Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 133 of 203
Found at i:42287111 original size:4 final size:4
Alignment explanation
Indices: 42287102--42287128 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
42287092 TTATGTCCTT
42287102 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
42287129 TTGAAATCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:42288317 original size:15 final size:14
Alignment explanation
Indices: 42288296--42288325 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
42288286 ACATTAAATA
42288296 GTCAATTTGGTACC
1 GTCAATTTGGTACC
42288310 GNTCAATTTGGTACC
1 G-TCAATTTGGTACC
42288325 G
1 G
42288326 ATTTTGGGCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 1 0.07
15 14 0.93
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.33
Consensus pattern (14 bp):
GTCAATTTGGTACC
Found at i:42289913 original size:56 final size:56
Alignment explanation
Indices: 42289827--42290058 Score: 446
Period size: 56 Copynumber: 4.1 Consensus size: 56
42289817 ACAAGGGATG
42289827 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
42289883 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
42289939 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
* *
42289995 ATGGGCAAAACATGTCATCAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
42290051 ATGGGCAA
1 ATGGGCAA
42290059 TAAACTAATA
Statistics
Matches: 174, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 174 1.00
ACGTcount: A:0.46, C:0.09, G:0.22, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:42291362 original size:40 final size:40
Alignment explanation
Indices: 42291124--42291348 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
42291114 TCGAATGATG
* * * *
42291124 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
42291164 TCCGGACTAAGAT-CCAAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
42291204 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
42291243 TCCGGGTTAAGTCCCGAAGACATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
42291283 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
42291324 T-CGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
42291349 AACGAGTAGC
Statistics
Matches: 161, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
39 33 0.20
40 117 0.73
41 11 0.07
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:42293606 original size:40 final size:39
Alignment explanation
Indices: 42293569--42293786 Score: 233
Period size: 40 Copynumber: 5.5 Consensus size: 39
42293559 ATATCCGGAC
42293569 TAAGATCCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGT
1 TAAG-TCCGAAGGCATTTGTGCGAGATACTAAA-TCCGGGT
* *
42293609 TAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGT
1 TAAG-TCCGAAGGCATTTGTGCGAGATACTAAATCCGGGT
* * *
42293649 TAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGT
1 TAAGT-CCGAAGGCATTTGTGCGAGATACTAAATCCGGGT
* * * *
42293689 TAAGTCCCGTAGGCATTCGTGCGAGTTATTAAATCCGGGT
1 TAAGT-CCGAAGGCATTTGTGCGAGATACTAAATCCGGGT
* * * *
42293729 TAAGTCCCGAAGGCA-TTGTGTGAGTTACTAAAACCGGGC
1 TAAGT-CCGAAGGCATTTGTGCGAGATACTAAATCCGGGT
*
42293768 TATGTCCCGAAGGCATTTG
1 TAAGT-CCGAAGGCATTTG
42293787 AACGAGGAGC
Statistics
Matches: 159, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
39 33 0.21
40 123 0.77
41 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
TAAGTCCGAAGGCATTTGTGCGAGATACTAAATCCGGGT
Found at i:42293738 original size:120 final size:120
Alignment explanation
Indices: 42293522--42293784 Score: 309
Period size: 120 Copynumber: 2.2 Consensus size: 120
42293512 TTGAATGCTG
* *
42293522 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
42293586 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * ** *
42293642 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGTAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* * * * *
42293705 TCGTGCGAGTTATTAAA-TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
42293761 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
42293785 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 38 0.31
120 74 0.61
121 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:42293804 original size:79 final size:80
Alignment explanation
Indices: 42293523--42293819 Score: 230
Period size: 80 Copynumber: 3.7 Consensus size: 80
42293513 TGAATGCTGT
* ** * * * **
42293523 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTCGAAC-GAGTGACTAAATCCGGGTTAAG-TCCCGAAGGCATT
* * *
42293586 TGTGCGAGATAC-AAATT
64 CGTGCGAGTTACTAAA-A
* * * * **
42293603 CCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGAT-ACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCATTC
* *
42293667 GTGCGAGTTATTAAAT
65 GTGCGAGTTACTAAAA
* * ** * *
42293683 CCGGGTTAAGTCCCGTAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT-G
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
*
42293747 TGTGAGTTACTAAAA
66 TGCGAGTTACTAAAA
* * * *
42293762 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
42293820 TACGTGATTT
Statistics
Matches: 183, Mismatches: 28, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
78 16 0.09
79 46 0.25
80 110 0.60
81 11 0.06
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
TGCGAGTTACTAAAA
Found at i:42304037 original size:29 final size:29
Alignment explanation
Indices: 42304002--42304075 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
42303992 GTTGTGAGAT
* *
42304002 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
* *
42304031 TGGCACTAAGTGTGCGAGTTTAAAGTACG
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
42304060 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
42304076 TGGTTGATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 5 0.12
29 35 0.88
ACGTcount: A:0.24, C:0.16, G:0.34, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:42310207 original size:24 final size:24
Alignment explanation
Indices: 42310180--42310231 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
42310170 TTTAGCTATC
*
42310180 ATCTCCTTATTTTAAGTGAAAAGA
1 ATCTCCTTATTCTAAGTGAAAAGA
42310204 ATCTCCTTATTCTAAGTGAAAAGA
1 ATCTCCTTATTCTAAGTGAAAAGA
42310228 ATCT
1 ATCT
42310232 TGGTTGACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37
Consensus pattern (24 bp):
ATCTCCTTATTCTAAGTGAAAAGA
Found at i:42314156 original size:25 final size:25
Alignment explanation
Indices: 42314114--42314164 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
42314104 GAGTATTTTA
42314114 TTAATATAATATTAAA-TTAATTATT
1 TTAATATAATATTAAATTTAA-TATT
*
42314139 TTAATATTAA-ATTTAATTTAATATT
1 TTAATA-TAATATTAAATTTAATATT
42314164 T
1 T
42314165 ATCAAGATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
TTAATATAATATTAAATTTAATATT
Found at i:42323560 original size:26 final size:26
Alignment explanation
Indices: 42323530--42323579 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
42323520 AAATTTATTG
42323530 AAATGA-TCGTTATAC-CCTTATGAGGT
1 AAATGACT-GTTATACTCC-TATGAGGT
42323556 AAATGACTGTTATACTCCTATGAG
1 AAATGACTGTTATACTCCTATGAG
42323580 ATGTGTGACT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 19 0.86
27 3 0.14
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (26 bp):
AAATGACTGTTATACTCCTATGAGGT
Found at i:42331252 original size:6 final size:6
Alignment explanation
Indices: 42331243--42331384 Score: 94
Period size: 6 Copynumber: 22.8 Consensus size: 6
42331233 AACTAGAACT
*
42331243 AGAATC AGAATC AGAATC AGAATC AGGTGAT- AGAATC AGAATC AGAATC
1 AGAATC AGAATC AGAATC AGAATC A-G-AATC AGAATC AGAATC AGAATC
* * * * *
42331292 AGTATC AGGTAAT- AGAATC AAAATC AAAATC AGTATC AGGTAA-C AAAATC
1 AGAATC A-G-AATC AGAATC AGAATC AGAATC AGAATC A-G-AATC AGAATC
* * *
42331342 AAAATC AGAATC AGTATC AGGTAA-C AGAATC AAAAATC AGAAT
1 AGAATC AGAATC AGAATC A-G-AATC AGAATC -AGAATC AGAAT
42331385 GTGAATGCAA
Statistics
Matches: 109, Mismatches: 14, Indels: 26
0.73 0.09 0.17
Matches are distributed among these distances:
5 9 0.08
6 79 0.72
7 15 0.14
8 6 0.06
ACGTcount: A:0.50, C:0.14, G:0.16, T:0.20
Consensus pattern (6 bp):
AGAATC
Found at i:42331279 original size:31 final size:31
Alignment explanation
Indices: 42331242--42331384 Score: 205
Period size: 31 Copynumber: 4.6 Consensus size: 31
42331232 GAACTAGAAC
* * *
42331242 TAGAATCAGAATCAGAATCAGAATCAGGTGA
1 TAGAATCAAAATCAGAATCAGTATCAGGTAA
*
42331273 TAGAATCAGAATCAGAATCAGTATCAGGTAA
1 TAGAATCAAAATCAGAATCAGTATCAGGTAA
*
42331304 TAGAATCAAAATCAAAATCAGTATCAGGTAA
1 TAGAATCAAAATCAGAATCAGTATCAGGTAA
* *
42331335 CAAAATCAAAATCAGAATCAGTATCAGGTAA
1 TAGAATCAAAATCAGAATCAGTATCAGGTAA
*
42331366 CAGAATCAAAAATCAGAAT
1 TAGAATC-AAAATCAGAAT
42331385 GTGAATGCAA
Statistics
Matches: 103, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
31 92 0.89
32 11 0.11
ACGTcount: A:0.50, C:0.14, G:0.16, T:0.20
Consensus pattern (31 bp):
TAGAATCAAAATCAGAATCAGTATCAGGTAA
Found at i:42331323 original size:25 final size:25
Alignment explanation
Indices: 42331277--42331349 Score: 71
Period size: 25 Copynumber: 2.9 Consensus size: 25
42331267 AGGTGATAGA
* **
42331277 ATCAGAATCAGAATCAGTATCAGGT
1 ATCAGAATCAAAATCAAAATCAGGT
42331302 AAT-AGAATCAAAATCAAAATCA-GT
1 -ATCAGAATCAAAATCAAAATCAGGT
42331326 ATCAGGTAA-CAAAATCAAAATCAG
1 ATCA-G-AATCAAAATCAAAATCAG
42331350 AATCAGTATC
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
23 2 0.05
24 3 0.08
25 31 0.77
26 4 0.10
ACGTcount: A:0.51, C:0.15, G:0.14, T:0.21
Consensus pattern (25 bp):
ATCAGAATCAAAATCAAAATCAGGT
Found at i:42331563 original size:27 final size:26
Alignment explanation
Indices: 42331521--42331622 Score: 132
Period size: 27 Copynumber: 3.8 Consensus size: 26
42331511 GCTCAGTTAT
* *
42331521 CAGATATTGTGACAGAGTCACCAGATA
1 CAGATATTGTGGCAGAGCCACCAGA-A
42331548 CAGATATTGTGGCAGAGCCACCAGAA
1 CAGATATTGTGGCAGAGCCACCAGAA
*
42331574 CAGATATTTGTGGCATAGCCACCAGAAA
1 CAGATA-TTGTGGCAGAGCCACCAG-AA
* *
42331602 CAGATAATGTGGCAAAGCCAC
1 CAGATATTGTGGCAGAGCCAC
42331623 TTAACAGAAT
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
26 7 0.10
27 53 0.78
28 8 0.12
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.19
Consensus pattern (26 bp):
CAGATATTGTGGCAGAGCCACCAGAA
Found at i:42332328 original size:27 final size:27
Alignment explanation
Indices: 42332272--42332690 Score: 590
Period size: 27 Copynumber: 15.6 Consensus size: 27
42332262 GAGGCAAAAT
* * *
42332272 GGTAATTTTACCCTACA-AGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
42332298 GGTAATTCTACGCTAAAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
*
42332325 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
42332352 GATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
42332379 GATAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
42332406 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
42332433 GATAATTCTACCCTGCAAGGGTA-TTC
1 GGTAATTCTACCCTACAGGGGTATTTC
42332459 TGGTAATTCTACCCTACAGGGGTATTTC
1 -GGTAATTCTACCCTACAGGGGTATTTC
* *
42332487 GGTAATTCTACCCTATAGGGGTATTGC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
42332514 GATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
42332541 GGTAATTCTACCCTATAGGGGTATTGC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
42332568 GATAATTTTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
42332595 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
42332622 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
42332649 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
**
42332676 AATAATTCTACCCTA
1 GGTAATTCTACCCTA
42332691 TATTTTGGTA
Statistics
Matches: 348, Mismatches: 42, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
26 17 0.05
27 328 0.94
28 3 0.01
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:42332721 original size:27 final size:27
Alignment explanation
Indices: 42332691--42332757 Score: 134
Period size: 27 Copynumber: 2.5 Consensus size: 27
42332681 TTCTACCCTA
42332691 TATTTTGGTAATTCCACAAATCAGGGG
1 TATTTTGGTAATTCCACAAATCAGGGG
42332718 TATTTTGGTAATTCCACAAATCAGGGG
1 TATTTTGGTAATTCCACAAATCAGGGG
42332745 TATTTTGGTAATT
1 TATTTTGGTAATT
42332758 TTATTGATCG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.39
Consensus pattern (27 bp):
TATTTTGGTAATTCCACAAATCAGGGG
Found at i:42332798 original size:27 final size:27
Alignment explanation
Indices: 42332708--42332881 Score: 107
Period size: 27 Copynumber: 6.4 Consensus size: 27
42332698 GTAATTCCAC
* ****
42332708 AAATCAGGGGTATTTTGGTAATTCCAC
1 AAATCAAGGGTATTTTGGTAATTTTGT
* *
42332735 AAATCAGGGGTATTTTGGTAATTTTAT
1 AAATCAAGGGTATTTTGGTAATTTTGT
** *
42332762 TGATCGAGGGTATTTTGGTAATTTTGT
1 AAATCAAGGGTATTTTGGTAATTTTGT
***
42332789 AAA-CTAAGGGTATTTCAATAATTTTGT
1 AAATC-AAGGGTATTTTGGTAATTTTGT
* *** *
42332816 AAATCGAGGGTAAAATGGTAATTTTAT
1 AAATCAAGGGTATTTTGGTAATTTTGT
* **** *
42332843 AAATCGAGGGTAAAACGGTAATTCTGT
1 AAATCAAGGGTATTTTGGTAATTTTGT
*
42332870 AAATCGAGGGTA
1 AAATCAAGGGTA
42332882 AAATGGTAAT
Statistics
Matches: 120, Mismatches: 25, Indels: 4
0.81 0.17 0.03
Matches are distributed among these distances:
26 1 0.01
27 118 0.98
28 1 0.01
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.36
Consensus pattern (27 bp):
AAATCAAGGGTATTTTGGTAATTTTGT
Found at i:42332853 original size:54 final size:54
Alignment explanation
Indices: 42332777--42332892 Score: 144
Period size: 54 Copynumber: 2.1 Consensus size: 54
42332767 GAGGGTATTT
* *** *
42332777 TGGTAATTTTGTAAACTAAGGGTATTTCAATAATTTTGTAAATCGAGGGTAAAA
1 TGGTAATTTTATAAACTAAGGGTAAAACAATAATTCTGTAAATCGAGGGTAAAA
* **
42332831 TGGTAATTTTATAAA-TCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAA
1 TGGTAATTTTATAAACT-AAGGGTAAAACAATAATTCTGTAAATCGAGGGTAAAA
42332885 TGGTAATT
1 TGGTAATT
42332893 CTATCTTACA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
53 1 0.02
54 52 0.98
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.34
Consensus pattern (54 bp):
TGGTAATTTTATAAACTAAGGGTAAAACAATAATTCTGTAAATCGAGGGTAAAA
Found at i:42332882 original size:27 final size:27
Alignment explanation
Indices: 42332807--42332894 Score: 140
Period size: 27 Copynumber: 3.3 Consensus size: 27
42332797 GGTATTTCAA
*
42332807 TAATTTTGTAAATCGAGGGTAAAATGG
1 TAATTCTGTAAATCGAGGGTAAAATGG
* * *
42332834 TAATTTTATAAATCGAGGGTAAAACGG
1 TAATTCTGTAAATCGAGGGTAAAATGG
42332861 TAATTCTGTAAATCGAGGGTAAAATGG
1 TAATTCTGTAAATCGAGGGTAAAATGG
42332888 TAATTCT
1 TAATTCT
42332895 ATCTTACAGG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.33
Consensus pattern (27 bp):
TAATTCTGTAAATCGAGGGTAAAATGG
Found at i:42332936 original size:27 final size:27
Alignment explanation
Indices: 42332906--42333097 Score: 210
Period size: 27 Copynumber: 7.1 Consensus size: 27
42332896 TCTTACAGGA
*
42332906 GTATTTCAGTAATTTTACAAATTGAGG
1 GTATTTCAGTAATTTTACAAATCGAGG
*
42332933 GTATTTCAGTAATTTTGCAAAAT-GAGG
1 GTATTTCAGTAATTTTAC-AAATCGAGG
42332960 GTATTTCAGTAATTTTACAAATCGAGG
1 GTATTTCAGTAATTTTACAAATCGAGG
* * *
42332987 ATATTT-ATGTAATTTTATAAATCGGGG
1 GTATTTCA-GTAATTTTACAAATCGAGG
* *
42333014 GTACTTT-GGTAATTTTACAAGTCGAGG
1 GTA-TTTCAGTAATTTTACAAATCGAGG
* * **
42333041 GTATTTTAATAATTTTACAGGTCGAGG
1 GTATTTCAGTAATTTTACAAATCGAGG
* * *
42333068 GTATTTTAGTAATTTCACAAATCAAGG
1 GTATTTCAGTAATTTTACAAATCGAGG
42333095 GTA
1 GTA
42333098 ATTTTATAAA
Statistics
Matches: 142, Mismatches: 18, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
26 8 0.06
27 127 0.89
28 7 0.05
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.39
Consensus pattern (27 bp):
GTATTTCAGTAATTTTACAAATCGAGG
Found at i:42333128 original size:27 final size:27
Alignment explanation
Indices: 42333094--42333191 Score: 151
Period size: 27 Copynumber: 3.6 Consensus size: 27
42333084 ACAAATCAAG
*
42333094 GGTAATTTTATAAACTAGGGGTATTCT
1 GGTAATTTTATAAACTAGGGGTATTTT
* *
42333121 GATAATTTTACAAACTAGGGGTATTTT
1 GGTAATTTTATAAACTAGGGGTATTTT
42333148 GGTAATTTTATAAACTAGGGGTATTTT
1 GGTAATTTTATAAACTAGGGGTATTTT
* *
42333175 GGTAATTTGAGAAACTA
1 GGTAATTTTATAAACTA
42333192 AAGTATTCTA
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 64 1.00
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.40
Consensus pattern (27 bp):
GGTAATTTTATAAACTAGGGGTATTTT
Found at i:42335829 original size:28 final size:27
Alignment explanation
Indices: 42335784--42335838 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
42335774 TATAATCTTG
42335784 AAATTGTATTTGAATGGGCTAAGGCCC
1 AAATTGTATTTGAATGGGCTAAGGCCC
*
42335811 AAATTG-ATTCTGTAATGGGCTCAGGCCC
1 AAATTGTATT-TG-AATGGGCTAAGGCCC
42335839 GAACTGTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 3 0.12
27 8 0.32
28 14 0.56
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.29
Consensus pattern (27 bp):
AAATTGTATTTGAATGGGCTAAGGCCC
Found at i:42339520 original size:43 final size:42
Alignment explanation
Indices: 42339377--42339520 Score: 155
Period size: 43 Copynumber: 3.4 Consensus size: 42
42339367 TACCGAGATG
* * *
42339377 TGATTACATGTAAGACCATGTCTAGGACATTGGCATTGTATTG
1 TGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTA-TA
42339420 TGATTACATGTAAGACCATGTCTGGGACATTGGCATCGT-TAA
1 TGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT-A
*** * * *
42339462 TCGATTTTGTTTAAGACCCTGTCTGGGACAGTGGCATCGATATA
1 T-GATTACATGTAAGACCATGTCTGGGACATTGGCATCG-TATA
*
42339506 TGATAACATGTAAGA
1 TGATTACATGTAAGA
42339521 TCATATCTAG
Statistics
Matches: 83, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 77 0.93
44 3 0.04
45 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (42 bp):
TGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTATA
Found at i:42344491 original size:29 final size:29
Alignment explanation
Indices: 42344432--42344560 Score: 172
Period size: 29 Copynumber: 4.5 Consensus size: 29
42344422 ATAGTAAGTC
* *
42344432 CGCACACTTAGTG-TTATATAATAAAACT
1 CGCACACTTAGTGCTTACATAATCAAACT
42344460 CGCACACTTAGTGCTTACATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCAAACT
42344489 CGCACACTTAGTGCTTACATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCAAACT
* * * * *
42344518 TGCACACTTAGTGCTATGCA-ATTTAAACC
1 CGCACACTTAGTGCT-TACATAATCAAACT
42344547 CGCACACTTAGTGC
1 CGCACACTTAGTGC
42344561 CAATCTCATG
Statistics
Matches: 91, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
28 13 0.14
29 75 0.82
30 3 0.03
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCTTACATAATCAAACT
Found at i:42349798 original size:43 final size:43
Alignment explanation
Indices: 42349737--42349820 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 43
42349727 ATTGAATTCG
42349737 ATCTCGAACAGCTCGTGGGTAAGCCCTGTACA-ATGTGTCCCTA
1 ATCTCGAACAGCTCGTGGGTAAGCCCTGTA-ATATGTGTCCCTA
*
42349780 ATCTCGAACAGCTTGTGGGTAAGCCCTGTAATATGTGTCCC
1 ATCTCGAACAGCTCGTGGGTAAGCCCTGTAATATGTGTCCC
42349821 CAAGAAAGGA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
42 1 0.03
43 38 0.97
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (43 bp):
ATCTCGAACAGCTCGTGGGTAAGCCCTGTAATATGTGTCCCTA
Found at i:42361222 original size:23 final size:21
Alignment explanation
Indices: 42361170--42361265 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
42361160 CCTGATCAGT
** * *
42361170 ATACGACACATAAAGTGCCTA
1 ATACGACACACGAGGTGCCTG
*
42361191 AAACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
42361212 ATACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
42361233 ATACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
42361254 AAATACGACACA
1 --ATACGACACA
42361266 TAAAGTGCCT
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
21 57 0.85
23 10 0.15
ACGTcount: A:0.36, C:0.27, G:0.23, T:0.14
Consensus pattern (21 bp):
ATACGACACACGAGGTGCCTG
Found at i:42361230 original size:42 final size:43
Alignment explanation
Indices: 42361170--42361275 Score: 142
Period size: 42 Copynumber: 2.5 Consensus size: 43
42361160 CCTGATCAGT
*
42361170 ATACGACACATAAAGTGCCTAAAACGACACACGAGGTGCCTG-
1 ATACGACACACAAAGTGCCTAAAACGACACACGAGGTGCCTGA
* * * *
42361212 ATACGACACACGAGGTGCCTGATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTAAAACGACACACGAGGTGCCTG-A
*
42361256 ATACGACACATAAAGTGCCT
1 ATACGACACACAAAGTGCCT
42361276 GATCGATAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
42 37 0.69
44 17 0.31
ACGTcount: A:0.36, C:0.26, G:0.23, T:0.15
Consensus pattern (43 bp):
ATACGACACACAAAGTGCCTAAAACGACACACGAGGTGCCTGA
Found at i:42361674 original size:15 final size:15
Alignment explanation
Indices: 42361649--42361706 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
42361639 TCATATATAT
42361649 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
42361665 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
42361680 AATAATTTCAATCAA
1 TATAAATTCAATCAA
42361695 TATAAATTCAAT
1 TATAAATTCAAT
42361707 AAAACATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:42361691 original size:30 final size:28
Alignment explanation
Indices: 42361652--42361710 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 28
42361642 TATATATTAT
42361652 ATAATTCAATCAATATAAATTCAATCAAA
1 ATAATTCAATCAATATAAATTCAAT-AAA
42361681 ATAATTTCAATCAATATAAATTCAATAAA
1 ATAA-TTCAATCAATATAAATTCAATAAA
42361710 A
1 A
42361711 CATATATTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 8 0.28
30 21 0.72
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (28 bp):
ATAATTCAATCAATATAAATTCAATAAA
Found at i:42364850 original size:17 final size:17
Alignment explanation
Indices: 42364828--42364860 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
42364818 TTTGGCCGAA
42364828 ACGGGCACATGGGCCCT
1 ACGGGCACATGGGCCCT
42364845 ACGGGCACATGGGCCC
1 ACGGGCACATGGGCCC
42364861 CACATGGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.36, G:0.36, T:0.09
Consensus pattern (17 bp):
ACGGGCACATGGGCCCT
Found at i:42367845 original size:35 final size:35
Alignment explanation
Indices: 42367791--42367861 Score: 108
Period size: 35 Copynumber: 2.0 Consensus size: 35
42367781 GGCAGCCCCT
* *
42367791 AGGGAAAGGCATCAGAAAATTCCCTTACTGTTCTC
1 AGGGAAAGACATCAGAAAATTCCCTAACTGTTCTC
42367826 AGGGAAAGACATCCA-AAAATTCCCTAACTGTTCTC
1 AGGGAAAGACAT-CAGAAAATTCCCTAACTGTTCTC
42367861 A
1 A
42367862 ACTCATTAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 31 0.94
36 2 0.06
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (35 bp):
AGGGAAAGACATCAGAAAATTCCCTAACTGTTCTC
Found at i:42372432 original size:40 final size:40
Alignment explanation
Indices: 42372388--42372492 Score: 151
Period size: 40 Copynumber: 2.6 Consensus size: 40
42372378 GCTACTCGTT
*
42372388 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
42372428 CAAATGCCTTCGGGACTTAACCAGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
42372468 CCAATGCCTTCGGG-CTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
42372493 CATCATTCGA
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
39 9 0.16
40 47 0.81
41 2 0.03
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:42380614 original size:39 final size:40
Alignment explanation
Indices: 42380497--42380678 Score: 210
Period size: 40 Copynumber: 4.6 Consensus size: 40
42380487 GCTACTCGTT
*
42380497 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
42380537 CAAATGCCTTCGGGCCTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
42380577 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
42380616 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
42380657 CAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGACTTAGCCC
42380679 AGACATCATT
Statistics
Matches: 121, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
38 2 0.02
39 32 0.26
40 74 0.61
41 13 0.11
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:42380641 original size:79 final size:80
Alignment explanation
Indices: 42380499--42380678 Score: 213
Period size: 79 Copynumber: 2.3 Consensus size: 80
42380489 TACTCGTTCA
* * *
42380499 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGCCTTAACCCGGAT
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGACCTTAACCCGGAT
* *
42380564 TTAGTAAC-TCGCACC
66 ATAGTAACTTAGCA-C
* * **
42380579 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGACCTTAACCCGGA
* *
42380642 TATGGTCACTTAGCAC
65 TATAGTAACTTAGCAC
*
42380658 AAAGCCTTCGGGACTTAGCCC
1 AATGCCTTCGGGACTTAGCCC
42380679 AGACATCATT
Statistics
Matches: 85, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
78 1 0.01
79 60 0.71
80 24 0.28
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (80 bp):
AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGACCTTAACCCGGAT
ATAGTAACTTAGCAC
Found at i:42382649 original size:29 final size:29
Alignment explanation
Indices: 42382604--42382719 Score: 121
Period size: 29 Copynumber: 4.0 Consensus size: 29
42382594 TACCTGTATC
* *
42382604 TGGCCCATTAAGCCC-AATCATATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
* *
42382632 TGGCCCCTTTAGGCCCAAATCACCTGT-ATA
1 TGG-CCCATTAGGCCCAAATCACAT-TCATA
* *
42382662 TGGCCCATTAGACCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
* *
42382691 TGGCCCGTTAGGCCC-AGTCACATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
42382719 T
1 T
42382720 TCATGCTCAC
Statistics
Matches: 73, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
28 16 0.22
29 44 0.60
30 12 0.16
31 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.28
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTCATA
Found at i:42382666 original size:58 final size:58
Alignment explanation
Indices: 42382595--42382706 Score: 156
Period size: 58 Copynumber: 1.9 Consensus size: 58
42382585 AAATTCACAT
* * *
42382595 ACCTGTATCTGGCCCATTA-AGCCC-AATCATATTCATATGGCCCCTTTAGGCCCAAATC
1 ACCTGTATATGGCCCATTAGA-CCCAAATCACATTCATATGG-CCCGTTAGGCCCAAATC
*
42382653 ACCTGTATATGGCCCATTAGACCCAAATCACATTTATATGGCCCGTTAGGCCCA
1 ACCTGTATATGGCCCATTAGACCCAAATCACATTCATATGGCCCGTTAGGCCCA
42382707 GTCACATTCA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
58 33 0.69
59 15 0.31
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (58 bp):
ACCTGTATATGGCCCATTAGACCCAAATCACATTCATATGGCCCGTTAGGCCCAAATC
Found at i:42386200 original size:27 final size:27
Alignment explanation
Indices: 42386170--42386347 Score: 171
Period size: 27 Copynumber: 6.6 Consensus size: 27
42386160 ATATTGAGCC
* * *
42386170 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
* * * *
42386197 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
42386224 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAGTCA-ACT
** * *
42386252 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
* **
42386279 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAACT
* *
42386306 CGCACACTTAGTGCAATATAGTCGAA-T
1 CGCACACTTAGTGCTACATAGTC-AACT
42386333 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42386348 GTACAATTTA
Statistics
Matches: 126, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
27 101 0.80
28 25 0.20
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:42386309 original size:82 final size:81
Alignment explanation
Indices: 42386191--42386346 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
42386181 TGCTATATAA
* * *
42386191 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTCAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTC-GAATCGCA
42386256 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
42386273 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAATATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTCGAATCGCA
42386337 CACTTAGTGC
65 CACTTAGTGC
42386347 TGTACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 19 0.29
82 46 0.71
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCGAATCGCAC
ACTTAGTGCCGCATGG
Found at i:42388701 original size:35 final size:35
Alignment explanation
Indices: 42388655--42388723 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
42388645 GTGGCTGCCT
*
42388655 TCAAACTTTCACGGATTACTTTTACTTTCTGTTCG
1 TCAAACTTTCACGGATTACCTTTACTTTCTGTTCG
42388690 TCAAACTTTCACGGATTACCTTTACTTTCTGTTC
1 TCAAACTTTCACGGATTACCTTTACTTTCTGTTC
42388724 AGCATCTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.20, C:0.25, G:0.10, T:0.45
Consensus pattern (35 bp):
TCAAACTTTCACGGATTACCTTTACTTTCTGTTCG
Found at i:42393732 original size:68 final size:68
Alignment explanation
Indices: 42393652--42393787 Score: 254
Period size: 68 Copynumber: 2.0 Consensus size: 68
42393642 CATGCCTACC
42393652 CTTGATCCAACTCAATCGAACATTCGTGCCATCTAAGCATGGCTTAAAGTTTACATGCCAAAGTT
1 CTTGATCCAACTCAATCGAACATTCGTGCCATCTAAGCATGGCTTAAAGTTTACATGCCAAAGTT
42393717 CAA
66 CAA
**
42393720 CTTGATCCAACTCAATCGAACATTCGTGCCATCTTCGCATGGCTTAAAGTTTACATGCCAAAGTT
1 CTTGATCCAACTCAATCGAACATTCGTGCCATCTAAGCATGGCTTAAAGTTTACATGCCAAAGTT
42393785 CAA
66 CAA
42393788 ACACAACGTA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.29
Consensus pattern (68 bp):
CTTGATCCAACTCAATCGAACATTCGTGCCATCTAAGCATGGCTTAAAGTTTACATGCCAAAGTT
CAA
Found at i:42394429 original size:27 final size:27
Alignment explanation
Indices: 42394397--42394574 Score: 169
Period size: 27 Copynumber: 6.6 Consensus size: 27
42394387 ATATTGAGTC
* *
42394397 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * *
42394424 CACACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
42394451 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** *** *
42394479 CGCACACTTAGTGCCGCAGGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
42394506 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
42394533 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
42394560 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42394575 GTACAATTTA
Statistics
Matches: 125, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
27 102 0.82
28 23 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:42404989 original size:12 final size:12
Alignment explanation
Indices: 42404970--42405003 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
42404960 TGTTATATTG
42404970 CATTATTATTAT
1 CATTATTATTAT
**
42404982 TGTTATTATTAT
1 CATTATTATTAT
42404994 CATTATTATT
1 CATTATTATT
42405004 TCTATACATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (12 bp):
CATTATTATTAT
Found at i:42405073 original size:21 final size:22
Alignment explanation
Indices: 42405021--42405076 Score: 69
Period size: 24 Copynumber: 2.5 Consensus size: 22
42405011 ATATACACAC
42405021 GTATATATTTTTTATAACATAT
1 GTATATATTTTTTATAACATAT
* *
42405043 ATATGCATATTTTTTA-AATATAT
1 GTAT--ATATTTTTTATAACATAT
42405066 GTATATATTTT
1 GTATATATTTT
42405077 CAGACTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 7 0.24
22 3 0.10
23 9 0.31
24 10 0.34
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.55
Consensus pattern (22 bp):
GTATATATTTTTTATAACATAT
Found at i:42405113 original size:18 final size:18
Alignment explanation
Indices: 42405090--42405128 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
42405080 ACTTTTATAA
*
42405090 ATACATGTATATATTTTT
1 ATACATATATATATTTTT
42405108 ATACATATATATATTTTT
1 ATACATATATATATTTTT
42405126 ATA
1 ATA
42405129 TTTTATTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (18 bp):
ATACATATATATATTTTT
Found at i:42415226 original size:492 final size:492
Alignment explanation
Indices: 42414302--42415289 Score: 1886
Period size: 492 Copynumber: 2.0 Consensus size: 492
42414292 GCTTAATCTA
42414302 ACAAAGTGCACCTTTGGAGCCAGATCAGGGAAGTTGCTAGGCTTTATAGTCAGTGGAAAAGGAAT
1 ACAAAGTGCACCTTTGGAGCCAGATCAGGGAAGTTGCTAGGCTTTATAGTCAGTGGAAAAGGAAT
42414367 TGAGGTTGACCCAGATAAAGTCAAGGTGATACGAGACTTGCCTCCACCACACACTCAGAAAGAGG
66 TGAGGTTGACCCAGATAAAGTCAAGGTGATACGAGACTTGCCTCCACCACACACTCAGAAAGAGG
*
42414432 TACGAGGTTTTCTAGGAAGATTGAATTACATTGCTCGGTTCATTTTACAGTTAACTAAGAAATGT
131 TACGAGGTTTTCTAGGAAGATTGAATTACATTGCTCGGTTCATTTCACAGTTAACTAAGAAATGT
42414497 GATCCCATATTCCGTCTTCTGAGGAAGCATAATCCGGGTGTATCGGATGAATAATATCAAAAAGC
196 GATCCCATATTCCGTCTTCTGAGGAAGCATAATCCGGGTGTATCGGATGAATAATATCAAAAAGC
42414562 TTTTGAAAAAATAAAATAGTTCTTGTCCATCACTCCAGTGCTATCACCACCTAGTCCGGATAGGC
261 TTTTGAAAAAATAAAATAGTTCTTGTCCATCACTCCAGTGCTATCACCACCTAGTCCGGATAGGC
42414627 CATTAATACTGTATTTAATAGTATTTGAAAATTCCATGGGGTGCGTGTTAGGCTAACATGATGAG
326 CATTAATACTGTATTTAATAGTATTTGAAAATTCCATGGGGTGCGTGTTAGGCTAACATGATGAG
42414692 ACAGGAAGAAAAGAAAGGGCAATATATTATCTTAGCAAGAAATTCACTGATTGTGAAACGAGGTA
391 ACAGGAAGAAAAGAAAGGGCAATATATTATCTTAGCAAGAAATTCACTGATTGTGAAACGAGGTA
*
42414757 CTCGTCTATCGAGAAGTTATGTTGTGCCCTGGTTTGG
456 CTCGTCTATCGAGAAGTTATGTTGTGCCCTGGTTTAG
42414794 ACAAAGTGCACCTTTGGAGCCAGATCAGGGAAGTTGCTAGGCTTTATAGTCAGTGGAAAAGGAAT
1 ACAAAGTGCACCTTTGGAGCCAGATCAGGGAAGTTGCTAGGCTTTATAGTCAGTGGAAAAGGAAT
*
42414859 TGAGGTTGACCCAGATAAAGTCAAGGTGATACGAGATTTGCCTCCACCACACACTCAGAAAGAGG
66 TGAGGTTGACCCAGATAAAGTCAAGGTGATACGAGACTTGCCTCCACCACACACTCAGAAAGAGG
* * *
42414924 TACGAGGTTTTCTAGGAAGATTGAATTACATTGCTCGTTTTATTTCACAGTTAACTGAGAAATGT
131 TACGAGGTTTTCTAGGAAGATTGAATTACATTGCTCGGTTCATTTCACAGTTAACTAAGAAATGT
* *
42414989 GATCCCATATTCCGTCTTCTGAGGAAGCATAATCCGGGTGTATGGGATGAATAATATCAAAATGC
196 GATCCCATATTCCGTCTTCTGAGGAAGCATAATCCGGGTGTATCGGATGAATAATATCAAAAAGC
42415054 TTTTGAAAAAATAAAATAGTTCTTGTCCATCACTCCAGTGCTATCACCACCTAGTCCGGATAGGC
261 TTTTGAAAAAATAAAATAGTTCTTGTCCATCACTCCAGTGCTATCACCACCTAGTCCGGATAGGC
42415119 CATTAATACTGTATTTAATAGTATTTGAAAATTCCATGGGGTGCGTGTTAGGCTAACATGATGAG
326 CATTAATACTGTATTTAATAGTATTTGAAAATTCCATGGGGTGCGTGTTAGGCTAACATGATGAG
**
42415184 ACAGGAAGAAAAGAAAGGGCAATATATTATCTTAGCAAGAAATTCACTGATTGTGAAGTGAGGTA
391 ACAGGAAGAAAAGAAAGGGCAATATATTATCTTAGCAAGAAATTCACTGATTGTGAAACGAGGTA
42415249 CTCGTCTATCGAGAAGTTATGTTGTGCCCTGGTTTAG
456 CTCGTCTATCGAGAAGTTATGTTGTGCCCTGGTTTAG
42415286 ACAA
1 ACAA
42415290 CTCGGAGATT
Statistics
Matches: 486, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
492 486 1.00
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (492 bp):
ACAAAGTGCACCTTTGGAGCCAGATCAGGGAAGTTGCTAGGCTTTATAGTCAGTGGAAAAGGAAT
TGAGGTTGACCCAGATAAAGTCAAGGTGATACGAGACTTGCCTCCACCACACACTCAGAAAGAGG
TACGAGGTTTTCTAGGAAGATTGAATTACATTGCTCGGTTCATTTCACAGTTAACTAAGAAATGT
GATCCCATATTCCGTCTTCTGAGGAAGCATAATCCGGGTGTATCGGATGAATAATATCAAAAAGC
TTTTGAAAAAATAAAATAGTTCTTGTCCATCACTCCAGTGCTATCACCACCTAGTCCGGATAGGC
CATTAATACTGTATTTAATAGTATTTGAAAATTCCATGGGGTGCGTGTTAGGCTAACATGATGAG
ACAGGAAGAAAAGAAAGGGCAATATATTATCTTAGCAAGAAATTCACTGATTGTGAAACGAGGTA
CTCGTCTATCGAGAAGTTATGTTGTGCCCTGGTTTAG
Found at i:42418586 original size:45 final size:45
Alignment explanation
Indices: 42418449--42418809 Score: 340
Period size: 45 Copynumber: 8.0 Consensus size: 45
42418439 AACAGATCGG
* * *
42418449 TGAAGATAGCAAATCCTATCTCCTTGAAGTTGCAGTAGAGTGGAT
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTAGAT
* * * * *
42418494 TGAAGATATGCAAGTCTTATCTCCATGAAGTTGCAGCGGAGCAGAT
1 TGAAGATA-GCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTAGAT
*
42418540 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGAT
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTAGAT
* * * * * * *
42418585 TGAAGATATGCAAGTCTTATCTCCCTGAAGTTACAGCGGAGCAAAC
1 TGAAGATA-GCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTAGAT
* * *
42418631 TGAAGATAGCAAATCTTATCTCGCT-AATGTTGCAGTGGAGTGGAT
1 TGAAGATAGCAAATCCTATCTCCCTGAA-GTTGCAGTGGAGTAGAT
* *
42418676 TGAAGATAGCAAGTCTTATC-CTCCTGAAGTTG-AGTGG-GATAGAT
1 TGAAGATAGCAAATCCTATCTC-CCTGAAGTTGCAGTGGAG-TAGAT
* ** ** *
42418720 TGAAGATGGTGAA-CCTTATCTCCCTGGGGTTGCAGTGGAGCAGAT
1 TGAAGATAGCAAATCC-TATCTCCCTGAAGTTGCAGTGGAGTAGAT
** *
42418765 TGAAGCCA--ATAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGAT
1 TGAAGATAGCA-AATCCTATCTCCCTGAAGTTGCAGTGGAGTAGAT
42418809 T
1 T
42418810 AAAACATCCA
Statistics
Matches: 256, Mismatches: 48, Indels: 25
0.78 0.15 0.08
Matches are distributed among these distances:
43 2 0.01
44 61 0.24
45 115 0.45
46 78 0.30
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (45 bp):
TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTAGAT
Found at i:42418604 original size:91 final size:90
Alignment explanation
Indices: 42418449--42418769 Score: 409
Period size: 91 Copynumber: 3.6 Consensus size: 90
42418439 AACAGATCGG
* *
42418449 TGAAGATAGCAAATCCTATCTCCTTGAAGTTGCAGTAGAGTGGATTGAAGATATGCAAGTCTTAT
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTGAAGATATGCAAGTCTTAT
42418514 CTCCATGAAGTTGCAGCGGAGCAGAT
66 CTCC-TGAAGTTGCAGCGGAGCAGAT
42418540 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTGAAGATATGCAAGTCTTAT
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTGAAGATATGCAAGTCTTAT
* * *
42418605 CTCCCTGAAGTTACAGCGGAGCAAAC
66 CT-CCTGAAGTTGCAGCGGAGCAGAT
* *
42418631 TGAAGATAGCAAATCTTATCTCGCT-AATGTTGCAGTGGAGTGGATTGAAGATA-GCAAGTCTTA
1 TGAAGATAGCAAATCCTATCTCCCTGAA-GTTGCAGTGGAGTGGATTGAAGATATGCAAGTCTTA
* *
42418694 TCCTCCTGAAGTTG-AGTGG-GATAGAT
65 T-CTCCTGAAGTTGCAGCGGAG-CAGAT
* ** ** **
42418720 TGAAGATGGTGAA-CCTTATCTCCCTGGGGTTGCAGTGGAGCAGATTGAAG
1 TGAAGATAGCAAATCC-TATCTCCCTGAAGTTGCAGTGGAGTGGATTGAAG
42418770 CCAATAATCC
Statistics
Matches: 203, Mismatches: 21, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
88 2 0.01
89 44 0.22
90 22 0.11
91 133 0.66
92 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (90 bp):
TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTGAAGATATGCAAGTCTTAT
CTCCTGAAGTTGCAGCGGAGCAGAT
Found at i:42420658 original size:89 final size:88
Alignment explanation
Indices: 42420554--42420728 Score: 253
Period size: 89 Copynumber: 2.0 Consensus size: 88
42420544 GAAAAGCAGC
* * *
42420554 GGATCTTGTCTTCATGTATTGACATGAAGTAGATC-GAAGATAGCGGATCTTATCTTCCCACACT
1 GGATCTTGTCTTCATGTATTGACATGAAGTAAATCAG-AGATAGCAGATCGTATCTTCCCACACT
*
42420618 GGTGGTGAAGTAAATCGAAGATAAT
65 AGT-GTGAAGTAAATCGAAGATAAT
* * *
42420643 GGATCTTGTCTTCATGTATTGACATGAAGTAAATCAGAGATAGTAGATCGTGTCTTCCCATACTA
1 GGATCTTGTCTTCATGTATTGACATGAAGTAAATCAGAGATAGCAGATCGTATCTTCCCACACTA
*
42420708 GTGTGAAGTAGATCGAAGATA
66 GTGTGAAGTAAATCGAAGATA
42420729 CAGGTCTTAC
Statistics
Matches: 77, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
88 18 0.23
89 58 0.75
90 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (88 bp):
GGATCTTGTCTTCATGTATTGACATGAAGTAAATCAGAGATAGCAGATCGTATCTTCCCACACTA
GTGTGAAGTAAATCGAAGATAAT
Found at i:42420728 original size:44 final size:44
Alignment explanation
Indices: 42420578--42420728 Score: 130
Period size: 44 Copynumber: 3.4 Consensus size: 44
42420568 TGTATTGACA
* * * * *
42420578 TGAAGTAGATCGAAGATAGCGGATCTTATCTTCCCACACTGGTGG
1 TGAAGTAAATCGAAGATAGTGGATCTTGTCTTCCCATACTAGT-G
* * *
42420623 TGAAGTAAATCGAAGATAATGGATCTTGTCTT--CAT-GTATTG
1 TGAAGTAAATCGAAGATAGTGGATCTTGTCTTCCCATACTAGTG
* *
42420664 ACATGAAGTAAATC-AGAGATAGTAGATCGTGTCTTCCCATACTAGTG
1 ---TGAAGTAAATCGA-AGATAGTGGATCTTGTCTTCCCATACTAGTG
*
42420711 TGAAGTAGATCGAAGATA
1 TGAAGTAAATCGAAGATA
42420729 CAGGTCTTAC
Statistics
Matches: 84, Mismatches: 14, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
41 1 0.01
42 2 0.02
43 3 0.04
44 42 0.50
45 29 0.35
46 3 0.04
47 4 0.05
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (44 bp):
TGAAGTAAATCGAAGATAGTGGATCTTGTCTTCCCATACTAGTG
Found at i:42421012 original size:45 final size:44
Alignment explanation
Indices: 42420957--42421107 Score: 139
Period size: 44 Copynumber: 3.4 Consensus size: 44
42420947 TGTATTGACA
* * *
42420957 TGAAGTAGATCGAAGATGGCAGATCTTGTCTTCCCATACTGGTGG
1 TGAAGTAGATCGAAGATAGTAGATCTTGTCTTCCCATACTAGT-G
* * * * *
42421002 TGAAGTAGATCAAAGATAATGGATCTTGTCTT--CAT-GTATTG
1 TGAAGTAGATCGAAGATAGTAGATCTTGTCTTCCCATACTAGTG
* *
42421043 ACATGAAGTAAATC-AGAGATAGTAGATCGTGTCTTCCCATACTAGTG
1 ---TGAAGTAGATCGA-AGATAGTAGATCTTGTCTTCCCATACTAGTG
42421090 TGAAGTAGATCGAAGATA
1 TGAAGTAGATCGAAGATA
42421108 CAGGTCTTAC
Statistics
Matches: 83, Mismatches: 15, Indels: 17
0.72 0.13 0.15
Matches are distributed among these distances:
41 1 0.01
42 2 0.02
43 4 0.05
44 41 0.49
45 28 0.34
46 3 0.04
47 4 0.05
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.30
Consensus pattern (44 bp):
TGAAGTAGATCGAAGATAGTAGATCTTGTCTTCCCATACTAGTG
Found at i:42421063 original size:44 final size:44
Alignment explanation
Indices: 42420910--42421078 Score: 169
Period size: 44 Copynumber: 3.8 Consensus size: 44
42420900 TACACAACAA
* *
42420910 ACATGAAGTAGATCAGAGATAGTGGATCTTGTCTTAATGTATTG
1 ACATGAAGTAGATCAGAGATAGTAGATCTTGTCTTCATGTATTG
* * *** *
42420954 ACATGAAGTAGATC-GAAGATGGCAGATCTTGTCTTCCCATACTGG
1 ACATGAAGTAGATCAG-AGATAGTAGATCTTGTCTTCATGTA-TTG
*** * * *
42420999 TGGTGAAGTAGATCAAAGATAATGGATCTTGTCTTCATGTATTG
1 ACATGAAGTAGATCAGAGATAGTAGATCTTGTCTTCATGTATTG
* *
42421043 ACATGAAGTAAATCAGAGATAGTAGATCGTGTCTTC
1 ACATGAAGTAGATCAGAGATAGTAGATCTTGTCTTC
42421079 CCATACTAGT
Statistics
Matches: 94, Mismatches: 28, Indels: 6
0.73 0.22 0.05
Matches are distributed among these distances:
43 1 0.01
44 62 0.66
45 31 0.33
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.31
Consensus pattern (44 bp):
ACATGAAGTAGATCAGAGATAGTAGATCTTGTCTTCATGTATTG
Found at i:42421070 original size:89 final size:88
Alignment explanation
Indices: 42420913--42421107 Score: 284
Period size: 89 Copynumber: 2.2 Consensus size: 88
42420903 ACAACAAACA
* * * *
42420913 TGAAGTAGATCAGAGATAGTGGATCTTGTCTTAATGTATTGACATGAAGTAGATCGAAGATGGCA
1 TGAAGTAGATCAAAGATAATGGATCTTGTCTTAATGTATTGACATGAAGTAAATCGAAGATAGCA
* *
42420978 GATCTTGTCTTCCCATACTGGTGG
66 GATCGTGTCTTCCCATACTAGT-G
* *
42421002 TGAAGTAGATCAAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAAATC-AGAGATAGT
1 TGAAGTAGATCAAAGATAATGGATCTTGTCTTAATGTATTGACATGAAGTAAATCGA-AGATAGC
42421066 AGATCGTGTCTTCCCATACTAGTG
65 AGATCGTGTCTTCCCATACTAGTG
*
42421090 TGAAGTAGATCGAAGATA
1 TGAAGTAGATCAAAGATA
42421108 CAGGTCTTAC
Statistics
Matches: 96, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
88 19 0.20
89 77 0.80
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.31
Consensus pattern (88 bp):
TGAAGTAGATCAAAGATAATGGATCTTGTCTTAATGTATTGACATGAAGTAAATCGAAGATAGCA
GATCGTGTCTTCCCATACTAGTG
Found at i:42421253 original size:379 final size:379
Alignment explanation
Indices: 42420554--42421288 Score: 1407
Period size: 379 Copynumber: 1.9 Consensus size: 379
42420544 GAAAAGCAGC
* *
42420554 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAGCGGATCTTATCTTCCCACACTG
1 GGATCTTGTCTTAATGTATTGACATGAAGTAGATCGAAGATAGCAGATCTTATCTTCCCACACTG
*
42420619 GTGGTGAAGTAAATCGAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAAATCAGAGAT
66 GTGGTGAAGTAAATCAAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAAATCAGAGAT
42420684 AGTAGATCGTGTCTTCCCATACTAGTGTGAAGTAGATCGAAGATACAGGTCTTACCTCCCCAACA
131 AGTAGATCGTGTCTTCCCATACTAGTGTGAAGTAGATCGAAGATACAGGTCTTACCTCCCCAACA
42420749 TTACAGTGGAGTAGATAGAAGCACCAATTCATGTACCTCTGAAGATGCAGTAGGAAGGAACGAGG
196 TTACAGTGGAGTAGATAGAAGCACCAATTCATGTACCTCTGAAGATGCAGTAGGAAGGAACGAGG
42420814 CTACCTGAAGAAGAGAAGCATTGAAGAAGTTGAGGCTCAGTAAGACCGGGCACAATTGGGCCTTG
261 CTACCTGAAGAAGAGAAGCATTGAAGAAGTTGAGGCTCAGTAAGACCGGGCACAATTGGGCCTTG
42420879 TAGTCTTTGCTCTGTTCCCATTACACAACAAACATGAAGTAGATCAGAGATAGT
326 TAGTCTTTGCTCTGTTCCCATTACACAACAAACATGAAGTAGATCAGAGATAGT
* * *
42420933 GGATCTTGTCTTAATGTATTGACATGAAGTAGATCGAAGATGGCAGATCTTGTCTTCCCATACTG
1 GGATCTTGTCTTAATGTATTGACATGAAGTAGATCGAAGATAGCAGATCTTATCTTCCCACACTG
*
42420998 GTGGTGAAGTAGATCAAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAAATCAGAGAT
66 GTGGTGAAGTAAATCAAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAAATCAGAGAT
42421063 AGTAGATCGTGTCTTCCCATACTAGTGTGAAGTAGATCGAAGATACAGGTCTTACCTCCCCAACA
131 AGTAGATCGTGTCTTCCCATACTAGTGTGAAGTAGATCGAAGATACAGGTCTTACCTCCCCAACA
42421128 TTACAGTGGAGTAGATAGAAGCACCAATTCATGTACCTCTGAAGATGCAGTAGGAAGGAACGAGG
196 TTACAGTGGAGTAGATAGAAGCACCAATTCATGTACCTCTGAAGATGCAGTAGGAAGGAACGAGG
42421193 CTACCTGAAGAAGAGAAGCATTGAAGAAGTTGAGGCTCAGTAAGACCGGGCACAATTGGGCCTTG
261 CTACCTGAAGAAGAGAAGCATTGAAGAAGTTGAGGCTCAGTAAGACCGGGCACAATTGGGCCTTG
42421258 TAGTCTTTGCTCTGTTCCCATTACACAACAA
326 TAGTCTTTGCTCTGTTCCCATTACACAACAA
42421289 CGAGCAAAGA
Statistics
Matches: 349, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
379 349 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (379 bp):
GGATCTTGTCTTAATGTATTGACATGAAGTAGATCGAAGATAGCAGATCTTATCTTCCCACACTG
GTGGTGAAGTAAATCAAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAAATCAGAGAT
AGTAGATCGTGTCTTCCCATACTAGTGTGAAGTAGATCGAAGATACAGGTCTTACCTCCCCAACA
TTACAGTGGAGTAGATAGAAGCACCAATTCATGTACCTCTGAAGATGCAGTAGGAAGGAACGAGG
CTACCTGAAGAAGAGAAGCATTGAAGAAGTTGAGGCTCAGTAAGACCGGGCACAATTGGGCCTTG
TAGTCTTTGCTCTGTTCCCATTACACAACAAACATGAAGTAGATCAGAGATAGT
Found at i:42423588 original size:40 final size:40
Alignment explanation
Indices: 42423542--42423866 Score: 195
Period size: 40 Copynumber: 7.7 Consensus size: 40
42423532 GGTTTCGACA
*
42423542 CTTATCTTTCTGAAGTTGCAGAGAGCAGATCGCATCTAGT
1 CTTATCTTTCTGAAGTTGCAGAGAGTAGATCGCATCTAGT
* ** * * ** * *
42423582 CCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACATCCAAAT
1 CTTATCTTTCTGAAGTTGCAG-AGAGTAGA-T--CGCAT-CTAGT
*
42423627 CTTATCTTTCTGAAGTTGCAGAGAGCAGATCGCATCTAGT
1 CTTATCTTTCTGAAGTTGCAGAGAGTAGATCGCATCTAGT
* * * * ** * *
42423667 CCTATC-TCCTTGAAGTTGCAGTGGAGTGGATTAAAACATCCAAAT
1 CTTATCTTTC-TGAAGTTGCAG-AGAGTAGA-T--CGCAT-CTAGT
*
42423712 CTTATCTTTCTGAAGTTGCAGAGAGCAGATCGCATCTAGT
1 CTTATCTTTCTGAAGTTGCAGAGAGTAGATCGCATCTAGT
* * * * ** *
42423752 CCTATC-TCCTTGAAGTTGCAGTGGAGTGGATTAAAACATCCAGAT
1 CTTATCTTTC-TGAAGTTGCAG-AGAGTAGA-T--CGCATCTAG-T
42423797 CTTATCTTTCTGAAGTTGCAGAGAGTAGATCGCATCTAGT
1 CTTATCTTTCTGAAGTTGCAGAGAGTAGATCGCATCTAGT
** * *
42423837 CTTATCTCCCTAAAGTTGTAGTAGAGTAGA
1 CTTATCTTTCTGAAGTTGCAG-AGAGTAGA
42423867 CTGAATGAAC
Statistics
Matches: 208, Mismatches: 57, Indels: 39
0.68 0.19 0.13
Matches are distributed among these distances:
39 4 0.02
40 74 0.36
41 35 0.17
42 3 0.01
43 3 0.01
44 28 0.13
45 57 0.27
46 4 0.02
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.31
Consensus pattern (40 bp):
CTTATCTTTCTGAAGTTGCAGAGAGTAGATCGCATCTAGT
Found at i:42423685 original size:85 final size:85
Alignment explanation
Indices: 42423542--42423863 Score: 572
Period size: 85 Copynumber: 3.8 Consensus size: 85
42423532 GGTTTCGACA
42423542 CTTATCTTTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCCTATCTCCCTGAAGTTGCAGTGGA
1 CTTATCTTTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCCTATCTCCCTGAAGTTGCAGTGGA
42423607 GTGGATTAAAACATCCAAAT
66 GTGGATTAAAACATCCAAAT
*
42423627 CTTATCTTTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCCTATCTCCTTGAAGTTGCAGTGGA
1 CTTATCTTTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCCTATCTCCCTGAAGTTGCAGTGGA
42423692 GTGGATTAAAACATCCAAAT
66 GTGGATTAAAACATCCAAAT
*
42423712 CTTATCTTTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCCTATCTCCTTGAAGTTGCAGTGGA
1 CTTATCTTTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCCTATCTCCCTGAAGTTGCAGTGGA
*
42423777 GTGGATTAAAACATCCAGAT
66 GTGGATTAAAACATCCAAAT
* * * * *
42423797 CTTATCTTTCTGAAGTTGCAGAGAGTAGATCGCATCTAGTCTTATCTCCCTAAAGTTGTAGTAGA
1 CTTATCTTTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCCTATCTCCCTGAAGTTGCAGTGGA
42423862 GT
66 GT
42423864 AGACTGAATG
Statistics
Matches: 229, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 229 1.00
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.31
Consensus pattern (85 bp):
CTTATCTTTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCCTATCTCCCTGAAGTTGCAGTGGA
GTGGATTAAAACATCCAAAT
Found at i:42425307 original size:3 final size:3
Alignment explanation
Indices: 42425288--42425338 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
42425278 GTTATATTGC
* * * *
42425288 ATT ATT AGT ATT -GT ATT ATTT ATT ATT ATT TTT ATT ATT ATC ATT
1 ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT
42425333 ATT ATT
1 ATT ATT
42425339 TCTATACATA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
2 1 0.03
3 34 0.89
4 3 0.08
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:42425410 original size:23 final size:24
Alignment explanation
Indices: 42425356--42425414 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 24
42425346 ATATACGCAC
42425356 GTATATATTTTTTATAACATATAT
1 GTATATATTTTTTATAACATATAT
* ** *
42425380 ATGCATATTTTTTTTAA-ATATAT
1 GTATATATTTTTTATAACATATAT
42425403 GTATATATTTTT
1 GTATATATTTTT
42425415 AGACTTTTAT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
23 15 0.54
24 13 0.46
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (24 bp):
GTATATATTTTTTATAACATATAT
Found at i:42425435 original size:30 final size:30
Alignment explanation
Indices: 42425389--42425445 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
42425379 TATGCATATT
* *
42425389 TTTTTTAAATATATGTATATATTTTTAGAC
1 TTTTATAAATACATGTATATATTTTTAGAC
42425419 TTTTATAAATACATGTATATATTTTTA
1 TTTTATAAATACATGTATATATTTTTA
42425446 TACATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.56
Consensus pattern (30 bp):
TTTTATAAATACATGTATATATTTTTAGAC
Found at i:42425450 original size:18 final size:18
Alignment explanation
Indices: 42425427--42425465 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
42425417 ACTTTTATAA
*
42425427 ATACATGTATATATTTTT
1 ATACATATATATATTTTT
42425445 ATACATATATATATTTTT
1 ATACATATATATATTTTT
42425463 ATA
1 ATA
42425466 TTTTATTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (18 bp):
ATACATATATATATTTTT
Found at i:42428091 original size:41 final size:42
Alignment explanation
Indices: 42427990--42428148 Score: 121
Period size: 41 Copynumber: 3.7 Consensus size: 42
42427980 ATATCGAACA
* * * *
42427990 ATGCCAACGTCCCAGAC-GTGGTCTTACATGCTAGCTCATAT-CG
1 ATGCCAATGTCCCAGACAG-GGTCTTACACG-TA-ATCAAATACG
*
42428033 ATGCCACTGTCCCAGACAGGGTCTTACACG-AATCAAATACG
1 ATGCCAATGTCCCAGACAGGGTCTTACACGTAATCAAATACG
* * *
42428074 ATGCCAATGTCCTAGACATGGTCTTATACGTAATCACATATATCG
1 ATGCCAATGTCCCAGACAGGGTCTTACACGTAATCA-A-ATA-CG
* *
42428119 ATGAC-ATCATCCCAGAC-GTGGTCTTACACG
1 ATGCCAAT-GTCCCAGACAG-GGTCTTACACG
42428149 AGAACACATA
Statistics
Matches: 94, Mismatches: 14, Indels: 14
0.77 0.11 0.11
Matches are distributed among these distances:
40 5 0.05
41 29 0.31
42 5 0.05
43 26 0.28
44 6 0.06
45 23 0.24
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACAGGGTCTTACACGTAATCAAATACG
Found at i:42429074 original size:28 final size:31
Alignment explanation
Indices: 42429042--42429100 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 31
42429032 TGTTTTGTTT
42429042 TTATTATAATAA-CATTAT-AAT-ATATAAA
1 TTATTATAATAACCATTATAAATAATATAAA
* *
42429070 TTATTATTATAACCTTTATAAATAATATAAA
1 TTATTATAATAACCATTATAAATAATATAAA
42429101 AACTATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 11 0.42
29 5 0.19
30 3 0.12
31 7 0.27
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (31 bp):
TTATTATAATAACCATTATAAATAATATAAA
Found at i:42430227 original size:30 final size:30
Alignment explanation
Indices: 42430166--42430227 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
42430156 TTACGGTCGG
* * * *
42430166 TAAAATTTTAATTTAATACTTTATAATTTA
1 TAAAATTTTAAATTAATAATGTATAAATTA
42430196 TAAAATTTTAAATTAATAATGGTA-AAATTA
1 TAAAATTTTAAATTAATAAT-GTATAAATTA
42430226 TA
1 TA
42430228 TTTTGACCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 25 0.93
31 2 0.07
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (30 bp):
TAAAATTTTAAATTAATAATGTATAAATTA
Found at i:42431429 original size:51 final size:52
Alignment explanation
Indices: 42431360--42431582 Score: 138
Period size: 51 Copynumber: 4.4 Consensus size: 52
42431350 TGGCACGGAT
* * * * * **
42431360 TATGTGTAGGCCATTATGTAAAAGAGAAAATGAT-GGTCATGTGTGTAGTAC
1 TATGTGCAGGCTACTATGTAAACGAGATAATGATAGGTCACATGTGTAGTAC
* * * *
42431411 TATGTGCAGGCTACTATGTGTACCG-G--AATGATAGGTCGCACGTGTAGTAC
1 TATGTGCAGGCTACTATGT-AAACGAGATAATGATAGGTCACATGTGTAGTAC
*** * * * * * *
42431461 TATGTGCAGGCTACTATGCGTACCAGATAGT-TTCGATCACGTGTGTAGTAC
1 TATGTGCAGGCTACTATGTAAACGAGATAATGATAGGTCACATGTGTAGTAC
* ** * *
42431512 TATGTGCAGGCTACTACGTGT-ATCGA-ATGGTAAT-GGTCATATGTGTAGTAC
1 TATGTGCAGGCTACTA--TGTAAACGAGATAATGATAGGTCACATGTGTAGTAC
42431563 TATGTGCAGGCTACTATGTA
1 TATGTGCAGGCTACTATGTA
42431583 TACCGAACAT
Statistics
Matches: 132, Mismatches: 31, Indels: 19
0.73 0.17 0.10
Matches are distributed among these distances:
49 10 0.08
50 32 0.24
51 81 0.61
52 7 0.05
53 2 0.02
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.31
Consensus pattern (52 bp):
TATGTGCAGGCTACTATGTAAACGAGATAATGATAGGTCACATGTGTAGTAC
Found at i:42439828 original size:19 final size:19
Alignment explanation
Indices: 42439777--42439861 Score: 64
Period size: 20 Copynumber: 4.2 Consensus size: 19
42439767 ATTACAAAAA
* * *
42439777 AAAAATCAAAGTAATTTTC
1 AAAATTCAAAATAATTTTT
*
42439796 AAAATTTGAAAATAATTTTT
1 AAAA-TTCAAAATAATTTTT
*
42439816 AAAATTCAAAAT-ATTTAT
1 AAAATTCAAAATAATTTTT
42439834 AGAAATTCTAAAATTTATATTTTT
1 A-AAATTC-AAAA--TA-ATTTTT
42439858 AAAA
1 AAAA
42439862 AAAATTATAA
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
18 6 0.12
19 17 0.33
20 19 0.37
22 1 0.02
23 3 0.06
24 6 0.12
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.40
Consensus pattern (19 bp):
AAAATTCAAAATAATTTTT
Found at i:42439849 original size:18 final size:19
Alignment explanation
Indices: 42439804--42439852 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
42439794 TCAAAATTTG
*
42439804 AAAATAATTTTTA-AAATTC
1 AAAAT-ATTTATAGAAATTC
42439823 AAAATATTTATAGAAATTC
1 AAAATATTTATAGAAATTC
*
42439842 TAAA-ATTTATA
1 AAAATATTTATA
42439853 TTTTTAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (19 bp):
AAAATATTTATAGAAATTC
Found at i:42439890 original size:18 final size:20
Alignment explanation
Indices: 42439843--42439884 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
42439833 TAGAAATTCT
*
42439843 AAAATT-TATATTTTTAAAA
1 AAAATTATAAATTTTTAAAA
42439862 AAAATTATAAATTTTTAAAA
1 AAAATTATAAATTTTTAAAA
42439882 AAA
1 AAA
42439885 TATAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAATTATAAATTTTTAAAA
Found at i:42439894 original size:21 final size:20
Alignment explanation
Indices: 42439852--42439904 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
42439842 TAAAATTTAT
* *
42439852 ATTTTTAAAAAAAATTATAA
1 ATTTTTAAAAAAAATAAAAA
42439872 ATTTTTAAAAAAATATAAAAA
1 ATTTTTAAAAAAA-ATAAAAA
* *
42439893 ATGTATAAAAAA
1 ATTTTTAAAAAA
42439905 TTTAATACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (20 bp):
ATTTTTAAAAAAAATAAAAA
Found at i:42440210 original size:21 final size:21
Alignment explanation
Indices: 42440186--42440225 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
42440176 ACCTTTTCTA
42440186 AAGTTAAAAGCCAAAACTATC
1 AAGTTAAAAGCCAAAACTATC
*
42440207 AAGTTAAAAGGCAAAACTA
1 AAGTTAAAAGCCAAAACTA
42440226 CGTTATTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.15, G:0.12, T:0.17
Consensus pattern (21 bp):
AAGTTAAAAGCCAAAACTATC
Found at i:42443393 original size:18 final size:19
Alignment explanation
Indices: 42443355--42443397 Score: 63
Period size: 18 Copynumber: 2.3 Consensus size: 19
42443345 TCTAAATGAA
42443355 TTCATTTCTCATTTTTATT
1 TTCATTTCTCATTTTTATT
42443374 TTCATTTCT-ATTTTCT-TT
1 TTCATTTCTCATTTT-TATT
42443392 TTCATT
1 TTCATT
42443398 CTGAAGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (19 bp):
TTCATTTCTCATTTTTATT
Found at i:42447364 original size:3 final size:3
Alignment explanation
Indices: 42447351--42447384 Score: 50
Period size: 3 Copynumber: 10.7 Consensus size: 3
42447341 TCTAAAATGG
42447351 TTC TTC TTTC TTC TTC TTC TTTC TTC TTC TTC TT
1 TTC TTC -TTC TTC TTC TTC -TTC TTC TTC TTC TT
42447385 TCTTAAGTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 23 0.79
4 6 0.21
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:42447369 original size:13 final size:13
Alignment explanation
Indices: 42447351--42447388 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
42447341 TCTAAAATGG
42447351 TTCTTCTTTCTTC
1 TTCTTCTTTCTTC
42447364 TTCTTCTTTCTTC
1 TTCTTCTTTCTTC
42447377 TTCTTCTTTCTT
1 TTCTTCTTTCTT
42447389 AAGTGGTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (13 bp):
TTCTTCTTTCTTC
Found at i:42447388 original size:10 final size:9
Alignment explanation
Indices: 42447351--42447384 Score: 50
Period size: 10 Copynumber: 3.6 Consensus size: 9
42447341 TCTAAAATGG
42447351 TTCTTCTTTC
1 TTCTTC-TTC
42447361 TTCTTCTTC
1 TTCTTCTTC
42447370 TTTCTTCTTC
1 -TTCTTCTTC
42447380 TTCTT
1 TTCTT
42447385 TCTTAAGTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (9 bp):
TTCTTCTTC
Found at i:42454769 original size:24 final size:24
Alignment explanation
Indices: 42454721--42454767 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
42454711 ATATTTTATG
42454721 TATCATTATATTAAATTATTTAAA
1 TATCATTATATTAAATTATTTAAA
42454745 TATCATT-TATTATAA-TATTTAAA
1 TATCATTATATTA-AATTATTTAAA
42454768 ATTTTAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (24 bp):
TATCATTATATTAAATTATTTAAA
Found at i:42454817 original size:26 final size:26
Alignment explanation
Indices: 42454767--42454819 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
42454757 TAATATTTAA
*
42454767 AATTTTAAAATATATTATGTATAATT
1 AATTTTAAAATATATTATATATAATT
42454793 AATTTTACAAATA-ATT-TATACTAATT
1 AATTTTA-AAATATATTATATA-TAATT
42454819 A
1 A
42454820 CTCAAGATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 3 0.12
26 16 0.67
27 5 0.21
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (26 bp):
AATTTTAAAATATATTATATATAATT
Found at i:42462233 original size:20 final size:20
Alignment explanation
Indices: 42462208--42462245 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
42462198 AATCAAGGAA
42462208 GCAATCAAGAAGGTTGATAT
1 GCAATCAAGAAGGTTGATAT
*
42462228 GCAATCAAGGAGGTTGAT
1 GCAATCAAGAAGGTTGAT
42462246 TGGATTGTGA
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:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GCAATCAAGAAGGTTGATAT
Found at i:42468226 original size:6 final size:6
Alignment explanation
Indices: 42468215--42468243 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
42468205 TGTTGTAGTT
42468215 TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
42468244 TTTCCCTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTC
Found at i:42470431 original size:20 final size:20
Alignment explanation
Indices: 42470408--42470446 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
42470398 CAATTTAAAA
42470408 TATAAAAAATTATTAATATG
1 TATAAAAAATTATTAATATG
* **
42470428 TATATAATTTTATTAATAT
1 TATAAAAAATTATTAATAT
42470447 ATGTAAAAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAAATTATTAATATG
Found at i:42470568 original size:20 final size:20
Alignment explanation
Indices: 42470543--42470582 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
42470533 AATATTTTCA
42470543 GTAAATCATTTTCCAGAAAT
1 GTAAATCATTTTCCAGAAAT
42470563 GTAAATCATTTTCCAGAAAT
1 GTAAATCATTTTCCAGAAAT
42470583 CATTTTCCGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (20 bp):
GTAAATCATTTTCCAGAAAT
Found at i:42470583 original size:34 final size:33
Alignment explanation
Indices: 42470532--42470595 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 33
42470522 AAACACCAGA
42470532 AAATATTTTCAGTAAATCATTTTCCAGAAATGT
1 AAATATTTTCAGTAAATCATTTTCCAGAAATGT
*
42470565 AAATCATTTTCCAG-AAATCATTTTCCGGAAA
1 AAAT-ATTTT-CAGTAAATCATTTTCCAGAAA
42470596 ACATTTTACT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 4 0.14
34 21 0.75
35 3 0.11
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (33 bp):
AAATATTTTCAGTAAATCATTTTCCAGAAATGT
Found at i:42470584 original size:14 final size:14
Alignment explanation
Indices: 42470565--42470602 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
42470555 CCAGAAATGT
42470565 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
42470579 AAATCATTTTCCGG
1 AAATCATTTTCCAG
*
42470593 AAAACATTTT
1 AAATCATTTT
42470603 ACTGGCAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:42472633 original size:44 final size:44
Alignment explanation
Indices: 42472585--42472677 Score: 177
Period size: 44 Copynumber: 2.1 Consensus size: 44
42472575 GGCTTTGGTG
42472585 AAAATGTGTTTTAGGTTCAAATCTCATAATAATAATATTTTATA
1 AAAATGTGTTTTAGGTTCAAATCTCATAATAATAATATTTTATA
*
42472629 AAAATGTGTTTTAGGTTCAAATCTCTTAATAATAATATTTTATA
1 AAAATGTGTTTTAGGTTCAAATCTCATAATAATAATATTTTATA
42472673 AAAAT
1 AAAAT
42472678 ATATATAAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.43
Consensus pattern (44 bp):
AAAATGTGTTTTAGGTTCAAATCTCATAATAATAATATTTTATA
Found at i:42473427 original size:31 final size:32
Alignment explanation
Indices: 42473354--42473430 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 32
42473344 ATCTATAAAA
42473354 ATTAAATCAAAACATTTAAAGTATAAAATTACAT
1 ATTAAATC-AAA-ATTTAAAGTATAAAATTACAT
* *
42473388 A--AAATCAAAATTT-ATGTATAATATTACAT
1 ATTAAATCAAAATTTAAAGTATAAAATTACAT
42473417 ATTAAATCAAAATT
1 ATTAAATCAAAATT
42473431 CATTTATACT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
29 15 0.38
30 4 0.10
31 14 0.36
32 5 0.13
34 1 0.03
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.35
Consensus pattern (32 bp):
ATTAAATCAAAATTTAAAGTATAAAATTACAT
Found at i:42474931 original size:17 final size:17
Alignment explanation
Indices: 42474905--42474938 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
42474895 TATGGTCTAT
*
42474905 ATATAGTATACTAAAAA
1 ATATAGTATAATAAAAA
*
42474922 ATATATTATAATAAAAA
1 ATATAGTATAATAAAAA
42474939 TTTAAGTCTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (17 bp):
ATATAGTATAATAAAAA
Found at i:42477111 original size:18 final size:18
Alignment explanation
Indices: 42477084--42477123 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
42477074 CTTTGCTTCA
*
42477084 ACTGCTGTGGAACCGTCG
1 ACTGCCGTGGAACCGTCG
*
42477102 ACTGCCGTGGAACCGTTG
1 ACTGCCGTGGAACCGTCG
42477120 ACTG
1 ACTG
42477124 GAAAAGAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.17, C:0.28, G:0.33, T:0.23
Consensus pattern (18 bp):
ACTGCCGTGGAACCGTCG
Found at i:42499476 original size:25 final size:26
Alignment explanation
Indices: 42499428--42499476 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
42499418 TGCACATAAA
*
42499428 TCGAATCATCTCGAGACACACATTAT
1 TCGAATCATATCGAGACACACATTAT
* *
42499454 TCGAAT-ATATCGCGACAGACATT
1 TCGAATCATATCGAGACACACATT
42499477 CATAGTATGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27
Consensus pattern (26 bp):
TCGAATCATATCGAGACACACATTAT
Found at i:42500047 original size:189 final size:190
Alignment explanation
Indices: 42499727--42500106 Score: 708
Period size: 189 Copynumber: 2.0 Consensus size: 190
42499717 TATCGTGACC
*
42499727 AAACTCTCCCTAATAACATACTATTACGAAAGCTACTCAATCAGTGCTCGTCCAGTGACCTTTGT
1 AAACTCTCCCTAATAACATACTATTACGAAAGCTACTCAATCAGTGCTCATCCAGTGACCTTTGT
42499792 GTTACTCTTATATGATACCTTAATCTCTTTGGGATAATATTCGTTCTCCTAATATGATCCTA-TT
66 GTTACTCTTATATGATACCTTAATCTCTTTGGGATAATATTCGTTCTCCTAATATGATCCTATTT
*
42499856 TTTTTATCATGGTAATCATTACATTTTTCTTCATAAAAAGTCATTTACTATCAAATAGTA
131 TTTTTATCATGGTAATCATTACATCTTTCTTCATAAAAAGTCATTTACTATCAAATAGTA
*
42499916 AAACTCTCCCTAATAACATACTATTACGAAAGCTACTCAATCAGTGCTCATCTAGTGACCTTTGT
1 AAACTCTCCCTAATAACATACTATTACGAAAGCTACTCAATCAGTGCTCATCCAGTGACCTTTGT
* *
42499981 GTTACTCTTATATGATACTTTAATCTCTTTGGGATAATATTTGTTCTCCTAATATGATCCTATTT
66 GTTACTCTTATATGATACCTTAATCTCTTTGGGATAATATTCGTTCTCCTAATATGATCCTATTT
42500046 TTTTTATCATGGTAATCATTACATCTTTCTTCATAAAAAGTCATTTACTATCAAATAGTA
131 TTTTTATCATGGTAATCATTACATCTTTCTTCATAAAAAGTCATTTACTATCAAATAGTA
42500106 A
1 A
42500107 TTAAGTCATG
Statistics
Matches: 185, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
189 123 0.66
190 62 0.34
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (190 bp):
AAACTCTCCCTAATAACATACTATTACGAAAGCTACTCAATCAGTGCTCATCCAGTGACCTTTGT
GTTACTCTTATATGATACCTTAATCTCTTTGGGATAATATTCGTTCTCCTAATATGATCCTATTT
TTTTTATCATGGTAATCATTACATCTTTCTTCATAAAAAGTCATTTACTATCAAATAGTA
Found at i:42502476 original size:43 final size:43
Alignment explanation
Indices: 42502350--42502455 Score: 160
Period size: 43 Copynumber: 2.5 Consensus size: 43
42502340 TGTATCAATA
* *
42502350 GATAAATCAAAAGAAATATACTGGCACACATAGTGCATCATCG
1 GATAAATCGAAACAAATATACTGGCACACATAGTGCATCATCG
* *
42502393 GATAAACCGAAGC-AATCATACTGGCACACATAGTGCATCATCG
1 GATAAATCGAAACAAAT-ATACTGGCACACATAGTGCATCATCG
42502436 GATAAATCGAAACAAATATA
1 GATAAATCGAAACAAATATA
42502456 TTGACATAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
42 3 0.05
43 49 0.89
44 3 0.05
ACGTcount: A:0.44, C:0.20, G:0.16, T:0.20
Consensus pattern (43 bp):
GATAAATCGAAACAAATATACTGGCACACATAGTGCATCATCG
Found at i:42504363 original size:19 final size:20
Alignment explanation
Indices: 42504339--42504377 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
42504329 AATTCATTGT
*
42504339 ATAATTTAA-AAATAAAATA
1 ATAATTGAAGAAATAAAATA
*
42504358 ATAATTGAAGTAATAAAATA
1 ATAATTGAAGAAATAAAATA
42504378 TATTTATTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (20 bp):
ATAATTGAAGAAATAAAATA
Found at i:42513060 original size:6 final size:6
Alignment explanation
Indices: 42513049--42513115 Score: 50
Period size: 6 Copynumber: 11.2 Consensus size: 6
42513039 CAACACATAG
* ***
42513049 AATAAA AATAAA AATAATA AA-AATA AA-AAT AATAAA AATTTT AAT-AA
1 AATAAA AATAAA AATAA-A AATAA-A AATAAA AATAAA AATAAA AATAAA
42513096 AATAAA AATAAA ATATAAA A
1 AATAAA AATAAA A-ATAAA A
42513116 CTGAAAACCT
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
5 5 0.10
6 36 0.72
7 9 0.18
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (6 bp):
AATAAA
Found at i:42513095 original size:15 final size:15
Alignment explanation
Indices: 42513049--42513087 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
42513039 CAACACATAG
42513049 AATAAAAATAAAAAT
1 AATAAAAATAAAAAT
42513064 AATAAAAATAAAAAT
1 AATAAAAATAAAAAT
42513079 AATAAAAAT
1 AATAAAAAT
42513088 TTTAATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
AATAAAAATAAAAAT
Found at i:42522323 original size:49 final size:50
Alignment explanation
Indices: 42522251--42522367 Score: 130
Period size: 50 Copynumber: 2.4 Consensus size: 50
42522241 CAAAGCTATG
* * * *
42522251 TCCCAGACATAGTTTTACATGAGATGTT-TCTTGTA-CTACCAATGCCATA
1 TCCCAGACATGGTCTTACATGAGA-GTTCTCATATAGCTACCAATGCCATA
* * * * *
42522300 TCCCAGATATGGTCTTACATGAGAGTTCTCATATAGGTGCCCATGCCCTA
1 TCCCAGACATGGTCTTACATGAGAGTTCTCATATAGCTACCAATGCCATA
42522350 TCCCAGACATGGTCTTAC
1 TCCCAGACATGGTCTTAC
42522368 GGGGGACCTC
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
48 3 0.05
49 26 0.46
50 27 0.48
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.32
Consensus pattern (50 bp):
TCCCAGACATGGTCTTACATGAGAGTTCTCATATAGCTACCAATGCCATA
Found at i:42522380 original size:50 final size:50
Alignment explanation
Indices: 42522289--42522484 Score: 167
Period size: 50 Copynumber: 3.8 Consensus size: 50
42522279 TCTTGTACTA
* * **
42522289 CCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATAGGTG
1 CCAATGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATATAGGTG
* * ** * *
42522339 CCCATGCCCTATCCCAGACATGGTCTTACGGGGGACCTCTCATCTTGGTG
1 CCAATGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATATAGGTG
* * * * * *
42522389 CCAACGCCATGTCCTAGACATAGTCTTACATCGGACCTCTCATAATCTCAATGATG
1 CCAATGCCATATCCCAGACATGGTCTTACATGGGACCTCTCAT-A--T--A-GGTG
* * *
42522445 CCAATGCCATGTTCCAGACATGGTCTTACATGGGATCTCT
1 CCAATGCCATATCCCAGACATGGTCTTACATGGGACCTCT
42522485 TTACCCAAAT
Statistics
Matches: 112, Mismatches: 28, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
50 74 0.66
53 1 0.01
56 37 0.33
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (50 bp):
CCAATGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATATAGGTG
Found at i:42526786 original size:16 final size:16
Alignment explanation
Indices: 42526762--42526792 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42526752 TCACCAAAGT
*
42526762 GAAGGGATGATGGTTG
1 GAAGAGATGATGGTTG
42526778 GAAGAGATGATGGTT
1 GAAGAGATGATGGTT
42526793 TTAGGGATGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.45, T:0.26
Consensus pattern (16 bp):
GAAGAGATGATGGTTG
Found at i:42531701 original size:20 final size:18
Alignment explanation
Indices: 42531654--42531704 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 18
42531644 CAAGATAAGC
42531654 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
42531671 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
42531691 ATTAAATTAATATT
1 ATTAAATTAATATT
42531705 ATTTTTGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
17 8 0.28
18 3 0.10
19 3 0.10
20 15 0.52
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:42539253 original size:585 final size:581
Alignment explanation
Indices: 42538147--42539317 Score: 2198
Period size: 585 Copynumber: 2.0 Consensus size: 581
42538137 TCAATTCAAT
*
42538147 AATCTCTTAATCAATATATTTTATAATATACAAAATCAATCCATTTCAAATCCACTATTAATTCA
1 AATCTCTTAATCAATATATTTCATAATATACAAAATCAATCCATTTCAAATCCACTATTAATTCA
*
42538212 ATTCAATCTCAAACTACCAAAGTACTCACCTCAAATGCTTACCATATGCAAATAATTTAAATATG
66 ATTCAATCTCAAACTAACAAAGTACTCACCTCAAATGCTTACCATATGCAAATAATTTAAATATG
*
42538277 CAATATTCTACTAGTTAATTCGAATTATAGAAACACAAACCGTGAATTTCGAGCTATTCAACGTC
131 CAACATTCTACTAGTTAATTCGAATTATAGAAACACAAACCGTGAATTTCGAGCTATTCAACGTC
42538342 GATTTTATCATTTCCCTTTTTACTCGAGGATTCCGGTACGACATTAGCTAAGGAATAAATTAAAA
196 GATTTTATCATTTCCCTTTTTACTCGAGGATTCCGGTACGACATTAGCTAAGGAATAAATTAAAA
*
42538407 TACGTTAATATTACACAATTAAATTTCACATTGAATTTCAATTTTTACACTATATTTTGCTTATT
261 TACGTTAATATTACACAACTAAATTTCACATTGAATTTCAATTTTTACACTATATTTTGCTTATT
* * *
42538472 TTTCAATTTAGTCCCTAAACTGAGATTAGTTTTTAACCTTCATATTTAAATTTATATTTTTATAC
326 TTTCAATTTAGTCCCTAAACTCAGACTAGTTTTTAACCTTCACATTTAAATTTATATTTTTATAC
*
42538537 TAATTTCACTCTAACTAAATTTAGCTTCCTCTTTTCCAATTCGACCTCTTAATTTCTAATTTTTC
391 TAATTTCACTCTAACGAAATTTAGCTTCCTCTTTTCCAATTCGACCTCTTAATTTCTAATTTTTC
* *
42538602 ACTATTTAGTCCTTATTACTCAAAATTAACAATTTATTCCATAATTTAGTCATTTTCCATTTTCA
456 ACAATTTAGTCATTATTACTCAAAATTAACAATTTATTCCATAATTTAGTCATTTTCCATTTTCA
42538667 ACTTAAAAATCTATCTATTTAATCCCTAATACTTAAACTATTCAACAATGTCAACACTTAA
521 ACTTAAAAATCTATCTATTTAATCCCTAATACTTAAACTATTCAACAATGTCAACACTTAA
42538728 AATCTCTTAATCAATATATTTCATAATATACAAAATCAATCCATTTCAAATCCACTATTAATTCA
1 AATCTCTTAATCAATATATTTCATAATATACAAAATCAATCCATTTCAAATCCACTATTAATTCA
42538793 ATTCAATCTCAAACTAACAAAGTACTCACCTCAAATGCTTACCATATGCAAATAATTTAAATATG
66 ATTCAATCTCAAACTAACAAAGTACTCACCTCAAATGCTTACCATATGCAAATAATTTAAATATG
42538858 CAACATTCTACTAGTTAATTCGAATTATAGAAACACAAACCGTGAATTTCGAGCTATTCAACGTC
131 CAACATTCTACTAGTTAATTCGAATTATAGAAACACAAACCGTGAATTTCGAGCTATTCAACGTC
*
42538923 GATTTTATCCTTTCCCTTTTTACTCGAGGATTCCGGTACGACATTAGCTAAGGAATACAACAATT
196 GATTTTATCATTTCCCTTTTTACTCGAGGATTCCGGTACGACATTAGCTAAGGAAT---A-AATT
42538988 AAAATACGTTAATATTACACAACTAAATTTCACATTGAATTTCAATTTTTACACTATATTTTGCT
257 AAAATACGTTAATATTACACAACTAAATTTCACATTGAATTTCAATTTTTACACTATATTTTGCT
42539053 TATTTTTCAATTTAGTCCCTAAACTCAGACTAGTTTTTAACCTTCACATTTAAATTTATATTTTT
322 TATTTTTCAATTTAGTCCCTAAACTCAGACTAGTTTTTAACCTTCACATTTAAATTTATATTTTT
42539118 ATACTAATTTCACTCTAACGAAATTTAGCTTCCTCTTTTCCAATTCGACCTCTTAATTTCTAATT
387 ATACTAATTTCACTCTAACGAAATTTAGCTTCCTCTTTTCCAATTCGACCTCTTAATTTCTAATT
42539183 TTTCACAATTTAGTCATTATTACTCAAAATTAACAATTTATTCCATAATTTAGTCATTTTCCATT
452 TTTCACAATTTAGTCATTATTACTCAAAATTAACAATTTATTCCATAATTTAGTCATTTTCCATT
*
42539248 TTCAACTTAAAAATCTATCTATTTAATCCTTAATACTTAAACTATTCAACAATGTCAACACTTAA
517 TTCAACTTAAAAATCTATCTATTTAATCCCTAATACTTAAACTATTCAACAATGTCAACACTTAA
42539313 AATCT
1 AATCT
42539318 TGAACAATAC
Statistics
Matches: 574, Mismatches: 12, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
581 247 0.43
584 1 0.00
585 326 0.57
ACGTcount: A:0.36, C:0.19, G:0.06, T:0.39
Consensus pattern (581 bp):
AATCTCTTAATCAATATATTTCATAATATACAAAATCAATCCATTTCAAATCCACTATTAATTCA
ATTCAATCTCAAACTAACAAAGTACTCACCTCAAATGCTTACCATATGCAAATAATTTAAATATG
CAACATTCTACTAGTTAATTCGAATTATAGAAACACAAACCGTGAATTTCGAGCTATTCAACGTC
GATTTTATCATTTCCCTTTTTACTCGAGGATTCCGGTACGACATTAGCTAAGGAATAAATTAAAA
TACGTTAATATTACACAACTAAATTTCACATTGAATTTCAATTTTTACACTATATTTTGCTTATT
TTTCAATTTAGTCCCTAAACTCAGACTAGTTTTTAACCTTCACATTTAAATTTATATTTTTATAC
TAATTTCACTCTAACGAAATTTAGCTTCCTCTTTTCCAATTCGACCTCTTAATTTCTAATTTTTC
ACAATTTAGTCATTATTACTCAAAATTAACAATTTATTCCATAATTTAGTCATTTTCCATTTTCA
ACTTAAAAATCTATCTATTTAATCCCTAATACTTAAACTATTCAACAATGTCAACACTTAA
Found at i:42541261 original size:16 final size:16
Alignment explanation
Indices: 42541240--42541270 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
42541230 AACATATATA
42541240 AAAAAATAATTACATG
1 AAAAAATAATTACATG
42541256 AAAAAATAATTACAT
1 AAAAAATAATTACAT
42541271 CCTAAAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (16 bp):
AAAAAATAATTACATG
Found at i:42543101 original size:44 final size:43
Alignment explanation
Indices: 42542732--42543753 Score: 325
Period size: 44 Copynumber: 23.6 Consensus size: 43
42542722 TAATGTGCCT
* *
42542732 CACTGCAACTTCA-GGAGGATAATACTTGCTGATTTAGTCTGC-C
1 CACTGCAACTTCAGGGA-GATAAGACTTGCT-AATTAGTCTGCTC
** *
42542775 TCACTGCAACTTCA-GGAGGATAAGACTTGCTTACCTAGTTTGCTC
1 -CACTGCAACTTCAGGGA-GATAAGACTTGC-TAATTAGTCTGCTC
* * * ***
42542820 CACTGCAACTTCA-GGAGGGTGAGGCTTGCTTACCCAGTCTGCTC
1 CACTGCAACTTCAGGGA-GATAAGACTTGC-TAATTAGTCTGCTC
* * ** *
42542864 CACTGTAACTTCAGGGAGATAAGACTAG---ATGCGATCCGCT-
1 CACTGCAACTTCAGGGAGATAAGACTTGCTAATTAG-TCTGCTC
* * * ** * * **
42542904 CTCTGCAACTTCAGAGAGATAATA-TCTGAGATTTTAATCCACT-
1 CACTGCAACTTCAGGGAGATAAGACT-TGCTA-ATTAGTCTGCTC
* * * * * * * *
42542947 TACTGCAACTTCAGCGAGATAGGA-TTGTCGACTTTAATATACTC
1 CACTGCAACTTCAGGGAGATAAGACTTG-CTA-ATTAGTCTGCTC
* * *
42542991 CACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGC-C
1 CACTGCAACTTCAGGGAGATAAGACTTGCTA-ATT-AGTCTGCTC
* *
42543035 TCGCTGCAACTCCA-GGAGGATAAGACTTGCTTAATTAGTCTGCTC
1 -CACTGCAACTTCAGGGA-GATAAGACTTGC-TAATTAGTCTGCTC
* * * **
42543080 CACTACAACTTCAGAGAGATAAGACTAG---ATGCGATCTGCT-
1 CACTGCAACTTCAGGGAGATAAGACTTGCTAATTAG-TCTGCTC
* * * * * ** *
42543120 CTCTGCAACTTCAGAGAGATAAGATCTAAGGT-TTTAACCCGCTC
1 CACTGCAACTTCAGGGAGATAAGA-CT-TGCTAATTAGTCTGCTC
* * * *
42543164 CACTGCAACTTTAGCGAGATAGGA-TTACCGGCT--TTAATCTGCTC
1 CACTGCAACTTCAGGGAGATAAGACTT----GCTAATTAGTCTGCTC
* * *
42543208 CACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGC-C
1 CACTGCAACTTCAGGGAGATAAGACTTGCTA-ATT-AGTCTGCTC
* * *
42543252 TCGCTACAACTTCA-GGAGGATAAGACTTGCTTAATTAGTTTGCTC
1 -CACTGCAACTTCAGGGA-GATAAGACTTGC-TAATTAGTCTGCTC
* **
42543297 CACTGCAACTTCAGGGAGATAAGACTAG---ATGCGATCTGCT-
1 CACTGCAACTTCAGGGAGATAAGACTTGCTAATTAG-TCTGCTC
* * * * * ** *
42543337 CTCTGCAACTTCAGAGAGATAAGATCTAAGGT-TTTAACCCGCTC
1 CACTGCAACTTCAGGGAGATAAGA-CT-TGCTAATTAGTCTGCTC
* * *
42543381 CACTGCAACTTCAGTGAGATAGGA-TTACCGGCT--TTAATCTGCTC
1 CACTGCAACTTCAGGGAGATAAGACTT----GCTAATTAGTCTGCTC
* * * * *
42543425 CATTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTAC-C
1 CACTGCAACTTCAGGGAGATAAGACTTGCTA-ATT-AGTCTGCTC
* *
42543469 TCGCTGCAACTTCA-GGAGGATAAGACTTGCTCAGTTAGTCTGCTC
1 -CACTGCAACTTCAGGGA-GATAAGACTTGCT-AATTAGTCTGCTC
* ** *
42543514 CACTGCAACTTCA-GG-GATAAGACTAG---ATGCGATATGCT-
1 CACTGCAACTTCAGGGAGATAAGACTTGCTAATTAG-TCTGCTC
* * * * * * **
42543552 CTCTGCAACTTCAGAGAGATAAGATCTAAGGT-TTTAATCCAC-C
1 CACTGCAACTTCAGGGAGATAAGA-CT-TGCTAATTAGTCTGCTC
* * * *
42543595 CACTGCAACTTCAGCGAGATAGGA-TTG-TCAGCTTTAATCTGCTC
1 CACTGCAACTTCAGGGAGATAAGACTTGCT-A--ATTAGTCTGCTC
* * * *
42543639 CACTGCAACTTCAGGGAGATAAGATTTTCCATCTTCAGTCTGC-C
1 CACTGCAACTTCAGGGAGATAAGACTTGCTA-ATT-AGTCTGCTC
* *
42543683 TCGCTGCAACTTCA-GGAGGATAAGACTTGCTTATTTAGTCTGCTC
1 -CACTGCAACTTCAGGGA-GATAAGACTTGC-TAATTAGTCTGCTC
42543728 CACTGCAACTTCAGGGAGATAAGACT
1 CACTGCAACTTCAGGGAGATAAGACT
42543754 CGATCTGTTA
Statistics
Matches: 747, Mismatches: 153, Indels: 156
0.71 0.14 0.15
Matches are distributed among these distances:
38 14 0.02
39 8 0.01
40 80 0.11
41 27 0.04
42 20 0.03
43 75 0.10
44 371 0.50
45 148 0.20
46 4 0.01
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (43 bp):
CACTGCAACTTCAGGGAGATAAGACTTGCTAATTAGTCTGCTC
Found at i:42543270 original size:217 final size:217
Alignment explanation
Indices: 42542822--42543753 Score: 1494
Period size: 217 Copynumber: 4.3 Consensus size: 217
42542812 GTTTGCTCCA
* * * *** *
42542822 CTGCAACTTCAGGAGGGTGAGGCTTGCTTACCCAGTCTGCTCCACTGTAACTTCAGGGAGATAAG
1 CTGCAACTTCAGGAGGATAAGACTTGCTTAATTAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
* * * * * *
42542887 ACTAGATGCGATCCGCTCTCTGCAACTTCAGAGAGATAATATCTGAGATTTTAATCCACT-TACT
66 ACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAACCCACTCCACT
** * * *
42542951 GCAACTTCAGCGAGATAGGATTGTCGACTTTAATATACTCCACTGCAACTTCAGGGAGATAAGAT
131 GCAACTTCAGCGAGATAGGATTACCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
42543016 TTGCCATCTTCAGTCTGCCTCG
196 TTGCCATCTTCAGTCTGCCTCG
* * *
42543038 CTGCAACTCCAGGAGGATAAGACTTGCTTAATTAGTCTGCTCCACTACAACTTCAGAGAGATAAG
1 CTGCAACTTCAGGAGGATAAGACTTGCTTAATTAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
*
42543103 ACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAACCCGCTCCACT
66 ACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAACCCACTCCACT
*
42543168 GCAACTTTAGCGAGATAGGATTACCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
131 GCAACTTCAGCGAGATAGGATTACCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
42543233 TTGCCATCTTCAGTCTGCCTCG
196 TTGCCATCTTCAGTCTGCCTCG
* *
42543255 CTACAACTTCAGGAGGATAAGACTTGCTTAATTAGTTTGCTCCACTGCAACTTCAGGGAGATAAG
1 CTGCAACTTCAGGAGGATAAGACTTGCTTAATTAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
*
42543320 ACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAACCCGCTCCACT
66 ACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAACCCACTCCACT
* *
42543385 GCAACTTCAGTGAGATAGGATTACCGGCTTTAATCTGCTCCATTGCAACTTCAGGGAGATAAGAT
131 GCAACTTCAGCGAGATAGGATTACCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
*
42543450 TTGCCATCTTCAGTCTACCTCG
196 TTGCCATCTTCAGTCTGCCTCG
* *
42543472 CTGCAACTTCAGGAGGATAAGACTTGCTCAGTTAGTCTGCTCCACTGCAACTTCA-GG-GATAAG
1 CTGCAACTTCAGGAGGATAAGACTTGCTTAATTAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
* *
42543535 ACTAGATGCGATATGCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAATCCAC-CCACT
66 ACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAACCCACTCCACT
** *
42543599 GCAACTTCAGCGAGATAGGATTGTCAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
131 GCAACTTCAGCGAGATAGGATTACCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
*
42543664 TTTCCATCTTCAGTCTGCCTCG
196 TTGCCATCTTCAGTCTGCCTCG
*
42543686 CTGCAACTTCAGGAGGATAAGACTTGCTTATTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
1 CTGCAACTTCAGGAGGATAAGACTTGCTTAATTAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
42543751 ACT
66 ACT
42543754 CGATCTGTTA
Statistics
Matches: 665, Mismatches: 48, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
214 138 0.21
215 64 0.10
216 120 0.18
217 343 0.52
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (217 bp):
CTGCAACTTCAGGAGGATAAGACTTGCTTAATTAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
ACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAACCCACTCCACT
GCAACTTCAGCGAGATAGGATTACCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
TTGCCATCTTCAGTCTGCCTCG
Found at i:42543603 original size:43 final size:43
Alignment explanation
Indices: 42543554--42543663 Score: 123
Period size: 43 Copynumber: 2.5 Consensus size: 43
42543544 GATATGCTCT
*
42543554 CTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAATCCAC-CCA
1 CTGCAACTTCAGAGAGATAAGATCTAA-GCTTTAATCCACTCCA
* * * * **
42543597 CTGCAACTTCAGCGAGATAGGATTGTCAGCTTTAATCTGCTCCA
1 CTGCAACTTCAGAGAGATAAGA-TCTAAGCTTTAATCCACTCCA
*
42543641 CTGCAACTTCAGGGAGATAAGAT
1 CTGCAACTTCAGAGAGATAAGAT
42543664 TTTCCATCTT
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
43 30 0.54
44 26 0.46
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (43 bp):
CTGCAACTTCAGAGAGATAAGATCTAAGCTTTAATCCACTCCA
Found at i:42551824 original size:24 final size:24
Alignment explanation
Indices: 42551795--42551840 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
42551785 ATCATCTTTT
*
42551795 GCTGCTCATT-CATTTGCTTTTGAA
1 GCTGCTC-TTGCATTTCCTTTTGAA
42551819 GCTGCTCTTGCATTTCCTTTTG
1 GCTGCTCTTGCATTTCCTTTTG
42551841 GGATTGTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (24 bp):
GCTGCTCTTGCATTTCCTTTTGAA
Found at i:42556106 original size:19 final size:16
Alignment explanation
Indices: 42556065--42556098 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
42556055 ATAAACATAT
42556065 ATAAAAAAATAATTAC
1 ATAAAAAAATAATTAC
42556081 ATAAAAAAATAATTAC
1 ATAAAAAAATAATTAC
42556097 AT
1 AT
42556099 CCTAAAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAAAAAAATAATTAC
Found at i:42559246 original size:19 final size:20
Alignment explanation
Indices: 42559211--42559250 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
42559201 AGCATTCCAT
*
42559211 AACTCAGGATAACATAAAAA
1 AACTCAGGATAAAATAAAAA
42559231 AACTCA-GATAAAATAAAAA
1 AACTCAGGATAAAATAAAAA
42559250 A
1 A
42559251 TCATACTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.65, C:0.12, G:0.07, T:0.15
Consensus pattern (20 bp):
AACTCAGGATAAAATAAAAA
Found at i:42567141 original size:5 final size:5
Alignment explanation
Indices: 42567131--42567156 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
42567121 GTAAAGATAG
42567131 AAATA AAATA AAATA AAATA AAATA A
1 AAATA AAATA AAATA AAATA AAATA A
42567157 CGAATCACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:42572924 original size:39 final size:40
Alignment explanation
Indices: 42572859--42572954 Score: 122
Period size: 40 Copynumber: 2.4 Consensus size: 40
42572849 TTTGAATAAA
* * *
42572859 AAAATGCCACTAAAAATCAAGCATTAGCGGCGCTTTTTGG
1 AAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTTAG
* *
42572899 AAAACGCCGCTAAAAAT-GAGCATTAGCGGCGTTTTTTAG
1 AAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTTAG
*
42572938 AAAAGCGCCGCAAAAAA
1 AAAA-CGCCGCTAAAAA
42572955 CCTAATCCCA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
39 23 0.47
40 26 0.53
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.21
Consensus pattern (40 bp):
AAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTTAG
Found at i:42573249 original size:122 final size:124
Alignment explanation
Indices: 42572992--42573307 Score: 458
Period size: 122 Copynumber: 2.6 Consensus size: 124
42572982 CCTTTCGAGG
* * * * *
42572992 CTTTAGCGGTGTTTTTGGAAAAGCGACACTAATGCTCAGACCTTTAGCGGCGTTTTTTGGAGAAG
1 CTTTAGCGGCGTTTATGGAAAAGCGACGCTAATGCTCAGACCTTTAGCGGCGTTTTTTGAAAAAG
* * * *
42573057 CGGCGCTAATGCTCAAACCTTTAGCTGTGTTTTTGTAAAAGTGCCGCTAATGCTCAGAC
66 CGCCGCTAATGCTCAAACCTTTAGCTGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAC
* * *
42573116 CTTTAGTGGCGTTTATGGAAAAGAGTCGCTAATGCTCAGACCTTTAGCGGCG-TTTTTGAAAAAG
1 CTTTAGCGGCGTTTATGGAAAAGCGACGCTAATGCTCAGACCTTTAGCGGCGTTTTTTGAAAAAG
** *
42573180 CGCCGCTAATGCTCGGACTTTTAGC-GCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAC
66 CGCCGCTAATGCTCAAACCTTTAGCTGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAC
* *
42573238 CTTTAGCGGCGTTAATGGAAAAGCGCCGCTAATGCTCAGACCTTTAGCGGCGTTTTTTGAAAAAG
1 CTTTAGCGGCGTTTATGGAAAAGCGACGCTAATGCTCAGACCTTTAGCGGCGTTTTTTGAAAAAG
42573303 -GCCGC
66 CGCCGC
42573308 AAAAACATTT
Statistics
Matches: 172, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
122 83 0.48
123 43 0.25
124 46 0.27
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (124 bp):
CTTTAGCGGCGTTTATGGAAAAGCGACGCTAATGCTCAGACCTTTAGCGGCGTTTTTTGAAAAAG
CGCCGCTAATGCTCAAACCTTTAGCTGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAC
Found at i:42573307 original size:41 final size:41
Alignment explanation
Indices: 42572992--42573300 Score: 422
Period size: 41 Copynumber: 7.5 Consensus size: 41
42572982 CCTTTCGAGG
* * *
42572992 CTTTAGCGGTGTTTTTGGAAAAGCGACACTAATGCTCAGAC
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAC
* * *
42573033 CTTTAGCGGCGTTTTTTGGAGAAGCGGCGCTAATGCTCAAAC
1 CTTTAGCGGCG-TTTTTGGAAAAGCGCCGCTAATGCTCAGAC
* * * *
42573075 CTTTAGCTGTGTTTTTGTAAAAGTGCCGCTAATGCTCAGAC
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAC
* * * *
42573116 CTTTAGTGGCGTTTATGGAAAAGAGTCGCTAATGCTCAGAC
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAC
* *
42573157 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGAC
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAC
*
42573198 TTTTAGC-GCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAC
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAC
**
42573238 CTTTAGCGGCGTTAATGGAAAAGCGCCGCTAATGCTCAGAC
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAC
*
42573279 CTTTAGCGGCGTTTTTTGAAAA
1 CTTTAGCGGCGTTTTTGGAAAA
42573301 AGGCCGCAAA
Statistics
Matches: 232, Mismatches: 34, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
40 37 0.16
41 160 0.69
42 35 0.15
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.30
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAC
Found at i:42573737 original size:14 final size:15
Alignment explanation
Indices: 42573709--42573741 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
42573699 AAGGTTTATA
42573709 GATTATGGAATTAGG
1 GATTATGGAATTAGG
42573724 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
42573738 GATT
1 GATT
42573742 CTAGTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:42573918 original size:7 final size:7
Alignment explanation
Indices: 42573908--42573933 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
42573898 GGGGTTAAGG
42573908 GTTAGTA
1 GTTAGTA
42573915 GTTAGTA
1 GTTAGTA
42573922 GTTAGTA
1 GTTAGTA
42573929 GTTAG
1 GTTAG
42573934 GGGTTGGGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.31, T:0.42
Consensus pattern (7 bp):
GTTAGTA
Found at i:42576558 original size:18 final size:18
Alignment explanation
Indices: 42576535--42576593 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
42576525 AACAGAACTT
42576535 ATGTAATTCTAATATAGA
1 ATGTAATTCTAATATAGA
* * ***
42576553 ATGTAA-AC-AATTTTCTT
1 ATGTAATTCTAA-TATAGA
42576570 ATGTAATTCTAATATAGA
1 ATGTAATTCTAATATAGA
42576588 ATGTAA
1 ATGTAA
42576594 CTTGTTTTAA
Statistics
Matches: 28, Mismatches: 10, Indels: 6
0.64 0.23 0.14
Matches are distributed among these distances:
16 2 0.07
17 9 0.32
18 15 0.54
19 2 0.07
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.41
Consensus pattern (18 bp):
ATGTAATTCTAATATAGA
Found at i:42576855 original size:43 final size:43
Alignment explanation
Indices: 42576801--42577098 Score: 373
Period size: 43 Copynumber: 6.9 Consensus size: 43
42576791 GTTTTTAGTG
* *
42576801 GCGTTTGTGGGAAAAGCGCCGCTATAGGTATTGGTCTTTAGCA
1 GCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCA
* ** * **
42576844 GCGTTTGTGGGAAATGAACTGCTAAATTTCTTGGTCTTTAGCA
1 GCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCA
* * * *
42576887 GCGTTTGTGGGATATGCGTCGCTAAAGGTCTTGGTCTTTAGCG
1 GCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCA
* * *
42576930 GCGTTTGTGGGAAATGCACCGCTAAAGTTCTTGGTCTTTAG-A
1 GCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCA
** *
42576972 GGCGTTTGTGGGATTAGCGCCGCTAAAGGTCTTGGTCTTTAGCG
1 -GCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCA
* * *
42577016 GCGTTTATGGGAAAAGCTCCGCTAAAGGTCTTGGTCTTTAGCG
1 GCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCA
* *
42577059 GCGCTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTATTTA
1 GCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTA
42577099 AAAAAATGCC
Statistics
Matches: 218, Mismatches: 35, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
43 218 1.00
ACGTcount: A:0.19, C:0.17, G:0.32, T:0.32
Consensus pattern (43 bp):
GCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCA
Found at i:42576939 original size:86 final size:86
Alignment explanation
Indices: 42576801--42577098 Score: 418
Period size: 86 Copynumber: 3.5 Consensus size: 86
42576791 GTTTTTAGTG
* * * * *
42576801 GCGTTTGTGGGAAAAGCGCCGCTATAGGTATTGGTCTTTAGCAGCGTTTGTGGGAAATGAACTGC
1 GCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAATGCACCGC
*
42576866 TAAATTTCTTGGTCTTTAGCA
66 TAAAGTTCTTGGTCTTTAGCA
* * *
42576887 GCGTTTGTGGGATATGCGTCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAATGCACCGC
1 GCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAATGCACCGC
42576952 TAAAGTTCTTGGTCTTTAG-A
66 TAAAGTTCTTGGTCTTTAGCA
** * * *
42576972 GGCGTTTGTGGGATTAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTATGGGAAAAGCTCCG
1 -GCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAATGCACCG
* *
42577037 CTAAAGGTCTTGGTCTTTAGCG
65 CTAAAGTTCTTGGTCTTTAGCA
* *
42577059 GCGCTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTATTTA
1 GCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTA
42577099 AAAAAATGCC
Statistics
Matches: 189, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
85 1 0.01
86 188 0.99
ACGTcount: A:0.19, C:0.17, G:0.32, T:0.32
Consensus pattern (86 bp):
GCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAATGCACCGC
TAAAGTTCTTGGTCTTTAGCA
Found at i:42577615 original size:12 final size:12
Alignment explanation
Indices: 42577598--42577622 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42577588 TTAGGACTTG
42577598 AATGATGTTGAT
1 AATGATGTTGAT
42577610 AATGATGTTGAT
1 AATGATGTTGAT
42577622 A
1 A
42577623 TTGTGAAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (12 bp):
AATGATGTTGAT
Found at i:42582312 original size:19 final size:20
Alignment explanation
Indices: 42582282--42582320 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
42582272 TTTTTAGTTT
*
42582282 TGTTTTTAGTAATTTTTTTA
1 TGTTTTTAGTAATTGTTTTA
42582302 TGTTTTT-GTAATTGTTTTA
1 TGTTTTTAGTAATTGTTTTA
42582321 GCTTAATCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.18, C:0.00, G:0.13, T:0.69
Consensus pattern (20 bp):
TGTTTTTAGTAATTGTTTTA
Found at i:42584131 original size:21 final size:21
Alignment explanation
Indices: 42584105--42584150 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
42584095 AGCAAGGGCT
* * *
42584105 TGTGGAGTGGCCATACGAGCA
1 TGTGGAATAGCCATACGAACA
42584126 TGTGGAATAGCCATACGAACA
1 TGTGGAATAGCCATACGAACA
42584147 TGTG
1 TGTG
42584151 TTTTTAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.17, G:0.33, T:0.22
Consensus pattern (21 bp):
TGTGGAATAGCCATACGAACA
Found at i:42584382 original size:20 final size:19
Alignment explanation
Indices: 42584337--42584383 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
42584327 GTGACCCCTG
*
42584337 TTTTCAAAATTTTCAAGTT
1 TTTTCAAAATTATCAAGTT
* *
42584356 TTTTCAAAATTATCTATTT
1 TTTTCAAAATTATCAAGTT
42584375 TGTTTCAAA
1 T-TTTCAAA
42584384 TTGATCCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.32, C:0.11, G:0.04, T:0.53
Consensus pattern (19 bp):
TTTTCAAAATTATCAAGTT
Found at i:42588246 original size:34 final size:33
Alignment explanation
Indices: 42588208--42588426 Score: 99
Period size: 34 Copynumber: 7.2 Consensus size: 33
42588198 TGTTGAAATG
42588208 GACTATGTATGATATATGGCTAAATTAATAATTT
1 GACTATGTATGATA-ATGGCTAAATTAATAATTT
* * * *
42588242 GAC----TA-G-TAATGG-TACATT-TTGAAATG
1 GACTATGTATGATAATGGCTAAATTAAT-AATTT
42588268 GACTATGTATGATACATGGCTAAATTAATAATTT
1 GACTATGTATGATA-ATGGCTAAATTAATAATTT
* * * *
42588302 GAC----TA-G-TAATGG-TACATT-TTGAAATG
1 GACTATGTATGATAATGGCTAAATTAAT-AATTT
42588328 GACTATGTATGATACATGGCTAAATTAATAATTT
1 GACTATGTATGATA-ATGGCTAAATTAATAATTT
* * * *
42588362 GAC----TA-G-TAATGG-TACATT-TTGAAATG
1 GACTATGTATGATAATGGCTAAATTAAT-AATTT
42588388 GACTATGTATGATACATGGCTAAATTAATAATTT
1 GACTATGTATGATA-ATGGCTAAATTAATAATTT
42588422 GACTA
1 GACTA
42588427 GTAATGGTAC
Statistics
Matches: 131, Mismatches: 24, Indels: 60
0.61 0.11 0.28
Matches are distributed among these distances:
25 3 0.02
26 33 0.25
27 12 0.09
28 6 0.05
29 3 0.02
30 12 0.09
31 3 0.02
32 6 0.05
33 12 0.09
34 38 0.29
35 3 0.02
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (33 bp):
GACTATGTATGATAATGGCTAAATTAATAATTT
Found at i:42588271 original size:26 final size:26
Alignment explanation
Indices: 42588242--42588392 Score: 72
Period size: 26 Copynumber: 5.2 Consensus size: 26
42588232 TTAATAATTT
42588242 GACTAGTAATGGTACATTTTGAAATG
1 GACTAGTAATGGTACATTTTGAAATG
* * *
42588268 GACTATGT-ATGATACATGGCTAAATTAATAATTT
1 GACTA-GTAATGGTACAT---T---TTGA-AA-TG
42588302 GACTAGTAATGGTACATTTTGAAATG
1 GACTAGTAATGGTACATTTTGAAATG
* * *
42588328 GACTATGT-ATGATACATGGCTAAATTAATAATTT
1 GACTA-GTAATGGTACAT---T---TTGA-AA-TG
42588362 GACTAGTAATGGTACATTTTGAAATG
1 GACTAGTAATGGTACATTTTGAAATG
42588388 GACTA
1 GACTA
42588393 TGTATGATAC
Statistics
Matches: 93, Mismatches: 12, Indels: 40
0.64 0.08 0.28
Matches are distributed among these distances:
26 33 0.35
27 8 0.09
28 6 0.06
29 2 0.02
31 2 0.02
32 6 0.06
33 8 0.09
34 28 0.30
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (26 bp):
GACTAGTAATGGTACATTTTGAAATG
Found at i:42588293 original size:60 final size:60
Alignment explanation
Indices: 42588200--42588441 Score: 475
Period size: 60 Copynumber: 4.0 Consensus size: 60
42588190 TATAAATATG
*
42588200 TTGAAATGGACTATGTATGATATATGGCTAAATTAATAATTTGACTAGTAATGGTACATT
1 TTGAAATGGACTATGTATGATACATGGCTAAATTAATAATTTGACTAGTAATGGTACATT
42588260 TTGAAATGGACTATGTATGATACATGGCTAAATTAATAATTTGACTAGTAATGGTACATT
1 TTGAAATGGACTATGTATGATACATGGCTAAATTAATAATTTGACTAGTAATGGTACATT
42588320 TTGAAATGGACTATGTATGATACATGGCTAAATTAATAATTTGACTAGTAATGGTACATT
1 TTGAAATGGACTATGTATGATACATGGCTAAATTAATAATTTGACTAGTAATGGTACATT
42588380 TTGAAATGGACTATGTATGATACATGGCTAAATTAATAATTTGACTAGTAATGGTACATT
1 TTGAAATGGACTATGTATGATACATGGCTAAATTAATAATTTGACTAGTAATGGTACATT
42588440 TT
1 TT
42588442 CGCTGTTAAA
Statistics
Matches: 181, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
60 181 1.00
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (60 bp):
TTGAAATGGACTATGTATGATACATGGCTAAATTAATAATTTGACTAGTAATGGTACATT
Found at i:42590718 original size:14 final size:14
Alignment explanation
Indices: 42590701--42590729 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
42590691 TATCCGGTTA
42590701 TTGATTTGAAATCG
1 TTGATTTGAAATCG
42590715 TTGATTTGAAATCG
1 TTGATTTGAAATCG
42590729 T
1 T
42590730 GATGGATCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.07, G:0.21, T:0.45
Consensus pattern (14 bp):
TTGATTTGAAATCG
Done.