Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12
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: 24583705
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1509421 characters in sequence are not A, C, G, or T
File 75 of 75
Found at i:24428065 original size:17 final size:16
Alignment explanation
Indices: 24428015--24428065 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
24428005 GACACTATTC
24428015 TAATATAAAATTATGGAA
1 TAATATAAAATTAT--AA
24428033 TAAT-TAAAA-TATTAA
1 TAATATAAAATTA-TAA
24428048 TAATTATAAAATTATAA
1 TAA-TATAAAATTATAA
24428065 T
1 T
24428066 CTCATTTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
15 5 0.17
16 3 0.10
17 15 0.52
18 6 0.21
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (16 bp):
TAATATAAAATTATAA
Found at i:24429027 original size:17 final size:18
Alignment explanation
Indices: 24428997--24429034 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
24428987 AAAAAATCTA
24428997 AAAAATTAAGAATTTTTT
1 AAAAATTAAGAATTTTTT
*
24429015 AAAAATT-ATAATTTTTT
1 AAAAATTAAGAATTTTTT
24429032 AAA
1 AAA
24429035 CTATACAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (18 bp):
AAAAATTAAGAATTTTTT
Found at i:24429772 original size:17 final size:19
Alignment explanation
Indices: 24429728--24429773 Score: 62
Period size: 17 Copynumber: 2.5 Consensus size: 19
24429718 TACACAAAAC
24429728 TATTTTTA-AATTTCACTA
1 TATTTTTATAATTTCACTA
24429746 TATCTTTTATAATTTCA-TA
1 TAT-TTTTATAATTTCACTA
24429765 -ATTTTTATA
1 TATTTTTATA
24429774 TACTTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 7 0.27
18 5 0.19
19 7 0.27
20 7 0.27
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.59
Consensus pattern (19 bp):
TATTTTTATAATTTCACTA
Found at i:24431689 original size:139 final size:139
Alignment explanation
Indices: 24431438--24431709 Score: 517
Period size: 139 Copynumber: 2.0 Consensus size: 139
24431428 GTTAAGAAAT
24431438 TTAATTGTTTAGATAGTAATTAAGTAAAAAGGATTAATTTGAAAAAAGGAACAAAAGTTGGCTTC
1 TTAATTGTTTAGATAGTAATTAAGTAAAAAGGATTAATTTGAAAAAAGGAACAAAAGTTGGCTTC
24431503 TTTTTATTTAAATGGATCAATTAGCTCTTAATAGGTAAATTACTGGACTTAATATATAATTGTTC
66 TTTTTATTTAAATGGATCAATTAGCTCTTAATAGGTAAATTACTGGACTTAATATATAATTGTTC
24431568 AATTATAAA
131 AATTATAAA
*
24431577 TTAATTGTTTAGATAGTAATTAAGTAAAAAGGATTAATTTGAAAAAAGGAGCAAAAGTTGGCTTC
1 TTAATTGTTTAGATAGTAATTAAGTAAAAAGGATTAATTTGAAAAAAGGAACAAAAGTTGGCTTC
* *
24431642 TTTTTATTTAAATGGATCAATTAGCTCTTAATAGGTAAATTATTGGACTTAATTTATAATTGTTC
66 TTTTTATTTAAATGGATCAATTAGCTCTTAATAGGTAAATTACTGGACTTAATATATAATTGTTC
24431707 AAT
131 AAT
24431710 GACTATTGCA
Statistics
Matches: 130, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
139 130 1.00
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.39
Consensus pattern (139 bp):
TTAATTGTTTAGATAGTAATTAAGTAAAAAGGATTAATTTGAAAAAAGGAACAAAAGTTGGCTTC
TTTTTATTTAAATGGATCAATTAGCTCTTAATAGGTAAATTACTGGACTTAATATATAATTGTTC
AATTATAAA
Found at i:24432643 original size:38 final size:38
Alignment explanation
Indices: 24432599--24432699 Score: 166
Period size: 38 Copynumber: 2.7 Consensus size: 38
24432589 ATCCAAATTG
*
24432599 GGTGTTATTCAGGCTTAGTGCCTAGTAGGCTTCATGCT
1 GGTGTTATTCAGGCTTAGTGCCTAGTAGGCTTCATGCC
* * *
24432637 GGTGTTATTCAAGCTTAATGCCTAGTAGGCTTCATTCC
1 GGTGTTATTCAGGCTTAGTGCCTAGTAGGCTTCATGCC
24432675 GGTGTTATTCAGGCTTAGTGCCTAG
1 GGTGTTATTCAGGCTTAGTGCCTAG
24432700 CAGGTTTCGT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 57 1.00
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.37
Consensus pattern (38 bp):
GGTGTTATTCAGGCTTAGTGCCTAGTAGGCTTCATGCC
Found at i:24433403 original size:17 final size:17
Alignment explanation
Indices: 24433381--24433423 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
24433371 CACAGGTTGT
24433381 CACACGGTCGTGTGACA
1 CACACGGTCGTGTGACA
24433398 CACACGGTCGTGTGACA
1 CACACGGTCGTGTGACA
24433415 CACACGGTC
1 CACACGGTC
24433424 TGTTTGCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.23, C:0.33, G:0.28, T:0.16
Consensus pattern (17 bp):
CACACGGTCGTGTGACA
Found at i:24437430 original size:44 final size:44
Alignment explanation
Indices: 24437375--24437461 Score: 165
Period size: 44 Copynumber: 2.0 Consensus size: 44
24437365 TTATGTGTGT
*
24437375 TTAATTCTTGGTTTAATATTTCTAGACTATTGATCCAACTTTGC
1 TTAATTATTGGTTTAATATTTCTAGACTATTGATCCAACTTTGC
24437419 TTAATTATTGGTTTAATATTTCTAGACTATTGATCCAACTTTG
1 TTAATTATTGGTTTAATATTTCTAGACTATTGATCCAACTTTG
24437462 ACGTGCTTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.26, C:0.14, G:0.11, T:0.48
Consensus pattern (44 bp):
TTAATTATTGGTTTAATATTTCTAGACTATTGATCCAACTTTGC
Found at i:24437449 original size:22 final size:22
Alignment explanation
Indices: 24437382--24437450 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 22
24437372 TGTTTAATTC
24437382 TTGGTTTAATATTTCTAGACTA
1 TTGGTTTAATATTTCTAGACTA
* ** * *
24437404 TTGATCCAACT-TTGCTTA-ATTA
1 TTGGTTTAA-TATTTC-TAGACTA
24437426 TTGGTTTAATATTTCTAGACTA
1 TTGGTTTAATATTTCTAGACTA
24437448 TTG
1 TTG
24437451 ATCCAACTTT
Statistics
Matches: 33, Mismatches: 10, Indels: 8
0.65 0.20 0.16
Matches are distributed among these distances:
21 3 0.09
22 27 0.82
23 3 0.09
ACGTcount: A:0.26, C:0.12, G:0.13, T:0.49
Consensus pattern (22 bp):
TTGGTTTAATATTTCTAGACTA
Found at i:24441117 original size:45 final size:45
Alignment explanation
Indices: 24441068--24441546 Score: 601
Period size: 45 Copynumber: 10.6 Consensus size: 45
24441058 ATCAAACGAG
* *
24441068 TAAGACCATAGTTGAAGGACACCATGGCACTATATCGAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCACTATATCGAAAATGAA
* *
24441113 TAAGACCATAGTTAAAAGACACTATGGAACTATATCGAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCACTATATCGAAAATGAA
* *
24441158 TAAGACCATAGTTAAAAGACACTATGGAACTATATCGAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCACTATATCGAAAATGAA
* *
24441203 TAAGACCATAGTTAAAAGACACTATGGAACTATATCGAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCACTATATCGAAAATGAA
* * *
24441248 TAAGACCATAGTTAAAAGACACTATGACACTATA-CAGGAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCACTATATC-GAAAATGAA
* * *
24441293 TAAGACCATAGTTGAAAGAAACTATGACACTATA-CTGGAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCACTATATC-GAAAATGAA
24441338 TAAGACCATAGTTGAAAGACACTATGGCACTATATCGAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCACTATATCGAAAATGAA
* * * * * *
24441383 TAATACCATAGTTGAAAGACAATACGGAACTATA-CCAAACTCGAA
1 TAAGACCATAGTTGAAAGACACTATGGCACTATATCGAAAAT-GAA
*
24441428 TAAGACCATAGTTGAAAGACAAC-ATGGCACTATA-CCAAAATTGAA
1 TAAGACCATAGTTGAAAGAC-ACTATGGCACTATATCGAAAA-TGAA
* * * * * *
24441473 TAAGACCATAGTTGAAAAACATTATGGAAATATGAT-AAAAATAAA
1 TAAGACCATAGTTGAAAGACACTATGGCACTAT-ATCGAAAATGAA
* *
24441518 TAAAACCATAGTTGAAAAACACTATGGCA
1 TAAGACCATAGTTGAAAGACACTATGGCA
24441547 TCATGTTGGA
Statistics
Matches: 393, Mismatches: 33, Indels: 16
0.89 0.07 0.04
Matches are distributed among these distances:
44 7 0.02
45 378 0.96
46 8 0.02
ACGTcount: A:0.48, C:0.15, G:0.16, T:0.22
Consensus pattern (45 bp):
TAAGACCATAGTTGAAAGACACTATGGCACTATATCGAAAATGAA
Found at i:24441333 original size:24 final size:24
Alignment explanation
Indices: 24441262--24441333 Score: 62
Period size: 24 Copynumber: 3.1 Consensus size: 24
24441252 ACCATAGTTA
* *
24441262 AAAGACACTATGACACTATACAGG
1 AAAGAAACTATGACACTATACTGG
* * *
24441286 AAATG-AA-TAAGAC-C-ATAGTTG
1 AAA-GAAACTATGACACTATACTGG
24441307 AAAGAAACTATGACACTATACTGG
1 AAAGAAACTATGACACTATACTGG
24441331 AAA
1 AAA
24441334 TGAATAAGAC
Statistics
Matches: 35, Mismatches: 8, Indels: 10
0.66 0.15 0.19
Matches are distributed among these distances:
20 1 0.03
21 9 0.26
22 6 0.17
23 6 0.17
24 12 0.34
25 1 0.03
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.19
Consensus pattern (24 bp):
AAAGAAACTATGACACTATACTGG
Found at i:24441354 original size:21 final size:21
Alignment explanation
Indices: 24441241--24441354 Score: 70
Period size: 21 Copynumber: 5.1 Consensus size: 21
24441231 ACTATATCGA
24441241 AAATGAATAAGACCATAGTT-
1 AAATGAATAAGACCATAGTTG
* * ***
24441261 AAAAGACACTATGACACTATACAGG
1 AAATGA-A-TAAGAC-C-ATAGTTG
24441286 AAATGAATAAGACCATAGTTG
1 AAATGAATAAGACCATAGTTG
* * *
24441307 AAA-GAAACTATGACACTATACTGG
1 AAATG-AA-TAAGAC-C-ATAGTTG
24441331 AAATGAATAAGACCATAGTTG
1 AAATGAATAAGACCATAGTTG
24441352 AAA
1 AAA
24441355 GACACTATGG
Statistics
Matches: 68, Mismatches: 16, Indels: 19
0.66 0.16 0.18
Matches are distributed among these distances:
20 6 0.09
21 18 0.26
22 12 0.18
23 12 0.18
24 14 0.21
25 6 0.09
ACGTcount: A:0.49, C:0.13, G:0.17, T:0.21
Consensus pattern (21 bp):
AAATGAATAAGACCATAGTTG
Found at i:24444303 original size:21 final size:22
Alignment explanation
Indices: 24444279--24444325 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
24444269 CAAAAATTAC
*
24444279 AAAATAATTCAAAATAA-TTTT
1 AAAATAATTCAAAAAAACTTTT
*
24444300 AAAA-AATTTAAAAAAACTTTT
1 AAAATAATTCAAAAAAACTTTT
24444321 AAAAT
1 AAAAT
24444326 TCAAAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (22 bp):
AAAATAATTCAAAAAAACTTTT
Found at i:24445004 original size:27 final size:27
Alignment explanation
Indices: 24444974--24445063 Score: 105
Period size: 27 Copynumber: 3.4 Consensus size: 27
24444964 TTACGGAGTT
*
24444974 TGCCGCAAAGGTGTTCCTTTT-ATATTG
1 TGCCACAAAGGTGTT-CTTTTAATATTG
24445001 TGCCACAAAGGTGTTCTTTTAATATTG
1 TGCCACAAAGGTGTTCTTTTAATATTG
*** *
24445028 CATCACAAA--TGTTCTTTTCATATTG
1 TGCCACAAAGGTGTTCTTTTAATATTG
24445053 TGCCACAAAGG
1 TGCCACAAAGG
24445064 CACTCTTTTC
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
25 21 0.40
26 5 0.10
27 26 0.50
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.38
Consensus pattern (27 bp):
TGCCACAAAGGTGTTCTTTTAATATTG
Found at i:24445059 original size:25 final size:25
Alignment explanation
Indices: 24444985--24445079 Score: 84
Period size: 27 Copynumber: 3.6 Consensus size: 25
24444975 GCCGCAAAGG
24444985 TGTTCCTTTT-ATATTGTGCCACAAA
1 TGTT-CTTTTCATATTGTGCCACAAA
* ***
24445010 GGTGTTCTTTTAATATTGCATCACAAA
1 --TGTTCTTTTCATATTGTGCCACAAA
24445037 TGTTCTTTTCATATTGTGCCACAAA
1 TGTTCTTTTCATATTGTGCCACAAA
* *
24445062 GGCACTCTTTTCATATTG
1 TG--TTCTTTTCATATTG
24445080 CACTACAAAG
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
25 22 0.39
26 5 0.09
27 29 0.52
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (25 bp):
TGTTCTTTTCATATTGTGCCACAAA
Found at i:24445087 original size:27 final size:27
Alignment explanation
Indices: 24445015--24445092 Score: 79
Period size: 27 Copynumber: 3.0 Consensus size: 27
24445005 ACAAAGGTGT
* * * *
24445015 TCTTTTAATATTGCATCACAAATG--T
1 TCTTTTCATATTGCACCACAAAGGCAC
**
24445040 TCTTTTCATATTGTGCCACAAAGGCAC
1 TCTTTTCATATTGCACCACAAAGGCAC
*
24445067 TCTTTTCATATTGCACTACAAAGGCA
1 TCTTTTCATATTGCACCACAAAGGCA
24445093 TTCCTTATCT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
25 19 0.45
27 23 0.55
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (27 bp):
TCTTTTCATATTGCACCACAAAGGCAC
Found at i:24448111 original size:119 final size:119
Alignment explanation
Indices: 24447918--24448149 Score: 446
Period size: 119 Copynumber: 1.9 Consensus size: 119
24447908 TTGTGGGAAC
24447918 CATCTTCAACCTTCTTCTTGCCATTGTCTTACATTGGAGGGGAGATTAGAGCCGTTTGAAGGGAG
1 CATCTTCAACCTTCTTCTTGCCATTGTCTTACATTGGAGGGGAGATTAGAGCCGTTTGAAGGGAG
*
24447983 TTGTGAAATCTTTCTTGATTTCAAGGCTTCTTAGGACTTTTTCTTTATGGGAGT
66 TTGTGAAATCTTTCTCGATTTCAAGGCTTCTTAGGACTTTTTCTTTATGGGAGT
*
24448037 CATCTTCAGCCTTCTTCTTGCCATTGTCTTACATTGGAGGGGAGATTAGAGCCGTTTGAAGGGAG
1 CATCTTCAACCTTCTTCTTGCCATTGTCTTACATTGGAGGGGAGATTAGAGCCGTTTGAAGGGAG
24448102 TTGTGAAATCTTTCTCGATTTCAAGGCTTCTTAGGACTTTTTCTTTAT
66 TTGTGAAATCTTTCTCGATTTCAAGGCTTCTTAGGACTTTTTCTTTAT
24448150 TTTCTTGCTG
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
119 111 1.00
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.40
Consensus pattern (119 bp):
CATCTTCAACCTTCTTCTTGCCATTGTCTTACATTGGAGGGGAGATTAGAGCCGTTTGAAGGGAG
TTGTGAAATCTTTCTCGATTTCAAGGCTTCTTAGGACTTTTTCTTTATGGGAGT
Found at i:24448961 original size:60 final size:60
Alignment explanation
Indices: 24448895--24449015 Score: 242
Period size: 60 Copynumber: 2.0 Consensus size: 60
24448885 AGTTGATAAA
24448895 TTCCTTTTATTATATAAAAATATTACAAAATTAATTTTATAATTAAATAAAAGCTTGGTT
1 TTCCTTTTATTATATAAAAATATTACAAAATTAATTTTATAATTAAATAAAAGCTTGGTT
24448955 TTCCTTTTATTATATAAAAATATTACAAAATTAATTTTATAATTAAATAAAAGCTTGGTT
1 TTCCTTTTATTATATAAAAATATTACAAAATTAATTTTATAATTAAATAAAAGCTTGGTT
24449015 T
1 T
24449016 GAAAATCCAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (60 bp):
TTCCTTTTATTATATAAAAATATTACAAAATTAATTTTATAATTAAATAAAAGCTTGGTT
Found at i:24450377 original size:18 final size:18
Alignment explanation
Indices: 24450367--24450415 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
24450357 AATTTTACAT
24450367 TTTTAAAAAATTATAATA
1 TTTTAAAAAATTATAATA
*
24450385 TTTTAAAAAATTATAAAAA
1 TTTTAAAAAATTAT-AATA
*
24450404 TTCTAAAAAATT
1 TTTTAAAAAATT
24450416 CTAAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
18 14 0.50
19 14 0.50
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
TTTTAAAAAATTATAATA
Found at i:24450403 original size:10 final size:10
Alignment explanation
Indices: 24450370--24450423 Score: 51
Period size: 10 Copynumber: 5.7 Consensus size: 10
24450360 TTTACATTTT
24450370 TAAAAAATTA
1 TAAAAAATTA
* *
24450380 T--AATATTT
1 TAAAAAATTA
24450388 TAAAAAATTA
1 TAAAAAATTA
*
24450398 T-AAAAATTC
1 TAAAAAATTA
*
24450407 TAAAAAATTC
1 TAAAAAATTA
24450417 TAAAAAA
1 TAAAAAA
24450424 AATTAAATTC
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
8 6 0.17
9 8 0.22
10 22 0.61
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:24450410 original size:19 final size:19
Alignment explanation
Indices: 24450370--24450422 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
24450360 TTTACATTTT
* *
24450370 TAAAAAATTAT-AATATTT
1 TAAAAAATTATAAAAATTC
24450388 TAAAAAATTATAAAAATTC
1 TAAAAAATTATAAAAATTC
*
24450407 TAAAAAATTCTAAAAA
1 TAAAAAATTATAAAAA
24450423 AAATTAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
18 11 0.35
19 20 0.65
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (19 bp):
TAAAAAATTATAAAAATTC
Found at i:24450421 original size:18 final size:18
Alignment explanation
Indices: 24450370--24450421 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
24450360 TTTACATTTT
* *
24450370 TAAAAAATTATAATATTT
1 TAAAAAATTATAAAATTC
24450388 TAAAAAATTATAAAAATTC
1 TAAAAAATTAT-AAAATTC
*
24450407 TAAAAAATTCTAAAA
1 TAAAAAATTATAAAA
24450422 AAAATTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
18 15 0.50
19 15 0.50
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAAAAATTATAAAATTC
Found at i:24450427 original size:12 final size:10
Alignment explanation
Indices: 24450388--24450423 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
24450378 TATAATATTT
*
24450388 TAAAAAATTA
1 TAAAAAATTC
24450398 T-AAAAATTC
1 TAAAAAATTC
24450407 TAAAAAATTC
1 TAAAAAATTC
24450417 TAAAAAA
1 TAAAAAA
24450424 AATTAAATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (10 bp):
TAAAAAATTC
Found at i:24459301 original size:20 final size:20
Alignment explanation
Indices: 24459260--24459301 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
24459250 ATTAATATTT
* *
24459260 TAATATTTTTAAATTTAAAA
1 TAATATTATTAAATATAAAA
24459280 TAATATTATT-AATATAATAA
1 TAATATTATTAAATATAA-AA
24459300 TA
1 TA
24459302 CTTGACTGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TAATATTATTAAATATAAAA
Found at i:24466939 original size:15 final size:16
Alignment explanation
Indices: 24466919--24466951 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
24466909 AATTGGTTCT
*
24466919 AATAATTGA-AAATTA
1 AATAATTCATAAATTA
24466934 AATAATTCATAAATTA
1 AATAATTCATAAATTA
24466950 AA
1 AA
24466952 AAGAAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (16 bp):
AATAATTCATAAATTA
Found at i:24471252 original size:20 final size:19
Alignment explanation
Indices: 24471225--24471262 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
24471215 AAGTAAAATG
24471225 AAAGAATAAAAAGAAACAA
1 AAAGAATAAAAAGAAACAA
*
24471244 AAAGAAATAGAAAGAAACA
1 AAAG-AATAAAAAGAAACA
24471263 GAATAGAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.76, C:0.05, G:0.13, T:0.05
Consensus pattern (19 bp):
AAAGAATAAAAAGAAACAA
Found at i:24472289 original size:38 final size:39
Alignment explanation
Indices: 24472187--24472295 Score: 105
Period size: 38 Copynumber: 2.8 Consensus size: 39
24472177 AACTTCAAGT
* * **
24472187 CGATGAGACACTGGGTGTCACTATTTTACTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA--ACTTTACTTCGGAGAGACC
* * * *
24472228 CAATGAGATACTGGGTATC-ACTTTACTTCGGCGAG-CC
1 CGATGAGACACTGGGTGTCAACTTTACTTCGGAGAGACC
*
24472265 CGATGAGACACTGGGTGTCAACTTTGCTTCG
1 CGATGAGACACTGGGTGTCAACTTTACTTCG
24472296 AACTATCCGA
Statistics
Matches: 55, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
37 16 0.29
38 23 0.42
41 16 0.29
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAACTTTACTTCGGAGAGACC
Found at i:24477000 original size:20 final size:18
Alignment explanation
Indices: 24476977--24477025 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
24476967 TTTTGTTTGC
24476977 AAAATCAAAGTTTTCTTTAA
1 AAAATCAAAGTTTTC-TT-A
* *
24476997 AAAATCACTACTTTTCTTA
1 AAAATCA-AAGTTTTCTTA
24477016 AAAATCAAAG
1 AAAATCAAAG
24477026 CTTTATTCCA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
18 1 0.04
19 8 0.33
20 9 0.38
21 6 0.25
ACGTcount: A:0.47, C:0.14, G:0.04, T:0.35
Consensus pattern (18 bp):
AAAATCAAAGTTTTCTTA
Found at i:24477029 original size:19 final size:21
Alignment explanation
Indices: 24476977--24477029 Score: 60
Period size: 19 Copynumber: 2.7 Consensus size: 21
24476967 TTTTGTTTGC
24476977 AAAATCAAAG-TTTTCTTTAA
1 AAAATCAAAGCTTTTCTTTAA
*
24476997 AAAATCACTA-CTTTTC-TT-A
1 AAAATCA-AAGCTTTTCTTTAA
24477016 AAAATCAAAGCTTT
1 AAAATCAAAGCTTT
24477030 ATTCCAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
18 1 0.04
19 12 0.43
20 9 0.32
21 6 0.21
ACGTcount: A:0.43, C:0.15, G:0.04, T:0.38
Consensus pattern (21 bp):
AAAATCAAAGCTTTTCTTTAA
Found at i:24481566 original size:23 final size:23
Alignment explanation
Indices: 24481540--24481591 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
24481530 TGATTTTTAA
*
24481540 ATTTTGAATTATTTAATCATAAT
1 ATTTAGAATTATTTAATCATAAT
* *
24481563 ATTTAGAATTATTTAGTGATAAT
1 ATTTAGAATTATTTAATCATAAT
24481586 ATTTAG
1 ATTTAG
24481592 GTAAAATCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.50
Consensus pattern (23 bp):
ATTTAGAATTATTTAATCATAAT
Found at i:24494707 original size:70 final size:70
Alignment explanation
Indices: 24494610--24495420 Score: 629
Period size: 70 Copynumber: 11.6 Consensus size: 70
24494600 CTGACGATTA
** ** * * **
24494610 AAGGCTCGCAGGTTCAATACTACAGCCTAGAAAACAATTAGCGCGAGTTTACGCTCCCAGCTAAT
1 AAGGCTCGCAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGCTTACGCTCCCAGCTGGT
*
24494675 ATCCT
66 ATCTT
* * * * * * *
24494680 AAGGCTCACAGGTTCAATACCGCAGCCTCTC-AAACAGTTAGTGTGAGTTTACGCTCCTAGTTGA
1 AAGGCTCGCAGGTTCAATACCGCAGCCTC-CAAAACAGTTAGCGCGAGCTTACGCTCCCAGCTGG
*
24494744 TATCAT
65 TATCTT
** * *
24494750 AAGGCTCGCAGGTTCAATATTGCAGCCTCCCAAACAGTTAGCGCGAGCTTACGCTCCCAACTGGT
1 AAGGCTCGCAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGCTTACGCTCCCAGCTGGT
*
24494815 ATTTT
66 ATCTT
** * * * **
24494820 AAGTATTGTAGGTTCAATACCGTAGCCTCCAAAACAGTTAGCGCGA-CTTATAC-CCCGAGCTGG
1 AAGGCTCGCAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGCTTACGCTCCC-AGCTGG
*
24494883 TATATT
65 TATCTT
* * * * * * * * * *
24494889 AAGGCTCCCAGGTTCAATATCACAGCCTTCAAAACAGTTGGCACGAGCCTACGCTCCTAGTTGAT
1 AAGGCTCGCAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGCTTACGCTCCCAGCTGGT
24494954 ATCTT
66 ATCTT
* ** * ** * * *
24494959 AAGGCTTGCAAATTCAATACTGCAGCCTAGAAAACAGTTAGTGCGAGCCTACGCTCCAAGCTGGT
1 AAGGCTCGCAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGCTTACGCTCCCAGCTGGT
24495024 ATCTT
66 ATCTT
** * ** * * * * * *
24495029 AAGGCTTACAAGTTCAATACAACAACCTTCAAAATAGTTAGCGCGAGCCTATGCTCCTAGCTGGT
1 AAGGCTCGCAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGCTTACGCTCCCAGCTGGT
24495094 ATCTT
66 ATCTT
* ** * * * * *
24495099 AAGGTTCATAGGTTCAATATCGCAACCTTCAACACAGTTAGCGCAAGCTTACGCTCCCAGCTGGT
1 AAGGCTCGCAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGCTTACGCTCCCAGCTGGT
24495164 ATCTT
66 ATCTT
* * * * * * *
24495169 AAGGATCGCCGGTTTAATACCTCAGCCTCCAAAATAGTTAGCGTGAGCCTACGCTCCCAGCTGGT
1 AAGGCTCGCAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGCTTACGCTCCCAGCTGGT
*
24495234 ATCCT
66 ATCTT
* * * * ** ** * ** *
24495239 AAGGCTTGCAGGTCCAATATCGTAGCCTTTAAAACAGTTAAAGCGAGCTTACACTCCCAATTGGC
1 AAGGCTCGCAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGCTTACGCTCCCAGCTGGT
24495304 ATCTT
66 ATCTT
** * * * * * * * ** ** *
24495309 AAACCTCGCAGGTTCAATACCACAGCTTCTAAAAAAGTTAACACGAGCCTACATTCCCAATTGAT
1 AAGGCTCGCAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGCTTACGCTCCCAGCTGGT
*
24495374 ATCCT
66 ATCTT
* * *
24495379 AAGGCTCGCAGGTTCAATACCGCAGCTTCTAAAAAAGTTAGC
1 AAGGCTCGCAGGTTCAATACCGCAGCCTCCAAAACAGTTAGC
24495421 ACGAACCTAC
Statistics
Matches: 587, Mismatches: 149, Indels: 10
0.79 0.20 0.01
Matches are distributed among these distances:
68 3 0.01
69 51 0.09
70 531 0.90
71 2 0.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (70 bp):
AAGGCTCGCAGGTTCAATACCGCAGCCTCCAAAACAGTTAGCGCGAGCTTACGCTCCCAGCTGGT
ATCTT
Found at i:24495310 original size:210 final size:208
Alignment explanation
Indices: 24494610--24495430 Score: 716
Period size: 210 Copynumber: 3.9 Consensus size: 208
24494600 CTGACGATTA
* ** * * ** **
24494610 AAGGCTCGCAGGTTCAATAC-TACAGCCTAGAAAACAATTAGCGCGAGTTTACGCTCCCAGCTAA
1 AAGGCTTGCAGGTTCAATACGT--AGCCTTCAAAACAGTTAGCGCGAGCTTATACTCCCAGCTGG
* * * * *
24494674 TATCCTAAGGCTCACAGGTTCAATACCGCAGCCTCTCAAACAGTTAGTGTGAGTTTACGCTCCTA
64 TATCTTAAGGCTCACAGGTTCAATATCGCAGCCT-TCAAACAGTTAGCGCGAGCTTACGCTCCTA
* * * *
24494739 GTTGATATCATAAGGCTCGCAGGTTCAATATTGCAGCCTCCCAAACAGTTAGCGCGAGCTTACGC
128 GTTGATATCTTAAGGCTCGCAGGTTCAATACTGCAGCCTCCAAAACAGTTAGCGCGAGCCTACGC
* *
24494804 TCCCAACTGGTATTTT
193 TCCCAGCTGGTATCTT
** * *
24494820 AAGTATTGTAGGTTCAATACCGTAGCCTCCAAAACAGTTAGCGCGA-CTTATAC-CCCGAGCTGG
1 AAGGCTTGCAGGTTCAATA-CGTAGCCTTCAAAACAGTTAGCGCGAGCTTATACTCCC-AGCTGG
* * * * * *
24494883 TATATTAAGGCTCCCAGGTTCAATATCACAGCCTTCAAAACAGTTGGCACGAGCCTACGCTCCTA
64 TATCTTAAGGCTCACAGGTTCAATATCGCAGCCTTC-AAACAGTTAGCGCGAGCTTACGCTCCTA
* ** ** *
24494948 GTTGATATCTTAAGGCTTGCAAATTCAATACTGCAGCCTAGAAAACAGTTAGTGCGAGCCTACGC
128 GTTGATATCTTAAGGCTCGCAGGTTCAATACTGCAGCCTCCAAAACAGTTAGCGCGAGCCTACGC
*
24495013 TCCAAGCTGGTATCTT
193 TCCCAGCTGGTATCTT
* * ** * * * * *
24495029 AAGGCTTACAAGTTCAATACAACAACCTTCAAAATAGTTAGCGCGAGCCTATGCTCCTAGCTGGT
1 AAGGCTTGCAGGTTCAATAC-GTAGCCTTCAAAACAGTTAGCGCGAGCTTATACTCCCAGCTGGT
* * * * *
24495094 ATCTTAAGGTTCATAGGTTCAATATCGCAACCTTCAACACAGTTAGCGCAAGCTTACGCTCCCAG
65 ATCTTAAGGCTCACAGGTTCAATATCGCAGCCTTCAA-ACAGTTAGCGCGAGCTTACGCTCCTAG
* * * * * * *
24495159 CTGGTATCTTAAGGATCGCCGGTTTAATACCT-CAGCCTCCAAAATAGTTAGCGTGAGCCTACGC
129 TTGATATCTTAAGGCTCGCAGGTTCAATA-CTGCAGCCTCCAAAACAGTTAGCGCGAGCCTACGC
*
24495223 TCCCAGCTGGTATCCT
193 TCCCAGCTGGTATCTT
* * ** * ** *
24495239 AAGGCTTGCAGGTCCAATATCGTAGCCTTTAAAACAGTTAAAGCGAGCTTACACTCCCAATTGGC
1 AAGGCTTGCAGGTTCAATA-CGTAGCCTTCAAAACAGTTAGCGCGAGCTTATACTCCCAGCTGGT
** * * * * * * * ** *
24495304 ATCTTAAACCTCGCAGGTTCAATACCACAG-CTTCTAAAAAAGTTAACACGAGCCTACATTCCCA
65 ATCTTAAGGCTCACAGGTTCAATATCGCAGCCTTC--AAACAGTTAGCGCGAGCTTACGCTCCTA
* * * * * * * *
24495368 ATTGATATCCTAAGGCTCGCAGGTTCAATACCGCAGCTTCTAAAAAAGTTAGCACGAACCTAC
128 GTTGATATCTTAAGGCTCGCAGGTTCAATACTGCAGCCTCCAAAACAGTTAGCGCGAGCCTAC
24495431 ATTCGCAGTT
Statistics
Matches: 477, Mismatches: 121, Indels: 26
0.76 0.19 0.04
Matches are distributed among these distances:
208 6 0.01
209 168 0.35
210 294 0.62
211 8 0.02
212 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.25
Consensus pattern (208 bp):
AAGGCTTGCAGGTTCAATACGTAGCCTTCAAAACAGTTAGCGCGAGCTTATACTCCCAGCTGGTA
TCTTAAGGCTCACAGGTTCAATATCGCAGCCTTCAAACAGTTAGCGCGAGCTTACGCTCCTAGTT
GATATCTTAAGGCTCGCAGGTTCAATACTGCAGCCTCCAAAACAGTTAGCGCGAGCCTACGCTCC
CAGCTGGTATCTT
Found at i:24495476 original size:70 final size:70
Alignment explanation
Indices: 24495322--24495461 Score: 183
Period size: 70 Copynumber: 2.0 Consensus size: 70
24495312 CCTCGCAGGT
* * *
24495322 TCAATACCACAGCTTCTAAAAAAGTTAACACGAGCCTACATTCCCAATTGATATCCTAAGGCTCG
1 TCAATAACGCAGCTTCTAAAAAAGTTAACACGAACCTACATTCCCAATTGATATCCTAAGGCTCG
***
24495387 CAGGT
66 CAAAA
* * * *
24495392 TCAATACCGCAGCTTCTAAAAAAGTTAGCACGAACCTACATTCGCAGTTGATATCCTAAGGCTC-
1 TCAATAACGCAGCTTCTAAAAAAGTTAACACGAACCTACATTCCCAATTGATATCCTAAGGCTCG
24495456 CAAAA
66 CAAAA
24495461 T
1 T
24495462 AGTTAACGCG
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
69 3 0.05
70 59 0.95
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.24
Consensus pattern (70 bp):
TCAATAACGCAGCTTCTAAAAAAGTTAACACGAACCTACATTCCCAATTGATATCCTAAGGCTCG
CAAAA
Found at i:24495530 original size:70 final size:70
Alignment explanation
Indices: 24495453--24495625 Score: 229
Period size: 70 Copynumber: 2.5 Consensus size: 70
24495443 TATCCTAAGG
* * * *
24495453 CTCCAAAATAGTTAACGCGAGCTTATGTTCCCAACTGGTATCCTAAGGCTCGCAGGTTCAATATC
1 CTCCAAAATAGTTAACGTGAGCTTACGTTCCCAACTGGTATCCTAAGGCTCACAGGTTCAATACC
24495518 GTAGC
66 GTAGC
** * * * **
24495523 CTCCAAAATAGTTAGTGTGAGCTTACGCTCCTAGCTGGTATTTTAAGGCTCACAGGTTCAATACC
1 CTCCAAAATAGTTAACGTGAGCTTACGTTCCCAACTGGTATCCTAAGGCTCACAGGTTCAATACC
24495588 GTAGC
66 GTAGC
* *
24495593 CTCCAAAACAGTTAACATGAGCTTACGTTCCCA
1 CTCCAAAATAGTTAACGTGAGCTTACGTTCCCA
24495626 GCCGATATTA
Statistics
Matches: 86, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
70 86 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (70 bp):
CTCCAAAATAGTTAACGTGAGCTTACGTTCCCAACTGGTATCCTAAGGCTCACAGGTTCAATACC
GTAGC
Found at i:24509532 original size:24 final size:24
Alignment explanation
Indices: 24509494--24509540 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
24509484 AGCTGCTGTT
24509494 GAGGCACCCACTC-AACTTGCTACC
1 GAGGCACCCACTCAAAC-TGCTACC
* *
24509518 GAGGCACCTATTCAAACTGCTAC
1 GAGGCACCCACTCAAACTGCTAC
24509541 TGGAGAACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.28, C:0.36, G:0.17, T:0.19
Consensus pattern (24 bp):
GAGGCACCCACTCAAACTGCTACC
Found at i:24513180 original size:19 final size:19
Alignment explanation
Indices: 24513158--24513197 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
24513148 TCATTTTAGA
* *
24513158 TAATTTATGTTATTTTGGT
1 TAATTAATGTTAATTTGGT
*
24513177 TAATTAATTTTAATTTGGT
1 TAATTAATGTTAATTTGGT
24513196 TA
1 TA
24513198 TTCATAATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (19 bp):
TAATTAATGTTAATTTGGT
Found at i:24514376 original size:26 final size:26
Alignment explanation
Indices: 24514345--24514426 Score: 89
Period size: 26 Copynumber: 3.3 Consensus size: 26
24514335 GCTTCATTGA
24514345 TTGTTTTGTTGCATTCATAAATAAAG
1 TTGTTTTGTTGCATTCATAAATAAAG
* * * ** *
24514371 TTGTTTTATT-TATAC-TTCAT-TAG
1 TTGTTTTGTTGCATTCATAAATAAAG
24514394 TTGTTTTGTTGCATTCATAAATAAAG
1 TTGTTTTGTTGCATTCATAAATAAAG
24514420 TTGTTTT
1 TTGTTTT
24514427 ATTTATGCTT
Statistics
Matches: 41, Mismatches: 12, Indels: 6
0.69 0.20 0.10
Matches are distributed among these distances:
23 11 0.27
24 6 0.15
25 6 0.15
26 18 0.44
ACGTcount: A:0.26, C:0.07, G:0.13, T:0.54
Consensus pattern (26 bp):
TTGTTTTGTTGCATTCATAAATAAAG
Found at i:24514389 original size:49 final size:51
Alignment explanation
Indices: 24514244--24514501 Score: 310
Period size: 49 Copynumber: 4.9 Consensus size: 51
24514234 AGGCATATTA
* * *
24514244 GCATTCATAAATAAAGTTGTGTTTTTGTTTATTTATGTTTCATTGAATGTTTTCTT
1 GCATTCATAAATAAAG-TGTG---TT-TTTATTTATGCTTCATTGATTGTTTTGTT
24514300 GCATTCATAAATAAAGTTGTGTTTTCTTTATTTATGCTTCATTGATTGTTTTGTT
1 GCATTCATAAATAAAG-TGTG--TT-TTTATTTATGCTTCATTGATTGTTTTGTT
*
24514355 GCATTCATAAATAAAGT-TG-TTTTATTTATACTTCATT-AGTTGTTTTGTT
1 GCATTCATAAATAAAGTGTGTTTTTATTTATGCTTCATTGA-TTGTTTTGTT
24514404 GCATTCATAAATAAAGT-TG-TTTTATTTATGCTTCATTGATTGTTTTGTT
1 GCATTCATAAATAAAGTGTGTTTTTATTTATGCTTCATTGATTGTTTTGTT
* * * *
24514453 GCATTCAGAAATAAGGTGGTGTTTTTAATTATGCTTCATTGTTTGTTTT
1 GCATTCATAAATAAAGT-GTGTTTTTATTTATGCTTCATTGATTGTTTT
24514502 TTGATTAGCT
Statistics
Matches: 187, Mismatches: 10, Indels: 14
0.89 0.05 0.07
Matches are distributed among these distances:
48 1 0.01
49 87 0.47
50 2 0.01
51 2 0.01
52 25 0.13
53 2 0.01
54 1 0.01
55 46 0.25
56 21 0.11
ACGTcount: A:0.24, C:0.08, G:0.15, T:0.53
Consensus pattern (51 bp):
GCATTCATAAATAAAGTGTGTTTTTATTTATGCTTCATTGATTGTTTTGTT
Found at i:24515891 original size:11 final size:12
Alignment explanation
Indices: 24515875--24515916 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
24515865 GAATTCAATC
24515875 ATTCAATGGAG-
1 ATTCAATGGAGA
24515886 ATTCAATGGATGA
1 ATTCAATGGA-GA
* *
24515899 ATTTAATGGAGT
1 ATTCAATGGAGA
24515911 ATTCAA
1 ATTCAA
24515917 GATGGAAGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
11 10 0.38
12 7 0.27
13 9 0.35
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.33
Consensus pattern (12 bp):
ATTCAATGGAGA
Found at i:24519281 original size:14 final size:14
Alignment explanation
Indices: 24519253--24519281 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
24519243 GCTTAGTTGC
24519253 TTTTGACTTGATTT
1 TTTTGACTTGATTT
24519267 TTTTG-CTTGATTT
1 TTTTGACTTGATTT
24519280 TT
1 TT
24519282 AAGCTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.10, C:0.07, G:0.14, T:0.69
Consensus pattern (14 bp):
TTTTGACTTGATTT
Found at i:24522307 original size:50 final size:51
Alignment explanation
Indices: 24522175--24522314 Score: 167
Period size: 50 Copynumber: 2.8 Consensus size: 51
24522165 NNNNNNNNNN
* * *
24522175 TACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATCTGA
1 TACACGTAGTAGCCTGCACATAGTACTACACACGCGACCGAAACTATCCGA
* * * * * *
24522226 TACGCATAGTAGCCTGCACATAGTACTACACATGCGACC-TATC-ATTCCGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGCGACCGAAACTA-TCCGA
*
24522276 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACC
1 TACACGTAGTAGCCTGCACATAGTACTACACACGCGACC
24522315 ATCACTTTAG
Statistics
Matches: 75, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
49 1 0.01
50 40 0.53
51 34 0.45
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.23
Consensus pattern (51 bp):
TACACGTAGTAGCCTGCACATAGTACTACACACGCGACCGAAACTATCCGA
Found at i:24522325 original size:26 final size:26
Alignment explanation
Indices: 24522296--24522348 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
24522286 AGCCTGCACA
24522296 TAGTACTACACACGTGACCATCACTT
1 TAGTACTACACACGTGACCATCACTT
24522322 TAGTACTACACACGTGACCATCACTT
1 TAGTACTACACACGTGACCATCACTT
24522348 T
1 T
24522349 CACTTTTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.30, G:0.11, T:0.28
Consensus pattern (26 bp):
TAGTACTACACACGTGACCATCACTT
Found at i:24527882 original size:98 final size:102
Alignment explanation
Indices: 24527756--24528001 Score: 320
Period size: 98 Copynumber: 2.4 Consensus size: 102
24527746 TTTTCTGTAT
* * **
24527756 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCC-CGCCATGTCC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCACGCCATGTCC
** *
24527820 CAGACATGGTCTTATGGGGGACCTCTC-ATC-CC-GG
66 CAGACATGGTCTTACAGGGGACCTCTCAATCTCCAGA
* * *
24527854 TGCCAACGCCATGTCCCAGACATTGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCC-ACGCCATGTC
*
24527919 CCAGACATGGTCTTACATGGGACCTCTCATAATCTCCATGA
65 CCAGACATGGTCTTACAGGGGACCTCTC--AATCTCCA-GA
*
24527960 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
24528002 TTACCCAAAT
Statistics
Matches: 126, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
98 47 0.37
100 34 0.27
103 3 0.02
104 2 0.02
106 40 0.32
ACGTcount: A:0.21, C:0.31, G:0.22, T:0.26
Consensus pattern (102 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCACGCCATGTCC
CAGACATGGTCTTACAGGGGACCTCTCAATCTCCAGA
Found at i:24527980 original size:56 final size:51
Alignment explanation
Indices: 24527707--24528001 Score: 298
Period size: 50 Copynumber: 5.8 Consensus size: 51
24527697 GATAATAACA
* * * ** ****
24527707 TGCCAAAGCCATGTCCCAGACATGGTATTACATGGGA--TGTTTTCTGTAT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCCGG
* * * ** *
24527756 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATAT-CGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCCGG
***
24527806 TGCC--CGCCATGTCCCAGACATGGTCTTATGGGGGACCTCTCATC-CCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCCGG
*
24527854 TGCCAACGCCATGTCCCAGACATTGTCTTACATGGGACCTCTCATCT-CGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCCGG
*
24527904 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCCATGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTCC--GG
* *
24527960 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
24528002 TTACCCAAAT
Statistics
Matches: 206, Mismatches: 28, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
48 38 0.18
49 33 0.16
50 85 0.41
51 4 0.02
53 4 0.02
54 1 0.00
56 41 0.20
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (51 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCCGG
Found at i:24534618 original size:35 final size:36
Alignment explanation
Indices: 24534579--24534648 Score: 99
Period size: 34 Copynumber: 2.0 Consensus size: 36
24534569 CCTCATTTTA
* *
24534579 CTTTCTTTTCCTTTTCTTTTTTC-T-TTTGGCCGAAC
1 CTTTCTTTT-CTTCTATTTTTTCTTCTTTGGCCGAAC
24534614 CTTTCTTTTCTTCTATTTTTTCTTCTTTGGCCGAA
1 CTTTCTTTTCTTCTATTTTTTCTTCTTTGGCCGAA
24534649 TAATCTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
34 11 0.35
35 10 0.32
36 10 0.32
ACGTcount: A:0.07, C:0.24, G:0.09, T:0.60
Consensus pattern (36 bp):
CTTTCTTTTCTTCTATTTTTTCTTCTTTGGCCGAAC
Found at i:24535335 original size:27 final size:27
Alignment explanation
Indices: 24535301--24535673 Score: 461
Period size: 27 Copynumber: 13.9 Consensus size: 27
24535291 CCGTAATGGG
24535301 ATCGAAATACCCTCGAAGGGTAAAATT
1 ATCGAAATACCCTCGAAGGGTAAAATT
* * ** * *
24535328 ACCAAAATACCCTTAAAGGATAGAATT
1 ATCGAAATACCCTCGAAGGGTAAAATT
24535355 A-CTGAAATACCCTCGAAGGGTAAAATT
1 ATC-GAAATACCCTCGAAGGGTAAAATT
* *
24535382 ACCGAAATAACCTCGAAGGGTAAAATT
1 ATCGAAATACCCTCGAAGGGTAAAATT
** ** *
24535409 ATTAAAATACAATTGAAGGGTAAAATT
1 ATCGAAATACCCTCGAAGGGTAAAATT
*
24535436 ATTGAAATACCCTCGAAGGGTAAAATT
1 ATCGAAATACCCTCGAAGGGTAAAATT
24535463 A--GAAATACCCTCGAAGGGTAAAATT
1 ATCGAAATACCCTCGAAGGGTAAAATT
*
24535488 ATCGAAATACCCTCGAA-GGTAGAATT
1 ATCGAAATACCCTCGAAGGGTAAAATT
24535514 ATCGAAATACCCTCGAAGGGTAAAATT
1 ATCGAAATACCCTCGAAGGGTAAAATT
24535541 ATCGAAATACCCTCGAAGGGTAAAATT
1 ATCGAAATACCCTCGAAGGGTAAAATT
* * * *
24535568 AACAAAATACCCTCAAAGGGTAAAATG
1 ATCGAAATACCCTCGAAGGGTAAAATT
*
24535595 ATCGAAATACCAC-CGAAAGGTAAAATT
1 ATCGAAATACC-CTCGAAGGGTAAAATT
* *
24535622 ATCGAAATACCCCCGAAGGGTAAAATG
1 ATCGAAATACCCTCGAAGGGTAAAATT
* *
24535649 A-CTGAAACACCCCCGAAGGGTAAAA
1 ATC-GAAATACCCTCGAAGGGTAAAA
24535674 CGATCGTTAT
Statistics
Matches: 301, Mismatches: 37, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
25 25 0.08
26 28 0.09
27 246 0.82
28 2 0.01
ACGTcount: A:0.44, C:0.18, G:0.18, T:0.20
Consensus pattern (27 bp):
ATCGAAATACCCTCGAAGGGTAAAATT
Found at i:24535897 original size:26 final size:26
Alignment explanation
Indices: 24535868--24535941 Score: 112
Period size: 26 Copynumber: 2.8 Consensus size: 26
24535858 ATGCCATATA
*
24535868 TACTGTTACTGGTAGCTTTGCTGCGT
1 TACTGTTACTGGCAGCTTTGCTGCGT
*
24535894 TACTGTTATTGGCAGCTTTGCTGCGT
1 TACTGTTACTGGCAGCTTTGCTGCGT
* *
24535920 TATTATTACTGGCAGCTTTGCT
1 TACTGTTACTGGCAGCTTTGCT
24535942 ACGATATTGG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.14, C:0.19, G:0.24, T:0.43
Consensus pattern (26 bp):
TACTGTTACTGGCAGCTTTGCTGCGT
Found at i:24536099 original size:28 final size:28
Alignment explanation
Indices: 24536059--24536143 Score: 136
Period size: 28 Copynumber: 3.1 Consensus size: 28
24536049 TACTGATTAT
*
24536059 TGTATTGGGCTAAGGCCCACATTGTTGC
1 TGTATTGGGCTAAGGCCCACATTGTTAC
24536087 TGTATTGGGCTAAGGCCCACATTGTTAC
1 TGTATTGGGCTAAGGCCCACATTGTTAC
* *
24536115 TGTAATGGGCTAAGGCCCACACTG-TAC
1 TGTATTGGGCTAAGGCCCACATTGTTAC
24536142 TG
1 TG
24536144 ATACTGTATA
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 5 0.09
28 49 0.91
ACGTcount: A:0.21, C:0.22, G:0.27, T:0.29
Consensus pattern (28 bp):
TGTATTGGGCTAAGGCCCACATTGTTAC
Found at i:24536158 original size:33 final size:31
Alignment explanation
Indices: 24536059--24536171 Score: 96
Period size: 28 Copynumber: 3.8 Consensus size: 31
24536049 TACTGATTAT
* *
24536059 TGTATTGGGCTAAGGCCCACATTGTTG---C
1 TGTATAGGGCTAAGGCCCACACTGTTGATAC
* *
24536087 TGTATTGGGCTAAGGCCCACA---TTGTTAC
1 TGTATAGGGCTAAGGCCCACACTGTTGATAC
24536115 TGTA-ATGGGCTAAGGCCCACACTGTACTGATAC
1 TGTATA-GGGCTAAGGCCCACACTGT--TGATAC
* *
24536148 TGTATAGGGCTTAGGCCCAGACTG
1 TGTATAGGGCTAAGGCCCACACTG
24536172 ATTCTGCATG
Statistics
Matches: 71, Mismatches: 4, Indels: 15
0.79 0.04 0.17
Matches are distributed among these distances:
25 3 0.04
28 41 0.58
31 1 0.01
33 25 0.35
34 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.28
Consensus pattern (31 bp):
TGTATAGGGCTAAGGCCCACACTGTTGATAC
Found at i:24536493 original size:36 final size:36
Alignment explanation
Indices: 24536448--24536519 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
24536438 TAGTTAGGTG
*
24536448 AAAACGAATTTTCAAAATAATCACTGTTTTCAAAGA
1 AAAACGAATTTTCAAAATAATCACTATTTTCAAAGA
* * *
24536484 AAAATGAATTTTTAAAATAATCACTATTTTTAAAGA
1 AAAACGAATTTTCAAAATAATCACTATTTTCAAAGA
24536520 CACGAACTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.35
Consensus pattern (36 bp):
AAAACGAATTTTCAAAATAATCACTATTTTCAAAGA
Found at i:24540801 original size:41 final size:36
Alignment explanation
Indices: 24540747--24540836 Score: 101
Period size: 37 Copynumber: 2.4 Consensus size: 36
24540737 GTGGAAAAAC
24540747 AAAAACAAAAGAGAATGAGATAACAAAAAAAAGAAAAAGA
1 AAAAACAAAAGAGAAT--G-TAA-AAAAAAAAGAAAAAGA
**
24540787 GAAAAACATGAGAGAATGTAAAAAAAAAAGAAAAAGA
1 -AAAAACAAAAGAGAATGTAAAAAAAAAAGAAAAAGA
24540824 AAAAGA-AAAAGAG
1 AAAA-ACAAAAGAG
24540837 CATGGGGGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
36 9 0.20
37 17 0.39
38 3 0.07
39 1 0.02
41 14 0.32
ACGTcount: A:0.73, C:0.03, G:0.18, T:0.06
Consensus pattern (36 bp):
AAAAACAAAAGAGAATGTAAAAAAAAAAGAAAAAGA
Found at i:24540854 original size:6 final size:6
Alignment explanation
Indices: 24540806--24540835 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
24540796 GAGAGAATGT
24540806 AAAAA- AAAAAG AAAAAG AAAAAG AAAAAG A
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG A
24540836 GCATGGGGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:24545845 original size:18 final size:19
Alignment explanation
Indices: 24545803--24545846 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
24545793 ATAGGCCAGC
*
24545803 ATAT-AAAAAACGGAAGAA
1 ATATAAAAAAAAGGAAGAA
24545821 ATAATAAAAAAAAGGAA-AA
1 AT-ATAAAAAAAAGGAAGAA
24545840 ATATAAA
1 ATATAAA
24545847 CCATTTTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 7 0.30
19 6 0.26
20 10 0.43
ACGTcount: A:0.73, C:0.02, G:0.11, T:0.14
Consensus pattern (19 bp):
ATATAAAAAAAAGGAAGAA
Found at i:24556414 original size:6 final size:7
Alignment explanation
Indices: 24556388--24556450 Score: 85
Period size: 7 Copynumber: 9.0 Consensus size: 7
24556378 TAAGTTGCAA
24556388 AAAATATG
1 AAAA-ATG
24556396 AAAAATG
1 AAAAATG
24556403 AAAAAATG
1 -AAAAATG
24556411 -AAAATG
1 AAAAATG
24556417 AAAAATG
1 AAAAATG
24556424 AAAAATG
1 AAAAATG
24556431 AAAAATG
1 AAAAATG
*
24556438 AAAAGT-
1 AAAAATG
24556444 AAAAATG
1 AAAAATG
24556451 GAGAGGCTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
6 11 0.22
7 28 0.56
8 11 0.22
ACGTcount: A:0.70, C:0.00, G:0.14, T:0.16
Consensus pattern (7 bp):
AAAAATG
Found at i:24558511 original size:132 final size:132
Alignment explanation
Indices: 24558210--24558734 Score: 783
Period size: 132 Copynumber: 4.0 Consensus size: 132
24558200 GGAGCAGGTT
* * *
24558210 GATGGTGGATTTTACCT-CCTGAGGTTACAGTGGAGTACATTGAAGCCGGTAATTCTA-TCTCCC
1 GATGGTGGATTTTACCTCCCTGTGATTACAGTGGAGTACATTGAAGCCAGTAATTCTACT-TCCC
* *
24558273 TGGGCAGCAGTGGAATAGATTGAAGATTACAGACCTTA----CCTAAGTAGTAGTGGAGTAGATC
65 TGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGTAGTAGTGGAGTAGATC
24558334 GAA
130 GAA
* *
24558337 GATGGTGGATTTTACCTCCCTGTGATTACAGTGGAGTACATTGAAGCCAGTAATTCTTCTTTCCT
1 GATGGTGGATTTTACCTCCCTGTGATTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT
* * * * *
24558402 GGGCAGCAGCGGAATAGATTGAAGATTTTAGATCTTACCTCCCTAAGTAGTAATGGAGTAAATCG
66 GGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGTAGTAGTGGAGTAGATCG
24558467 AA
131 AA
*
24558469 GATGGTGGATTTTACCTCCCTGTGATTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTTCCT
1 GATGGTGGATTTTACCTCCCTGTGATTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT
* **
24558534 GGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATAA
66 GGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGTAGTAGTGGAGTAGATCG
24558599 AA
131 AA
* *
24558601 AATGGCGGATTTTACCTCCCTGTGATTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT
1 GATGGTGGATTTTACCTCCCTGTGATTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT
* * * * * *
24558666 GGGCAGTAGTGGAATAGATTGAAGATTTCAGAACTTATCTCCCAAAGTAGTAGCGGAGCAGATTG
66 GGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGTAGTAGTGGAGTAGATCG
24558731 AA
131 AA
24558733 GA
1 GA
24558735 CGGCGAATCT
Statistics
Matches: 362, Mismatches: 30, Indels: 7
0.91 0.08 0.02
Matches are distributed among these distances:
127 17 0.05
128 73 0.20
129 1 0.00
132 271 0.75
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (132 bp):
GATGGTGGATTTTACCTCCCTGTGATTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT
GGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGTAGTAGTGGAGTAGATCG
AA
Found at i:24558995 original size:50 final size:50
Alignment explanation
Indices: 24558859--24559025 Score: 172
Period size: 50 Copynumber: 3.3 Consensus size: 50
24558849 GTGGAGGGTT
* * *
24558859 GAATCTTACTTCTCCGGGCGGTGTAGTGGAACAGATTAAAGCTACAACGGC
1 GAATCTTACTTC-CCCGGCGGTGTAGTGGAAAAGATTAAAGCCACAACGGC
* * ** ** * ** *
24558910 AAATCTTGCTTCCCCAACATTGCAGTTAAAAAGATTAAAGCCACAACGAC
1 GAATCTTACTTCCCCGGCGGTGTAGTGGAAAAGATTAAAGCCACAACGGC
* *
24558960 GAATCTTACTTCCCTGGCGGTGTAGTGGAATAGATTAAAGCCACAACGGC
1 GAATCTTACTTCCCCGGCGGTGTAGTGGAAAAGATTAAAGCCACAACGGC
**
24559010 GAATCTTGTTTCCCCG
1 GAATCTTACTTCCCCG
24559026 ACATTGTAGT
Statistics
Matches: 88, Mismatches: 28, Indels: 1
0.75 0.24 0.01
Matches are distributed among these distances:
50 78 0.89
51 10 0.11
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.25
Consensus pattern (50 bp):
GAATCTTACTTCCCCGGCGGTGTAGTGGAAAAGATTAAAGCCACAACGGC
Found at i:24559034 original size:50 final size:50
Alignment explanation
Indices: 24558880--24559035 Score: 177
Period size: 50 Copynumber: 3.1 Consensus size: 50
24558870 CTCCGGGCGG
* * * *
24558880 TGTAGTGGAACAGATTAAAGCTACAACGGCAAATCTTGCTTCCCCAACAT
1 TGTAGTGGAAAAGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGACAT
* ** * * * * **
24558930 TGCAGTTAAAAAGATTAAAGCCACAACGACGAATCTTACTTCCCTGGCGG
1 TGTAGTGGAAAAGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGACAT
* *
24558980 TGTAGTGGAATAGATTAAAGCCACAACGGCGAATCTTGTTTCCCCGACAT
1 TGTAGTGGAAAAGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGACAT
24559030 TGTAGT
1 TGTAGT
24559036 CAGACAGTAC
Statistics
Matches: 82, Mismatches: 24, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
50 82 1.00
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (50 bp):
TGTAGTGGAAAAGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGACAT
Found at i:24562118 original size:55 final size:53
Alignment explanation
Indices: 24562005--24562178 Score: 221
Period size: 55 Copynumber: 3.3 Consensus size: 53
24561995 TTAGGCATAT
* *
24562005 TTGCATTCATAAATAAAGTTGTGTTTTTATTTATTTATGTTTCATTAAATGTTTTG
1 TTGCATTCATAAATAAAGTTGTG--TTTATTTATTTATG-TTCATTGATTGTTTTG
* *
24562061 TTGCATTCATAAATAAATTTGTGTTTCCTTTATTTATGTTGCATTGATTGTTTTG
1 TTGCATTCATAAATAAAGTTGTGTTT-ATTTATTTATGTT-CATTGATTGTTTTG
* *
24562116 TTGCATTCATAAATAAAGTTG-ATTTATTTA--TA-CTTCATTGATTGTTTTG
1 TTGCATTCATAAATAAAGTTGTGTTTATTTATTTATGTTCATTGATTGTTTTG
24562165 TTGCATTCATAAAT
1 TTGCATTCATAAAT
24562179 TGTAACACCC
Statistics
Matches: 108, Mismatches: 8, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
49 28 0.26
50 2 0.02
51 2 0.02
53 4 0.04
54 8 0.07
55 42 0.39
56 22 0.20
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (53 bp):
TTGCATTCATAAATAAAGTTGTGTTTATTTATTTATGTTCATTGATTGTTTTG
Found at i:24563022 original size:18 final size:19
Alignment explanation
Indices: 24562995--24563030 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
24562985 CAATATAGGG
*
24562995 TCATTGATTT-AACTTAAA
1 TCATTCATTTCAACTTAAA
24563013 TCATTCATTTCAACTTAA
1 TCATTCATTTCAACTTAA
24563031 GCAAACAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.36, C:0.17, G:0.03, T:0.44
Consensus pattern (19 bp):
TCATTCATTTCAACTTAAA
Found at i:24568191 original size:56 final size:51
Alignment explanation
Indices: 24568113--24568305 Score: 176
Period size: 50 Copynumber: 3.7 Consensus size: 51
24568103 GGGGATGAGA
* * **
24568113 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGAATTATTGAGGTTATGAGAGG-
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGG---CACCGA-G--ATGAGAGGT
*
24568169 TCCCACGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGT
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGT
* * ** * *
24568220 TCCC-CGTGAGACCATGTCTGGGACATGGCATGGGCACATATATGAGAAGT
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGT
* * * *
24568270 T-CCATGTAAGACCATATCTGGGATATGACATTGGCA
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA
24568306 GTACAGGAAA
Statistics
Matches: 117, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
49 2 0.02
50 74 0.63
51 4 0.03
52 1 0.01
53 3 0.03
56 33 0.28
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (51 bp):
TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGT
Found at i:24568219 original size:50 final size:49
Alignment explanation
Indices: 24568161--24568354 Score: 167
Period size: 50 Copynumber: 3.9 Consensus size: 49
24568151 TATTGAGGTT
* *
24568161 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA-CGAC
* * * *
24568211 ATGAGAGGTTCCC-CGTGAGACCATGTCTGGGACATGGCATGGGCACATAT
1 ATGAGAGG-TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCAC-GAC
* * * * * *
24568261 ATGAGAAGTTCCATGTAAGACCATATCTGGGATATGACATTGGCA-GTAC
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACG-AC
* * ** * * *
24568310 AGGAAACATCCCATGTAAGACCATGTCTAGGACATGGCTTTGGCA
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA
24568355 TGTTATTATC
Statistics
Matches: 115, Mismatches: 25, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
49 40 0.35
50 71 0.62
51 4 0.03
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (49 bp):
ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACGAC
Found at i:24568583 original size:20 final size:20
Alignment explanation
Indices: 24568558--24568605 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
24568548 GAGTTATTTG
*
24568558 AGTAAGCAAGTAAGTAAACA
1 AGTAAGCAAGTAAATAAACA
*
24568578 AGTAAG-AGAGTAAATAAAGA
1 AGTAAGCA-AGTAAATAAACA
24568598 AG-AAGCAA
1 AGTAAGCAA
24568606 AGACCATGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.58, C:0.06, G:0.23, T:0.12
Consensus pattern (20 bp):
AGTAAGCAAGTAAATAAACA
Found at i:24572318 original size:18 final size:18
Alignment explanation
Indices: 24572295--24572359 Score: 121
Period size: 18 Copynumber: 3.6 Consensus size: 18
24572285 TAAGTACACT
24572295 TTAATTATTTTGTAAAAA
1 TTAATTATTTTGTAAAAA
*
24572313 TTAATTATTTTATAAAAA
1 TTAATTATTTTGTAAAAA
24572331 TTAATTATTTTGTAAAAA
1 TTAATTATTTTGTAAAAA
24572349 TTAATTATTTT
1 TTAATTATTTT
24572360 TTCGACAAGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TTAATTATTTTGTAAAAA
Found at i:24580834 original size:24 final size:24
Alignment explanation
Indices: 24580802--24580850 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
24580792 CAACAAAGCT
24580802 ATCCCTAAATTTCCCTAAAATTAG
1 ATCCCTAAATTTCCCTAAAATTAG
*
24580826 ATCCTTAAATTTCCCTAAAATTAG
1 ATCCCTAAATTTCCCTAAAATTAG
24580850 A
1 A
24580851 CTCATATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.35
Consensus pattern (24 bp):
ATCCCTAAATTTCCCTAAAATTAG
Found at i:24582080 original size:50 final size:50
Alignment explanation
Indices: 24581956--24582150 Score: 196
Period size: 50 Copynumber: 3.9 Consensus size: 50
24581946 AATAATGACA
* * ** * * *
24581956 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCCTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATAT-CGG
* * * **
24582005 TGCCAATGCCATATCCCATATATGGTCTTACATGAGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGG
* * ** * *
24582055 TGCCCATGCCATGTCCCAAACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGG
*
24582105 TGCCAATGCCATGTCCTAGACATGGTCTTACATGAGACCTCTCATA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATA
24582151 GTCTCAATAA
Statistics
Matches: 117, Mismatches: 27, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
48 1 0.01
49 37 0.32
50 79 0.68
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGG
Done.