Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: 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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 128 of 135
Found at i:46180891 original size:17 final size:18
Alignment explanation
Indices: 46180859--46180894 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
46180849 CAATTTTTGA
46180859 AAAAATATCATAATTTTT
1 AAAAATATCATAATTTTT
*
46180877 AAAAATA-CATTATTTTT
1 AAAAATATCATAATTTTT
46180894 A
1 A
46180895 TAATAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (18 bp):
AAAAATATCATAATTTTT
Found at i:46184464 original size:11 final size:11
Alignment explanation
Indices: 46184448--46184474 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
46184438 TTTGATATTT
46184448 TAATTGAGTTC
1 TAATTGAGTTC
46184459 TAATTGAGTTC
1 TAATTGAGTTC
46184470 TAATT
1 TAATT
46184475 AATGATGGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (11 bp):
TAATTGAGTTC
Found at i:46184829 original size:440 final size:440
Alignment explanation
Indices: 46184008--46184892 Score: 1563
Period size: 440 Copynumber: 2.0 Consensus size: 440
46183998 AATACTCTAG
*
46184008 TAATTGAGCTCTAATCAAATTCTAATTAATGATGGACTAGTTAGGAATTAGAACCAATATGCCAA
1 TAATTGAGCTCTAATCAAATTCTAATTAATGATGGACTAATTAGGAATTAGAACCAATATGCCAA
*
46184073 TGTTATAAATATTGGGGTTATGGTCCTCAAATTAAACACAAGATATCTTTTTTAGTATCCCATCC
66 TGTTATAAATATTGGGGTTATGGTCCTCAAATTAAACACAAAATATCTTTTTTAGTATCCCATCC
*
46184138 TTAGCAAAGAGAGAGCAAATATTCTCTGAAGTTCTTATGTGCTAATTTGGAAGATCAAATCCCCA
131 TTAGCAAAGAGAGAGCAAATATTCTCTGAAGTTCTTATGTACTAATTTGGAAGATCAAATCCCCA
* *
46184203 AGATCCGTAGATTTCAAGGAATTCATGGATTCAGGTACGCTGTTGCATCTAATTTTGTTCTTGAT
196 AGATCCGTAGATTTCAAGGAATTCATAGATTCAAGTACGCTGTTGCATCTAATTTTGTTCTTGAT
*
46184268 TTATTCATGATGATTTGACATGATAGATCATGGTTTATTAAGTTTTATTTTAGATTTATTTTACA
261 TTATTCATGATGATTTGACATGATAGATCATGATTTATTAAGTTTTATTTTAGATTTATTTTACA
46184333 AATCTAACAAGTGGTATCAGAGTTTTGTCACGTTGAATCATTGCGAATGAATTGATTCTTTATTA
326 AATCTAACAAGTGGTATCAGAGTTTTGTCACGTTGAATCATTGCGAATGAATTGATTCTTTATTA
46184398 TTTTTGGATTGATTCGTTTTTCTTTTTTTAATTTTATGGATTTGATATTT
391 TTTTTGGATTGATTCGTTTTTCTTTTTTTAATTTTATGGATTTGATATTT
* ** * *
46184448 TAATTGAGTTCTAATTGAGTTCTAATTAATGATGGACTAATTAGGAATTAGAACTAATATGCCAA
1 TAATTGAGCTCTAATCAAATTCTAATTAATGATGGACTAATTAGGAATTAGAACCAATATGCCAA
* *
46184513 TGTTATAAATATTGGGGTTATGGTCTTCAAATTACACACAAAATATCTTTTTTAGTATCCCATCC
66 TGTTATAAATATTGGGGTTATGGTCCTCAAATTAAACACAAAATATCTTTTTTAGTATCCCATCC
* * * *
46184578 TTAGTAAAGAGAGAGCAAATATTCTCTGAATTTCTTATGTACTAATTTGGAAGATCAAATTCTCA
131 TTAGCAAAGAGAGAGCAAATATTCTCTGAAGTTCTTATGTACTAATTTGGAAGATCAAATCCCCA
*
46184643 AGATCCGTAGATTTCAAGGAATTCATAGATTCAAGTACGTTGTTGCATCTAATTTTGTTCTTGAT
196 AGATCCGTAGATTTCAAGGAATTCATAGATTCAAGTACGCTGTTGCATCTAATTTTGTTCTTGAT
* *
46184708 TTATTCTTGATGATTTGACATGATAGATCTTGATTTATTAAGTTTTATTTTAGATTTATTTTACA
261 TTATTCATGATGATTTGACATGATAGATCATGATTTATTAAGTTTTATTTTAGATTTATTTTACA
* *
46184773 AATCTAGCAAGTGGTATCAGAGTTTTGTCATGTTGAATCATTGCGAATGAATTGATTCTTTATTA
326 AATCTAACAAGTGGTATCAGAGTTTTGTCACGTTGAATCATTGCGAATGAATTGATTCTTTATTA
*
46184838 TTTTTGGATTGTTTCGTTTTTCTTTTTTTAATTTTATGGATTTGATATTT
391 TTTTTGGATTGATTCGTTTTTCTTTTTTTAATTTTATGGATTTGATATTT
46184888 TAATT
1 TAATT
46184893 ATTTATTATG
Statistics
Matches: 422, Mismatches: 23, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
440 422 1.00
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (440 bp):
TAATTGAGCTCTAATCAAATTCTAATTAATGATGGACTAATTAGGAATTAGAACCAATATGCCAA
TGTTATAAATATTGGGGTTATGGTCCTCAAATTAAACACAAAATATCTTTTTTAGTATCCCATCC
TTAGCAAAGAGAGAGCAAATATTCTCTGAAGTTCTTATGTACTAATTTGGAAGATCAAATCCCCA
AGATCCGTAGATTTCAAGGAATTCATAGATTCAAGTACGCTGTTGCATCTAATTTTGTTCTTGAT
TTATTCATGATGATTTGACATGATAGATCATGATTTATTAAGTTTTATTTTAGATTTATTTTACA
AATCTAACAAGTGGTATCAGAGTTTTGTCACGTTGAATCATTGCGAATGAATTGATTCTTTATTA
TTTTTGGATTGATTCGTTTTTCTTTTTTTAATTTTATGGATTTGATATTT
Found at i:46197698 original size:26 final size:26
Alignment explanation
Indices: 46197642--46197699 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
46197632 TTTTAATTAA
* *
46197642 GAAAATTACTTAAAAATAATATAGTT
1 GAAAATTAATTAAAAACAATATAGTT
* *
46197668 TAAAATTAATTAATAAACATTATA-TT
1 GAAAATTAATTAA-AAACAATATAGTT
46197694 GAAAAT
1 GAAAAT
46197700 AGGGGTGTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 18 0.69
27 8 0.31
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.36
Consensus pattern (26 bp):
GAAAATTAATTAAAAACAATATAGTT
Found at i:46201334 original size:28 final size:28
Alignment explanation
Indices: 46201269--46201461 Score: 164
Period size: 28 Copynumber: 6.9 Consensus size: 28
46201259 ATTCAATGTA
* * * *
46201269 CGCCGCAAAGGCTTTCC-TCTCAAGATT
1 CGCCACAAAGGCTTTCCTTTTTATGATT
*
46201296 CGCCACGAAGGCTTTCCTTTTTATGATT
1 CGCCACAAAGGCTTTCCTTTTTATGATT
46201324 CGCCACAAAGGCTATT-CTTTTTATGATT
1 CGCCACAAAGGCT-TTCCTTTTTATGATT
* *
46201352 CACCACAAAGGCTTTCCTTTCTATGAATT
1 CGCCACAAAGGCTTTCCTTTTTATG-ATT
* *
46201381 -GTCACAAAAGCTTTCCTTTTTATGATT
1 CGCCACAAAGGCTTTCCTTTTTATGATT
** *
46201408 CGTCC-CAAAGG-TTATTATTTTTATGAAT
1 CG-CCACAAAGGCTT-TCCTTTTTATGATT
* * *
46201436 CACCATAAAGG-TTTATCTTTTTATGA
1 CGCCACAAAGGCTTT-CCTTTTTATGA
46201462 ATCACCACTA
Statistics
Matches: 137, Mismatches: 20, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
27 25 0.18
28 106 0.77
29 6 0.04
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.38
Consensus pattern (28 bp):
CGCCACAAAGGCTTTCCTTTTTATGATT
Found at i:46201417 original size:84 final size:84
Alignment explanation
Indices: 46201306--46201463 Score: 230
Period size: 84 Copynumber: 1.9 Consensus size: 84
46201296 CGCCACGAAG
* *
46201306 GCTTTCCTTTTTATGATTCGCCACAAAGGCTATTCTTTTTATGATTCACCACAAAGGCTTT-CCT
1 GCTTTCCTTTTTATGATTCGCCACAAAGGCTATTATTTTTATGAATCACCACAAAGG-TTTACCT
46201370 TTCTATGAATTGTCACAAAA
65 TTCTATGAATTGTCACAAAA
* * *
46201390 GCTTTCCTTTTTATGATTCGTCC-CAAAGGTTATTATTTTTATGAATCACCATAAAGGTTTATCT
1 GCTTTCCTTTTTATGATTCG-CCACAAAGGCTATTATTTTTATGAATCACCACAAAGGTTTACCT
*
46201454 TTTTATGAAT
65 TTCTATGAAT
46201464 CACCACTATG
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
83 3 0.05
84 61 0.92
85 2 0.03
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.43
Consensus pattern (84 bp):
GCTTTCCTTTTTATGATTCGCCACAAAGGCTATTATTTTTATGAATCACCACAAAGGTTTACCTT
TCTATGAATTGTCACAAAA
Found at i:46202857 original size:15 final size:15
Alignment explanation
Indices: 46202837--46202868 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
46202827 AAGTTCCAAG
46202837 TTTGATTCCTTTCCC
1 TTTGATTCCTTTCCC
46202852 TTTGATTCCTTTCCC
1 TTTGATTCCTTTCCC
46202867 TT
1 TT
46202869 GCAAAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.31, G:0.06, T:0.56
Consensus pattern (15 bp):
TTTGATTCCTTTCCC
Found at i:46209962 original size:14 final size:15
Alignment explanation
Indices: 46209945--46209985 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
46209935 TTATTTATTA
46209945 AATTAATTTT-AATT
1 AATTAATTTTCAATT
46209959 AATTAATTTTTCAATT
1 AATTAA-TTTTCAATT
*
46209975 AAATAATTTTC
1 AATTAATTTTC
46209986 TCAACCCAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 6 0.25
15 9 0.38
16 9 0.38
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (15 bp):
AATTAATTTTCAATT
Found at i:46209976 original size:16 final size:16
Alignment explanation
Indices: 46209945--46209989 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
46209935 TTATTTATTA
46209945 AATTAA-TTTT-AATT
1 AATTAATTTTTCAATT
46209959 AATTAATTTTTCAATT
1 AATTAATTTTTCAATT
*
46209975 AAATAATTTTCTCAA
1 AATTAATTTT-TCAA
46209990 CCCAATTCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 6 0.22
15 4 0.15
16 13 0.48
17 4 0.15
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (16 bp):
AATTAATTTTTCAATT
Found at i:46238661 original size:24 final size:22
Alignment explanation
Indices: 46238611--46238670 Score: 61
Period size: 24 Copynumber: 2.7 Consensus size: 22
46238601 TAACAAAAGA
*
46238611 GAAAAAGAAAG-AAGAGCAATC
1 GAAAAAGAAAGAAAGACCAATC
*
46238632 GGAAAAGAAAGAAAGAACCCAATC
1 GAAAAAGAAAGAAAG-A-CCAATC
46238656 GAAAAAGGAAA-AAAG
1 GAAAAA-GAAAGAAAG
46238671 GAAAACCTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
21 10 0.31
22 3 0.09
23 1 0.03
24 14 0.44
25 4 0.12
ACGTcount: A:0.63, C:0.10, G:0.23, T:0.03
Consensus pattern (22 bp):
GAAAAAGAAAGAAAGACCAATC
Found at i:46241742 original size:17 final size:17
Alignment explanation
Indices: 46241717--46241750 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
46241707 CACTAACATT
46241717 AAAAGGCAATGACAATG
1 AAAAGGCAATGACAATG
* *
46241734 AAAATGCAATGATAATG
1 AAAAGGCAATGACAATG
46241751 TATACTTATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.09, G:0.21, T:0.18
Consensus pattern (17 bp):
AAAAGGCAATGACAATG
Found at i:46242197 original size:18 final size:18
Alignment explanation
Indices: 46242174--46242210 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
46242164 TCTTTTTTTT
46242174 CTTTCTCATT-TTCAGCAA
1 CTTTCTC-TTGTTCAGCAA
46242192 CTTTCTCTTGTTCAGCAA
1 CTTTCTCTTGTTCAGCAA
46242210 C
1 C
46242211 AACTTCCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.19, C:0.30, G:0.08, T:0.43
Consensus pattern (18 bp):
CTTTCTCTTGTTCAGCAA
Found at i:46246881 original size:23 final size:23
Alignment explanation
Indices: 46246855--46246902 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
46246845 TAGAAAGACA
* * *
46246855 TATTGTAATATCCCGAAAATTAC
1 TATTGAAATACCCCGAAAACTAC
46246878 TATTGAAATACCCCGAAAACTAC
1 TATTGAAATACCCCGAAAACTAC
46246901 TA
1 TA
46246903 CAGTAAGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (23 bp):
TATTGAAATACCCCGAAAACTAC
Found at i:46249550 original size:15 final size:15
Alignment explanation
Indices: 46249530--46249560 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
46249520 ACACTAAAGG
46249530 TGACTTGCTCATCAT
1 TGACTTGCTCATCAT
46249545 TGACTTGCTCATCAT
1 TGACTTGCTCATCAT
46249560 T
1 T
46249561 AAGTCGTCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.26, G:0.13, T:0.42
Consensus pattern (15 bp):
TGACTTGCTCATCAT
Found at i:46269882 original size:18 final size:19
Alignment explanation
Indices: 46269861--46269900 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
46269851 TTTTTTTAGA
46269861 TTTTCCAAAAATAATTT-T
1 TTTTCCAAAAATAATTTCT
**
46269879 TTTTTGAAAAATAATTTCT
1 TTTTCCAAAAATAATTTCT
46269898 TTT
1 TTT
46269901 GTTTTTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (19 bp):
TTTTCCAAAAATAATTTCT
Found at i:46269901 original size:17 final size:18
Alignment explanation
Indices: 46269867--46269901 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
46269857 TAGATTTTCC
*
46269867 AAAAATAATTTTTTTTTG
1 AAAAATAATTTTCTTTTG
46269885 AAAAATAA-TTTCTTTTG
1 AAAAATAATTTTCTTTTG
46269902 TTTTTATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (18 bp):
AAAAATAATTTTCTTTTG
Found at i:46273069 original size:19 final size:18
Alignment explanation
Indices: 46273041--46273082 Score: 75
Period size: 19 Copynumber: 2.3 Consensus size: 18
46273031 ACTTATGTAG
46273041 TTTTTAATTTTGAATTAT
1 TTTTTAATTTTGAATTAT
46273059 TTTTATAATTTTGAATTAT
1 TTTT-TAATTTTGAATTAT
46273078 TTTTT
1 TTTTT
46273083 GATGTGAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (18 bp):
TTTTTAATTTTGAATTAT
Found at i:46275822 original size:24 final size:25
Alignment explanation
Indices: 46275795--46275841 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
46275785 ACTGGTCATA
*
46275795 GAGAGAATTGAGGA-AGCATATTTG
1 GAGAGAATTGAGGAGAGAATATTTG
*
46275819 GAGAGATTTGAGGAGAGAATATT
1 GAGAGAATTGAGGAGAGAATATT
46275842 GGGATTTGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.38, C:0.02, G:0.34, T:0.26
Consensus pattern (25 bp):
GAGAGAATTGAGGAGAGAATATTTG
Found at i:46275843 original size:24 final size:24
Alignment explanation
Indices: 46275795--46275854 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
46275785 ACTGGTCATA
* *
46275795 GAGAGAATTGAGGA-AGCATATTT
1 GAGAGATTTGAGGAGAGAATATTT
46275818 GGAGAGATTTGAGGAGAGAATA-TT
1 -GAGAGATTTGAGGAGAGAATATTT
46275842 G-G-GATTTGAGGAG
1 GAGAGATTTGAGGAG
46275855 GTTGTTGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
21 11 0.33
22 1 0.03
23 1 0.03
24 15 0.45
25 5 0.15
ACGTcount: A:0.35, C:0.02, G:0.38, T:0.25
Consensus pattern (24 bp):
GAGAGATTTGAGGAGAGAATATTT
Found at i:46276459 original size:27 final size:27
Alignment explanation
Indices: 46276421--46276559 Score: 190
Period size: 27 Copynumber: 5.2 Consensus size: 27
46276411 TTACACTATT
** *
46276421 ATGACCAAAATACCTTCATAGGGTAAA
1 ATGACCAAAATACCCCCATAGGGTAGA
* *
46276448 ATGACCGAAATACCCCCATAAGGTAGA
1 ATGACCAAAATACCCCCATAGGGTAGA
* *
46276475 ATGAACAAAATACCCTCATAGGGTAGA
1 ATGACCAAAATACCCCCATAGGGTAGA
46276502 ATGACC-AAATACCCCCATAGGGTAGA
1 ATGACCAAAATACCCCCATAGGGTAGA
* *
46276528 ATGACCGAAATACCCCCATAGGGTAAA
1 ATGACCAAAATACCCCCATAGGGTAGA
46276555 ATGAC
1 ATGAC
46276560 TGTTATGGCT
Statistics
Matches: 99, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
26 25 0.25
27 74 0.75
ACGTcount: A:0.42, C:0.23, G:0.18, T:0.17
Consensus pattern (27 bp):
ATGACCAAAATACCCCCATAGGGTAGA
Found at i:46276539 original size:53 final size:54
Alignment explanation
Indices: 46276421--46276559 Score: 217
Period size: 53 Copynumber: 2.6 Consensus size: 54
46276411 TTACACTATT
*
46276421 ATGACCAAAATACCTTCATAGGGTAAAATGACCGAAATACCCCCATAAGGTAGA
1 ATGACCAAAATACCCTCATAGGGTAAAATGACCGAAATACCCCCATAAGGTAGA
* * *
46276475 ATGAACAAAATACCCTCATAGGGTAGAATGACC-AAATACCCCCATAGGGTAGA
1 ATGACCAAAATACCCTCATAGGGTAAAATGACCGAAATACCCCCATAAGGTAGA
* *
46276528 ATGACCGAAATACCCCCATAGGGTAAAATGAC
1 ATGACCAAAATACCCTCATAGGGTAAAATGAC
46276560 TGTTATGGCT
Statistics
Matches: 77, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
53 47 0.61
54 30 0.39
ACGTcount: A:0.42, C:0.23, G:0.18, T:0.17
Consensus pattern (54 bp):
ATGACCAAAATACCCTCATAGGGTAAAATGACCGAAATACCCCCATAAGGTAGA
Found at i:46284502 original size:66 final size:66
Alignment explanation
Indices: 46284393--46284516 Score: 178
Period size: 66 Copynumber: 1.9 Consensus size: 66
46284383 AATTGGATGC
* * * *
46284393 GTTTTCAGAAAATTTTGTAAGAAAACGCTTCTAGTTGGTTGCGCTTTTCTGCTCAGTCTTGGACG
1 GTTTTCAGAAAATTTTGTAAGAAAACGCTTCCAGCTGGATGCGCTTTCCTGCTCAGTCTTGGACG
46284458 T
66 T
* *
46284459 GTTTTCA-ACAAATTTTGTAAGAAAATGCTTCCAGCTGGATGCGCTTTCCTGTTCAGTC
1 GTTTTCAGA-AAATTTTGTAAGAAAACGCTTCCAGCTGGATGCGCTTTCCTGCTCAGTC
46284517 AGCAAAGCTC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
65 1 0.02
66 50 0.98
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.38
Consensus pattern (66 bp):
GTTTTCAGAAAATTTTGTAAGAAAACGCTTCCAGCTGGATGCGCTTTCCTGCTCAGTCTTGGACG
T
Found at i:46284695 original size:11 final size:11
Alignment explanation
Indices: 46284651--46284711 Score: 68
Period size: 11 Copynumber: 5.5 Consensus size: 11
46284641 CAAATTTCCC
*
46284651 TCTCTCTCGAT
1 TCTCTCTCAAT
* *
46284662 TCACTCTCAAC
1 TCTCTCTCAAT
46284673 TCTCTCTCAAT
1 TCTCTCTCAAT
*
46284684 TCTCTCTTAAT
1 TCTCTCTCAAT
* *
46284695 TATCACTCAAT
1 TCTCTCTCAAT
46284706 TCTCTC
1 TCTCTC
46284712 ATATCACTCT
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 39 1.00
ACGTcount: A:0.20, C:0.36, G:0.02, T:0.43
Consensus pattern (11 bp):
TCTCTCTCAAT
Found at i:46284861 original size:11 final size:11
Alignment explanation
Indices: 46284834--46284875 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
46284824 TCTCCCTTTC
* *
46284834 AATTCACTCTC
1 AATTCTCTCTT
46284845 AATTCTCTCTT
1 AATTCTCTCTT
*
46284856 AATTCTCACTT
1 AATTCTCTCTT
46284867 AATTCTCTC
1 AATTCTCTC
46284876 AGTTCACTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.24, C:0.31, G:0.00, T:0.45
Consensus pattern (11 bp):
AATTCTCTCTT
Found at i:46284950 original size:161 final size:163
Alignment explanation
Indices: 46284676--46284980 Score: 510
Period size: 161 Copynumber: 1.9 Consensus size: 163
46284666 TCTCAACTCT
*
46284676 CTCTCAATTCTCTCTTAATTATCACTCAATTCTCTCATATCACTCTTATTTTTTATTAAAATTTT
1 CTCTCAATTCTCTCTTAATTATCACTCAATTCTCTCATATCACTCTGATTTTTTATTAAAATTTT
*
46284741 CTTAAGGTTTTTTTAATTAATTTTGTATTACAATTTTTATTTGTATTTATTGAAATTCTTAATGG
66 CTTAAGG-TTTTTTAATTAATTTTGTATTACAATTTTTATTCGTATTTATTGAAATTCTTAATGG
46284806 AAAATTCTCTTATTCGCTTCTCCCTTTCAATTCA
130 AAAATTCTCTTATTCGCTTCTCCCTTTCAATTCA
* *
46284840 CTCTCAATTCTCTCTTAATTCTCACTTAATTCTCTCAGT-TCACTCTGA-TTTTTATTAAAATTG
1 CTCTCAATTCTCTCTTAATTATCACTCAATTCTCTCA-TATCACTCTGATTTTTTATTAAAATT-
46284903 TT-TTAAGG-TTTTTAATTAATTTTGTATTACAATTTTTATTCGTATTTATTGAAATTCTTAATG
64 TTCTTAAGGTTTTTTAATTAATTTTGTATTACAATTTTTATTCGTATTTATTGAAATTCTTAATG
*
46284966 GCAAATTCTCTTATT
129 GAAAATTCTCTTATT
46284981 TGTTTAGATG
Statistics
Matches: 134, Mismatches: 5, Indels: 7
0.92 0.03 0.05
Matches are distributed among these distances:
161 68 0.51
163 20 0.15
164 45 0.34
165 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.06, T:0.52
Consensus pattern (163 bp):
CTCTCAATTCTCTCTTAATTATCACTCAATTCTCTCATATCACTCTGATTTTTTATTAAAATTTT
CTTAAGGTTTTTTAATTAATTTTGTATTACAATTTTTATTCGTATTTATTGAAATTCTTAATGGA
AAATTCTCTTATTCGCTTCTCCCTTTCAATTCA
Found at i:46291410 original size:18 final size:20
Alignment explanation
Indices: 46291375--46291413 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
46291365 ATTACACGGG
46291375 TAATTTTAATATTTTCAAAA
1 TAATTTTAATATTTTCAAAA
46291395 TAATTTTAA-A-TTTCAAAA
1 TAATTTTAATATTTTCAAAA
46291413 T
1 T
46291414 TTATATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
19 1 0.05
20 9 0.47
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (20 bp):
TAATTTTAATATTTTCAAAA
Found at i:46291474 original size:21 final size:19
Alignment explanation
Indices: 46291424--46291477 Score: 56
Period size: 22 Copynumber: 2.7 Consensus size: 19
46291414 TTATATTTTT
*
46291424 AAAATATAAAAATTATAAA
1 AAAATCTAAAAATTATAAA
46291443 AAAATCCTAAAGAATATATAAA
1 AAAAT-CTAAA-AAT-TATAAA
46291465 AAAAGT-TAAAAAT
1 AAAA-TCTAAAAAT
46291478 GTAAAATGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
19 5 0.17
20 7 0.23
21 7 0.23
22 10 0.33
23 1 0.03
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.24
Consensus pattern (19 bp):
AAAATCTAAAAATTATAAA
Found at i:46299733 original size:20 final size:22
Alignment explanation
Indices: 46299704--46299744 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
46299694 TTTTAACATT
*
46299704 ATAAATGGAT-AATTT-TTTTA
1 ATAAAAGGATCAATTTGTTTTA
46299724 ATAAAAGGATCAATTTGTTTT
1 ATAAAAGGATCAATTTGTTTT
46299745 TAATGTAACG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 5 0.28
22 4 0.22
ACGTcount: A:0.39, C:0.02, G:0.12, T:0.46
Consensus pattern (22 bp):
ATAAAAGGATCAATTTGTTTTA
Found at i:46308818 original size:18 final size:19
Alignment explanation
Indices: 46308779--46308819 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
46308769 ATTATTCATA
46308779 ATTTT-ATATTTTTACAGT
1 ATTTTAATATTTTTACAGT
*
46308797 -TTTTAATATTTTTATA-T
1 ATTTTAATATTTTTACAGT
46308814 ATTTTA
1 ATTTTA
46308820 TTTAATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (19 bp):
ATTTTAATATTTTTACAGT
Found at i:46310701 original size:7 final size:7
Alignment explanation
Indices: 46310689--46310732 Score: 88
Period size: 7 Copynumber: 6.3 Consensus size: 7
46310679 ATTTATGTCT
46310689 TTTTGTA
1 TTTTGTA
46310696 TTTTGTA
1 TTTTGTA
46310703 TTTTGTA
1 TTTTGTA
46310710 TTTTGTA
1 TTTTGTA
46310717 TTTTGTA
1 TTTTGTA
46310724 TTTTGTA
1 TTTTGTA
46310731 TT
1 TT
46310733 CAGCGTTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.73
Consensus pattern (7 bp):
TTTTGTA
Found at i:46310741 original size:21 final size:21
Alignment explanation
Indices: 46310695--46310741 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
46310685 GTCTTTTTGT
** *
46310695 ATTTTGTATTTTGTATTTTGT
1 ATTTTGTATTTTGTATTCAGC
46310716 ATTTTGTATTTTGTATTCAGC
1 ATTTTGTATTTTGTATTCAGC
*
46310737 GTTTT
1 ATTTT
46310742 AATAACATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.15, C:0.04, G:0.15, T:0.66
Consensus pattern (21 bp):
ATTTTGTATTTTGTATTCAGC
Found at i:46311255 original size:17 final size:17
Alignment explanation
Indices: 46311226--46311267 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
46311216 TTGAACTAGA
46311226 TTTTATAATTTTAT-ATT
1 TTTTA-AATTTTATAATT
46311243 TTTTAAATGTTTATGAATT
1 TTTTAAAT-TTTAT-AATT
46311262 TTTTAA
1 TTTTAA
46311268 TAATTGACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 3 0.14
17 10 0.45
19 9 0.41
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (17 bp):
TTTTAAATTTTATAATT
Found at i:46313217 original size:25 final size:25
Alignment explanation
Indices: 46313162--46313219 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
46313152 TGGCTCTTAC
** *
46313162 GAGCTTCCCGATTGATGGCTCTTTT
1 GAGCTTCCCGATTGATGGCTAGTAT
* * *
46313187 GTGCTTCTCGATTTATGGCTAGTAT
1 GAGCTTCCCGATTGATGGCTAGTAT
46313212 GAGCTTCC
1 GAGCTTCC
46313220 TGATATACAG
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.14, C:0.22, G:0.24, T:0.40
Consensus pattern (25 bp):
GAGCTTCCCGATTGATGGCTAGTAT
Found at i:46313282 original size:25 final size:25
Alignment explanation
Indices: 46313238--46313298 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
46313228 AGCTCGATAA
*
46313238 AGCTTCCCGTTACTTAGCTCACATG
1 AGCTTCCCGTTACTTAGCTCACAAG
* *
46313263 AGCTTCCCGTTA-TATGGCTCAGAAG
1 AGCTTCCCGTTACT-TAGCTCACAAG
46313288 AGCTTCCCGTT
1 AGCTTCCCGTT
46313299 CACATCCTCG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
24 1 0.03
25 31 0.97
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.31
Consensus pattern (25 bp):
AGCTTCCCGTTACTTAGCTCACAAG
Found at i:46322181 original size:18 final size:18
Alignment explanation
Indices: 46322158--46322192 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
46322148 CGGTAGGTGC
*
46322158 GTATCCTAGCCCTTATAT
1 GTATCCTAACCCTTATAT
46322176 GTATCCTAACCCTTATA
1 GTATCCTAACCCTTATA
46322193 CGTTTCATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.29, G:0.09, T:0.37
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:46322475 original size:21 final size:21
Alignment explanation
Indices: 46322451--46322491 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
46322441 ACAACCAGAA
46322451 CAACCACAACCCCCGCCGGAG
1 CAACCACAACCCCCGCCGGAG
46322472 CAACCACAACCCCCGCCGGA
1 CAACCACAACCCCCGCCGGA
46322492 AGCTGAACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.54, G:0.17, T:0.00
Consensus pattern (21 bp):
CAACCACAACCCCCGCCGGAG
Found at i:46325978 original size:126 final size:125
Alignment explanation
Indices: 46325743--46326140 Score: 584
Period size: 126 Copynumber: 3.2 Consensus size: 125
46325733 TAAGGCCAAA
*
46325743 CAAGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGATAGTGC
1 CAAGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
* *
46325808 ATCCTGCTTAAAGCGTTTTTGACACTATTTTTTCAGAATTGTCTTCTCAAAATTATTTTTT
66 ATCCTACTTAAAGCGTTTTTGACACTATTTTTT-AGAATCGTCTTCTCAAAATTATTTTTT
* * * * *
46325869 CAAGAACCACTGTAGAAAAAGAGTGTTCATGTGGTAGCTTTTTTCAGTAATTTTGCTGACAGTGC
1 CAAGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
* * * *
46325934 ATCCTACTTGAAGTGTTTTTGAAACTACTTTTTTAGAACCGTCTTCTCAAAATTATTTTTT
66 ATCCTACTTAAAGCGTTTTTGACACTA-TTTTTTAGAATCGTCTTCTCAAAATTATTTTTT
* *
46325995 CAAGAACTATTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTTAGTAATTTTGCTGACAGTGC
1 CAAGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
* *
46326060 ATCCTACTTCAAGCGTTTTTGACATTATCTTTTTAGAATCGTCTTCTCAAAATTAAATTTTTT
66 ATCCTACTTAAAGCGTTTTTGACACTAT-TTTTTAGAATCGTCTTCTCAAAATT--ATTTTTT
*
46326123 -GA-AACTACTGTAGAAAAA
1 CAAGAACTACTGTAGAAAAA
46326141 AAACAAAATT
Statistics
Matches: 242, Mismatches: 26, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
125 1 0.00
126 227 0.94
127 7 0.03
128 7 0.03
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (125 bp):
CAAGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
ATCCTACTTAAAGCGTTTTTGACACTATTTTTTAGAATCGTCTTCTCAAAATTATTTTTT
Found at i:46326327 original size:35 final size:34
Alignment explanation
Indices: 46326196--46326330 Score: 155
Period size: 34 Copynumber: 3.9 Consensus size: 34
46326186 CTAAACACAA
**
46326196 AATTATTTTTAAAAAAACTAAACCCTAATTTAATT
1 AATT-TTTTTAAAAACTCTAAACCCTAATTTAATT
* * *
46326231 AATTTTCTTAAAAATTCTAAACCCTCATTTAATT
1 AATTTTTTTAAAAACTCTAAACCCTAATTTAATT
** *
46326265 AATTTATTTTAAATCCT-TAAAACCTAATTTAATT
1 AATTT-TTTTAAAAACTCTAAACCCTAATTTAATT
*
46326299 AAATTTTTTTAAAAACTCTAAACTCTAATTTA
1 -AATTTTTTTAAAAACTCTAAACCCTAATTTA
46326331 TTTTTTAAAA
Statistics
Matches: 83, Mismatches: 14, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
34 55 0.66
35 28 0.34
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.44
Consensus pattern (34 bp):
AATTTTTTTAAAAACTCTAAACCCTAATTTAATT
Found at i:46326421 original size:22 final size:23
Alignment explanation
Indices: 46326382--46326427 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
46326372 TTATTTTAAC
*
46326382 AAAACCCTAACACTAC-AACCCT
1 AAAACCCTAACACCACAAACCCT
46326404 AAAACCCTAA-ACCCACAAACCCT
1 AAAACCCTAACA-CCACAAACCCT
46326427 A
1 A
46326428 GGGACTAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 1 0.05
22 13 0.62
23 7 0.33
ACGTcount: A:0.48, C:0.41, G:0.00, T:0.11
Consensus pattern (23 bp):
AAAACCCTAACACCACAAACCCT
Found at i:46328421 original size:42 final size:42
Alignment explanation
Indices: 46328362--46328443 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
46328352 TTTTTTTATG
46328362 TATTGTTGGAAAATAATTATTGAGTGAAGAATGATAATTGAA
1 TATTGTTGGAAAATAATTATTGAGTGAAGAATGATAATTGAA
*
46328404 TATTGTTGGAAAATAATTATTGAGTGATGAATGATAATTG
1 TATTGTTGGAAAATAATTATTGAGTGAAGAATGATAATTG
46328444 TATCTCTTGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.40, C:0.00, G:0.22, T:0.38
Consensus pattern (42 bp):
TATTGTTGGAAAATAATTATTGAGTGAAGAATGATAATTGAA
Found at i:46328440 original size:21 final size:21
Alignment explanation
Indices: 46328374--46328442 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
46328364 TTGTTGGAAA
*
46328374 ATAATTATTGAGTGAAGAATG
1 ATAATTATTGAGTGATGAATG
* * * *
46328395 ATAATTGAAT-ATTGTTGGAA-A
1 ATAATT-ATTGAGTGAT-GAATG
46328416 ATAATTATTGAGTGATGAATG
1 ATAATTATTGAGTGATGAATG
46328437 ATAATT
1 ATAATT
46328443 GTATCTCTTG
Statistics
Matches: 35, Mismatches: 9, Indels: 8
0.67 0.17 0.15
Matches are distributed among these distances:
20 5 0.14
21 25 0.71
22 5 0.14
ACGTcount: A:0.42, C:0.00, G:0.20, T:0.38
Consensus pattern (21 bp):
ATAATTATTGAGTGATGAATG
Found at i:46328639 original size:14 final size:15
Alignment explanation
Indices: 46328615--46328655 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
46328605 CCAAGTTAGG
46328615 ATATT-TCAAAAAC-
1 ATATTATCAAAAACT
46328628 ATATTATCAAAAACT
1 ATATTATCAAAAACT
*
46328643 ATCAATATCAAAA
1 AT-ATTATCAAAA
46328656 CTTCCTTCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 5 0.21
14 8 0.33
15 2 0.08
16 9 0.38
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (15 bp):
ATATTATCAAAAACT
Found at i:46332924 original size:15 final size:15
Alignment explanation
Indices: 46332904--46332939 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
46332894 GGTAAGTCGA
*
46332904 GACACATGCGTCGTC
1 GACACATGCGTCATC
46332919 GACACATGCGTCATC
1 GACACATGCGTCATC
46332934 GACACA
1 GACACA
46332940 ATACCATAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.28, C:0.33, G:0.22, T:0.17
Consensus pattern (15 bp):
GACACATGCGTCATC
Found at i:46337244 original size:20 final size:19
Alignment explanation
Indices: 46337208--46337254 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
46337198 ATAAAAAAAC
*
46337208 TTAAAAAATATATTTATTAA
1 TTAAAAAATATAGTTA-TAA
*
46337228 TTAAAAACAT-TAGTTATAT
1 TTAAAAA-ATATAGTTATAA
46337247 TTAAAAAA
1 TTAAAAAA
46337255 ATTCTTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 1 0.04
19 9 0.38
20 12 0.50
21 2 0.08
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (19 bp):
TTAAAAAATATAGTTATAA
Found at i:46338857 original size:20 final size:19
Alignment explanation
Indices: 46338821--46338867 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
46338811 ATAAAAAAAC
*
46338821 TTAAAAAATATATTTATTAA
1 TTAAAAAATATAGTTA-TAA
*
46338841 TTAAAAACAT-TAGTTATAT
1 TTAAAAA-ATATAGTTATAA
46338860 TTAAAAAA
1 TTAAAAAA
46338868 ATTCTTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 1 0.04
19 9 0.38
20 12 0.50
21 2 0.08
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (19 bp):
TTAAAAAATATAGTTATAA
Found at i:46340266 original size:18 final size:16
Alignment explanation
Indices: 46340245--46340297 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 16
46340235 TACCAACTTC
46340245 ATTTATTTAAAAAATATT
1 ATTTATTT--AAAATATT
*
46340263 ATTTATTTTAAATATT
1 ATTTATTTAAAATATT
*
46340279 ATTTACATTAAATATATT
1 ATTTA-TTTAAA-ATATT
46340297 A
1 A
46340298 AATTATATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 12 0.40
17 4 0.13
18 14 0.47
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTATTTAAAATATT
Found at i:46340277 original size:16 final size:16
Alignment explanation
Indices: 46340256--46340293 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
46340246 TTTATTTAAA
**
46340256 AAATATTATTTATTTT
1 AAATATTATTTACATT
46340272 AAATATTATTTACATT
1 AAATATTATTTACATT
46340288 AAATAT
1 AAATAT
46340294 ATTAAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
AAATATTATTTACATT
Found at i:46340281 original size:19 final size:18
Alignment explanation
Indices: 46340245--46340283 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
46340235 TACCAACTTC
46340245 ATTTATTTAAAAAATATT
1 ATTTATTTAAAAAATATT
*
46340263 ATTTATTT--TAAATATT
1 ATTTATTTAAAAAATATT
46340279 ATTTA
1 ATTTA
46340284 CATTAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
18 8 0.40
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTATTTAAAAAATATT
Found at i:46341401 original size:31 final size:31
Alignment explanation
Indices: 46341363--46341437 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
46341353 TGGCTATTAC
* *
46341363 TCCCTTTACTTTATGAAAATTGTGGACTTAG
1 TCCCTTTACTTTATGAAAACTGTAGACTTAG
* * *
46341394 TCCCTTTACTTTGTGGAAACTGTAGATTTAG
1 TCCCTTTACTTTATGAAAACTGTAGACTTAG
46341425 T-CCTTGTACTTTA
1 TCCCTT-TACTTTA
46341438 ATTTGATCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
30 4 0.11
31 33 0.89
ACGTcount: A:0.23, C:0.17, G:0.16, T:0.44
Consensus pattern (31 bp):
TCCCTTTACTTTATGAAAACTGTAGACTTAG
Found at i:46344469 original size:90 final size:89
Alignment explanation
Indices: 46344260--46344480 Score: 286
Period size: 89 Copynumber: 2.5 Consensus size: 89
46344250 AGGCTTAAGG
* * * *
46344260 GTAT-AAAAAGCCCTTAAACTTTTTCAAAAAAAGCAATTAAGCCCTTCCTTTTTTTTTGTATTCA
1 GTATCAAAAAGCCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTCCTTTTTTTTTGCACTCA
46344324 ATTGAGCACTTAAACTTTCAAAAT
66 ATTGAGCACTTAAACTTTCAAAAT
** * *
46344348 ACATCAAAAATGCCCTCAAACTTCTTCAAAAAAAGCAATTAAGCCCCTGCTTTTTTTTT-CACTC
1 GTATCAAAAA-GCCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTCCTTTTTTTTTGCACTC
* * *
46344412 AATTGCGTACTTGAACTTTCAAAAT
65 AATTGAGCACTTAAACTTTCAAAAT
* *
46344437 GTATCAAAAAGACCCTCAAAATTTTTCAAAAAATG-AATTAAGCC
1 GTATCAAAAAG-CCCTCAAACTTTTTCAAAAAAAGCAATTAAGCC
46344481 TCTGTTCTTA
Statistics
Matches: 114, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
88 12 0.11
89 58 0.51
90 44 0.39
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (89 bp):
GTATCAAAAAGCCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTCCTTTTTTTTTGCACTCA
ATTGAGCACTTAAACTTTCAAAAT
Found at i:46346384 original size:2 final size:2
Alignment explanation
Indices: 46346377--46346408 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
46346367 NNNNNNNNNN
46346377 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46346409 GAATTAGGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46347737 original size:18 final size:19
Alignment explanation
Indices: 46347714--46347749 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
46347704 ATAATACAAC
*
46347714 ATATTATTTA-ATTTAAAA
1 ATATTATATATATTTAAAA
46347732 ATATTATATATATTTAAA
1 ATATTATATATATTTAAA
46347750 CAATGCATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATATTATATATATTTAAAA
Found at i:46348079 original size:19 final size:19
Alignment explanation
Indices: 46348044--46348081 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
46348034 AATATAAAAC
*
46348044 TTTTAACAATAACATATTA
1 TTTTAACAAGAACATATTA
46348063 TTTTAACACAGAA-ATATTA
1 TTTTAACA-AGAACATATTA
46348082 AACTAATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.47, C:0.11, G:0.03, T:0.39
Consensus pattern (19 bp):
TTTTAACAAGAACATATTA
Found at i:46350500 original size:2 final size:2
Alignment explanation
Indices: 46350493--46350517 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
46350483 TTTTTGCTTT
46350493 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
46350518 TTGTGATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:46357911 original size:439 final size:439
Alignment explanation
Indices: 46357087--46357964 Score: 1438
Period size: 439 Copynumber: 2.0 Consensus size: 439
46357077 AAATTGGAAA
46357087 TGGTCAGTTCATAAATGTTGAAGGAAGAGGAGATGTGCTGATTTGTACCCCTACAGGTGGCAAAA
1 TGGTCAGTTCATAAATGTTGAAGGAAGAGGAGATGTGCTGATTTGTACCCCTACAGGTGGCAAAA
46357152 TCATTTCAAATGTACTTTTGGTACCTGAAATTGATAGGAACCTTCTCAGTATAACTCAATTACTT
66 TCATTTCAAATGTACTTTTGGTACCTGAAATTGATAGGAACCTTCTCAGTATAACTCAATTACTT
* *
46357217 GAGAAAGGTTACTCAGTTGTGTTCAAGGAGAAAGAATGCCAAATTTTTGATCTAAGTGGATCAAA
131 GAGAAAGGTTACTCAGTTGTGTTCAAGGAGAAAGAATGCCAAATTTTTGACCCAAGTGGATCAAA
*
46357282 CCTCATAACAGTCACCATGACTGACAAATGTTTTGAAGTAGACTGGCCAAATGACTTGCATTCAG
196 CCTCATAACAGTCACCATGACTGACAAATGTTTTGAAGTAGACTGGCCAAATGACTTACATTCAG
* * *
46357347 CCTGCATAGACTCCACTGATGACTCTAGACTCTGGCACCAGAGGCTTGGACATGCAAATTACAAA
261 CCTGCATAGACTCCACTGATGACTCAAGACTCTGGCACCAAAGGCTTGGACATGCAAACTACAAA
* *
46357412 TCCATAGCTCGAATGGCCAATAAAGGACTTGCTGAAAACTTCATCGATTCAGTAAAGAATGATGA
326 TCCATAGCTAGAATGGCCAATAAAGGACTAGCTGAAAACTTCATCGATTCAGTAAAGAATGATGA
** * *
46357477 GCTTTGTGAAATATGTCAACAAGGAAAATTGGCAAGATTGCCATTTCCT
391 AATTTGTGAAATATGTCAACAAGGAAAATAGGCAAGACTGCCATTTCCT
46357526 TGGTCAGTTCATAAATGTTGAAGGAAGAGGAGATGTGCTGATTTGTACCCCTACAGGTGGCAAAA
1 TGGTCAGTTCATAAATGTTGAAGGAAGAGGAGATGTGCTGATTTGTACCCCTACAGGTGGCAAAA
*
46357591 TCATTTCAAATGTACTTTTGGTACCTGAAATTGATAGGAACCTTCTCAGTATAACTCAATTGCTT
66 TCATTTCAAATGTACTTTTGGTACCTGAAATTGATAGGAACCTTCTCAGTATAACTCAATTACTT
* *
46357656 GAGAAAGGTTACTCAGTTGTGTTTAAGGAGAAAGAATGCCAAATTTTTGACCCCAA-TGGATCCA
131 GAGAAAGGTTACTCAGTTGTGTTCAAGGAGAAAGAATGCCAAATTTTTGA-CCCAAGTGGATCAA
** * * * *
46357720 ATTTCATAACAGTCACTATGACTGACAAGTGTTTTGAAGTAGACTGGTCAAATGACTTATATTCA
195 ACCTCATAACAGTCACCATGACTGACAAATGTTTTGAAGTAGACTGGCCAAATGACTTACATTCA
* * *
46357785 GCCTGTATAGCCTCCACTGATGACTCAAGGCTCTGGCACCAAAGGCTTGGACA-GACAAACTACA
260 GCCTGCATAGACTCCACTGATGACTCAAGACTCTGGCACCAAAGGCTTGGACATG-CAAACTACA
* * * *
46357849 AATCCATAGCTA-AGATGGTCAATGAAGGGCTAGCTGAAAACTTCATCGATTCAGTGAAGAATGA
324 AATCCATAGCTAGA-ATGGCCAATAAAGGACTAGCTGAAAACTTCATCGATTCAGTAAAGAATGA
* *
46357913 TGAAATTTGTGAGATATGTCAACAAGGAAAGTAGGCAAGACTGCCATTTCCT
388 TGAAATTTGTGAAATATGTCAACAAGGAAAATAGGCAAGACTGCCATTTCCT
46357965 ACAAGCACAG
Statistics
Matches: 406, Mismatches: 30, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
438 2 0.00
439 401 0.99
440 3 0.01
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (439 bp):
TGGTCAGTTCATAAATGTTGAAGGAAGAGGAGATGTGCTGATTTGTACCCCTACAGGTGGCAAAA
TCATTTCAAATGTACTTTTGGTACCTGAAATTGATAGGAACCTTCTCAGTATAACTCAATTACTT
GAGAAAGGTTACTCAGTTGTGTTCAAGGAGAAAGAATGCCAAATTTTTGACCCAAGTGGATCAAA
CCTCATAACAGTCACCATGACTGACAAATGTTTTGAAGTAGACTGGCCAAATGACTTACATTCAG
CCTGCATAGACTCCACTGATGACTCAAGACTCTGGCACCAAAGGCTTGGACATGCAAACTACAAA
TCCATAGCTAGAATGGCCAATAAAGGACTAGCTGAAAACTTCATCGATTCAGTAAAGAATGATGA
AATTTGTGAAATATGTCAACAAGGAAAATAGGCAAGACTGCCATTTCCT
Found at i:46362959 original size:22 final size:21
Alignment explanation
Indices: 46362900--46362964 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 21
46362890 TGCTAGTAAC
46362900 CAGAATGGCTAAGAGCCATAAA
1 CAGAATGGCTAA-AGCCATAAA
* ** *
46362922 CAGGATAACTATAAGCTATAAA
1 CAGAATGGCTA-AAGCCATAAA
46362944 CAGAATGGCTACAAGCCATAA
1 CAGAATGGCTA-AAGCCATAA
46362965 GTACAGTAAT
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
22 32 0.97
23 1 0.03
ACGTcount: A:0.46, C:0.18, G:0.18, T:0.17
Consensus pattern (21 bp):
CAGAATGGCTAAAGCCATAAA
Found at i:46363011 original size:32 final size:32
Alignment explanation
Indices: 46362956--46363094 Score: 163
Period size: 32 Copynumber: 4.4 Consensus size: 32
46362946 GAATGGCTAC
* *
46362956 AAGCCATAAGT-ACAGTAATATGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* *
46362987 AAGCCATCAGTAGCAGTGATATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* *
46363019 CAGCCATCAGTAACGGTAATATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * * * *
46363051 GAGCCATTAGTAACGGTAATATGACCGACACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
*
46363083 AAGGCATCAGTA
1 AAGCCATCAGTA
46363095 GTATCGCAAC
Statistics
Matches: 92, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
31 10 0.11
32 82 0.89
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.19
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATCGGCACA
Found at i:46363279 original size:24 final size:24
Alignment explanation
Indices: 46363248--46363315 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
46363238 GTCGTGTATG
46363248 CAGA-AAATCAGTCATACTA-ATCA
1 CAGACAAATCAGTCAT-CTACATCA
* *
46363271 CAGACAAATTAGTCATTTACATCA
1 CAGACAAATCAGTCATCTACATCA
* * *
46363295 CGGACAAATCAATCATTTACA
1 CAGACAAATCAGTCATCTACA
46363316 CTCGAGGGGA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
23 6 0.16
24 32 0.84
ACGTcount: A:0.44, C:0.22, G:0.09, T:0.25
Consensus pattern (24 bp):
CAGACAAATCAGTCATCTACATCA
Found at i:46363375 original size:27 final size:27
Alignment explanation
Indices: 46363336--46363520 Score: 133
Period size: 27 Copynumber: 7.0 Consensus size: 27
46363326 AAAATAGTTA
* * *
46363336 TTTACCCTCCAGGGGCATTACGGTCAT
1 TTTACCTTACAGGGGTATTACGGTCAT
*
46363363 TTTACCTTACAGGGGTATTTCGGTCAT
1 TTTACCTTACAGGGGTATTACGGTCAT
* * * *
46363390 TTAACCTTATAGAGGTATTACGGTTAT
1 TTTACCTTACAGGGGTATTACGGTCAT
* * * *
46363417 TTTACCCTACAGGGGCATTAGGGTCGT
1 TTTACCTTACAGGGGTATTACGGTCAT
* * * * *
46363444 TTTACC--ATA-TGATTTTTCGGTCAT
1 TTTACCTTACAGGGGTATTACGGTCAT
* * * *
46363468 TTTACCTTAAAAGGGTATTACAGTCGT
1 TTTACCTTACAGGGGTATTACGGTCAT
* * *
46363495 TTTACCTTATAAGGGCATTACGGTCA
1 TTTACCTTACAGGGGTATTACGGTCA
46363521 AACTACAACA
Statistics
Matches: 119, Mismatches: 36, Indels: 6
0.74 0.22 0.04
Matches are distributed among these distances:
24 14 0.12
25 2 0.02
26 2 0.02
27 101 0.85
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (27 bp):
TTTACCTTACAGGGGTATTACGGTCAT
Found at i:46365036 original size:51 final size:51
Alignment explanation
Indices: 46364960--46365298 Score: 286
Period size: 51 Copynumber: 6.7 Consensus size: 51
46364950 TGTCGATGAA
* * ** *
46364960 CACATGTGTAGTACTGTGTGGAGGCTACTACGTGTATTGATAAATAATGGT
1 CACATGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTGGT
* * *
46365011 CACATGTGTAGTACAAAGTGAAGGCTACTATGTGTACCGA-AAAGCT-TTGAG-
1 CACATGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAA--TATTG-GT
* * * *
46365062 CACATGTGTAGTACTGTGTGAATGCTACTACGTGTATCGGTAAAT-TATGGT
1 CACATGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATAT-TGGT
* * * * *
46365113 TACATGTGTAGTACTAAGTGAAGGCTACAATGGGTACCGA-AAAGCT-TTGGT
1 CACATGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAA--TATTGGT
* * *
46365164 CACGTATGTAGTACTATGTGAAGGCTACTACGTG-AGCCG-TAAA-ACTTGAT
1 CACATGTGTAGTACTATGTGAAGGCTACTACGTGTA-CCGATAAATA-TTGGT
* * * * * *
46365214 CGCGTGTGTAGTACTATGTGAAGGCTACTACGTGAACTG-TAAA-ACTGAT
1 CACATGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTGGT
*
46365263 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
1 CACATGTGTAGTACTATGTGAAGGCTACTACGTGTA
46365299 TCGAATGATA
Statistics
Matches: 237, Mismatches: 38, Indels: 28
0.78 0.13 0.09
Matches are distributed among these distances:
49 38 0.16
50 53 0.22
51 139 0.59
52 7 0.03
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (51 bp):
CACATGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTGGT
Found at i:46365136 original size:102 final size:102
Alignment explanation
Indices: 46364960--46365301 Score: 390
Period size: 102 Copynumber: 3.4 Consensus size: 102
46364950 TGTCGATGAA
* * * * *
46364960 CACATGTGTAGTACTGTGTGGAGGCTACTACGTGTATTGATAAATAATGGTCACATGTGTAGTAC
1 CACATGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGTAAATTATGGTCACATGTGTAGTAC
*
46365025 AAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGAG
66 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGAG
* * *
46365062 CACATGTGTAGTACTGTGTGAATGCTACTACGTGTATCGGTAAATTATGGTTACATGTGTAGTAC
1 CACATGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGTAAATTATGGTCACATGTGTAGTAC
* *
46365127 TAAGTGAAGGCTACAATGGGTACCGAAAAGCTTTG-G
66 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGAG
* * * * * * * *
46365163 TCACGTATGTAGTACTATGTGAAGGCTACTACGTG-AGCCGTAAAACT-TGATCGCGTGTGTAGT
1 -CACATGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGT-AAATTATGGTCACATGTGTAGT
* * * * *
46365226 ACTATGTGAAGGCTACTACGTGAACTGTAAAA-C--TGAT
64 ACTAAGTGAAGGCTACTATGTGTACCG-AAAAGCTTTGAG
*
46365263 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCG
1 CACATGTGTAGTACTATGTGAAGGCTACTACGTGTATCG
46365302 AATGATAAAA
Statistics
Matches: 205, Mismatches: 30, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
99 35 0.17
100 2 0.01
101 39 0.19
102 129 0.63
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (102 bp):
CACATGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGTAAATTATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGAG
Found at i:46370504 original size:164 final size:164
Alignment explanation
Indices: 46370233--46370594 Score: 697
Period size: 164 Copynumber: 2.2 Consensus size: 164
46370223 CCTCTGCCGA
46370233 TTTCCTTGTTGGTAAGTTAATCCCCTTCAGATTTCCTTGTTGCTGAAGCCTTAGCTGCAGCTTCT
1 TTTCCTTGTTGGTAAGTTAATCCCCTTCAGATTTCCTTGTTGCTGAAGCCTTAGCTGCAGCTTCT
* *
46370298 TGAAGCTTTCGAACTGTACTTTCTGATTTCCTTGTTGGTAAGTTAATAGGTTCATCAAGTTTTCT
66 TCAAGCTTTCAAACTGTACTTTCTGATTTCCTTGTTGGTAAGTTAATAGGTTCATCAAGTTTTCT
46370363 TCTTTTATGATATTATTGGCTTAACTGAGTAGTT
131 TCTTTTATGATATTATTGGCTTAACTGAGTAGTT
*
46370397 TTTCCTTGTCGGTAAGTTAATCCCCTTCAGATTTCCTTGTTGCTGAAGCCTTAGCTGCAGCTTCT
1 TTTCCTTGTTGGTAAGTTAATCCCCTTCAGATTTCCTTGTTGCTGAAGCCTTAGCTGCAGCTTCT
46370462 TCAAGCTTTCAAACTGTACTTTCTGATTTCCTTGTTGGTAAGTTAATAGGTTCATCAAGTTTTCT
66 TCAAGCTTTCAAACTGTACTTTCTGATTTCCTTGTTGGTAAGTTAATAGGTTCATCAAGTTTTCT
46370527 TCTTTTATGATATTATTGGCTTAACTGAGTAGTT
131 TCTTTTATGATATTATTGGCTTAACTGAGTAGTT
46370561 TTTCCTTGTTGGTAAGTTAATCCCCTTCAGATTT
1 TTTCCTTGTTGGTAAGTTAATCCCCTTCAGATTT
46370595 GTTTCACTCT
Statistics
Matches: 194, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
164 194 1.00
ACGTcount: A:0.20, C:0.19, G:0.17, T:0.44
Consensus pattern (164 bp):
TTTCCTTGTTGGTAAGTTAATCCCCTTCAGATTTCCTTGTTGCTGAAGCCTTAGCTGCAGCTTCT
TCAAGCTTTCAAACTGTACTTTCTGATTTCCTTGTTGGTAAGTTAATAGGTTCATCAAGTTTTCT
TCTTTTATGATATTATTGGCTTAACTGAGTAGTT
Found at i:46373718 original size:39 final size:40
Alignment explanation
Indices: 46373675--46373779 Score: 113
Period size: 44 Copynumber: 2.5 Consensus size: 40
46373665 TTCCATTATG
46373675 CTATTACACCTCTATTCCATTCAACCAAACACAAGA-TTA
1 CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
* *** *
46373714 CTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATTTG
1 CTATTACACCTCTATT-C----CATTCAACCAAACACAAGATTTA
46373759 CTATTACACCTCTATTCCATT
1 CTATTACACCTCTATTCCATT
46373780 ACACCTCTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
39 15 0.28
40 5 0.09
44 17 0.31
45 17 0.31
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34
Consensus pattern (40 bp):
CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
Found at i:46373773 original size:45 final size:44
Alignment explanation
Indices: 46373673--46373782 Score: 131
Period size: 45 Copynumber: 2.6 Consensus size: 44
46373663 TTTTCCATTA
46373673 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * ***
46373712 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
46373757 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
46373783 CCTCTAATCC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 25 0.43
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:46373782 original size:16 final size:16
Alignment explanation
Indices: 46373761--46373798 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
46373751 TTGATTTGCT
*
46373761 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
46373777 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
46373793 AATACA
1 ATTACA
46373799 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:46376489 original size:36 final size:36
Alignment explanation
Indices: 46376415--46376648 Score: 208
Period size: 35 Copynumber: 6.5 Consensus size: 36
46376405 CTTAGACGTA
* *
46376415 TCTATTCCAATTTTTTTAAGGTTGCCTTAG--AAGTG
1 TCTATCCCAACTTTTTTAAGGTTGCCTTAGATAAG-G
*
46376450 TCTATCCCAACTTTTTTAAGGTTGTCTTAGATAAGG
1 TCTATCCCAACTTTTTTAAGGTTGCCTTAGATAAGG
** **
46376486 TCTATCTAAACTTTTTTAAGGTTGCCTTAGACGA-G
1 TCTATCCCAACTTTTTTAAGGTTGCCTTAGATAAGG
* *
46376521 TCTATCCCAAACTTTTTTAAAGGTTGCTTTAGACAAGG
1 TCTATCCC-AACTTTTTT-AAGGTTGCCTTAGATAAGG
* * * *
46376559 TCTATCCCAACCTTTTTAAGTTTGTCTTAGAT-GGG
1 TCTATCCCAACTTTTTTAAGGTTGCCTTAGATAAGG
* ** * * *
46376594 CCTATATCAACCTTTTTAAGATTGCCTTAGATGA-G
1 TCTATCCCAACTTTTTTAAGGTTGCCTTAGATAAGG
* *
46376629 TTTATCCAAATCTTTTTTAA
1 TCTATCCCAA-CTTTTTTAA
46376649 ATGTCGGTAT
Statistics
Matches: 162, Mismatches: 30, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
35 69 0.43
36 58 0.36
37 26 0.16
38 9 0.06
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.42
Consensus pattern (36 bp):
TCTATCCCAACTTTTTTAAGGTTGCCTTAGATAAGG
Found at i:46376502 original size:37 final size:36
Alignment explanation
Indices: 46376426--46376589 Score: 190
Period size: 36 Copynumber: 4.6 Consensus size: 36
46376416 CTATTCCAAT
*
46376426 TTTTTTAAGGTTGCCTTAG--AAGTGTCTATCCCAAC
1 TTTTTTAAGGTTGCCTTAGACAAG-GTCTATCCAAAC
* * *
46376461 TTTTTTAAGGTTGTCTTAGATAAGGTCTATCTAAAC
1 TTTTTTAAGGTTGCCTTAGACAAGGTCTATCCAAAC
*
46376497 TTTTTTAAGGTTGCCTTAGACGA-GTCTATCCCAAAC
1 TTTTTTAAGGTTGCCTTAGACAAGGTCTAT-CCAAAC
* *
46376533 TTTTTTAAAGGTTGCTTTAGACAAGGTCTATCCCAAC
1 TTTTTT-AAGGTTGCCTTAGACAAGGTCTATCCAAAC
* * *
46376570 CTTTTTAAGTTTGTCTTAGA
1 TTTTTTAAGGTTGCCTTAGA
46376590 TGGGCCTATA
Statistics
Matches: 110, Mismatches: 14, Indels: 9
0.83 0.11 0.07
Matches are distributed among these distances:
35 24 0.22
36 52 0.47
37 28 0.25
38 6 0.05
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.41
Consensus pattern (36 bp):
TTTTTTAAGGTTGCCTTAGACAAGGTCTATCCAAAC
Found at i:46376559 original size:73 final size:71
Alignment explanation
Indices: 46376426--46376648 Score: 225
Period size: 71 Copynumber: 3.1 Consensus size: 71
46376416 CTATTCCAAT
* *
46376426 TTTTTTAAGGTTGCCTTAGAAGTGTCTATCCCAACTTTTTTAAGGTTGTCTTAGATAAGGTCTAT
1 TTTTTTAAGGTTGCCTTAGAAGAGTCTATCCCAACTTTTTTAAGGTTGTCTTAGACAAGGTCTAT
*
46376491 CTAAAC
66 CCAAAC
*
46376497 TTTTTTAAGGTTGCCTTAGACGAGTCTATCCCAAACTTTTTTAAAGGTTG-CTTTAGACAAGGTC
1 TTTTTTAAGGTTGCCTTAGAAGAGTCTATCCC-AACTTTTTT-AAGGTTGTC-TTAGACAAGGTC
*
46376561 TATCCCAAC
63 TATCCAAAC
* * * * * * ** * * * ** *
46376570 CTTTTTAAGTTTGTCTTAGATGGGCCTATATCAACCTTTTTAAGATTGCCTTAGATGA-GTTTAT
1 TTTTTTAAGGTTGCCTTAGAAGAGTCTATCCCAACTTTTTTAAGGTTGTCTTAGACAAGGTCTAT
46376634 CCAAATC
66 CCAAA-C
46376641 TTTTTTAA
1 TTTTTTAA
46376649 ATGTCGGTAT
Statistics
Matches: 127, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
70 9 0.07
71 50 0.39
72 19 0.15
73 49 0.39
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.42
Consensus pattern (71 bp):
TTTTTTAAGGTTGCCTTAGAAGAGTCTATCCCAACTTTTTTAAGGTTGTCTTAGACAAGGTCTAT
CCAAAC
Found at i:46376635 original size:108 final size:108
Alignment explanation
Indices: 46376404--46376649 Score: 299
Period size: 108 Copynumber: 2.3 Consensus size: 108
46376394 GAAAAAATTA
*
46376404 CCTTAGACGTA-TCTATTCC-AAT-TTTTTT-AAGGTTGCCTTAGAAGTGTCTATCCCAACTTTT
1 CCTTAGACG-AGTCTA-TCCAAATCTTTTTTAAAGGTTGCCTTAGAAGTGTCTATCCCAACCTTT
* * * *
46376465 TTAAGGTTGTCTTAGATAAGGTCTATCTAAACTTTTTTAAGGTTG
64 TTAAGGTTGTCTTAGATAAGGCCTATATAAACCTTTTTAAGATTG
*
46376510 CCTTAGACGAGTCTATCCCAAA-CTTTTTTAAAGGTTGCTTTAGACAAG-GTCTATCCCAACCTT
1 CCTTAGACGAGTCTAT-CCAAATCTTTTTTAAAGGTTGCCTTAG--AAGTGTCTATCCCAACCTT
* * *
46376573 TTTAAGTTTGTCTTAGAT-GGGCCTATATCAACCTTTTTAAGATTG
63 TTTAAGGTTGTCTTAGATAAGGCCTATATAAACCTTTTTAAGATTG
* *
46376618 CCTTAGATGAGTTTATCCAAATCTTTTTTAAA
1 CCTTAGACGAGTCTATCCAAATCTTTTTTAAA
46376650 TGTCGGTATT
Statistics
Matches: 121, Mismatches: 11, Indels: 14
0.83 0.08 0.10
Matches are distributed among these distances:
105 2 0.02
106 15 0.12
107 13 0.11
108 57 0.47
109 31 0.26
110 3 0.02
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (108 bp):
CCTTAGACGAGTCTATCCAAATCTTTTTTAAAGGTTGCCTTAGAAGTGTCTATCCCAACCTTTTT
AAGGTTGTCTTAGATAAGGCCTATATAAACCTTTTTAAGATTG
Found at i:46380673 original size:18 final size:18
Alignment explanation
Indices: 46380639--46380672 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
46380629 AATTGGTTAT
46380639 TTTTATTATTTTATTTTA
1 TTTTATTATTTTATTTTA
46380657 TTTTATT-TTTTATTTT
1 TTTTATTATTTTATTTT
46380673 TGGTAAAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTATTATTTTATTTTA
Found at i:46381611 original size:21 final size:21
Alignment explanation
Indices: 46381539--46381612 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
46381529 GATCGTGTAC
* *
46381539 CTCAGTCACACAAGCGTGTAT
1 CTCAGACACACAAGCGTGTCT
46381560 CTCA-AC-CACATAGCTGTGTCT
1 CTCAGACACACA-AGC-GTGTCT
* * *
46381581 CTTAGGCACACAGGCGTGTCT
1 CTCAGACACACAAGCGTGTCT
46381602 CTCAGACACAC
1 CTCAGACACAC
46381613 GACCATGTAT
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
19 4 0.10
20 4 0.10
21 27 0.64
22 3 0.07
23 4 0.10
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.23
Consensus pattern (21 bp):
CTCAGACACACAAGCGTGTCT
Found at i:46383982 original size:2 final size:2
Alignment explanation
Indices: 46383977--46384011 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
46383967 TGTATATATA
*
46383977 TG TG TG TG TG TG TG TG TG TA TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
46384012 ACATATTAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.03, C:0.00, G:0.46, T:0.51
Consensus pattern (2 bp):
TG
Found at i:46391804 original size:26 final size:26
Alignment explanation
Indices: 46391775--46391824 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
46391765 AAATAATTTG
46391775 GGGAATCAACACTTAGCAACCCCTCA
1 GGGAATCAACACTTAGCAACCCCTCA
**
46391801 GGGAATCTGCACTTAGCAACCCCT
1 GGGAATCAACACTTAGCAACCCCT
46391825 TTTTTATCAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.18, T:0.18
Consensus pattern (26 bp):
GGGAATCAACACTTAGCAACCCCTCA
Found at i:46391858 original size:41 final size:41
Alignment explanation
Indices: 46391801--46391948 Score: 224
Period size: 41 Copynumber: 3.6 Consensus size: 41
46391791 CAACCCCTCA
** * *
46391801 GGGAATCTGCACTTAGCAACCCCTTTTTTATCAGTGATTTG
1 GGGAATCTGCACTTAGCAACCCCTTTTCGATCAATGATTCG
*
46391842 GGGAATCTGCACTTAGCAACCCCTTTTCGATCAATGATACG
1 GGGAATCTGCACTTAGCAACCCCTTTTCGATCAATGATTCG
* * *
46391883 GGGAATTTGCACTTGGCAACCCCTTTTCGATCAATGATTCA
1 GGGAATCTGCACTTAGCAACCCCTTTTCGATCAATGATTCG
46391924 GGGAATCTGCACTTAGCAACCCCTT
1 GGGAATCTGCACTTAGCAACCCCTT
46391949 ACATTCAATG
Statistics
Matches: 96, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 96 1.00
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (41 bp):
GGGAATCTGCACTTAGCAACCCCTTTTCGATCAATGATTCG
Found at i:46397547 original size:31 final size:30
Alignment explanation
Indices: 46397512--46397571 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
46397502 GGAGGTGGGA
*
46397512 TGGGAAGAGAATAAAAGTTTTAGGGGAAAAG
1 TGGG-AGAGAATAAAAATTTTAGGGGAAAAG
* * *
46397543 TGGGAGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAGAGAATAAAAATTTTAGGGGAAAA
46397572 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (30 bp):
TGGGAGAGAATAAAAATTTTAGGGGAAAAG
Found at i:46399522 original size:22 final size:24
Alignment explanation
Indices: 46399485--46399528 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
46399475 AAAACGCCTA
46399485 TTCTTCTTCTCTTTTTTCTTTTGG
1 TTCTTCTTCTCTTTTTTCTTTTGG
46399509 TTCTT-TT-TCTTTTTTCTTTT
1 TTCTTCTTCTCTTTTTTCTTTT
46399529 TAATAACTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 13 0.65
23 2 0.10
24 5 0.25
ACGTcount: A:0.00, C:0.18, G:0.05, T:0.77
Consensus pattern (24 bp):
TTCTTCTTCTCTTTTTTCTTTTGG
Found at i:46403166 original size:62 final size:62
Alignment explanation
Indices: 46403089--46403247 Score: 165
Period size: 62 Copynumber: 2.6 Consensus size: 62
46403079 GAATTGGAGG
* * * ** * *
46403089 CACACGAGCTAGGGACATGGGCGTGTTTCTAGGTTATGTAACTCATTGTTTGTATTTTTGGT
1 CACACAAGCTAGGGACATGGGCGTGTGTCCAGGCCATGTAACTCACTGTTTGTATTTCTGGT
* *** * *
46403151 CACACAAGCCAGGGACACCCGCATGTGTCCAGGCCGTGTAACTCACTGTTTGTATTTCTGGT
1 CACACAAGCTAGGGACATGGGCGTGTGTCCAGGCCATGTAACTCACTGTTTGTATTTCTGGT
* * * *
46403213 CACACAGGCTAGGGACATAGGTGCGTGTCCAGGCC
1 CACACAAGCTAGGGACATGGGCGTGTGTCCAGGCC
46403248 GTGTGAGGGG
Statistics
Matches: 76, Mismatches: 21, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
62 76 1.00
ACGTcount: A:0.21, C:0.23, G:0.28, T:0.28
Consensus pattern (62 bp):
CACACAAGCTAGGGACATGGGCGTGTGTCCAGGCCATGTAACTCACTGTTTGTATTTCTGGT
Found at i:46407871 original size:23 final size:23
Alignment explanation
Indices: 46407820--46407864 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
46407810 ACCAAAATAA
46407820 TAAATTATTACAACGGTAGTGAC
1 TAAATTATTACAACGGTAGTGAC
*
46407843 TAAATTATT-CTAACGGTTGTGA
1 TAAATTATTAC-AACGGTAGTGA
46407865 TCAAATTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.36
Consensus pattern (23 bp):
TAAATTATTACAACGGTAGTGAC
Found at i:46413386 original size:21 final size:21
Alignment explanation
Indices: 46413332--46413402 Score: 85
Period size: 20 Copynumber: 3.4 Consensus size: 21
46413322 GTATATCATG
46413332 TATGTTATGTATATT-ACTATT
1 TATG-TATGTATATTAACTATT
*
46413353 TATGTATGTATATTAAGTATGT
1 TATGTATGTATATTAACTAT-T
*
46413375 TATGTA-GTATATT-ACTGTT
1 TATGTATGTATATTAACTATT
46413394 TATGTATGT
1 TATGTATGT
46413403 TATGTATTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
19 7 0.16
20 15 0.34
21 15 0.34
22 7 0.16
ACGTcount: A:0.28, C:0.03, G:0.15, T:0.54
Consensus pattern (21 bp):
TATGTATGTATATTAACTATT
Found at i:46413393 original size:18 final size:19
Alignment explanation
Indices: 46413319--46413402 Score: 66
Period size: 20 Copynumber: 4.3 Consensus size: 19
46413309 AAAAAAATAA
*
46413319 TATGTATATCA-TG-TATG
1 TATGTATATTACTGTTATG
*
46413336 TTATGTATATTACTATTTATG
1 -TATGTATATTACT-GTTATG
*
46413357 TATGTATATTAAGTATGTTATG
1 TATGTATATT-A--CTGTTATG
46413379 TA-GTATATTACTGTTTATG
1 TATGTATATTACTG-TTATG
46413398 TATGT
1 TATGT
46413403 TATGTATTAT
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
18 12 0.23
19 8 0.15
20 13 0.25
21 12 0.23
22 7 0.13
23 1 0.02
ACGTcount: A:0.29, C:0.04, G:0.15, T:0.52
Consensus pattern (19 bp):
TATGTATATTACTGTTATG
Found at i:46413397 original size:41 final size:38
Alignment explanation
Indices: 46413319--46413402 Score: 114
Period size: 41 Copynumber: 2.1 Consensus size: 38
46413309 AAAAAAATAA
*
46413319 TATGTATATCATGTATGTTATGTATATTACTATTTATG
1 TATGTATATCAAGTATGTTATGTATATTACTATTTATG
* *
46413357 TATGTATATTAAGTATGTTATGTAGTATATTACTGTTTATG
1 TATGTATATCAAGTATGTTA--T-GTATATTACTATTTATG
46413398 TATGT
1 TATGT
46413403 TATGTATTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
38 18 0.45
40 1 0.03
41 21 0.52
ACGTcount: A:0.29, C:0.04, G:0.15, T:0.52
Consensus pattern (38 bp):
TATGTATATCAAGTATGTTATGTATATTACTATTTATG
Found at i:46413401 original size:28 final size:28
Alignment explanation
Indices: 46413369--46413465 Score: 124
Period size: 28 Copynumber: 3.4 Consensus size: 28
46413359 TGTATATTAA
46413369 GTATGTTATGTAGTATATTACTGTTTAT
1 GTATGTTATGTAGTATATTACTGTTTAT
* * *
46413397 GTATGTTATGTATTATATTATTGTTAAT
1 GTATGTTATGTAGTATATTACTGTTTAT
* *
46413425 GTATTTTATGTATGT-TATGTAGTGTTTAT
1 GTATGTTATGTA-GTATAT-TACTGTTTAT
46413454 GTATGTTATGTA
1 GTATGTTATGTA
46413466 TATTACCAGT
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
28 39 0.66
29 20 0.34
ACGTcount: A:0.25, C:0.01, G:0.19, T:0.56
Consensus pattern (28 bp):
GTATGTTATGTAGTATATTACTGTTTAT
Found at i:46413407 original size:9 final size:9
Alignment explanation
Indices: 46413319--46413466 Score: 101
Period size: 9 Copynumber: 15.8 Consensus size: 9
46413309 AAAAAAATAA
*
46413319 TATGTATAT
1 TATGTATGT
*
46413328 CATGTATGT
1 TATGTATGT
*
46413337 TATGTATAT
1 TATGTATGT
*
46413346 TA-CTAT-T
1 TATGTATGT
46413353 TATGTATGT
1 TATGTATGT
46413362 ATATTAAGTATGT
1 -TA-T--GTATGT
46413375 TATGTA-GT
1 TATGTATGT
46413383 ATAT-TACTGTT
1 -TATGTA-TG-T
46413394 TATGTATGT
1 TATGTATGT
46413403 TATGTAT-T
1 TATGTATGT
46413411 ATAT-TATTGT
1 -TATGTA-TGT
*
46413421 TAATGTATTT
1 T-ATGTATGT
46413431 TATGTATGT
1 TATGTATGT
46413440 TATGTAGTGTT
1 TATGTA-TG-T
46413451 TATGTATGT
1 TATGTATGT
46413460 TATGTAT
1 TATGTAT
46413467 ATTACCAGTT
Statistics
Matches: 113, Mismatches: 8, Indels: 36
0.72 0.05 0.23
Matches are distributed among these distances:
7 3 0.03
8 13 0.12
9 57 0.50
10 18 0.16
11 14 0.12
12 2 0.02
13 6 0.05
ACGTcount: A:0.27, C:0.02, G:0.16, T:0.55
Consensus pattern (9 bp):
TATGTATGT
Found at i:46413922 original size:18 final size:18
Alignment explanation
Indices: 46413886--46413923 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
46413876 GGGGAACCAC
*
46413886 ATTGTAATGAAGAATTTA
1 ATTGTAATGAAGAAGTTA
46413904 ATTGTAATG-AGAGAGTTA
1 ATTGTAATGAAGA-AGTTA
46413922 AT
1 AT
46413924 AGCGGGGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.37
Consensus pattern (18 bp):
ATTGTAATGAAGAAGTTA
Found at i:46418838 original size:25 final size:25
Alignment explanation
Indices: 46418810--46418901 Score: 111
Period size: 25 Copynumber: 3.8 Consensus size: 25
46418800 TGGCTCGTAT
46418810 GAGCTTCCTGATAATTGGCTCTCCG
1 GAGCTTCCTGATAATTGGCTCTCCG
* **
46418835 GAGCTTCCCGATAATTGGCTCTCAT
1 GAGCTTCCTGATAATTGGCTCTCCG
* *
46418860 GAGCTT-CT--TGATTAGCTCTCCG
1 GAGCTTCCTGATAATTGGCTCTCCG
46418882 GAGCTTCCTGAT-ATTGGCTC
1 GAGCTTCCTGATAATTGGCTC
46418902 ACACGAGCTT
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
22 16 0.29
23 2 0.04
24 8 0.15
25 29 0.53
ACGTcount: A:0.16, C:0.27, G:0.23, T:0.34
Consensus pattern (25 bp):
GAGCTTCCTGATAATTGGCTCTCCG
Found at i:46418888 original size:47 final size:46
Alignment explanation
Indices: 46418827--46418919 Score: 134
Period size: 47 Copynumber: 2.0 Consensus size: 46
46418817 CTGATAATTG
* *
46418827 GCTCTCCGGAGCTTCCCGATAATTGGCTCTCATGAGC-TTCTTGATTA
1 GCTCTCCGGAGCTTCCCGAT-ATTGGCTCACACGAGCTTTC-TGATTA
*
46418874 GCTCTCCGGAGCTTCCTGATATTGGCTCACACGAGCTTTCTGATTA
1 GCTCTCCGGAGCTTCCCGATATTGGCTCACACGAGCTTTCTGATTA
46418920 TGGTTCTTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
46 20 0.48
47 22 0.52
ACGTcount: A:0.17, C:0.28, G:0.22, T:0.33
Consensus pattern (46 bp):
GCTCTCCGGAGCTTCCCGATATTGGCTCACACGAGCTTTCTGATTA
Found at i:46418918 original size:46 final size:47
Alignment explanation
Indices: 46418827--46418919 Score: 136
Period size: 46 Copynumber: 2.0 Consensus size: 47
46418817 CTGATAATTG
* *
46418827 GCTCTCCGGAGCTTCCCGATAATTGGCTCTCATGAGCTTCTTGATTA
1 GCTCTCCGGAGCTTCCCGATAATTGGCTCACACGAGCTTCTTGATTA
*
46418874 GCTCTCCGGAGCTTCCTGAT-ATTGGCTCACACGAGCTT-TCTGATTA
1 GCTCTCCGGAGCTTCCCGATAATTGGCTCACACGAGCTTCT-TGATTA
46418920 TGGTTCTTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
45 1 0.02
46 22 0.52
47 19 0.45
ACGTcount: A:0.17, C:0.28, G:0.22, T:0.33
Consensus pattern (47 bp):
GCTCTCCGGAGCTTCCCGATAATTGGCTCACACGAGCTTCTTGATTA
Found at i:46422540 original size:21 final size:21
Alignment explanation
Indices: 46422516--46422555 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
46422506 GAGAAAAATG
* *
46422516 AAAGAGATAGCAGCGAAAACA
1 AAAGAGATAGAAGAGAAAACA
46422537 AAAGAGATAGAAGAGAAAA
1 AAAGAGATAGAAGAGAAAA
46422556 AGGTTGAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.62, C:0.07, G:0.25, T:0.05
Consensus pattern (21 bp):
AAAGAGATAGAAGAGAAAACA
Found at i:46425438 original size:25 final size:25
Alignment explanation
Indices: 46425409--46425523 Score: 212
Period size: 25 Copynumber: 4.6 Consensus size: 25
46425399 TATTTAAATA
46425409 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
46425434 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
*
46425459 TTATTTGATGTAATAAAATATAAGT
1 TTATTTGATGTAATAAAATAGAAGT
*
46425484 TTATTTGATGTAATAAAATATAAGT
1 TTATTTGATGTAATAAAATAGAAGT
46425509 TTATTTGATGTAATA
1 TTATTTGATGTAATA
46425524 TAATTAAATA
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
25 89 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:46425606 original size:38 final size:31
Alignment explanation
Indices: 46425519--46426118 Score: 445
Period size: 33 Copynumber: 20.5 Consensus size: 31
46425509 TTATTTGATG
* * *
46425519 TAATATAATTAAATACCCT-AATCCTAA-CC
1 TAATTTAATTAAAAACCCTAAACCCTAATCC
46425548 TAATTTAATTAAAAACCCTAAAAACCCTAATCC
1 TAATTTAATTAAAAACCCT--AAACCCTAATCC
* *
46425581 TAATTTAATTAAAAA-CCTTAA-CCTAAACC
1 TAATTTAATTAAAAACCCTAAACCCTAATCC
* * *
46425610 ----CTAATTAAATACCCT-AATCCTAA-CC
1 TAATTTAATTAAAAACCCTAAACCCTAATCC
46425635 TAATTTAATTAAAAACCCTAAAAACCCTAATCC
1 TAATTTAATTAAAAACCCT--AAACCCTAATCC
* *
46425668 TAATTTAATTAAAAA-CCTTAA-CCTAAACC
1 TAATTTAATTAAAAACCCTAAACCCTAATCC
* * *
46425697 ----CTAATTAAATACCCT-AATCCTAA-CC
1 TAATTTAATTAAAAACCCTAAACCCTAATCC
46425722 TAATTTAATTAAAAACCCTAAAAACCCTAATCC
1 TAATTTAATTAAAAACCCT--AAACCCTAATCC
* *
46425755 TAATTTAATTAAAAA-CCTTAA-CCTAAACC
1 TAATTTAATTAAAAACCCTAAACCCTAATCC
* * *
46425784 ----CTAATTAAATACCCT-AATCCTAA-CC
1 TAATTTAATTAAAAACCCTAAACCCTAATCC
46425809 TAATTTAATTAAAAAACCCTAAAACCCTAATCC
1 TAATTTAATT-AAAAACCCT-AAACCCTAATCC
* *
46425842 TAATTTAATTAAAAA-CCTTAA-CCTAAACC
1 TAATTTAATTAAAAACCCTAAACCCTAATCC
* * *
46425871 ----CTAATTAAATACCCT-AATCCTAA-CC
1 TAATTTAATTAAAAACCCTAAACCCTAATCC
46425896 TAATTTAATTAAAAACCCTAAAAACCCTAATCC
1 TAATTTAATTAAAAACCCT--AAACCCTAATCC
*
46425929 TAATTTAATTAAAAACCCT-AA-CCTAAACC
1 TAATTTAATTAAAAACCCTAAACCCTAATCC
* *
46425958 ----CTAATTAAATACCCTAAA-CCTAA-CC
1 TAATTTAATTAAAAACCCTAAACCCTAATCC
*
46425983 TAATTTAATTAAAAACCCTAAAAACCTTAATCC
1 TAATTTAATTAAAAACCCT--AAACCCTAATCC
* *
46426016 TAATTTAATTAAAAACCCT-AA-TCTAAACCC
1 TAATTTAATTAAAAACCCTAAACCCT-AATCC
*
46426046 TAA-TT-A--AAATACCCT-AACCCTAA-CC
1 TAATTTAATTAAAAACCCTAAACCCTAATCC
46426071 TAATTTAATTAAAAACCCTAAAAACCCTAATCC
1 TAATTTAATTAAAAACCCT--AAACCCTAATCC
46426104 TAATTTAATTAAAAA
1 TAATTTAATTAAAAA
46426119 TTCTAACCTA
Statistics
Matches: 465, Mismatches: 43, Indels: 122
0.74 0.07 0.19
Matches are distributed among these distances:
25 72 0.15
26 53 0.11
27 3 0.01
28 1 0.00
29 120 0.26
30 27 0.06
31 6 0.01
32 61 0.13
33 122 0.26
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.29
Consensus pattern (31 bp):
TAATTTAATTAAAAACCCTAAACCCTAATCC
Found at i:46425642 original size:25 final size:24
Alignment explanation
Indices: 46425566--46425639 Score: 87
Period size: 24 Copynumber: 3.0 Consensus size: 24
46425556 TTAAAAACCC
**
46425566 TAAAAACCCTAATCCTAATTTAAT
1 TAAAAACCCTAATCCTAACCTAAT
*
46425590 TAAAAACCTTAA-CCTAAACCCTAAT
1 TAAAAACCCTAATCCT-AA-CCTAAT
*
46425615 TAAATACCCTAATCCTAACCTAAT
1 TAAAAACCCTAATCCTAACCTAAT
46425639 T
1 T
46425640 TAATTAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
23 3 0.07
24 20 0.48
25 16 0.38
26 3 0.07
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.30
Consensus pattern (24 bp):
TAAAAACCCTAATCCTAACCTAAT
Found at i:46425670 original size:87 final size:87
Alignment explanation
Indices: 46425524--46426179 Score: 1199
Period size: 87 Copynumber: 7.5 Consensus size: 87
46425514 TGATGTAATA
46425524 TAATTAAATACCCTAATCCTAACCTAATTTAATTAAAAACCCTAAAAACCCTAATCCTAATTTAA
1 TAATTAAATACCCTAATCCTAACCTAATTTAATTAAAAACCCTAAAAACCCTAATCCTAATTTAA
46425589 TTAAAAACCTTAACCTAAACCC
66 TTAAAAACCTTAACCTAAACCC
46425611 TAATTAAATACCCTAATCCTAACCTAATTTAATTAAAAACCCTAAAAACCCTAATCCTAATTTAA
1 TAATTAAATACCCTAATCCTAACCTAATTTAATTAAAAACCCTAAAAACCCTAATCCTAATTTAA
46425676 TTAAAAACCTTAACCTAAACCC
66 TTAAAAACCTTAACCTAAACCC
46425698 TAATTAAATACCCTAATCCTAACCTAATTTAATTAAAAACCCTAAAAACCCTAATCCTAATTTAA
1 TAATTAAATACCCTAATCCTAACCTAATTTAATTAAAAACCCTAAAAACCCTAATCCTAATTTAA
46425763 TTAAAAACCTTAACCTAAACCC
66 TTAAAAACCTTAACCTAAACCC
46425785 TAATTAAATACCCTAATCCTAACCTAATTTAATTAAAAAACCCT-AAAACCCTAATCCTAATTTA
1 TAATTAAATACCCTAATCCTAACCTAATTTAATT-AAAAACCCTAAAAACCCTAATCCTAATTTA
46425849 ATTAAAAACCTTAACCTAAACCC
65 ATTAAAAACCTTAACCTAAACCC
46425872 TAATTAAATACCCTAATCCTAACCTAATTTAATTAAAAACCCTAAAAACCCTAATCCTAATTTAA
1 TAATTAAATACCCTAATCCTAACCTAATTTAATTAAAAACCCTAAAAACCCTAATCCTAATTTAA
*
46425937 TTAAAAACCCTAACCTAAACCC
66 TTAAAAACCTTAACCTAAACCC
* *
46425959 TAATTAAATACCCTAAACCTAACCTAATTTAATTAAAAACCCTAAAAACCTTAATCCTAATTTAA
1 TAATTAAATACCCTAATCCTAACCTAATTTAATTAAAAACCCTAAAAACCCTAATCCTAATTTAA
* *
46426024 TTAAAAACCCTAATCTAAACCC
66 TTAAAAACCTTAACCTAAACCC
*
46426046 TAATTAAAATACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAAAACCCTAATCCTAATTTA
1 TAATT-AAATACCCTAATCCTAACCTAATTTAATTAAAAACCCTAAAAACCCTAATCCTAATTTA
*
46426111 ATTAAAAA-TTCTAACCTAAACCC
65 ATTAAAAACCT-TAACCTAAACCC
*
46426134 TAATTAAATACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAA
1 TAATTAAATACCCTAATCCTAACCTAATTTAATTAAAAACCCTAAA
46426180 CCCTTAACTT
Statistics
Matches: 556, Mismatches: 9, Indels: 8
0.97 0.02 0.01
Matches are distributed among these distances:
86 9 0.02
87 457 0.82
88 90 0.16
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.29
Consensus pattern (87 bp):
TAATTAAATACCCTAATCCTAACCTAATTTAATTAAAAACCCTAAAAACCCTAATCCTAATTTAA
TTAAAAACCTTAACCTAAACCC
Found at i:46425729 original size:25 final size:24
Alignment explanation
Indices: 46425653--46425726 Score: 87
Period size: 24 Copynumber: 3.0 Consensus size: 24
46425643 TTAAAAACCC
**
46425653 TAAAAACCCTAATCCTAATTTAAT
1 TAAAAACCCTAATCCTAACCTAAT
*
46425677 TAAAAACCTTAA-CCTAAACCCTAAT
1 TAAAAACCCTAATCCT-AA-CCTAAT
*
46425702 TAAATACCCTAATCCTAACCTAAT
1 TAAAAACCCTAATCCTAACCTAAT
46425726 T
1 T
46425727 TAATTAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
23 3 0.07
24 20 0.48
25 16 0.38
26 3 0.07
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.30
Consensus pattern (24 bp):
TAAAAACCCTAATCCTAACCTAAT
Found at i:46425816 original size:25 final size:24
Alignment explanation
Indices: 46425740--46425813 Score: 87
Period size: 24 Copynumber: 3.0 Consensus size: 24
46425730 TTAAAAACCC
**
46425740 TAAAAACCCTAATCCTAATTTAAT
1 TAAAAACCCTAATCCTAACCTAAT
*
46425764 TAAAAACCTTAA-CCTAAACCCTAAT
1 TAAAAACCCTAATCCT-AA-CCTAAT
*
46425789 TAAATACCCTAATCCTAACCTAAT
1 TAAAAACCCTAATCCTAACCTAAT
46425813 T
1 T
46425814 TAATTAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
23 3 0.07
24 20 0.48
25 16 0.38
26 3 0.07
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.30
Consensus pattern (24 bp):
TAAAAACCCTAATCCTAACCTAAT
Found at i:46425829 original size:24 final size:24
Alignment explanation
Indices: 46425741--46425830 Score: 65
Period size: 24 Copynumber: 3.5 Consensus size: 24
46425731 TAAAAACCCT
46425741 AAAAACCCTAATCCTAATTTAATT-
1 AAAAACCCTAA-CCTAATTTAATTA
* **
46425765 AAAAACCTTAACCTAAACCCTAATTA
1 AAAAACCCTAACCT-AA-TTTAATTA
*
46425791 AATACCCTAATCCTAACCTAATTTAATTA
1 AA-A----AACCCTAACCTAATTTAATTA
46425820 AAAAACCCTAA
1 AAAAACCCTAA
46425831 AACCCTAATC
Statistics
Matches: 50, Mismatches: 8, Indels: 16
0.68 0.11 0.22
Matches are distributed among these distances:
23 3 0.06
24 19 0.38
25 5 0.10
26 2 0.04
27 1 0.02
28 1 0.02
29 8 0.16
30 2 0.04
31 9 0.18
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (24 bp):
AAAAACCCTAACCTAATTTAATTA
Found at i:46425878 original size:25 final size:24
Alignment explanation
Indices: 46425829--46425900 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
46425819 AAAAAACCCT
**
46425829 AAAACCCTAATCCTAATTTAATTA
1 AAAACCCTAATCCTAACCTAATTA
*
46425853 AAAACCTTAA-CCTAAACCCTAATTA
1 AAAACCCTAATCCT-AA-CCTAATTA
*
46425878 AATACCCTAATCCTAACCTAATT
1 AAAACCCTAATCCTAACCTAATT
46425901 TAATTAAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
23 3 0.08
24 18 0.45
25 16 0.40
26 3 0.08
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.29
Consensus pattern (24 bp):
AAAACCCTAATCCTAACCTAATTA
Found at i:46425962 original size:25 final size:25
Alignment explanation
Indices: 46425934--46426064 Score: 84
Period size: 25 Copynumber: 4.7 Consensus size: 25
46425924 AATCCTAATT
46425934 TAATTAAAAACCCTAACCTAAACCC
1 TAATTAAAAACCCTAACCTAAACCC
* *
46425959 TAATTAAATACCCTAAACCT-AACCTAATT
1 TAATTAAAAACCCT-AACCTAAACC----C
* *
46425988 TAATTAAAAACCCTAAAAACCTTAATCC
1 TAATTAAAAACCCT---AACCTAAACCC
*
46426016 TAATTTAATTAAAAACCCTAATCTAAACCC
1 T-A----ATTAAAAACCCTAACCTAAACCC
46426046 TAATTAAAATACCCTAACC
1 TAATTAAAA-ACCCTAACC
46426065 CTAACCTAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 27
0.70 0.08 0.23
Matches are distributed among these distances:
25 24 0.29
26 13 0.16
28 1 0.01
29 15 0.18
30 9 0.11
31 6 0.07
32 3 0.04
33 12 0.14
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.27
Consensus pattern (25 bp):
TAATTAAAAACCCTAACCTAAACCC
Found at i:46426110 original size:33 final size:29
Alignment explanation
Indices: 46426093--46426252 Score: 106
Period size: 29 Copynumber: 6.1 Consensus size: 29
46426083 AAACCCTAAA
**
46426093 AACCCTAATCCTAATTTAATTAAAAATTCT
1 AACCCTAA-CCTAATTTAATTAAAAACCCT
* *
46426123 AA-CCTAAACC----CTAATTAAATACCCT
1 AACCCT-AACCTAATTTAATTAAAAACCCT
46426148 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
46426177 AAACCCT----T-A---ACTTAAAAACCCT
1 -AACCCTAACCTAATTTAATTAAAAACCCT
*
46426199 AACCTTAACCTAATTTAATT--AAA----
1 AACCCTAACCTAATTTAATTAAAAACCCT
46426222 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
46426251 AA
1 AA
46426253 ACTAAGTTAA
Statistics
Matches: 99, Mismatches: 10, Indels: 43
0.65 0.07 0.28
Matches are distributed among these distances:
21 5 0.05
22 12 0.12
23 19 0.19
25 22 0.22
26 5 0.05
27 3 0.03
29 23 0.23
30 10 0.10
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.29
Consensus pattern (29 bp):
AACCCTAACCTAATTTAATTAAAAACCCT
Found at i:46426178 original size:23 final size:23
Alignment explanation
Indices: 46426148--46426262 Score: 117
Period size: 23 Copynumber: 4.8 Consensus size: 23
46426138 TAAATACCCT
46426148 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
*
46426171 AACCCTAAACCCTTAACTTAA--AAA
1 AACCCT-AA-CC-TAATTTAATTAAA
*
46426195 CCCTAACCTTAACCTAATTTAATTAAA
1 ----AACCCTAACCTAATTTAATTAAA
46426222 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
* *
46426245 AACCCTAAACTAAGTTAA
1 AACCCTAACCTAATTTAA
46426263 CAATGTTACA
Statistics
Matches: 77, Mismatches: 6, Indels: 18
0.76 0.06 0.18
Matches are distributed among these distances:
23 44 0.57
24 5 0.06
25 9 0.12
26 9 0.12
27 5 0.06
28 5 0.06
ACGTcount: A:0.47, C:0.24, G:0.01, T:0.28
Consensus pattern (23 bp):
AACCCTAACCTAATTTAATTAAA
Found at i:46426194 original size:22 final size:20
Alignment explanation
Indices: 46426162--46426207 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 20
46426152 CTAACCTAAT
46426162 TTAA-TTAAAAACCCTAAACCC
1 TTAACTTAAAAACCCT-AA-CC
46426183 TTAACTTAAAAACCCTAACC
1 TTAACTTAAAAACCCTAACC
46426203 TTAAC
1 TTAAC
46426208 CTAATTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 7 0.29
21 6 0.25
22 11 0.46
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.26
Consensus pattern (20 bp):
TTAACTTAAAAACCCTAACC
Found at i:46426208 original size:51 final size:49
Alignment explanation
Indices: 46426125--46426236 Score: 174
Period size: 51 Copynumber: 2.3 Consensus size: 49
46426115 AAAATTCTAA
*
46426125 CCTAAACCCTAATTAAATACCCTAACCCTAACCTAATTTAATTAAAAAC
1 CCTAAACCCTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAAC
*
46426174 CCTAAACCCTTAACTTAAAAACCCTAACCTTAACCTAATTTAATTAAAAAC
1 CCTAAACCC-TAA-TTAAAAACCCTAACCCTAACCTAATTTAATTAAAAAC
46426225 CCT-AA-CCTAATT
1 CCTAAACCCTAATT
46426237 TAATTAAAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
47 2 0.03
48 3 0.05
49 11 0.19
50 5 0.08
51 38 0.64
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.28
Consensus pattern (49 bp):
CCTAAACCCTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAAC
Found at i:46426483 original size:116 final size:116
Alignment explanation
Indices: 46426259--46426475 Score: 323
Period size: 116 Copynumber: 1.9 Consensus size: 116
46426249 CTAAACTAAG
* *
46426259 TTAACAATGTTACATTTACGTAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
1 TTAACAATGTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
* *
46426324 TAATTTTACATAATTTGATAGTTTTACTAACCATTAACACAATTTTTTGAC
66 TAATTTTACATAATTTGATAATTTTACTAACAATTAACACAATTTTTTGAC
* *
46426375 TTAATAATTTTACATTCACATAATGTTAGATTT-GATAAAATGTTTTGACTGGTACTAACAATTA
1 TTAACAATGTTACATTCACATAATGTTAGATTTGGA-AAAATGTTTTGACTGGTACTAACAATTA
*
46426439 ATAAATTTATAC-T-ATTTGATAATTTTAGTAACAATTA
65 AT-AATTT-TACATAATTTGATAATTTTACTAACAATTA
46426476 GTACAATTAT
Statistics
Matches: 91, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
115 2 0.02
116 80 0.88
117 6 0.07
118 3 0.03
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (116 bp):
TTAACAATGTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
TAATTTTACATAATTTGATAATTTTACTAACAATTAACACAATTTTTTGAC
Found at i:46428606 original size:892 final size:892
Alignment explanation
Indices: 46426883--46428666 Score: 2941
Period size: 892 Copynumber: 2.0 Consensus size: 892
46426873 CCCACAGTCG
46426883 CAAGTCCTATTTCGCAAATGTACACGATATTGCCCGCCAACAACACCTTGGTGCGGTCTGTCAAA
1 CAAGTCCTATTTCGCAAATGTACACGATATTGCCCGCCAACAACACCTTGGTGCGGTCTGTCAAA
* * *
46426948 CTCTGTCACGTGAAACCATAAATTGTCTCGATCGTGACACACTGTGTGCATGGTGTTTGCCCTCG
66 CTCTGTCACGCGAAACCATAAACTGTCTCGATCATGACACACTGTGTGCATGGTGTTTGCCCTCG
*
46427013 CCTTGGCCTTGTTAATTTCTTGAACTACCTTACTGCACCATACATGGCCCCCCTGCATTTGGCCT
131 CCTTGGCCTTGTTAATTTCTTGAACTACCTTACTGCACCATACATGGCCCCCCTGCATCTGGCCT
* * *
46427078 ACATAACTTGCCGCTCGCTTTGGAAATAGCGCCGCTAAACAGAACTATGTCTCTCGCACAACCGA
196 ACATAACTTGCCGCTCGCTTTAGAAATAGCGCCGCCAAACAGAAATATGTCTCTCGCACAACCGA
* * *
46427143 TGTTATCGGTAGATGGCGCGTTCCTTTAAGAACAGAATTTATGCATTCTGCCAGGTTTGACGTCA
261 TGTTATCGGTAGATGACGCGTTCCTTTAAGAACAGAATTTATGCATTCAGCCAGGTTCGACGTCA
* * *
46427208 TATGGTCATATCGTAGGCCGCCGTCGTATGATTGTGCCCACTGTTCGAAACGTATGTTACAAAGG
326 TATGGCCATATCGTAGGCCGCCGTCGTATGATTGTGCCCACTATTCGAAACATATGTTACAAAGG
* * * *
46427273 TAGTCCGCCCCTTCTCCGTTTTGGGATCGTAAAATTGCCAACATCTCGTTAAAATGATCTGTATT
391 TAGTCCGCCCCTTCTCCGTTTTGGGAACGTAAAATGGCCAACATCTCGTGAAAACGATCTGTATT
46427338 TATTTCATACTCTACCAATATAAGATCATAGCGAATAATTTATACCACTTCTACCAATAAAACTA
456 TATTTCATACTCTACCAATATAAGATCATAGCGAATAATTTATACCACTTCTACCAATAAAACTA
*
46427403 ATTCAAATTGACAAACGAAATAACACAGATATAGACTAAATACCCATGTTGGTCACTTGTCGTCG
521 ATTCAAATTGACAAACGAAATAACACAGATATAGACTAAATACCCAGGTTGGTCACTTGTCGTCG
46427468 TTCGCTCTTAGATGGATATTGCCTGTAGTAGTTCGAAGCAACGTATCTTAGGCAATATCTATGGT
586 TTCGCTCTTAGATGGATATTGCCTGTAGTAGTTCGAAGCAACGTATCTTAGGCAATATCTATGGT
* *
46427533 GCGCGCGCTGCCATAAGCTTCCCTGTCGATCAAATGCAGCTAGTATACTGGCGGCCCGATCTGAA
651 GCGCGCACTGCCATAAGCTTCCCTGTCGATCAAATGCAGCTAGTATACCGGCGGCCCGATCTGAA
* *
46427598 ATAACACAGTTATCAGGTTGGGGGCACACATGCCTCCTTAACCTAGAGAGAAAGAAATCTCAGTC
716 ATAAAACAGTTATCAGGTTGGGGGCACACATGCCTCCTTAACCTAGAGAGAAAGAAATCACAGTC
**
46427663 ATCAGACGACTCCCCCGGTGTTATTGCAAATGCAATTGGAAAAATTCTCCCACCGCCATCCTGTG
781 ATCAGACGACTCCCCCGGTGTTATTGCAAATGCAATTCAAAAAATTCTCCCACCGCCATCCTGTG
* ** * *
46427728 CCACTACAAGCAATATCCGATGAGTATGGCTACCGCATATAAAGGTA
846 CCACTACAAGCAATAGCCGATGAGTATACCTACCGAACATAAAGGTA
*
46427775 CAAGTCCTATTTCGCAAGTGTACACGATATTGCCCGCCAACAACACCTTGGTGCGGTCTGTCAAA
1 CAAGTCCTATTTCGCAAATGTACACGATATTGCCCGCCAACAACACCTTGGTGCGGTCTGTCAAA
* *
46427840 CTCTGTCACGCGAAATCATAAACTGTCTCGATCATGACCCACTGTGTGCATGGTGTTTGCCCTCG
66 CTCTGTCACGCGAAACCATAAACTGTCTCGATCATGACACACTGTGTGCATGGTGTTTGCCCTCG
*
46427905 CCTTGGCCTTGTTAATTTCTTGAACTACCTTACTGCACCATACATGGCCTCCCTGCATCTGGCCT
131 CCTTGGCCTTGTTAATTTCTTGAACTACCTTACTGCACCATACATGGCCCCCCTGCATCTGGCCT
* * * *
46427970 GCATAACTTGCTGCTCGCTTTAGAAATAGCGTCGCCAAA-AGAAAATATGTCTCTCGCAGAACCG
196 ACATAACTTGCCGCTCGCTTTAGAAATAGCGCCGCCAAACAG-AAATATGTCTCTCGCACAACCG
* * *
46428034 ATGTTATTGGTAGATGACGCGTTCCTTTGAA-AATAGAATTTATGCATTCAGCCAGGTTCGATGT
260 ATGTTATCGGTAGATGACGCGTTCCTTT-AAGAACAGAATTTATGCATTCAGCCAGGTTCGACGT
** * *
46428098 CATATGGCCATATCGTAGGCCGTTGTCGTATGCTTGTGCCCACTATTCGAAACATATGTTGCAAA
324 CATATGGCCATATCGTAGGCCGCCGTCGTATGATTGTGCCCACTATTCGAAACATATGTTACAAA
* * * *
46428163 GGTAGTCTGCCCCTTCTGCGTTATT-TGAACGTAAAATGGCCAACATCTCGTGAAAACGATTTGT
389 GGTAGTCCGCCCCTTCTCCGTT-TTGGGAACGTAAAATGGCCAACATCTCGTGAAAACGATCTGT
46428227 ATTTATTTCATACTCTACCAATATAAGATCATAGCGAATAATTTATACCACTTCTACCAATAAAA
453 ATTTATTTCATACTCTACCAATATAAGATCATAGCGAATAATTTATACCACTTCTACCAATAAAA
*
46428292 CTAATTCAAATTGACAAACGAAATAACACAGATATAGACTAAATACCCAGGTTGGTTACTTGTCG
518 CTAATTCAAATTGACAAACGAAATAACACAGATATAGACTAAATACCCAGGTTGGTCACTTGTCG
* *
46428357 TTGTTCGCTCTTAGATGGATATTGCCTGTAGTAGTTCGAAGCAACGTGTCTTAGGCAATATCTAT
583 TCGTTCGCTCTTAGATGGATATTGCCTGTAGTAGTTCGAAGCAACGTATCTTAGGCAATATCTAT
* * ** *
46428422 GGTGTGTGCACTGCCATAAGCTTTTCTGTCGATCAAATGCAGCTAGTATACCGGC-GCCATGATC
648 GGTGCGCGCACTGCCATAAGCTTCCCTGTCGATCAAATGCAGCTAGTATACCGGCGGCC-CGATC
*
46428486 TGAAATAAAACA-TATATCAGGTTGGGGGCACACATGCCTCCTTAACCTAGAGAGAAATAAATCA
712 TGAAATAAAACAGT-TATCAGGTTGGGGGCACACATGCCTCCTTAACCTAGAGAGAAAGAAATCA
46428550 CAGTCATCAGACGACTCCCCCGGTGTTATTGCAAATGCAA-TCAAAAGAATTCTCCCACCGCCAT
776 CAGTCATCAGACGACTCCCCCGGTGTTATTGCAAATGCAATTCAAAA-AATTCTCCCACCGCCAT
* *
46428614 CCTGTGTCACTGCAAGCAATAGCCGATGAGTATACCTACCGAACATAAAGGTA
840 CCTGTGCCACTACAAGCAATAGCCGATGAGTATACCTACCGAACATAAAGGTA
46428667 TCGTCAATTT
Statistics
Matches: 827, Mismatches: 59, Indels: 12
0.92 0.07 0.01
Matches are distributed among these distances:
891 10 0.01
892 813 0.98
893 4 0.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (892 bp):
CAAGTCCTATTTCGCAAATGTACACGATATTGCCCGCCAACAACACCTTGGTGCGGTCTGTCAAA
CTCTGTCACGCGAAACCATAAACTGTCTCGATCATGACACACTGTGTGCATGGTGTTTGCCCTCG
CCTTGGCCTTGTTAATTTCTTGAACTACCTTACTGCACCATACATGGCCCCCCTGCATCTGGCCT
ACATAACTTGCCGCTCGCTTTAGAAATAGCGCCGCCAAACAGAAATATGTCTCTCGCACAACCGA
TGTTATCGGTAGATGACGCGTTCCTTTAAGAACAGAATTTATGCATTCAGCCAGGTTCGACGTCA
TATGGCCATATCGTAGGCCGCCGTCGTATGATTGTGCCCACTATTCGAAACATATGTTACAAAGG
TAGTCCGCCCCTTCTCCGTTTTGGGAACGTAAAATGGCCAACATCTCGTGAAAACGATCTGTATT
TATTTCATACTCTACCAATATAAGATCATAGCGAATAATTTATACCACTTCTACCAATAAAACTA
ATTCAAATTGACAAACGAAATAACACAGATATAGACTAAATACCCAGGTTGGTCACTTGTCGTCG
TTCGCTCTTAGATGGATATTGCCTGTAGTAGTTCGAAGCAACGTATCTTAGGCAATATCTATGGT
GCGCGCACTGCCATAAGCTTCCCTGTCGATCAAATGCAGCTAGTATACCGGCGGCCCGATCTGAA
ATAAAACAGTTATCAGGTTGGGGGCACACATGCCTCCTTAACCTAGAGAGAAAGAAATCACAGTC
ATCAGACGACTCCCCCGGTGTTATTGCAAATGCAATTCAAAAAATTCTCCCACCGCCATCCTGTG
CCACTACAAGCAATAGCCGATGAGTATACCTACCGAACATAAAGGTA
Found at i:46430628 original size:125 final size:125
Alignment explanation
Indices: 46430406--46430774 Score: 562
Period size: 124 Copynumber: 3.0 Consensus size: 125
46430396 CCCAAACATG
* *
46430406 CTACTGTAGCAAAATCGCGTCCACGACGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* * *
46430471 TAGAAGCGATTTTACACTATTTGCTCAAAAACGTCAACTAAAAATTATTTTTTCCGGGAC
66 TAGAAGCTATTTTATACTATTTGCTCAAAAACGTCAACTAAAAATTATTTATTCCGGGAC
* *
46430531 CTACTGTAGCAAAAGCGCGTCCATGAGGGCGCGATATCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* * * *
46430596 TACAAGCTATTTTATACTATTTGCTCAAAAACGTCAA-AAAAAATTATTTCTTCCGTGAC
66 TAGAAGCTATTTTATACTATTTGCTCAAAAACGTCAACTAAAAATTATTTATTCCGGGAC
* *
46430655 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCATAAATTCTTCTCAAATATCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* * **
46430720 TAGAAG-TGATTTTATACTATTTGATCAGAAACGTCAACTCGAAATTATTTATTCC
66 TAGAAGCT-ATTTTATACTATTTGCTCAAAAACGTCAACTAAAAATTATTTATTCC
46430775 ATGACCTAAA
Statistics
Matches: 221, Mismatches: 21, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
123 1 0.00
124 112 0.51
125 108 0.49
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCTATTTTATACTATTTGCTCAAAAACGTCAACTAAAAATTATTTATTCCGGGAC
Found at i:46433277 original size:39 final size:39
Alignment explanation
Indices: 46433223--46433302 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
46433213 GTATAATTTA
46433223 GAACTTTTGTTTGCATTCCTCATCCTCATCTTAGCTTTG
1 GAACTTTTGTTTGCATTCCTCATCCTCATCTTAGCTTTG
*
46433262 GAACTTTTGTTTGCATTCCTCATCCTTATCTTAGCTTTG
1 GAACTTTTGTTTGCATTCCTCATCCTCATCTTAGCTTTG
46433301 GA
1 GA
46433303 CTTCTCATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.16, C:0.24, G:0.14, T:0.46
Consensus pattern (39 bp):
GAACTTTTGTTTGCATTCCTCATCCTCATCTTAGCTTTG
Found at i:46435227 original size:22 final size:22
Alignment explanation
Indices: 46435202--46435248 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
46435192 TCAGCTCTAT
*
46435202 CTTCCTTTCCATATCTCTTAAC
1 CTTCCTTTACATATCTCTTAAC
*
46435224 CTTCCTTTATATATCTCTTAAC
1 CTTCCTTTACATATCTCTTAAC
46435246 CTT
1 CTT
46435249 GGCTCTTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.19, C:0.32, G:0.00, T:0.49
Consensus pattern (22 bp):
CTTCCTTTACATATCTCTTAAC
Found at i:46439922 original size:31 final size:31
Alignment explanation
Indices: 46439887--46439951 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
46439877 TTAATCATTG
*
46439887 AACTTGACACTTG-TTCTTATATTAGGGCCTA
1 AACTTGACACTTGTTTC-AATATTAGGGCCTA
* *
46439918 AACTTGACAGTTGTTTCAATATTGGGGCCTA
1 AACTTGACACTTGTTTCAATATTAGGGCCTA
46439949 AAC
1 AAC
46439952 CCTAAGGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 27 0.90
32 3 0.10
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Consensus pattern (31 bp):
AACTTGACACTTGTTTCAATATTAGGGCCTA
Found at i:46440457 original size:20 final size:20
Alignment explanation
Indices: 46440432--46440471 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
46440422 CGTAAAATAA
*
46440432 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
46440452 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
46440472 GGAAAATATT
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:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:46440461 original size:34 final size:35
Alignment explanation
Indices: 46440417--46440483 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
46440407 CAGTAAAATA
*
46440417 TTTTCCGTAAAATAATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATAATTTACTGGAAAATATTTTAC
* *
46440451 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATAATTTACTGGAAAATATTTT
46440484 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATAATTTACTGGAAAATATTTTAC
Found at i:46440548 original size:32 final size:31
Alignment explanation
Indices: 46440464--46440549 Score: 91
Period size: 33 Copynumber: 2.6 Consensus size: 31
46440454 TCTGTAAAAT
* **
46440464 GATTTACTGGAAAATATTTTCTGGTGTTTGATT
1 GATTT-CT-GAAAATATTTTCTGCTGTTTGACA
*
46440497 GAATTTGTGTAAAATATTTTCTGCTGTTTGACA
1 G-ATTTCTG-AAAATATTTTCTGCTGTTTGACA
46440530 GATTTCCTGAAAATATTTTC
1 GATTT-CTGAAAATATTTTC
46440550 CGAAAAAGTT
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
32 16 0.36
33 25 0.56
34 4 0.09
ACGTcount: A:0.27, C:0.09, G:0.17, T:0.47
Consensus pattern (31 bp):
GATTTCTGAAAATATTTTCTGCTGTTTGACA
Found at i:46443510 original size:3 final size:3
Alignment explanation
Indices: 46443502--46443530 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
46443492 GAGCACACGC
46443502 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
46443531 ACAATATCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:46447573 original size:20 final size:21
Alignment explanation
Indices: 46447548--46447596 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
46447538 CGCCCCTAAT
*
46447548 TTATAAAAAAT-CATAAAAAA
1 TTATAAAAAATACAAAAAAAA
* *
46447568 TTATAAAATATAGAAAAAAAA
1 TTATAAAAAATACAAAAAAAA
46447589 TTATAAAA
1 TTATAAAA
46447597 TTCTATAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (21 bp):
TTATAAAAAATACAAAAAAAA
Found at i:46447596 original size:10 final size:10
Alignment explanation
Indices: 46447548--46447596 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
46447538 CGCCCCTAAT
46447548 TTATAAAAAA
1 TTATAAAAAA
*
46447558 TCATAAAAAA
1 TTATAAAAAA
*
46447568 TTATAAAATA
1 TTATAAAAAA
* *
46447578 TAGAAAAAAAA
1 T-TATAAAAAA
46447589 TTATAAAA
1 TTATAAAA
46447597 TTCTATAAAG
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
10 23 0.77
11 7 0.23
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:46447626 original size:41 final size:42
Alignment explanation
Indices: 46447572--46447666 Score: 99
Period size: 41 Copynumber: 2.3 Consensus size: 42
46447562 AAAAAATTAT
* * *
46447572 AAAATATAGAAAAAAAAT-TATAA-AATTCTATAAAGTCGT-AAG
1 AAAAT-TATAAAAAAAATGTA-AAGAAATCTA-AAAGTCGTAAAA
*
46447614 AAAATTAT-AAAAAAATGTAAAGAAATCTAAAATTCGTAAAA
1 AAAATTATAAAAAAAATGTAAAGAAATCTAAAAGTCGTAAAA
46447655 AAAATTATAAAA
1 AAAATTATAAAA
46447667 GTTATCGTAC
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
40 17 0.38
41 20 0.44
42 8 0.18
ACGTcount: A:0.63, C:0.04, G:0.07, T:0.25
Consensus pattern (42 bp):
AAAATTATAAAAAAAATGTAAAGAAATCTAAAAGTCGTAAAA
Found at i:46448162 original size:90 final size:85
Alignment explanation
Indices: 46448021--46448254 Score: 265
Period size: 90 Copynumber: 2.6 Consensus size: 85
46448011 TAACGGTTAA
* * *
46448021 AGGGCCTTTTTGATACATTTTGACAGTTTAAGTACCCAATTGAGTGTAAAAAAAAAGCAGGGGCC
1 AGGGCCTTTTTGATGCATTTTGAAAGTTCAAGTA-CCAATTGAGTG-AAAAAAAAA--A-GGGCC
* *
46448086 TAATTACTTATCT-TGAAAAAGTTTG
61 TAATGACTT-TCTCTGAAAAAATTTG
* *
46448111 AGGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCTAATTGAGTG-AAAAAAAAAGGGCTTTAT
1 AGGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACC-AATTGAGTGAAAAAAAAAAGGGCCTAAT
* *
46448175 GGCTTTTTCTGAAAAAATTTG
65 GACTTTCTCTGAAAAAATTTG
*
46448196 AGGGCCTTTTTTTTATGCATTTTGAAAGTTCAAGTATCCAATTGAGTGCAAAAAAAAAA
1 AGGGCC--TTTTTGATGCATTTTGAAAGTTCAAGTA-CCAATTGAGTG-AAAAAAAAAA
46448255 TTAATTGTTT
Statistics
Matches: 127, Mismatches: 10, Indels: 15
0.84 0.07 0.10
Matches are distributed among these distances:
84 2 0.02
85 27 0.21
86 1 0.01
87 36 0.28
88 10 0.08
89 11 0.09
90 40 0.31
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.34
Consensus pattern (85 bp):
AGGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCAATTGAGTGAAAAAAAAAAGGGCCTAATG
ACTTTCTCTGAAAAAATTTG
Found at i:46450113 original size:246 final size:247
Alignment explanation
Indices: 46449390--46450269 Score: 1241
Period size: 248 Copynumber: 3.6 Consensus size: 247
46449380 AAAAAATAAT
* * *
46449390 AATAACATACAATAGATAATGAACT-TATGGTTTGAAACTAGTTAACAATAACACATGAAATATG
1 AATAACATACAATAGATAATGAAATGTATGGTTTGAAACTAATTAATAATAACACATGAAATATG
*** * * * *
46449454 TACGATGTTAAAATTGAAAATTTTAGGTTAAAAATGGTTATCATGGTGTTGGCATCAATCTTGAG
66 TACGATGTTAAAA-TGAAAAAAATAGATTAAAATTGTTTATCATGGTGTTGTCATCAATCTTGAG
*
46449519 TGGATGTCGAGTTAACTTATGACACCAACTCAATCAAATACATTAATATATACTAGAATCCCTAT
130 TGGATGTCGAGTTAACTTATGACACCAACTCAATCAAATACATTAATATATACTAGAATTCCTAT
46449584 CACATGCGTATGAGCGT-GAAAACAAAAATTTGTGAACACAAATGTGTGTTTAAA
195 CACATGCGTATGAGCGTGGAAAA-AAAAATTT-TGAACACAAATGTGTGTTTAAA
* * *
46449638 AATAGCATACAATAGATAATGAAACGTATGGTTTGAAAATAATTAATAATAACACATGAAATATG
1 AATAACATACAATAGATAATGAAATGTATGGTTTGAAACTAATTAATAATAACACATGAAATATG
46449703 TACGATGTTAAAATGAAAAAAATAGATTAAAATTGTTTATCATGGTGTTGTCATCAATCTTGAGT
66 TACGATGTTAAAATGAAAAAAATAGATTAAAATTGTTTATCATGGTGTTGTCATCAATCTTGAGT
* *
46449768 GGATGTCGAGTTAAGTTATGACACCAACTCAATCAAATACATTAATATATACTAGAA-TCTTTAT
131 GGATGTCGAGTTAACTTATGACACCAACTCAATCAAATACATTAATATATACTAGAATTC-CTAT
* * *
46449832 CACATGCGTATGTGGGTGGAAACAACAAATTTTGAACACAAATGTGTGTTTAAA
195 CACATGCGTATGAGCGTGGAAA-AAAAAATTTTGAACACAAATGTGTGTTTAAA
* *
46449886 AATAACATACAATAGATAATGAAATGTATGGTTTGAAACTAATTAATAATAACAAATGAAAAATG
1 AATAACATACAATAGATAATGAAATGTATGGTTTGAAACTAATTAATAATAACACATGAAATATG
* * * *
46449951 TATGATGTTAAAATGAAAAAAA-A-ATTTAAATTTTTTATCATGATGTTGTCATCAATCTTGAGT
66 TACGATGTTAAAATGAAAAAAATAGATTAAAATTGTTTATCATGGTGTTGTCATCAATCTTGAGT
* ** * *
46450014 TGATGTCGAGTTAACTTATGTTACCAACTCAATCAAACATATTAATATATACTAGAATTCCTATC
131 GGATGTCGAGTTAACTTATGACACCAACTCAATCAAATACATTAATATATACTAGAATTCCTATC
* * * * * * *
46450079 ACACGCATATGCGTGTGGATATAAAAAATTTTGAACACAAATCTGTGTTCAAA
196 ACATGCGTATGAGCGTGGA-AAAAAAAATTTTGAACACAAATGTGTGTTTAAA
* * * *
46450132 TATAACATAAAATAGATAACGAAATATATGGTTTGAAACTAATTAATAATAACACATGAAATATG
1 AATAACATACAATAGATAATGAAATGTATGGTTTGAAACTAATTAATAATAACACATGAAATATG
** * * *
46450197 TATAATGTTAAAAT-AAAAAAATAGATTAAAATTGTTTAACATGGTTTTGTCATCAATCTTAAGT
66 TACGATGTTAAAATGAAAAAAATAGATTAAAATTGTTTATCATGGTGTTGTCATCAATCTTGAGT
*
46450261 TGATGTCGA
131 GGATGTCGA
46450270 TTATACACAC
Statistics
Matches: 568, Mismatches: 56, Indels: 17
0.89 0.09 0.03
Matches are distributed among these distances:
245 7 0.01
246 208 0.37
247 48 0.08
248 244 0.43
249 60 0.11
250 1 0.00
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (247 bp):
AATAACATACAATAGATAATGAAATGTATGGTTTGAAACTAATTAATAATAACACATGAAATATG
TACGATGTTAAAATGAAAAAAATAGATTAAAATTGTTTATCATGGTGTTGTCATCAATCTTGAGT
GGATGTCGAGTTAACTTATGACACCAACTCAATCAAATACATTAATATATACTAGAATTCCTATC
ACATGCGTATGAGCGTGGAAAAAAAAATTTTGAACACAAATGTGTGTTTAAA
Found at i:46452261 original size:8 final size:8
Alignment explanation
Indices: 46452248--46452281 Score: 68
Period size: 8 Copynumber: 4.2 Consensus size: 8
46452238 TCCACCTACA
46452248 TTAACACT
1 TTAACACT
46452256 TTAACACT
1 TTAACACT
46452264 TTAACACT
1 TTAACACT
46452272 TTAACACT
1 TTAACACT
46452280 TT
1 TT
46452282 CACAAGCCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (8 bp):
TTAACACT
Found at i:46457392 original size:125 final size:125
Alignment explanation
Indices: 46457170--46457421 Score: 468
Period size: 125 Copynumber: 2.0 Consensus size: 125
46457160 TTTTAAACTA
*
46457170 ATCTATAACACCTCGTAATCCAACCCGATCACTGGTATAGTTGAAATGTGATTCTGTTTCCTGAT
1 ATCTATAACACCTCGTAATCCAACCCGATCACTGGTATAGTTGAAATGTGATTCTGTTTCCTGAG
*
46457235 ATATGGGTTTGAGATTGGCACAAGGAATGGGTCGTTGATAACCATGTAGGGTTGTAGGAG
66 ATATGGGTTTGAGATTGGCACAAGGAATGGGTCGTTGATAACCATGCAGGGTTGTAGGAG
*
46457295 ATCTATAACACCTCGTAATCCAACCCGATCACTGGTATAGTTGAAATGTGATTCTGTTTCTTGAG
1 ATCTATAACACCTCGTAATCCAACCCGATCACTGGTATAGTTGAAATGTGATTCTGTTTCCTGAG
*
46457360 ATATGGGTTTGAGGTTGGCACAAGGAATGGGTCGTTGATAACCATGCAGGGTTGTAGGAG
66 ATATGGGTTTGAGATTGGCACAAGGAATGGGTCGTTGATAACCATGCAGGGTTGTAGGAG
46457420 AT
1 AT
46457422 GTGTATAAGT
Statistics
Matches: 123, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
125 123 1.00
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (125 bp):
ATCTATAACACCTCGTAATCCAACCCGATCACTGGTATAGTTGAAATGTGATTCTGTTTCCTGAG
ATATGGGTTTGAGATTGGCACAAGGAATGGGTCGTTGATAACCATGCAGGGTTGTAGGAG
Found at i:46462296 original size:26 final size:26
Alignment explanation
Indices: 46462107--46462297 Score: 159
Period size: 26 Copynumber: 7.6 Consensus size: 26
46462097 AAGCTGATCT
*
46462107 GAGCAATATAACGGGAAGCTCACAAA
1 GAGCCATATAACGGGAAGCTCACAAA
*
46462133 GAGCC-TATAACGGGTAGCTC-CAAA
1 GAGCCATATAACGGGAAGCTCACAAA
* * *
46462157 GAGCAAT-TAACGGGAAGCAC-CAGA
1 GAGCCATATAACGGGAAGCTCACAAA
* * * * *
46462181 TAGCCATATAACAGGCAGTTCA-AGCA
1 GAGCCATATAACGGGAAGCTCACA-AA
*
46462207 -AG-CA-CTAACGGGAAGCTCACAAA
1 GAGCCATATAACGGGAAGCTCACAAA
*
46462230 GAGCC-TTTAATCGGGAAGCTCACAAA
1 GAGCCATATAA-CGGGAAGCTCACAAA
* *
46462256 GAGCC-TTTAATCGGGAAGCTCACGAA
1 GAGCCATATAA-CGGGAAGCTCACAAA
46462282 GAGCCATATAACGGGA
1 GAGCCATATAACGGGA
46462298 CGCTTATAAG
Statistics
Matches: 134, Mismatches: 21, Indels: 20
0.77 0.12 0.11
Matches are distributed among these distances:
23 12 0.09
24 32 0.24
25 31 0.23
26 55 0.41
27 4 0.03
ACGTcount: A:0.38, C:0.23, G:0.25, T:0.15
Consensus pattern (26 bp):
GAGCCATATAACGGGAAGCTCACAAA
Found at i:46462297 original size:52 final size:49
Alignment explanation
Indices: 46462115--46462297 Score: 160
Period size: 49 Copynumber: 3.7 Consensus size: 49
46462105 CTGAGCAATA
* *
46462115 TAACGGGAAGCTCACAAAGAGCCTATAACGGGTAGCTC-CAAAGAGCAAT
1 TAACGGGAAGCTCACAAAGAGCCTATAACGGGAAGCTCACAAAGAGC-CT
* * * * * * *
46462164 TAACGGGAAGCAC-CAGATAGCCATATAACAGGCAGTTCA-AGCA-AGCAC-
1 TAACGGGAAGCTCACAAAGAGCC-TATAACGGGAAGCTCACA-AAGAGC-CT
*
46462212 TAACGGGAAGCTCACAAAGAGCCTTTAATCGGGAAGCTCACAAAGAGCCTT
1 TAACGGGAAGCTCACAAAGAGCCTATAA-CGGGAAGCTCACAAAGAGCC-T
*
46462263 TAATCGGGAAGCTCACGAAGAGCCATATAACGGGA
1 TAA-CGGGAAGCTCACAAAGAGCC-TATAACGGGA
46462298 CGCTTATAAG
Statistics
Matches: 105, Mismatches: 18, Indels: 19
0.74 0.13 0.13
Matches are distributed among these distances:
48 23 0.22
49 46 0.44
50 5 0.05
51 3 0.03
52 24 0.23
53 4 0.04
ACGTcount: A:0.38, C:0.23, G:0.25, T:0.15
Consensus pattern (49 bp):
TAACGGGAAGCTCACAAAGAGCCTATAACGGGAAGCTCACAAAGAGCCT
Done.