Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 6 of 279
Found at i:1649261 original size:26 final size:26
Alignment explanation
Indices: 1649232--1649283 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1649222 AGTTGTAAAG
*
1649232 AGAAAATTATCTGAAGAGAT-TATTTT
1 AGAAAATT-TCTAAAGAGATATATTTT
*
1649258 AGAAAATTTCTAAAGATATATATTTT
1 AGAAAATTTCTAAAGAGATATATTTT
1649284 TTATTTACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.44, C:0.04, G:0.12, T:0.40
Consensus pattern (26 bp):
AGAAAATTTCTAAAGAGATATATTTT
Found at i:1649647 original size:43 final size:43
Alignment explanation
Indices: 1649599--1649682 Score: 123
Period size: 43 Copynumber: 2.0 Consensus size: 43
1649589 TGCCCTCATA
* * *
1649599 GTGCATCATTGAGTAAGCCGAAGCAATTATAATGGCACACAAG
1 GTGCATCATCGAGCAAGCCGAAGCAATTATAATGCCACACAAG
* *
1649642 GTGCATCATCGAGCAAGCTGAAGCAATTATATTGCCACACA
1 GTGCATCATCGAGCAAGCCGAAGCAATTATAATGCCACACA
1649683 TAGTGTTGGA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (43 bp):
GTGCATCATCGAGCAAGCCGAAGCAATTATAATGCCACACAAG
Found at i:1655388 original size:57 final size:58
Alignment explanation
Indices: 1655289--1655400 Score: 151
Period size: 57 Copynumber: 1.9 Consensus size: 58
1655279 AGAAATGGTG
*
1655289 AAAATAGAGAAATGGGTAATATTTAGAAATGATATTAATTTTCTCTAAAATGAAAAAC
1 AAAATAGAGAAATGGGTAATATTTAGAAATGATATTAATTTTCTCCAAAATGAAAAAC
*
1655347 AAAATAGAGAAAT-GG-AATTATTTTA-AAATGA-ATGTAGTTTTCTCCAAAATGAAA
1 AAAATAGAGAAATGGGTAA-TA-TTTAGAAATGATAT-TAATTTTCTCCAAAATGAAA
1655401 TGAAAATGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
56 4 0.08
57 28 0.57
58 17 0.35
ACGTcount: A:0.49, C:0.05, G:0.14, T:0.31
Consensus pattern (58 bp):
AAAATAGAGAAATGGGTAATATTTAGAAATGATATTAATTTTCTCCAAAATGAAAAAC
Found at i:1655409 original size:6 final size:6
Alignment explanation
Indices: 1655392--1655420 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1655382 AGTTTTCTCC
1655392 AAAATG -AAATG AAAATG AAAATG AAAATG
1 AAAATG AAAATG AAAATG AAAATG AAAATG
1655421 GAGAAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (6 bp):
AAAATG
Found at i:1661485 original size:23 final size:23
Alignment explanation
Indices: 1661459--1661504 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1661449 TTGTTATGGC
1661459 AAGTTATCATTTTGCCTATAACA
1 AAGTTATCATTTTGCCTATAACA
1661482 AAGTTATCATTTTGCCTATAACA
1 AAGTTATCATTTTGCCTATAACA
1661505 CCCGCCTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (23 bp):
AAGTTATCATTTTGCCTATAACA
Found at i:1661997 original size:37 final size:35
Alignment explanation
Indices: 1661946--1662019 Score: 103
Period size: 37 Copynumber: 2.1 Consensus size: 35
1661936 GGATTAAAGG
*
1661946 AAAGAGAGGGATAAGGGCTCTAAAAGCTTTTGTAT
1 AAAGAGAGGAATAAGGGCTCTAAAAGCTTTTGTAT
* *
1661981 ANNAAGAGTGGAATAAGGGCTCTCAAAGCTTTTGTAT
1 A--AAGAGAGGAATAAGGGCTCTAAAAGCTTTTGTAT
1662018 AA
1 AA
1662020 TTTAAGATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
35 2 0.06
37 32 0.94
ACGTcount: A:0.36, C:0.09, G:0.26, T:0.26
Consensus pattern (35 bp):
AAAGAGAGGAATAAGGGCTCTAAAAGCTTTTGTAT
Found at i:1663382 original size:13 final size:14
Alignment explanation
Indices: 1663366--1663394 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1663356 TTTCCATCTA
1663366 TCTTCTTTATT-TT
1 TCTTCTTTATTGTT
1663379 TCTTCTTTATTGTT
1 TCTTCTTTATTGTT
1663393 TC
1 TC
1663395 AATATTTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.07, C:0.17, G:0.03, T:0.72
Consensus pattern (14 bp):
TCTTCTTTATTGTT
Found at i:1663627 original size:94 final size:94
Alignment explanation
Indices: 1663460--1663763 Score: 324
Period size: 94 Copynumber: 3.2 Consensus size: 94
1663450 TATTTGACTC
** * ** * *
1663460 GACTATAACAATATAGAGTGTTTGTCGAGGCATTAAACACGTGGTAGTCTGCTAAAACATTAAAC
1 GACTATAACAATATAGAAAGTCTGTCGAGATATTAAACACGGGGTAGTCTGCTAGAACATTAAAC
* *
1663525 ATGGGGTTACCTGTGTAAGACCATAGCTCA
66 ATGAGGTTACATGTGTAAGACCATAGCT-A
*
1663555 G-TTATAACAATATAGAAAGTCTGTCGAGATATTAAACACGGGGTAGTCTGCTAGAACATTAAAC
1 GACTATAACAATATAGAAAGTCTGTCGAGATATTAAACACGGGGTAGTCTGCTAGAACATTAAAC
* * * * *
1663619 ATGTGGTTACAAGTGTAATACCATAACTT
66 ATGAGGTTACATGTGTAAGACCATAGCTA
* * ** * * * *
1663648 GACTATGATAGCATAGAAAGTCTGTCGGGATATTAAACATGGGGTAGT-TCACTAGGACATTAAA
1 GACTATAACAATATAGAAAGTCTGTCGAGATATTAAACACGGGGTAGTCT-GCTAGAACATTAAA
* *
1663712 CATCAGGTTACATGTGTAAGACCATAGCTT
65 CATGAGGTTACATGTGTAAGACCATAGCTA
* * *
1663742 GACTATGACAACATAGAGAGTC
1 GACTATAACAATATAGAAAGTC
1663764 CGCTGGGATG
Statistics
Matches: 176, Mismatches: 31, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
93 2 0.01
94 173 0.98
95 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (94 bp):
GACTATAACAATATAGAAAGTCTGTCGAGATATTAAACACGGGGTAGTCTGCTAGAACATTAAAC
ATGAGGTTACATGTGTAAGACCATAGCTA
Found at i:1663772 original size:94 final size:94
Alignment explanation
Indices: 1663491--1663763 Score: 325
Period size: 94 Copynumber: 2.9 Consensus size: 94
1663481 TTGTCGAGGC
* * * * * *
1663491 ATTAAACACGTGGTAGTCTGCTAAAACATTAAACATGGGGTTACCTGTGTAAGACCATAGC-TCA
1 ATTAAACACGGGGTAGTCTACTAGAACATTAAACATGAGGTTACATGTGTAAGACCATAGCTTGA
* * * *
1663555 GTTATAACAATATAGAAAGTCTGTCGAGAT
66 -CTATGACAACATAGAAAGTCTGTCGGGAT
* * * * *
1663585 ATTAAACACGGGGTAGTCTGCTAGAACATTAAACATGTGGTTACAAGTGTAATACCATAACTTGA
1 ATTAAACACGGGGTAGTCTACTAGAACATTAAACATGAGGTTACATGTGTAAGACCATAGCTTGA
* *
1663650 CTATGATAGCATAGAAAGTCTGTCGGGAT
66 CTATGACAACATAGAAAGTCTGTCGGGAT
* * *
1663679 ATTAAACATGGGGTAGT-TCACTAGGACATTAAACATCAGGTTACATGTGTAAGACCATAGCTTG
1 ATTAAACACGGGGTAGTCT-ACTAGAACATTAAACATGAGGTTACATGTGTAAGACCATAGCTTG
*
1663743 ACTATGACAACATAGAGAGTC
65 ACTATGACAACATAGAAAGTC
1663764 CGCTGGGATG
Statistics
Matches: 152, Mismatches: 25, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
93 1 0.01
94 149 0.98
95 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (94 bp):
ATTAAACACGGGGTAGTCTACTAGAACATTAAACATGAGGTTACATGTGTAAGACCATAGCTTGA
CTATGACAACATAGAAAGTCTGTCGGGAT
Found at i:1669483 original size:55 final size:55
Alignment explanation
Indices: 1669411--1669553 Score: 144
Period size: 55 Copynumber: 2.6 Consensus size: 55
1669401 TGCAAGCCCC
** * * **
1669411 ACGCCCGTGTTAATTTAACAGGTTCGACCACGGGTGTTCCACCCGGGTGTGTCGA
1 ACGCCCGTGTTGTTTTAACAGGTTCGACCACGGGTCTTCCACACGGGCATGTCGA
* ** * *
1669466 ATGCCCGTGTTGTTTTAACAGGTT-TTCCTACGGTTCTTCCACACGGGCATGTCGT
1 ACGCCCGTGTTGTTTTAACAGGTTCGACC-ACGGGTCTTCCACACGGGCATGTCGA
** *
1669521 ACGCCCGTGTTGTTTTGGCAGGCTCGACCACGG
1 ACGCCCGTGTTGTTTTAACAGGTTCGACCACGG
1669554 TCATATCACA
Statistics
Matches: 69, Mismatches: 17, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
54 2 0.03
55 65 0.94
56 2 0.03
ACGTcount: A:0.15, C:0.27, G:0.28, T:0.29
Consensus pattern (55 bp):
ACGCCCGTGTTGTTTTAACAGGTTCGACCACGGGTCTTCCACACGGGCATGTCGA
Found at i:1673535 original size:35 final size:35
Alignment explanation
Indices: 1673489--1673559 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
1673479 CCAGTTGCTG
1673489 AGATGGGTCAATCGGCTTCCTTAGAGTAATTCCTT
1 AGATGGGTCAATCGGCTTCCTTAGAGTAATTCCTT
*
1673524 AGATGGGTCAATCGGCTTCCTTGGAGTAATTCCTT
1 AGATGGGTCAATCGGCTTCCTTAGAGTAATTCCTT
1673559 A
1 A
1673560 CTCCCCCTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.34
Consensus pattern (35 bp):
AGATGGGTCAATCGGCTTCCTTAGAGTAATTCCTT
Found at i:1678238 original size:27 final size:27
Alignment explanation
Indices: 1678208--1678260 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
1678198 TATCCTGGGA
1678208 GTAAGATTTCTTACTTCTTTGAATGGT
1 GTAAGATTTCTTACTTCTTTGAATGGT
1678235 GTAAGATTTCTTACTTCTTTGAATGG
1 GTAAGATTTCTTACTTCTTTGAATGG
1678261 CCTCATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.23, C:0.11, G:0.19, T:0.47
Consensus pattern (27 bp):
GTAAGATTTCTTACTTCTTTGAATGGT
Found at i:1680573 original size:1 final size:1
Alignment explanation
Indices: 1680569--1680600 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
1680559 TTTAGAATGC
1680569 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1680601 CTGTGTATGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1682049 original size:74 final size:74
Alignment explanation
Indices: 1681925--1682147 Score: 338
Period size: 74 Copynumber: 3.0 Consensus size: 74
1681915 AACAAAGGCA
* *
1681925 ACAATCCACGTGTTAGAATACATCAACTGCTTTACATGCTAACAATCTTAACTTGCTATCTAAAC
1 ACAATCCACGTGCTAGAATACATCAACTGCTTTACATGCTAACAATCTTAACTCGCTATCTAAAC
*
1681990 ACACAACAT
66 ACAAAACAT
* * * * * *
1681999 GCAATCCACATGCTAGAATTCATCAACTTCTTTACATGCTAACAACCTTAACGCGCTATCTAAAC
1 ACAATCCACGTGCTAGAATACATCAACTGCTTTACATGCTAACAATCTTAACTCGCTATCTAAAC
1682064 ACAAAACAT
66 ACAAAACAT
* *
1682073 AAAATCCACGTGCTAGAATCCATCAACTGCTTTACATGCTAACAATCTTAACTCGCTATCTAAAC
1 ACAATCCACGTGCTAGAATACATCAACTGCTTTACATGCTAACAATCTTAACTCGCTATCTAAAC
*
1682138 ACATAACAT
66 ACAAAACAT
1682147 A
1 A
1682148 TAATAGAGTA
Statistics
Matches: 132, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
74 132 1.00
ACGTcount: A:0.38, C:0.27, G:0.08, T:0.27
Consensus pattern (74 bp):
ACAATCCACGTGCTAGAATACATCAACTGCTTTACATGCTAACAATCTTAACTCGCTATCTAAAC
ACAAAACAT
Found at i:1689072 original size:25 final size:25
Alignment explanation
Indices: 1689038--1689090 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
1689028 AAAACAACAA
1689038 TGAGCGACATTTATGGGCCAAAGAG
1 TGAGCGACATTTATGGGCCAAAGAG
1689063 TGAGCGACATTTATGGGCCAAAGAG
1 TGAGCGACATTTATGGGCCAAAGAG
1689088 TGA
1 TGA
1689091 ACTGTAGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.32, C:0.15, G:0.32, T:0.21
Consensus pattern (25 bp):
TGAGCGACATTTATGGGCCAAAGAG
Found at i:1690428 original size:43 final size:43
Alignment explanation
Indices: 1690364--1690445 Score: 146
Period size: 43 Copynumber: 1.9 Consensus size: 43
1690354 TTGTATGTTG
*
1690364 TAATGATTGATTTTGGATGTAGTTATAAGAATGTGTTATATCT
1 TAATGATTAATTTTGGATGTAGTTATAAGAATGTGTTATATCT
*
1690407 TAATGATTAATTTTGGCTGTAGTTATAAGAATGTGTTAT
1 TAATGATTAATTTTGGATGTAGTTATAAGAATGTGTTAT
1690446 GCCTTGTATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.30, C:0.02, G:0.21, T:0.46
Consensus pattern (43 bp):
TAATGATTAATTTTGGATGTAGTTATAAGAATGTGTTATATCT
Found at i:1691406 original size:18 final size:19
Alignment explanation
Indices: 1691383--1691420 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
1691373 TCGAAACCGG
1691383 TCAGTTAACC-AAAAAAAT
1 TCAGTTAACCGAAAAAAAT
1691401 TCAGTTAACCGAAAAAAAT
1 TCAGTTAACCGAAAAAAAT
1691420 T
1 T
1691421 AATAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.53, C:0.16, G:0.08, T:0.24
Consensus pattern (19 bp):
TCAGTTAACCGAAAAAAAT
Found at i:1691581 original size:6 final size:6
Alignment explanation
Indices: 1691570--1691615 Score: 67
Period size: 6 Copynumber: 7.5 Consensus size: 6
1691560 ATAATTTAAC
1691570 AAATAA AAAT-A AAATAA AAATCTAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAA--TAA AAATAA AAATAA AAATAA AAA
1691616 ACATATAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.14
6 26 0.70
8 6 0.16
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:1691597 original size:19 final size:20
Alignment explanation
Indices: 1691573--1691610 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1691563 ATTTAACAAA
1691573 TAAAAAT-AAAATAAAAATC
1 TAAAAATAAAAATAAAAATC
1691592 TAAAAATAAAAATAAAAAT
1 TAAAAATAAAAATAAAAAT
1691611 AAAAAACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (20 bp):
TAAAAATAAAAATAAAAATC
Found at i:1691616 original size:20 final size:19
Alignment explanation
Indices: 1691574--1691616 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
1691564 TTTAACAAAT
**
1691574 AAAAATAAAATAAAAATCT
1 AAAAATAAAATAAAAATAA
1691593 AAAAATAAAAATAAAAATAA
1 AAAAAT-AAAATAAAAATAA
1691613 AAAA
1 AAAA
1691617 CATATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.16
Consensus pattern (19 bp):
AAAAATAAAATAAAAATAA
Found at i:1691649 original size:9 final size:9
Alignment explanation
Indices: 1691635--1691720 Score: 136
Period size: 9 Copynumber: 9.6 Consensus size: 9
1691625 TTTATACAAA
1691635 TAATTCGGT
1 TAATTCGGT
1691644 TAATTCGGT
1 TAATTCGGT
1691653 TAATTCGGT
1 TAATTCGGT
* *
1691662 TAATTTGGG
1 TAATTCGGT
*
1691671 TAATTCGGG
1 TAATTCGGT
1691680 TAATTCGGT
1 TAATTCGGT
*
1691689 TAATTCGAT
1 TAATTCGGT
1691698 TAATTCGGT
1 TAATTCGGT
1691707 TAATTCGGT
1 TAATTCGGT
1691716 TAATT
1 TAATT
1691721 TTATACTTAT
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 71 1.00
ACGTcount: A:0.24, C:0.09, G:0.22, T:0.44
Consensus pattern (9 bp):
TAATTCGGT
Found at i:1695470 original size:30 final size:30
Alignment explanation
Indices: 1695436--1695496 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1695426 TCCTTAACTC
1695436 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
1695466 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
1695496 A
1 A
1695497 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:1696396 original size:43 final size:43
Alignment explanation
Indices: 1696316--1696485 Score: 159
Period size: 43 Copynumber: 4.0 Consensus size: 43
1696306 TACACGTACA
* * * *
1696316 ATGCCAACGTCCTAGAC-GTGGTCTTACATGTAATCAAATATTG
1 ATGCCAATGTCCCAGACAG-GGTCTTACACGAAATCAAATATTG
* **
1696359 ATGTCTTTGTCCCAGACAGGGTCTTACACGAAATCAAATA-TG
1 ATGCCAATGTCCCAGACAGGGTCTTACACGAAATCAAATATTG
* * * *
1696401 ATGCCGATGTCCCAGACATGGTCTTACACGTAAATCTCAA-ATCG
1 ATGCCAATGTCCCAGACAGGGTCTTACACG-AAATC-AAATATTG
* *
1696445 ATGCCAATGTTCCAGAC-GTGGTCTTACACGAAATCACATAT
1 ATGCCAATGTCCCAGACAG-GGTCTTACACGAAATCAAATAT
1696486 CGGAATCCTA
Statistics
Matches: 103, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
42 29 0.28
43 44 0.43
44 30 0.29
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.28
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACAGGGTCTTACACGAAATCAAATATTG
Found at i:1696460 original size:44 final size:44
Alignment explanation
Indices: 1696366--1696479 Score: 153
Period size: 44 Copynumber: 2.6 Consensus size: 44
1696356 TTGATGTCTT
* * *
1696366 TGTCCCAGACAGGGTCTTACACGAAA--TCAAATATGATGCCGA
1 TGTCCCAGACATGGTCTTACACGAAATCTCAAATACGATGCCAA
1696408 TGTCCCAGACATGGTCTTACACGTAAATCTCAAAT-CGATGCCAA
1 TGTCCCAGACATGGTCTTACACG-AAATCTCAAATACGATGCCAA
* *
1696452 TGTTCCAGACGTGGTCTTACACGAAATC
1 TGTCCCAGACATGGTCTTACACGAAATC
1696480 ACATATCGGA
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
42 22 0.34
43 8 0.12
44 28 0.44
45 6 0.09
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (44 bp):
TGTCCCAGACATGGTCTTACACGAAATCTCAAATACGATGCCAA
Found at i:1700727 original size:30 final size:30
Alignment explanation
Indices: 1700676--1700732 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1700666 ACGGCCATGA
*
1700676 CACACGGGCGTGTGTCCTGCCCGTGTGTCC
1 CACACGGGCGTATGTCCTGCCCGTGTGTCC
*
1700706 CACACGGGCGTATAGT-TTGCCCGTGTG
1 CACACGGGCGTAT-GTCCTGCCCGTGTG
1700733 AAAGTGCCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.11, C:0.32, G:0.33, T:0.25
Consensus pattern (30 bp):
CACACGGGCGTATGTCCTGCCCGTGTGTCC
Found at i:1704226 original size:19 final size:21
Alignment explanation
Indices: 1704202--1704243 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
1704192 AATCATAATA
1704202 AATAACA-AAT-ATAATGAAG
1 AATAACAGAATAATAATGAAG
1704221 AATAACAGTAATAATAATGAAG
1 AATAACAG-AATAATAATGAAG
1704243 A
1 A
1704244 CTAATAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.35
21 3 0.15
22 10 0.50
ACGTcount: A:0.62, C:0.05, G:0.12, T:0.21
Consensus pattern (21 bp):
AATAACAGAATAATAATGAAG
Found at i:1714882 original size:48 final size:48
Alignment explanation
Indices: 1714803--1715082 Score: 234
Period size: 48 Copynumber: 5.9 Consensus size: 48
1714793 CACATAGTAG
* * * * * *
1714803 GATGCTAATGCCATATCCTAAATATGGTCTTACATGGGATCAAATGTC
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATGTC
* * *
1714851 AATGCCAATGCTATGTCCCAGACATGGTCTTACATGAGAT--CATG-C
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATGTC
* * * * * *
1714896 -ATACCGAA-GCCGATAG-CCCAG-CTATGGTCTTACACGATG-TCTCATATT
1 GATGCC-AATGCC-AT-GTCCCAGAC-ATGGTCTTACATG-GGATCACATGTC
* *
1714944 GATGCCAATGCCATGTCCCAGACACGGTCTTACATGGGATCACATTTC
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATGTC
* *
1714992 GATACCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATTTC
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATGTC
* * * ** *
1715040 GATGCCAATACAATGACCTGGACATGATCTTACATGGGATCAC
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCAC
1715083 TCATATCCCT
Statistics
Matches: 188, Mismatches: 31, Indels: 26
0.77 0.13 0.11
Matches are distributed among these distances:
44 7 0.04
45 23 0.12
46 5 0.03
47 5 0.03
48 140 0.74
49 8 0.04
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.27
Consensus pattern (48 bp):
GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATGTC
Found at i:1718843 original size:33 final size:34
Alignment explanation
Indices: 1718779--1718869 Score: 87
Period size: 33 Copynumber: 2.7 Consensus size: 34
1718769 ACGTTCAAGG
* * * *
1718779 TGCCATAACCCAGTTACGGTCTTTTCATTAAA-A-
1 TGCCATAGCCCAGCTATGGTC-TTCCATTAAACAC
1718812 TGCCATAGCCCAGCTATGGTCTTCCATTTAAACAC
1 TGCCATAGCCCAGCTATGGTCTTCCA-TTAAACAC
* * *
1718847 TGCCATAGTCCAACCATGGTCTT
1 TGCCATAGCCCAGCTATGGTCTT
1718870 ATCTGTCAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
32 4 0.08
33 23 0.48
34 1 0.02
35 20 0.42
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (34 bp):
TGCCATAGCCCAGCTATGGTCTTCCATTAAACAC
Found at i:1721586 original size:48 final size:48
Alignment explanation
Indices: 1721527--1721642 Score: 137
Period size: 47 Copynumber: 2.4 Consensus size: 48
1721517 TATGTGTGCT
* * *
1721527 AGTGTAAGACCATGTTTGGGACATGACATTGGCCACGAT-ATGAGAGCC
1 AGTGTAAGACCATGTTTGGGACATGACATTGG-CAAGATAATAAAAGCC
* * * *
1721575 AGTGTAAGACCATG-TTGGAACATGGCATTGGCAATATAATAAAAGCT
1 AGTGTAAGACCATGTTTGGGACATGACATTGGCAAGATAATAAAAGCC
*
1721622 AGTGTGAGACCATGTTTGGGA
1 AGTGTAAGACCATGTTTGGGA
1721643 TATGGCATCG
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
46 4 0.07
47 34 0.60
48 19 0.33
ACGTcount: A:0.32, C:0.15, G:0.28, T:0.25
Consensus pattern (48 bp):
AGTGTAAGACCATGTTTGGGACATGACATTGGCAAGATAATAAAAGCC
Found at i:1721827 original size:144 final size:143
Alignment explanation
Indices: 1721565--1721828 Score: 320
Period size: 144 Copynumber: 1.8 Consensus size: 143
1721555 TTGGCCACGA
* * * *
1721565 TATGAGAGCCAGTGTAAGACCATGTTGGAACATGGCATTGGCAATATAATAAAAGCTAGTGTGAG
1 TATGAGAGCCAGTGTAAGACCATGTTGGAACATAGCATCGACAATATAATAAAAGCTAGTGTAAG
* * * * * * *
1721630 ACCATGTTTGGGATATGGCATCGGTATTGATATGTGCGCTAGTGTAAGACCATGTCTGACACACA
66 ACCATGTCTGGGATATGGCATCGGTATCGACATGTGAGCCAATATAAGACCATGTCTGACACACA
1721695 GCACCAGCTACAT
131 GCACCAGCTACAT
* * *
1721708 TATGAGAGCCAGTGTAAGACCATGTCT-GAGACATAGCATCGACATTGA-AACT-AGAGTTAGTG
1 TATGAGAGCCAGTGTAAGACCATGT-TGGA-ACATAGCATCGACAAT-ATAA-TAAAAGCTAGTG
*
1721770 TAAGACCATGTCTGGGATATGGCATCGG-ACTCGACGTGTGAGCCAATATAAGACCATGT
62 TAAGACCATGTCTGGGATATGGCATCGGTA-TCGACATGTGAGCCAATATAAGACCATGT
1721829 TTAGAATATG
Statistics
Matches: 101, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
143 28 0.28
144 71 0.70
145 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (143 bp):
TATGAGAGCCAGTGTAAGACCATGTTGGAACATAGCATCGACAATATAATAAAAGCTAGTGTAAG
ACCATGTCTGGGATATGGCATCGGTATCGACATGTGAGCCAATATAAGACCATGTCTGACACACA
GCACCAGCTACAT
Found at i:1723002 original size:43 final size:43
Alignment explanation
Indices: 1722954--1723039 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
1722944 CACGGGCTTG
1722954 TCCAAATATGCGCAGGCCATGTGAGCTGCACGGGCTTTCAGCA
1 TCCAAATATGCGCAGGCCATGTGAGCTGCACGGGCTTTCAGCA
*
1722997 TCCAAATATGCGCAGGCCATGTGAGCTGCACGGTCTTTCAGCA
1 TCCAAATATGCGCAGGCCATGTGAGCTGCACGGGCTTTCAGCA
1723040 GGATCATGTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.23, C:0.28, G:0.27, T:0.22
Consensus pattern (43 bp):
TCCAAATATGCGCAGGCCATGTGAGCTGCACGGGCTTTCAGCA
Found at i:1729374 original size:48 final size:48
Alignment explanation
Indices: 1729314--1729634 Score: 285
Period size: 48 Copynumber: 6.7 Consensus size: 48
1729304 TATGTGTGCT
*
1729314 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGATATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCCACGATATGAGAGCC
* * * * * *
1729362 AGTGTAAGACCATGTTTGGAACATGGTATCAGCAATG-TAATGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCCACGAT-ATGAGAGCC
* * * * *
1729410 AGTGTAAGACCATGTCTGGGACATGGTAT-AGACATTGATATGTGCA-CT
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCCA-CGATATGAG-AGCC
* * *
1729458 AGTGTAAGACCATGTCTGGGACATAGCATTAACCAC-ATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCCACGA-TATGAGAGCC
* * * ** **
1729506 AGTGTAAGACCATGTCTGGGACATGGCATC-GGCATTGAGACAAGAGTT
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCCA-CGATATGAGAGCC
* * * *
1729554 AGTGTAAGACCATGTCTAGGACATGGCATC-GACCTCGACATGTGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCAG-CCACGATATGAGAGCC
* * *
1729602 AGTATAAGACCATGTTTGGAACATGGCATCAGC
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGC
1729635 AATTCACCCT
Statistics
Matches: 219, Mismatches: 43, Indels: 22
0.77 0.15 0.08
Matches are distributed among these distances:
47 8 0.04
48 203 0.93
49 8 0.04
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCAGCCACGATATGAGAGCC
Found at i:1729478 original size:144 final size:143
Alignment explanation
Indices: 1729308--1729632 Score: 395
Period size: 144 Copynumber: 2.3 Consensus size: 143
1729298 GGGTCATATG
**
1729308 TGTG-CTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGA-TATGAGAGCCAGTGTAAGA
1 TGTGACTAGTGTAAGACCATGTCTGGGACATGGCATCAACCAC-ATTATGAGAGCCAGTGTAAGA
* * ** *
1729371 CCATGTTTGGAACATGGTATCAGCAATGTA-ATGAGAGCTAGTGTAAGACCATGTCTGGGACATG
65 CCATGTCTGGAACATGGCATCAGCAATG-AGACAAGAGCTAGTGTAAGACCATGTCTAGGACATG
* *
1729435 GTATAGACATTGATA
129 GCATAGACATCGATA
* *
1729450 TGTGCACTAGTGTAAGACCATGTCTGGGACATAGCATTAACCACATTATGAGAGCCAGTGTAAGA
1 TGTG-ACTAGTGTAAGACCATGTCTGGGACATGGCATCAACCACATTATGAGAGCCAGTGTAAGA
* * * *
1729515 CCATGTCTGGGACATGGCATCGGCATTGAGACAAGAGTTAGTGTAAGACCATGTCTAGGACATGG
65 CCATGTCTGGAACATGGCATCAGCAATGAGACAAGAGCTAGTGTAAGACCATGTCTAGGACATGG
* * *
1729580 CATCGACCTCGACA
130 CATAGACATCGATA
* * * *
1729594 TGTGAGCCAGTATAAGACCATGTTTGGAACATGGCATCA
1 TGTGA-CTAGTGTAAGACCATGTCTGGGACATGGCATCA
1729633 GCAATTCACC
Statistics
Matches: 154, Mismatches: 24, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
142 4 0.03
143 3 0.02
144 147 0.95
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.24
Consensus pattern (143 bp):
TGTGACTAGTGTAAGACCATGTCTGGGACATGGCATCAACCACATTATGAGAGCCAGTGTAAGAC
CATGTCTGGAACATGGCATCAGCAATGAGACAAGAGCTAGTGTAAGACCATGTCTAGGACATGGC
ATAGACATCGATA
Found at i:1729542 original size:96 final size:96
Alignment explanation
Indices: 1729314--1729631 Score: 322
Period size: 96 Copynumber: 3.3 Consensus size: 96
1729304 TATGTGTGCT
* * *
1729314 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCA-CGATATGAGAGCCAGTGTAAGACCATGTT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG-CATTGATATGAGAGCTAGTGTAAGACCATGTC
* * * * *
1729378 TGGAACATGGTA-TCAGCA-ATGTAATGAGAGCT
65 TGGGACATGGCATTAACCACAT-T-ATGAGAGCC
* * * *
1729410 AGTGTAAGACCATGTCTGGGACATGGTATAGACATTGATATGTGCA-CTAGTGTAAGACCATGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATATGAG-AGCTAGTGTAAGACCATGTC
*
1729474 TGGGACATAGCATTAACCACATTATGAGAGCC
65 TGGGACATGGCATTAACCACATTATGAGAGCC
* ** *
1729506 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACAAGAGTTAGTGTAAGACCATGTCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATATGAGAGCTAGTGTAAGACCATGTCT
* ** * * *
1729571 AGGACATGGCATCGACCTCGA-CATGTGAGCC
66 GGGACATGGCATTAACCAC-ATTATGAGAGCC
* * *
1729602 AGTATAAGACCATGTTTGGAACATGGCATC
1 AGTGTAAGACCATGTCTGGGACATGGCATC
1729632 AGCAATTCAC
Statistics
Matches: 185, Mismatches: 31, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
95 3 0.02
96 173 0.94
97 7 0.04
98 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (96 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATATGAGAGCTAGTGTAAGACCATGTCT
GGGACATGGCATTAACCACATTATGAGAGCC
Found at i:1736104 original size:11 final size:11
Alignment explanation
Indices: 1736088--1736128 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
1736078 TTGATTAATT
1736088 TTAAAAAATAA
1 TTAAAAAATAA
1736099 TTAAAAAATAA
1 TTAAAAAATAA
*
1736110 --AATAAAATAT
1 TTAA-AAAATAA
1736120 TTAAAAAAT
1 TTAAAAAAT
1736129 GAAAAAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
9 2 0.08
10 6 0.23
11 16 0.62
12 2 0.08
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
TTAAAAAATAA
Found at i:1736117 original size:21 final size:21
Alignment explanation
Indices: 1736090--1736137 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1736080 GATTAATTTT
1736090 AAAAAATAATTAAAAAAT-AA
1 AAAAAATAATTAAAAAATGAA
*
1736110 AATAAAATATTTAAAAAATGAA
1 AA-AAAATAATTAAAAAATGAA
1736132 AAAAAA
1 AAAAAA
1736138 GCAACCAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 2 0.08
21 19 0.76
22 4 0.16
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (21 bp):
AAAAAATAATTAAAAAATGAA
Found at i:1741465 original size:48 final size:48
Alignment explanation
Indices: 1741398--1741679 Score: 323
Period size: 48 Copynumber: 5.9 Consensus size: 48
1741388 ATACTAGGGT
* * *
1741398 TATGTGAGCCAGTGTAAGACCATGTTTGGAATATGGCATCGGCATTGA
1 TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGA
* * * * * * *
1741446 TATGAGAGCTAATGTAAGACTATGTATGGGACATGGTATCGGCCTCGA
1 TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGA
* * *
1741494 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTGA
1 TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGA
* * * * * *
1741542 TATGAGAGCTAGTGTAAGACAATGTCTGGGACATGGCATTGGCCTCGA
1 TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGA
* *
1741590 CATGTGAGCTAGTGTAAGACCATGTTTGGAACATGGCAT-GGCATTGATA
1 TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTG--A
* * *
1741639 TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCG
1 TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCG
1741680 ACATCTTACC
Statistics
Matches: 190, Mismatches: 41, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
47 5 0.03
48 149 0.78
49 35 0.18
50 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.27
Consensus pattern (48 bp):
TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGA
Found at i:1741572 original size:96 final size:96
Alignment explanation
Indices: 1741398--1741679 Score: 440
Period size: 96 Copynumber: 2.9 Consensus size: 96
1741388 ATACTAGGGT
* *
1741398 TATGTGAGCCAGTGTAAGACCATGTTTGGAATATGGCATCGGCATTGATATGAGAGCTAATGTAA
1 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGATATGAGAGCTAGTGTAA
* * *
1741463 GACTATGTATGGGACATGGTATCGGCCTCGA
66 GACAATGTCTGGGACATGGCATCGGCCTCGA
*
1741494 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTGATATGAGAGCTAGTGTAA
1 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGATATGAGAGCTAGTGTAA
*
1741559 GACAATGTCTGGGACATGGCATTGGCCTCGA
66 GACAATGTCTGGGACATGGCATCGGCCTCGA
* * *
1741590 CATGTGAGCTAGTGTAAGACCATGTTTGGAACATGGCAT-GGCATTGATATATGAGAGCCAGTGT
1 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTG--ATATGAGAGCTAGTGT
*
1741654 AAGACCATGTCTGGGACATGGCATCG
64 AAGACAATGTCTGGGACATGGCATCG
1741680 ACATCTTACC
Statistics
Matches: 171, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
95 6 0.04
96 126 0.74
97 39 0.23
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.27
Consensus pattern (96 bp):
TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGATATGAGAGCTAGTGTAA
GACAATGTCTGGGACATGGCATCGGCCTCGA
Found at i:1744469 original size:58 final size:60
Alignment explanation
Indices: 1744405--1744523 Score: 215
Period size: 60 Copynumber: 2.0 Consensus size: 60
1744395 TCATATTCCA
*
1744405 GAAAGTTTTCCATAAAATTTCCCAGTTG-CAT-GCCAGATTTTCGGAATAATAGCCTATG
1 GAAAGTTTCCCATAAAATTTCCCAGTTGACATAGCCAGATTTTCGGAATAATAGCCTATG
1744463 GAAAGTTTCCCATAAAATTTCCCAGTTGACATAGCCAGATTTTCGGAATAATAGCCTATG
1 GAAAGTTTCCCATAAAATTTCCCAGTTGACATAGCCAGATTTTCGGAATAATAGCCTATG
1744523 G
1 G
1744524 GAACATCATG
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
58 27 0.47
59 3 0.05
60 28 0.48
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (60 bp):
GAAAGTTTCCCATAAAATTTCCCAGTTGACATAGCCAGATTTTCGGAATAATAGCCTATG
Found at i:1747333 original size:26 final size:25
Alignment explanation
Indices: 1747294--1747367 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 25
1747284 CTAACCTATT
*
1747294 AATTAAACTTTAATTATCTTATCTA
1 AATTAAACTCTAATTATCTTATCTA
* *
1747319 AATTAAAACTCTAATTATCCTAATTTA
1 AATT-AAACTCTAATTAT-CTTATCTA
*
1747346 AATTTAACTCCTAATTATCTTA
1 AATTAAACT-CTAATTATCTTA
1747368 ATTAAAATCT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
25 4 0.10
26 19 0.46
27 18 0.44
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.45
Consensus pattern (25 bp):
AATTAAACTCTAATTATCTTATCTA
Found at i:1747336 original size:21 final size:21
Alignment explanation
Indices: 1747312--1747379 Score: 57
Period size: 26 Copynumber: 3.0 Consensus size: 21
1747302 TTTAATTATC
1747312 TTATCTAAATTAAAACTCTAA
1 TTATCTAAATTAAAACTCTAA
*
1747333 TTATCCTAATTTAAATTTAACTCCTAA
1 TTAT-CTAAATT-AA---AACT-CTAA
*
1747360 TTATCTTAATTAAAA-TCTAA
1 TTATCTAAATTAAAACTCTAA
1747380 AATTATTATC
Statistics
Matches: 38, Mismatches: 3, Indels: 13
0.70 0.06 0.24
Matches are distributed among these distances:
20 4 0.11
21 5 0.13
22 8 0.21
23 2 0.05
25 2 0.05
26 9 0.24
27 8 0.21
ACGTcount: A:0.43, C:0.15, G:0.00, T:0.43
Consensus pattern (21 bp):
TTATCTAAATTAAAACTCTAA
Found at i:1747364 original size:53 final size:52
Alignment explanation
Indices: 1747230--1747480 Score: 171
Period size: 53 Copynumber: 4.8 Consensus size: 52
1747220 TCACTCTAAC
* * * * *
1747230 TATCCTAATATAATTTAAAATTCTAATTATTTTAATTAAAATCT-AAA-TT-AT
1 TATCCTAATTTAATTTAAACTACTAATTATCTTAACT-AAAT-TAAAACTTAAT
* *
1747281 TAT-CTAACCTATTAA-TTAAACT-TTAATTATCTTATCTAAATTAAAACTCTAAT
1 TATCCTAA--T-TTAATTTAAACTACTAATTATCTTAACTAAATTAAAACT-TAAT
* *
1747334 TATCCTAATTTAAATTT-AACTCCTAATTATCTTAATTAAAATCTAAAA-TT-AT
1 TATCCTAATTT-AATTTAAACTACTAATTATCTTAACT-AAAT-TAAAACTTAAT
* * * * * *
1747386 TAT-CTAACCTATTAATTTAAATTATTAATGATCTTAAATAGATTAGAACTTTAAT
1 TATCCTAA--T-TTAATTTAAACTACTAATTATCTTAACTAAATTAAAAC-TTAAT
*
1747441 TATCCTAATTTAATTTAAACTTCTAATTATCTTAACTAAA
1 TATCCTAATTTAATTTAAACTACTAATTATCTTAACTAAA
1747481 ATCTAAATTA
Statistics
Matches: 157, Mismatches: 22, Indels: 40
0.72 0.10 0.18
Matches are distributed among these distances:
49 1 0.01
50 11 0.07
51 21 0.13
52 24 0.15
53 57 0.36
54 29 0.18
55 10 0.06
56 4 0.03
ACGTcount: A:0.42, C:0.12, G:0.01, T:0.45
Consensus pattern (52 bp):
TATCCTAATTTAATTTAAACTACTAATTATCTTAACTAAATTAAAACTTAAT
Found at i:1747372 original size:26 final size:26
Alignment explanation
Indices: 1747222--1747480 Score: 94
Period size: 27 Copynumber: 9.8 Consensus size: 26
1747212 CGACCGCATC
* * *
1747222 ACTCTAACTATCCTAATATAATTTAAA
1 ACTCTAATTATCTTAAT-TAAATTAAA
* *
1747249 ATTCTAATTATTTTAATTAAAATCT-AA
1 ACTCTAATTATCTTAATT-AAAT-TAAA
*
1747276 A-T-T-ATTATC-TAACCTATTAATT-AA
1 ACTCTAATTATCTTAA--T-TAAATTAAA
*
1747300 ACTTTAATTATCTT-ATCTAAATTAAA
1 ACTCTAATTATCTTAAT-TAAATTAAA
* *
1747326 ACTCTAATTATCCTAATTTAAATT-TA
1 ACTCTAATTATCTTAA-TTAAATTAAA
1747352 ACTCCTAATTATCTTAATTAAAATCTAAA
1 ACT-CTAATTATCTTAATT-AAAT-TAAA
* *
1747381 A-T-T-ATTATCTAACCTATTAATTTAAA
1 ACTCTAATTATCTTA---ATTAAATTAAA
* * * *
1747407 TTA-T-TAATGATCTTAAATAGATTAGA
1 --ACTCTAATTATCTTAATTAAATTAAA
* * * *
1747433 ACTTTAATTATCCTAATTTAATTTAA
1 ACTCTAATTATCTTAATTAAATTAAA
*
1747459 ACTTCTAATTATCTTAACTAAA
1 AC-TCTAATTATCTTAATTAAA
1747481 ATCTAAATTA
Statistics
Matches: 174, Mismatches: 33, Indels: 50
0.68 0.13 0.19
Matches are distributed among these distances:
23 3 0.02
24 10 0.06
25 21 0.12
26 53 0.30
27 67 0.39
28 11 0.06
29 9 0.05
ACGTcount: A:0.42, C:0.13, G:0.01, T:0.44
Consensus pattern (26 bp):
ACTCTAATTATCTTAATTAAATTAAA
Found at i:1747467 original size:107 final size:104
Alignment explanation
Indices: 1747222--1747495 Score: 388
Period size: 107 Copynumber: 2.6 Consensus size: 104
1747212 CGACCGCATC
* * * *
1747222 ACTCTAACTATCCTAATATAATTTAAAATTCTAATTATTTTAATTAAAATCTAAATTATTATCTA
1 ACTCTAATTATCCTAATTTAATTTAAACTTCTAATTATCTTAATTAAAATCTAAATTATTATCTA
* **
1747287 ACCTATTAATTAAACTTTAATTATCTTATCTAAATTAAA
66 ACCTATTAATTAAACTTTAATGATCTTAAATAAATTAAA
*
1747326 ACTCTAATTATCCTAATTTAAATTT-AACTCCTAATTATCTTAATTAAAATCTAAAATTATTATC
1 ACTCTAATTATCCTAATTT-AATTTAAACTTCTAATTATCTTAATTAAAATCT-AAATTATTATC
* * *
1747390 TAACCTATTAATTTAAATTATTAATGATCTTAAATAGATTAGA
64 TAACCTATTAA-TTAAACT-TTAATGATCTTAAATAAATTAAA
* *
1747433 ACTTTAATTATCCTAATTTAATTTAAACTTCTAATTATCTTAACTAAAATCTAAATTATTATC
1 ACTCTAATTATCCTAATTTAATTTAAACTTCTAATTATCTTAATTAAAATCTAAATTATTATC
1747496 GGGAAGAAAT
Statistics
Matches: 151, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
104 41 0.27
105 27 0.18
106 22 0.15
107 61 0.40
ACGTcount: A:0.42, C:0.13, G:0.01, T:0.44
Consensus pattern (104 bp):
ACTCTAATTATCCTAATTTAATTTAAACTTCTAATTATCTTAATTAAAATCTAAATTATTATCTA
ACCTATTAATTAAACTTTAATGATCTTAAATAAATTAAA
Found at i:1750093 original size:31 final size:31
Alignment explanation
Indices: 1750055--1750118 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
1750045 TTGACTCATG
1750055 TAATTTGCAGGATCTTGGATTTATAGGTCCA
1 TAATTTGCAGGATCTTGGATTTATAGGTCCA
1750086 TAATTTGCAGGATCTTGGATTTATAGGTCCA
1 TAATTTGCAGGATCTTGGATTTATAGGTCCA
1750117 TA
1 TA
1750119 CTTTACCTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (31 bp):
TAATTTGCAGGATCTTGGATTTATAGGTCCA
Found at i:1754021 original size:19 final size:20
Alignment explanation
Indices: 1753993--1754031 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1753983 TCCCATTATT
1753993 TATTTATTTTT-TGTTTTAA
1 TATTTATTTTTATGTTTTAA
*
1754012 TATTTGTTTTTATGTTTTAA
1 TATTTATTTTTATGTTTTAA
1754032 ATGTATTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.72
Consensus pattern (20 bp):
TATTTATTTTTATGTTTTAA
Found at i:1754049 original size:25 final size:23
Alignment explanation
Indices: 1754012--1754057 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
1754002 TTTGTTTTAA
*
1754012 TATTTGTTTTTATGTTTTAAATG
1 TATTTGTTTTTATATTTTAAATG
1754035 TATTTGATTTATTATATTTTAAA
1 TATTTG-TTT-TTATATTTTAAA
1754058 GTTTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 3 0.15
25 11 0.55
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (23 bp):
TATTTGTTTTTATATTTTAAATG
Found at i:1754423 original size:21 final size:20
Alignment explanation
Indices: 1754399--1754470 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 20
1754389 CCTAATTATC
1754399 TTATCTAAATTAAAAATCTAA
1 TTATCTAAATT-AAAATCTAA
*
1754420 TTATCCTAATTTATTTAAACTCCTAA
1 TTAT-CTAA---A-TTAAAAT-CTAA
*
1754446 TTATCTTAATTAAAATCTAAA
1 TTATCTAAATTAAAATCT-AA
1754467 TTAT
1 TTAT
1754471 TATCTAACCT
Statistics
Matches: 41, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
20 2 0.05
21 16 0.39
22 5 0.12
25 8 0.20
26 10 0.24
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.44
Consensus pattern (20 bp):
TTATCTAAATTAAAATCTAA
Found at i:1759059 original size:41 final size:42
Alignment explanation
Indices: 1758997--1759078 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 42
1758987 GAATCGGTGC
* * *
1758997 CGATACCATGTCCCGGACATGGT-TTATACGGGACCTCATAT
1 CGATACCATGTCCCAGACATGGTCTTACACGAGACCTCATAT
* *
1759038 CGATGCCATGTCCCAGACATGGTCTTACACGAGAGCTCATA
1 CGATACCATGTCCCAGACATGGTCTTACACGAGACCTCATA
1759079 AATCATGGTG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
41 21 0.60
42 14 0.40
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (42 bp):
CGATACCATGTCCCAGACATGGTCTTACACGAGACCTCATAT
Found at i:1761354 original size:26 final size:26
Alignment explanation
Indices: 1761321--1761385 Score: 98
Period size: 24 Copynumber: 2.5 Consensus size: 26
1761311 AAACTCTTCT
1761321 AAAAGAAAACTCAAGAGAAATTCTTG
1 AAAAGAAAACTCAAGAGAAATTCTTG
*
1761347 AAAAGAAAACTC--GAGAGATTCTTG
1 AAAAGAAAACTCAAGAGAAATTCTTG
1761371 AAAAGAAAACCTCAA
1 AAAAGAAAA-CTCAA
1761386 AAAGACTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
24 20 0.57
25 3 0.09
26 12 0.34
ACGTcount: A:0.54, C:0.14, G:0.15, T:0.17
Consensus pattern (26 bp):
AAAAGAAAACTCAAGAGAAATTCTTG
Found at i:1775140 original size:135 final size:138
Alignment explanation
Indices: 1774870--1775147 Score: 375
Period size: 135 Copynumber: 2.0 Consensus size: 138
1774860 AATAATAAGA
*
1774870 TCTAATAAATAAAATATTGGGCTCATATATAATAATAATTAAGCCTAAAAATTGAACCCAATATG
1 TCTAATAAATAAAATATTGGGCTC--A-ATAATAATAATTAAGCCTAAAAATCGAACCCAATATG
* * * *
1774935 ATTTAAACTTGAATTAAAAGCCTGAAACTCGTAATTTTCGTAATAATCTCATCCAAAAAGTTTGC
63 ATTTAAACTTGAATTAAAAGCCCGAAACTCGTAATTTCCGTAATAATCCCATCCAAAAAGTTTAC
*
1775000 CCACACAGTCT
128 CCACACAATCT
* *
1775011 TCTAATAAATAAAATATTGGGCTC-AT-AT-ATAATTAAGCCTAAAAATCGATCCTAATATGATT
1 TCTAATAAATAAAATATTGGGCTCAATAATAATAATTAAGCCTAAAAATCGAACCCAATATGATT
* * * **
1775073 TAAACTTGAATTAAAAGCCCGAAACTTGTAATTTCCGTAATAATCCCGTCCAGAAA-TTCTATTC
66 TAAACTTGAATTAAAAGCCCGAAACTCGTAATTTCCGTAATAATCCCATCCAAAAAGTT-TACCC
1775137 ACACAATCT
130 ACACAATCT
1775146 TC
1 TC
1775148 ACTAAAATGA
Statistics
Matches: 123, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
134 2 0.02
135 93 0.76
136 2 0.02
137 2 0.02
141 24 0.20
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.32
Consensus pattern (138 bp):
TCTAATAAATAAAATATTGGGCTCAATAATAATAATTAAGCCTAAAAATCGAACCCAATATGATT
TAAACTTGAATTAAAAGCCCGAAACTCGTAATTTCCGTAATAATCCCATCCAAAAAGTTTACCCA
CACAATCT
Found at i:1781898 original size:5 final size:5
Alignment explanation
Indices: 1781867--1781920 Score: 72
Period size: 5 Copynumber: 10.2 Consensus size: 5
1781857 GAGATTATGA
*
1781867 AATTG AATGTG AAATTG CATATG AATTG AATTG AATTG AATTG AATTG
1 AATTG AAT-TG -AATTG AAT-TG AATTG AATTG AATTG AATTG AATTG
1781915 AATTG A
1 AATTG A
1781921 GATTTATGAT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
5 33 0.75
6 8 0.18
7 3 0.07
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.37
Consensus pattern (5 bp):
AATTG
Found at i:1781985 original size:31 final size:31
Alignment explanation
Indices: 1781950--1782096 Score: 163
Period size: 31 Copynumber: 4.7 Consensus size: 31
1781940 ATAAAATAGA
*
1781950 GTATGAATATGAAAATATGAATGATTACAGG
1 GTATGAATATGAAAATATGAATGATTACAAG
*
1781981 GTATGGATAT-AAAAGTATGAATGATTACAAG
1 GTATGAATATGAAAA-TATGAATGATTACAAG
* * * *
1782012 ATATGAATATGACAGTATGAATGATTACAGG
1 GTATGAATATGAAAATATGAATGATTACAAG
* * *
1782043 GCATGACTAT-AAAGGTATGAATGATTACAAG
1 GTATGAATATGAAA-ATATGAATGATTACAAG
* *
1782074 GTATGAACATGTAAATATGAATG
1 GTATGAATATGAAAATATGAATG
1782097 GTTGATGCCC
Statistics
Matches: 95, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
30 6 0.06
31 85 0.89
32 4 0.04
ACGTcount: A:0.44, C:0.05, G:0.22, T:0.29
Consensus pattern (31 bp):
GTATGAATATGAAAATATGAATGATTACAAG
Found at i:1782018 original size:17 final size:17
Alignment explanation
Indices: 1781965--1782080 Score: 97
Period size: 17 Copynumber: 7.4 Consensus size: 17
1781955 AATATGAAAA
*
1781965 TATGAATGATTACAGGG
1 TATGAATGATTACAAGG
* *
1781982 TATGGAT-A-TA-AAAG
1 TATGAATGATTACAAGG
*
1781996 TATGAATGATTACAAGA
1 TATGAATGATTACAAGG
*
1782013 TATGAAT-ATGAC-A-G
1 TATGAATGATTACAAGG
*
1782027 TATGAATGATTACAGGG
1 TATGAATGATTACAAGG
* *
1782044 CATGACT-A-TA-AAGG
1 TATGAATGATTACAAGG
1782058 TATGAATGATTACAAGG
1 TATGAATGATTACAAGG
1782075 TATGAA
1 TATGAA
1782081 CATGTAAATA
Statistics
Matches: 75, Mismatches: 15, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
14 23 0.31
15 11 0.15
16 10 0.13
17 31 0.41
ACGTcount: A:0.42, C:0.06, G:0.23, T:0.28
Consensus pattern (17 bp):
TATGAATGATTACAAGG
Found at i:1782020 original size:62 final size:62
Alignment explanation
Indices: 1781951--1782096 Score: 213
Period size: 62 Copynumber: 2.4 Consensus size: 62
1781941 TAAAATAGAG
*
1781951 TATGAATATGAAAATATGAATGATTACAGGGTATGGA-TATAAAAGTATGAATGATTACAAGA
1 TATGAATATGAAAATATGAATGATTACAGGGCAT-GACTATAAAAGTATGAATGATTACAAGA
* * * *
1782013 TATGAATATGACAGTATGAATGATTACAGGGCATGACTATAAAGGTATGAATGATTACAAGG
1 TATGAATATGAAAATATGAATGATTACAGGGCATGACTATAAAAGTATGAATGATTACAAGA
* *
1782075 TATGAACATGTAAATATGAATG
1 TATGAATATGAAAATATGAATG
1782097 GTTGATGCCC
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
61 2 0.03
62 72 0.97
ACGTcount: A:0.44, C:0.05, G:0.22, T:0.29
Consensus pattern (62 bp):
TATGAATATGAAAATATGAATGATTACAGGGCATGACTATAAAAGTATGAATGATTACAAGA
Found at i:1782032 original size:14 final size:14
Alignment explanation
Indices: 1781949--1782033 Score: 53
Period size: 14 Copynumber: 5.6 Consensus size: 14
1781939 GATAAAATAG
*
1781949 AGTATGAATATGAA
1 AGTATGAATATGAC
* *
1781963 AATATGAATGATTAC
1 AGTATGAAT-ATGAC
* * *
1781978 AGGGTATGGATATAAA
1 A--GTATGAATATGAC
*
1781994 AGTATGAATGATTAC
1 AGTATGAAT-ATGAC
1782009 AAGATATGAATATGAC
1 -AG-TATGAATATGAC
1782025 AGTATGAAT
1 AGTATGAAT
1782034 GATTACAGGG
Statistics
Matches: 54, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
14 22 0.41
15 9 0.17
16 10 0.19
17 13 0.24
ACGTcount: A:0.46, C:0.04, G:0.21, T:0.29
Consensus pattern (14 bp):
AGTATGAATATGAC
Found at i:1785441 original size:19 final size:20
Alignment explanation
Indices: 1785400--1785442 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
1785390 TTTTGTAAAG
* *
1785400 TTTGTAAAATAGATGGTACT
1 TTTGTAAAATAGATGGAAAT
*
1785420 TTTGTGAAATA-ATGGAAAT
1 TTTGTAAAATAGATGGAAAT
1785439 TTTG
1 TTTG
1785443 GGTTGCTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.35, C:0.02, G:0.21, T:0.42
Consensus pattern (20 bp):
TTTGTAAAATAGATGGAAAT
Found at i:1786627 original size:12 final size:12
Alignment explanation
Indices: 1786612--1786641 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1786602 ACAATAATAC
1786612 TATATATAAATG
1 TATATATAAATG
*
1786624 TATATATATATG
1 TATATATAAATG
1786636 TATATA
1 TATATA
1786642 ATAGAAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (12 bp):
TATATATAAATG
Found at i:1786744 original size:19 final size:17
Alignment explanation
Indices: 1786720--1786766 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
1786710 AATTAAAGTA
*
1786720 ATAAAAAATAATACTATAT
1 ATAAAAAAT-ATA-TATAC
*
1786739 ATAAAATATATATATAC
1 ATAAAAAATATATATAC
1786756 AT-AAAAATATA
1 ATAAAAAATATA
1786767 CACTAATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 8 0.32
17 6 0.24
18 3 0.12
19 8 0.32
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAAAAAATATATATAC
Found at i:1786762 original size:18 final size:19
Alignment explanation
Indices: 1786723--1786771 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 19
1786713 TAAAGTAATA
*
1786723 AAAAATA-ATACTATATAT
1 AAAAATATATACTATACAT
1786741 -AAAATATATA-TATACAT
1 AAAAATATATACTATACAT
*
1786758 AAAAATATACACTA
1 AAAAATATATACTA
1786772 ATATATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 12 0.46
18 12 0.46
19 2 0.08
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAAATATATACTATACAT
Found at i:1786998 original size:3 final size:3
Alignment explanation
Indices: 1786985--1787070 Score: 60
Period size: 3 Copynumber: 29.3 Consensus size: 3
1786975 GAGGGCATAT
1786985 ATA AT- ATA ATA ATA AT- ATA A-A A-A ATA ATA TATA CATGA GA-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA -AT-A -ATA ATA
* *
1787029 ATA ATA ATA AT- ATAA ATA ATA GTA AAA ATA ATA A-A ATA ATA A
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1787071 AACAAAGCTC
Statistics
Matches: 68, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
2 13 0.19
3 46 0.68
4 7 0.10
5 2 0.03
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:1787011 original size:18 final size:18
Alignment explanation
Indices: 1786990--1787070 Score: 76
Period size: 18 Copynumber: 4.4 Consensus size: 18
1786980 CATATATAAT
1786990 ATAATAATAATATAAAAA
1 ATAATAATAATATAAAAA
* *
1787008 ATAATATATACATGAGAAATA
1 ATAATA-ATA-AT-ATAAAAA
*
1787029 ATAATAATAATATAAATA
1 ATAATAATAATATAAAAA
*
1787047 ATAGTAA-AA-ATAATAAA
1 ATAATAATAATATAA-AAA
1787064 ATAATAA
1 ATAATAA
1787071 AACAAAGCTC
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
16 4 0.08
17 10 0.19
18 18 0.34
19 5 0.09
20 5 0.09
21 11 0.21
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (18 bp):
ATAATAATAATATAAAAA
Found at i:1787433 original size:40 final size:40
Alignment explanation
Indices: 1787389--1787540 Score: 196
Period size: 40 Copynumber: 3.8 Consensus size: 40
1787379 GTGTTTTTAG
*
1787389 TCTGCTCCACTACTACTTAGGGAGATAAGACTTGATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
* * * * ***
1787429 TCTGCTTCACTATTGCTTAGGGAAATAAGATCTGTGGTTTTA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGATGCGA
*
1787471 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTAATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
*
1787511 TCTACTCCACTACTGCTTAGGGAGATAAGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA
1787541 TTGTAATCTT
Statistics
Matches: 93, Mismatches: 17, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
40 58 0.62
41 4 0.04
42 31 0.33
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (40 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
Found at i:1787480 original size:82 final size:83
Alignment explanation
Indices: 1787373--1787541 Score: 259
Period size: 82 Copynumber: 2.0 Consensus size: 83
1787363 CATGGGGATG
* * * * *
1787373 AGATTTGTGTTTTTAGTCTGCTCCACTACTACTTAGGGAGATAAGACTTGATGCGATCTGCTTCA
1 AGATCTGTGGTTTTAGTCTGCTCCACTACTACTTAGGGAGATAAGACTTAATGCGATCTACTCCA
*
1787438 CTATTGCTTAGGGAAATA
66 CTACTGCTTAGGGAAATA
*
1787456 AGATCTGTGGTTTTA-TCTGCTCCACTACTGCTTAGGGAGATAAGACTTAATGCGATCTACTCCA
1 AGATCTGTGGTTTTAGTCTGCTCCACTACTACTTAGGGAGATAAGACTTAATGCGATCTACTCCA
*
1787520 CTACTGCTTAGGGAGATA
66 CTACTGCTTAGGGAAATA
1787538 AGAT
1 AGAT
1787542 TGTAATCTTC
Statistics
Matches: 78, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
82 65 0.83
83 13 0.17
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (83 bp):
AGATCTGTGGTTTTAGTCTGCTCCACTACTACTTAGGGAGATAAGACTTAATGCGATCTACTCCA
CTACTGCTTAGGGAAATA
Found at i:1788013 original size:134 final size:134
Alignment explanation
Indices: 1787703--1788275 Score: 957
Period size: 134 Copynumber: 4.3 Consensus size: 134
1787693 ACTTCCTACC
* *
1787703 AATATAGGAAGGCAGGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTT
1 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTT
1787768 ATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCG
66 ATCGGCTTCAATGTACTCCACTGTAGT--CAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCG
*
1787833 CTGCCT
129 CTGCCA
*
1787839 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGTGAGATAGAGTT
1 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTT
1787904 ATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCT
66 ATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCT
* *
1787969 ACCG
131 GCCA
*
1787973 AATACAGGAAGGCAAGATCTGCAATATTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTT
1 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTT
* *
1788038 ATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCT
66 ATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCT
1788103 GCCA
131 GCCA
* * *
1788107 AATATAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATT
1 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTT
* * * * * *
1788172 ATCGGCTTCAGTGTACTCCACTGTGGTCAGGAAGGTAAAATCTGCCATTTTTGATTTGCTTCGCT
66 ATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCT
1788237 GCCA
131 GCCA
*
1788241 AATACAGGAAGGCAAGATCTGCAATCTTAAATCTA
1 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTA
1788276 CTTCATCACC
Statistics
Matches: 416, Mismatches: 21, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
134 327 0.79
136 89 0.21
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.27
Consensus pattern (134 bp):
AATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTT
ATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCT
GCCA
Found at i:1788478 original size:132 final size:132
Alignment explanation
Indices: 1788271--1788925 Score: 1184
Period size: 132 Copynumber: 5.0 Consensus size: 132
1788261 GCAATCTTAA
** * *
1788271 ATCTACTTCATCACCAGTATGGGAAGACAAGATCTGCATCTTGGATCGACTTCCTATCAATATAG
1 ATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAG
1788336 GAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTG
66 GAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTG
1788401 CG
131 CG
*
1788403 ATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATATTGGATCCACTTCCTATCAATATAG
1 ATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAG
1788468 GAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTG
66 GAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTG
1788533 CG
131 CG
*
1788535 ATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATATTGGATCCACTTCCTATCAATATAG
1 ATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAG
1788600 GAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTG
66 GAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTG
1788665 CG
131 CG
* *
1788667 ATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAG
1 ATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAG
* * *
1788732 AAAGATAGGATCTGCTACCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTG
66 GAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTG
1788797 CG
131 CG
*
1788799 ATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCCTGGATCCACTTCCTATCAATATAG
1 ATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAG
* *
1788864 GAAGATAGGACCTGCTATCTTCGATCTGCTTCACGCCAATACATGAAGACAAGATCTACTTT
66 GAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTT
1788926 AATGACTTCA
Statistics
Matches: 504, Mismatches: 19, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
132 504 1.00
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.27
Consensus pattern (132 bp):
ATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAG
GAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTG
CG
Found at i:1810977 original size:51 final size:51
Alignment explanation
Indices: 1810864--1810969 Score: 144
Period size: 51 Copynumber: 2.1 Consensus size: 51
1810854 ATACCACATA
* *
1810864 ACATGTAA-CACATCCATAAGAAACTCGTACCTCTCAACGAGCTCAGATGTT
1 ACATG-AATCACATCCATAAGAAACTCGGACCTCTCAACGAGCTCAGATGCT
* *
1810915 ACATGAATCACATCCACTATG-AACTCGGACCTCTCAACGAGCTCGGATGCT
1 ACATGAATCACATCCA-TAAGAAACTCGGACCTCTCAACGAGCTCAGATGCT
1810966 ACAT
1 ACAT
1810970 ATCTCACAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
50 2 0.04
51 44 0.90
52 3 0.06
ACGTcount: A:0.33, C:0.29, G:0.15, T:0.23
Consensus pattern (51 bp):
ACATGAATCACATCCATAAGAAACTCGGACCTCTCAACGAGCTCAGATGCT
Found at i:1817870 original size:13 final size:13
Alignment explanation
Indices: 1817842--1817885 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
1817832 TTGTCATGAG
*
1817842 AAATTAATTTAGTT
1 AAATTAA-TTAATT
* *
1817856 AATTTGATTAATT
1 AAATTAATTAATT
1817869 AAATTAATTAATT
1 AAATTAATTAATT
1817882 AAAT
1 AAAT
1817886 AAAACTTATT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 20 0.80
14 5 0.20
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (13 bp):
AAATTAATTAATT
Found at i:1818236 original size:20 final size:19
Alignment explanation
Indices: 1818206--1818243 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1818196 AATTAGTGAG
1818206 AATTAATTTTCTAAGAATA
1 AATTAATTTTCTAAGAATA
*
1818225 AATTATATTTTCTAGGAAT
1 AATTA-ATTTTCTAAGAAT
1818244 TACAATTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (19 bp):
AATTAATTTTCTAAGAATA
Found at i:1822847 original size:48 final size:48
Alignment explanation
Indices: 1822791--1823005 Score: 358
Period size: 48 Copynumber: 4.5 Consensus size: 48
1822781 ATAAGCTATT
*
1822791 GCTAATGTGAAATATGTATGAGATAGGTATATGTGGTAAATCCGAATG
1 GCTAATGTGAAATATGTATGAGATAGGTATATGTGGTAAAGCCGAATG
1822839 GCTAATGTGAAATATGTATGAGATAGGTATATGTGGTAAAGCCGAATG
1 GCTAATGTGAAATATGTATGAGATAGGTATATGTGGTAAAGCCGAATG
* * *
1822887 GCTATTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCAAATG
1 GCTAATGTGAAATATGTATGAGATAGGTATATGTGGTAAAGCCGAATG
* *
1822935 GCTAATGTGAAATATGTATGAGATACGTATATGTGGTAAAGCCGAAGG
1 GCTAATGTGAAATATGTATGAGATAGGTATATGTGGTAAAGCCGAATG
* *
1822983 GCTAGTGTGAAATATGTAGGAGA
1 GCTAATGTGAAATATGTATGAGA
1823006 CGTGTGTATA
Statistics
Matches: 157, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 157 1.00
ACGTcount: A:0.35, C:0.07, G:0.28, T:0.30
Consensus pattern (48 bp):
GCTAATGTGAAATATGTATGAGATAGGTATATGTGGTAAAGCCGAATG
Found at i:1823292 original size:37 final size:37
Alignment explanation
Indices: 1823147--1823291 Score: 227
Period size: 37 Copynumber: 3.9 Consensus size: 37
1823137 GGAAATATAT
*
1823147 TCCGGGTAAGACCCGATGATTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* *
1823184 TCCAGGTAAGATCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
1823221 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* * *
1823258 TCCGGGTAAGACCAGATAACTTCGTGTGGAGATT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATT
1823292 TCATCTGAGC
Statistics
Matches: 99, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 99 1.00
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:1827423 original size:49 final size:48
Alignment explanation
Indices: 1827214--1827528 Score: 195
Period size: 49 Copynumber: 6.6 Consensus size: 48
1827204 GTGGTATGTG
* * * *
1827214 AGCCAGTGTAAGACATGTCTGGGACAT-GCATC-AGCATTGAGA--TGAG
1 AGCCAGTGTAAGACCTGTCTGGGACATGGCATCGA-C-TTCATATGTGAA
* * * * * ** *
1827260 AGCTAGTGTAAGACATGTCTGGGACAT-GCATTGGCCTCGGATAT-ACA
1 AGCCAGTGTAAGACCTGTCTGGGACATGGCATCGACTTCATATGTGA-A
* * *
1827307 AGCTAGTGTAAGACCTGTGTCTGGGACATGGCGTC-AGCTT-GT-TGTG--
1 AGCCAGTGTAAGACC--TGTCTGGGACATGGCATCGA-CTTCATATGTGAA
* * ** * *
1827353 TGTCAGTGTAAGACCTGTCTGGGACATGGCATCGACACCTATAGGTGAG
1 AGCCAGTGTAAGACCTGTCTGGGACATGGCATCGACTTC-ATATGTGAA
* * *
1827402 AGCCAGTGTAAGACCTTTCTGGGACATGGCATCGGCTTCGATATATGAA
1 AGCCAGTGTAAGACCTGTCTGGGACATGGCATCGACTTC-ATATGTGAA
* * * **
1827451 AGTCAGTGTAAGACCTGTCTGGGACACGGCATCGATTTCA-ATGTGCT
1 AGCCAGTGTAAGACCTGTCTGGGACATGGCATCGACTTCATATGTGAA
*
1827498 AGCCAGTGTAAGACCATATCTGGGACATGGC
1 AGCCAGTGTAAGACC-TGTCTGGGACATGGC
1827529 GTCAGCATTT
Statistics
Matches: 210, Mismatches: 43, Indels: 30
0.74 0.15 0.11
Matches are distributed among these distances:
44 18 0.09
45 4 0.02
46 45 0.21
47 36 0.17
48 16 0.08
49 86 0.41
50 5 0.02
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (48 bp):
AGCCAGTGTAAGACCTGTCTGGGACATGGCATCGACTTCATATGTGAA
Found at i:1827470 original size:142 final size:138
Alignment explanation
Indices: 1827217--1827476 Score: 323
Period size: 142 Copynumber: 1.8 Consensus size: 138
1827207 GTATGTGAGC
*
1827217 CAGTGTAAGACATGTCTGGGACATGCATCAGCATTGAGATGAGAGCTAGTGTAAGACATGTCTGG
1 CAGTGTAAGACATGTCTGGGACATGCATCAGCATTGAGATGAGAGCCAGTGTAAGACATGTCTGG
* *
1827282 GACATGCATTGGCCTCGGATATACAAGCTAGTGTAAGACCTGTGTCTGGGACATGGCGTCAGCTT
66 GACATGCATCGGCCTCGGATATAAAAGCTAGTGTAAGACC-GTGTCTGGGACATGGCGTCAGCTT
1827347 GTTGTGTGT
130 GTTGTGTGT
* * * *
1827356 CAGTGTAAGACCTGTCTGGGACATGGCATC-GACACCTAT-AGGTGAGAGCCAGTGTAAGACCTT
1 CAGTGTAAGACATGTCTGGGACAT-GCATCAG-CA--T-TGAGATGAGAGCCAGTGTAAGACATG
*
1827419 TCTGGGACATGGCATCGGCTTC-GATATATGAAAG-TCAGTGTAAGACC-TGTCTGGGACA
61 TCTGGGACAT-GCATCGGCCTCGGATATA--AAAGCT-AGTGTAAGACCGTGTCTGGGACA
1827477 CGGCATCGAT
Statistics
Matches: 104, Mismatches: 8, Indels: 15
0.82 0.06 0.12
Matches are distributed among these distances:
139 24 0.23
140 7 0.07
142 48 0.46
143 11 0.11
144 14 0.13
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (138 bp):
CAGTGTAAGACATGTCTGGGACATGCATCAGCATTGAGATGAGAGCCAGTGTAAGACATGTCTGG
GACATGCATCGGCCTCGGATATAAAAGCTAGTGTAAGACCGTGTCTGGGACATGGCGTCAGCTTG
TTGTGTGT
Found at i:1839712 original size:5 final size:5
Alignment explanation
Indices: 1839704--1839736 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
1839694 TTCTTTGATT
1839704 TTTAA TTTAA TTTAA TTTAA TTT-A TTTAA TTTA
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTA
1839737 TTATCTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTAA
Found at i:1839732 original size:9 final size:9
Alignment explanation
Indices: 1839708--1839738 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
1839698 TTGATTTTTA
1839708 ATTTAATTT
1 ATTTAATTT
1839717 AATTTAATTT
1 -ATTTAATTT
1839727 ATTTAATTT
1 ATTTAATTT
1839736 ATT
1 ATT
1839739 ATCTTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
ATTTAATTT
Found at i:1839745 original size:14 final size:14
Alignment explanation
Indices: 1839704--1839736 Score: 57
Period size: 14 Copynumber: 2.3 Consensus size: 14
1839694 TTCTTTGATT
1839704 TTTAATTTAATTTAA
1 TTTAATTT-ATTTAA
1839719 TTTAATTTATTTAA
1 TTTAATTTATTTAA
1839733 TTTA
1 TTTA
1839737 TTATCTTTAT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTAATTTATTTAA
Found at i:1839938 original size:23 final size:22
Alignment explanation
Indices: 1839899--1839958 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 22
1839889 GGTTCTTTTC
*
1839899 TTTTTATC-TATTGATTATTATT
1 TTTTTCTCTTATT-ATTATTATT
*
1839921 ATTTTTCTCTTATTATTATTCTT
1 -TTTTTCTCTTATTATTATTATT
*
1839944 TTTATTCTATTATTA
1 TTT-TTCTCTTATTA
1839959 CTTTTTACTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 3 0.09
23 25 0.78
24 4 0.12
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.68
Consensus pattern (22 bp):
TTTTTCTCTTATTATTATTATT
Found at i:1839954 original size:20 final size:20
Alignment explanation
Indices: 1839896--1839958 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 20
1839886 GTAGGTTCTT
1839896 TTCTTTTTA-TCTATTGATTA
1 TTCTTTTTATTCTATT-ATTA
* *
1839916 TTATTATTTTTCTCTTATTATTA
1 TTCTT-TTTAT-TC-TATTATTA
1839939 TTCTTTTTATTCTATTATTA
1 TTCTTTTTATTCTATTATTA
1839959 CTTTTTACTT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
20 12 0.34
21 5 0.14
22 4 0.11
23 10 0.29
24 4 0.11
ACGTcount: A:0.21, C:0.10, G:0.02, T:0.68
Consensus pattern (20 bp):
TTCTTTTTATTCTATTATTA
Found at i:1842518 original size:18 final size:19
Alignment explanation
Indices: 1842482--1842520 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1842472 TCTTAAATTC
* *
1842482 TTTTAATTGATGCACTTGT
1 TTTTAATTCATGCAATTGT
1842501 TTTTAATTCA-GCAATTGT
1 TTTTAATTCATGCAATTGT
1842519 TT
1 TT
1842521 GTTTTTTCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.23, C:0.10, G:0.13, T:0.54
Consensus pattern (19 bp):
TTTTAATTCATGCAATTGT
Found at i:1845836 original size:11 final size:11
Alignment explanation
Indices: 1845820--1845848 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1845810 GGGATTTTTG
1845820 AATAATTGAAA
1 AATAATTGAAA
1845831 AATAATTGAAA
1 AATAATTGAAA
1845842 AATAATT
1 AATAATT
1845849 TTTGAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (11 bp):
AATAATTGAAA
Found at i:1848018 original size:22 final size:22
Alignment explanation
Indices: 1847992--1848033 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1847982 CGTGGATTGC
*
1847992 GATACCTAAAATTGGATATCGT
1 GATACCCAAAATTGGATATCGT
* *
1848014 GATACCCAGAGTTGGATATC
1 GATACCCAAAATTGGATATC
1848034 ACGATATCCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (22 bp):
GATACCCAAAATTGGATATCGT
Found at i:1852375 original size:18 final size:18
Alignment explanation
Indices: 1852347--1852394 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
1852337 TATTATGGAA
* *
1852347 AACTGTGTTAATCTAGTG
1 AACTGTATTAATATAGTG
* *
1852365 ATCTGTATTAATATGGTG
1 AACTGTATTAATATAGTG
1852383 AACTGTATTAAT
1 AACTGTATTAAT
1852395 TTTCCAAACC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (18 bp):
AACTGTATTAATATAGTG
Found at i:1854864 original size:228 final size:228
Alignment explanation
Indices: 1854467--1854923 Score: 905
Period size: 228 Copynumber: 2.0 Consensus size: 228
1854457 TTACATTTAC
1854467 TTTCTTTAGCTTAATTAACATCATCAATTCAACTCATCATTCCCTTTTTCATCACTCATTTCATA
1 TTTCTTTAGCTTAATTAACATCATCAATTCAACTCATCATTCCCTTTTTCATCACTCATTTCATA
*
1854532 TGCATAATACACAAGAAATAAGCATATCATCAACTATAGCCACAAGCTAGTGCATTTAAACATAG
66 TGCATAATACACAAGAAACAAGCATATCATCAACTATAGCCACAAGCTAGTGCATTTAAACATAG
1854597 CTCTTTTAGAATTAATCACATGATAAACCATTTCATAAGAATTTTCATAATTTAAACCTTACCAT
131 CTCTTTTAGAATTAATCACATGATAAACCATTTCATAAGAATTTTCATAATTTAAACCTTACCAT
1854662 TTTTTCATGAGTACAAGCATATTTTCATTTGAG
196 TTTTTCATGAGTACAAGCATATTTTCATTTGAG
1854695 TTTCTTTAGCTTAATTAACATCATCAATTCAACTCATCATTCCCTTTTTCATCACTCATTTCATA
1 TTTCTTTAGCTTAATTAACATCATCAATTCAACTCATCATTCCCTTTTTCATCACTCATTTCATA
1854760 TGCATAATACACAAGAAACAAGCATATCATCAACTATAGCCACAAGCTAGTGCATTTAAACATAG
66 TGCATAATACACAAGAAACAAGCATATCATCAACTATAGCCACAAGCTAGTGCATTTAAACATAG
1854825 CTCTTTTAGAATTAATCACATGATAAACCATTTCATAAGAATTTTCATAATTTAAACCTTACCAT
131 CTCTTTTAGAATTAATCACATGATAAACCATTTCATAAGAATTTTCATAATTTAAACCTTACCAT
1854890 TTTTTCATGAGTACAAGCATATTTTCATTTGAG
196 TTTTTCATGAGTACAAGCATATTTTCATTTGAG
1854923 T
1 T
1854924 ACTTACCATT
Statistics
Matches: 228, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
228 228 1.00
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.37
Consensus pattern (228 bp):
TTTCTTTAGCTTAATTAACATCATCAATTCAACTCATCATTCCCTTTTTCATCACTCATTTCATA
TGCATAATACACAAGAAACAAGCATATCATCAACTATAGCCACAAGCTAGTGCATTTAAACATAG
CTCTTTTAGAATTAATCACATGATAAACCATTTCATAAGAATTTTCATAATTTAAACCTTACCAT
TTTTTCATGAGTACAAGCATATTTTCATTTGAG
Found at i:1869759 original size:46 final size:46
Alignment explanation
Indices: 1869644--1869763 Score: 152
Period size: 48 Copynumber: 2.6 Consensus size: 46
1869634 TATGTGTGCT
* * * *
1869644 AGTGTAAGACATGTCTAGGACATGCATCGGCCTTGCGATATTTAAGTC
1 AGTGTAAGACATGTCTAGGACATGCATCGGCATTGAGAGA--TAAGCC
*
1869692 AGTGTAAGACATGTCTAGGACATGCATCGGCATTGAGACGA-GAGCC
1 AGTGTAAGACATGTCTAGGACATGCATCGGCATTGAGA-GATAAGCC
*
1869738 AGTGTAAGACATGTCTGGGACATGCA
1 AGTGTAAGACATGTCTAGGACATGCA
1869764 CTGACCTCGC
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
46 28 0.43
48 36 0.55
49 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTAGGACATGCATCGGCATTGAGAGATAAGCC
Found at i:1876635 original size:40 final size:40
Alignment explanation
Indices: 1876552--1876814 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
1876542 TTGAATGCTG
* * * * * *
1876552 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
* * * *
1876592 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
*
1876632 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
1876672 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
**
1876712 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
1876752 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
1876791 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
1876815 TGAACGAGGA
Statistics
Matches: 199, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 35 0.18
40 156 0.78
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:1876834 original size:79 final size:80
Alignment explanation
Indices: 1876591--1876849 Score: 265
Period size: 80 Copynumber: 3.3 Consensus size: 80
1876581 AAGTGAATAT
* * * * * *
1876591 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
1876655 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* *
1876671 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
1876736 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
1876751 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
1876815 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
1876830 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
1876850 TACGTGATTT
Statistics
Matches: 158, Mismatches: 19, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
78 14 0.09
79 49 0.31
80 95 0.60
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:1884580 original size:40 final size:40
Alignment explanation
Indices: 1884497--1884839 Score: 467
Period size: 40 Copynumber: 8.6 Consensus size: 40
1884487 TTGAATGCTG
* * * * * *
1884497 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
1884537 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
1884577 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1884617 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
1884657 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
1884697 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
1884737 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
1884777 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
1884816 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
1884840 TGAACGAGGA
Statistics
Matches: 281, Mismatches: 19, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
39 35 0.12
40 238 0.85
41 8 0.03
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:1892298 original size:44 final size:43
Alignment explanation
Indices: 1892226--1892313 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 43
1892216 AACTCTGTTT
1892226 TTAGTTTACCACTTAAATCTGATTAGTGTAGGTTATTTTAATA
1 TTAGTTTACCACTTAAATCTGATTAGTGTAGGTTATTTTAATA
* *
1892269 TTAGTTTCCCATTTAAACTCTGATTAGTGTAGGTTATTTTAATA
1 TTAGTTTACCACTTAAA-TCTGATTAGTGTAGGTTATTTTAATA
1892313 T
1 T
1892314 CATTTGACCT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
43 15 0.36
44 27 0.64
ACGTcount: A:0.28, C:0.10, G:0.14, T:0.48
Consensus pattern (43 bp):
TTAGTTTACCACTTAAATCTGATTAGTGTAGGTTATTTTAATA
Found at i:1894015 original size:25 final size:23
Alignment explanation
Indices: 1893970--1894016 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1893960 TTTTAGTTTT
**
1893970 TAAAAAAAATTAACTTTTAAAAG
1 TAAAAAAAATTAACTACTAAAAG
1893993 TAAAAAAAATGTAAACTACTAAAA
1 TAAAAAAAAT-T-AACTACTAAAA
1894017 TAGTCATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 1 0.05
25 9 0.45
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26
Consensus pattern (23 bp):
TAAAAAAAATTAACTACTAAAAG
Found at i:1895853 original size:46 final size:47
Alignment explanation
Indices: 1895768--1895867 Score: 121
Period size: 46 Copynumber: 2.1 Consensus size: 47
1895758 TAACAACTTG
* *
1895768 ACTGCAAATATAGTGGCTCGACCACACATATCTGTTCTGGCAGCTTA
1 ACTGCAAATATAGTGGCTCGACCACACATATATGATCTGGCAGCTTA
* * * * **
1895815 ACTGCAAA-ATAGTGGTTTGACTACATATATATGATCTGGCATTTTA
1 ACTGCAAATATAGTGGCTCGACCACACATATATGATCTGGCAGCTTA
1895861 ACTGCAA
1 ACTGCAA
1895868 CTCTGGTGAC
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
46 37 0.82
47 8 0.18
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (47 bp):
ACTGCAAATATAGTGGCTCGACCACACATATATGATCTGGCAGCTTA
Found at i:1903674 original size:30 final size:30
Alignment explanation
Indices: 1903640--1903702 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
1903630 ACTTAACAAG
*
1903640 CAAATG-CTTCTAAAATAATAAAAAAATTAA
1 CAAATGCCTT-TAAAATAACAAAAAAATTAA
*
1903670 CAAATGCCTTTAAAATAACAAGAAAATTAA
1 CAAATGCCTTTAAAATAACAAAAAAATTAA
1903700 CAA
1 CAA
1903703 TAAAATAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 27 0.90
31 3 0.10
ACGTcount: A:0.59, C:0.13, G:0.05, T:0.24
Consensus pattern (30 bp):
CAAATGCCTTTAAAATAACAAAAAAATTAA
Found at i:1904891 original size:3 final size:3
Alignment explanation
Indices: 1904883--1904907 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1904873 TTTTAGTTAA
1904883 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
1904908 TAGACCACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1905395 original size:2 final size:2
Alignment explanation
Indices: 1905388--1905415 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1905378 CCTTGAGCTT
1905388 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1905416 CAAATTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1905950 original size:33 final size:32
Alignment explanation
Indices: 1905877--1905950 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 32
1905867 ATTGTATAAC
* * *
1905877 TATTGTTTTCTTGTTAATTTACAACTATTTTA
1 TATTATTTTCTTGTTAAGTTACAAATATTTTA
* *
1905909 AAGGTATTTTCTTGTTAAGTTACAAATATTTTA
1 TA-TTATTTTCTTGTTAAGTTACAAATATTTTA
1905942 GTATTATTT
1 -TATTATTT
1905951 AAATATAAAG
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
32 1 0.03
33 31 0.94
34 1 0.03
ACGTcount: A:0.28, C:0.07, G:0.09, T:0.55
Consensus pattern (32 bp):
TATTATTTTCTTGTTAAGTTACAAATATTTTA
Found at i:1908194 original size:29 final size:29
Alignment explanation
Indices: 1908157--1908251 Score: 81
Period size: 29 Copynumber: 3.3 Consensus size: 29
1908147 TATTAATTAT
*
1908157 TTAATATTTATGAGGTCATTAGTGTCATG
1 TTAAAATTTATGAGGTCATTAGTGTCATG
* ** *
1908186 TTAAAATTTGACTATAAAT-ATTAAT-T-AT-
1 TTAAAATTT-A-T-GAGGTCATTAGTGTCATG
*
1908214 TTAATATTTATGAGGTCATTAGTGTCATG
1 TTAAAATTTATGAGGTCATTAGTGTCATG
1908243 TTAAAATTT
1 TTAAAATTT
1908252 GGTCTAGAAA
Statistics
Matches: 48, Mismatches: 11, Indels: 14
0.66 0.15 0.19
Matches are distributed among these distances:
25 2 0.04
26 6 0.12
27 2 0.04
28 10 0.21
29 18 0.38
30 2 0.04
31 6 0.12
32 2 0.04
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.46
Consensus pattern (29 bp):
TTAAAATTTATGAGGTCATTAGTGTCATG
Found at i:1908228 original size:57 final size:57
Alignment explanation
Indices: 1908140--1908252 Score: 226
Period size: 57 Copynumber: 2.0 Consensus size: 57
1908130 ATGTGTGAGT
1908140 CTATAAATATTAATTATTTAATATTTATGAGGTCATTAGTGTCATGTTAAAATTTGA
1 CTATAAATATTAATTATTTAATATTTATGAGGTCATTAGTGTCATGTTAAAATTTGA
1908197 CTATAAATATTAATTATTTAATATTTATGAGGTCATTAGTGTCATGTTAAAATTTG
1 CTATAAATATTAATTATTTAATATTTATGAGGTCATTAGTGTCATGTTAAAATTTG
1908253 GTCTAGAAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.46
Consensus pattern (57 bp):
CTATAAATATTAATTATTTAATATTTATGAGGTCATTAGTGTCATGTTAAAATTTGA
Found at i:1916401 original size:13 final size:13
Alignment explanation
Indices: 1916383--1916416 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
1916373 GCATGAGTGA
1916383 CCACACGGCCTGC
1 CCACACGGCCTGC
1916396 CCACACGGCCTGC
1 CCACACGGCCTGC
1916409 CCACACGG
1 CCACACGG
1916417 GCGTGTCCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.18, C:0.53, G:0.24, T:0.06
Consensus pattern (13 bp):
CCACACGGCCTGC
Found at i:1919879 original size:20 final size:20
Alignment explanation
Indices: 1919854--1919893 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1919844 CTTACCATCC
* *
1919854 TGGAAAAACTAATGTGGTGG
1 TGGAAAAAATAATGTAGTGG
1919874 TGGAAAAAATAATGTAGTGG
1 TGGAAAAAATAATGTAGTGG
1919894 CAGATGTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.03, G:0.33, T:0.25
Consensus pattern (20 bp):
TGGAAAAAATAATGTAGTGG
Found at i:1921362 original size:29 final size:27
Alignment explanation
Indices: 1921308--1921363 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
1921298 AAAGTGATTT
*
1921308 TTGACAAAATGTCAATTAGGGATTAAA
1 TTGACAAAATGTAAATTAGGGATTAAA
* *
1921335 TTGAGAAAAGTGTAAATTGAGGGGTTAAA
1 TTGACAAAA-TGTAAATT-AGGGATTAAA
1921364 ATGTGAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 8 0.33
28 7 0.29
29 9 0.38
ACGTcount: A:0.43, C:0.04, G:0.25, T:0.29
Consensus pattern (27 bp):
TTGACAAAATGTAAATTAGGGATTAAA
Found at i:1921371 original size:29 final size:27
Alignment explanation
Indices: 1921313--1921371 Score: 64
Period size: 29 Copynumber: 2.1 Consensus size: 27
1921303 GATTTTTGAC
* *
1921313 AAAATGTCAATTAGGGATTAAATTGAG
1 AAAATGTAAATTAGGGATTAAAATGAG
* *
1921340 AAAAGTGTAAATTGAGGGGTTAAAATGTG
1 AAAA-TGTAAATT-AGGGATTAAAATGAG
1921369 AAA
1 AAA
1921372 TAAATGAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 4 0.15
28 7 0.27
29 15 0.58
ACGTcount: A:0.46, C:0.02, G:0.25, T:0.27
Consensus pattern (27 bp):
AAAATGTAAATTAGGGATTAAAATGAG
Found at i:1924333 original size:8 final size:8
Alignment explanation
Indices: 1924320--1924344 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1924310 AATCCAAGCC
1924320 AAAAATTT
1 AAAAATTT
1924328 AAAAATTT
1 AAAAATTT
1924336 AAAAATTT
1 AAAAATTT
1924344 A
1 A
1924345 TTTTATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
AAAAATTT
Found at i:1933520 original size:40 final size:40
Alignment explanation
Indices: 1933475--1933666 Score: 231
Period size: 40 Copynumber: 4.8 Consensus size: 40
1933465 TATAACCACA
** *
1933475 AGCACAAATGCCTTCGGGTCTTAGCCCGGATTTAGTAACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATAACT
* * * *
1933515 CGCACAAATGCCTTCGGATCTTAGTCCGGATAAAATCACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATAACT
* * * * **
1933555 AGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATAACT
* *
1933595 CGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATAACT
* *
1933635 AGCACAATTGCCTTCGGGACTTAGCCCGGATA
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATA
1933667 TCATTCAAAT
Statistics
Matches: 124, Mismatches: 28, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 124 1.00
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATAACT
Found at i:1933595 original size:80 final size:79
Alignment explanation
Indices: 1933447--1933667 Score: 318
Period size: 80 Copynumber: 2.8 Consensus size: 79
1933437 ACCCAAGTTT
* * * * * *
1933447 CTTCGGAAT-TTAGCCGGATATAACCACAAGCACAAATGCCTTCGGGTCTTAGCCCGGATTTAGT
1 CTTCGG-ATCTTAGCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATATAGC
1933511 AACTCGCACAAATGC
65 AACTCGCACAAATGC
* *
1933526 CTTCGGATCTTAGTCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGC
1 CTTCGGATCTTAG-CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATATAGC
1933591 AACTCGCACAAATGC
65 AACTCGCACAAATGC
* *
1933606 CTTCGGGTCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGACTTAGCCCGGATAT
1 CTTCGGATCTTAG-CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATAT
1933668 CATTCAAATG
Statistics
Matches: 127, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
78 2 0.02
79 10 0.08
80 115 0.91
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (79 bp):
CTTCGGATCTTAGCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCA
ACTCGCACAAATGC
Found at i:1942790 original size:20 final size:20
Alignment explanation
Indices: 1942767--1942833 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
1942757 GCAACTTGTT
*
1942767 TGCATTACTAGCAGTTTATC
1 TGCATTACTGGCAGTTTATC
* * *
1942787 TGCATTACTGGCAGCTTGTT
1 TGCATTACTGGCAGTTTATC
1942807 TGC-TCTACTGGCAGTTTATC
1 TGCAT-TACTGGCAGTTTATC
1942827 TGCATTA
1 TGCATTA
1942834 TTGGTGAGTT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
19 1 0.03
20 36 0.95
21 1 0.03
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.40
Consensus pattern (20 bp):
TGCATTACTGGCAGTTTATC
Found at i:1942821 original size:40 final size:40
Alignment explanation
Indices: 1942750--1942833 Score: 125
Period size: 40 Copynumber: 2.1 Consensus size: 40
1942740 GCATGTCCAT
*
1942750 ATTATTGGCAACTTGTTTGCATTACTAGCAGTTTATCTGC
1 ATTACTGGCAACTTGTTTGCATTACTAGCAGTTTATCTGC
* *
1942790 ATTACTGGCAGCTTGTTTGC-TCTACTGGCAGTTTATCTGC
1 ATTACTGGCAACTTGTTTGCAT-TACTAGCAGTTTATCTGC
1942830 ATTA
1 ATTA
1942834 TTGGTGAGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
39 1 0.03
40 39 0.98
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.42
Consensus pattern (40 bp):
ATTACTGGCAACTTGTTTGCATTACTAGCAGTTTATCTGC
Found at i:1948291 original size:6 final size:6
Alignment explanation
Indices: 1948273--1948306 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
1948263 TGCAAATGAA
*
1948273 TCATTT CTCATTT TCATTT TCATTT CCATTT TCA
1 TCATTT -TCATTT TCATTT TCATTT TCATTT TCA
1948307 GAAAACCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.18, C:0.24, G:0.00, T:0.59
Consensus pattern (6 bp):
TCATTT
Found at i:1952074 original size:14 final size:14
Alignment explanation
Indices: 1952055--1952082 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1952045 CTTTGTATAC
1952055 CTTACCATACAAGA
1 CTTACCATACAAGA
1952069 CTTACCATACAAGA
1 CTTACCATACAAGA
1952083 GAGCCAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.29, G:0.07, T:0.21
Consensus pattern (14 bp):
CTTACCATACAAGA
Found at i:1960423 original size:14 final size:14
Alignment explanation
Indices: 1960404--1960437 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
1960394 ATAACAGTTG
1960404 ACCTCAAGAATTCA
1 ACCTCAAGAATTCA
1960418 ACCTCAAGAATTCA
1 ACCTCAAGAATTCA
1960432 ACCTCA
1 ACCTCA
1960438 TATTCTGTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.41, C:0.32, G:0.06, T:0.21
Consensus pattern (14 bp):
ACCTCAAGAATTCA
Found at i:1961333 original size:26 final size:26
Alignment explanation
Indices: 1961296--1961367 Score: 90
Period size: 26 Copynumber: 2.8 Consensus size: 26
1961286 ATTTTCTCAT
*
1961296 AATTTTACTAGGGGCAAAATCGTCAA
1 AATTTTACTAGGGGCAAAATCATCAA
* *
1961322 GATTTTACTAGGGGTAAAATCATCAA
1 AATTTTACTAGGGGCAAAATCATCAA
** *
1961348 AATTTTGTTGGGGGCAAAAT
1 AATTTTACTAGGGGCAAAAT
1961368 AGGGATGAGA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (26 bp):
AATTTTACTAGGGGCAAAATCATCAA
Found at i:1963635 original size:34 final size:34
Alignment explanation
Indices: 1963548--1963623 Score: 102
Period size: 34 Copynumber: 2.2 Consensus size: 34
1963538 GATCAATACG
* *
1963548 ATAGCAATTAATATGCTTATAATAATTCGATATA
1 ATAGCAAATAATATGCTTATAACAATTCGATATA
1963582 ATAGCAAATAATATGCTTATAACAGA-TCGAT-TCA
1 ATAGCAAATAATATGCTTATAACA-ATTCGATAT-A
1963616 ATAGCAAA
1 ATAGCAAA
1963624 AGTTATGCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
33 1 0.03
34 36 0.95
35 1 0.03
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.32
Consensus pattern (34 bp):
ATAGCAAATAATATGCTTATAACAATTCGATATA
Found at i:1964287 original size:22 final size:20
Alignment explanation
Indices: 1964255--1964294 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
1964245 TAGAATTGCA
1964255 TGACTTTTAGGATGAGATCC
1 TGACTTTTAGGATGAGATCC
*
1964275 TGACATTTCTAGGTTGAGAT
1 TGAC-TTT-TAGGATGAGAT
1964295 GTCTTCATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 3 0.18
22 10 0.59
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (20 bp):
TGACTTTTAGGATGAGATCC
Found at i:1967989 original size:21 final size:21
Alignment explanation
Indices: 1967963--1968018 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
1967953 TATATGGCAT
1967963 ATTAAAAAATA-AATTAAAAA
1 ATTAAAAAATATAATTAAAAA
**
1967983 ATATAAAAAATATTTTTAAAAA
1 AT-TAAAAAATATAATTAAAAA
1968005 ATTAAAATAATATA
1 ATTAAAA-AATATA
1968019 TATAAAGTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 2 0.07
21 14 0.47
22 14 0.47
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
ATTAAAAAATATAATTAAAAA
Found at i:1968024 original size:22 final size:20
Alignment explanation
Indices: 1967963--1968024 Score: 70
Period size: 22 Copynumber: 2.9 Consensus size: 20
1967953 TATATGGCAT
*
1967963 ATTAAAAAATAAATTAAAAA
1 ATTAAAAAATATATTAAAAA
*
1967983 ATATAAAAAATATTTTTAAAAA
1 AT-TAAAAAATA-TATTAAAAA
1968005 ATTAAAATAATATATATAAA
1 ATTAAAA-AATATAT-TAAA
1968025 GTTCATAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
20 2 0.06
21 16 0.46
22 17 0.49
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
ATTAAAAAATATATTAAAAA
Found at i:1968576 original size:21 final size:21
Alignment explanation
Indices: 1968510--1968583 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 21
1968500 GGTTTCTTGG
1968510 TTTAGGGTTTTGTTAAAATAA
1 TTTAGGGTTTTGTTAAAATAA
* ** *** ***
1968531 TTTAAGGTTAGGTTTGTAGGG
1 TTTAGGGTTTTGTTAAAATAA
1968552 TTTAGGGTTTTGTTAAAATAA
1 TTTAGGGTTTTGTTAAAATAA
*
1968573 TTTAGAGTTTT
1 TTTAGGGTTTT
1968584 AGATTTTAGA
Statistics
Matches: 34, Mismatches: 19, Indels: 0
0.64 0.36 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (21 bp):
TTTAGGGTTTTGTTAAAATAA
Found at i:1968677 original size:34 final size:33
Alignment explanation
Indices: 1968632--1968723 Score: 114
Period size: 34 Copynumber: 2.7 Consensus size: 33
1968622 GTTCTTTTTT
1968632 AAAAATTAATTAAATTATGGTTTAG-GGGTTTAA
1 AAAAATTAATTAAATT-TGGTTTAGTGGGTTTAA
**
1968665 AATAAATTAATTAAATTTGGGTTTAGTGTTTTTAA
1 AA-AAATTAATTAAATTT-GGTTTAGTGGGTTTAA
*
1968700 GAAAATTAATTAAATTTGGATTTA
1 AAAAATTAATTAAATTTGG-TTTA
1968724 ATTTTTTTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
33 5 0.10
34 40 0.77
35 7 0.13
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.43
Consensus pattern (33 bp):
AAAAATTAATTAAATTTGGTTTAGTGGGTTTAA
Found at i:1969239 original size:126 final size:126
Alignment explanation
Indices: 1969015--1969442 Score: 682
Period size: 126 Copynumber: 3.4 Consensus size: 126
1969005 TGCACGCAAA
* * * *
1969015 ATGCACTATCTGCAAAATTGAT-AAAAAAGCTCACACGTAGACGCTCTTTTTCTACAGTAGTTCC
1 ATGCACTATCAGCAAAATTGATGAAAAAAGCTCATACATGGACGCTCTTTTTCTACAGTAGTTCC
1969079 TGAAAAAATAATTTTGAGAAGACGTTTCTAAACAAATAATGTCAAAAACGCTTCAAGCAGG
66 TGAAAAAATAATTTTGAGAAGACGTTTCTAAACAAATAATGTCAAAAACGCTTCAAGCAGG
1969140 ATGCACTATCAGCAAAATTGATGAAAAAAGCTCATACATGGACGCTCTTTTTCTACAGTAGTTCC
1 ATGCACTATCAGCAAAATTGATGAAAAAAGCTCATACATGGACGCTCTTTTTCTACAGTAGTTCC
1969205 TGAAAAAATAATTTTGAGAAGACGTTTCTAAACAAATAATGTCAAAAACGCTTCAAGCAGG
66 TGAAAAAATAATTTTGAGAAGACGTTTCTAAACAAATAATGTCAAAAACGCTTCAAGCAGG
*
1969266 ATGCACTATCAGCAAAGTTGATGAAAAAAGCTCATACATGGACGCTCTTTTTCTACAGTAGTTCC
1 ATGCACTATCAGCAAAATTGATGAAAAAAGCTCATACATGGACGCTCTTTTTCTACAGTAGTTCC
* * * * * * * *
1969331 TAAAAAAATAATTTTAAGAAGATGTTTTTGAACAAATAGTGTCAAAAATGCTTCAAGTAGG
66 TGAAAAAATAATTTTGAGAAGACGTTTCTAAACAAATAATGTCAAAAACGCTTCAAGCAGG
* *
1969392 ATGCACTATCAGCAAAATT-ACTGCAAAAAGCTC-TCACGTGGACGCTCTTTT
1 ATGCACTATCAGCAAAATTGA-TGAAAAAAGCTCAT-ACATGGACGCTCTTTT
1969443 CAATAGTAGT
Statistics
Matches: 284, Mismatches: 16, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
125 23 0.08
126 261 0.92
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (126 bp):
ATGCACTATCAGCAAAATTGATGAAAAAAGCTCATACATGGACGCTCTTTTTCTACAGTAGTTCC
TGAAAAAATAATTTTGAGAAGACGTTTCTAAACAAATAATGTCAAAAACGCTTCAAGCAGG
Found at i:1969386 original size:252 final size:256
Alignment explanation
Indices: 1968798--1969442 Score: 845
Period size: 252 Copynumber: 2.5 Consensus size: 256
1968788 GATTTTGGTT
* * * *
1968798 TTTTTTTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGATGGTTCTGAACAAATAGTGTAAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGATGTTTCTGAACAAATAGTGTCAAAA
* * * * *
1968863 ACGCTTCAAGTAGGTTGCACTGTCAACAAAATTACTGAAAAAAAGCTCTCAGATGGACACTCTTT
66 ACGCTTCAAGTAGGATGCACTATCAGCAAAATTACTG-AAAAAAGCTCTCACATGGACGCTCTTT
* * ** *
1968928 TTCTAGAGTAGTTCCTAAAAAAATAATTTTGAGAAGACAATTCTGAACAAATGGTGTCAAAAATA
130 TTCTACAGTAGTTCCTAAAAAAATAATTTTGAGAAGACAATTCTAAACAAATAATGTCAAAAACA
* *
1968993 CTTAAAGCAGAATGCACGCAAAATGCACTATCTGCAAAATTGATAAAAAAGCTCACACGTAGACG
195 CTT--A-CA-AATGCACG--AAATGCACTATCAGCAAAATTGATAAAAAAGCTCACACATAGACG
1969058 CTC
254 CTC
* * *
1969061 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGTTTCTAAACAAATAATGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGATGTTTCTGAACAAATAGTGTCAAAA
*
1969126 ACGCTTCAAGCAGGATGCACTATCAGCAAAATTGA-TGAAAAAAGCTCAT-ACATGGACGCTCTT
66 ACGCTTCAAGTAGGATGCACTATCAGCAAAATT-ACTGAAAAAAGCTC-TCACATGGACGCTCTT
* **
1969189 TTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGTTTCTAAACAAATAATGTCAAAAAC
129 TTTCTACAGTAGTTCCTAAAAAAATAATTTTGAGAAGACAATTCTAAACAAATAATGTCAAAAAC
* * * * *
1969254 GCTT-C-AA-GCA-G-GATGCACTATCAGCAAAGTTGATGAAAAAAGCTCATACATGGACGCTC
194 ACTTACAAATGCACGAAATGCACTATCAGCAAAATTGAT-AAAAAAGCTCACACATAGACGCTC
* * *
1969313 TTTTTCTACAGTAGTTCCTAAAAAAATAATTTTAAGAAGATGTTTTTGAACAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGATGTTTCTGAACAAATAGTGTCAAAA
* * *
1969378 ATGCTTCAAGTAGGATGCACTATCAGCAAAATTACTGCAAAAAGCTCTCACGTGGACGCTCTTTT
66 ACGCTTCAAGTAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTCTCACATGGACGCTCTTTT
1969443 CAATAGTAGT
Statistics
Matches: 339, Mismatches: 38, Indels: 21
0.85 0.10 0.05
Matches are distributed among these distances:
251 22 0.06
252 137 0.40
254 1 0.00
255 3 0.01
256 2 0.01
258 1 0.00
262 82 0.24
263 90 0.27
264 1 0.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.28
Consensus pattern (256 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGATGTTTCTGAACAAATAGTGTCAAAA
ACGCTTCAAGTAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTCTCACATGGACGCTCTTTT
TCTACAGTAGTTCCTAAAAAAATAATTTTGAGAAGACAATTCTAAACAAATAATGTCAAAAACAC
TTACAAATGCACGAAATGCACTATCAGCAAAATTGATAAAAAAGCTCACACATAGACGCTC
Found at i:1972531 original size:24 final size:24
Alignment explanation
Indices: 1972499--1972577 Score: 149
Period size: 24 Copynumber: 3.3 Consensus size: 24
1972489 GTTGCATTAT
*
1972499 TTCTATTGCCTTACTCAAAAGAAC
1 TTCTATTGCCTTATTCAAAAGAAC
1972523 TTCTATTGCCTTATTCAAAAGAAC
1 TTCTATTGCCTTATTCAAAAGAAC
1972547 TTCTATTGCCTTATTCAAAAGAAC
1 TTCTATTGCCTTATTCAAAAGAAC
1972571 TTCTATT
1 TTCTATT
1972578 TTATTAAAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.39
Consensus pattern (24 bp):
TTCTATTGCCTTATTCAAAAGAAC
Found at i:1972587 original size:21 final size:22
Alignment explanation
Indices: 1972499--1972587 Score: 99
Period size: 24 Copynumber: 3.8 Consensus size: 22
1972489 GTTGCATTAT
*
1972499 TTCTATTGCCTTACTCAAAAGAAC
1 TTCTATT--CTTATTCAAAAGAAC
1972523 TTCTATTGCCTTATTCAAAAGAAC
1 TTCTATT--CTTATTCAAAAGAAC
1972547 TTCTATTGCCTTATTCAAAAGAAC
1 TTCTATT--CTTATTCAAAAGAAC
*
1972571 TTCTATT-TTATTAAAAA
1 TTCTATTCTTATTCAAAA
1972588 TATAAAACTA
Statistics
Matches: 63, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
21 9 0.14
24 54 0.86
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.39
Consensus pattern (22 bp):
TTCTATTCTTATTCAAAAGAAC
Found at i:1978329 original size:28 final size:28
Alignment explanation
Indices: 1978281--1978335 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
1978271 TTATTAACCC
1978281 CATAAGTTATAAAACTCTTCCTATACCT
1 CATAAGTTATAAAACTCTTCCTATACCT
* * *
1978309 CATAAGTTATGAGACTTTTCCTATACC
1 CATAAGTTATAAAACTCTTCCTATACC
1978336 CCATTAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.36
Consensus pattern (28 bp):
CATAAGTTATAAAACTCTTCCTATACCT
Done.