Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 93 of 198
Found at i:29639438 original size:13 final size:13
Alignment explanation
Indices: 29639415--29639439 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29639405 CAAATCCCCC
29639415 TCCAAAATCCTCA
1 TCCAAAATCCTCA
29639428 TCCAAAATCCTC
1 TCCAAAATCCTC
29639440 TGTTTTCTTT
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:0.36, C:0.40, G:0.00, T:0.24
Consensus pattern (13 bp):
TCCAAAATCCTCA
Found at i:29645449 original size:27 final size:27
Alignment explanation
Indices: 29645411--29645463 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
29645401 ACAGTACGAG
29645411 TTGGAATGAGTTCGTTGTCATCATTGC
1 TTGGAATGAGTTCGTTGTCATCATTGC
29645438 TTGGAATGAGTTCGTTGTCATCATTG
1 TTGGAATGAGTTCGTTGTCATCATTG
29645464 TGAACCACAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.19, C:0.13, G:0.26, T:0.42
Consensus pattern (27 bp):
TTGGAATGAGTTCGTTGTCATCATTGC
Found at i:29647166 original size:13 final size:13
Alignment explanation
Indices: 29647143--29647167 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29647133 CAAATCCCCC
29647143 TCCAAAATCCTCA
1 TCCAAAATCCTCA
29647156 TCCAAAATCCTC
1 TCCAAAATCCTC
29647168 TTTCTTTCTT
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:0.36, C:0.40, G:0.00, T:0.24
Consensus pattern (13 bp):
TCCAAAATCCTCA
Found at i:29662993 original size:27 final size:27
Alignment explanation
Indices: 29662958--29663022 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
29662948 AGCAGAGCTG
29662958 CCAGT-ACAGT-ATATGTGGCAAAGCCA
1 CCAGTAACAGTAAT-TGTGGCAAAGCCA
*
29662984 CCAGTAACAGTAATTGTGGCAGAGCCA
1 CCAGTAACAGTAATTGTGGCAAAGCCA
*
29663011 CCAGTAATAGTA
1 CCAGTAACAGTA
29663023 CTTCCTCCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
26 5 0.14
27 28 0.80
28 2 0.06
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (27 bp):
CCAGTAACAGTAATTGTGGCAAAGCCA
Found at i:29663185 original size:27 final size:26
Alignment explanation
Indices: 29663155--29663287 Score: 106
Period size: 27 Copynumber: 4.9 Consensus size: 26
29663145 TCAATTCCTA
*
29663155 GGGGTATAATAGTCATTTTACCCTAT-G
1 GGGGTAT-ATGGTCATTTTACCCT-TCG
* *
29663182 GGGGTATTTTGGTTATTTTACCCTTCG
1 GGGGTA-TATGGTCATTTTACCCTTCG
*
29663209 GGGGTATGTCGGTCATTTTACCCTTCG
1 GGGGTATAT-GGTCATTTTACCCTTCG
* * * *
29663236 AGGGTATTTCGATCATTTTACCTTTCG
1 GGGGTATAT-GGTCATTTTACCCTTCG
* * *
29663263 AGGATATTTGGGTCATTTTACCCTT
1 GGGGTATAT-GGTCATTTTACCCTT
29663288 TAAGGGTATT
Statistics
Matches: 90, Mismatches: 13, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
26 3 0.03
27 86 0.96
28 1 0.01
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.42
Consensus pattern (26 bp):
GGGGTATATGGTCATTTTACCCTTCG
Found at i:29663241 original size:54 final size:53
Alignment explanation
Indices: 29663166--29663405 Score: 162
Period size: 54 Copynumber: 4.5 Consensus size: 53
29663156 GGGTATAATA
* * * * * *
29663166 GTCATTTTACCCTATGGGGGTATTTTGGTTATTTTACCCTTCGGGGGTATGTCG
1 GTCATTTTACCCT-TGAGGGTATTTCGATCATTTTACCCTTCGAGGATATGTCG
* * *
29663220 GTCATTTTACCCTTCGAGGGTATTTCGATCATTTTACCTTTCGAGGATATTTGG
1 GTCATTTTACCCTT-GAGGGTATTTCGATCATTTTACCCTTCGAGGATATGTCG
* * * * *
29663274 GTCATTTTACCCTTTAAGGGTATTTCTG-TCATTTTACACATCGAGGGTATTTC-
1 GTCATTTTACCC-TTGAGGGTATTTC-GATCATTTTACCCTTCGAGGATATGTCG
*** * * * * * * * *
29663327 AAAATTTTACACCTCGGGGGTATTTCGATAATTTTACTCTT-TAGGGTATTTTG
1 GTCATTTTAC-CCTTGAGGGTATTTCGATCATTTTACCCTTCGAGGATATGTCG
* *
29663380 GTAATTTTACCCATCGAGGGTATTTC
1 GTCATTTTACCC-TTGAGGGTATTTC
29663406 AGTAATTTAC
Statistics
Matches: 150, Mismatches: 29, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
52 12 0.08
53 48 0.32
54 87 0.58
55 3 0.02
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.42
Consensus pattern (53 bp):
GTCATTTTACCCTTGAGGGTATTTCGATCATTTTACCCTTCGAGGATATGTCG
Found at i:29663641 original size:26 final size:26
Alignment explanation
Indices: 29663183--29663648 Score: 447
Period size: 26 Copynumber: 17.7 Consensus size: 26
29663173 TACCCTATGG
* * * *
29663183 GGGTATTTTGGTTATTTTACCCTTCGG
1 GGGTATTTCGG-TAATTTACCCATCGA
* * *
29663210 GGGTATGTCGGTCATTTTACCCTTCGA
1 GGGTATTTCGGT-AATTTACCCATCGA
* * **
29663237 GGGTATTTCGATCATTTTACCTTTCGA
1 GGGTATTTCGGT-AATTTACCCATCGA
* * * * **
29663264 GGATATTTGGGTCATTTTACCCTTTAA
1 GGGTATTTCGGT-AATTTACCCATCGA
* * *
29663291 GGGTATTTCTGTCATTTTACACATCGA
1 GGGTATTTCGGT-AATTTACCCATCGA
** *
29663318 GGGTATTTC-AAAATTTTACACC-TCGG
1 GGGTATTTCGGTAA-TTTAC-CCATCGA
* * **
29663344 GGGTATTTCGATAATTTTACTC-TTTA
1 GGGTATTTCGGTAA-TTTACCCATCGA
*
29663370 GGGTATTTTGGTAATTTTACCCATCGA
1 GGGTATTTCGGTAA-TTTACCCATCGA
*
29663397 GGGTATTTCAGTAATTTACCCATCGA
1 GGGTATTTCGGTAATTTACCCATCGA
29663423 GGGTATTTCGAG-AATTTACCCATCGA
1 GGGTATTTCG-GTAATTTACCCATCGA
* *
29663449 GGGTATTTCAAG-AATTTACCCATCGT
1 GGGTATTTC-GGTAATTTACCCATCGA
*
29663475 GGGTATTTCGATAATTTACCCATCGA
1 GGGTATTTCGGTAATTTACCCATCGA
*
29663501 GGGTATTTCAGTAATTTACCCATCGA
1 GGGTATTTCGGTAATTTACCCATCGA
*
29663527 GGGTATTTCGGTAATTTACCCATCAA
1 GGGTATTTCGGTAATTTACCCATCGA
* * * *
29663553 AGGTATTTCAGTAATTTACCTATCAA
1 GGGTATTTCGGTAATTTACCCATCGA
*
29663579 GGGTATTTCGGTAATTTACCCAACGA
1 GGGTATTTCGGTAATTTACCCATCGA
29663605 GGGTATTTCGGTAATTTACCCATCGA
1 GGGTATTTCGGTAATTTACCCATCGA
29663631 GGGTATTTCGGTAATTTA
1 GGGTATTTCGGTAATTTA
29663649 GGCCCATTAC
Statistics
Matches: 376, Mismatches: 55, Indels: 17
0.84 0.12 0.04
Matches are distributed among these distances:
25 1 0.00
26 254 0.68
27 121 0.32
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.38
Consensus pattern (26 bp):
GGGTATTTCGGTAATTTACCCATCGA
Found at i:29665533 original size:50 final size:50
Alignment explanation
Indices: 29665455--29665647 Score: 269
Period size: 50 Copynumber: 3.8 Consensus size: 50
29665445 ATTTGGGTAA
29665455 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* **
29665505 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGCTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* ** * * *
29665555 ATAGGTCCCCCGTAAGACCATGTCTGGGATATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** *
29665605 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
29665648 TGTTCTTGTC
Statistics
Matches: 122, Mismatches: 20, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
50 89 0.73
51 33 0.27
ACGTcount: A:0.25, C:0.23, G:0.31, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:29666240 original size:32 final size:32
Alignment explanation
Indices: 29666187--29666269 Score: 132
Period size: 32 Copynumber: 2.6 Consensus size: 32
29666177 ATGATGAATG
** *
29666187 GTTGTTA-AAATGGCTAAGTATGAAGGTGTTT
1 GTTGTTACAAATGTTTAGGTATGAAGGTGTTT
29666218 GTTGTTACAAATGTTTAGGTATGAAGGTGTTT
1 GTTGTTACAAATGTTTAGGTATGAAGGTGTTT
29666250 GTTGTTACAAATGTTTAGGT
1 GTTGTTACAAATGTTTAGGT
29666270 GATAAATCAT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
31 7 0.15
32 41 0.85
ACGTcount: A:0.27, C:0.04, G:0.28, T:0.42
Consensus pattern (32 bp):
GTTGTTACAAATGTTTAGGTATGAAGGTGTTT
Found at i:29673133 original size:51 final size:50
Alignment explanation
Indices: 29673011--29673141 Score: 163
Period size: 50 Copynumber: 2.6 Consensus size: 50
29673001 GGTAAAGATG
* * * * **
29673011 TCCCATGTAAGACCATTTCTGGGACATGCCATTGGCACCGAGATGATAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAAACA
** * *
29673061 TCCCCCGTAAGACCATGTCTGGGACATGGCATGGGTACCGATATGAGAACA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGA-AACA
29673112 TCCCATGTAAGACCATGTCTGGGACATGGC
1 TCCCATGTAAGACCATGTCTGGGACATGGC
29673142 TTTGGCATGT
Statistics
Matches: 68, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
50 39 0.57
51 29 0.43
ACGTcount: A:0.26, C:0.25, G:0.27, T:0.22
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAAACA
Found at i:29678900 original size:21 final size:21
Alignment explanation
Indices: 29678876--29678944 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
29678866 GAACTATAAT
29678876 CAACACACTCAGATGCATCCA
1 CAACACACTCAGATGCATCCA
*
29678897 CAACAAAGC-CAGATGCATCCA
1 CAACACA-CTCAGATGCATCCA
* * * * *
29678918 CACCAGAATCAGATGTAGCCA
1 CAACACACTCAGATGCATCCA
29678939 CAACAC
1 CAACAC
29678945 TCTTCAATGC
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
21 37 0.97
22 1 0.03
ACGTcount: A:0.41, C:0.35, G:0.13, T:0.12
Consensus pattern (21 bp):
CAACACACTCAGATGCATCCA
Found at i:29698521 original size:21 final size:21
Alignment explanation
Indices: 29698473--29698522 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
29698463 GGTGGCTAAA
* *
29698473 AATATTTTGTTTTGAAAAATC
1 AATATTTTCTTTTAAAAAATC
*
29698494 AAAATTTTCTTTTAAAAAATC
1 AATATTTTCTTTTAAAAAATC
*
29698515 ATTATTTT
1 AATATTTT
29698523 TCTTAAGAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.50
Consensus pattern (21 bp):
AATATTTTCTTTTAAAAAATC
Found at i:29699010 original size:3 final size:3
Alignment explanation
Indices: 29699002--29699030 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
29698992 AATAGAATAC
29699002 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
29699031 TTTTACTCTT
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:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:29699159 original size:3 final size:3
Alignment explanation
Indices: 29699153--29699196 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
29699143 TAATAATATT
*
29699153 TAG TAG TAG TAG TAG CAG TAG TAG TAG TAG TAG TAG TAG TAG TA
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TA
29699197 ATGATAATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.34, C:0.02, G:0.32, T:0.32
Consensus pattern (3 bp):
TAG
Found at i:29699693 original size:42 final size:42
Alignment explanation
Indices: 29699641--29699777 Score: 222
Period size: 42 Copynumber: 3.3 Consensus size: 42
29699631 CTTCATATAC
* *
29699641 AATGCAATGAAACGTAAATGGACCTCTC-CACCTGGGCCTCTA
1 AATGCAATGAAAAGTAAATGGACCTC-CACACCTAGGCCTCTA
* *
29699683 AATGCAATGAAAGGTAAATGGACCTCCACATCTAGGCCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTAGGCCTCTA
29699725 AATGCAATGAAAAGTAAATGGACCTCCACACCTAGGCCTCTA
1 AATGCAATGAAAAGTAAATGGACCTCCACACCTAGGCCTCTA
29699767 AATGCAATGAA
1 AATGCAATGAA
29699778 TGCTTTCCTT
Statistics
Matches: 89, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
41 1 0.01
42 88 0.99
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.20
Consensus pattern (42 bp):
AATGCAATGAAAAGTAAATGGACCTCCACACCTAGGCCTCTA
Found at i:29700215 original size:14 final size:15
Alignment explanation
Indices: 29700196--29700231 Score: 65
Period size: 14 Copynumber: 2.5 Consensus size: 15
29700186 TTTTTTTCCA
29700196 TTTTTTTGGTTTC-T
1 TTTTTTTGGTTTCGT
29700210 TTTTTTTGGTTTCGT
1 TTTTTTTGGTTTCGT
29700225 TTTTTTT
1 TTTTTTT
29700232 ATTCTTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.00, C:0.06, G:0.14, T:0.81
Consensus pattern (15 bp):
TTTTTTTGGTTTCGT
Found at i:29703811 original size:16 final size:15
Alignment explanation
Indices: 29703780--29703820 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
29703770 AAACGTTATA
29703780 AATTAATTTT-AATT
1 AATTAATTTTCAATT
29703794 AATTAACTTTTCAATT
1 AATTAA-TTTTCAATT
*
29703810 AAATAATTTTC
1 AATTAATTTTC
29703821 TCAACTCGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 6 0.25
15 9 0.38
16 9 0.38
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.51
Consensus pattern (15 bp):
AATTAATTTTCAATT
Found at i:29710364 original size:23 final size:23
Alignment explanation
Indices: 29710311--29710371 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
29710301 TATCAAGTTG
*
29710311 AACGGTAAGCTCCAT-AGAGCTAA
1 AACGGTAAGCT-CATAAGAACTAA
** *
29710334 AATAGTAAGCTCATAAGAACTGA
1 AACGGTAAGCTCATAAGAACTAA
29710357 AACGGTAAGCTCATA
1 AACGGTAAGCTCATA
29710372 TGAGCTATGG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
22 3 0.10
23 28 0.90
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.20
Consensus pattern (23 bp):
AACGGTAAGCTCATAAGAACTAA
Found at i:29717278 original size:22 final size:23
Alignment explanation
Indices: 29717253--29717337 Score: 77
Period size: 23 Copynumber: 3.7 Consensus size: 23
29717243 CAGTAAATAA
* *
29717253 TAAGCTCTATCGAGCTG-AACGG
1 TAAGCTCTATAGAGCTGAAACAG
*
29717275 TAAGCTCTGTAGAGCTGAAACAG
1 TAAGCTCTATAGAGCTGAAACAG
* **
29717298 TAAGCTC-ATAAGAGCTAAAATGG
1 TAAGCTCTAT-AGAGCTGAAACAG
29717321 TAAGCTCATATA-AGCTG
1 TAAGCTC-TATAGAGCTG
29717338 TGGTGAGTCC
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
22 16 0.31
23 32 0.63
24 1 0.02
25 2 0.04
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.24
Consensus pattern (23 bp):
TAAGCTCTATAGAGCTGAAACAG
Found at i:29723497 original size:42 final size:43
Alignment explanation
Indices: 29723450--29723535 Score: 147
Period size: 42 Copynumber: 2.0 Consensus size: 43
29723440 TTCTGAGGTG
*
29723450 TGATTTCGTGTAAGACCATGTCTGGGACATTGGCATC-ATATA
1 TGATTTCGTGTAAGACCATGTCTGGGACAGTGGCATCGATATA
*
29723492 TGATTTCGTGTAAGACCCTGTCTGGGACAGTGGCATCGATATA
1 TGATTTCGTGTAAGACCATGTCTGGGACAGTGGCATCGATATA
29723535 T
1 T
29723536 TATAACATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 35 0.85
43 6 0.15
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (43 bp):
TGATTTCGTGTAAGACCATGTCTGGGACAGTGGCATCGATATA
Found at i:29723549 original size:43 final size:42
Alignment explanation
Indices: 29723460--29723553 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 42
29723450 TGATTTCGTG
* ** * *
29723460 TAAGACCATGTCTGGGACATTGGCATCATATATGATTTCGTG
1 TAAGACCATGTCTGGGACAGTGGCATCATATATGATAACATA
* *
29723502 TAAGACCCTGTCTGGGACAGTGGCATCGATATATTATAACATA
1 TAAGACCATGTCTGGGACAGTGGCATC-ATATATGATAACATA
29723545 TAAGACCAT
1 TAAGACCAT
29723554 ATTTGGGATA
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
42 25 0.58
43 18 0.42
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (42 bp):
TAAGACCATGTCTGGGACAGTGGCATCATATATGATAACATA
Found at i:29723561 original size:43 final size:41
Alignment explanation
Indices: 29723460--29723569 Score: 112
Period size: 42 Copynumber: 2.6 Consensus size: 41
29723450 TGATTTCGTG
** * *
29723460 TAAGACCATGTCTGGGACATTGGCATCATATATGATTTCGTG
1 TAAGACCATGTCTGGGACA-TGGCATCATATATGATAACATA
* *
29723502 TAAGACCCTGTCTGGGACAGTGGCATCGATATATTATAACATA
1 TAAGACCATGTCTGGGACA-TGGCATC-ATATATGATAACATA
* * *
29723545 TAAGACCATATTTGGGATATGGCAT
1 TAAGACCATGTCTGGGACATGGCAT
29723570 TGTATAAGCT
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
42 31 0.55
43 25 0.45
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (41 bp):
TAAGACCATGTCTGGGACATGGCATCATATATGATAACATA
Found at i:29725197 original size:59 final size:59
Alignment explanation
Indices: 29725121--29725244 Score: 221
Period size: 59 Copynumber: 2.1 Consensus size: 59
29725111 TGGTATAATA
* * *
29725121 TAATTTGTTTTAACTTGTTATGTGAAAGTGCATAGGTATATAAAATGGTTCGTATTTGT
1 TAATTTGTTTTAACTTGTTATGTGAAAGTACACAGGTATATAAAATGGTTCATATTTGT
29725180 TAATTTGTTTTAACTTGTTATGTGAAAGTACACAGGTATATAAAATGGTTCATATTTGT
1 TAATTTGTTTTAACTTGTTATGTGAAAGTACACAGGTATATAAAATGGTTCATATTTGT
29725239 TAATTT
1 TAATTT
29725245 TTTATGTGAA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.31, C:0.06, G:0.18, T:0.46
Consensus pattern (59 bp):
TAATTTGTTTTAACTTGTTATGTGAAAGTACACAGGTATATAAAATGGTTCATATTTGT
Found at i:29725310 original size:48 final size:48
Alignment explanation
Indices: 29725177--29725319 Score: 193
Period size: 49 Copynumber: 3.0 Consensus size: 48
29725167 GGTTCGTATT
* * *
29725177 TGTTAATTTGTTTTAACTTGTTATGTGAAAGTACACAGGTATATAAAA
1 TGTTAATTTGTTTTAACTTGTTTTGTGAAAGTGCATAGGTATATAAAA
*
29725225 TGGTTCATATTTG--TTAA-TTTTTTATGTGAAAGTGCATAGGTATATAAAA
1 T-GTT-A-ATTTGTTTTAACTTGTTT-TGTGAAAGTGCATAGGTATATAAAA
29725274 TGTTAATTTGTTTTAACTTGTTTTGTGAAAGTGCATAGGTATATAA
1 TGTTAATTTGTTTTAACTTGTTTTGTGAAAGTGCATAGGTATATAA
29725320 TAGGTATATA
Statistics
Matches: 83, Mismatches: 5, Indels: 14
0.81 0.05 0.14
Matches are distributed among these distances:
46 5 0.06
47 1 0.01
48 35 0.42
49 36 0.43
50 1 0.01
51 5 0.06
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (48 bp):
TGTTAATTTGTTTTAACTTGTTTTGTGAAAGTGCATAGGTATATAAAA
Found at i:29728984 original size:23 final size:23
Alignment explanation
Indices: 29728954--29729002 Score: 82
Period size: 23 Copynumber: 2.1 Consensus size: 23
29728944 TTTTTCATGA
29728954 TTTTTATAAAATTTT-AATATGGT
1 TTTTTATAAAATTTTAAATAT-GT
29728977 TTTTTATAAAATTTTAAATATGT
1 TTTTTATAAAATTTTAAATATGT
29729000 TTT
1 TTT
29729003 ATTTTTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (23 bp):
TTTTTATAAAATTTTAAATATGT
Found at i:29729017 original size:13 final size:13
Alignment explanation
Indices: 29728999--29729024 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29728989 TTTAAATATG
29728999 TTTTATTTTTTAT
1 TTTTATTTTTTAT
29729012 TTTTATTTTTTAT
1 TTTTATTTTTTAT
29729025 AATTTATTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTATTTTTTAT
Found at i:29729083 original size:9 final size:9
Alignment explanation
Indices: 29729010--29729179 Score: 81
Period size: 9 Copynumber: 19.1 Consensus size: 9
29729000 TTTATTTTTT
29729010 ATTTTTAT-
1 ATTTTTATA
29729018 -TTTTTATA
1 ATTTTTATA
*
29729026 ATTTATTA-G
1 ATTT-TTATA
*
29729035 ATTTATTA-G
1 ATTT-TTATA
29729044 ATTTTTATA
1 ATTTTTATA
*
29729053 ATATTTATA
1 ATTTTTATA
29729062 ATATTTTAT-
1 AT-TTTTATA
29729071 ATTTTTATA
1 ATTTTTATA
*
29729080 ATTTTCATA
1 ATTTTTATA
**
29729089 AGTTCATATCA
1 A-TTTTTAT-A
* *
29729100 CTTTTCAT-
1 ATTTTTATA
29729108 ATTTTTA-A
1 ATTTTTATA
29729116 ATATTTT-TA
1 AT-TTTTATA
* *
29729125 ATATTTAATC
1 AT-TTTTATA
29729135 ATTTTTAT-
1 ATTTTTATA
*
29729143 TTTTTTATA
1 ATTTTTATA
* *
29729152 ATTTTTGTG
1 ATTTTTATA
29729161 ATTTTTA-A
1 ATTTTTATA
29729169 TATTTTTATA
1 -ATTTTTATA
29729179 A
1 A
29729180 ACAGAATATT
Statistics
Matches: 124, Mismatches: 23, Indels: 29
0.70 0.13 0.16
Matches are distributed among these distances:
7 7 0.06
8 23 0.19
9 73 0.59
10 20 0.16
11 1 0.01
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (9 bp):
ATTTTTATA
Found at i:29729084 original size:36 final size:36
Alignment explanation
Indices: 29728977--29729174 Score: 111
Period size: 36 Copynumber: 5.7 Consensus size: 36
29728967 TTAATATGGT
*
29728977 TTTTTATAAAATTT-TAAATATGTTT-TATTTTT-T-A
1 TTTTTATAATATTTAT-AATAT-TTTATATTTTTATAA
* * *
29729011 TTTTTAT--TTTTTATAAT-TTATTAGATTTATTA-GA
1 TTTTTATAATATTTATAATATT-TTATATTT-TTATAA
29729045 TTTTTATAATATTTATAATATTTTATATTTTTATAA
1 TTTTTATAATATTTATAATATTTTATATTTTTATAA
* * *
29729081 TTTTCATAA-GTTCAT-ATCACTTTTCATATTTTTA-AA
1 TTTTTATAATATTTATAAT-A-TTTT-ATATTTTTATAA
* *
29729117 TATTTT-TAATATTTAATCAT-TTTTATTTTTTTATAA
1 T-TTTTATAATATTT-ATAATATTTTATATTTTTATAA
* *
29729153 TTTTTGTGAT-TTT-TAATATTTT
1 TTTTTATAATATTTATAATATTTT
29729175 TATAAACAGA
Statistics
Matches: 129, Mismatches: 15, Indels: 40
0.70 0.08 0.22
Matches are distributed among these distances:
30 1 0.01
31 3 0.02
32 10 0.08
33 6 0.05
34 21 0.16
35 23 0.18
36 45 0.35
37 16 0.12
38 2 0.02
39 2 0.02
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (36 bp):
TTTTTATAATATTTATAATATTTTATATTTTTATAA
Found at i:29729849 original size:24 final size:23
Alignment explanation
Indices: 29729817--29729863 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
29729807 TTTCAATAAA
29729817 TAATTTTAAAAATTAAAAAACAT
1 TAATTTTAAAAATTAAAAAACAT
*
29729840 TAATATTTAAAATTTAAAAAACAT
1 TAAT-TTTAAAAATTAAAAAACAT
29729864 ATAAAAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (23 bp):
TAATTTTAAAAATTAAAAAACAT
Found at i:29732078 original size:42 final size:42
Alignment explanation
Indices: 29731996--29732080 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
29731986 AAAAAGAAAC
*
29731996 AGAAAAGCATCAGATAAGTTGGCTCCACTAATCCCAAATTTG
1 AGAAAAGCATCAGATAAGTTGGCTCCACTAATACCAAATTTG
* * *
29732038 AGAAAAGCATCAGATTAGTTGGCTCCGA-TAATATCGAATTTG
1 AGAAAAGCATCAGATAAGTTGGCTCC-ACTAATACCAAATTTG
29732080 A
1 A
29732081 AAGCTTTTCT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 37 0.97
43 1 0.03
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.26
Consensus pattern (42 bp):
AGAAAAGCATCAGATAAGTTGGCTCCACTAATACCAAATTTG
Found at i:29734928 original size:2 final size:2
Alignment explanation
Indices: 29734921--29734953 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
29734911 ACAATGCACT
*
29734921 AG AG AG AG AG AG AG AG AG AA AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
29734954 TGGGGGGGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:29737322 original size:80 final size:80
Alignment explanation
Indices: 29737189--29737337 Score: 244
Period size: 80 Copynumber: 1.9 Consensus size: 80
29737179 TACAATGAGG
* * *
29737189 GTTTAAATTTCGATTAAAATTAAATTAATCAACCAAATCAATTTAATTTAGTTAATCAATCGATT
1 GTTTAAATTTCGATTAAAACTAAATTAATCAACCAAACCAATCTAATTTAGTTAATCAATCGATT
29737254 AATTTTAGTAAGAGT
66 AATTTTAGTAAGAGT
* * *
29737269 GTTTAAATTTCGATTAGAACTAAATTAATCAATCAAACCAATCTAATTTAGTTAATCAGTCGATT
1 GTTTAAATTTCGATTAAAACTAAATTAATCAACCAAACCAATCTAATTTAGTTAATCAATCGATT
29737334 AATT
66 AATT
29737338 GATCTAATTT
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 63 1.00
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.39
Consensus pattern (80 bp):
GTTTAAATTTCGATTAAAACTAAATTAATCAACCAAACCAATCTAATTTAGTTAATCAATCGATT
AATTTTAGTAAGAGT
Found at i:29737846 original size:22 final size:24
Alignment explanation
Indices: 29737801--29737846 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
29737791 AAATAATTTC
*
29737801 ATAAAAATAACATTCTTTTGAATA
1 ATAAAAATAACATTCTTTTAAATA
*
29737825 ATAAAAATCACA-T-TTTTAAATA
1 ATAAAAATAACATTCTTTTAAATA
29737847 CAATTAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 8 0.40
23 1 0.05
24 11 0.55
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.37
Consensus pattern (24 bp):
ATAAAAATAACATTCTTTTAAATA
Found at i:29742840 original size:29 final size:29
Alignment explanation
Indices: 29742807--29742867 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
29742797 TCAAATATTT
29742807 ATTGCGTAAAGCAAAAATTAAATAATAAG
1 ATTGCGTAAAGCAAAAATTAAATAATAAG
*
29742836 ATTGCGTAAAGCAGAAATTAAATAATAAG
1 ATTGCGTAAAGCAAAAATTAAATAATAAG
29742865 ATT
1 ATT
29742868 CATCATAGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.52, C:0.07, G:0.15, T:0.26
Consensus pattern (29 bp):
ATTGCGTAAAGCAAAAATTAAATAATAAG
Found at i:29756394 original size:50 final size:50
Alignment explanation
Indices: 29756327--29756463 Score: 184
Period size: 50 Copynumber: 2.7 Consensus size: 50
29756317 GGGAATGAGA
* * * **
29756327 TCCCATGTAAGACCATGTCTGGGACATTGCGTTGGCACCGAGATGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAAC
* * *
29756377 TCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAAC
* *
29756427 TCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA
29756464 TGTTATTATC
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 75 1.00
ACGTcount: A:0.24, C:0.25, G:0.29, T:0.22
Consensus pattern (50 bp):
TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAAC
Found at i:29760135 original size:24 final size:25
Alignment explanation
Indices: 29760088--29760138 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
29760078 AGAAACATAC
*
29760088 TTAAAAATTCATGCGAAATCCCTTA
1 TTAAAAATTCATGCAAAATCCCTTA
*
29760113 TTAAAAATTCATGCAAAATCCTTTA
1 TTAAAAATTCATGCAAAATCCCTTA
29760138 T
1 T
29760139 CCCCCTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (25 bp):
TTAAAAATTCATGCAAAATCCCTTA
Found at i:29762401 original size:6 final size:6
Alignment explanation
Indices: 29762387--29762449 Score: 65
Period size: 6 Copynumber: 10.5 Consensus size: 6
29762377 CCTTTATTAA
* * * * *
29762387 AAAAAT AAAACT AAAATT AAAATT AAAAAT AAAGATT AAAATT GAAACT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAA-ATT AAAATT AAAATT
29762436 -AAATT AAAATT AAA
1 AAAATT AAAATT AAA
29762450 GACAAAGATA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
5 4 0.08
6 39 0.81
7 5 0.10
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.25
Consensus pattern (6 bp):
AAAATT
Found at i:29762415 original size:19 final size:19
Alignment explanation
Indices: 29762393--29762449 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
29762383 TTAAAAAAAT
29762393 AAAACTAAAATTAAAATTA
1 AAAACTAAAATTAAAATTA
29762412 AAAA-TAAAGATTAAAATT-
1 AAAACTAAA-ATTAAAATTA
*
29762430 GAAACT-AAATTAAAATTA
1 AAAACTAAAATTAAAATTA
29762448 AA
1 AA
29762450 GACAAAGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
17 9 0.27
18 10 0.30
19 14 0.42
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.26
Consensus pattern (19 bp):
AAAACTAAAATTAAAATTA
Found at i:29762440 original size:36 final size:37
Alignment explanation
Indices: 29762394--29762498 Score: 110
Period size: 36 Copynumber: 2.9 Consensus size: 37
29762384 TAAAAAAATA
* *
29762394 AAACTAAAATTAAAATTAAAAATAAAGATTAAAATTG
1 AAACTAAAATTAAAATTAAAAACAAAGATAAAAATTG
*
29762431 AAACT-AAATTAAAATTAAAGACAAAGATAAAAA-TG
1 AAACTAAAATTAAAATTAAAAACAAAGATAAAAATTG
* * * *
29762466 AGAAATAAAAATAAAACT-AAGA-AAAGATAAAAA
1 A-AACTAAAATTAAAATTAAAAACAAAGATAAAAA
29762499 CGAATTAAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
35 14 0.23
36 32 0.53
37 14 0.23
ACGTcount: A:0.69, C:0.04, G:0.08, T:0.20
Consensus pattern (37 bp):
AAACTAAAATTAAAATTAAAAACAAAGATAAAAATTG
Found at i:29767736 original size:37 final size:37
Alignment explanation
Indices: 29767667--29767739 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 37
29767657 CGCAATGAGT
* *
29767667 ATGGAAACAATTTTAACCTGAGTGTATCTTCAGTCAA
1 ATGGAAACAATTTTAACCTCAGTGCATCTTCAGTCAA
* *
29767704 ATGGAAACAATTTTAACCTCATTGCATTTTCAGTCA
1 ATGGAAACAATTTTAACCTCAGTGCATCTTCAGTCA
29767740 CACTAGCTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (37 bp):
ATGGAAACAATTTTAACCTCAGTGCATCTTCAGTCAA
Found at i:29770192 original size:6 final size:6
Alignment explanation
Indices: 29770181--29770208 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
29770171 CCACTTAAGG
29770181 AAGAGA AAGAGA AAGAGA AAGAGA AAGA
1 AAGAGA AAGAGA AAGAGA AAGAGA AAGA
29770209 AGAACCCCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (6 bp):
AAGAGA
Found at i:29776647 original size:17 final size:17
Alignment explanation
Indices: 29776625--29776659 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
29776615 CACGGGCTGT
29776625 CACATGGCC-GTGTGACA
1 CACATGGCCTG-GTGACA
29776642 CACATGGCCTGGTGACA
1 CACATGGCCTGGTGACA
29776659 C
1 C
29776660 GGTTGTGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.94
18 1 0.06
ACGTcount: A:0.23, C:0.31, G:0.29, T:0.17
Consensus pattern (17 bp):
CACATGGCCTGGTGACA
Found at i:29788091 original size:18 final size:19
Alignment explanation
Indices: 29788068--29788103 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
29788058 CAAGGTACCA
29788068 AAAAAT-ATTTAAATAAAT
1 AAAAATAATTTAAATAAAT
*
29788086 AAAAATAATTTAAGTAAA
1 AAAAATAATTTAAATAAA
29788104 AATTAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (19 bp):
AAAAATAATTTAAATAAAT
Found at i:29796993 original size:24 final size:24
Alignment explanation
Indices: 29796961--29797006 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
29796951 TAATTATTTT
*
29796961 AAATTAAGGGCAATGTATGTTCCA
1 AAATTAAGGGCAATGTACGTTCCA
29796985 AAATTAAGGGCAATGTACGTTC
1 AAATTAAGGGCAATGTACGTTC
29797007 GTGTGTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (24 bp):
AAATTAAGGGCAATGTACGTTCCA
Found at i:29801200 original size:17 final size:17
Alignment explanation
Indices: 29801178--29801229 Score: 63
Period size: 17 Copynumber: 3.0 Consensus size: 17
29801168 TTATATTTCC
29801178 TATTTTAATTTTTGT-TT
1 TATTTTAATTTTT-TATT
29801195 TATTTTAAATTTTTTCATT
1 TATTTT-AATTTTTT-ATT
29801214 TATTTT-ATTTTTTATT
1 TATTTTAATTTTTTATT
29801230 AATCTTAGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
16 3 0.09
17 14 0.44
18 7 0.22
19 8 0.25
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (17 bp):
TATTTTAATTTTTTATT
Found at i:29808086 original size:22 final size:22
Alignment explanation
Indices: 29808058--29808108 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
29808048 CATGCCAATA
29808058 GGGTTTGAACGCGGACTTGTAT
1 GGGTTTGAACGCGGACTTGTAT
*
29808080 GGGTTTGAACGCGGACTTTTAT
1 GGGTTTGAACGCGGACTTGTAT
29808102 GGGTTTG
1 GGGTTTG
29808109 CACTTCGGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.16, C:0.12, G:0.37, T:0.35
Consensus pattern (22 bp):
GGGTTTGAACGCGGACTTGTAT
Found at i:29808150 original size:20 final size:20
Alignment explanation
Indices: 29808106--29808144 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
29808096 TTTTATGGGT
29808106 TTGCACTTCGGTGCCTCTGA
1 TTGCACTTCGGTGCCTCTGA
29808126 TTGCACATTC-GTGCCTCTG
1 TTGCAC-TTCGGTGCCTCTG
29808145 TCTGCATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.10, C:0.31, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCACTTCGGTGCCTCTGA
Found at i:29816508 original size:26 final size:28
Alignment explanation
Indices: 29816451--29816510 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 28
29816441 CCCCTAATAT
* *
29816451 AATAAAAAAGAGAAGAAAAAGAAAAACT
1 AATAAAAAAGAGAAGAAAAACAAAAACA
**
29816479 AATAAAAAAG-G-AGAAAAACAAGTACA
1 AATAAAAAAGAGAAGAAAAACAAAAACA
29816505 AATAAA
1 AATAAA
29816511 TATCTTTGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 17 0.61
27 1 0.04
28 10 0.36
ACGTcount: A:0.73, C:0.05, G:0.13, T:0.08
Consensus pattern (28 bp):
AATAAAAAAGAGAAGAAAAACAAAAACA
Found at i:29827258 original size:10 final size:10
Alignment explanation
Indices: 29827245--29827279 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
29827235 TTGTGACTAA
*
29827245 ATGTGCTCAT
1 ATGTGCTTAT
*
29827255 ATGTGATTAT
1 ATGTGCTTAT
29827265 ATGTGCTTAT
1 ATGTGCTTAT
29827275 ATGTG
1 ATGTG
29827280 GATAGTACAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.46
Consensus pattern (10 bp):
ATGTGCTTAT
Found at i:29833780 original size:50 final size:50
Alignment explanation
Indices: 29833720--29833891 Score: 272
Period size: 50 Copynumber: 3.4 Consensus size: 50
29833710 CTACCAATTT
* ** * *
29833720 CATGTCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGC
1 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGC
** *
29833770 CATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGC
1 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGC
29833820 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGC
1 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGC
29833870 CATGTCCCAGACATGGTCTTAC
1 CATGTCCCAGACATGGTCTTAC
29833892 GTGTGATCTC
Statistics
Matches: 111, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 111 1.00
ACGTcount: A:0.20, C:0.31, G:0.23, T:0.26
Consensus pattern (50 bp):
CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGC
Found at i:29836549 original size:36 final size:36
Alignment explanation
Indices: 29836509--29836598 Score: 180
Period size: 36 Copynumber: 2.5 Consensus size: 36
29836499 TTTAAAAAAT
29836509 CTTGAGCTAGTTCTTTTTCGGTGTGAAGAGACTAAC
1 CTTGAGCTAGTTCTTTTTCGGTGTGAAGAGACTAAC
29836545 CTTGAGCTAGTTCTTTTTCGGTGTGAAGAGACTAAC
1 CTTGAGCTAGTTCTTTTTCGGTGTGAAGAGACTAAC
29836581 CTTGAGCTAGTTCTTTTT
1 CTTGAGCTAGTTCTTTTT
29836599 GAAGGTATTG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.40
Consensus pattern (36 bp):
CTTGAGCTAGTTCTTTTTCGGTGTGAAGAGACTAAC
Found at i:29840128 original size:23 final size:22
Alignment explanation
Indices: 29840102--29840157 Score: 53
Period size: 21 Copynumber: 2.5 Consensus size: 22
29840092 ATGCTTTTTT
29840102 CATTTTTACATGTGTCTTTCA-TG
1 CATTTTTACAT-TGT-TTTCATTG
**
29840125 CATTCATA-ATTGTTTTCATTG
1 CATTTTTACATTGTTTTCATTG
29840146 CATTTTCTACAT
1 CATTTT-TACAT
29840158 ATCTATTTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
20 5 0.19
21 9 0.35
22 4 0.15
23 8 0.31
ACGTcount: A:0.21, C:0.18, G:0.09, T:0.52
Consensus pattern (22 bp):
CATTTTTACATTGTTTTCATTG
Found at i:29854781 original size:12 final size:12
Alignment explanation
Indices: 29854756--29854794 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
29854746 ACTCGCTTCT
* *
29854756 TTACTTACTCAC
1 TTACTTGCTTAC
*
29854768 TTACTTGTTTAC
1 TTACTTGCTTAC
29854780 TTACTTGCTTAC
1 TTACTTGCTTAC
29854792 TTA
1 TTA
29854795 AATAACTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:29855119 original size:50 final size:50
Alignment explanation
Indices: 29855045--29855239 Score: 185
Period size: 50 Copynumber: 3.8 Consensus size: 50
29855035 CTCTGTACTA
* * * **
29855045 CCAATGTCATGCCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTG
* * *
29855095 CCTATGCCATGTCCCAGACATGGTCTTAC-GGAGGACCTCTCATCTCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATG-GGACCTCTCATATCGGTG
** * * *
29855145 CCAACACCATGTCCCGGACATGGTCTTACATGGGACCTCTCATAATCTTAATGAG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-ATC----GGTG
* * *
29855200 CCAATGTCATGTCCCAGACATGGTCTTACATTGGATCTCT
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
29855240 TTCCCCAAAT
Statistics
Matches: 116, Mismatches: 22, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
49 1 0.01
50 76 0.66
51 3 0.03
55 36 0.31
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (50 bp):
CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTG
Found at i:29862346 original size:12 final size:12
Alignment explanation
Indices: 29862321--29862359 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
29862311 ACTCGCTTCT
* *
29862321 TTACTTACTCAC
1 TTACTTGCTTAC
*
29862333 TTACTTGTTTAC
1 TTACTTGCTTAC
29862345 TTACTTGCTTAC
1 TTACTTGCTTAC
29862357 TTA
1 TTA
29862360 AATAACTCAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:29878923 original size:34 final size:34
Alignment explanation
Indices: 29878880--29878948 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
29878870 CGTCTTAGGT
29878880 TTGAAACAATTTAATCACACAAATCTAAAAACTA
1 TTGAAACAATTTAATCACACAAATCTAAAAACTA
29878914 TTGAAACAATTTAATCACACAAATCTAAAAACTA
1 TTGAAACAATTTAATCACACAAATCTAAAAACTA
29878948 T
1 T
29878949 GTAGATAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.52, C:0.17, G:0.03, T:0.28
Consensus pattern (34 bp):
TTGAAACAATTTAATCACACAAATCTAAAAACTA
Found at i:29879971 original size:14 final size:14
Alignment explanation
Indices: 29879952--29879979 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
29879942 CCAATTTATT
29879952 AATGAATTATTAAA
1 AATGAATTATTAAA
29879966 AATGAATTATTAAA
1 AATGAATTATTAAA
29879980 TATAACTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
AATGAATTATTAAA
Found at i:29880803 original size:29 final size:29
Alignment explanation
Indices: 29880761--29880846 Score: 136
Period size: 29 Copynumber: 3.0 Consensus size: 29
29880751 GTGTGCTAAA
29880761 CGATGGTCGAAACCATCCCTTTTCATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
29880790 CGATGGTCGAAACCATCCCTTTTCATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
* * **
29880819 CTATGGTCGTAACCATCATTTTTCATAT
1 CGATGGTCGAAACCATCCCTTTTCATAT
29880847 ATGCTCATAT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.24, C:0.26, G:0.13, T:0.37
Consensus pattern (29 bp):
CGATGGTCGAAACCATCCCTTTTCATATT
Found at i:29883690 original size:50 final size:51
Alignment explanation
Indices: 29883595--29883729 Score: 175
Period size: 50 Copynumber: 2.7 Consensus size: 51
29883585 CCAAACACCA
* * * *
29883595 TTTGTGGACAAGCCACCACTGATTTGCATATA-AACTACCACTGATAACAC
1 TTTGTGGACAAGCCACCATTGATATGCAGATATACCTACCACTGATAACAC
* * *
29883645 TTTGTGGACAAGCCACCATTGATATGCAGATATACCT-CTATTGATAACAT
1 TTTGTGGACAAGCCACCATTGATATGCAGATATACCTACCACTGATAACAC
* *
29883695 TTTGTGGATAAGCCACCATTGATATGAAGATATAC
1 TTTGTGGACAAGCCACCATTGATATGCAGATATAC
29883730 TGCCACTTAC
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
50 72 0.96
51 3 0.04
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (51 bp):
TTTGTGGACAAGCCACCATTGATATGCAGATATACCTACCACTGATAACAC
Found at i:29888762 original size:20 final size:21
Alignment explanation
Indices: 29888739--29888781 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
29888729 CAATTTAAAA
29888739 TATAAAAAATTATTAAT-ATG
1 TATAAAAAATTATTAATAATG
* *
29888759 TATATAAATTTATTAATAATG
1 TATAAAAAATTATTAATAATG
29888780 TA
1 TA
29888782 AAAGAAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (21 bp):
TATAAAAAATTATTAATAATG
Found at i:29888905 original size:20 final size:20
Alignment explanation
Indices: 29888876--29888913 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
29888866 ATATTTTCAC
29888876 TAAATCATTTTCCAGAAAAG
1 TAAATCATTTTCCAGAAAAG
*
29888896 TAAATTATTTTCCAGAAA
1 TAAATCATTTTCCAGAAA
29888914 TCATTTTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.13, G:0.08, T:0.34
Consensus pattern (20 bp):
TAAATCATTTTCCAGAAAAG
Found at i:29893051 original size:18 final size:18
Alignment explanation
Indices: 29893028--29893067 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
29893018 CTTTAGGAAT
*
29893028 TAATTAATTTTAATAATG
1 TAATTAATTTTAATAATA
* *
29893046 TAATTATTTTTCATAATA
1 TAATTAATTTTAATAATA
29893064 TAAT
1 TAAT
29893068 CATTATTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (18 bp):
TAATTAATTTTAATAATA
Found at i:29904262 original size:34 final size:34
Alignment explanation
Indices: 29904219--29904286 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
29904209 CTGAAGTGGA
29904219 GTAGATTGAAGCTGTAGGCATCGAATCCTATCTC
1 GTAGATTGAAGCTGTAGGCATCGAATCCTATCTC
29904253 GTAGATTGAAGCTGTAGGCATCGAATCCTATCTC
1 GTAGATTGAAGCTGTAGGCATCGAATCCTATCTC
29904287 TTTGGCATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (34 bp):
GTAGATTGAAGCTGTAGGCATCGAATCCTATCTC
Found at i:29904739 original size:45 final size:44
Alignment explanation
Indices: 29904688--29904797 Score: 114
Period size: 45 Copynumber: 2.5 Consensus size: 44
29904678 GAAAATGGCG
*
29904688 AATCTTATCTCCCTGAAGTTGCAGGG-GAGCAGACTCAATAAAGCA
1 AATCTTATCTCCCTGAAGTTGCAGGGAG-GCAGACTAAATAAA-CA
* * * * *
29904733 AGTCTTATCCCCCTGAAATTGTAGTGAGGCAGACTAAATAAACA
1 AATCTTATCTCCCTGAAGTTGCAGGGAGGCAGACTAAATAAACA
* * *
29904777 AATCCTGTCTCCCTAAAGTTG
1 AATCTTATCTCCCTGAAGTTG
29904798 TAGTGGAGTG
Statistics
Matches: 52, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
44 17 0.33
45 34 0.65
46 1 0.02
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGGGAGGCAGACTAAATAAACA
Found at i:29906417 original size:18 final size:18
Alignment explanation
Indices: 29906394--29906433 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
29906384 CTTTAGGAAT
*
29906394 TAATTAATTTTAATAATG
1 TAATTAATTTTAATAATA
* *
29906412 TAATTATTTTTCATAATA
1 TAATTAATTTTAATAATA
29906430 TAAT
1 TAAT
29906434 CATTATTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (18 bp):
TAATTAATTTTAATAATA
Found at i:29906717 original size:2 final size:2
Alignment explanation
Indices: 29906710--29906738 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29906700 TATACCTACC
29906710 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29906739 CTTCTTTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29918012 original size:26 final size:25
Alignment explanation
Indices: 29917943--29918012 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 25
29917933 TTTTTATCCT
*
29917943 TATTTTACCCCCAATAAATTTTTAA
1 TATTTTACCCCTAATAAATTTTTAA
* ** *
29917968 TAATTTTACCCTTGGTAAATTTTTTAC
1 T-ATTTTACCCCTAATAAA-TTTTTAA
29917995 TATTTTACCCCTAATAAA
1 TATTTTACCCCTAATAAA
29918013 AGTTCGAGAA
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
25 1 0.03
26 27 0.77
27 7 0.20
ACGTcount: A:0.33, C:0.19, G:0.03, T:0.46
Consensus pattern (25 bp):
TATTTTACCCCTAATAAATTTTTAA
Found at i:29928060 original size:40 final size:41
Alignment explanation
Indices: 29927992--29928103 Score: 109
Period size: 40 Copynumber: 2.7 Consensus size: 41
29927982 ATTTCTGAGG
* ** *
29927992 TATGATTTCGTGTAAGACCATGTTTGGGACATTGGCATCTA
1 TATGATTTCGTGTAAGACCATGTCTGGGACAGAGGCATCGA
* *
29928033 TATGA-TTCGTGTACGACCCTGTCTGGGACAGAGGCATCGA
1 TATGATTTCGTGTAAGACCATGTCTGGGACAGAGGCATCGA
** * *
29928073 TATGTGATAACATGTAAGACCATATCTGGGA
1 TA--TGATTTCGTGTAAGACCATGTCTGGGA
29928104 TATGGCATTG
Statistics
Matches: 56, Mismatches: 12, Indels: 4
0.78 0.17 0.06
Matches are distributed among these distances:
40 31 0.55
41 5 0.09
42 3 0.05
43 17 0.30
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (41 bp):
TATGATTTCGTGTAAGACCATGTCTGGGACAGAGGCATCGA
Found at i:29945035 original size:35 final size:35
Alignment explanation
Indices: 29944970--29945036 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
29944960 TACGTTATAA
*
29944970 AAAAATATATTCAATTATTTATTTTGTTTTCTCTT
1 AAAAATATATTAAATTATTTATTTTGTTTTCTCTT
29945005 AAAAAT-TATTAAATTCATATTATTTT-TTTTCT
1 AAAAATATATTAAATT-AT-TTATTTTGTTTTCT
29945037 TTTTACTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 8 0.28
35 14 0.48
36 7 0.24
ACGTcount: A:0.34, C:0.07, G:0.01, T:0.57
Consensus pattern (35 bp):
AAAAATATATTAAATTATTTATTTTGTTTTCTCTT
Found at i:29945320 original size:5 final size:5
Alignment explanation
Indices: 29945310--29945345 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
29945300 CAAAAACACA
*
29945310 TTCTT TTCTT TTCTT TTC-T TTCTT TTTTT TTCTT TT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TT
29945346 TTGGGTGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTCTT
Found at i:29945333 original size:14 final size:14
Alignment explanation
Indices: 29945314--29945344 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
29945304 AACACATTCT
29945314 TTTCTTTTCTTTTC
1 TTTCTTTTCTTTTC
*
29945328 TTTCTTTTTTTTTC
1 TTTCTTTTCTTTTC
29945342 TTT
1 TTT
29945345 TTTGGGTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTCTTTTCTTTTC
Found at i:29953584 original size:22 final size:22
Alignment explanation
Indices: 29953546--29953596 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
29953536 TCTGCTTTCG
29953546 GAAA-GAAAAAAAAAAGAAAAA
1 GAAAGGAAAAAAAAAAGAAAAA
* * *
29953567 GAAAGGAAAAAGAGAAGAGAAA
1 GAAAGGAAAAAAAAAAGAAAAA
*
29953589 GAAGGGAA
1 GAAAGGAA
29953597 TTGATGCCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (22 bp):
GAAAGGAAAAAAAAAAGAAAAA
Found at i:29956560 original size:46 final size:44
Alignment explanation
Indices: 29956468--29956560 Score: 125
Period size: 44 Copynumber: 2.1 Consensus size: 44
29956458 TTACAAATCT
*
29956468 ATTCCATTCAACCAAACACAATAAGACTATTACAGTTCTATTCC
1 ATTCCATTCAACCAAACACAATAAGACTATTACAGCTCTATTCC
* *
29956512 ATTCCATTCAACCAAACA-ATTGAATTACTGATTACAGCTCTATTCC
1 ATTCCATTCAACCAAACACAAT-AA-GACT-ATTACAGCTCTATTCC
29956558 ATT
1 ATT
29956561 ACAGCTTTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 2 0.05
44 20 0.47
45 3 0.07
46 18 0.42
ACGTcount: A:0.37, C:0.26, G:0.05, T:0.32
Consensus pattern (44 bp):
ATTCCATTCAACCAAACACAATAAGACTATTACAGCTCTATTCC
Found at i:29956563 original size:16 final size:16
Alignment explanation
Indices: 29956542--29956612 Score: 74
Period size: 16 Copynumber: 4.4 Consensus size: 16
29956532 TGAATTACTG
*
29956542 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCA
*
29956558 ATTACAGCTTTATTCA
1 ATTACAGCTCTATTCA
29956574 ATTA-ATGCTCTATTCA
1 ATTACA-GCTCTATTCA
* *
29956590 ATTATAGCCCTATTGC-
1 ATTACAGCTCTATT-CA
29956606 ATTACAG
1 ATTACAG
29956613 TGAACCAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
15 1 0.02
16 44 0.94
17 2 0.04
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (16 bp):
ATTACAGCTCTATTCA
Found at i:29964574 original size:15 final size:16
Alignment explanation
Indices: 29964545--29964576 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
29964535 GTCTATAGTT
29964545 TTCTATAGTTTTCACA
1 TTCTATAGTTTTCACA
29964561 TTCTATAG-TTTCACA
1 TTCTATAGTTTTCACA
29964576 T
1 T
29964577 CTAAAGATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.25, C:0.19, G:0.06, T:0.50
Consensus pattern (16 bp):
TTCTATAGTTTTCACA
Found at i:29975383 original size:2 final size:2
Alignment explanation
Indices: 29975370--29975405 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
29975360 TGGTTGTCTT
*
29975370 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29975406 ACAATTTAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:29975701 original size:43 final size:43
Alignment explanation
Indices: 29975635--29975746 Score: 197
Period size: 43 Copynumber: 2.6 Consensus size: 43
29975625 TTATTTCCAT
* *
29975635 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTGTCGC
1 AAACGCCGCTAAAGACCACGACCTTTAGCGGCGCTTTTGTCAC
29975678 AAACGCCGCTAAAGACCACGACCTTTAGCGGCGCTTTTGTCAC
1 AAACGCCGCTAAAGACCACGACCTTTAGCGGCGCTTTTGTCAC
*
29975721 AAACGCCGCTAAAGACCACAACCTTT
1 AAACGCCGCTAAAGACCACGACCTTT
29975747 CGACAAAAGC
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 66 1.00
ACGTcount: A:0.28, C:0.32, G:0.20, T:0.21
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCACGACCTTTAGCGGCGCTTTTGTCAC
Found at i:29980444 original size:22 final size:21
Alignment explanation
Indices: 29980409--29980474 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
29980399 TCAACCCTTG
*
29980409 AATCCTTAAATCCTAAACCCTA
1 AATCCCTAAATCCT-AACCCTA
*
29980431 AATCCCTAACTCCTAACCCTTA
1 AATCCCTAAATCCTAACCC-TA
* * *
29980453 AA-CCTTAAATCCCAACCTTA
1 AATCCCTAAATCCTAACCCTA
29980473 AA
1 AA
29980475 CTATAATCCC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
20 4 0.11
21 17 0.46
22 16 0.43
ACGTcount: A:0.39, C:0.35, G:0.00, T:0.26
Consensus pattern (21 bp):
AATCCCTAAATCCTAACCCTA
Found at i:29980494 original size:14 final size:14
Alignment explanation
Indices: 29980475--29980501 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29980465 CAACCTTAAA
29980475 CTATAATCCCTAAT
1 CTATAATCCCTAAT
29980489 CTATAATCCCTAA
1 CTATAATCCCTAA
29980502 ATCCATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.30, G:0.00, T:0.33
Consensus pattern (14 bp):
CTATAATCCCTAAT
Found at i:29980572 original size:18 final size:21
Alignment explanation
Indices: 29980549--29980599 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 21
29980539 CAAAACACGC
29980549 AAAAAACTGAACTG-G-A-TA
1 AAAAAACTGAACTGAGCACTA
*
29980567 AAAAAAATGAACTGAGCACTA
1 AAAAAACTGAACTGAGCACTA
*
29980588 AAAATACTGAAC
1 AAAAAACTGAAC
29980600 CGGGATGGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 13 0.48
19 1 0.04
20 1 0.04
21 12 0.44
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.16
Consensus pattern (21 bp):
AAAAAACTGAACTGAGCACTA
Found at i:29980767 original size:7 final size:7
Alignment explanation
Indices: 29980755--29980908 Score: 80
Period size: 7 Copynumber: 21.9 Consensus size: 7
29980745 ACTAGTTAAT
29980755 CTAAACC
1 CTAAACC
29980762 CTAAACC
1 CTAAACC
*
29980769 ATAAA-C
1 CTAAACC
*
29980775 TTAAACC
1 CTAAACC
29980782 CTAAAACC
1 CT-AAACC
*
29980790 ATAAACC
1 CTAAACC
* *
29980797 CTTAACA
1 CTAAACC
29980804 C-ATAACC
1 CTA-AACC
29980811 TCTAAACC
1 -CTAAACC
*
29980819 TTAAACC
1 CTAAACC
*
29980826 CT-AGCC
1 CTAAACC
*
29980832 TTTAAACC
1 -CTAAACC
*
29980840 ATAAACC
1 CTAAACC
*
29980847 ATAAACC
1 CTAAACC
* *
29980854 ATAACCC
1 CTAAACC
29980861 CTAAACC
1 CTAAACC
*
29980868 ATAAACC
1 CTAAACC
* *
29980875 ATAACCC
1 CTAAACC
29980882 CTAAACC
1 CTAAACC
* *
29980889 ATAAACT
1 CTAAACC
**
29980896 AAAAACC
1 CTAAACC
29980903 CTAAAC
1 CTAAAC
29980909 TGTAGTGATA
Statistics
Matches: 112, Mismatches: 28, Indels: 14
0.73 0.18 0.09
Matches are distributed among these distances:
6 8 0.07
7 89 0.79
8 14 0.12
9 1 0.01
ACGTcount: A:0.47, C:0.34, G:0.01, T:0.18
Consensus pattern (7 bp):
CTAAACC
Found at i:29980790 original size:21 final size:20
Alignment explanation
Indices: 29980756--29980908 Score: 93
Period size: 21 Copynumber: 7.6 Consensus size: 20
29980746 CTAGTTAATC
29980756 TAAACCCTAAACCATAAACT
1 TAAACCCTAAACCATAAACT
29980776 TAAACCCTAAAACC----A--
1 TAAACCCT-AAACCATAAACT
* *
29980791 TAAACCCTTAACACATAACCT
1 TAAACCCTAAAC-CATAAACT
* * **
29980812 CTAAACCTTAAACCCTAGCCTT
1 -TAAACCCTAAACCATAAAC-T
* *
29980834 TAAACCATAAACCATAAACCA
1 TAAACCCTAAACCATAAA-CT
* *
29980855 TAACCCCTAAACCATAAACCA
1 TAAACCCTAAACCATAAA-CT
*
29980876 TAACCCCTAAACCATAAACT
1 TAAACCCTAAACCATAAACT
*
29980896 AAAAACCCTAAAC
1 -TAAACCCTAAAC
29980909 TGTAGTGATA
Statistics
Matches: 105, Mismatches: 16, Indels: 23
0.73 0.11 0.16
Matches are distributed among these distances:
14 3 0.03
15 9 0.09
17 1 0.01
20 9 0.09
21 71 0.68
22 12 0.11
ACGTcount: A:0.48, C:0.33, G:0.01, T:0.18
Consensus pattern (20 bp):
TAAACCCTAAACCATAAACT
Found at i:29980851 original size:14 final size:14
Alignment explanation
Indices: 29980756--29980908 Score: 96
Period size: 14 Copynumber: 10.9 Consensus size: 14
29980746 CTAGTTAATC
*
29980756 TAAACCCTAAACCA
1 TAAACCATAAACCA
* *
29980770 TAAA-CTTAAACCC
1 TAAACCATAAACCA
*
29980783 TAAAACCATAAACCC
1 T-AAACCATAAACCA
* *
29980798 TTAACACAT-AACCTC
1 TAAAC-CATAAACC-A
* *
29980813 TAAACCTTAAACCC
1 TAAACCATAAACCA
* *
29980827 T-AGCCTTTAAACCA
1 TAAACC-ATAAACCA
29980841 TAAACCATAAACCA
1 TAAACCATAAACCA
* *
29980855 TAACCCCTAAACCA
1 TAAACCATAAACCA
* *
29980869 TAAACCATAACCCC
1 TAAACCATAAACCA
*
29980883 TAAACCATAAACTA
1 TAAACCATAAACCA
* *
29980897 AAAACCCTAAAC
1 TAAACCATAAAC
29980909 TGTAGTGATA
Statistics
Matches: 111, Mismatches: 21, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
13 11 0.10
14 76 0.68
15 24 0.22
ACGTcount: A:0.48, C:0.33, G:0.01, T:0.18
Consensus pattern (14 bp):
TAAACCATAAACCA
Found at i:29981243 original size:41 final size:41
Alignment explanation
Indices: 29981181--29981313 Score: 169
Period size: 41 Copynumber: 3.2 Consensus size: 41
29981171 TTTAGGGAAG
* * * **
29981181 CGCCGCTAAAGCTCTAAGCATTAGCAGCGCTTTCTTAAAAA
1 CGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCCAAAAAA
* * *
29981222 TGCCGTTACAGCCCT-AGGCATTAGCGGCGCTTTCCAAAAAA
1 CGCCGCTAAAGCCCTGA-GCATTAGCGGCGCTTTCCAAAAAA
*
29981263 CGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCCCAAAAA
1 CGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCCAAAAAA
29981304 CGCCGCTAAA
1 CGCCGCTAAA
29981314 TCCCCGAAAG
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
40 1 0.01
41 77 0.97
42 1 0.01
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (41 bp):
CGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCCAAAAAA
Found at i:29990797 original size:50 final size:49
Alignment explanation
Indices: 29990648--29990824 Score: 227
Period size: 50 Copynumber: 3.6 Consensus size: 49
29990638 CAAAGTCATA
* * * *
29990648 TCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATG
1 TCCCAGACATGGTCTTACATGGGA-CTCTCATCTCGGTGCCAATGCCATG
* *
29990698 TCCCAGACATGCTCTT--ATGGGGAC-CTCATCTCGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACAT-GGGACTCTCATCTCGGTGCCAATGCCATG
*
29990745 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGTCAATGCCATG
1 TCCCAGACATGGTCTTACATGGGA-CTCTCATCTCGGTGCCAATGCCATG
*
29990795 TCCCAAACATGGTCTTACATGGGA-TCTCAT
1 TCCCAGACATGGTCTTACATGGGACTCTCAT
29990825 TCCCTTAATG
Statistics
Matches: 112, Mismatches: 10, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
47 35 0.31
48 12 0.11
49 7 0.06
50 58 0.52
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.28
Consensus pattern (49 bp):
TCCCAGACATGGTCTTACATGGGACTCTCATCTCGGTGCCAATGCCATG
Found at i:29994332 original size:14 final size:15
Alignment explanation
Indices: 29994313--29994345 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
29994303 TCAATTCTTT
*
29994313 CAATTCTA-ACGGAG
1 CAATTCTATAAGGAG
29994327 CAATTCTATAAGGAG
1 CAATTCTATAAGGAG
29994342 CAAT
1 CAAT
29994346 AGAAATAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.24
Consensus pattern (15 bp):
CAATTCTATAAGGAG
Found at i:29997843 original size:50 final size:49
Alignment explanation
Indices: 29997750--29997986 Score: 267
Period size: 50 Copynumber: 4.7 Consensus size: 49
29997740 CTTCTTGTAC
* * ** *
29997750 TGCCAATGCCATATCCCAAATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCC-ATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
* * * * **
29997800 TGTCCATGCAACGTCCCAGACATGCTCTTACGGGGGACCTCTCATCTCGG
1 TG-CCATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
*
29997850 TGCCATTGCCATGTCCCAAACATGGTCTTACATGAGACCTCTCATCTCGG
1 TGCCA-TGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
* *
29997900 TGCCAACGCCATGCCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCC-ATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
29997950 TGTCAATGCCATGACCCAGACATGGTCTTTCATGGGA
1 TG-CCATGCCATGTCCCAAACATGGTCTTACATGGGA
29997987 TCTCATTCCC
Statistics
Matches: 157, Mismatches: 26, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
49 3 0.02
50 150 0.96
51 4 0.03
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.26
Consensus pattern (49 bp):
TGCCATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:29998789 original size:23 final size:24
Alignment explanation
Indices: 29998762--29998830 Score: 65
Period size: 22 Copynumber: 3.0 Consensus size: 24
29998752 CATAACTAGT
*
29998762 CGCATGGTATAACATATAGGGTT-
1 CGCATGATATAACATATAGGGTTC
* *
29998785 TGCAT-ATATAACATCTA-GGTTC
1 CGCATGATATAACATATAGGGTTC
*
29998807 CGCATGTTA-ACACATATAGGGTTC
1 CGCATGATATA-ACATATAGGGTTC
29998831 ATACAATACA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
21 4 0.11
22 15 0.42
23 12 0.33
24 5 0.14
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32
Consensus pattern (24 bp):
CGCATGATATAACATATAGGGTTC
Found at i:29999018 original size:14 final size:14
Alignment explanation
Indices: 29998999--29999029 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
29998989 TTAGAGATCT
29998999 ACACATTAGGGTTA
1 ACACATTAGGGTTA
*
29999013 ACACATTTGGGTTA
1 ACACATTAGGGTTA
29999027 ACA
1 ACA
29999030 TTCCTATGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (14 bp):
ACACATTAGGGTTA
Found at i:29999096 original size:15 final size:15
Alignment explanation
Indices: 29999050--29999101 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
29999040 TCGTACATAG
*
29999050 GGGTTCACACAACTA
1 GGGTTCGCACAACTA
29999065 GGGTTCGCACATA-TA
1 GGGTTCGCACA-ACTA
* *
29999080 GGGTTTGCACACCTA
1 GGGTTCGCACAACTA
*
29999095 GGTTTCG
1 GGGTTCG
29999102 TAAATACAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 29 0.97
16 1 0.03
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (15 bp):
GGGTTCGCACAACTA
Found at i:30000166 original size:20 final size:20
Alignment explanation
Indices: 30000134--30000173 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
30000124 TAACTTTTAG
*
30000134 GTAATTAATGCTATAGATAT
1 GTAATTAATGCTATAAATAT
30000154 GTAA-TAATAGCTATAAATAT
1 GTAATTAAT-GCTATAAATAT
30000174 ATAAAATGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.38
Consensus pattern (20 bp):
GTAATTAATGCTATAAATAT
Found at i:30002255 original size:778 final size:778
Alignment explanation
Indices: 30000761--30002320 Score: 3120
Period size: 778 Copynumber: 2.0 Consensus size: 778
30000751 TCCATCTCAT
30000761 GGACATAGAGAATGGATACTTTCTGGCTAAATTTCAGTCCACCGAAGACTATGCAAAAGTTCTTC
1 GGACATAGAGAATGGATACTTTCTGGCTAAATTTCAGTCCACCGAAGACTATGCAAAAGTTCTTC
30000826 GCAAGGTCCTTAGCTAATTTATGGTCAATATCTGACTGTTCAACCTTGGACCAAAGAATTCAACC
66 GCAAGGTCCTTAGCTAATTTATGGTCAATATCTGACTGTTCAACCTTGGACCAAAGAATTCAACC
30000891 CCTTACAACCATACCCAAGCATGGTGATGGCTTGTATACGGTTACTAGGCCTCCCAGGGTTTCTG
131 CCTTACAACCATACCCAAGCATGGTGATGGCTTGTATACGGTTACTAGGCCTCCCAGGGTTTCTG
30000956 TACAAAAGGAAAATTCTTGAAGAAATAAGAGAGACCATAGGAAAGGTTGTTCGGTTAGATTTCAA
196 TACAAAAGGAAAATTCTTGAAGAAATAAGAGAGACCATAGGAAAGGTTGTTCGGTTAGATTTCAA
30001021 TACTAATAGTAGAATTAGAGGCCACTTCGCCAAGATGGTTGTTTATGTCAACCTGGACAAGCCTC
261 TACTAATAGTAGAATTAGAGGCCACTTCGCCAAGATGGTTGTTTATGTCAACCTGGACAAGCCTC
30001086 TGGTCGCTCAAGTTCTTATGAGTGGTTTACATCAGAAAGTTGAGCATGAAGCGCTGCCTATGATT
326 TGGTCGCTCAAGTTCTTATGAGTGGTTTACATCAGAAAGTTGAGCATGAAGCGCTGCCTATGATT
30001151 TGCTTCACCTGCGGGAAGTACGGACATGCTAAGGAGCTATGTGCTTCGCCACAACCGGATCTGGC
391 TGCTTCACCTGCGGGAAGTACGGACATGCTAAGGAGCTATGTGCTTCGCCACAACCGGATCTGGC
30001216 AGTGGGGAAGGATCAGAAGGGTACTAATCTGACAGAGGCTGTAAGCAGAGGAGAAGGTGCTGTTT
456 AGTGGGGAAGGATCAGAAGGGTACTAATCTGACAGAGGCTGTAAGCAGAGGAGAAGGTGCTGTTT
30001281 ACGGGCCATGGATTATGGTTGAAAGGAAAGGAAGGTGTAGTTCTAGGAACAACAATATTAAAAAA
521 ACGGGCCATGGATTATGGTTGAAAGGAAAGGAAGGTGTAGTTCTAGGAACAACAATATTAAAAAA
30001346 ACTGATTTTACGGAGAAAGGAAAATTGGGTTCTCGATTTGATGCTCTGGCTAATATGGAAGTTTT
586 ACTGATTTTACGGAGAAAGGAAAATTGGGTTCTCGATTTGATGCTCTGGCTAATATGGAAGTTTT
30001411 GCTTGATCTAAAAGATGAGTTAAATAAGGAAGATACTGGAAAGTTGGCTGGTTTTAAGAATAAAT
651 GCTTGATCTAAAAGATGAGTTAAATAAGGAAGATACTGGAAAGTTGGCTGGTTTTAAGAATAAAT
30001476 TGAAGGTTGGAGAGAATGTTATGTAACAGGGGTTTAAGACACAGGGCAACCCTAAGTCAACAA
716 TGAAGGTTGGAGAGAATGTTATGTAACAGGGGTTTAAGACACAGGGCAACCCTAAGTCAACAA
30001539 GGACATAGAGAATGGATACTTTCTGGCTAAATTTCAGTCCACCGAAGACTATGCAAAAGTTCTTC
1 GGACATAGAGAATGGATACTTTCTGGCTAAATTTCAGTCCACCGAAGACTATGCAAAAGTTCTTC
30001604 GCAAGGTCCTTAGCTAATTTATGGTCAATATCTGACTGTTCAACCTTGGACCAAAGAATTCAACC
66 GCAAGGTCCTTAGCTAATTTATGGTCAATATCTGACTGTTCAACCTTGGACCAAAGAATTCAACC
30001669 CCTTACAACCATACCCAAGCATGGTGATGGCTTGTATACGGTTACTAGGCCTCCCAGGGTTTCTG
131 CCTTACAACCATACCCAAGCATGGTGATGGCTTGTATACGGTTACTAGGCCTCCCAGGGTTTCTG
30001734 TACAAAAGGAAAATTCTTGAAGAAATAAGAGAGACCATAGGAAAGGTTGTTCGGTTAGATTTCAA
196 TACAAAAGGAAAATTCTTGAAGAAATAAGAGAGACCATAGGAAAGGTTGTTCGGTTAGATTTCAA
30001799 TACTAATAGTAGAATTAGAGGCCACTTCGCCAAGATGGTTGTTTATGTCAACCTGGACAAGCCTC
261 TACTAATAGTAGAATTAGAGGCCACTTCGCCAAGATGGTTGTTTATGTCAACCTGGACAAGCCTC
30001864 TGGTCGCTCAAGTTCTTATGAGTGGTTTACATCAGAAAGTTGAGCATGAAGCGCTGCCTATGATT
326 TGGTCGCTCAAGTTCTTATGAGTGGTTTACATCAGAAAGTTGAGCATGAAGCGCTGCCTATGATT
30001929 TGCTTCACCTGCGGGAAGTACGGACATGCTAAGGAGCTATGTGCTTCGCCACAACCGGATCTGGC
391 TGCTTCACCTGCGGGAAGTACGGACATGCTAAGGAGCTATGTGCTTCGCCACAACCGGATCTGGC
30001994 AGTGGGGAAGGATCAGAAGGGTACTAATCTGACAGAGGCTGTAAGCAGAGGAGAAGGTGCTGTTT
456 AGTGGGGAAGGATCAGAAGGGTACTAATCTGACAGAGGCTGTAAGCAGAGGAGAAGGTGCTGTTT
30002059 ACGGGCCATGGATTATGGTTGAAAGGAAAGGAAGGTGTAGTTCTAGGAACAACAATATTAAAAAA
521 ACGGGCCATGGATTATGGTTGAAAGGAAAGGAAGGTGTAGTTCTAGGAACAACAATATTAAAAAA
30002124 ACTGATTTTACGGAGAAAGGAAAATTGGGTTCTCGATTTGATGCTCTGGCTAATATGGAAGTTTT
586 ACTGATTTTACGGAGAAAGGAAAATTGGGTTCTCGATTTGATGCTCTGGCTAATATGGAAGTTTT
30002189 GCTTGATCTAAAAGATGAGTTAAATAAGGAAGATACTGGAAAGTTGGCTGGTTTTAAGAATAAAT
651 GCTTGATCTAAAAGATGAGTTAAATAAGGAAGATACTGGAAAGTTGGCTGGTTTTAAGAATAAAT
30002254 TGAAGGTTGGAGAGAATGTTATGTAACAGGGGTTTAAGACACAGGGCAACCCTAAGTCAACAA
716 TGAAGGTTGGAGAGAATGTTATGTAACAGGGGTTTAAGACACAGGGCAACCCTAAGTCAACAA
30002317 GGAC
1 GGAC
30002321 TGAGCAATCG
Statistics
Matches: 782, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
778 782 1.00
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (778 bp):
GGACATAGAGAATGGATACTTTCTGGCTAAATTTCAGTCCACCGAAGACTATGCAAAAGTTCTTC
GCAAGGTCCTTAGCTAATTTATGGTCAATATCTGACTGTTCAACCTTGGACCAAAGAATTCAACC
CCTTACAACCATACCCAAGCATGGTGATGGCTTGTATACGGTTACTAGGCCTCCCAGGGTTTCTG
TACAAAAGGAAAATTCTTGAAGAAATAAGAGAGACCATAGGAAAGGTTGTTCGGTTAGATTTCAA
TACTAATAGTAGAATTAGAGGCCACTTCGCCAAGATGGTTGTTTATGTCAACCTGGACAAGCCTC
TGGTCGCTCAAGTTCTTATGAGTGGTTTACATCAGAAAGTTGAGCATGAAGCGCTGCCTATGATT
TGCTTCACCTGCGGGAAGTACGGACATGCTAAGGAGCTATGTGCTTCGCCACAACCGGATCTGGC
AGTGGGGAAGGATCAGAAGGGTACTAATCTGACAGAGGCTGTAAGCAGAGGAGAAGGTGCTGTTT
ACGGGCCATGGATTATGGTTGAAAGGAAAGGAAGGTGTAGTTCTAGGAACAACAATATTAAAAAA
ACTGATTTTACGGAGAAAGGAAAATTGGGTTCTCGATTTGATGCTCTGGCTAATATGGAAGTTTT
GCTTGATCTAAAAGATGAGTTAAATAAGGAAGATACTGGAAAGTTGGCTGGTTTTAAGAATAAAT
TGAAGGTTGGAGAGAATGTTATGTAACAGGGGTTTAAGACACAGGGCAACCCTAAGTCAACAA
Found at i:30007708 original size:20 final size:20
Alignment explanation
Indices: 30007665--30007708 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
30007655 TGGTTTTCTT
*
30007665 AAAAAAGAATCACCTTCTGC
1 AAAAAAGAATCACCTTCAGC
*
30007685 AAAAATAGATTCACCTTCAG-
1 AAAAA-AGAATCACCTTCAGC
30007705 AAAA
1 AAAA
30007709 CCATTATTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.50, C:0.20, G:0.09, T:0.20
Consensus pattern (20 bp):
AAAAAAGAATCACCTTCAGC
Found at i:30009190 original size:35 final size:35
Alignment explanation
Indices: 30009141--30009220 Score: 115
Period size: 35 Copynumber: 2.3 Consensus size: 35
30009131 CCCCTTTCAA
* *
30009141 GGTGTCACCGTGAAGGACCTATATATCATTTGCAC
1 GGTGTCACCCTGAAGGACCTATATATCATTTACAC
* * *
30009176 GGTGTCGCCCTGAAGGACCTATATATCGTTTACAT
1 GGTGTCACCCTGAAGGACCTATATATCATTTACAC
30009211 GGTGTCACCC
1 GGTGTCACCC
30009221 CAAAAGACTT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.29
Consensus pattern (35 bp):
GGTGTCACCCTGAAGGACCTATATATCATTTACAC
Found at i:30010782 original size:21 final size:21
Alignment explanation
Indices: 30010738--30010783 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
30010728 GCTTAAGCCT
* *
30010738 AAATTGATGTCCTACATGCCC
1 AAATTGATGCCCTACATACCC
* *
30010759 AAATTGATGCCCTACGTACTC
1 AAATTGATGCCCTACATACCC
30010780 AAAT
1 AAAT
30010784 AAACCATTCG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.28
Consensus pattern (21 bp):
AAATTGATGCCCTACATACCC
Found at i:30010928 original size:16 final size:17
Alignment explanation
Indices: 30010907--30010946 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
30010897 TGATATAACA
30010907 AATAAA-TATGTTTTTG
1 AATAAAGTATGTTTTTG
*
30010923 AATAAAGTTTGTTTTTG
1 AATAAAGTATGTTTTTG
*
30010940 AACAAAG
1 AATAAAG
30010947 AAATTATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.40, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAAGTATGTTTTTG
Found at i:30011010 original size:34 final size:34
Alignment explanation
Indices: 30010972--30011041 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
30010962 AATAATAAAA
30010972 ATCATTTCAAGACTTCCAAACATATTAGAAAATG
1 ATCATTTCAAGACTTCCAAACATATTAGAAAATG
30011006 ATCATTTCAAGACTTCCAAACATATTAGAAAATG
1 ATCATTTCAAGACTTCCAAACATATTAGAAAATG
30011040 AT
1 AT
30011042 TTGAACACTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.44, C:0.17, G:0.09, T:0.30
Consensus pattern (34 bp):
ATCATTTCAAGACTTCCAAACATATTAGAAAATG
Found at i:30018116 original size:27 final size:27
Alignment explanation
Indices: 30017740--30018122 Score: 443
Period size: 27 Copynumber: 14.2 Consensus size: 27
30017730 TGTAATAACT
* * *
30017740 GTAATACCCTTGA-AGGGCAAAATGATC
1 GTAATACCCCT-ATAGGGTAAAATGACC
* *
30017767 GTAATGCCCCTGTAGGGTAAAATGACC
1 GTAATACCCCTATAGGGTAAAATGACC
* *
30017794 GTAATACCCCCATAGGGTAAAATGATC
1 GTAATACCCCTATAGGGTAAAATGACC
** *
30017821 GTAATACCCCTGCAGGGTAAAATGATC
1 GTAATACCCCTATAGGGTAAAATGACC
**
30017848 GTAATACCCCTATAGGGTAAAATGATA
1 GTAATACCCCTATAGGGTAAAATGACC
*
30017875 GTAATACCCC-ATAGGGTAAAATGATC
1 GTAATACCCCTATAGGGTAAAATGACC
*
30017901 GTAATACCCTTATAGGGTAAAATGACC
1 GTAATACCCCTATAGGGTAAAATGACC
* *
30017928 GTAATA-CCCTCATAAGGTAAAATAACC
1 GTAATACCCCT-ATAGGGTAAAATGACC
* *
30017955 GTAATA-CCTTCATAGGGTAAAATGATC
1 GTAATACCCCT-ATAGGGTAAAATGACC
30017982 GTAATACCCCTATAGGGTAAAATGACC
1 GTAATACCCCTATAGGGTAAAATGACC
* *
30018009 ATAATACCCCCCATAGGGTAAAATGACC
1 GTAATA-CCCCTATAGGGTAAAATGACC
* * * * *
30018037 ATAATACCCCCATAAGGTAAAATGTCT
1 GTAATACCCCTATAGGGTAAAATGACC
30018064 GTAATA-CCCTCATAGGGTAAAATGACC
1 GTAATACCCCT-ATAGGGTAAAATGACC
*
30018091 GTAATACCCCTGTAGGGTAAAATGACC
1 GTAATACCCCTATAGGGTAAAATGACC
*
30018118 ATAAT
1 GTAAT
30018123 GCCCTTGTGG
Statistics
Matches: 310, Mismatches: 39, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
26 30 0.10
27 247 0.80
28 33 0.11
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (27 bp):
GTAATACCCCTATAGGGTAAAATGACC
Found at i:30018218 original size:24 final size:23
Alignment explanation
Indices: 30018161--30018230 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
30018151 CCTCAAGGTC
*
30018161 AAATGATTGTTTTGTCTGTGGTT
1 AAATGATTGATTTGTCTGTGGTT
* *
30018184 AAATGACTGATTTGTCTGTGTTT
1 AAATGATTGATTTGTCTGTGGTT
** *
30018207 GGTATGATTGATTTGTCTATGGTT
1 -AAATGATTGATTTGTCTGTGGTT
30018231 TGAATGACTG
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
23 20 0.53
24 18 0.47
ACGTcount: A:0.19, C:0.06, G:0.26, T:0.50
Consensus pattern (23 bp):
AAATGATTGATTTGTCTGTGGTT
Found at i:30018237 original size:24 final size:24
Alignment explanation
Indices: 30018162--30018243 Score: 87
Period size: 24 Copynumber: 3.5 Consensus size: 24
30018152 CTCAAGGTCA
* * *
30018162 AATGATTGTTTTGTCTGTGG-TTA
1 AATGACTGATTTGTCTGTGGTTTG
30018185 AATGACTGATTTGTCTGT-GTTTGG
1 AATGACTGATTTGTCTGTGGTTT-G
* * *
30018209 TATGATTGATTTGTCTATGGTTTG
1 AATGACTGATTTGTCTGTGGTTTG
30018233 AATGACTGATT
1 AATGACTGATT
30018244 CTGAGCATGG
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
22 1 0.02
23 18 0.38
24 25 0.52
25 4 0.08
ACGTcount: A:0.20, C:0.06, G:0.26, T:0.49
Consensus pattern (24 bp):
AATGACTGATTTGTCTGTGGTTTG
Found at i:30018345 original size:27 final size:27
Alignment explanation
Indices: 30018306--30018371 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
30018296 TATGGAGGAA
30018306 ATACTG-TACTGGTGGCTCT-GCCACA-
1 ATACTGTTACTGGTGGCT-TGGCCACAT
30018331 ATCACTGTTACTGGTGGCTTGGCCACAT
1 AT-ACTGTTACTGGTGGCTTGGCCACAT
*
30018359 ATACTATTACTGG
1 ATACTGTTACTGG
30018372 CAGCTTTGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
25 2 0.06
26 5 0.14
27 27 0.75
28 2 0.06
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.32
Consensus pattern (27 bp):
ATACTGTTACTGGTGGCTTGGCCACAT
Found at i:30018377 original size:27 final size:27
Alignment explanation
Indices: 30018325--30018377 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
30018315 TGGTGGCTCT
* **
30018325 GCCACAATCACTGTTACTGGTGGCTTG
1 GCCACAATCACTATTACTGGCAGCTTG
30018352 GCCACATAT-ACTATTACTGGCAGCTT
1 GCCACA-ATCACTATTACTGGCAGCTT
30018378 TGTTGCGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (27 bp):
GCCACAATCACTATTACTGGCAGCTTG
Found at i:30018477 original size:32 final size:32
Alignment explanation
Indices: 30018418--30018666 Score: 227
Period size: 32 Copynumber: 7.8 Consensus size: 32
30018408 GCAATGCTAT
* * * *
30018418 TGATAGCTTTGTGCCGGTCCTAGTACCGTTAC
1 TGATGGCTTTGTGCCGATCATATTACCGTTAC
* * *
30018450 TGATGGTTTTGTGCCGATCATAATACCGTTAT
1 TGATGGCTTTGTGCCGATCATATTACCGTTAC
* * *
30018482 TGATGGTTTTATACCGATCATATTACCGTTA-
1 TGATGGCTTTGTGCCGATCATATTACCGTTAC
* * *
30018513 TCGATGGCTGTGTACCGATCAT-TTCACTGTTAC
1 T-GATGGCTTTGTGCCGATCATATT-ACCGTTAC
*
30018546 TGATGGCTTTGTACCGATCA-ATTACCGTTAC
1 TGATGGCTTTGTGCCGATCATATTACCGTTAC
* * *
30018577 TAATGGCTTTGTGTCGAACATATTACCGTTAC
1 TGATGGCTTTGTGCCGATCATATTACCGTTAC
* * * * * *
30018609 TAATGG-TTGTGTGTCAATCATATCACTGCTAC
1 TGATGGCTT-TGTGCCGATCATATTACCGTTAC
*
30018641 TGATGGCTTTGTGCCAATCATATTAC
1 TGATGGCTTTGTGCCGATCATATTAC
30018667 TATACTTATG
Statistics
Matches: 183, Mismatches: 27, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
31 28 0.15
32 152 0.83
33 3 0.02
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (32 bp):
TGATGGCTTTGTGCCGATCATATTACCGTTAC
Found at i:30018620 original size:95 final size:96
Alignment explanation
Indices: 30018445--30018666 Score: 259
Period size: 95 Copynumber: 2.3 Consensus size: 96
30018435 TCCTAGTACC
* * * * * *
30018445 GTTACTGATGGTTTTGTGCCGATCATAATACCGTTATTGATGGTTTTATACCGATCATATTACCG
1 GTTACTGATGGCTTTGTGCCGATCATATTACCGTTACTAATGGCTTTATACCGAACATATTACCG
* * *
30018510 TTATCGATGGCTGTGTACCGATCATTTCACT
66 TTATCAATGGCTGTGTACCAATCATATCACT
* * **
30018541 GTTACTGATGGCTTTGTACCGATCA-ATTACCGTTACTAATGGCTTTGTGTCGAACATATTACCG
1 GTTACTGATGGCTTTGTGCCGATCATATTACCGTTACTAATGGCTTTATACCGAACATATTACCG
* **
30018605 TTA-CTAATGGTTGTGTGTCAATCATATCACT
66 TTATC-AATGGCTGTGTACCAATCATATCACT
* *
30018636 GCTACTGATGGCTTTGTGCCAATCATATTAC
1 GTTACTGATGGCTTTGTGCCGATCATATTAC
30018667 TATACTTATG
Statistics
Matches: 105, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
94 1 0.01
95 76 0.72
96 28 0.27
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (96 bp):
GTTACTGATGGCTTTGTGCCGATCATATTACCGTTACTAATGGCTTTATACCGAACATATTACCG
TTATCAATGGCTGTGTACCAATCATATCACT
Found at i:30018702 original size:22 final size:22
Alignment explanation
Indices: 30018672--30018718 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
30018662 ATTACTATAC
* * *
30018672 TTATGGCTTGTAGCCATTCTGT
1 TTATAGCTTATAGCCATCCTGT
*
30018694 TTATAGCTTATAGCTATCCTGT
1 TTATAGCTTATAGCCATCCTGT
30018716 TTA
1 TTA
30018719 CGGTTCTTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.47
Consensus pattern (22 bp):
TTATAGCTTATAGCCATCCTGT
Found at i:30026441 original size:20 final size:20
Alignment explanation
Indices: 30026416--30026503 Score: 77
Period size: 20 Copynumber: 4.3 Consensus size: 20
30026406 TTGTACGAAA
* *
30026416 TTTGCACTTCGGTGTCTCTG
1 TTTGCACTTCGGTGCCCCTG
* * *
30026436 TTTGCACTTCAGTGCCACTA
1 TTTGCACTTCGGTGCCCCTG
* * *
30026456 TATACACTTTCGGTGTCCCTG
1 TTTGCAC-TTCGGTGCCCCTG
* *
30026477 TTCGCACTACGGTGCCCCTG
1 TTTGCACTTCGGTGCCCCTG
30026497 TTTGCAC
1 TTTGCAC
30026504 AATTGTGCCC
Statistics
Matches: 51, Mismatches: 16, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 38 0.75
21 13 0.25
ACGTcount: A:0.12, C:0.31, G:0.20, T:0.36
Consensus pattern (20 bp):
TTTGCACTTCGGTGCCCCTG
Found at i:30038734 original size:14 final size:14
Alignment explanation
Indices: 30038714--30038748 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
30038704 TTATAAATAC
30038714 ATAATAACATACAAT
1 ATAATAACAT-CAAT
30038729 -TAATAACATCAAT
1 ATAATAACATCAAT
30038742 ATAATAA
1 ATAATAA
30038749 TCCGTACGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.29
Consensus pattern (14 bp):
ATAATAACATCAAT
Found at i:30053751 original size:14 final size:14
Alignment explanation
Indices: 30053713--30053755 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
30053703 CAAAATGTAC
30053713 AATATAATTAAA-T
1 AATATAATTAAATT
30053726 AATATAAATTAAATT
1 AATAT-AATTAAATT
*
30053741 AA-ATAATTTAATT
1 AATATAATTAAATT
30053754 AA
1 AA
30053756 CTGTTTACCC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 15 0.56
14 9 0.33
15 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATAATTAAATT
Found at i:30056470 original size:3 final size:3
Alignment explanation
Indices: 30056462--30056491 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
30056452 CTTTCTAAAG
30056462 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
30056492 TTTTTCTCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:30056556 original size:31 final size:29
Alignment explanation
Indices: 30056515--30056611 Score: 80
Period size: 30 Copynumber: 3.4 Consensus size: 29
30056505 TATGAGTTTA
30056515 TAAATATTTGGGTCAATGCAAGATTCTTCTT
1 TAAATATTTGGGTC-ATGCAA-ATTCTTCTT
* * *
30056546 TAAATTTTTGGG-C-T-C--TTTCATT-TA
1 TAAATATTTGGGTCATGCAAATTC-TTCTT
30056570 TAAATATTTGGGTCATGCAATATTCTTCTT
1 TAAATATTTGGGTCATGCAA-ATTCTTCTT
*
30056600 TAAATTTTTGGG
1 TAAATATTTGGG
30056612 CTCTTTCATT
Statistics
Matches: 51, Mismatches: 7, Indels: 17
0.68 0.09 0.23
Matches are distributed among these distances:
24 15 0.29
25 3 0.06
26 1 0.02
27 2 0.04
28 1 0.02
29 2 0.04
30 16 0.31
31 11 0.22
ACGTcount: A:0.26, C:0.11, G:0.15, T:0.47
Consensus pattern (29 bp):
TAAATATTTGGGTCATGCAAATTCTTCTT
Found at i:30056595 original size:54 final size:55
Alignment explanation
Indices: 30056511--30056624 Score: 212
Period size: 54 Copynumber: 2.1 Consensus size: 55
30056501 CTAATATGAG
30056511 TTTATAAATATTTGGGTCAATGCAAGATTCTTCTTTAAATTTTTGGGCTCTTTCA
1 TTTATAAATATTTGGGTCAATGCAAGATTCTTCTTTAAATTTTTGGGCTCTTTCA
*
30056566 TTTATAAATATTTGGGTC-ATGCAATATTCTTCTTTAAATTTTTGGGCTCTTTCA
1 TTTATAAATATTTGGGTCAATGCAAGATTCTTCTTTAAATTTTTGGGCTCTTTCA
30056620 TTTAT
1 TTTAT
30056625 TGTTTCTAAA
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
54 40 0.69
55 18 0.31
ACGTcount: A:0.25, C:0.12, G:0.13, T:0.50
Consensus pattern (55 bp):
TTTATAAATATTTGGGTCAATGCAAGATTCTTCTTTAAATTTTTGGGCTCTTTCA
Found at i:30056789 original size:24 final size:23
Alignment explanation
Indices: 30056757--30056830 Score: 85
Period size: 24 Copynumber: 3.1 Consensus size: 23
30056747 CATTGGAAAC
30056757 TTAACTATAAAGTACATGTCATAT
1 TTAACTATAAAGTACAT-TCATAT
* * * *
30056781 TTAACTATAAATTTCATTGGAAAT
1 TTAACTATAAAGTACATT-CATAT
*
30056805 TTAACTATAAAGTACATTTATAT
1 TTAACTATAAAGTACATTCATAT
30056828 TTA
1 TTA
30056831 CTCAAGGGAC
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
23 7 0.17
24 34 0.83
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (23 bp):
TTAACTATAAAGTACATTCATAT
Found at i:30068389 original size:16 final size:15
Alignment explanation
Indices: 30068362--30068395 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
30068352 ATAACTAGTA
*
30068362 TATAATTATATTTAT
1 TATAATTATATTGAT
30068377 TATAATATATATTGAT
1 TATAAT-TATATTGAT
30068393 TAT
1 TAT
30068396 TATCAGCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (15 bp):
TATAATTATATTGAT
Found at i:30069117 original size:17 final size:18
Alignment explanation
Indices: 30069095--30069132 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
30069085 AAATTTCAAT
* *
30069095 TTTATTTAATTTTTAA-A
1 TTTATTGAATTGTTAATA
30069112 TTTATTGAATTGTTAATA
1 TTTATTGAATTGTTAATA
30069130 TTT
1 TTT
30069133 TATACTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (18 bp):
TTTATTGAATTGTTAATA
Found at i:30071767 original size:37 final size:37
Alignment explanation
Indices: 30071726--30071805 Score: 135
Period size: 37 Copynumber: 2.2 Consensus size: 37
30071716 TATGTATACT
30071726 TAAGTAGCA-TAAATATCAAATTTCTTATTCTTGAGCA
1 TAAGTA-CACTAAATATCAAATTTCTTATTCTTGAGCA
*
30071763 TAAGTATACTAAATATCAAATTTCTTATTCTTGAGCA
1 TAAGTACACTAAATATCAAATTTCTTATTCTTGAGCA
30071800 TAAGTA
1 TAAGTA
30071806 TAACCAAGAA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
36 1 0.02
37 40 0.98
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (37 bp):
TAAGTACACTAAATATCAAATTTCTTATTCTTGAGCA
Found at i:30071806 original size:37 final size:37
Alignment explanation
Indices: 30071735--30071807 Score: 146
Period size: 37 Copynumber: 2.0 Consensus size: 37
30071725 TTAAGTAGCA
30071735 TAAATATCAAATTTCTTATTCTTGAGCATAAGTATAC
1 TAAATATCAAATTTCTTATTCTTGAGCATAAGTATAC
30071772 TAAATATCAAATTTCTTATTCTTGAGCATAAGTATA
1 TAAATATCAAATTTCTTATTCTTGAGCATAAGTATA
30071808 ACCAAGAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.41
Consensus pattern (37 bp):
TAAATATCAAATTTCTTATTCTTGAGCATAAGTATAC
Found at i:30074983 original size:17 final size:16
Alignment explanation
Indices: 30074956--30074987 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
30074946 TGATACGTCT
30074956 CTGATGAGCTTCCAAA
1 CTGATGAGCTTCCAAA
30074972 CTGATCGAGCTTCCAA
1 CTGAT-GAGCTTCCAA
30074988 TAATCTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (16 bp):
CTGATGAGCTTCCAAA
Found at i:30098900 original size:27 final size:27
Alignment explanation
Indices: 30098840--30098900 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 27
30098830 TAGTAACAAT
30098840 ACAGTGTGGGCCTTAGCCCAATACAGA
1 ACAGTGTGGGCCTTAGCCCAATACAGA
*
30098867 ATTAGTGTGGGCCTTAGCCC-ATACAGTA
1 A-CAGTGTGGGCCTTAGCCCAATACAG-A
30098895 ACAGTG
1 ACAGTG
30098901 GCAAATGGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 11 0.37
28 19 0.63
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (27 bp):
ACAGTGTGGGCCTTAGCCCAATACAGA
Found at i:30099406 original size:27 final size:26
Alignment explanation
Indices: 30099376--30099463 Score: 88
Period size: 27 Copynumber: 3.3 Consensus size: 26
30099366 GGGTAAAACA
* *
30099376 GTCATTTTATCCTATAAGGGTATTTTG
1 GTCATTTTACCCT-TGAGGGTATTTTG
30099403 GTCATTTTACCCTTCGAGGGT-TTTTCG
1 GTCATTTTACCCTT-GAGGGTATTTT-G
* * *
30099430 GTAATTTTACCCTTTGAGGATATTTTA
1 GTCATTTTACCC-TTGAGGGTATTTTG
30099457 GTCATTT
1 GTCATTT
30099464 AACAACCTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
26 5 0.10
27 40 0.78
28 6 0.12
ACGTcount: A:0.19, C:0.15, G:0.18, T:0.48
Consensus pattern (26 bp):
GTCATTTTACCCTTGAGGGTATTTTG
Found at i:30099837 original size:24 final size:23
Alignment explanation
Indices: 30099802--30099846 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
30099792 CGTAGTCGTA
*
30099802 CTTTTGGCTTTTCGACTTTTTAG
1 CTTTTGGCTTTTCGACATTTTAG
30099825 CTTTTGGGCTTTTCGACATTTT
1 CTTTT-GGCTTTTCGACATTTT
30099847 GAGATTTCGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.09, C:0.18, G:0.18, T:0.56
Consensus pattern (23 bp):
CTTTTGGCTTTTCGACATTTTAG
Done.