTTGACCCACTATCTAACGAGATAGGAACCAAAGGTATAGC
42618732 GAAATCAATAAATAAACCTTGACCCACTATCTAACGAGATAGGAACCAAAGGTATAGC
1 GAAATCAATAAATAAACCTTGACCCACTATCTAACGAGATAGGAACCAAAGGTATAGC
42618790 GAA
1 GAA
42618793 CGCCACACTT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.45, C:0.20, G:0.17, T:0.18
Consensus pattern (58 bp):
GAAATCAATAAATAAACCTTGACCCACTATCTAACGAGATAGGAACCAAAGGTATAGC
Found at i:42619724 original size:52 final size:50
Alignment explanation
Indices: 42619630--42619732 Score: 136
Period size: 52 Copynumber: 2.0 Consensus size: 50
42619620 GGTTTTAATT
* *
42619630 AAGATGGAAACTAAATGAACAATGAATTACTTAATGCATGACTTCATTAA
1 AAGATGCAAACTAAATGAACAATGAATTACATAATGCATGACTTCATTAA
* *
42619680 AAGATGCAAACTATAATTAAC-ATGAGAGTTACATAATGCATGACTTTATTAA
1 AAGATGCAAACTA-AATGAACAATGA-A-TTACATAATGCATGACTTCATTAA
42619732 A
1 A
42619733 TGCAGAACAC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
50 16 0.35
51 7 0.15
52 23 0.50
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.29
Consensus pattern (50 bp):
AAGATGCAAACTAAATGAACAATGAATTACATAATGCATGACTTCATTAA
Found at i:42622979 original size:13 final size:12
Alignment explanation
Indices: 42622946--42622987 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
42622936 TAAAAATTTA
42622946 TTTT-ATATTAT
1 TTTTAATATTAT
42622957 AATTTTAATATTAT
1 --TTTTAATATTAT
42622971 TTTTAAATATTAT
1 TTTT-AATATTAT
42622984 TTTT
1 TTTT
42622988 TATGCCGGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.15
13 16 0.59
14 7 0.26
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTTAATATTAT
Found at i:42625343 original size:3 final size:3
Alignment explanation
Indices: 42625335--42625363 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
42625325 ATGGGCTGTT
42625335 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
42625364 GTTGTTGCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:42629364 original size:40 final size:40
Alignment explanation
Indices: 42629276--42629364 Score: 105
Period size: 40 Copynumber: 2.3 Consensus size: 40
42629266 ATAAATATAT
*
42629276 ATTTTA-TTT-TTATTTTTTAATTTTAAAATACTTTTAAA
1 ATTTTATTTTATTATTTTTTAATTTTAAAATAATTTTAAA
* *
42629314 ATTATT-TTTTATTATTTTTTATTTTTAAAATAATTTT-TA
1 ATT-TTATTTTATTATTTTTTAATTTTAAAATAATTTTAAA
42629353 ATGTTTATTTTA
1 AT-TTTATTTTA
42629365 AAAATGGGCC
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
38 3 0.07
39 10 0.23
40 30 0.70
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (40 bp):
ATTTTATTTTATTATTTTTTAATTTTAAAATAATTTTAAA
Found at i:42630855 original size:11 final size:11
Alignment explanation
Indices: 42630839--42630863 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
42630829 AAACACAAGA
42630839 GAGTATCTATT
1 GAGTATCTATT
42630850 GAGTATCTATT
1 GAGTATCTATT
42630861 GAG
1 GAG
42630864 CTTACCTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40
Consensus pattern (11 bp):
GAGTATCTATT
Found at i:42636120 original size:20 final size:21
Alignment explanation
Indices: 42636087--42636126 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
42636077 CCAAGTGCAA
* *
42636087 AATGAAGCTTAATTTTAGCTC
1 AATGAAGCTCAATTCTAGCTC
42636108 AATG-AGCTCAATTCTAGCT
1 AATGAAGCTCAATTCTAGCT
42636127 TCTTCAAGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (21 bp):
AATGAAGCTCAATTCTAGCTC
Found at i:42636248 original size:19 final size:19
Alignment explanation
Indices: 42636224--42636316 Score: 77
Period size: 19 Copynumber: 5.1 Consensus size: 19
42636214 AATAAATTAC
*
42636224 TCATCTTAGTTAATTGAGT
1 TCATCTTAGTTAATTAAGT
42636243 TCATCTTAGTTAATTAAGT
1 TCATCTTAGTTAATTAAGT
** * * *
42636262 TGC-T-GGAATAAATT-A-C
1 T-CATCTTAGTTAATTAAGT
*
42636278 TCATCTTAGTTAATTAAAT
1 TCATCTTAGTTAATTAAGT
*
42636297 TCATCTTAGTTAATTTAGT
1 TCATCTTAGTTAATTAAGT
42636316 T
1 T
42636317 GCTGGAATAA
Statistics
Matches: 56, Mismatches: 13, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
15 1 0.02
16 2 0.04
17 7 0.12
18 7 0.12
19 38 0.68
20 1 0.02
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.46
Consensus pattern (19 bp):
TCATCTTAGTTAATTAAGT
Found at i:42636268 original size:54 final size:54
Alignment explanation
Indices: 42636205--42636326 Score: 217
Period size: 54 Copynumber: 2.3 Consensus size: 54
42636195 ATAAGTATTT
* *
42636205 AGTTGCTGGAATAAATTACTCATCTTAGTTAATTGAGTTCATCTTAGTTAATTA
1 AGTTGCTGGAATAAATTACTCATCTTAGTTAATTAAATTCATCTTAGTTAATTA
*
42636259 AGTTGCTGGAATAAATTACTCATCTTAGTTAATTAAATTCATCTTAGTTAATTT
1 AGTTGCTGGAATAAATTACTCATCTTAGTTAATTAAATTCATCTTAGTTAATTA
42636313 AGTTGCTGGAATAA
1 AGTTGCTGGAATAA
42636327 TTTATTGTTG
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 65 1.00
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.42
Consensus pattern (54 bp):
AGTTGCTGGAATAAATTACTCATCTTAGTTAATTAAATTCATCTTAGTTAATTA
Found at i:42636515 original size:74 final size:75
Alignment explanation
Indices: 42636404--42636552 Score: 228
Period size: 74 Copynumber: 2.0 Consensus size: 75
42636394 ATTAATTAAA
* *
42636404 CTTATTAAGTCTAATATGTGTTTAATGTGTTTTAATGTGTTTGTGAATAAATGCTTGCAGGTGAC
1 CTTATTAAGTCTAATATGTGTTAAATGTGTTTTAATGTGTTTGTGAATAAATACTTGCAGGTGAC
*
42636469 TATTTAGTTG
66 TATGTAGTTG
* * * *
42636479 CTTATTAAGTTTAGTATGT-TTAAATGTGTTTTAATGTGTTTGTTAATAAATATTTGCAGGTGAC
1 CTTATTAAGTCTAATATGTGTTAAATGTGTTTTAATGTGTTTGTGAATAAATACTTGCAGGTGAC
42636543 TATGTAGTTG
66 TATGTAGTTG
42636553 GAGTAAGTTA
Statistics
Matches: 67, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
74 50 0.75
75 17 0.25
ACGTcount: A:0.26, C:0.05, G:0.21, T:0.48
Consensus pattern (75 bp):
CTTATTAAGTCTAATATGTGTTAAATGTGTTTTAATGTGTTTGTGAATAAATACTTGCAGGTGAC
TATGTAGTTG
Found at i:42638476 original size:14 final size:13
Alignment explanation
Indices: 42638429--42638480 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 13
42638419 TTTTGTAATG
* *
42638429 AAAAGAAGAGAGA
1 AAAAGAAAAGAAA
42638442 AAAAGAAATTGAGAAA
1 AAAAGAAA---AGAAA
42638458 AAAAGAAAAGAAA
1 AAAAGAAAAGAAA
42638471 ATAAAGAAAA
1 A-AAAGAAAA
42638481 AGCAATTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
13 13 0.39
14 8 0.24
16 12 0.36
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (13 bp):
AAAAGAAAAGAAA
Found at i:42638482 original size:36 final size:36
Alignment explanation
Indices: 42638439--42638519 Score: 94
Period size: 36 Copynumber: 2.2 Consensus size: 36
42638429 AAAAGAAGAG
*
42638439 AGAAAAAGAAATTG-AGAA-AAAAAGAAAAGAAAATAA
1 AGAAAAAGAAATTGAAAAAGAAAAAG-AAAGAAAA-AA
* **
42638475 AGAAAAAGCAATTGAAAAAGAAAAAGAAAGTGAAAA
1 AGAAAAAGAAATTGAAAAAGAAAAAGAAAGAAAAAA
42638511 AGAAAAAGA
1 AGAAAAAGA
42638520 GAGTGAGAGT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
36 23 0.61
37 9 0.24
38 6 0.16
ACGTcount: A:0.73, C:0.01, G:0.19, T:0.07
Consensus pattern (36 bp):
AGAAAAAGAAATTGAAAAAGAAAAAGAAAGAAAAAA
Found at i:42638496 original size:18 final size:18
Alignment explanation
Indices: 42638473--42638525 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
42638463 AAAAGAAAAT
* *
42638473 AAAGAAAAAGCAATTGAA
1 AAAGAAAAAGAAAGTGAA
42638491 AAAGAAAAAGAAAGTGAA
1 AAAGAAAAAGAAAGTGAA
*
42638509 AAAGAAAAAGAGAGTGA
1 AAAGAAAAAGAAAGTGA
42638526 GAGTTAGAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.68, C:0.02, G:0.23, T:0.08
Consensus pattern (18 bp):
AAAGAAAAAGAAAGTGAA
Found at i:42638516 original size:5 final size:6
Alignment explanation
Indices: 42638457--42638519 Score: 54
Period size: 6 Copynumber: 10.2 Consensus size: 6
42638447 AAATTGAGAA
* * ** **
42638457 AAAAAG AAAAGAA AATAAAG AAAAAG CAATTG AAAAAG AAAAAG AAAGTG
1 AAAAAG AAAA-AG AA-AAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
42638507 AAAAAG AAAAAG A
1 AAAAAG AAAAAG A
42638520 GAGTGAGAGT
Statistics
Matches: 43, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
6 35 0.81
7 6 0.14
8 2 0.05
ACGTcount: A:0.75, C:0.02, G:0.17, T:0.06
Consensus pattern (6 bp):
AAAAAG
Found at i:42640188 original size:20 final size:21
Alignment explanation
Indices: 42640155--42640194 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
42640145 CCAAGTGCAA
* *
42640155 AATGAAGCTTAATTTTAGCTC
1 AATGAAGCTCAATTCTAGCTC
42640176 AATG-AGCTCAATTCTAGCT
1 AATGAAGCTCAATTCTAGCT
42640195 TCTTCAAGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (21 bp):
AATGAAGCTCAATTCTAGCTC
Found at i:42640318 original size:19 final size:19
Alignment explanation
Indices: 42640294--42640330 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
42640284 TAAATTACTT
*
42640294 ATCTTAGTTAATTGAGTTC
1 ATCTTAGTTAATTAAGTTC
42640313 ATCTTAGTTAATTAAGTT
1 ATCTTAGTTAATTAAGTT
42640331 GCTGGAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (19 bp):
ATCTTAGTTAATTAAGTTC
Found at i:42644595 original size:40 final size:40
Alignment explanation
Indices: 42644539--42644727 Score: 227
Period size: 40 Copynumber: 4.8 Consensus size: 40
42644529 AATTTTTAAA
* * *
42644539 TGATTGCACTTGCGTGCCCCTGTTTGTACTTTGGTACTCC
1 TGATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCC
* *
42644579 TGATTGCATTTACGTGCCCCTGTTTGTACTTCGGTACCCT
1 TGATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCC
* * * * *
42644619 TGATTACAGTTACATGGCCCTGTTTGTACTT-TGTACCCC
1 TGATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCC
* * *
42644658 TGATTGTACTTACATGCCCCTGTTTGTACTCCGGTACCCC
1 TGATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCC
** *
42644698 TGATTGCACTTTTGTGCCCCTGTTTATACT
1 TGATTGCACTTACGTGCCCCTGTTTGTACT
42644728 CGAGTAACTC
Statistics
Matches: 126, Mismatches: 22, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
39 32 0.25
40 94 0.75
ACGTcount: A:0.14, C:0.28, G:0.19, T:0.40
Consensus pattern (40 bp):
TGATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCC
Found at i:42644664 original size:19 final size:19
Alignment explanation
Indices: 42644636--42644719 Score: 60
Period size: 20 Copynumber: 4.3 Consensus size: 19
42644626 AGTTACATGG
*
42644636 CCCTGTTTGTACTTTGTAC
1 CCCTGATTGTACTTTGTAC
** *
42644655 CCCTGATTGTACTTACATGC
1 CCCTGATTGTACTT-TGTAC
* **
42644675 CCCTGTTTGTACTCCGGTAC
1 CCCTGATTGTACT-TTGTAC
* *
42644695 CCCTGATTGCACTTTTGTGC
1 CCCTGATTGTAC-TTTGTAC
42644715 CCCTG
1 CCCTG
42644720 TTTATACTCG
Statistics
Matches: 48, Mismatches: 14, Indels: 5
0.72 0.21 0.07
Matches are distributed among these distances:
19 13 0.27
20 34 0.71
21 1 0.02
ACGTcount: A:0.12, C:0.32, G:0.18, T:0.38
Consensus pattern (19 bp):
CCCTGATTGTACTTTGTAC
Found at i:42644719 original size:79 final size:80
Alignment explanation
Indices: 42644539--42644727 Score: 245
Period size: 79 Copynumber: 2.4 Consensus size: 80
42644529 AATTTTTAAA
* * * *
42644539 TGATTGCACTTGCGTGCCCCTGTTTGTACTTTGGTACTCCTGATTGCATTTACGTGCCCCTGTTT
1 TGATTGCACTTACGTGCCCCTGTTTGTACTTTGGTACCCCTGATTGCACTTACATGCCCCTGTTT
* *
42644604 GTACTTCGGTACCCT
66 GTACTCCGGTACCCC
* * * * *
42644619 TGATTACAGTTACATGGCCCTGTTTGTACTTT-GTACCCCTGATTGTACTTACATGCCCCTGTTT
1 TGATTGCACTTACGTGCCCCTGTTTGTACTTTGGTACCCCTGATTGCACTTACATGCCCCTGTTT
42644683 GTACTCCGGTACCCC
66 GTACTCCGGTACCCC
** *
42644698 TGATTGCACTTTTGTGCCCCTGTTTATACT
1 TGATTGCACTTACGTGCCCCTGTTTGTACT
42644728 CGAGTAACTC
Statistics
Matches: 91, Mismatches: 18, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
79 64 0.70
80 27 0.30
ACGTcount: A:0.14, C:0.28, G:0.19, T:0.40
Consensus pattern (80 bp):
TGATTGCACTTACGTGCCCCTGTTTGTACTTTGGTACCCCTGATTGCACTTACATGCCCCTGTTT
GTACTCCGGTACCCC
Found at i:42647601 original size:23 final size:24
Alignment explanation
Indices: 42647575--42647626 Score: 79
Period size: 25 Copynumber: 2.2 Consensus size: 24
42647565 CTGTCAATTC
*
42647575 CTGTACAT-GTATGCTCACACGAG
1 CTGTAAATCGTATGCTCACACGAG
42647598 CTGTAAATCGGTATGCTCACACGAG
1 CTGTAAATC-GTATGCTCACACGAG
42647623 CTGT
1 CTGT
42647627 GGGTCAGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 7 0.27
25 19 0.73
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (24 bp):
CTGTAAATCGTATGCTCACACGAG
Found at i:42656854 original size:19 final size:19
Alignment explanation
Indices: 42656811--42656855 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
42656801 CAATTTAATT
42656811 AATA-AAATAAAATTTTAA
1 AATATAAATAAAATTTTAA
*
42656829 CAT-TAAATAAAATTTTAA
1 AATATAAATAAAATTTTAA
42656847 AATATAAAT
1 AATATAAAT
42656856 TATATAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
AATATAAATAAAATTTTAA
Found at i:42659014 original size:2 final size:2
Alignment explanation
Indices: 42659009--42659034 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42658999 GGGGGGGGGG
42659009 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
42659035 CCTGGTGGGA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:42660227 original size:22 final size:22
Alignment explanation
Indices: 42660196--42660238 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
42660186 TTCATAATTT
42660196 TTAAAATCCAAATT-ATTTTTC
1 TTAAAATCCAAATTAATTTTTC
*
42660217 TTAAATATCCAATTTAATTTTT
1 TTAAA-ATCCAAATTAATTTTT
42660239 AAAACCGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 8 0.42
23 6 0.32
ACGTcount: A:0.37, C:0.12, G:0.00, T:0.51
Consensus pattern (22 bp):
TTAAAATCCAAATTAATTTTTC
Found at i:42660712 original size:19 final size:19
Alignment explanation
Indices: 42660688--42660726 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
42660678 CTTAATTTCG
*
42660688 TCCCATTATATGTTTATTA
1 TCCCATCATATGTTTATTA
* *
42660707 TCCCATCCTATTTTTATTA
1 TCCCATCATATGTTTATTA
42660726 T
1 T
42660727 TTACTTCACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.23, C:0.21, G:0.03, T:0.54
Consensus pattern (19 bp):
TCCCATCATATGTTTATTA
Found at i:42662588 original size:18 final size:20
Alignment explanation
Indices: 42662559--42662596 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
42662549 ATTCAAAAAT
42662559 TCATTAAAACATTCA-TTAA
1 TCATTAAAACATTCAGTTAA
42662578 TCATT-AAACATTCAGTTAA
1 TCATTAAAACATTCAGTTAA
42662597 AACATGTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.45, C:0.16, G:0.03, T:0.37
Consensus pattern (20 bp):
TCATTAAAACATTCAGTTAA
Found at i:42672132 original size:27 final size:26
Alignment explanation
Indices: 42672096--42672482 Score: 261
Period size: 27 Copynumber: 14.3 Consensus size: 26
42672086 ACCCAAGGAT
*
42672096 GGGTAAAATGACAGAAATACCCTCAA
1 GGGTAAAATTACAGAAATACCCTCAA
* * *
42672122 TGGGTAAAATGACTGAAATACCCTTAA
1 -GGGTAAAATTACAGAAATACCCTCAA
* *
42672149 TGGGTAAAATGATC-GAAATACCCTCGAT
1 -GGGTAAAATTA-CAGAAATACCCTC-AA
* *
42672177 GGGTAAAATAATCA-AAATACCCTCGAT
1 GGGTAAAATTA-CAGAAATACCCTC-AA
* *
42672204 GGGTAAAATGATC-GAAATACCCTAGAA
1 GGGTAAAATTA-CAGAAATACCCT-CAA
* * *
42672231 GGGTAAAATCACCGAAAAACCCTCGAA
1 GGGTAAAATTACAGAAATACCCTC-AA
*
42672258 GGATAAAATTATCA-AAATACCCTCGAA
1 GGGTAAAATTA-CAGAAATACCCTC-AA
* *
42672285 GGATAAAATTATC-GAAATACCCTTGAAA
1 GGGTAAAATTA-CAGAAATACCC-T-CAA
* * * *
42672313 GGTTAAAATTACTGAAA-GCCTTCAAA
1 GGGTAAAATTACAGAAATACCCTC-AA
*
42672339 GGGTAAAATTACTA-AAATACCCTTGAA
1 GGGTAAAATTAC-AGAAATACCC-TCAA
42672366 GGGTAAAATTATC-GAAATACCCTCGAA
1 GGGTAAAATTA-CAGAAATACCCTC-AA
42672393 GGGTAAAATTACTA-AAATACCCTCGAA
1 GGGTAAAATTAC-AGAAATACCCTC-AA
* *
42672420 AGGTAAAATTACAGAAATACCCCCAAA
1 GGGTAAAATTACAGAAATACCCTC-AA
* * * *
42672447 GGGTAAAAGTACCGGAATACCCCCGAA
1 GGGTAAAATTACAGAAATACCCTC-AA
42672474 GGGTAAAAT
1 GGGTAAAAT
42672483 GACTGTTATA
Statistics
Matches: 303, Mismatches: 35, Indels: 44
0.79 0.09 0.12
Matches are distributed among these distances:
26 21 0.07
27 260 0.86
28 22 0.07
ACGTcount: A:0.44, C:0.18, G:0.18, T:0.21
Consensus pattern (26 bp):
GGGTAAAATTACAGAAATACCCTCAA
Found at i:42672466 original size:54 final size:53
Alignment explanation
Indices: 42672096--42672482 Score: 336
Period size: 54 Copynumber: 7.2 Consensus size: 53
42672086 ACCCAAGGAT
* * * *
42672096 GGGTAAAATGA-CAGAAATACCCTCAATGGGTAAAATGACTGAAATACCCT-TAA
1 GGGTAAAATTATC-GAAATACCCTCAAAGGGTAAAAT-ACCGAAATACCCTCGAA
* * * * * *
42672149 TGGGTAAAATGATCGAAATACCCTCGATGGGTAAAATAATCAAAATACCCTCGAT
1 -GGGTAAAATTATCGAAATACCCTCAAAGGGTAAAAT-ACCGAAATACCCTCGAA
* *
42672204 GGGTAAAATGATCGAAATACCCT-AGAAGGGTAAAATCACCGAAAAACCCTCGAA
1 GGGTAAAATTATCGAAATACCCTCA-AAGGGTAAAAT-ACCGAAATACCCTCGAA
* * * * * *
42672258 GGATAAAATTATCAAAATACCCTCGAAGGATAAAATTATCGAAATACCCTTGAAA
1 GGGTAAAATTATCGAAATACCCTCAAAGGGTAAAA-TACCGAAATACCCTCG-AA
* * * ** *
42672313 GGTTAAAATTA-CTGAAA-GCCTTCAAAGGGTAAAATTACTAAAATACCCTTGAA
1 GGGTAAAATTATC-GAAATACCCTCAAAGGGTAAAA-TACCGAAATACCCTCGAA
* **
42672366 GGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTACTAAAATACCCTCGAA
1 GGGTAAAATTATCGAAATACCCTCAAAGGGTAAAA-TACCGAAATACCCTCGAA
* * * *
42672420 AGGTAAAATTA-CAGAAATACCCCCAAAGGGTAAAAGTACCGGAATACCCCCGAA
1 GGGTAAAATTATC-GAAATACCCTCAAAGGGTAAAA-TACCGAAATACCCTCGAA
42672474 GGGTAAAAT
1 GGGTAAAAT
42672483 GACTGTTATA
Statistics
Matches: 278, Mismatches: 45, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
53 17 0.06
54 243 0.87
55 18 0.06
ACGTcount: A:0.44, C:0.18, G:0.18, T:0.21
Consensus pattern (53 bp):
GGGTAAAATTATCGAAATACCCTCAAAGGGTAAAATACCGAAATACCCTCGAA
Found at i:42672494 original size:81 final size:79
Alignment explanation
Indices: 42672097--42672487 Score: 364
Period size: 81 Copynumber: 4.8 Consensus size: 79
42672087 CCCAAGGATG
* *
42672097 GGTAAAATGACAGAAATACCCTC-AATGGGTAAAATGA-CTGAAATACCCT-TAATGGGTAAAAT
1 GGTAAAATTACA-AAATACCCTCGAA-GGGTAAAAT-ATC-GAAATACCCTCGAA-GGGTAAAAT
**
42672159 GA-TCGAAATACCCTCGATG
61 GACT-GAAATACCCTCGAAA
* * * *
42672178 GGTAAAATAATCAAAATACCCTCGATGGGTAAAATGATCGAAATACCCTAGAAGGGTAAAATCAC
1 GGTAAAATTA-CAAAATACCCTCGAAGGGTAAAAT-ATCGAAATACCCTCGAAGGGTAAAATGAC
* *
42672243 CGAAAAACCCTCG-AA
64 TGAAATACCCTCGAAA
* * * *
42672258 GGATAAAATTATCAAAATACCCTCGAAGGATAAAATTATCGAAATACCCTTGAAAGGTTAAAATT
1 GG-TAAAATTA-CAAAATACCCTCGAAGGGTAAAA-TATCGAAATACCCTCG-AAGGGTAAAATG
* *
42672323 ACTGAAA-GCCTTC-AAA
62 ACTGAAATACCCTCGAAA
* *
42672339 GGGTAAAATTACTAAAATACCCTTGAAGGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTA
1 -GGTAAAATTAC-AAAATACCCTCGAAGGGTAAAA-TATCGAAATACCCTCGAAGGGTAAAATGA
*
42672404 CTAAAATACCCTCGAAA
63 CTGAAATACCCTCGAAA
* * * * *
42672421 GGTAAAATTACAGAAATACCCCCAAAGGGTAAAAGTACCGGAATACCCCCGAAGGGTAAAATGAC
1 GGTAAAATTACA-AAATACCCTCGAAGGGTAAAA-TATCGAAATACCCTCGAAGGGTAAAATGAC
42672486 TG
64 TG
42672488 TTATACCTCT
Statistics
Matches: 263, Mismatches: 33, Indels: 28
0.81 0.10 0.09
Matches are distributed among these distances:
80 21 0.08
81 214 0.81
82 28 0.11
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.21
Consensus pattern (79 bp):
GGTAAAATTACAAAATACCCTCGAAGGGTAAAATATCGAAATACCCTCGAAGGGTAAAATGACTG
AAATACCCTCGAAA
Found at i:42673085 original size:27 final size:26
Alignment explanation
Indices: 42673049--42673440 Score: 251
Period size: 27 Copynumber: 14.5 Consensus size: 26
42673039 ACCCAAGGAT
*
42673049 GGGTAAAATGACAGAAATACCCTCAA
1 GGGTAAAATTACAGAAATACCCTCAA
* * *
42673075 TGGGTAAAATGACTGAAATACCCTTAA
1 -GGGTAAAATTACAGAAATACCCTCAA
* *
42673102 TGGGTAAAATGATC-GAAATACCCTCGAT
1 -GGGTAAAATTA-CAGAAATACCCTC-AA
* *
42673130 GGGTAAAATAATCA-AAATACCCTCGAT
1 GGGTAAAATTA-CAGAAATACCCTC-AA
* ** *
42673157 GGGTAAAATGATTGAAATACCCTAGAA
1 GGGTAAAATTACAGAAATACCCT-CAA
* * *
42673184 GGGTAAAATCACCGAAAAACCCTCGAA
1 GGGTAAAATTACAGAAATACCCTC-AA
*
42673211 GGATAAAATTATCA-AAATACCCTCGAA
1 GGGTAAAATTA-CAGAAATACCCTC-AA
* *
42673238 GGATAAAATTATC-GAAATACCCTTGAAA
1 GGGTAAAATTA-CAGAAATACCC-T-CAA
* * * *
42673266 GGTTAAAATTACTGAAA-GCCTTCAAA
1 GGGTAAAATTACAGAAATACCCTC-AA
* *
42673292 GGGTAAAATTACTGAAATACCCTTGAA
1 GGGTAAAATTACAGAAATACCC-TCAA
42673319 GGGTAAAATTATC-GAAATACCCTCGAA
1 GGGTAAAATTA-CAGAAATACCCTC-AA
42673346 GGGTAAAATTACTA-AAATACCCTCAAA
1 GGGTAAAATTAC-AGAAATACCCTC-AA
* * *
42673373 AGGTAAAATTACAAAAATACCCCCAAA
1 GGGTAAAATTACAGAAATACCCTC-AA
* * *
42673400 GGGTAAAAGTACCGGAATACTCC-CGAA
1 GGGTAAAATTACAGAAATAC-CCTC-AA
*
42673427 GGGTAAAATGACAG
1 GGGTAAAATTACAG
42673441 TTATACCTCT
Statistics
Matches: 304, Mismatches: 41, Indels: 40
0.79 0.11 0.10
Matches are distributed among these distances:
26 22 0.07
27 258 0.85
28 24 0.08
ACGTcount: A:0.44, C:0.18, G:0.18, T:0.21
Consensus pattern (26 bp):
GGGTAAAATTACAGAAATACCCTCAA
Found at i:42673378 original size:54 final size:54
Alignment explanation
Indices: 42673062--42673407 Score: 296
Period size: 54 Copynumber: 6.4 Consensus size: 54
42673052 TAAAATGACA
* * * * *
42673062 GAAATACCCTC-AATGGGTAAAATGACTGAAATACCCT-TAATGGGTAAAATGATC
1 GAAATACCCTCGAA-GGGTAAAATTACTAAAATACCCTCGAA-AGGTAAAATTATC
* * ** * *
42673116 GAAATACCCTCGATGGGTAAAA-TAATCAAAATACCCTCGATGGGTAAAATGATT
1 GAAATACCCTCGAAGGGTAAAATTACT-AAAATACCCTCGAAAGGTAAAATTATC
* * *
42673170 GAAATACCCTAGAAGGGTAAAATCACCGAAAA-ACCCTCG-AAGGATAAAATTATC
1 GAAATACCCTCGAAGGGTAAAATTA-CTAAAATACCCTCGAAAGG-TAAAATTATC
* * * *
42673224 AAAATACCCTCGAAGGATAAAATTA-TCGAAATACCCTTGAAAGGTTAAAATTA-C
1 GAAATACCCTCGAAGGGTAAAATTACT-AAAATACCCTCGAAAGG-TAAAATTATC
* * * * * *
42673278 TGAAA-GCCTTCAAAGGGTAAAATTACTGAAATACCCTTGAAGGGTAAAATTATC
1 -GAAATACCCTCGAAGGGTAAAATTACTAAAATACCCTCGAAAGGTAAAATTATC
*
42673332 GAAATACCCTCGAAGGGTAAAATTACTAAAATACCCTCAAAAGGTAAAATTA-C
1 GAAATACCCTCGAAGGGTAAAATTACTAAAATACCCTCGAAAGGTAAAATTATC
* * *
42673385 AAAAATACCCCCAAAGGGTAAAA
1 -GAAATACCCTCGAAGGGTAAAA
42673408 GTACCGGAAT
Statistics
Matches: 238, Mismatches: 40, Indels: 28
0.78 0.13 0.09
Matches are distributed among these distances:
53 20 0.08
54 195 0.82
55 23 0.10
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.22
Consensus pattern (54 bp):
GAAATACCCTCGAAGGGTAAAATTACTAAAATACCCTCGAAAGGTAAAATTATC
Found at i:42673419 original size:81 final size:79
Alignment explanation
Indices: 42673050--42673435 Score: 332
Period size: 81 Copynumber: 4.8 Consensus size: 79
42673040 CCCAAGGATG
* * *
42673050 GGTAAAATGACAGAAATACCCTC-AATGGGTAAAATGA-CTGAAATACCCT-TAATGGGTAAAAT
1 GGTAAAATTACA-AAATACCCTCGAA-GGGTAAAATTATC-GAAATACCCTCGAA-GGGTAAAAT
* * * * **
42673112 GATCGAAATACCCTCGATG
62 TA-CTAAAAACCCTCAAAA
* * * * * *
42673131 GGTAAAATAATCAAAATACCCTCGATGGGTAAAATGATTGAAATACCCTAGAAGGGTAAAATCAC
1 GGTAAAATTA-CAAAATACCCTCGAAGGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTA-
* *
42673196 CGAAAAACCCTC-GAA
64 CTAAAAACCCTCAAAA
* * *
42673211 GGATAAAATTATCAAAATACCCTCGAAGGATAAAATTATCGAAATACCCTTGAAAGGTTAAAATT
1 GG-TAAAATTA-CAAAATACCCTCGAAGGGTAAAATTATCGAAATACCCTCG-AAGGGTAAAATT
* * * *
42673276 ACTGAAAGCCTTCAAAG
63 ACTAAAAACCCTCAAAA
* *
42673293 GGTAAAATTACTGAAATACCCTTGAAGGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTAC
1 GGTAAAATTAC-AAAATACCCTCGAAGGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTAC
42673358 TAAAATACCCTCAAAA
65 TAAAA-ACCCTCAAAA
* * * * *
42673374 GGTAAAATTACAAAAATACCCCCAAAGGGTAAAAGTACCGGAATACTCC-CGAAGGGTAAAAT
1 GGTAAAATTAC-AAAATACCCTCGAAGGGTAAAATTATCGAAATAC-CCTCGAAGGGTAAAAT
42673436 GACAGTTATA
Statistics
Matches: 254, Mismatches: 41, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
80 20 0.08
81 213 0.84
82 21 0.08
ACGTcount: A:0.44, C:0.18, G:0.17, T:0.21
Consensus pattern (79 bp):
GGTAAAATTACAAAATACCCTCGAAGGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTACT
AAAAACCCTCAAAA
Found at i:42673550 original size:953 final size:953
Alignment explanation
Indices: 42671704--42673608 Score: 3684
Period size: 953 Copynumber: 2.0 Consensus size: 953
42671694 GCAGAAACCC
*
42671704 GTCTAAAAGATCATAGGCAGCTTTCGTCAATGGTATAAGTGGGCTAAGCCACTGTTGTCGGTCGA
1 GTCTAAAAGATCATAGGCAGCTTTCGTCAATGGTATAAGTGGGCTAAGCCACTATTGTCGGTCGA
*
42671769 GGTAAGTGTTTTGGGTTAAGGGTATAGTAAGGTGGAGATCAACTCTTTCGTTTAACGACTAATGA
66 GGTAAGTGTTTTGGGTTAAGGGTATAGTAAGGTAGAGATCAACTCTTTCGTTTAACGACTAATGA
42671834 AAAACTAGTATGAATGCAAATTCTGGGTGTTCGTGGATCCTAGTGCATTTTCGCAAACAAGTGTG
131 AAAACTAGTATGAATGCAAATTCTGGGTGTTCGTGGATCCTAGTGCATTTTCGCAAACAAGTGTG
*
42671899 TAATCACACCCTCCATCAACTGCAAATCGCCAAAAGCCGAAAAGCCGAAAAAGACGGCGTTGAGA
196 TAATCACACCCTCCATCAACTGCAAATCGCCAAAAACCGAAAAGCCGAAAAAGACGGCGTTGAGA
42671964 CCCTGTGAGCGCGCGAACGCTCGTGTGGTAAATCGAGCCCTCGAAACATGGTGTCGGCCTGTAGA
261 CCCTGTGAGCGCGCGAACGCTCGTGTGGTAAATCGAGCCCTCGAAACATGGTGTCGGCCTGTAGA
42672029 GGCATCCATGAGCGTTTTCATGGGCTTAGGCTGTAATGGGCCATGAATGACCAAAATACCCAAGG
326 GGCATCCATGAGCGTTTTCATGGGCTTAGGCTGTAATGGGCCATGAATGACCAAAATACCCAAGG
42672094 ATGGGTAAAATGACAGAAATACCCTCAATGGGTAAAATGACTGAAATACCCTTAATGGGTAAAAT
391 ATGGGTAAAATGACAGAAATACCCTCAATGGGTAAAATGACTGAAATACCCTTAATGGGTAAAAT
42672159 GATCGAAATACCCTCGATGGGTAAAATAATCAAAATACCCTCGATGGGTAAAATGATCGAAATAC
456 GATCGAAATACCCTCGATGGGTAAAATAATCAAAATACCCTCGATGGGTAAAATGATCGAAATAC
42672224 CCTAGAAGGGTAAAATCACCGAAAAACCCTCGAAGGATAAAATTATCAAAATACCCTCGAAGGAT
521 CCTAGAAGGGTAAAATCACCGAAAAACCCTCGAAGGATAAAATTATCAAAATACCCTCGAAGGAT
42672289 AAAATTATCGAAATACCCTTGAAAGGTTAAAATTACTGAAAGCCTTCAAAGGGTAAAATTACTAA
586 AAAATTATCGAAATACCCTTGAAAGGTTAAAATTACTGAAAGCCTTCAAAGGGTAAAATTACTAA
*
42672354 AATACCCTTGAAGGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTACTAAAATACCCTCGA
651 AATACCCTTGAAGGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTACTAAAATACCCTCAA
*
42672419 AAGGTAAAATTACAGAAATACCCCCAAAGGGTAAAAGTACCGGAATACCCCCGAAGGGTAAAATG
716 AAGGTAAAATTACAAAAATACCCCCAAAGGGTAAAAGTACCGGAATACCCCCGAAGGGTAAAATG
*
42672484 ACTGTTATACCTCTAGGAGTTGAAATGAGTGTATGATCAAATTACTCTAAGTTATATATTTGACT
781 ACAGTTATACCTCTAGGAGTTGAAATGAGTGTATGATCAAATTACTCTAAGTTATATATTTGACT
*
42672549 GTTACTGAGTATGACATACTGCATATACGTATGATTTATGACATGACATACTGCATGGGGTTGGG
846 ATTACTGAGTATGACATACTGCATATACGTATGATTTATGACATGACATACTGCATGGGGTTGGG
42672614 ATATTGATATAGGGGAAGTATATTGTACTGGTGGCTATGCCAT
911 ATATTGATATAGGGGAAGTATATTGTACTGGTGGCTATGCCAT
*
42672657 GTCTAAAGGATCATAGGCAGCTTTCGTCAATGGTATAAGTGGGCTAAGCCACTATTGTCGGTCGA
1 GTCTAAAAGATCATAGGCAGCTTTCGTCAATGGTATAAGTGGGCTAAGCCACTATTGTCGGTCGA
42672722 GGTAAGTGTTTTGGGTTAAGGGTATAGTAAGGTAGAGATCAACTCTTTCGTTTAACGACTAATGA
66 GGTAAGTGTTTTGGGTTAAGGGTATAGTAAGGTAGAGATCAACTCTTTCGTTTAACGACTAATGA
42672787 AAAACTAGTATGAATGCAAATTCTGGGTGTTCGTGGATCCTAGTGCATTTTCGCAAACAAGTGTG
131 AAAACTAGTATGAATGCAAATTCTGGGTGTTCGTGGATCCTAGTGCATTTTCGCAAACAAGTGTG
*
42672852 TAATCACACCCTCCATCAACTGCAAATCGCCAAAAACTGAAAAGCCGAAAAAGACGGCGTTGAGA
196 TAATCACACCCTCCATCAACTGCAAATCGCCAAAAACCGAAAAGCCGAAAAAGACGGCGTTGAGA
42672917 CCCTGTGAGCGCGCGAACGCTCGTGTGGTAAATCGAGCCCTCGAAACATGGTGTCGGCCTGTAGA
261 CCCTGTGAGCGCGCGAACGCTCGTGTGGTAAATCGAGCCCTCGAAACATGGTGTCGGCCTGTAGA
42672982 GGCATCCATGAGCGTTTTCATGGGCTTAGGCTGTAATGGGCCATGAATGACCAAAATACCCAAGG
326 GGCATCCATGAGCGTTTTCATGGGCTTAGGCTGTAATGGGCCATGAATGACCAAAATACCCAAGG
42673047 ATGGGTAAAATGACAGAAATACCCTCAATGGGTAAAATGACTGAAATACCCTTAATGGGTAAAAT
391 ATGGGTAAAATGACAGAAATACCCTCAATGGGTAAAATGACTGAAATACCCTTAATGGGTAAAAT
*
42673112 GATCGAAATACCCTCGATGGGTAAAATAATCAAAATACCCTCGATGGGTAAAATGATTGAAATAC
456 GATCGAAATACCCTCGATGGGTAAAATAATCAAAATACCCTCGATGGGTAAAATGATCGAAATAC
42673177 CCTAGAAGGGTAAAATCACCGAAAAACCCTCGAAGGATAAAATTATCAAAATACCCTCGAAGGAT
521 CCTAGAAGGGTAAAATCACCGAAAAACCCTCGAAGGATAAAATTATCAAAATACCCTCGAAGGAT
*
42673242 AAAATTATCGAAATACCCTTGAAAGGTTAAAATTACTGAAAGCCTTCAAAGGGTAAAATTACTGA
586 AAAATTATCGAAATACCCTTGAAAGGTTAAAATTACTGAAAGCCTTCAAAGGGTAAAATTACTAA
42673307 AATACCCTTGAAGGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTACTAAAATACCCTCAA
651 AATACCCTTGAAGGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTACTAAAATACCCTCAA
*
42673372 AAGGTAAAATTACAAAAATACCCCCAAAGGGTAAAAGTACCGGAATACTCCCGAAGGGTAAAATG
716 AAGGTAAAATTACAAAAATACCCCCAAAGGGTAAAAGTACCGGAATACCCCCGAAGGGTAAAATG
*
42673437 ACAGTTATACCTCTAGGAGTTGAAATGAGTGTATGATCAAATTGCTCTAAGTTATATATTTGACT
781 ACAGTTATACCTCTAGGAGTTGAAATGAGTGTATGATCAAATTACTCTAAGTTATATATTTGACT
42673502 ATTACTGAGTATGACATACTGCATATACGTATGATTTATGACATGACATACTGCATGGGGTTGGG
846 ATTACTGAGTATGACATACTGCATATACGTATGATTTATGACATGACATACTGCATGGGGTTGGG
*
42673567 ATTTTGATATAGGGGAAGTATATTGTACTGGTGGCTATGCCA
911 ATATTGATATAGGGGAAGTATATTGTACTGGTGGCTATGCCA
42673609 CGTATACTGT
Statistics
Matches: 938, Mismatches: 14, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
953 938 1.00
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (953 bp):
GTCTAAAAGATCATAGGCAGCTTTCGTCAATGGTATAAGTGGGCTAAGCCACTATTGTCGGTCGA
GGTAAGTGTTTTGGGTTAAGGGTATAGTAAGGTAGAGATCAACTCTTTCGTTTAACGACTAATGA
AAAACTAGTATGAATGCAAATTCTGGGTGTTCGTGGATCCTAGTGCATTTTCGCAAACAAGTGTG
TAATCACACCCTCCATCAACTGCAAATCGCCAAAAACCGAAAAGCCGAAAAAGACGGCGTTGAGA
CCCTGTGAGCGCGCGAACGCTCGTGTGGTAAATCGAGCCCTCGAAACATGGTGTCGGCCTGTAGA
GGCATCCATGAGCGTTTTCATGGGCTTAGGCTGTAATGGGCCATGAATGACCAAAATACCCAAGG
ATGGGTAAAATGACAGAAATACCCTCAATGGGTAAAATGACTGAAATACCCTTAATGGGTAAAAT
GATCGAAATACCCTCGATGGGTAAAATAATCAAAATACCCTCGATGGGTAAAATGATCGAAATAC
CCTAGAAGGGTAAAATCACCGAAAAACCCTCGAAGGATAAAATTATCAAAATACCCTCGAAGGAT
AAAATTATCGAAATACCCTTGAAAGGTTAAAATTACTGAAAGCCTTCAAAGGGTAAAATTACTAA
AATACCCTTGAAGGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTACTAAAATACCCTCAA
AAGGTAAAATTACAAAAATACCCCCAAAGGGTAAAAGTACCGGAATACCCCCGAAGGGTAAAATG
ACAGTTATACCTCTAGGAGTTGAAATGAGTGTATGATCAAATTACTCTAAGTTATATATTTGACT
ATTACTGAGTATGACATACTGCATATACGTATGATTTATGACATGACATACTGCATGGGGTTGGG
ATATTGATATAGGGGAAGTATATTGTACTGGTGGCTATGCCAT
Found at i:42673623 original size:27 final size:27
Alignment explanation
Indices: 42673600--42673655 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
42673590 TGTACTGGTG
42673600 GCTATGCCACGTATACTGTTACTGGCA
1 GCTATGCCACGTATACTGTTACTGGCA
* **
42673627 GCTTTGCTGCGT-TACTGTTACTGGCA
1 GCTATGCCACGTATACTGTTACTGGCA
42673653 GCT
1 GCT
42673656 TTGCTGCATC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 17 0.65
27 9 0.35
ACGTcount: A:0.16, C:0.25, G:0.25, T:0.34
Consensus pattern (27 bp):
GCTATGCCACGTATACTGTTACTGGCA
Found at i:42673644 original size:26 final size:26
Alignment explanation
Indices: 42673613--42673685 Score: 101
Period size: 26 Copynumber: 2.8 Consensus size: 26
42673603 ATGCCACGTA
*
42673613 TACTGTTACTGGCAGCTTTGCTGCGT
1 TACTGTTACTGGCAGCTTTGCTGCAT
42673639 TACTGTTACTGGCAGCTTTGCTGCAT
1 TACTGTTACTGGCAGCTTTGCTGCAT
* * * *
42673665 CACTATTGCTGGCAACTTTGC
1 TACTGTTACTGGCAGCTTTGC
42673686 CGCGATATTG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.15, C:0.25, G:0.23, T:0.37
Consensus pattern (26 bp):
TACTGTTACTGGCAGCTTTGCTGCAT
Found at i:42674984 original size:25 final size:25
Alignment explanation
Indices: 42674968--42675056 Score: 86
Period size: 25 Copynumber: 3.8 Consensus size: 25
42674958 CAAAGGTGAG
42674968 ATACATA-A-TACGCCACAAAGGCA
1 ATACATAGAGTACGCCACAAAGGCA
42674991 ATACATAGAGTACGCCACAAAGGC-
1 ATACATAGAGTACGCCACAAAGGCA
*
42675015 -TAGC--AGA--ATGCCACAAAGGCA
1 ATA-CATAGAGTACGCCACAAAGGCA
* *
42675036 ATACACAGAGTACACCACAAA
1 ATACATAGAGTACGCCACAAA
42675057 TGCTAGCAGA
Statistics
Matches: 54, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
20 12 0.22
21 1 0.02
22 5 0.09
23 12 0.22
24 2 0.04
25 22 0.41
ACGTcount: A:0.46, C:0.26, G:0.17, T:0.11
Consensus pattern (25 bp):
ATACATAGAGTACGCCACAAAGGCA
Found at i:42675029 original size:20 final size:20
Alignment explanation
Indices: 42675004--42675088 Score: 80
Period size: 20 Copynumber: 4.0 Consensus size: 20
42674994 CATAGAGTAC
*
42675004 GCCACAAAGGCTAGCAGAAT
1 GCCACAAAGGCTAACAGAAT
*
42675024 GCCACAAAGGCAATACACAGAGTAC
1 GCCACAAAGGC--TA-ACAGA--AT
* * *
42675049 ACCACAAATGCTAGCAGAAT
1 GCCACAAAGGCTAACAGAAT
42675069 GCCACAAAGGCTAACAGAAT
1 GCCACAAAGGCTAACAGAAT
42675089 ATGCCATAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
20 29 0.57
22 6 0.12
23 6 0.12
25 10 0.20
ACGTcount: A:0.44, C:0.26, G:0.20, T:0.11
Consensus pattern (20 bp):
GCCACAAAGGCTAACAGAAT
Found at i:42675030 original size:45 final size:45
Alignment explanation
Indices: 42674979--42675079 Score: 175
Period size: 45 Copynumber: 2.2 Consensus size: 45
42674969 TACATAATAC
* *
42674979 GCCACAAAGGCAATACATAGAGTACGCCACAAAGGCTAGCAGAAT
1 GCCACAAAGGCAATACACAGAGTACACCACAAAGGCTAGCAGAAT
*
42675024 GCCACAAAGGCAATACACAGAGTACACCACAAATGCTAGCAGAAT
1 GCCACAAAGGCAATACACAGAGTACACCACAAAGGCTAGCAGAAT
42675069 GCCACAAAGGC
1 GCCACAAAGGC
42675080 TAACAGAATA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.43, C:0.27, G:0.21, T:0.10
Consensus pattern (45 bp):
GCCACAAAGGCAATACACAGAGTACACCACAAAGGCTAGCAGAAT
Found at i:42675114 original size:20 final size:21
Alignment explanation
Indices: 42675058--42675115 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
42675048 CACCACAAAT
* *
42675058 GCTAGCAG-AATGCCACAAAG
1 GCTAACAGAAATGCCATAAAG
42675078 GCTAACAGAATATGCCATAAAG
1 GCTAACAGAA-ATGCCATAAAG
* *
42675100 GTTATC-GAAATGCCAT
1 GCTAACAGAAATGCCAT
42675116 CTAAGCACCC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 14 0.44
21 4 0.12
22 14 0.44
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.19
Consensus pattern (21 bp):
GCTAACAGAAATGCCATAAAG
Found at i:42677532 original size:24 final size:26
Alignment explanation
Indices: 42677505--42677554 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
42677495 ATATAATTTC
42677505 CAAATCA-TGT-ATATATATCATGTA
1 CAAATCATTGTCATATATATCATGTA
* *
42677529 CAAATCATTTTCATATATCTCATGTA
1 CAAATCATTGTCATATATATCATGTA
42677555 AATACCTGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 2 0.09
26 13 0.59
ACGTcount: A:0.38, C:0.16, G:0.06, T:0.40
Consensus pattern (26 bp):
CAAATCATTGTCATATATATCATGTA
Found at i:42677745 original size:25 final size:24
Alignment explanation
Indices: 42677712--42677798 Score: 88
Period size: 25 Copynumber: 3.5 Consensus size: 24
42677702 ACGAGCTGTA
42677712 AATGGTAAGCTCCCCTTAGCTGAAT
1 AATGGTAAGCTCCCCTTAG-TGAAT
*
42677737 AATGGTAAGCTCCTCC-AAGTCGAAT
1 AATGGTAAGCTCC-CCTTAGT-GAAT
**
42677762 AATGGTAAGCT-CTTTTGAGTTGAAT
1 AATGGTAAGCTCCCCTT-AG-TGAAT
42677787 AATGGTAAGCTC
1 AATGGTAAGCTC
42677799 ATACGAGTTG
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
24 2 0.04
25 47 0.90
26 3 0.06
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (24 bp):
AATGGTAAGCTCCCCTTAGTGAAT
Found at i:42677806 original size:25 final size:25
Alignment explanation
Indices: 42677732--42677809 Score: 93
Period size: 25 Copynumber: 3.1 Consensus size: 25
42677722 TCCCCTTAGC
* * *
42677732 TGAATAATGGTAAGCTCCTCCAAGT
1 TGAATAATGGTAAGCTCATACGAGT
* * **
42677757 CGAATAATGGTAAGCTCTTTTGAGT
1 TGAATAATGGTAAGCTCATACGAGT
42677782 TGAATAATGGTAAGCTCATACGAGT
1 TGAATAATGGTAAGCTCATACGAGT
42677807 TGA
1 TGA
42677810 GTATCGGTAA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (25 bp):
TGAATAATGGTAAGCTCATACGAGT
Found at i:42686108 original size:17 final size:16
Alignment explanation
Indices: 42686081--42686136 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 16
42686071 AATCTATTTA
42686081 TTTTCTCTTTCATTCTC
1 TTTT-TCTTTCATTCTC
*
42686098 TTTTTATTTTCCAATT-TC
1 TTTTT-CTTT-C-ATTCTC
42686116 TTTTTCTTTCATCTCTC
1 TTTTTCTTTCAT-TCTC
42686133 TTTT
1 TTTT
42686137 CTCCTCTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
15 2 0.06
16 3 0.09
17 16 0.50
18 8 0.25
19 3 0.09
ACGTcount: A:0.09, C:0.23, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTCTTTCATTCTC
Found at i:42687117 original size:20 final size:21
Alignment explanation
Indices: 42687094--42687142 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 21
42687084 CTTTCAAGAC
42687094 TTTTTTTTA-ACTTCGTAA-A-
1 TTTTTTTTATACTTCG-AATAG
42687113 TTTTTTTTATACTTCGAATATG
1 TTTTTTTTATACTTCGAATA-G
42687135 TTTTTTTT
1 TTTTTTTT
42687143 TCAATTACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 11 0.42
20 7 0.27
22 8 0.31
ACGTcount: A:0.20, C:0.08, G:0.06, T:0.65
Consensus pattern (21 bp):
TTTTTTTTATACTTCGAATAG
Found at i:42690085 original size:30 final size:30
Alignment explanation
Indices: 42690041--42690110 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
42690031 TTAATTTTTG
* *
42690041 AGTTTAGGGACAAAAGTGTAAATATGGAAA
1 AGTTTGGGGGCAAAAGTGTAAATATGGAAA
* * * *
42690071 AGTTTGGGGGCAAAATTGTAATTTTTGAAA
1 AGTTTGGGGGCAAAAGTGTAAATATGGAAA
*
42690101 AGTTGGGGGG
1 AGTTTGGGGG
42690111 AGGATTATTT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.36, C:0.03, G:0.33, T:0.29
Consensus pattern (30 bp):
AGTTTGGGGGCAAAAGTGTAAATATGGAAA
Found at i:42690509 original size:33 final size:32
Alignment explanation
Indices: 42690440--42690621 Score: 130
Period size: 33 Copynumber: 5.6 Consensus size: 32
42690430 TAAAAAATGG
**
42690440 GGTTGCTAAGTGCTGATTCCC-CCT-A--GG-
1 GGTTGCTAAGTGCTGATTCCCTATTAATTGGT
*
42690467 GGTTGCTAAGTGCTGATTCTCCTATTCATTGGT
1 GGTTGCTAAGTGCTGATTC-CCTATTAATTGGT
*
42690500 GGTTGCTAAGTGCTGATTCCACCATATTTTAAATTTGAAGG
1 GGTTGCTAAGTGCTGATT-C-CC-TA--TT-AA-TTG--GT
***
42690541 GGTTGCTAAGTGCTGATTCCC-CCGAA--GG-
1 GGTTGCTAAGTGCTGATTCCCTATTAATTGGT
*
42690569 GGTTGCTAAGTGCTGATTCCCCGATTAATTGGT
1 GGTTGCTAAGTGCTGATT-CCCTATTAATTGGT
42690602 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
42690622 ACCATATCTT
Statistics
Matches: 125, Mismatches: 11, Indels: 33
0.74 0.07 0.20
Matches are distributed among these distances:
27 19 0.15
28 20 0.16
29 5 0.04
30 3 0.02
31 1 0.01
32 6 0.05
33 36 0.29
34 5 0.04
35 2 0.02
37 2 0.02
38 1 0.01
39 5 0.04
40 1 0.01
41 19 0.15
ACGTcount: A:0.19, C:0.20, G:0.27, T:0.35
Consensus pattern (32 bp):
GGTTGCTAAGTGCTGATTCCCTATTAATTGGT
Found at i:42690576 original size:28 final size:28
Alignment explanation
Indices: 42690536--42690621 Score: 111
Period size: 28 Copynumber: 2.9 Consensus size: 28
42690526 TTTTAAATTT
42690536 GAAGGGGTTGCTAAGTGCTGATTCCCCC
1 GAAGGGGTTGCTAAGTGCTGATTCCCCC
42690564 GAAGGGGTTGCTAAGTGCTGATT-CCCC
1 GAAGGGGTTGCTAAGTGCTGATTCCCCC
42690591 GATTAATTGGTGGTTGCTAAGTGCTGATTCC
1 G---AA--GG-GGTTGCTAAGTGCTGATTCC
42690622 ACCATATCTT
Statistics
Matches: 51, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
27 5 0.10
28 23 0.45
30 2 0.04
32 2 0.04
33 18 0.35
34 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.31, T:0.30
Consensus pattern (28 bp):
GAAGGGGTTGCTAAGTGCTGATTCCCCC
Found at i:42690613 original size:102 final size:103
Alignment explanation
Indices: 42690438--42690665 Score: 379
Period size: 102 Copynumber: 2.2 Consensus size: 103
42690428 AATAAAAAAT
* * * *
42690438 GGGGTTGCTAAGTGCTGATTCCCCCTAGGGGTTGCTAAGTGCTGATTCTCCTATTCATTGGTGGT
1 GGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGATTAATTGGTGGT
*
42690503 TGCTAAGTGCTGATTCCACCATAT-TTTAAATTTG-AA
66 TGCTAAGTGCTGATTCCACCATATCTTTAAATGTGAAA
42690539 GGGGTTGCTAAGTGCTGATTCCCCCGAAGGGGTTGCTAAGTGCTGATTCCCCGATTAATTGGTGG
1 GGGGTTGCTAAGTGCTGATTCCCCC-AAGGGGTTGCTAAGTGCTGATTCCCCGATTAATTGGTGG
*
42690604 TTGCTAAGTGCTGATTCCACCATATCTTTGAATGTGAAA
65 TTGCTAAGTGCTGATTCCACCATATCTTTAAATGTGAAA
42690643 GGGGTTGCTAAGTGCTGATTCCC
1 GGGGTTGCTAAGTGCTGATTCCC
42690666 TGAATCACTG
Statistics
Matches: 118, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
101 25 0.21
102 60 0.51
103 8 0.07
104 25 0.21
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (103 bp):
GGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGATTAATTGGTGGT
TGCTAAGTGCTGATTCCACCATATCTTTAAATGTGAAA
Found at i:42698265 original size:13 final size:13
Alignment explanation
Indices: 42698247--42698271 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42698237 TAATGGTATA
42698247 TTGAATCCATGAT
1 TTGAATCCATGAT
42698260 TTGAATCCATGA
1 TTGAATCCATGA
42698272 AAATTTAGTA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TTGAATCCATGAT
Found at i:42699734 original size:47 final size:47
Alignment explanation
Indices: 42699665--42700113 Score: 754
Period size: 47 Copynumber: 9.5 Consensus size: 47
42699655 ATAGTATGGC
* *
42699665 GTGAAATTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAAT
1 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
42699712 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
1 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
42699759 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
1 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
* *
42699806 GTGAAATTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAAT
1 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
42699853 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
1 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
*
42699900 GTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAAT
1 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
42699947 GTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
1 GTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
*
42699996 ATGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
1 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
* * * * * * *
42700043 GTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGAT
1 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
*
42700090 GTGAAAGTGTATAAATGTGATAAG
1 GTGAAAGTGTATATATGTGATAAG
42700114 TCCCGAAGGG
Statistics
Matches: 380, Mismatches: 20, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
47 335 0.88
49 45 0.12
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (47 bp):
GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
Found at i:42709898 original size:15 final size:15
Alignment explanation
Indices: 42709878--42709914 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
42709868 AAAGAGATTG
42709878 AAAAGAAGAAAAAGA
1 AAAAGAAGAAAAAGA
42709893 AAAAGAAGAAAAAGA
1 AAAAGAAGAAAAAGA
*
42709908 GAAAGAA
1 AAAAGAA
42709915 TTTGAGAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAAAGAAGAAAAAGA
Found at i:42712150 original size:49 final size:47
Alignment explanation
Indices: 42711883--42712287 Score: 643
Period size: 47 Copynumber: 8.6 Consensus size: 47
42711873 CCCTTCGGGA
* * * * * *
42711883 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGG-
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
42711929 CTCTGTCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CT-TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42711977 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42712024 CTTATCACATATATACACTTTCACATTCATCACATCGG-CATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42712070 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42712117 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
42712166 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42712215 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
42712262 CTTATCACATATATATACATTCACAT
1 CTTATCACATATATACACTTTCACAT
42712288 CACAATTATC
Statistics
Matches: 338, Mismatches: 16, Indels: 9
0.93 0.04 0.02
Matches are distributed among these distances:
46 48 0.14
47 194 0.57
48 2 0.01
49 94 0.28
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:42730757 original size:17 final size:19
Alignment explanation
Indices: 42730722--42730758 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
42730712 TCTATAATCC
42730722 AAGCATTAAGTACAATATA
1 AAGCATTAAGTACAATATA
42730741 AAGCATTAAG-A-AATATA
1 AAGCATTAAGTACAATATA
42730758 A
1 A
42730759 TTATGGAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 1 0.06
19 10 0.56
ACGTcount: A:0.57, C:0.08, G:0.11, T:0.24
Consensus pattern (19 bp):
AAGCATTAAGTACAATATA
Found at i:42734053 original size:41 final size:41
Alignment explanation
Indices: 42733966--42734115 Score: 169
Period size: 41 Copynumber: 3.7 Consensus size: 41
42733956 AGGCTAAGCG
* *** *
42733966 CCTAGCAGGCTAAATGCCGGTGA-ATTTTTCAGACTATAAA
1 CCTAGCAGGCTAAGTGCCGGTGATATGAATCAGGCTATAAA
* * *
42734006 TCTAGCAGGCTAAGTGCCTGTGAT-TGGAATCAGGTTATAAA
1 CCTAGCAGGCTAAGTGCCGGTGATAT-GAATCAGGCTATAAA
* *
42734047 CCTAGCAGGCTACGTGCCGGTGATATGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATATGAATCAGGCTATAAA
*
42734088 CCTAGCAGGCTATGTGCCGGTGAATATG
1 CCTAGCAGGCTAAGTGCCGGTG-ATATG
42734116 TTAAATTATG
Statistics
Matches: 92, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
40 21 0.23
41 65 0.71
42 6 0.07
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (41 bp):
CCTAGCAGGCTAAGTGCCGGTGATATGAATCAGGCTATAAA
Found at i:42738178 original size:43 final size:43
Alignment explanation
Indices: 42738125--42738409 Score: 256
Period size: 43 Copynumber: 6.7 Consensus size: 43
42738115 GTTTATATGG
* * * *
42738125 AAAAACGCCGCTAGAGAACATGACCTTTAGCGACG-TTTCTCAC
1 AAAAATGCCACTAAAGAACATGACCTTTAGCGACGCTTT-TCCC
* * * * ***
42738168 AAAAATGCCGCTATAGAGCATGACC-TTAGTGGTTCTTTTCCC
1 AAAAATGCCACTAAAGAACATGACCTTTAGCGACGCTTTTCCC
** * *
42738210 TCAAATGCCGCTAAAGAACATGACCTTTAGC-AGCACTTTTCCC
1 AAAAATGCCACTAAAGAACATGACCTTTAGCGA-CGCTTTTCCC
* * * *
42738253 ACAAAA-ACCACTATAGAACATGACCTTTAGTGGCGCTTTTCCC
1 A-AAAATGCCACTAAAGAACATGACCTTTAGCGACGCTTTTCCC
* * **
42738296 AAAAATTCCACTAAAGAACATGACCTTTACCGGTGCTTTTCCC
1 AAAAATGCCACTAAAGAACATGACCTTTAGCGACGCTTTTCCC
**
42738339 ACAAAA-GCCACTAAAGAACATGACCTTTAGCGGTGCTTTTCCC
1 A-AAAATGCCACTAAAGAACATGACCTTTAGCGACGCTTTTCCC
* *
42738382 ACAAACGCCACTAAAGAACATGACCTTT
1 AAAAATGCCACTAAAGAACATGACCTTT
42738410 CCCCACAAAC
Statistics
Matches: 202, Mismatches: 32, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
42 36 0.18
43 159 0.79
44 7 0.03
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (43 bp):
AAAAATGCCACTAAAGAACATGACCTTTAGCGACGCTTTTCCC
Found at i:42738323 original size:86 final size:84
Alignment explanation
Indices: 42738139--42738409 Score: 337
Period size: 86 Copynumber: 3.2 Consensus size: 84
42738129 ACGCCGCTAG
* * * * *
42738139 AGAACATGACCTTTAGCGACGTTTCTCACAAAAATGCCGCTATAGAGCATGACC-TTAGTGGTTC
1 AGAACATGACCTTTAGCGACTTTTCCCACAAAAA--CCACTATAGAACATGACCTTTAGTGGTGC
* *
42738203 TTTTCCCTCAAATGCCGCTAA
64 TTTTCCCACAAATGCCACTAA
*
42738224 AGAACATGACCTTTAGCAGCACTTTTCCCACAAAAACCACTATAGAACATGACCTTTAGTGGCGC
1 AGAACATGACCTTTAGC-G-ACTTTTCCCACAAAAACCACTATAGAACATGACCTTTAGTGGTGC
* *
42738289 TTTTCCCAAAAATTCCACTAA
64 TTTTCCCACAAATGCCACTAA
* * * * *
42738310 AGAACATGACCTTTACCGGTGCTTTTCCCACAAAAGCCACTAAAGAACATGACCTTTAGCGGTGC
1 AGAACATGACCTTTAGC-G-ACTTTTCCCACAAAAACCACTATAGAACATGACCTTTAGTGGTGC
*
42738375 TTTTCCCACAAACGCCACTAA
64 TTTTCCCACAAATGCCACTAA
42738396 AGAACATGACCTTT
1 AGAACATGACCTTT
42738410 CCCCACAAAC
Statistics
Matches: 162, Mismatches: 21, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
85 33 0.20
86 115 0.71
87 14 0.09
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (84 bp):
AGAACATGACCTTTAGCGACTTTTCCCACAAAAACCACTATAGAACATGACCTTTAGTGGTGCTT
TTCCCACAAATGCCACTAA
Found at i:42738378 original size:129 final size:128
Alignment explanation
Indices: 42738139--42738409 Score: 346
Period size: 129 Copynumber: 2.1 Consensus size: 128
42738129 ACGCCGCTAG
* * * ** *
42738139 AGAACATGACCTTTAGCGACGTTTCTCACAAAAATGCCGCTATAGAGCATGACCTTAGTGGTTCT
1 AGAACATGACCTTTAGCGACGTTTCTCACAAAAATGCCACTAAAGAACATGACCTTACCGGTGCT
* * * *
42738204 TTTCCCTCAAATGCCGCTAAAGAACATGACCTTTAGCAGCACTTTTCCCACAAAAACCACTAT
66 TTTCCCACAAAAGCCACTAAAGAACATGACCTTTAGCAGCACTTTTCCCACAAAAACCACTAA
* * * *
42738267 AGAACATGACCTTTAGTGGCGCTTT-TCCCAAAAATTCCACTAAAGAACATGACCTTTACCGGTG
1 AGAACATGACCTTTAGCGACG-TTTCTCACAAAAATGCCACTAAAGAACATGACC-TTACCGGTG
* ** **
42738331 CTTTTCCCACAAAAGCCACTAAAGAACATGACCTTTAGCGGTGCTTTTCCCACAAACGCCACTAA
64 CTTTTCCCACAAAAGCCACTAAAGAACATGACCTTTAGCAGCACTTTTCCCACAAAAACCACTAA
42738396 AGAACATGACCTTT
1 AGAACATGACCTTT
42738410 CCCCACAAAC
Statistics
Matches: 122, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
128 43 0.35
129 79 0.65
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (128 bp):
AGAACATGACCTTTAGCGACGTTTCTCACAAAAATGCCACTAAAGAACATGACCTTACCGGTGCT
TTTCCCACAAAAGCCACTAAAGAACATGACCTTTAGCAGCACTTTTCCCACAAAAACCACTAA
Found at i:42738427 original size:31 final size:32
Alignment explanation
Indices: 42738374--42738436 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
42738364 TTTAGCGGTG
*
42738374 CTTTTCCCACAAACGCCACTAAAGAACATGAC
1 CTTTCCCCACAAACGCCACTAAAGAACATGAC
42738406 CTTTCCCCACAAACGCC-CTAAAGAACATGAC
1 CTTTCCCCACAAACGCCACTAAAGAACATGAC
42738437 TTTTAGCGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 14 0.47
32 16 0.53
ACGTcount: A:0.37, C:0.37, G:0.10, T:0.17
Consensus pattern (32 bp):
CTTTCCCCACAAACGCCACTAAAGAACATGAC
Found at i:42744341 original size:9 final size:9
Alignment explanation
Indices: 42744327--42744415 Score: 57
Period size: 9 Copynumber: 10.6 Consensus size: 9
42744317 TATTTATGCA
42744327 TTATGTAAG
1 TTATGTAAG
42744336 TTATGTAAG
1 TTATGTAAG
* *
42744345 TTATATAGG
1 TTATGTAAG
*
42744354 TTACGTAAG
1 TTATGTAAG
42744363 TTA--TAA-
1 TTATGTAAG
*
42744369 -TATGATATG
1 TTATG-TAAG
* * *
42744378 ATATAT-AT
1 TTATGTAAG
42744386 TTATGT-A-
1 TTATGTAAG
42744393 TTATGTAAG
1 TTATGTAAG
42744402 TTATGTAAG
1 TTATGTAAG
42744411 TTATG
1 TTATG
42744416 ATCCAAAGTT
Statistics
Matches: 62, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
5 2 0.03
7 9 0.15
8 8 0.13
9 40 0.65
10 3 0.05
ACGTcount: A:0.35, C:0.01, G:0.18, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:42744484 original size:13 final size:13
Alignment explanation
Indices: 42744466--42744492 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
42744456 TGATTATCAT
42744466 CTTTAAATTTTAA
1 CTTTAAATTTTAA
42744479 CTTTAAATTTTAA
1 CTTTAAATTTTAA
42744492 C
1 C
42744493 CCTTTAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (13 bp):
CTTTAAATTTTAA
Found at i:42749784 original size:76 final size:75
Alignment explanation
Indices: 42749691--42749888 Score: 249
Period size: 76 Copynumber: 2.6 Consensus size: 75
42749681 ACGCGCTTTG
* * *
42749691 GGGAAAAGAATTAGGGATTTTGGGGAGGGGGAAC-GAATTTGGGGAAAAGAAGTTGGGG-AAAAA
1 GGGAAAAAAATTAGGGATTTTAGGGAGGGGGAACTG-ATTTGGGGAAAAGAAATTGGGGAAAAAA
42749754 AGAAAGGGAATT
65 AGAAAGGG-ATT
* * * * *
42749766 GGGAAAAAAAGTTGGGGATTTCAGGGAGGGGGAACTGGTTTGGTGAAAATAAATTGGGGAAAAAA
1 GGGAAAAAAA-TTAGGGATTTTAGGGAGGGGGAACTGATTTGGGGAAAAGAAATTGGGGAAAAAA
42749831 AGAAAGGGATT
65 AGAAAGGGATT
* * *
42749842 GGGAAAACAATTAGGGATTTTAGGG-GGTGGAACTGATTTAGGGAAAA
1 GGGAAAAAAATTAGGGATTTTAGGGAGGGGGAACTGATTTGGGGAAAA
42749889 AATTAGGGAT
Statistics
Matches: 105, Mismatches: 15, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
74 18 0.17
75 22 0.21
76 51 0.49
77 14 0.13
ACGTcount: A:0.39, C:0.03, G:0.39, T:0.20
Consensus pattern (75 bp):
GGGAAAAAAATTAGGGATTTTAGGGAGGGGGAACTGATTTGGGGAAAAGAAATTGGGGAAAAAAA
GAAAGGGATT
Found at i:42754124 original size:21 final size:22
Alignment explanation
Indices: 42754088--42754128 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
42754078 CAATTCTACC
*
42754088 TTTATTTTCTGATTTGAATGGT
1 TTTATTTTCAGATTTGAATGGT
42754110 TTTATTTT-AGATTTGAATG
1 TTTATTTTCAGATTTGAATG
42754129 TCCAATCCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.22, C:0.02, G:0.17, T:0.59
Consensus pattern (22 bp):
TTTATTTTCAGATTTGAATGGT
Found at i:42756924 original size:20 final size:20
Alignment explanation
Indices: 42756899--42756938 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
42756889 AACAACTTAT
42756899 GACAGAGCCA-CAGAAGTGCA
1 GACAGAGCCACCA-AAGTGCA
*
42756919 GACAGAGGCACCAAAGTGCA
1 GACAGAGCCACCAAAGTGCA
42756939 AACCCGAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.40, C:0.25, G:0.30, T:0.05
Consensus pattern (20 bp):
GACAGAGCCACCAAAGTGCA
Found at i:42757077 original size:170 final size:170
Alignment explanation
Indices: 42756795--42757136 Score: 675
Period size: 170 Copynumber: 2.0 Consensus size: 170
42756785 CGGATTCAGG
42756795 CTGGATCAAAATAGGTTCCTGAGACAAAATAGATTTGAGCTTCTCAAAGCTCAATTATTGCTCAT
1 CTGGATCAAAATAGGTTCCTGAGACAAAATAGATTTGAGCTTCTCAAAGCTCAATTATTGCTCAT
42756860 CGGTCCACACAAAAGGTGTGTTCTTACGCAACAACTTATGACAGAGCCACAGAAGTGCAGACAGA
66 CGGTCCACACAAAAGGTGTGTTCTTACGCAACAACTTATGACAGAGCCACAGAAGTGCAGACAGA
42756925 GGCACCAAAGTGCAAACCCGAACAAGCCTGCGTTTAAACC
131 GGCACCAAAGTGCAAACCCGAACAAGCCTGCGTTTAAACC
42756965 CTGGATCAAAATAGGTTCCTGAGACAAAATAGATTTGAGCTTCTCAAAGCTCAATTATTGCTCAT
1 CTGGATCAAAATAGGTTCCTGAGACAAAATAGATTTGAGCTTCTCAAAGCTCAATTATTGCTCAT
*
42757030 CGGTCCACACAAAAGGTGTGTTCTTACGCAACAACTTATGACAGAGCCACTGAAGTGCAGACAGA
66 CGGTCCACACAAAAGGTGTGTTCTTACGCAACAACTTATGACAGAGCCACAGAAGTGCAGACAGA
42757095 GGCACCAAAGTGCAAACCCGAACAAGCCTGCGTTTAAACC
131 GGCACCAAAGTGCAAACCCGAACAAGCCTGCGTTTAAACC
42757135 CT
1 CT
42757137 ATTGGCATGC
Statistics
Matches: 171, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
170 171 1.00
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (170 bp):
CTGGATCAAAATAGGTTCCTGAGACAAAATAGATTTGAGCTTCTCAAAGCTCAATTATTGCTCAT
CGGTCCACACAAAAGGTGTGTTCTTACGCAACAACTTATGACAGAGCCACAGAAGTGCAGACAGA
GGCACCAAAGTGCAAACCCGAACAAGCCTGCGTTTAAACC
Found at i:42758112 original size:16 final size:16
Alignment explanation
Indices: 42758088--42758130 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
42758078 GGAAGATGAT
*
42758088 GTTTTATTTTAATTAA
1 GTTTAATTTTAATTAA
42758104 GTTTAATTTTAATTAA
1 GTTTAATTTTAATTAA
42758120 -TTATAATTTTA
1 GTT-TAATTTTA
42758131 CCCTTATAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (16 bp):
GTTTAATTTTAATTAA
Found at i:42761410 original size:10 final size:9
Alignment explanation
Indices: 42761393--42761443 Score: 50
Period size: 10 Copynumber: 5.2 Consensus size: 9
42761383 TAACGATCTT
42761393 AATGAGCTG
1 AATGAGCTG
42761402 AATTGAGCTCG
1 AA-TGAGCT-G
42761413 AATGAGCT-
1 AATGAGCTG
42761421 AACTTGAGCTCG
1 AA--TGAGCT-G
42761433 AATGAGCTG
1 AATGAGCTG
42761442 AA
1 AA
42761444 CCACATGAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
8 2 0.06
9 5 0.14
10 24 0.67
11 3 0.08
12 2 0.06
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (9 bp):
AATGAGCTG
Found at i:42761416 original size:20 final size:21
Alignment explanation
Indices: 42761393--42761444 Score: 90
Period size: 20 Copynumber: 2.6 Consensus size: 21
42761383 TAACGATCTT
42761393 AATGAGCTGAA-TTGAGCTCG
1 AATGAGCTGAACTTGAGCTCG
42761413 AATGAGCT-AACTTGAGCTCG
1 AATGAGCTGAACTTGAGCTCG
42761433 AATGAGCTGAAC
1 AATGAGCTGAAC
42761445 CACATGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 2 0.07
20 25 0.83
21 3 0.10
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.23
Consensus pattern (21 bp):
AATGAGCTGAACTTGAGCTCG
Found at i:42768958 original size:29 final size:29
Alignment explanation
Indices: 42768926--42769068 Score: 153
Period size: 29 Copynumber: 4.8 Consensus size: 29
42768916 GGTATAGCTT
* *
42768926 CGACTATCGATTATGAAAAGGGATGGTGA
1 CGACCATCAATTATGAAAAGGGATGGTGA
42768955 CGACCATCAATTATGAAAAGGGATGGTGA
1 CGACCATCAATTATGAAAAGGGATGGTGA
* * *
42768984 CGACCATCAACTATGAAAACGTATAGTGATGA
1 CGACCATCAATTATGAAAAGGGAT-G-G-TGA
* *
42769016 CGACCATCGATTAATGAAAAGGGATGGT-T
1 CGACCATCAATT-ATGAAAAGGGATGGTGA
* *
42769045 CTTACCATCAAATATGAAAAGGGA
1 C-GACCATCAATTATGAAAAGGGA
42769069 CTGTTAAAGT
Statistics
Matches: 96, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
29 60 0.62
30 10 0.10
31 2 0.02
32 14 0.15
33 10 0.10
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.22
Consensus pattern (29 bp):
CGACCATCAATTATGAAAAGGGATGGTGA
Found at i:42772452 original size:13 final size:13
Alignment explanation
Indices: 42772409--42772451 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
42772399 TACATGCCCA
42772409 TGTGCCACACGGT
1 TGTGCCACACGGT
42772422 TGTGCCACACGGT
1 TGTGCCACACGGT
* *
42772435 TGTGTCACACGCT
1 TGTGCCACACGGT
42772448 TGTG
1 TGTG
42772452 TGCCAGGCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.14, C:0.28, G:0.30, T:0.28
Consensus pattern (13 bp):
TGTGCCACACGGT
Found at i:42773273 original size:22 final size:22
Alignment explanation
Indices: 42773242--42773353 Score: 101
Period size: 22 Copynumber: 5.4 Consensus size: 22
42773232 ATACCCACAA
*
42773242 TAAGCTTGAATAACACTGGCAC
1 TAAGCCTGAATAACACTGGCAC
**
42773264 TAAGCCTGAATAACACCAGCAC
1 TAAGCCTGAATAACACTGGCAC
* * *
42773286 TAAGCTTG-CT-AGACT----C
1 TAAGCCTGAATAACACTGGCAC
* *
42773302 TAAGCCTGAACAACACCGGCAC
1 TAAGCCTGAATAACACTGGCAC
*
42773324 TAAGCCTGAATAGCACTGGCAC
1 TAAGCCTGAATAACACTGGCAC
42773346 TAAGCCTG
1 TAAGCCTG
42773354 CTAGGCACTA
Statistics
Matches: 69, Mismatches: 15, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
16 8 0.12
18 3 0.04
20 3 0.04
21 1 0.01
22 54 0.78
ACGTcount: A:0.34, C:0.29, G:0.19, T:0.19
Consensus pattern (22 bp):
TAAGCCTGAATAACACTGGCAC
Found at i:42773335 original size:60 final size:60
Alignment explanation
Indices: 42773242--42773371 Score: 179
Period size: 60 Copynumber: 2.2 Consensus size: 60
42773232 ATACCCACAA
* * * * *
42773242 TAAGCTTGAATAACACTGGCACTAAGCCTGAATAACACCAGCACTAAGCTTGCTAGACTC
1 TAAGCCTGAACAACACCGGCACTAAGCCTGAATAACACCAGCACTAAGCCTGCTAGACAC
* ** *
42773302 TAAGCCTGAACAACACCGGCACTAAGCCTGAATAGCACTGGCACTAAGCCTGCTAGGCAC
1 TAAGCCTGAACAACACCGGCACTAAGCCTGAATAACACCAGCACTAAGCCTGCTAGACAC
42773362 TAAGCCTGAA
1 TAAGCCTGAA
42773372 TAATAGTATG
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.18
Consensus pattern (60 bp):
TAAGCCTGAACAACACCGGCACTAAGCCTGAATAACACCAGCACTAAGCCTGCTAGACAC
Found at i:42777638 original size:27 final size:27
Alignment explanation
Indices: 42777608--42777660 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
42777598 TGTCTGAAAT
* *
42777608 ACCCCCATAGGGTAGAATGACCGTAAC
1 ACCCCCATAGGGTAAAATAACCGTAAC
**
42777635 ACCCCTGTAGGGTAAAATAACCGTAA
1 ACCCCCATAGGGTAAAATAACCGTAA
42777661 TGCCCTGGTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (27 bp):
ACCCCCATAGGGTAAAATAACCGTAAC
Found at i:42777776 original size:24 final size:23
Alignment explanation
Indices: 42777725--42777782 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
42777715 TTTGTGGTTA
*
42777725 AATGACTGATTTTTTGTGTTTGG
1 AATGACTGATTTTCTGTGTTTGG
*
42777748 TATGACTGATTTGTCTGTGATTT-G
1 AATGACTGATTT-TCTGTG-TTTGG
*
42777772 AATGATTGATT
1 AATGACTGATT
42777783 CTGAGCATGG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 11 0.38
24 15 0.52
25 3 0.10
ACGTcount: A:0.21, C:0.05, G:0.24, T:0.50
Consensus pattern (23 bp):
AATGACTGATTTTCTGTGTTTGG
Found at i:42777886 original size:27 final size:27
Alignment explanation
Indices: 42777846--42777905 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
42777836 ATGGAGGAAG
42777846 TACTG-TACTAGTGGCTCT-GCCACA-A
1 TACTGTTACTAGTGGCT-TGGCCACATA
*
42777871 TCACTGTTACTGGTGGCTTGGCCACATA
1 T-ACTGTTACTAGTGGCTTGGCCACATA
42777899 TACTGTT
1 TACTGTT
42777906 GATGGCAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
25 1 0.03
26 5 0.17
27 22 0.73
28 2 0.07
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.33
Consensus pattern (27 bp):
TACTGTTACTAGTGGCTTGGCCACATA
Found at i:42777974 original size:32 final size:33
Alignment explanation
Indices: 42777928--42778161 Score: 216
Period size: 32 Copynumber: 7.4 Consensus size: 33
42777918 GCTACGATGC
* * *
42777928 TACTGATGGCTTTGTTCCGGTCATAGT-ACTGT
1 TACTGATGGCTTTGTGCCGATCATATTCACTGT
* * * *
42777960 TACTAATGGCTTTGTGTCAATTATATT-ACTGT
1 TACTGATGGCTTTGTGCCGATCATATTCACTGT
* *
42777992 TACTGGTGGCTATGTGCCGATCAT-TTCACTGT
1 TACTGATGGCTTTGTGCCGATCATATTCACTGT
* *
42778024 TACTGATGGCTATGTGCCGATCATA-TCACTGC
1 TACTGATGGCTTTGTGCCGATCATATTCACTGT
* * *
42778056 TACT-ATGGCTTTGTACCGATCATGTT-ACCGT
1 TACTGATGGCTTTGTGCCGATCATATTCACTGT
* * * *
42778087 TGCTGATGGCTGTGTGCCAATCATA-TCACTGC
1 TACTGATGGCTTTGTGCCGATCATATTCACTGT
* *
42778119 TACTGATGGCTTTGTGCCAATCACATT-ACTG-
1 TACTGATGGCTTTGTGCCGATCATATTCACTGT
*
42778150 TACTTATGGCTT
1 TACTGATGGCTT
42778162 GTAGCCATTC
Statistics
Matches: 165, Mismatches: 31, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
31 37 0.22
32 127 0.77
33 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (33 bp):
TACTGATGGCTTTGTGCCGATCATATTCACTGT
Found at i:42778104 original size:95 final size:93
Alignment explanation
Indices: 42777925--42778161 Score: 258
Period size: 95 Copynumber: 2.5 Consensus size: 93
42777915 TTTGCTACGA
* * ** * *
42777925 TGCTACTGATGGCTTTGTTCCGGTCATAGTACTGTTACTAATGGCTTTGTGTCAATTATATTACT
1 TGCTACTGATGGCTTTGTGCCGATCATA-TACTG-TACT-ATGGCTTTGTACCAATCATATTACC
* * *
42777990 GTTACTGGTGGCTATGTGCCGATCATTTCAC
63 GTTACTGATGGCTATGTGCCAATCATATCAC
* * * *
42778021 TGTTACTGATGGCTATGTGCCGATCATATCACTGCTACTATGGCTTTGTACCGATCATGTTACCG
1 TGCTACTGATGGCTTTGTGCCGATCATAT-ACTG-TACTATGGCTTTGTACCAATCATATTACCG
* *
42778086 TTGCTGATGGCTGTGTGCCAATCATATCAC
64 TTACTGATGGCTATGTGCCAATCATATCAC
* *
42778116 TGCTACTGATGGCTTTGTGCCAATCACATTACTGTACTTATGGCTT
1 TGCTACTGATGGCTTTGTGCCGATCATA-TACTGTAC-TATGGCTT
42778162 GTAGCCATTC
Statistics
Matches: 118, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
94 3 0.03
95 82 0.69
96 33 0.28
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (93 bp):
TGCTACTGATGGCTTTGTGCCGATCATATACTGTACTATGGCTTTGTACCAATCATATTACCGTT
ACTGATGGCTATGTGCCAATCATATCAC
Found at i:42780932 original size:38 final size:38
Alignment explanation
Indices: 42780852--42780924 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
42780842 ACACCAACAA
* * *
42780852 TAAGCCTGAATAACACCGGCACTAAGCTTGCTAGGAAC
1 TAAGCCTGAACAACACCGACACTAAGCCTGCTAGGAAC
*
42780890 TAAGCCTGACCAACACCGACACTAAGCCTGCTAGG
1 TAAGCCTGAACAACACCGACACTAAGCCTGCTAGG
42780925 CATTAAGCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.33, C:0.30, G:0.21, T:0.16
Consensus pattern (38 bp):
TAAGCCTGAACAACACCGACACTAAGCCTGCTAGGAAC
Found at i:42784728 original size:39 final size:36
Alignment explanation
Indices: 42784656--42784804 Score: 113
Period size: 38 Copynumber: 3.9 Consensus size: 36
42784646 TAAAGGCATG
* *
42784656 TATTAAATATGTCTAAACTAGGACAT-ATATAAAACAT
1 TATTAAAGATGTC-AAACTATGACATAAT-TAAAACAT
* *
42784693 GTATTTAAGATGTCCTAAACTATGACATAATTAAAAACCCT
1 -TATTAAAGATGT-C-AAACTATGACATAATT-AAAA-CAT
* *
42784734 TATTAAAGATGATCAGATTATGACATAATTAAAAC-T
1 TATTAAAGATG-TCAAACTATGACATAATTAAAACAT
* *
42784770 CATATTAATGATGTTCAAATTATGACATAATTAAA
1 --TATTAAAGATG-TCAAACTATGACATAATTAAA
42784805 GACTTAAACT
Statistics
Matches: 94, Mismatches: 10, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
36 1 0.01
37 1 0.01
38 44 0.47
39 28 0.30
40 17 0.18
41 3 0.03
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.34
Consensus pattern (36 bp):
TATTAAAGATGTCAAACTATGACATAATTAAAACAT
Found at i:42784777 original size:38 final size:38
Alignment explanation
Indices: 42784713--42784804 Score: 130
Period size: 38 Copynumber: 2.4 Consensus size: 38
42784703 TGTCCTAAAC
* *
42784713 TATGACATAATTAAAAACCCTTATTAAAGATGATCAGAT
1 TATGACATAATT-AAAACCCATATTAAAGATGATCAAAT
* * *
42784752 TATGACATAATTAAAACTCATATTAATGATGTTCAAAT
1 TATGACATAATTAAAACCCATATTAAAGATGATCAAAT
42784790 TATGACATAATTAAA
1 TATGACATAATTAAA
42784805 GACTTAAACT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
38 36 0.75
39 12 0.25
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.34
Consensus pattern (38 bp):
TATGACATAATTAAAACCCATATTAAAGATGATCAAAT
Found at i:42787887 original size:24 final size:25
Alignment explanation
Indices: 42787860--42787910 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
42787850 ACTGGTCATA
42787860 GAGAGAATTGA-GAAAGAATATTTG
1 GAGAGAATTGAGGAAAGAATATTTG
* *
42787884 GAGAGATTTGAGGAGAGAATATTTG
1 GAGAGAATTGAGGAAAGAATATTTG
42787909 GA
1 GA
42787911 TTTGGGGAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.41, C:0.00, G:0.33, T:0.25
Consensus pattern (25 bp):
GAGAGAATTGAGGAAAGAATATTTG
Found at i:42788525 original size:27 final size:26
Alignment explanation
Indices: 42788495--42788632 Score: 118
Period size: 27 Copynumber: 5.2 Consensus size: 26
42788485 TTACACTGTT
*
42788495 ATGACCAAAATACCTCCATAGGGTAAA
1 ATGACCGAAATACC-CCATAGGGTAAA
*
42788522 ATGACC-AAGATACCCCCATAGGGT-AG
1 ATGACCGAA-ATA-CCCCATAGGGTAAA
* * * *
42788548 ATAACTGAAATACCTCCATATGCTAAA
1 ATGACCGAAATACC-CCATAGGGTAAA
* *
42788575 ATGATCGAAATACCCCTATAGGGTAGA
1 ATGACCGAAATACCCC-ATAGGGTAAA
* *
42788602 ATGACCGTAATACCCCCTAAGGGTAAA
1 ATGACCGAAATACCCCAT-AGGGTAAA
42788629 ATGA
1 ATGA
42788633 TCTTTATACC
Statistics
Matches: 88, Mismatches: 16, Indels: 14
0.75 0.14 0.12
Matches are distributed among these distances:
25 2 0.02
26 20 0.23
27 64 0.73
28 2 0.02
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.20
Consensus pattern (26 bp):
ATGACCGAAATACCCCATAGGGTAAA
Found at i:42788565 original size:53 final size:54
Alignment explanation
Indices: 42788502--42788634 Score: 155
Period size: 53 Copynumber: 2.5 Consensus size: 54
42788492 GTTATGACCA
*
42788502 AAATACCTCCATAGGGTAAAATGA-CCAAGATACCCCCATAGGGTAG-ATAACTG
1 AAATACCTCCATAGGGTAAAATGATCCAA-ATACCCCCATAGGGTAGAATAACCG
* * * * *
42788555 AAATACCTCCATATGCTAAAATGATCGAAATACCCCTATAGGGTAGAATGACCG
1 AAATACCTCCATAGGGTAAAATGATCCAAATACCCCCATAGGGTAGAATAACCG
* *
42788609 TAATACC-CCCTAAGGGTAAAATGATC
1 AAATACCTCCAT-AGGGTAAAATGATC
42788635 TTTATACCCC
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
53 41 0.61
54 26 0.39
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.21
Consensus pattern (54 bp):
AAATACCTCCATAGGGTAAAATGATCCAAATACCCCCATAGGGTAGAATAACCG
Found at i:42790157 original size:20 final size:21
Alignment explanation
Indices: 42790127--42790167 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
42790117 TTACCTCTTG
*
42790127 CTTTTCTTTTTTTTCAGTTTT
1 CTTTTCTTTTTTTTCACTTTT
42790148 CTTTTC-TTTTTTTCACTTTT
1 CTTTTCTTTTTTTTCACTTTT
42790168 TTCTTTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.05, C:0.17, G:0.02, T:0.76
Consensus pattern (21 bp):
CTTTTCTTTTTTTTCACTTTT
Found at i:42790168 original size:21 final size:22
Alignment explanation
Indices: 42790127--42790174 Score: 64
Period size: 20 Copynumber: 2.2 Consensus size: 22
42790117 TTACCTCTTG
42790127 CTTTTCTTTTTTTTCA-GTTTT
1 CTTTTCTTTTTTTTCATGTTTT
*
42790148 CTTTTC-TTTTTTTCACTTTTTT
1 CTTTTCTTTTTTTTCA-TGTTTT
42790170 CTTTT
1 CTTTT
42790175 TCTTCTTTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 9 0.38
21 6 0.25
22 9 0.38
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.77
Consensus pattern (22 bp):
CTTTTCTTTTTTTTCATGTTTT
Found at i:42791736 original size:9 final size:9
Alignment explanation
Indices: 42791722--42791752 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
42791712 GGAATCATTC
42791722 TTCTAATTG
1 TTCTAATTG
42791731 TTCTAATTG
1 TTCTAATTG
42791740 TTCTAATTG
1 TTCTAATTG
42791749 TTCT
1 TTCT
42791753 TGTACAGGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.19, C:0.13, G:0.10, T:0.58
Consensus pattern (9 bp):
TTCTAATTG
Found at i:42794400 original size:29 final size:29
Alignment explanation
Indices: 42794344--42794400 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
42794334 ATGTATTTGA
* *
42794344 CCCTTAACTTTTCATTAATTATACATTTT
1 CCCTAAACTTTTCATTAATTACACATTTT
*
42794373 CCCTAAACTTTTACATTTATTACA-ATTT
1 CCCTAAACTTTT-CATTAATTACACATTT
42794401 AGTCCCTAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.30, C:0.21, G:0.00, T:0.49
Consensus pattern (29 bp):
CCCTAAACTTTTCATTAATTACACATTTT
Found at i:42796263 original size:17 final size:18
Alignment explanation
Indices: 42796226--42796279 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
42796216 CTTTCATTCC
*
42796226 ATAACATTTTCTAGTTT-A
1 ATAACATTTTCCA-TTTCA
42796244 ATAACA-TTTCCATTTCA
1 ATAACATTTTCCATTTCA
*
42796261 ATATCATTTTCCATTTCA
1 ATAACATTTTCCATTTCA
42796279 A
1 A
42796280 AATCATGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 3 0.09
17 11 0.34
18 18 0.56
ACGTcount: A:0.33, C:0.19, G:0.02, T:0.46
Consensus pattern (18 bp):
ATAACATTTTCCATTTCA
Found at i:42796271 original size:18 final size:18
Alignment explanation
Indices: 42796250--42796285 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
42796240 TTTAATAACA
*
42796250 TTTCCATTTCAATATCAT
1 TTTCCATTTCAAAATCAT
42796268 TTTCCATTTCAAAATCAT
1 TTTCCATTTCAAAATCAT
42796286 GATTTTGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.22, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTCCATTTCAAAATCAT
Found at i:42808398 original size:25 final size:25
Alignment explanation
Indices: 42808374--42808455 Score: 119
Period size: 25 Copynumber: 3.3 Consensus size: 25
42808364 AGAATAGTAT
* * *
42808374 GCTCTCACAAGCTATAAATTGGTAT
1 GCTCTTACAAGCTATAAATCGGTAC
* *
42808399 GCTCTTACGAGCTATAAATCGATAC
1 GCTCTTACAAGCTATAAATCGGTAC
42808424 GCTCTTACAAGCTATAAATCGGTAC
1 GCTCTTACAAGCTATAAATCGGTAC
42808449 GCTCTTA
1 GCTCTTA
42808456 TGAGCTGTGG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 50 1.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (25 bp):
GCTCTTACAAGCTATAAATCGGTAC
Found at i:42816864 original size:49 final size:49
Alignment explanation
Indices: 42816811--42817377 Score: 899
Period size: 49 Copynumber: 11.4 Consensus size: 49
42816801 TTGTGATGTG
42816811 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
42816860 AGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAA--T----GTG---A-A
* *
42816917 TATGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
1 -A-GTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
42816968 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
42817017 AGTGTATATATATGTGATTAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
42817066 AGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
42817113 AGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
42817162 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
42817211 AGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
42817260 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
42817309 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
42817358 AGTGTATATATATGTGATAA
1 AGTGTATATATATGTGATAA
42817378 TGTGAAAGTG
Statistics
Matches: 488, Mismatches: 14, Indels: 32
0.91 0.03 0.06
Matches are distributed among these distances:
47 79 0.16
49 356 0.73
50 1 0.00
51 1 0.00
52 1 0.00
53 3 0.01
55 3 0.01
56 1 0.00
57 1 0.00
58 1 0.00
59 4 0.01
61 37 0.08
ACGTcount: A:0.34, C:0.08, G:0.28, T:0.31
Consensus pattern (49 bp):
AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
Found at i:42816925 original size:12 final size:12
Alignment explanation
Indices: 42816908--42816934 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
42816898 GAATGTGAAA
42816908 GTGTATATATAT
1 GTGTATATATAT
42816920 GTGTATATATAT
1 GTGTATATATAT
42816932 GTG
1 GTG
42816935 ATAAGGCCGA
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:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (12 bp):
GTGTATATATAT
Found at i:42816935 original size:61 final size:61
Alignment explanation
Indices: 42816864--42816983 Score: 240
Period size: 61 Copynumber: 2.0 Consensus size: 61
42816854 TGTGAAAGTG
42816864 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGTA
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGTA
42816925 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTG
42816984 ATAAGGCCTA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.34, C:0.07, G:0.27, T:0.33
Consensus pattern (61 bp):
TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGTA
Found at i:42817382 original size:26 final size:26
Alignment explanation
Indices: 42817342--42817403 Score: 115
Period size: 26 Copynumber: 2.3 Consensus size: 26
42817332 CTAATGGCCG
42817342 ATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAT-AATGTGAAAGTGTATATAT
42817369 ATGTGATAATGTGAAAGTGTATATAT
1 ATGTGATAATGTGAAAGTGTATATAT
42817395 ATGTGATAA
1 ATGTGATAA
42817404 GGCCTAATGG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 28 0.80
27 7 0.20
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.37
Consensus pattern (26 bp):
ATGTGATAATGTGAAAGTGTATATAT
Found at i:42817389 original size:75 final size:73
Alignment explanation
Indices: 42817293--42817450 Score: 289
Period size: 75 Copynumber: 2.1 Consensus size: 73
42817283 CTAATGGCCG
42817293 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 ATGTGAT-AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
42817358 AGTGTATATAT
65 AGTG--TATAT
42817369 ATGTGATAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 ATGTGATAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
42817434 GTGTATAT
66 GTGTATAT
42817442 ATGTGATAA
1 ATGTGATAA
42817451 GGCCTAATAG
Statistics
Matches: 82, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
73 14 0.17
75 61 0.74
76 7 0.09
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (73 bp):
ATGTGATAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
GTGTATAT
Found at i:42817396 original size:124 final size:120
Alignment explanation
Indices: 42817244--42817497 Score: 454
Period size: 124 Copynumber: 2.1 Consensus size: 120
42817234 CGAATGGCCA
42817244 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 ATGTGAT-AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
42817309 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
65 AGTG--TATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG--TATAT
42817369 ATGTGATAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 ATGTGATAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
42817434 GTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
66 GTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
42817489 ATGTGATAA
1 ATGTGATAA
42817498 GGCCGAATGG
Statistics
Matches: 128, Mismatches: 1, Indels: 5
0.96 0.01 0.04
Matches are distributed among these distances:
120 14 0.11
122 46 0.36
124 61 0.48
125 7 0.05
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.32
Consensus pattern (120 bp):
ATGTGATAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
GTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
Found at i:42817455 original size:47 final size:47
Alignment explanation
Indices: 42817369--42817688 Score: 498
Period size: 47 Copynumber: 6.7 Consensus size: 47
42817359 GTGTATATAT
42817369 ATGTGAT-AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
*
42817417 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* *
42817464 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
42817511 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
42817560 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
42817607 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
42817654 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
42817689 TCCCGAAGGG
Statistics
Matches: 253, Mismatches: 16, Indels: 7
0.92 0.06 0.03
Matches are distributed among these distances:
47 189 0.75
48 7 0.03
49 57 0.23
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:42817480 original size:96 final size:94
Alignment explanation
Indices: 42817369--42817688 Score: 498
Period size: 96 Copynumber: 3.4 Consensus size: 94
42817359 GTGTATATAT
42817369 ATGTGAT-AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
42817433 AGTGTATATATGTGATAAGGCCTAATAGCCG
64 AGTGTATATATGTGATAAGGCCTAATGGCCG
* *
42817464 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
42817529 TGTATATATATGTGATAAGGCCTAATGGCCG
66 TG--TATATATGTGATAAGGCCTAATGGCCG
42817560 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
* * * * *
42817625 TGTATATATGTGACAGGGCCGAGTGGCCA
66 TGTATATATGTGATAAGGCCTAATGGCCG
* * *
42817654 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
42817689 TCCCGAAGGG
Statistics
Matches: 209, Mismatches: 13, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
94 99 0.47
95 7 0.03
96 103 0.49
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (94 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
TGTATATATGTGATAAGGCCTAATGGCCG
Found at i:42817535 original size:143 final size:143
Alignment explanation
Indices: 42817369--42817688 Score: 565
Period size: 143 Copynumber: 2.3 Consensus size: 143
42817359 GTGTATATAT
42817369 ATGTGAT-AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
42817433 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
66 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAA
42817498 GGCCGAATGGCCA
131 GGCCGAATGGCCA
42817511 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
42817576 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAG
66 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAA
*
42817641 GGCCGAGTGGCCA
131 GGCCGAATGGCCA
* *
42817654 ACGTGATGGATGTGAAAGTGTATA-A-ATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
42817689 TCCCGAAGGG
Statistics
Matches: 171, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
141 10 0.06
142 8 0.05
143 153 0.89
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (143 bp):
ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAA
GGCCGAATGGCCA
Found at i:42822016 original size:51 final size:51
Alignment explanation
Indices: 42821882--42822077 Score: 200
Period size: 51 Copynumber: 3.9 Consensus size: 51
42821872 AGTGAAAGTG
* *
42821882 ATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGA-A-TG
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTA
* * * *
42821931 ATAGGTCGCATGTGTAGTACTATGTGCAGCCTACTATGCGTACCGGATAGT-
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTA
* * * * * *
42821982 TTCGATCACGTGTGTAGTACTATGTTCAGGCTACTACGTGTATCGGATGGTA
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTA
* ** * *
42822034 ATGGTCAAATGTGTAGTACTATGTATAGGCTACTATGTGAACCG
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCG
42822078 AACATCATTG
Statistics
Matches: 118, Mismatches: 25, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
49 2 0.02
50 39 0.33
51 75 0.64
52 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (51 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTA
Found at i:42822131 original size:45 final size:45
Alignment explanation
Indices: 42822080--42822167 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 45
42822070 GTGAACCGAA
* * *
42822080 CATCATTGATTAGTAAGGTGGTTGTTATGTGCT-AATTCCACCGGG
1 CATCATTGATTAATAAGGTGGTTGCTATGTACTGAA-TCCACCGGG
42822125 CATCATTGATTAATAAGGTGGTTGCTATGTACTGAATCCACCG
1 CATCATTGATTAATAAGGTGGTTGCTATGTACTGAATCCACCG
42822168 AGTATATGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
45 37 0.95
46 2 0.05
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (45 bp):
CATCATTGATTAATAAGGTGGTTGCTATGTACTGAATCCACCGGG
Found at i:42830458 original size:35 final size:35
Alignment explanation
Indices: 42830406--42830483 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 35
42830396 ATTTGTTGAT
* * * *
42830406 ATTCTGATTCACATGTTAAGCATGCCATTATTTTG
1 ATTCTGATACACATGTTAACCATGCCACTATTCTG
* *
42830441 ATTCTGATACACTTGTTAACCATGTCACTATTCTG
1 ATTCTGATACACATGTTAACCATGCCACTATTCTG
42830476 ATTCTGAT
1 ATTCTGAT
42830484 TCGTATGTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (35 bp):
ATTCTGATACACATGTTAACCATGCCACTATTCTG
Found at i:42830493 original size:35 final size:35
Alignment explanation
Indices: 42830406--42830494 Score: 99
Period size: 35 Copynumber: 2.5 Consensus size: 35
42830396 ATTTGTTGAT
* * * *
42830406 ATTCTGATTCACATGTTAAGCATGCCATTATTTTG
1 ATTCTGATTCATATGTTAACCATGCCACTATTCTG
* *
42830441 ATTCTGATACACT-TGTTAACCATGTCACTATTCTG
1 ATTCTGATTCA-TATGTTAACCATGCCACTATTCTG
*
42830476 ATTCTGATTCGTATGTTAA
1 ATTCTGATTCATATGTTAA
42830495 GTATGCAACT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
34 1 0.02
35 43 0.98
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.43
Consensus pattern (35 bp):
ATTCTGATTCATATGTTAACCATGCCACTATTCTG
Found at i:42832098 original size:22 final size:22
Alignment explanation
Indices: 42832073--42832123 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
42832063 GTTAATCTGT
42832073 CATTGATTTGTAGATAAACAAC
1 CATTGATTTGTAGATAAACAAC
* *
42832095 CATTGGTTTGTAGATAAACTAC
1 CATTGATTTGTAGATAAACAAC
*
42832117 CACTGAT
1 CATTGAT
42832124 AACACTAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (22 bp):
CATTGATTTGTAGATAAACAAC
Found at i:42833214 original size:15 final size:16
Alignment explanation
Indices: 42833194--42833226 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
42833184 TGGTTCGGCT
42833194 AAGGAGAAGG-GAAGA
1 AAGGAGAAGGTGAAGA
*
42833209 AAGGAGTAGGTGAAGA
1 AAGGAGAAGGTGAAGA
42833225 AA
1 AA
42833227 AATAGAACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.52, C:0.00, G:0.42, T:0.06
Consensus pattern (16 bp):
AAGGAGAAGGTGAAGA
Found at i:42837161 original size:28 final size:28
Alignment explanation
Indices: 42837096--42837165 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
42837086 TTTTTATTCT
* *
42837096 GAACCCCAAATCCTAAATCTTAAAATTA
1 GAACCCCAAACCCTAAATCTTAAAACTA
* * *
42837124 GAATCTCAAACCCTAAATCTT-AAACTC
1 GAACCCCAAACCCTAAATCTTAAAACTA
42837151 GTAACCCCAAACCCT
1 G-AACCCCAAACCCT
42837166 TAAACTTTGA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
27 5 0.15
28 29 0.85
ACGTcount: A:0.41, C:0.31, G:0.04, T:0.23
Consensus pattern (28 bp):
GAACCCCAAACCCTAAATCTTAAAACTA
Found at i:42837210 original size:26 final size:27
Alignment explanation
Indices: 42837173--42837231 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 27
42837163 CCTTAAACTT
* * *
42837173 TGAA-CTTAAAATTCAAACTCAAGCCC
1 TGAACCTTAAAATCCAAACCCAAACCC
*
42837199 TGAACCTT-AAATCCAAACCCAAACCT
1 TGAACCTTAAAATCCAAACCCAAACCC
42837225 TGAACCT
1 TGAACCT
42837232 CGAGGTTCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 25 0.89
27 3 0.11
ACGTcount: A:0.41, C:0.31, G:0.07, T:0.22
Consensus pattern (27 bp):
TGAACCTTAAAATCCAAACCCAAACCC
Found at i:42840016 original size:43 final size:43
Alignment explanation
Indices: 42839962--42840129 Score: 171
Period size: 43 Copynumber: 3.9 Consensus size: 43
42839952 TTTGATATGT
*
42839962 GATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGATTTGA
1 GATTTAGTGTAAGACCATGTCTGGGACATTGGCATCGATTTGA
* * ** * *
42840005 GAATTT-GTGTAAGACTACGTCTGGGATGTTGCCATCAATTTGA
1 G-ATTTAGTGTAAGACCATGTCTGGGACATTGGCATCGATTTGA
* *
42840048 GATTTACGTGTAAGACCATGTTTGGGACATTGGCATCG-TAT-A
1 GATTTA-GTGTAAGACCATGTCTGGGACATTGGCATCGATTTGA
* * * *
42840090 TGATTTAATGTAAGACCTTGTCTAGGACAGTGGCATCGAT
1 -GATTTAGTGTAAGACCATGTCTGGGACATTGGCATCGAT
42840130 AGTTGATTAC
Statistics
Matches: 101, Mismatches: 19, Indels: 10
0.78 0.15 0.08
Matches are distributed among these distances:
42 31 0.31
43 42 0.42
44 28 0.28
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (43 bp):
GATTTAGTGTAAGACCATGTCTGGGACATTGGCATCGATTTGA
Found at i:42840137 original size:43 final size:42
Alignment explanation
Indices: 42840051--42840150 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 42
42840041 AATTTGAGAT
* * * *
42840051 TTACGTGTAAGACCATGTTTGGGACATTGGCATCGTATATGA
1 TTACATGTAAGACCATGTCTAGGACAGTGGCATCGTATATGA
*
42840093 TTTA-ATGTAAGACCTTGTCTAGGACAGTGGCATCG-ATAGTTGA
1 -TTACATGTAAGACCATGTCTAGGACAGTGGCATCGTATA--TGA
42840136 TTACATGTAAGACCA
1 TTACATGTAAGACCA
42840151 CGTCCGAGAC
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
41 3 0.06
42 29 0.60
43 16 0.33
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (42 bp):
TTACATGTAAGACCATGTCTAGGACAGTGGCATCGTATATGA
Found at i:42842568 original size:31 final size:32
Alignment explanation
Indices: 42842531--42842590 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
42842521 CGGAAGCTTA
* *
42842531 ATTTAAAACAAA-TGATTTGCGAAAATGTGTT
1 ATTTAAAAAAAATTGAGTTGCGAAAATGTGTT
42842562 ATTTAAAAAAAATTGAGTTGCGAAAATGT
1 ATTTAAAAAAAATTGAGTTGCGAAAATGT
42842591 AGCATTTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 11 0.42
32 15 0.58
ACGTcount: A:0.45, C:0.05, G:0.17, T:0.33
Consensus pattern (32 bp):
ATTTAAAAAAAATTGAGTTGCGAAAATGTGTT
Found at i:42843255 original size:22 final size:22
Alignment explanation
Indices: 42843226--42843277 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
42843216 AATGTCTAAG
* *
42843226 AGCCATAAACAAGATAGCTATA
1 AGCCATAAACAAAATAGCTACA
* *
42843248 AGCTATAAACAAAATGGCTACA
1 AGCCATAAACAAAATAGCTACA
42843270 AGCCATAA
1 AGCCATAA
42843278 GTATAGTAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.50, C:0.19, G:0.13, T:0.17
Consensus pattern (22 bp):
AGCCATAAACAAAATAGCTACA
Found at i:42843403 original size:63 final size:64
Alignment explanation
Indices: 42843267--42843441 Score: 225
Period size: 63 Copynumber: 2.8 Consensus size: 64
42843257 CAAAATGGCT
* * *
42843267 ACAAGCCATAAGT-ATAGTAATATGATTGGCACAAAGCCATCAATAGCAGTAATATGATCGACAC
1 ACAAGCCATCAGTAATGGTAATATGATTGGCACAAAGCCATC-ATAGAAGTAATATGATCGACAC
42843331 ACAA-CCATCAGTAATGGTAATATGATTGGCACAAAGCCA-C-TAGTAATGTAATATGATCGACA
1 ACAAGCCATCAGTAATGGTAATATGATTGGCACAAAGCCATCATAG-AA-GTAATATGATCGACA
42843393 C
64 C
* * *
42843394 A-AAGCCATCAGTAACGGTAATATGATCGACACAAAGCCATCAGTAGAA
1 ACAAGCCATCAGTAATGGTAATATGATTGGCACAAAGCCATCA-TAGAA
42843442 TCGCAGCAAA
Statistics
Matches: 98, Mismatches: 6, Indels: 13
0.84 0.05 0.11
Matches are distributed among these distances:
61 3 0.03
62 3 0.03
63 57 0.58
64 30 0.31
65 2 0.02
66 3 0.03
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (64 bp):
ACAAGCCATCAGTAATGGTAATATGATTGGCACAAAGCCATCATAGAAGTAATATGATCGACAC
Found at i:42843414 original size:37 final size:32
Alignment explanation
Indices: 42843283--42843438 Score: 192
Period size: 32 Copynumber: 4.9 Consensus size: 32
42843273 CATAAGTATA
* * * * *
42843283 GTAATATGATTGGCACAAAGCCATCAATAGCA
1 GTAATATGATCGACACAAAGCCATCAGTAACG
*
42843315 GTAATATGATCGACACACAA-CCATCAGTAATG
1 GTAATATGATCGACACA-AAGCCATCAGTAACG
* * *
42843347 GTAATATGATTGGCACAAAGCCA-CTAGTAA-T
1 GTAATATGATCGACACAAAGCCATC-AGTAACG
42843378 GTAATATGATCGACACAAAGCCATCAGTAACG
1 GTAATATGATCGACACAAAGCCATCAGTAACG
42843410 GTAATATGATCGACACAAAGCCATCAGTA
1 GTAATATGATCGACACAAAGCCATCAGTA
42843439 GAATCGCAGC
Statistics
Matches: 107, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
31 29 0.27
32 76 0.71
33 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Consensus pattern (32 bp):
GTAATATGATCGACACAAAGCCATCAGTAACG
Found at i:42843515 original size:27 final size:26
Alignment explanation
Indices: 42843485--42843546 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 26
42843475 AAAGCTTCCC
42843485 GTAATAGTATATGTGGCCA-AGCCACCA
1 GTAATAGTAT-TGTGG-CAGAGCCACCA
*
42843512 GTAACAGTGATTGTGGCAGAGCCACCA
1 GTAATAGT-ATTGTGGCAGAGCCACCA
42843539 GT-ATAGTA
1 GTAATAGTA
42843547 CTTCCTCGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
25 1 0.03
26 6 0.19
27 22 0.71
28 2 0.06
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (26 bp):
GTAATAGTATTGTGGCAGAGCCACCA
Found at i:42843643 original size:24 final size:24
Alignment explanation
Indices: 42843616--42843667 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
42843606 TCAGAACTAG
42843616 TCATACAAATCACAGAAAAATCAA
1 TCATACAAATCACAGAAAAATCAA
* * *
42843640 TCATACCAATCACAGACAAATCAG
1 TCATACAAATCACAGAAAAATCAA
42843664 TCAT
1 TCAT
42843668 TTAAATCATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.25, G:0.06, T:0.19
Consensus pattern (24 bp):
TCATACAAATCACAGAAAAATCAA
Found at i:42843674 original size:24 final size:24
Alignment explanation
Indices: 42843622--42843718 Score: 104
Period size: 24 Copynumber: 4.0 Consensus size: 24
42843612 CTAGTCATAC
* **
42843622 AAATCACAGAAAAATCAATCATAC
1 AAATCACAGACAAATCAATCATTT
* *
42843646 CAATCACAGACAAATCAGTCATTT
1 AAATCACAGACAAATCAATCATTT
* * *
42843670 AAATCATAGACAAATTAGTCATTT
1 AAATCACAGACAAATCAATCATTT
* *
42843694 ACATCACGGACAAATCAATCATTT
1 AAATCACAGACAAATCAATCATTT
42843718 A
1 A
42843719 CACTCGAGGG
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.47, C:0.21, G:0.07, T:0.25
Consensus pattern (24 bp):
AAATCACAGACAAATCAATCATTT
Found at i:42843800 original size:27 final size:27
Alignment explanation
Indices: 42843726--42843782 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
42843716 TTACACTCGA
*
42843726 GGGG-CATTACGGTCATTTTACCTTAT
1 GGGGTCATTACGGTCATTTTACCCTAT
42843752 GGGGTCATTACGGTCATTTTACCCTAT
1 GGGGTCATTACGGTCATTTTACCCTAT
42843779 GGGG
1 GGGG
42843783 ATTTTTCGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 4 0.14
27 25 0.86
ACGTcount: A:0.18, C:0.19, G:0.28, T:0.35
Consensus pattern (27 bp):
GGGGTCATTACGGTCATTTTACCCTAT
Found at i:42846056 original size:97 final size:97
Alignment explanation
Indices: 42845945--42846153 Score: 328
Period size: 97 Copynumber: 2.2 Consensus size: 97
42845935 TTAAATTTTT
* * *
42845945 GTTATGAAATTTTAATGTTTAAATTGTTAATTAAATGAAAAGGATTAAATCGTAAAAATAGAAAA
1 GTTATGAAATTTTAATGTTTAAATGGTTAATTAAATGAAAAGGACTAAATCATAAAAATAGAAAA
* * *
42846010 ATTTAAGTTCTATTAGTTAAAAGGGTCAAATG
66 AGTTAAGTTATATTAGTTAAAAGAGTCAAATG
* * *
42846042 GTTATGAAATTTTAATGTTTAAATGGTTAATTAAATTAAAAGGACTAAATCATAAAAATGGTAAA
1 GTTATGAAATTTTAATGTTTAAATGGTTAATTAAATGAAAAGGACTAAATCATAAAAATAGAAAA
42846107 AGTTAAGTTATATTAGTTAAAAGAGTCAAATG
66 AGTTAAGTTATATTAGTTAAAAGAGTCAAATG
*
42846139 GCTATGAAATTTTAA
1 GTTATGAAATTTTAA
42846154 ACTAAGGGAC
Statistics
Matches: 102, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
97 102 1.00
ACGTcount: A:0.45, C:0.03, G:0.15, T:0.36
Consensus pattern (97 bp):
GTTATGAAATTTTAATGTTTAAATGGTTAATTAAATGAAAAGGACTAAATCATAAAAATAGAAAA
AGTTAAGTTATATTAGTTAAAAGAGTCAAATG
Found at i:42849900 original size:16 final size:17
Alignment explanation
Indices: 42849877--42849914 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
42849867 AATAAACAAT
42849877 TAAA-TAAATT-GGAAA
1 TAAATTAAATTGGGAAA
42849892 TAAATTAAATTGGGAAA
1 TAAATTAAATTGGGAAA
*
42849909 CAAATT
1 TAAATT
42849915 TCGGTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 4 0.20
16 6 0.30
17 10 0.50
ACGTcount: A:0.55, C:0.03, G:0.13, T:0.29
Consensus pattern (17 bp):
TAAATTAAATTGGGAAA
Done.