Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 122 of 311
Found at i:40624692 original size:120 final size:122
Alignment explanation
Indices: 40624434--40624732 Score: 330
Period size: 120 Copynumber: 2.5 Consensus size: 122
40624424 AAATCACGTA
* ** * * *
40624434 CCTTCGGAATTTAA-CCGGATATAGCTC-CTC-GTTCAAATGCCTTCGGGACATGGCCCGG-TTA
1 CCTTCGGAACTTAACCCGGATATAG-TCACTCAGCACAAATGCCTTCGGGACTTAGCCCGGAATA
* *
40624495 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATG
65 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCACAAAGG
* *
40624553 CCTTCGGGACTTAACCCGGA-ATTAGT-ATCTCA-CACAAATGCCTTCGGGACTTAACCCGGAAT
1 CCTTCGGAACTTAACCCGGATA-TAGTCA-CTCAGCACAAATGCCTTCGGGACTTAGCCCGGAAT
* ** *
40624615 -TAGTATCTCGCACAAATGCCTTCGGGACTTAACTTGGAATTAGTATCTCGCACAAAGG
64 ATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCACAAAGG
** * *
40624673 CCTTC-GAATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 CCTTCGGAA-CTTAACCCGGATATAGTCACTCAGCACAAATGCCTTCGGGACTTAGCCCGGA
40624733 CATCATTCAA
Statistics
Matches: 150, Mismatches: 20, Indels: 19
0.79 0.11 0.10
Matches are distributed among these distances:
119 16 0.11
120 125 0.83
121 9 0.06
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (122 bp):
CCTTCGGAACTTAACCCGGATATAGTCACTCAGCACAAATGCCTTCGGGACTTAGCCCGGAATAT
AGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCACAAAGG
Found at i:40638842 original size:40 final size:40
Alignment explanation
Indices: 40638640--40638835 Score: 297
Period size: 40 Copynumber: 4.9 Consensus size: 40
40638630 CCTTTGGAAT
* *
40638640 TTAG-CCGGATATAG-CAACTCGCACGAATGCCTTCGGGAC
1 TTAGCCCGGATATAGTC-ACTAGCACAAATGCCTTCGGGAC
*
40638679 TTAGCCCGGACATAGTCACTAGCACAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGAC
** *
40638719 TTAGCCTAGATATAGTCACTAGCGCAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGAC
*
40638759 TTAGCCTGGATATAGTCACTAGCACAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGAC
*
40638799 TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGG
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGG
40638836 ATCTTAGTCC
Statistics
Matches: 144, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
39 4 0.03
40 139 0.97
41 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (40 bp):
TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGAC
Found at i:40659258 original size:10 final size:10
Alignment explanation
Indices: 40659243--40659278 Score: 63
Period size: 10 Copynumber: 3.5 Consensus size: 10
40659233 TGCTTTTCTA
40659243 CATGATATGC
1 CATGATATGC
40659253 CATGATATGC
1 CATGATATGC
40659263 ACATGATATGC
1 -CATGATATGC
40659274 CATGA
1 CATGA
40659279 CATATTCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 15 0.60
11 10 0.40
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (10 bp):
CATGATATGC
Found at i:40664674 original size:22 final size:22
Alignment explanation
Indices: 40664646--40664688 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
40664636 AGGAGGGTAG
40664646 AGTTGTAACATCCTGATTTTCA
1 AGTTGTAACATCCTGATTTTCA
40664668 AGTTGTAACATCCTGATTTTC
1 AGTTGTAACATCCTGATTTTC
40664689 GGGTTTTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.42
Consensus pattern (22 bp):
AGTTGTAACATCCTGATTTTCA
Found at i:40666481 original size:10 final size:10
Alignment explanation
Indices: 40666466--40666504 Score: 69
Period size: 10 Copynumber: 3.8 Consensus size: 10
40666456 TGCTTTTCTA
40666466 CATGATATGC
1 CATGATATGC
40666476 CATGATATGC
1 CATGATATGC
40666486 ACATGATATGC
1 -CATGATATGC
40666497 CATGATAT
1 CATGATAT
40666505 ATTCACATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 18 0.64
11 10 0.36
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (10 bp):
CATGATATGC
Found at i:40666490 original size:21 final size:21
Alignment explanation
Indices: 40666465--40666504 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
40666455 CTGCTTTTCT
40666465 ACATGATATGCCATGATATGC
1 ACATGATATGCCATGATATGC
40666486 ACATGATATGCCATGATAT
1 ACATGATATGCCATGATAT
40666505 ATTCACATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (21 bp):
ACATGATATGCCATGATATGC
Found at i:40676250 original size:6 final size:6
Alignment explanation
Indices: 40676239--40676269 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
40676229 AAATGAATTA
40676239 ATATAC ATATAC ATATAC ATATAC ATATAC A
1 ATATAC ATATAC ATATAC ATATAC ATATAC A
40676270 AATGCCGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (6 bp):
ATATAC
Found at i:40677504 original size:45 final size:43
Alignment explanation
Indices: 40677398--40677512 Score: 122
Period size: 45 Copynumber: 2.6 Consensus size: 43
40677388 GATGTCGATG
* * *
40677398 TCCCAGACACGGTCTTACACGTAACCATATTTATCGATGCCAACG
1 TCCCAGACATGGTCTTACACG-AA-AATATTTATCGATGCCAACA
* * *
40677443 TCCTATACATGATCTTACACGAAAATACTTATATCGATGCCAACA
1 TCCCAGACATGGTCTTACACGAAAATA-TT-TATCGATGCCAACA
* *
40677488 TCCCAGACGTGGTCTTACATGAAAA
1 TCCCAGACATGGTCTTACACGAAAA
40677513 CACATATCGG
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
43 3 0.05
44 4 0.07
45 50 0.88
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.26
Consensus pattern (43 bp):
TCCCAGACATGGTCTTACACGAAAATATTTATCGATGCCAACA
Found at i:40682991 original size:25 final size:25
Alignment explanation
Indices: 40682957--40683026 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
40682947 CTCTTTTAAT
* *
40682957 AACTAGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
* *
40682982 AACTGGGGCAAATCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
40683007 AACTGGGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
40683027 AGCACTTCAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.29
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:40683261 original size:27 final size:27
Alignment explanation
Indices: 40683231--40683389 Score: 210
Period size: 27 Copynumber: 5.9 Consensus size: 27
40683221 GGCAAAATGA
* * * *
40683231 TAATTTTACCCCACAAGAGTATGTCGG
1 TAATTCTACCCTACAAGGGTATTTCGG
* *
40683258 TAATTCTACCCTACAGGGGTATTTCGT
1 TAATTCTACCCTACAAGGGTATTTCGG
*
40683285 TATTTCTACCCTACAAGGGTATTTCGG
1 TAATTCTACCCTACAAGGGTATTTCGG
* * *
40683312 TAATTCTACCCTATAGGGGTATTTCAG
1 TAATTCTACCCTACAAGGGTATTTCGG
*
40683339 TAATTCTACCCTACAGGGGTATTTCGG
1 TAATTCTACCCTACAAGGGTATTTCGG
*
40683366 TAATGCTACCCTACAAGGGTATTT
1 TAATTCTACCCTACAAGGGTATTT
40683390 TGATATTTTA
Statistics
Matches: 115, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 115 1.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (27 bp):
TAATTCTACCCTACAAGGGTATTTCGG
Found at i:40683468 original size:54 final size:54
Alignment explanation
Indices: 40683379--40683506 Score: 143
Period size: 54 Copynumber: 2.4 Consensus size: 54
40683369 TGCTACCCTA
* *
40683379 CAAGGGTATTTTGAT-ATTTTACAAATCGAGAGTATTTCGATAA-TTTCACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAATCGAGAGTATTTCGATAATTTTC-CAAAC
* ** * * * *
40683432 CAGGGGTATTTTGGTAATTTTACTGATCGAGGGTATTTTGGTAATTTTCTAAAC
1 CAAGGGTATTTTGGTAATTTTACAAATCGAGAGTATTTCGATAATTTTCCAAAC
*
40683486 CAAGGGTATTTTAGTAATTTT
1 CAAGGGTATTTTGGTAATTTT
40683507 GTAAATTGAG
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
53 13 0.21
54 45 0.73
55 4 0.06
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (54 bp):
CAAGGGTATTTTGGTAATTTTACAAATCGAGAGTATTTCGATAATTTTCCAAAC
Found at i:40683557 original size:81 final size:81
Alignment explanation
Indices: 40683472--40683706 Score: 222
Period size: 81 Copynumber: 2.9 Consensus size: 81
40683462 GGGTATTTTG
* * *** *
40683472 GTAATTTTCTAAACCAAGGGTATTTTAGTAATTTTGTAAATTGAGGGTAAAACGATAATTCTGTA
1 GTAATTCTATAAACCAAGGGTAAAATAGTAATTTTGTAAATCGAGGGTAAAACGATAATTCTGTA
* *
40683537 AATTGAGGGTAAAGCA
66 AATCGAGGATAAAGCA
* * * * * *
40683553 GTAATTCTATAAATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTTTGTA
1 GTAATTCTATAAACCAAGGGTAAAATAGTAATTTTGTAAATCGAGGGTAAAACGATAATTCTGTA
**
40683618 AATCGAGGATAAAATA
66 AATCGAGGATAAAGCA
* * * * * * * *
40683634 GGT-ATTCTATAAATCGAGGATAAAAT-GATTATTCTATAAATCGAGGGTAAAATGGTAATTCTG
1 -GTAATTCTATAAACCAAGGGTAAAATAG-TAATTTTGTAAATCGAGGGTAAAACGATAATTCTG
40683697 TAAATCGAGG
64 TAAATCGAGG
40683707 GTACTTTGGT
Statistics
Matches: 131, Mismatches: 21, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
80 1 0.01
81 128 0.98
82 2 0.02
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.33
Consensus pattern (81 bp):
GTAATTCTATAAACCAAGGGTAAAATAGTAATTTTGTAAATCGAGGGTAAAACGATAATTCTGTA
AATCGAGGATAAAGCA
Found at i:40683720 original size:27 final size:27
Alignment explanation
Indices: 40683499--40683709 Score: 253
Period size: 27 Copynumber: 7.8 Consensus size: 27
40683489 GGGTATTTTA
* * *
40683499 GTAATTTTGTAAATTGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAATG
* * ***
40683526 ATAATTCTGTAAATTGAGGGTAAAGCA
1 GTAATTCTGTAAATCGAGGGTAAAATG
*
40683553 GTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
*
40683580 GTAATTTTGTAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
* *
40683607 GTAATTTTGTAAATCGAGGATAAAATAG
1 GTAATTCTGTAAATCGAGGGTAAAAT-G
* *
40683635 GT-ATTCTATAAATCGAGGATAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
* * *
40683661 ATTATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
40683688 GTAATTCTGTAAATCGAGGGTA
1 GTAATTCTGTAAATCGAGGGTA
40683710 CTTTGGTAAT
Statistics
Matches: 162, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
26 2 0.01
27 157 0.97
28 3 0.02
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAATG
Found at i:40683728 original size:27 final size:27
Alignment explanation
Indices: 40683381--40683748 Score: 125
Period size: 27 Copynumber: 13.7 Consensus size: 27
40683371 CTACCCTACA
* *
40683381 AGGGTATTTTGAT-ATTTTACAAATCG
1 AGGGTAATTTGGTAATTTTACAAATCG
* * *
40683407 AGAGT-ATTTCGATAATTTCACAAATC-
1 AGGGTAATTT-GGTAATTTTACAAATCG
* **
40683433 AGGGGTATTTTGGTAATTTTACTGATCG
1 A-GGGTAATTTGGTAATTTTACAAATCG
* * *
40683461 AGGGTATTTTGGTAATTTT-CTAAACCA
1 AGGGTAATTTGGTAATTTTAC-AAATCG
* * ** *
40683488 AGGGTATTTTAGTAATTTTGTAAATTG
1 AGGGTAATTTGGTAATTTTACAAATCG
*** * * ** *
40683515 AGGGTAAAACGATAATTCTGTAAATTG
1 AGGGTAATTTGGTAATTTTACAAATCG
**** * *
40683542 AGGGTAAAGCAGTAATTCTATAAATCG
1 AGGGTAATTTGGTAATTTTACAAATCG
** **
40683569 AGGGTAAAATGGTAATTTTGTAAATCG
1 AGGGTAATTTGGTAATTTTACAAATCG
** **
40683596 AGGGTAAAATGGTAATTTTGTAAATCG
1 AGGGTAATTTGGTAATTTTACAAATCG
* * * * *
40683623 AGGATAAAATAGGT-ATTCTATAAATCG
1 AGGGT-AATTTGGTAATTTTACAAATCG
* ** * * * *
40683650 AGGATAAAATGATTATTCTATAAATCG
1 AGGGTAATTTGGTAATTTTACAAATCG
** * **
40683677 AGGGTAAAATGGTAATTCTGTAAATCG
1 AGGGTAATTTGGTAATTTTACAAATCG
* *
40683704 AGGGTACTTTGGTAATTTTACAAATTG
1 AGGGTAATTTGGTAATTTTACAAATCG
* * *
40683731 AGGGCATTTTAGTAATTT
1 AGGGTAATTTGGTAATTT
40683749 GGTAAACTCA
Statistics
Matches: 276, Mismatches: 57, Indels: 17
0.79 0.16 0.05
Matches are distributed among these distances:
25 3 0.01
26 14 0.05
27 249 0.90
28 10 0.04
ACGTcount: A:0.35, C:0.07, G:0.21, T:0.36
Consensus pattern (27 bp):
AGGGTAATTTGGTAATTTTACAAATCG
Found at i:40683734 original size:54 final size:54
Alignment explanation
Indices: 40683499--40683734 Score: 249
Period size: 54 Copynumber: 4.4 Consensus size: 54
40683489 GGGTATTTTA
* * * * * ***
40683499 GTAATTTTGTAAATTGAGGGTAAAACGATAATTCTGTAAATTGAGGGTAAAGCA
1 GTAATTTTATAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAATTG
* * *
40683553 GTAATTCTATAAATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAATG
1 GTAATTTTATAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAATTG
* * * * *
40683607 GTAATTTTGTAAATCGAGGATAAAATAGGT-ATTCTATAAATCGAGGATAAAATG
1 GTAATTTTATAAATCGAGGGTAAAAT-GGTAATTCTGTAAATCGAGGGTAAATTG
* * * **
40683661 ATTATTCTATAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTACTTTG
1 GTAATTTTATAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAATTG
* *
40683715 GTAATTTTACAAATTGAGGG
1 GTAATTTTATAAATCGAGGG
40683735 CATTTTAGTA
Statistics
Matches: 149, Mismatches: 31, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
53 3 0.02
54 143 0.96
55 3 0.02
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.33
Consensus pattern (54 bp):
GTAATTTTATAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAATTG
Found at i:40686147 original size:24 final size:25
Alignment explanation
Indices: 40686120--40686170 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
40686110 GCCTAGCCTC
40686120 TTTTAAT-AACAGGGGCAAAGCCCT
1 TTTTAATAAACAGGGGCAAAGCCCT
* **
40686144 TTTTGATAAACTTGGGCAAAGCCCT
1 TTTTAATAAACAGGGGCAAAGCCCT
40686169 TT
1 TT
40686171 ACGGTAAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 6 0.26
25 17 0.74
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (25 bp):
TTTTAATAAACAGGGGCAAAGCCCT
Found at i:40686165 original size:25 final size:25
Alignment explanation
Indices: 40686131--40686196 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
40686121 TTTAATAACA
*
40686131 GGGGCAAAGCCCTTTTTGATAAACT
1 GGGGCAAAGCCCTTTTCGATAAACT
* * *
40686156 TGGGCAAAGCCCTTTACGGTAAACT
1 GGGGCAAAGCCCTTTTCGATAAACT
*
40686181 GGGGCATAGCCCTTTT
1 GGGGCAAAGCCCTTTT
40686197 AGCACTTCCT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (25 bp):
GGGGCAAAGCCCTTTTCGATAAACT
Found at i:40686428 original size:27 final size:27
Alignment explanation
Indices: 40686398--40686533 Score: 146
Period size: 27 Copynumber: 5.0 Consensus size: 27
40686388 GGGGCAAAAT
* * *
40686398 GGTAATTTTACCCTACAAGGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
**
40686425 GGTAATTCTACCCTATGGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
** * * *
40686452 GGTGTTTTTACCCTACAAGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
40686479 AGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
40686506 GATAATTCTACCCTAGAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
40686533 G
1 G
40686534 ATATTTTACA
Statistics
Matches: 88, Mismatches: 21, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 88 1.00
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:40686582 original size:27 final size:26
Alignment explanation
Indices: 40686522--40686584 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 26
40686512 TCTACCCTAG
*
40686522 AGGGGTATTTCGATATTTTACAAATT
1 AGGGGTATTTCGATATTTCACAAATT
* * *
40686548 -GAGAGTATTTCTATAATTTCATAAATT
1 AG-GGGTATTTCGAT-ATTTCACAAATT
40686575 AGGGGTATTT
1 AGGGGTATTT
40686585 TGGTAATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
25 1 0.03
26 10 0.34
27 17 0.59
28 1 0.03
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.43
Consensus pattern (26 bp):
AGGGGTATTTCGATATTTCACAAATT
Found at i:40686591 original size:27 final size:27
Alignment explanation
Indices: 40686575--40686719 Score: 211
Period size: 27 Copynumber: 5.4 Consensus size: 27
40686565 TTCATAAATT
*
40686575 AGGGGTATTTTGGTAATTTTACAAGCC
1 AGGGGTATTTTGGTAATTTTACAAACC
40686602 AGGGGTATTTTGGTAATTTTACAAACC
1 AGGGGTATTTTGGTAATTTTACAAACC
*
40686629 AGGGGTATTTTAGTAATTTTACAAACC
1 AGGGGTATTTTGGTAATTTTACAAACC
* *
40686656 AGGGGTATTTTGGTAATTTTACTAATC
1 AGGGGTATTTTGGTAATTTTACAAACC
**
40686683 -GAGGGTATTTTGGTAATTTTGTAAACC
1 AG-GGGTATTTTGGTAATTTTACAAACC
*
40686710 AAGGGTATTT
1 AGGGGTATTT
40686720 CAGTAATTCT
Statistics
Matches: 106, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
26 1 0.01
27 105 0.99
ACGTcount: A:0.28, C:0.09, G:0.23, T:0.39
Consensus pattern (27 bp):
AGGGGTATTTTGGTAATTTTACAAACC
Found at i:40686660 original size:81 final size:81
Alignment explanation
Indices: 40686575--40686754 Score: 236
Period size: 81 Copynumber: 2.2 Consensus size: 81
40686565 TTCATAAATT
*
40686575 AGGGGTATTTTGGTAATTTTAC-AAGCCAGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTT
1 AGGGGTATTTTGGTAATTTTACTAAGCCA-GGGTATTTTGGTAATTTTACAAACCAAGGGTATTT
* *
40686639 TAGTAATTTTACAAACC
65 CAGTAATTCTACAAACC
* * **
40686656 AGGGGTATTTTGGTAATTTTACTAATCGAGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTC
1 AGGGGTATTTTGGTAATTTTACTAAGCCAGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTC
* *
40686721 AGTAATTCTATAAATC
66 AGTAATTCTACAAACC
* **
40686737 AAGGGTAAATTGGTAATT
1 AGGGGTATTTTGGTAATT
40686755 CTGTAAATCG
Statistics
Matches: 86, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
81 82 0.95
82 4 0.05
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (81 bp):
AGGGGTATTTTGGTAATTTTACTAAGCCAGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTC
AGTAATTCTACAAACC
Found at i:40686725 original size:27 final size:27
Alignment explanation
Indices: 40686577--40686754 Score: 203
Period size: 27 Copynumber: 6.6 Consensus size: 27
40686567 CATAAATTAG
* *
40686577 GGGTATTTTGGTAATTTTACAAGCCAG
1 GGGTATTTTGGTAATTTTACAAACCAA
*
40686604 GGGTATTTTGGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAA
* *
40686631 GGGTATTTTAGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAA
* * *
40686658 GGGTATTTTGGTAATTTTACTAATCGA
1 GGGTATTTTGGTAATTTTACAAACCAA
**
40686685 GGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAA
** * * *
40686712 GGGTATTTCAGTAATTCTATAAATCAA
1 GGGTATTTTGGTAATTTTACAAACCAA
**
40686739 GGGTAAATTGGTAATT
1 GGGTATTTTGGTAATT
40686755 CTGTAAATCG
Statistics
Matches: 130, Mismatches: 21, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 130 1.00
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.39
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACCAA
Found at i:40686764 original size:81 final size:81
Alignment explanation
Indices: 40686679--40686946 Score: 270
Period size: 81 Copynumber: 3.3 Consensus size: 81
40686669 TAATTTTACT
* * **
40686679 AATCGAGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTCAGTAATTCTATAAATCAAGGGTA
1 AATCGAGGGTAATTTGGTAATTTTATAAACCAAGGGTAAATCAGTAATTCTATAAATCAAGGGTA
**
40686744 AATTGGTAATTCTGTA
66 AAACGGTAATTCTGTA
** * * * * * *
40686760 AATCGAGGGTAAAATGGTAATTCTATAAATCGAA-GGTAAAACGGTAATTCTATAAATCGAGGAT
1 AATCGAGGGTAATTTGGTAATTTTATAAA-CCAAGGGTAAATCAGTAATTCTATAAATCAAGGGT
* *
40686824 AAAACGATAATTCTATA
65 AAAACGGTAATTCTGTA
** * * * * *
40686841 AATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAAT-GGTAATTCTATAAATCGAGGGT
1 AATCGAGGGTAATTTGGTAATTTTATAAACCAAGGGT-AAATCAGTAATTCTATAAATCAAGGGT
*
40686905 AAAACAGTAATTCTGTA
65 AAAACGGTAATTCTGTA
* *
40686922 AATCGATGGTACTTTGGTAATTTTA
1 AATCGAGGGTAATTTGGTAATTTTA
40686947 CAAATTGAAG
Statistics
Matches: 155, Mismatches: 29, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
80 1 0.01
81 148 0.95
82 6 0.04
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (81 bp):
AATCGAGGGTAATTTGGTAATTTTATAAACCAAGGGTAAATCAGTAATTCTATAAATCAAGGGTA
AAACGGTAATTCTGTA
Found at i:40686943 original size:27 final size:27
Alignment explanation
Indices: 40686722--40686932 Score: 314
Period size: 27 Copynumber: 7.8 Consensus size: 27
40686712 GGGTATTTCA
* *
40686722 GTAATTCTATAAATCAAGGGTAAATTG
1 GTAATTCTATAAATCGAGGGTAAAATG
*
40686749 GTAATTCTGTAAATCGAGGGTAAAATG
1 GTAATTCTATAAATCGAGGGTAAAATG
* *
40686776 GTAATTCTATAAATCGAAGGTAAAACG
1 GTAATTCTATAAATCGAGGGTAAAATG
* *
40686803 GTAATTCTATAAATCGAGGATAAAACG
1 GTAATTCTATAAATCGAGGGTAAAATG
*
40686830 ATAATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTATAAATCGAGGGTAAAATG
40686857 GTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTATAAATCGAGGGTAAAATG
**
40686884 GTAATTCTATAAATCGAGGGTAAAACA
1 GTAATTCTATAAATCGAGGGTAAAATG
* *
40686911 GTAATTCTGTAAATCGATGGTA
1 GTAATTCTATAAATCGAGGGTA
40686933 CTTTGGTAAT
Statistics
Matches: 168, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 168 1.00
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.29
Consensus pattern (27 bp):
GTAATTCTATAAATCGAGGGTAAAATG
Found at i:40686969 original size:81 final size:80
Alignment explanation
Indices: 40686719--40686970 Score: 299
Period size: 81 Copynumber: 3.1 Consensus size: 80
40686709 CAAGGGTATT
* **
40686719 TCAGTAATTCTATAAATCAAGGGTAAATTGGTAATTCTGTAAATCGAGGGTAAAATGGTAATTCT
1 TCAGTAATTCTATAAATCGAGGGTAAA-ACGTAATTCTGTAAATCGAGGGTAAAATGGTAATTCT
40686784 ATAAATCGAAGGTAAA
65 ATAAATCGAAGGTAAA
* * * *
40686800 ACGGTAATTCTATAAATCGAGGATAAAACGATAATTCTATAAATCGAGGGTAAAATGGTAATTCT
1 TCAGTAATTCTATAAATCGAGGGTAAAACG-TAATTCTGTAAATCGAGGGTAAAATGGTAATTCT
*
40686865 ATAAATCGAGGGTAAAA
65 ATAAATCGAAGGT-AAA
* * *** *
40686882 T-GGTAATTCTATAAATCGAGGGTAAAACAGTAATTCTGTAAATCGATGGTACTTTGGTAATTTT
1 TCAGTAATTCTATAAATCGAGGGTAAAAC-GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCT
* * **
40686946 ACAAATTGAAGGTATT
65 ATAAATCGAAGGTAAA
40686962 TCAGTAATT
1 TCAGTAATT
40686971 TGGTAAACTA
Statistics
Matches: 145, Mismatches: 22, Indels: 8
0.83 0.13 0.05
Matches are distributed among these distances:
80 3 0.02
81 138 0.95
82 4 0.03
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.32
Consensus pattern (80 bp):
TCAGTAATTCTATAAATCGAGGGTAAAACGTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTA
TAAATCGAAGGTAAA
Found at i:40689367 original size:24 final size:25
Alignment explanation
Indices: 40689340--40689417 Score: 97
Period size: 25 Copynumber: 3.2 Consensus size: 25
40689330 GCCTAGCCTC
40689340 TTTTAAT-AACTGGGGCAAAGCCCT
1 TTTTAATAAACTGGGGCAAAGCCCT
* *
40689364 TTTTGATAAACTAGGGCAAAGCCCT
1 TTTTAATAAACTGGGGCAAAGCCCT
** *
40689389 TTTTGGTAAACTGGGGCATAG-CCT
1 TTTTAATAAACTGGGGCAAAGCCCT
40689413 TTTTA
1 TTTTA
40689418 GCACTTCCTC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
24 13 0.28
25 34 0.72
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (25 bp):
TTTTAATAAACTGGGGCAAAGCCCT
Found at i:40689375 original size:25 final size:25
Alignment explanation
Indices: 40689347--40689416 Score: 106
Period size: 25 Copynumber: 2.8 Consensus size: 25
40689337 CTCTTTTAAT
40689347 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTTGATA
* *
40689372 AACTAGGGCAAAGCCCTTTTTGGTA
1 AACTGGGGCAAAGCCCTTTTTGATA
*
40689397 AACTGGGGCATAG-CCTTTTT
1 AACTGGGGCAAAGCCCTTTTT
40689417 AGCACTTCCT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
24 7 0.17
25 34 0.83
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTTGATA
Found at i:40689657 original size:27 final size:27
Alignment explanation
Indices: 40689619--40689752 Score: 178
Period size: 27 Copynumber: 5.0 Consensus size: 27
40689609 GGGGCAAAAT
* * *
40689619 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
40689646 GGTAATTATACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
40689673 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
40689700 GGTGATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
40689727 AGTAATTCTACCCTACAAGGGTATTT
1 GGTAATTCTACCCTACAAGGGTATTT
40689753 TGATATTTTA
Statistics
Matches: 92, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 92 1.00
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:40689896 original size:54 final size:54
Alignment explanation
Indices: 40689798--40689950 Score: 175
Period size: 54 Copynumber: 2.8 Consensus size: 54
40689788 CATAAATCAG
* * * *
40689798 GGGTATTTT-GATAATTTTACAAGCTAGAGGTGTTTTGGTAATTTTACA-AACCA
1 GGGTATTTTAG-TAATTTTACAAACCAGGGGTATTTTGGTAATTTTACAGAACCA
* *
40689851 GGGATATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTACAGATCGA
1 GGG-TATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTACAGAACCA
** * **
40689906 GGGTATTTTAGTAATTTTGTAAACCAAGGGTATTTCAGTAATTTT
1 GGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTT
40689951 GTAAATCGAG
Statistics
Matches: 86, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
53 3 0.03
54 76 0.88
55 7 0.08
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.41
Consensus pattern (54 bp):
GGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTACAGAACCA
Found at i:40689923 original size:27 final size:26
Alignment explanation
Indices: 40689798--40689950 Score: 155
Period size: 27 Copynumber: 5.7 Consensus size: 26
40689788 CATAAATCAG
* *
40689798 GGGTATTTT-GATAATTTTACAAGCTA
1 GGGTATTTTAG-TAATTTTACAAACCA
* *
40689824 GAGGTGTTTTGGTAATTTTACAAACCA
1 G-GGTATTTTAGTAATTTTACAAACCA
40689851 GGGATATTTTAGTAATTTTACAAACCA
1 GGG-TATTTTAGTAATTTTACAAACCA
* * *
40689878 GGGGTATTTTGGTAATTTTACAGATCGA
1 -GGGTATTTTAGTAATTTTACA-AACCA
**
40689906 GGGTATTTTAGTAATTTTGTAAACCAA
1 GGGTATTTTAGTAATTTTACAAACC-A
*
40689933 GGGTATTTCAGTAATTTT
1 GGGTATTTTAGTAATTTT
40689951 GTAAATCGAG
Statistics
Matches: 107, Mismatches: 14, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
26 5 0.05
27 95 0.89
28 7 0.07
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.41
Consensus pattern (26 bp):
GGGTATTTTAGTAATTTTACAAACCA
Found at i:40689955 original size:27 final size:27
Alignment explanation
Indices: 40689742--40689950 Score: 151
Period size: 27 Copynumber: 7.8 Consensus size: 27
40689732 TTCTACCCTA
*
40689742 CAAGGGTATTTT-G-ATATTTTACAAAT
1 CAAGGGTATTTTAGTA-ATTTTACAAAC
* * * * * *
40689768 CGAGAGTA-TTTCGATAATTTCATAAAT
1 CAAGGGTATTTTAG-TAATTTTACAAAC
* *
40689795 CAGGGGTATTTT-GATAATTTTAC-AAG
1 CAAGGGTATTTTAG-TAATTTTACAAAC
* * *
40689821 CTAGAGGTGTTTTGGTAATTTTACAAAC
1 CAAG-GGTATTTTAGTAATTTTACAAAC
40689849 C-AGGGATATTTTAGTAATTTTACAAAC
1 CAAGGG-TATTTTAGTAATTTTACAAAC
* * * *
40689876 CAGGGGTATTTTGGTAATTTTACAGAT
1 CAAGGGTATTTTAGTAATTTTACAAAC
* **
40689903 CGAGGGTATTTTAGTAATTTTGTAAAC
1 CAAGGGTATTTTAGTAATTTTACAAAC
*
40689930 CAAGGGTATTTCAGTAATTTT
1 CAAGGGTATTTTAGTAATTTT
40689951 GTAAATCGAG
Statistics
Matches: 145, Mismatches: 29, Indels: 17
0.76 0.15 0.09
Matches are distributed among these distances:
25 3 0.02
26 13 0.09
27 118 0.81
28 11 0.08
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.40
Consensus pattern (27 bp):
CAAGGGTATTTTAGTAATTTTACAAAC
Found at i:40689959 original size:54 final size:54
Alignment explanation
Indices: 40689718--40689964 Score: 170
Period size: 54 Copynumber: 4.6 Consensus size: 54
40689708 TACCTTACAG
* ** * * *
40689718 GGGTATTTCAGTAATTCTAC-CCTACAAGGGTATTTT-G-ATATTTTACAAATCGA
1 GGGTATTTCAGTAATTTTACAAAT-CGAGGGTATTTTAGTA-ATTTTACAAACCAA
* * * * *
40689771 GAGTATTTC-GATAATTTCATAAATC-AGGGGTATTTT-GATAATTTTACAAGCTAGA
1 GGGTATTTCAG-TAATTTTACAAATCGA-GGGTATTTTAG-TAATTTTACAAACCA-A
* * *
40689826 GGTGT-TTT-GGTAATTTTACAAA-CCAGGGATATTTTAGTAATTTTACAAACCAG
1 GG-GTATTTCAGTAATTTTACAAATCGAGGG-TATTTTAGTAATTTTACAAACCAA
** * **
40689879 GGGTATTTTGGTAATTTTACAGATCGAGGGTATTTTAGTAATTTTGTAAACCAA
1 GGGTATTTCAGTAATTTTACAAATCGAGGGTATTTTAGTAATTTTACAAACCAA
**
40689933 GGGTATTTCAGTAATTTTGTAAATCGAGGGTA
1 GGGTATTTCAGTAATTTTACAAATCGAGGGTA
40689965 AAATGGTAAT
Statistics
Matches: 154, Mismatches: 26, Indels: 27
0.74 0.13 0.13
Matches are distributed among these distances:
52 4 0.03
53 34 0.22
54 101 0.66
55 13 0.08
56 2 0.01
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.38
Consensus pattern (54 bp):
GGGTATTTCAGTAATTTTACAAATCGAGGGTATTTTAGTAATTTTACAAACCAA
Found at i:40689962 original size:27 final size:27
Alignment explanation
Indices: 40689901--40689964 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
40689891 AATTTTACAG
*
40689901 ATCGAGGGTATTTTAGTAATTTTGTAA
1 ATCGAGGGTATTTCAGTAATTTTGTAA
* *
40689928 ACCAAGGGTATTTCAGTAATTTTGTAA
1 ATCGAGGGTATTTCAGTAATTTTGTAA
40689955 ATCGAGGGTA
1 ATCGAGGGTA
40689965 AAATGGTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (27 bp):
ATCGAGGGTATTTCAGTAATTTTGTAA
Found at i:40689964 original size:81 final size:80
Alignment explanation
Indices: 40689757--40689962 Score: 218
Period size: 81 Copynumber: 2.5 Consensus size: 80
40689747 GTATTTTGAT
* * *
40689757 ATTTTACAAATCGAGAGTATTTC-GATAATTTCATAAATCAGGGGTATTTTGATAATTTTACAAG
1 ATTTTACAAA-CCAGGGTATTTCAG-TAATTTTATAAATCAGGGGTATTTTGATAATTTTACAAG
* * *
40689821 CTAGAGGTGTTTTGGTA
64 CGAGAGGTATTTTAGTA
* * * * *
40689838 ATTTTACAAACCAGGGATATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTACAGAT
1 ATTTTACAAACCAGGG-TATTTCAGTAATTTTATAAATCAGGGGTATTTTGATAATTTTACA-AG
40689903 CGAG-GGTATTTTAGTA
64 CGAGAGGTATTTTAGTA
** *
40689919 ATTTTGTAAACCAAGGGTATTTCAGTAATTTTGTAAATCGAGGG
1 ATTTTACAAACC-AGGGTATTTCAGTAATTTTATAAATC-AGGG
40689963 TAAAATGGTA
Statistics
Matches: 103, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
80 4 0.04
81 86 0.83
82 13 0.13
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.38
Consensus pattern (80 bp):
ATTTTACAAACCAGGGTATTTCAGTAATTTTATAAATCAGGGGTATTTTGATAATTTTACAAGCG
AGAGGTATTTTAGTA
Found at i:40689973 original size:27 final size:27
Alignment explanation
Indices: 40689943--40690126 Score: 242
Period size: 27 Copynumber: 6.8 Consensus size: 27
40689933 GGGTATTTCA
* *
40689943 GTAATTTTGTAAATCGAGGGTAAAATG
1 GTAATTCTATAAATCGAGGGTAAAATG
*
40689970 GTAATTCTATAAATCAAGGGTAAAATG
1 GTAATTCTATAAATCGAGGGTAAAATG
* * * *
40689997 ATAATTCTGTAAATCGAGGATAAAACG
1 GTAATTCTATAAATCGAGGGTAAAATG
* *
40690024 ATAATTCTATAAACCGAGGGTAAAATG
1 GTAATTCTATAAATCGAGGGTAAAATG
40690051 GTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTATAAATCGAGGGTAAAATG
* *
40690078 GTAATTCTATAAATCAAGGGTAAAATA
1 GTAATTCTATAAATCGAGGGTAAAATG
* * *
40690105 ATAATTTTGTAAATCGAGGGTA
1 GTAATTCTATAAATCGAGGGTA
40690127 CTTTCTTAAT
Statistics
Matches: 137, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 137 1.00
ACGTcount: A:0.42, C:0.08, G:0.20, T:0.30
Consensus pattern (27 bp):
GTAATTCTATAAATCGAGGGTAAAATG
Found at i:40689974 original size:54 final size:54
Alignment explanation
Indices: 40689916--40690126 Score: 255
Period size: 54 Copynumber: 3.9 Consensus size: 54
40689906 GGGTATTTTA
* * **
40689916 GTAATTTTGTAAACCAAGGGT-ATTTCAGTAATTTTGTAAATCGAGGGTAAAATG
1 GTAATTCTATAAACCAAGGGTAAAAT-AGTAATTTTGTAAATCGAGGGTAAAATG
* * * *
40689970 GTAATTCTATAAATCAAGGGTAAAAT-GATAATTCTGTAAATCGAGGATAAAACG
1 GTAATTCTATAAACCAAGGGTAAAATAG-TAATTTTGTAAATCGAGGGTAAAATG
* * * * *
40690024 ATAATTCTATAAACCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTATAAACCAAGGGTAAAATAGTAATTTTGTAAATCGAGGGTAAAATG
* *
40690078 GTAATTCTATAAATCAAGGGTAAAATAATAATTTTGTAAATCGAGGGTA
1 GTAATTCTATAAACCAAGGGTAAAATAGTAATTTTGTAAATCGAGGGTA
40690127 CTTTCTTAAT
Statistics
Matches: 133, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
53 1 0.01
54 129 0.97
55 3 0.02
ACGTcount: A:0.41, C:0.08, G:0.20, T:0.31
Consensus pattern (54 bp):
GTAATTCTATAAACCAAGGGTAAAATAGTAATTTTGTAAATCGAGGGTAAAATG
Found at i:40689990 original size:81 final size:80
Alignment explanation
Indices: 40689916--40690126 Score: 255
Period size: 81 Copynumber: 2.6 Consensus size: 80
40689906 GGGTATTTTA
* * **
40689916 GTAATTTTGTAAACCAAGGGTATTTCAGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATA
1 GTAATTCTGTAAATCAAGGGTAAATCAGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATA
*
40689981 AATCAAGGGTAAAAT
66 AATCGAGGGTAAAAT
* * * * * *
40689996 GATAATTCTGTAAATCGAGGATAAAAC-GATAATTCTATAAACCGAGGGTAAAATGGTAATTCTA
1 G-TAATTCTGTAAATCAAGGGTAAATCAG-TAATTTTGTAAATCGAGGGTAAAATGGTAATTCTA
40690060 TAAATCGAGGGTAAAAT
64 TAAATCGAGGGTAAAAT
* *
40690077 GGTAATTCTATAAATCAAGGGTAAAAT-AATAATTTTGTAAATCGAGGGTA
1 -GTAATTCTGTAAATCAAGGGT-AAATCAGTAATTTTGTAAATCGAGGGTA
40690127 CTTTCTTAAT
Statistics
Matches: 107, Mismatches: 19, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
80 2 0.02
81 101 0.94
82 4 0.04
ACGTcount: A:0.41, C:0.08, G:0.20, T:0.31
Consensus pattern (80 bp):
GTAATTCTGTAAATCAAGGGTAAATCAGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATA
AATCGAGGGTAAAAT
Found at i:40690151 original size:81 final size:81
Alignment explanation
Indices: 40689944--40690126 Score: 276
Period size: 81 Copynumber: 2.3 Consensus size: 81
40689934 GGTATTTCAG
* *
40689944 TAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCAAGGGTAAAATGATAATTCTGTAA
1 TAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATGATAATTCTATAA
* *
40690009 ATCGAGGATAAAACGA
66 ATCAAGGATAAAACAA
* * * *
40690025 TAATTCTATAAACCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTATAA
1 TAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATGATAATTCTATAA
* *
40690090 ATCAAGGGTAAAATAA
66 ATCAAGGATAAAACAA
40690106 TAATTTTGTAAATCGAGGGTA
1 TAATTTTGTAAATCGAGGGTA
40690127 CTTTCTTAAT
Statistics
Matches: 89, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
81 89 1.00
ACGTcount: A:0.43, C:0.08, G:0.20, T:0.30
Consensus pattern (81 bp):
TAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATGATAATTCTATAA
ATCAAGGATAAAACAA
Found at i:40694023 original size:16 final size:16
Alignment explanation
Indices: 40694004--40694035 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40693994 AATTATTTTA
40694004 TTACAAAATTTCACTT
1 TTACAAAATTTCACTT
*
40694020 TTACATAATTTCACTT
1 TTACAAAATTTCACTT
40694036 ACTCCATTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (16 bp):
TTACAAAATTTCACTT
Found at i:40694343 original size:50 final size:50
Alignment explanation
Indices: 40694235--40694629 Score: 296
Period size: 50 Copynumber: 7.9 Consensus size: 50
40694225 ACTGAAGCTC
* * * *** * *
40694235 TCTGGTACGCAAAATAG-CTGCACTTAGTACTACACATACGACCTATCAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACTTAACAA
* * * * *
40694284 TCTAGTACACGTACTAGCCTGCACTTAGAACTACACACGTGACTTAACCA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACTTAACAA
* * * * *
40694334 TCTGATACACGTAGTAGCCTACACTTAGTACTACACACGTGA-TCGAAGTTAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACT-TAA--CAA
* * * * * * *
40694386 T-GGGTACGCATAATAGCCTGCACTTAGTACTACACATGCGACCTATCAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACTTAACAA
** * * *
40694435 TCTGGTACAGGTAGTAGCCTGCACTTAGTACTACACACGTGAATTAGCCA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACTTAACAA
* * * * * * * *
40694485 TCTGATACACTTAGTAGCCTACAATTAGAACTACACACATGA-TCGAAGTTAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACT-TAA--CAA
* * * * * *
40694537 -CGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACTTAACAA
*
40694586 TCTGGTACACATAGTAGCCTGCACTTAGCACTACACACGTGACT
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACT
40694630 CACAACGGAT
Statistics
Matches: 261, Mismatches: 74, Indels: 21
0.73 0.21 0.06
Matches are distributed among these distances:
49 19 0.07
50 174 0.67
51 65 0.25
52 3 0.01
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (50 bp):
TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACTTAACAA
Found at i:40694528 original size:151 final size:151
Alignment explanation
Indices: 40694238--40694627 Score: 629
Period size: 151 Copynumber: 2.6 Consensus size: 151
40694228 GAAGCTCTCT
* * * *
40694238 GGTACGCAAAATAG-CTGCACTTAGTACTACACATACGACCTATCAATCTAGTACACGTACTAGC
1 GGTACGCATAATAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTAGC
* * *
40694302 CTGCACTTAGAACTACACACGTGACTTAACCATCTGATACACGTAGTAGCCTACACTTAGTACTA
66 CTGCACTTAGAACTACACACGTGAATTAACCATCTGATACACGTAGTAGCCTACAATTAGAACTA
* *
40694367 CACACGTGATCGAAGTTAATG
131 CACACATGATCGAAGTTAACG
*
40694388 GGTACGCATAATAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACAGGTAGTAGC
1 GGTACGCATAATAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTAGC
* * *
40694453 CTGCACTTAGTACTACACACGTGAATTAGCCATCTGATACACTTAGTAGCCTACAATTAGAACTA
66 CTGCACTTAGAACTACACACGTGAATTAACCATCTGATACACGTAGTAGCCTACAATTAGAACTA
40694518 CACACATGATCGAAGTTAACG
131 CACACATGATCGAAGTTAACG
* *
40694539 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACATAGTAGC
1 GGTACGCATAATAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTAGC
*
40694604 CTGCACTTAGCACTACACACGTGA
66 CTGCACTTAGAACTACACACGTGA
40694628 CTCACAACGG
Statistics
Matches: 222, Mismatches: 17, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
150 13 0.06
151 209 0.94
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (151 bp):
GGTACGCATAATAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTAGC
CTGCACTTAGAACTACACACGTGAATTAACCATCTGATACACGTAGTAGCCTACAATTAGAACTA
CACACATGATCGAAGTTAACG
Found at i:40700528 original size:29 final size:27
Alignment explanation
Indices: 40700510--40700579 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
40700500 ATATTAAGTC
40700510 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
40700537 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
40700565 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
40700580 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:40700573 original size:28 final size:28
Alignment explanation
Indices: 40700510--40700607 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
40700500 ATATTAAGTC
*
40700510 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
40700537 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
40700565 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
40700594 CGCACACTTAGTGC
1 CGCACACTTAGTGC
40700608 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:40708483 original size:29 final size:27
Alignment explanation
Indices: 40708465--40708534 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
40708455 ATATTAAGTC
40708465 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
40708492 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
40708520 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
40708535 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:40708528 original size:28 final size:28
Alignment explanation
Indices: 40708465--40708562 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
40708455 ATATTAAGTC
*
40708465 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
40708492 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
40708520 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
40708549 CGCACACTTAGTGC
1 CGCACACTTAGTGC
40708563 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:40712259 original size:42 final size:42
Alignment explanation
Indices: 40712212--40712303 Score: 166
Period size: 42 Copynumber: 2.2 Consensus size: 42
40712202 TGGCCCTTAG
*
40712212 GCCCATTTCAATATCACATGTAATGGCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGGCAATGAATGTATACAA
*
40712254 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATACAA
1 GCCCATTTCAATATCACATGTAATGGCAATGAATGTATACAA
40712296 GCCCATTT
1 GCCCATTT
40712304 GGGGAGACTA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGTAATGGCAATGAATGTATACAA
Found at i:40713322 original size:27 final size:28
Alignment explanation
Indices: 40713291--40713359 Score: 83
Period size: 27 Copynumber: 2.6 Consensus size: 28
40713281 TACGGAACAT
*
40713291 AAGGGCATATT-C-GTCATTTTACCATAC
1 AAGGGC-TATTACGGTCACTTTACCATAC
*
40713318 AAGGG-TATTACGGTCACTTTACCCTAC
1 AAGGGCTATTACGGTCACTTTACCATAC
40713345 AAGGGCT-TTACGGTC
1 AAGGGCTATTACGGTC
40713360 TTTTTACCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
25 4 0.11
26 1 0.03
27 31 0.84
28 1 0.03
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.30
Consensus pattern (28 bp):
AAGGGCTATTACGGTCACTTTACCATAC
Found at i:40713365 original size:27 final size:27
Alignment explanation
Indices: 40713303--40713367 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
40713293 GGGCATATTC
40713303 GTCATTTTACCATACAAGGGTATTACG
1 GTCATTTTACCATACAAGGGTATTACG
* *
40713330 GTCACTTTACCCTACAAGGGCT-TTACG
1 GTCATTTTACCATACAAGGG-TATTACG
*
40713357 GTCTTTTTACC
1 GTCATTTTACC
40713368 TATTAGGGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 32 0.97
28 1 0.03
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCATACAAGGGTATTACG
Found at i:40713451 original size:27 final size:27
Alignment explanation
Indices: 40713421--40713506 Score: 95
Period size: 27 Copynumber: 3.1 Consensus size: 27
40713411 GTAAATCTAC
40713421 AAACCAAGGGTATTTC-AGTAATTTTGT
1 AAACCAAGGGTATTTCTA-TAATTTTGT
*
40713448 AAACCAATGGTATTTCTATAATTTT-T
1 AAACCAAGGGTATTTCTATAATTTTGT
* *
40713474 AGAAAGTCAAGGATATTTCTATAATTTTGT
1 --AAA-CCAAGGGTATTTCTATAATTTTGT
40713504 AAA
1 AAA
40713507 TCAGGGCTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
26 1 0.02
27 22 0.44
28 7 0.14
29 19 0.38
30 1 0.02
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (27 bp):
AAACCAAGGGTATTTCTATAATTTTGT
Found at i:40713525 original size:27 final size:26
Alignment explanation
Indices: 40713509--40713634 Score: 144
Period size: 27 Copynumber: 4.7 Consensus size: 26
40713499 TTTGTAAATC
* *
40713509 AGGGCTATTTTGGTAATTTTAAAAATT
1 AGGG-TATTTTGGTAATTTTACAAACT
* * *
40713536 GAGGGTATTTCGGTAATTTCACAAACCA
1 -AGGGTATTTTGGTAATTTTACAAA-CT
* *
40713564 ATGGTATTTTGGTAATTTCACAAACT
1 AGGGTATTTTGGTAATTTTACAAACT
40713590 AGGGGTATTTTGGTAATTTTACAAACT
1 A-GGGTATTTTGGTAATTTTACAAACT
40713617 AGGGGTATTTTGGTAATT
1 A-GGGTATTTTGGTAATT
40713635 CTATCCTATA
Statistics
Matches: 86, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
26 2 0.02
27 80 0.93
28 4 0.05
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (26 bp):
AGGGTATTTTGGTAATTTTACAAACT
Found at i:40713704 original size:27 final size:27
Alignment explanation
Indices: 40713666--40713971 Score: 339
Period size: 27 Copynumber: 11.3 Consensus size: 27
40713656 ATAATTTCAC
*
40713666 AATCGAGGGTAAAATGATAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTTTGTA
*
40713693 AA-CTTAGGGTAAAATGGTAATTTTGTA
1 AATC-GAGGGTAAAATGGTAATTTTGTA
** * *
40713720 AATAAAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAATGGTAATTTTGTA
* * *
40713747 AATCGAGGGTAAAATAGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTTTGTA
*
40713774 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTTTGTA
40713801 AA-CTGAGGGTAAAATGGTAATTTTGTA
1 AATC-GAGGGTAAAATGGTAATTTTGTA
* *
40713828 AATCGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTTTGTA
* *
40713855 AATCGAGGGTAAAATGGTAATTTTATT
1 AATCGAGGGTAAAATGGTAATTTTGTA
* *
40713882 AATCGAGGGTAAAACGGTAATGTTGTA
1 AATCGAGGGTAAAATGGTAATTTTGTA
* * * *
40713909 AA-CTGAGGGTGAAACGGTAATTGTATA
1 AATC-GAGGGTAAAATGGTAATTTTGTA
* * * **
40713936 AATCGAGGATAAAATGATAATTCTACA
1 AATCGAGGGTAAAATGGTAATTTTGTA
40713963 AATCGAGGG
1 AATCGAGGG
40713972 CATTTCAGTA
Statistics
Matches: 238, Mismatches: 35, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
26 3 0.01
27 233 0.98
28 2 0.01
ACGTcount: A:0.40, C:0.07, G:0.24, T:0.30
Consensus pattern (27 bp):
AATCGAGGGTAAAATGGTAATTTTGTA
Found at i:40716187 original size:41 final size:43
Alignment explanation
Indices: 40716091--40716193 Score: 113
Period size: 41 Copynumber: 2.4 Consensus size: 43
40716081 TAACAACGTT
* **
40716091 CTAGACATGGTCTTACATGCTATCTCATATCAATGCCACTGTC
1 CTAGACATGGTCTTACATGCAATCAAATATCAATGCCACTGTC
* * * *
40716134 CCAAACAGGGTCTTACATG-AATCAAATAT-GATGCCGA-TGTC
1 CTAGACATGGTCTTACATGCAATCAAATATCAATGCC-ACTGTC
40716175 CTAGACATGGTCTTACATG
1 CTAGACATGGTCTTACATG
40716194 TAACCATATT
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
41 25 0.51
42 8 0.16
43 16 0.33
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29
Consensus pattern (43 bp):
CTAGACATGGTCTTACATGCAATCAAATATCAATGCCACTGTC
Found at i:40716256 original size:45 final size:45
Alignment explanation
Indices: 40716220--40716339 Score: 195
Period size: 45 Copynumber: 2.7 Consensus size: 45
40716210 TGCCAAAATT
* *
40716220 CCAGACGCGGTCTTACACGAAAACACATATACCGATGCCAACGCC
1 CCAGACGTGGTCTTACACGAAAACACATATACCGATGCCAACGTC
*
40716265 CCAGACGTGGTCTTACACGAAAACACATATATCGATGCCAACGTC
1 CCAGACGTGGTCTTACACGAAAACACATATACCGATGCCAACGTC
* *
40716310 CCAGACTTGGTCTTACACAAAAACACATAT
1 CCAGACGTGGTCTTACACGAAAACACATAT
40716340 CAAAATCCTA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 70 1.00
ACGTcount: A:0.35, C:0.31, G:0.16, T:0.18
Consensus pattern (45 bp):
CCAGACGTGGTCTTACACGAAAACACATATACCGATGCCAACGTC
Found at i:40718890 original size:34 final size:36
Alignment explanation
Indices: 40718824--40718895 Score: 112
Period size: 34 Copynumber: 2.1 Consensus size: 36
40718814 GTAATTTAAG
*
40718824 TTAAATTAAATAAAAACAAGGGATAAAATTGATTCA
1 TTAAATTAAATAAAAACAACGGATAAAATTGATTCA
*
40718860 TTAAATTAAAT-AAAA-AACGGTTAAAATTGATTCA
1 TTAAATTAAATAAAAACAACGGATAAAATTGATTCA
40718894 TT
1 TT
40718896 CATCCTTGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 19 0.56
35 4 0.12
36 11 0.32
ACGTcount: A:0.53, C:0.06, G:0.10, T:0.32
Consensus pattern (36 bp):
TTAAATTAAATAAAAACAACGGATAAAATTGATTCA
Found at i:40730552 original size:43 final size:43
Alignment explanation
Indices: 40730455--40730558 Score: 117
Period size: 43 Copynumber: 2.4 Consensus size: 43
40730445 ATCGAGATGT
* * *
40730455 GATTA-CATGTAAGACCATGTCTGGGACATTGGTATTGTGTTGA
1 GATTATCATGTAAGACCATGTCTGGGACATTAGCATCGTGTT-A
*
40730498 GATTAT-GTGTAAGACCATGTCTGGGACATTAGCATCGATG-TA
1 GATTATCATGTAAGACCATGTCTGGGACATTAGCATCG-TGTTA
40730540 TG-TTATCATGTAAGACCAT
1 -GATTATCATGTAAGACCAT
40730559 ATTTGGGATA
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
42 5 0.10
43 45 0.87
44 2 0.04
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.34
Consensus pattern (43 bp):
GATTATCATGTAAGACCATGTCTGGGACATTAGCATCGTGTTA
Found at i:40732325 original size:30 final size:30
Alignment explanation
Indices: 40732280--40732339 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
40732270 TTCCCGAGCC
40732280 AGGGGCAAAAGTGTAAATATGCAAAAGTTT
1 AGGGGCAAAAGTGTAAATATGCAAAAGTTT
* * * * *
40732310 AGGGGTAAAATTGTAATTTTGTAAAAGTTT
1 AGGGGCAAAAGTGTAAATATGCAAAAGTTT
40732340 GAGTTAAGGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.40, C:0.03, G:0.25, T:0.32
Consensus pattern (30 bp):
AGGGGCAAAAGTGTAAATATGCAAAAGTTT
Found at i:40733122 original size:68 final size:66
Alignment explanation
Indices: 40733050--40733197 Score: 165
Period size: 67 Copynumber: 2.2 Consensus size: 66
40733040 CATCATGTGT
* * * *
40733050 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTA-TG-TGTACACCA
1 ACAAGAGAGCTAC-AG-CA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCA
40733113 TGTAG
62 TGTAG
* * * *
40733118 ACAAGAGAGCTACTGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGT
1 ACAAGAGAGCTACAGCATATATGTAGCTAGGTCGCATGCGTGATACCA-GTGAAGGACACCATGT
40733183 AG
65 AG
40733185 ACAAGAGAGCTAC
1 ACAAGAGAGCTAC
40733198 GAGATAAATT
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
64 24 0.35
65 3 0.04
66 3 0.04
67 26 0.38
68 13 0.19
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.22
Consensus pattern (66 bp):
ACAAGAGAGCTACAGCATATATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCATGTA
G
Found at i:40733155 original size:64 final size:64
Alignment explanation
Indices: 40733074--40733257 Score: 187
Period size: 67 Copynumber: 2.8 Consensus size: 64
40733064 AGACATTATG
* * *
40733074 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACTG-GATAT
1 ATGTAGCTAGGTCGCATGCGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTAC-GAGATAA
* * * *
40733138 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGCGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
40733203 AA
63 AA
* * * *
40733205 AT-TGGCTAGGTCACATGTGTGGTACTGA-GTGTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGCGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGAGC
40733258 CGAACTATAT
Statistics
Matches: 99, Mismatches: 15, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 25 0.25
66 22 0.22
67 32 0.32
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.24
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGCGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:40736466 original size:40 final size:40
Alignment explanation
Indices: 40736404--40736538 Score: 216
Period size: 40 Copynumber: 3.4 Consensus size: 40
40736394 CGGATGTAAC
* ** *
40736404 AACCAGCACGAATAACTTCGGGACTTAACCTGGTTATAAT
1 AACCTGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
*
40736444 AACCTGTACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCTGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
*
40736484 AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCTGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
40736524 AACCTGCACGAATGC
1 AACCTGCACGAATGC
40736539 TATGCACATA
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 87 1.00
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (40 bp):
AACCTGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
Found at i:40744946 original size:40 final size:40
Alignment explanation
Indices: 40744897--40744991 Score: 172
Period size: 40 Copynumber: 2.4 Consensus size: 40
40744887 CAGATGTAAC
40744897 AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
*
40744937 AACCTGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
*
40744977 AACCCGCACGAATGC
1 AACCAGCACGAATGC
40744992 TATGCACATA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.21
Consensus pattern (40 bp):
AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
Found at i:40753060 original size:36 final size:34
Alignment explanation
Indices: 40753004--40753075 Score: 92
Period size: 36 Copynumber: 2.1 Consensus size: 34
40752994 AATTTAAAGA
40753004 GAAAAGAAAATAATTCAATTCCAAATGGAAATAG
1 GAAAAGAAAATAATTCAATTCCAAATGGAAATAG
* *
40753038 GAAAAGAGAGAATAA-TCTAATTCCAAATTGAAGTAG
1 GAAAAGA-A-AATAATTC-AATTCCAAATGGAAATAG
40753074 GA
1 GA
40753076 GTACAAAAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 7 0.21
35 3 0.09
36 23 0.70
ACGTcount: A:0.53, C:0.08, G:0.18, T:0.21
Consensus pattern (34 bp):
GAAAAGAAAATAATTCAATTCCAAATGGAAATAG
Found at i:40754561 original size:20 final size:19
Alignment explanation
Indices: 40754538--40754594 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 19
40754528 GTATAAACTA
40754538 TAATTCATC-TGTATCAATAG
1 TAATTCATCAT-T-TCAATAG
40754558 TAATTCATTCATTTCAATAG
1 TAATTCA-TCATTTCAATAG
40754578 TAATTCATCCATTTCAA
1 TAATTCAT-CATTTCAA
40754595 CATGGCTCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
19 1 0.03
20 29 0.85
21 3 0.09
22 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.05, T:0.42
Consensus pattern (19 bp):
TAATTCATCATTTCAATAG
Found at i:40754795 original size:23 final size:23
Alignment explanation
Indices: 40754766--40754841 Score: 91
Period size: 23 Copynumber: 3.3 Consensus size: 23
40754756 CTAATAAATA
40754766 GTAAGCTCTATTGAGTTGAAACG
1 GTAAGCTCTATTGAGTTGAAACG
* * *
40754789 GTAAGCTCTATCGAGCTG-AACA
1 GTAAGCTCTATTGAGTTGAAACG
* * *
40754811 GTAAGCTCAAATGAGTTGAATCG
1 GTAAGCTCTATTGAGTTGAAACG
40754834 GTAAGCTC
1 GTAAGCTC
40754842 CAATGAGCTA
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
22 17 0.40
23 26 0.60
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (23 bp):
GTAAGCTCTATTGAGTTGAAACG
Found at i:40754850 original size:45 final size:45
Alignment explanation
Indices: 40754765--40754850 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
40754755 GCTAATAAAT
* * *
40754765 AGTAAGCTCTATTGAGTTGAAACGGTAAGCTCTATCGAGCTGAAC
1 AGTAAGCTCAAATGAGTTGAAACGGTAAGCTCAATCGAGCTGAAC
*
40754810 AGTAAGCTCAAATGAGTTGAATCGGTAAGCTCCAAT-GAGCT
1 AGTAAGCTCAAATGAGTTGAAACGGTAAGCT-CAATCGAGCT
40754851 AAAAATAGTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
45 33 0.92
46 3 0.08
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (45 bp):
AGTAAGCTCAAATGAGTTGAAACGGTAAGCTCAATCGAGCTGAAC
Found at i:40757582 original size:21 final size:21
Alignment explanation
Indices: 40757541--40757591 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
40757531 TTGATCTAAA
* * *
40757541 TTAAT-ACAAATTTTACTAAT
1 TTAATCACACATTTAACCAAT
40757561 TTAATCACACATTTAACCAAT
1 TTAATCACACATTTAACCAAT
*
40757582 TCAATC-CACA
1 TTAATCACACA
40757592 AATACATAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.43, C:0.22, G:0.00, T:0.35
Consensus pattern (21 bp):
TTAATCACACATTTAACCAAT
Found at i:40758890 original size:24 final size:24
Alignment explanation
Indices: 40758858--40758933 Score: 134
Period size: 24 Copynumber: 3.2 Consensus size: 24
40758848 AGTCTGTCAA
*
40758858 GAGAGGATTTAGGAGTTGATAAGG
1 GAGAGGATTTAGGAGCTGATAAGG
40758882 GAGAGGATTTAGGAGCTGATAAGG
1 GAGAGGATTTAGGAGCTGATAAGG
*
40758906 GAGAGGATTTAGGAGCTGATTAGG
1 GAGAGGATTTAGGAGCTGATAAGG
40758930 GAGA
1 GAGA
40758934 ACAATGTTGG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.33, C:0.03, G:0.42, T:0.22
Consensus pattern (24 bp):
GAGAGGATTTAGGAGCTGATAAGG
Found at i:40760417 original size:26 final size:26
Alignment explanation
Indices: 40760309--40760419 Score: 132
Period size: 27 Copynumber: 4.2 Consensus size: 26
40760299 AGGAAGCGTC
* * *
40760309 CTGGTGGCTATGCCACAATTATTTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGTT
40760336 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGTT
40760363 CTGGTGGCTCTGCCACGATTATCTGTT
1 CTGGTGGCTCTGCCAC-ATTATCTGTT
* * * *
40760390 CTGGTGACACTGTCACATTATCTATT
1 CTGGTGGCTCTGCCACATTATCTGTT
40760416 CTGG
1 CTGG
40760420 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
26 15 0.20
27 58 0.77
28 2 0.03
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGTT
Found at i:40764917 original size:93 final size:93
Alignment explanation
Indices: 40764752--40764924 Score: 283
Period size: 93 Copynumber: 1.9 Consensus size: 93
40764742 CGCCCATAAG
* * * *
40764752 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAGGTGAACTCGGACTCAACTTA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
40764817 GCAAGTTCGGATGCCTAGTTACATTTCA
66 ACAAGTTCGGATGCCTAGTTACATTTCA
*
40764845 CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
40764910 ACGAGTTCGGATGCC
66 ACAAGTTCGGATGCC
40764925 CAAATATCCC
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.27, C:0.29, G:0.23, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACAAGTTCGGATGCCTAGTTACATTTCA
Found at i:40764920 original size:46 final size:46
Alignment explanation
Indices: 40764745--40764920 Score: 185
Period size: 46 Copynumber: 3.8 Consensus size: 46
40764735 TGTAACCCGC
* * *
40764745 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* * * * * * * *
40764791 CCATAGGTGAACTCGGACTCAACTTAGCAAGTTCGGATGCCTAG-TT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCGCAT
* *
40764837 ACATTTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCA--TAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
*
40764884 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
40764921 TGCCCAAATA
Statistics
Matches: 101, Mismatches: 24, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
45 2 0.02
46 66 0.65
47 32 0.32
48 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:40770772 original size:22 final size:23
Alignment explanation
Indices: 40770747--40770789 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
40770737 CGCAATTTTC
*
40770747 TAGCT-TTGGCTTTTTGTTTTGG
1 TAGCTATTCGCTTTTTGTTTTGG
*
40770769 TAGCTATTCTCTTTTTGTTTT
1 TAGCTATTCGCTTTTTGTTTT
40770790 TCTCTCTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.07, C:0.12, G:0.19, T:0.63
Consensus pattern (23 bp):
TAGCTATTCGCTTTTTGTTTTGG
Found at i:40775087 original size:20 final size:20
Alignment explanation
Indices: 40775016--40775101 Score: 72
Period size: 20 Copynumber: 4.3 Consensus size: 20
40775006 GGATTGCAAA
40775016 TATATGAAATGGAAAAT-AT
1 TATATGAAATGGAAAATGAT
* *
40775035 ATATATGAAAT-GACATATAAT
1 -TATATGAAATGGA-AAATGAT
* *
40775056 TCA-ATGATATGGAAAATGGT
1 T-ATATGAAATGGAAAATGAT
40775076 TATATGAAATGGAAAAGTG-T
1 TATATGAAATGGAAAA-TGAT
40775096 TATATG
1 TATATG
40775102 TGAAAGAGGA
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
19 3 0.06
20 44 0.81
21 7 0.13
ACGTcount: A:0.47, C:0.02, G:0.19, T:0.33
Consensus pattern (20 bp):
TATATGAAATGGAAAATGAT
Found at i:40776368 original size:43 final size:44
Alignment explanation
Indices: 40776319--40776445 Score: 179
Period size: 43 Copynumber: 3.0 Consensus size: 44
40776309 TACCGAGATA
40776319 AGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT-TG
1 AGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATGTG
* * *
40776362 TGATTACGTGTAAGACCATGTCTGGGACATTGGCATCG-ATGTG
1 AGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATGTG
* * *
40776405 AGATAACATGTAAGACCATATCTGGGATA-TGGCATTGTATG
1 AGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATG
40776446 AGCTTTATGT
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
42 9 0.12
43 64 0.88
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.31
Consensus pattern (44 bp):
AGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATGTG
Found at i:40780011 original size:46 final size:45
Alignment explanation
Indices: 40779940--40780105 Score: 167
Period size: 46 Copynumber: 3.6 Consensus size: 45
40779930 GTGTCAATGC
* *
40779940 CATGTCCCAAACATGGTCTTACACTGACTATCATCTCATAACCGATG
1 CATGTCCCAGACATGGTCTTACACTGACT-TCATCTCA-AGCCGATG
* * * *
40779987 CATGTCACAGACAT-GTCTTACACTGGCTTACGTCTCGAGGCCGATG
1 CATGTCCCAGACATGGTCTTACACTGACTT-CATCTC-AAGCCGATG
*
40780033 CATGTCCCAGACAT-GTCTTACAAT-AGCTCTCATCTCAATGCCGATG
1 CATGTCCCAGACATGGTCTTACACTGA-CT-TCATCTCAA-GCCGATG
*
40780079 CCATATCCCAGACATGGTCTTACACTG
1 -CATGTCCCAGACATGGTCTTACACTG
40780106 GCTCTCATAA
Statistics
Matches: 98, Mismatches: 13, Indels: 14
0.78 0.10 0.11
Matches are distributed among these distances:
45 2 0.02
46 60 0.61
47 27 0.28
48 9 0.09
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27
Consensus pattern (45 bp):
CATGTCCCAGACATGGTCTTACACTGACTTCATCTCAAGCCGATG
Found at i:40780124 original size:48 final size:47
Alignment explanation
Indices: 40780025--40780155 Score: 119
Period size: 47 Copynumber: 2.8 Consensus size: 47
40780015 TACGTCTCGA
*
40780025 GGCCGATG-CATGTCCCAGACATGTCTTACAATAGCTCTCATCTCAAT
1 GGCCGATGCCATATCCCAGACATGTCTTACAATAGCTCTCA-CTCAAT
* *
40780072 -GCCGATGCCATATCCCAGACATGGTCTTACACTGGCTCTCA-T-AATGT
1 GGCCGATGCCATATCCCAGACAT-GTCTTACAATAGCTCTCACTCAA--T
* * * * *
40780119 GGCCGATG-CATGTTCTAGACATCTCTTACACTAGCTC
1 GGCCGATGCCATATCCCAGACATGTCTTACAATAGCTC
40780156 ATGCAAGTGA
Statistics
Matches: 71, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
45 2 0.03
46 21 0.30
47 25 0.35
48 23 0.32
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (47 bp):
GGCCGATGCCATATCCCAGACATGTCTTACAATAGCTCTCACTCAAT
Found at i:40780127 original size:94 final size:92
Alignment explanation
Indices: 40779940--40780155 Score: 233
Period size: 94 Copynumber: 2.3 Consensus size: 92
40779930 GTGTCAATGC
* * *
40779940 CATGTCCCAAACATGGTCTTACACT-GACTATCATCTCATAACCGATGCATGTCACAGACATGTC
1 CATGTCCCAGACAT-GTCTTACACTAG-CTCTCATCTCATAACCGATGCATATCACAGACATGTC
* *
40780004 TTACACTGGCTTACGTCTCGAGGCCGATG
64 TTACACTGGCTTACATATCGAGGCCGATG
* * *
40780033 CATGTCCCAGACATGTCTTACAATAGCTCTCATCTCA-ATGCCGATGCCATATCCCAGACATGGT
1 CATGTCCCAGACATGTCTTACACTAGCTCTCATCTCATA-ACCGATG-CATATCACAGACAT-GT
*
40780097 CTTACACTGGCTCT-CATAAT-GTGGCCGATG
63 CTTACACTGGCT-TACAT-ATCGAGGCCGATG
* * *
40780127 CATGTTCTAGACATCTCTTACACTAGCTC
1 CATGTCCCAGACATGTCTTACACTAGCTC
40780156 ATGCAAGTGA
Statistics
Matches: 104, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
91 1 0.01
92 25 0.24
93 26 0.25
94 50 0.48
95 2 0.02
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (92 bp):
CATGTCCCAGACATGTCTTACACTAGCTCTCATCTCATAACCGATGCATATCACAGACATGTCTT
ACACTGGCTTACATATCGAGGCCGATG
Found at i:40792388 original size:452 final size:451
Alignment explanation
Indices: 40791539--40792434 Score: 1560
Period size: 452 Copynumber: 2.0 Consensus size: 451
40791529 CAAAGCCTCT
*
40791539 AGTACGTGGTCAAGCCACTTTCAGTACTTCCTCCATCAATAACCTAGTCCCATGCATCAGATAAT
1 AGTACGTGGTCAAGCCACTTTCAGTACTTCCTCCATCAATAACCCAGTCCCATGCATCAGATAAT
* *
40791604 AATAACATGGCATGCAGTAAATAGTAACAGTCAAACATGCATTCAGGTTAACCTTAACCCTAGGG
66 AATAACATGGCATGCAGCAAATAGTAACAGTCAAACATGCATTCAGGTCAACCTTAACCCTAGGG
* *
40791669 GTATATCAGTAATTTTGCTCTTAGGAGTAAAACTGTAAACTTTCCACCTATAAAGGTATTTCAGT
131 GTATATCAGTAATTTTGCTCCTAGGAGTAAAACTGTAAACTTTCCACCTATAAAGGTATTTCAAT
* *
40791734 AATTTTATCAGTTTTAAGGGTTCTCATGAATGTTACGGTCCTTACTAGCCCATTTGTCATCGTAG
196 AATTTTATCAATTTTAAGGGTTCTCATGAATGTTACGGTCCTTACTAGCCCATTTGTCATCGCAG
* * *
40791799 TAATTTATTTATCTCAATTTCACAATTTTAGCCATTAGGCCCTAAAACCCCTAATGGGCCCTATA
261 TAATTTATTTATCTCAATTTAACAAGTTTAGCCATTAGGCCCTAAAACCCCTAATGGGCCCTACA
* * *
40791864 GTGTCCATTAGCAATTTAAGCCCATTTAATTCAAGTTTTATGACCAGTTTACTGGTTTAAGTAGT
326 GTGTCCATTAGAAATTTAAGCCCATTTAATTCAAGTTTTATGACCAGTTTACCGGTTTAAATAGT
* * *
40791929 TTCGATTCTACAGTCTAACATAACATACTTATTGCCTATT-TTTTTCATATATATATTCCTTC
391 GTCGATTCTACAGTATAACAGAACATACTTATTGCCTATTATTTTT-ATAT-TATATTCCTTC
*
40791991 AGTACGTGGTCAAGCCACTTTCAGTACTTCCTCCATCAATAACCCAGTCCCATGCATTAGATAAT
1 AGTACGTGGTCAAGCCACTTTCAGTACTTCCTCCATCAATAACCCAGTCCCATGCATCAGATAAT
*
40792056 AATAACATGGCATGCAGCAAATAGTAATAGTCAAACATGCATTCAGGTCAACCTTAACCCTAGGG
66 AATAACATGGCATGCAGCAAATAGTAACAGTCAAACATGCATTCAGGTCAACCTTAACCCTAGGG
*
40792121 GTATATCAGTAATTTTGCTCCTAGGAGTAAAGCTGTAAACTTTCCACCTATAAAGGTATTTCAAT
131 GTATATCAGTAATTTTGCTCCTAGGAGTAAAACTGTAAACTTTCCACCTATAAAGGTATTTCAAT
*
40792186 AATTTTATCAATTTTAAGGGTTCTCATGAATGTTACGGTCCTTACTAGCCTATTTGTCATCGCAG
196 AATTTTATCAATTTTAAGGGTTCTCATGAATGTTACGGTCCTTACTAGCCCATTTGTCATCGCAG
*
40792251 TAATTTATTTATCTCAATTTAACAAGTTTAGCCATTGGGCCCTAAAACCCCTAATGGGCCCTACA
261 TAATTTATTTATCTCAATTTAACAAGTTTAGCCATTAGGCCCTAAAACCCCTAATGGGCCCTACA
*
40792316 GTGTCCATTAGAAATTTAAGCCCATTTAATTCAAGTTTTATGACTAGTTTACCGGTTTAAATAGT
326 GTGTCCATTAGAAATTTAAGCCCATTTAATTCAAGTTTTATGACCAGTTTACCGGTTTAAATAGT
*
40792381 GTCGATTCTACAGTATAATAGAACATACTTATTGCCTATTATTTTTATATTATA
391 GTCGATTCTACAGTATAACAGAACATACTTATTGCCTATTATTTTTATATTATA
40792435 CATTTTATTA
Statistics
Matches: 420, Mismatches: 23, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
451 4 0.01
452 411 0.98
453 5 0.01
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (451 bp):
AGTACGTGGTCAAGCCACTTTCAGTACTTCCTCCATCAATAACCCAGTCCCATGCATCAGATAAT
AATAACATGGCATGCAGCAAATAGTAACAGTCAAACATGCATTCAGGTCAACCTTAACCCTAGGG
GTATATCAGTAATTTTGCTCCTAGGAGTAAAACTGTAAACTTTCCACCTATAAAGGTATTTCAAT
AATTTTATCAATTTTAAGGGTTCTCATGAATGTTACGGTCCTTACTAGCCCATTTGTCATCGCAG
TAATTTATTTATCTCAATTTAACAAGTTTAGCCATTAGGCCCTAAAACCCCTAATGGGCCCTACA
GTGTCCATTAGAAATTTAAGCCCATTTAATTCAAGTTTTATGACCAGTTTACCGGTTTAAATAGT
GTCGATTCTACAGTATAACAGAACATACTTATTGCCTATTATTTTTATATTATATTCCTTC
Found at i:40800534 original size:18 final size:18
Alignment explanation
Indices: 40800505--40800563 Score: 70
Period size: 17 Copynumber: 3.4 Consensus size: 18
40800495 ACATGATTGG
40800505 ATTCAT-TTTTCAATTAA
1 ATTCATGTTTTCAATTAA
* **
40800522 ATTCATGTTTTC-AGTCG
1 ATTCATGTTTTCAATTAA
40800539 A-TCATGTTTTCAATTAA
1 ATTCATGTTTTCAATTAA
40800556 ATTCATGT
1 ATTCATGT
40800564 ACTTCATTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
16 10 0.30
17 12 0.36
18 11 0.33
ACGTcount: A:0.29, C:0.14, G:0.08, T:0.49
Consensus pattern (18 bp):
ATTCATGTTTTCAATTAA
Found at i:40811966 original size:8 final size:8
Alignment explanation
Indices: 40811953--40811980 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
40811943 CACGAAATTT
40811953 TCATGAAA
1 TCATGAAA
40811961 TCATGAAA
1 TCATGAAA
40811969 TCATGAAA
1 TCATGAAA
40811977 TCAT
1 TCAT
40811981 ATCATAAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.29
Consensus pattern (8 bp):
TCATGAAA
Found at i:40814645 original size:27 final size:27
Alignment explanation
Indices: 40814614--40814678 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
40814604 GATCACTAAA
* *
40814614 CACTTTGCTATGTTTGGCACACTATAT
1 CACTTTGCCATGATTGGCACACTATAT
*
40814641 CACTTTGCCATGATTGGCACACTTTAT
1 CACTTTGCCATGATTGGCACACTATAT
40814668 CACTTTGCCAT
1 CACTTTGCCAT
40814679 AGTTCAACTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.22, C:0.26, G:0.14, T:0.38
Consensus pattern (27 bp):
CACTTTGCCATGATTGGCACACTATAT
Found at i:40814816 original size:31 final size:31
Alignment explanation
Indices: 40814735--40814912 Score: 171
Period size: 31 Copynumber: 5.7 Consensus size: 31
40814725 TCAGATAAAT
* * * **
40814735 GTAGCTAAAGCTACCACTTATCACTTGTTACTT
1 GTAGCTGAAGCTACCACTTTTCAC-TGAT-CAG
* * *
40814768 GTAGCCGAAGCTACCACTATTCACTGATCAA
1 GTAGCTGAAGCTACCACTTTTCACTGATCAG
* * *
40814799 GTAGCTGGAGCTGCCACTTTTCACTAATCAG
1 GTAGCTGAAGCTACCACTTTTCACTGATCAG
* *
40814830 GTAG-TCGAAGCTACTACTTTTCACTCATCAG
1 GTAGCT-GAAGCTACCACTTTTCACTGATCAG
* *
40814861 GTAGCCGAAACTACCACTTTTCACTGATCAG
1 GTAGCTGAAGCTACCACTTTTCACTGATCAG
40814892 GTAG-TCGAAGCTACCACTTTT
1 GTAGCT-GAAGCTACCACTTTT
40814913 TACATTGTAC
Statistics
Matches: 119, Mismatches: 23, Indels: 8
0.79 0.15 0.05
Matches are distributed among these distances:
30 1 0.01
31 95 0.80
32 3 0.03
33 20 0.17
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (31 bp):
GTAGCTGAAGCTACCACTTTTCACTGATCAG
Found at i:40814865 original size:62 final size:62
Alignment explanation
Indices: 40814768--40814912 Score: 200
Period size: 62 Copynumber: 2.3 Consensus size: 62
40814758 CTTGTTACTT
* * * * * * *
40814768 GTAGCCGAAGCTACCACTATTCACTGATCAAGTAGCTGGAGCTGCCACTTTTCACTAATCAG
1 GTAGTCGAAGCTACCACTTTTCACTCATCAAGTAGCCGAAACTACCACTTTTCACTAATCAG
* * *
40814830 GTAGTCGAAGCTACTACTTTTCACTCATCAGGTAGCCGAAACTACCACTTTTCACTGATCAG
1 GTAGTCGAAGCTACCACTTTTCACTCATCAAGTAGCCGAAACTACCACTTTTCACTAATCAG
40814892 GTAGTCGAAGCTACCACTTTT
1 GTAGTCGAAGCTACCACTTTT
40814913 TACATTGTAC
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
62 72 1.00
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (62 bp):
GTAGTCGAAGCTACCACTTTTCACTCATCAAGTAGCCGAAACTACCACTTTTCACTAATCAG
Found at i:40814992 original size:33 final size:32
Alignment explanation
Indices: 40814918--40815020 Score: 118
Period size: 33 Copynumber: 3.2 Consensus size: 32
40814908 CTTTTTACAT
* *
40814918 TGTACACACAAGGCGTACATTTCCTTTTCAAG
1 TGTACACACAAAGTGTACATTTCCTTTTCAAG
** *
40814950 TGTACACACAAAGTGTATGTTTCCTTTTTAAG
1 TGTACACACAAAGTGTACATTTCCTTTTCAAG
*
40814982 CTGTACACACACAA-TGTACATTTCCTTTTCTAG
1 -TGTACACACA-AAGTGTACATTTCCTTTTCAAG
40815015 TTGTAC
1 -TGTAC
40815021 CTTTTAGGTA
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
32 27 0.46
33 30 0.51
34 2 0.03
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (32 bp):
TGTACACACAAAGTGTACATTTCCTTTTCAAG
Found at i:40824229 original size:15 final size:15
Alignment explanation
Indices: 40824211--40824243 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
40824201 ACATAATAAA
40824211 AATTAACATGAAAAT
1 AATTAACATGAAAAT
40824226 AATTAACATGAAAAT
1 AATTAACATGAAAAT
40824241 AAT
1 AAT
40824244 ATAATTTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.27
Consensus pattern (15 bp):
AATTAACATGAAAAT
Found at i:40824244 original size:18 final size:16
Alignment explanation
Indices: 40824201--40824243 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
40824191 TGAACCCACT
*
40824201 ACAT-AATAAAAATTA
1 ACATGAATAATAATTA
40824216 ACATGAA-AATAATTA
1 ACATGAATAATAATTA
40824231 ACATGAA-AATAAT
1 ACATGAATAATAAT
40824244 ATAATTTATG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 24 0.92
16 2 0.08
ACGTcount: A:0.63, C:0.07, G:0.05, T:0.26
Consensus pattern (16 bp):
ACATGAATAATAATTA
Found at i:40824669 original size:20 final size:20
Alignment explanation
Indices: 40824616--40824669 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
40824606 AACAGGGGTC
*
40824616 ACACGCCCATGTGACTTGTG
1 ACACGCCCATGTGGCTTGTG
*
40824636 ACACGCCCGTGTGGCTTGTG
1 ACACGCCCATGTGGCTTGTG
40824656 ACACGCCCATGTGG
1 ACACGCCCATGTGG
40824670 GCAGGCCGGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.17, C:0.31, G:0.30, T:0.22
Consensus pattern (20 bp):
ACACGCCCATGTGGCTTGTG
Found at i:40832448 original size:40 final size:40
Alignment explanation
Indices: 40832378--40832593 Score: 285
Period size: 40 Copynumber: 5.4 Consensus size: 40
40832368 AAACCAAGTA
* * * * *
40832378 CCTTCGGGATTTA-ACCAGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
40832417 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
40832457 CCTTCGAGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
40832497 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * *
40832537 CCTTCGGGACTTAGCCC-GAAACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
40832577 CCTTCGGGACTTAGCCC
1 CCTTCGGGACTTAGCCC
40832594 AGTTATCATC
Statistics
Matches: 160, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
39 15 0.09
40 145 0.91
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:40841386 original size:16 final size:16
Alignment explanation
Indices: 40841365--40841395 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40841355 CAAATTGACT
40841365 CAAAATCATATTTTTA
1 CAAAATCATATTTTTA
*
40841381 CAAAATTATATTTTT
1 CAAAATCATATTTTT
40841396 GCCCCTAAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (16 bp):
CAAAATCATATTTTTA
Found at i:40845261 original size:32 final size:32
Alignment explanation
Indices: 40845220--40845283 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
40845210 TGGCTTAATC
40845220 GAGTGATCATAAATCAAACAAATGGATCTCCT
1 GAGTGATCATAAATCAAACAAATGGATCTCCT
*
40845252 GAGTGATCATACATCAAACAAATGGATCTCCT
1 GAGTGATCATAAATCAAACAAATGGATCTCCT
40845284 TACTCCCAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (32 bp):
GAGTGATCATAAATCAAACAAATGGATCTCCT
Found at i:40845658 original size:20 final size:20
Alignment explanation
Indices: 40845633--40845671 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40845623 GGACTAAACC
*
40845633 GATAACTCACGAAATTTTTG
1 GATAACTCAAGAAATTTTTG
*
40845653 GATAACTTAAGAAATTTTT
1 GATAACTCAAGAAATTTTT
40845672 CAAAAATACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (20 bp):
GATAACTCAAGAAATTTTTG
Found at i:40846729 original size:11 final size:11
Alignment explanation
Indices: 40846713--40846737 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40846703 ATGTAAAACT
40846713 TACAATTCAAG
1 TACAATTCAAG
40846724 TACAATTCAAG
1 TACAATTCAAG
40846735 TAC
1 TAC
40846738 TTAAACATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.28
Consensus pattern (11 bp):
TACAATTCAAG
Found at i:40849560 original size:17 final size:16
Alignment explanation
Indices: 40849536--40849585 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 16
40849526 CCCTTATTAA
40849536 AAAATAAAATAAAATT
1 AAAATAAAATAAAATT
40849552 AACAATAAAA-AAATATT
1 AA-AATAAAATAAA-ATT
*
40849569 AAAATGGAAATAAAATT
1 AAAAT-AAAATAAAATT
40849586 TTCAAAGTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 8 0.28
17 18 0.62
18 3 0.10
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (16 bp):
AAAATAAAATAAAATT
Found at i:40856251 original size:43 final size:43
Alignment explanation
Indices: 40856080--40856252 Score: 199
Period size: 43 Copynumber: 4.0 Consensus size: 43
40856070 ACATAGGATT
* * * *
40856080 TCGATATGTGATTTCATGTAAGACCACGTCTGGGACGTTGGAA
1 TCGATATTTGATTACATGTAAGACCATGTCTGGGACGTTGGCA
* * * *
40856123 TCGAT-TTGAGATTTACGTGTAAGACCATGTCTGGGACATCGGCA
1 TCGATATT-TGA-TTACATGTAAGACCATGTCTGGGACGTTGGCA
* *
40856167 TCG-TATTTGATTTCGTGTAAGACCATGTCTGGGACAG-TGGCA
1 TCGATATTTGATTACATGTAAGACCATGTCTGGGAC-GTTGGCA
*
40856209 TCGATATTTGATTACATGTAAGACCATGTCTGGGGCGTTGGCA
1 TCGATATTTGATTACATGTAAGACCATGTCTGGGACGTTGGCA
40856252 T
1 T
40856253 TATACGAGTT
Statistics
Matches: 109, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
42 33 0.30
43 45 0.41
44 31 0.28
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.32
Consensus pattern (43 bp):
TCGATATTTGATTACATGTAAGACCATGTCTGGGACGTTGGCA
Found at i:40868486 original size:46 final size:46
Alignment explanation
Indices: 40868364--40868488 Score: 214
Period size: 46 Copynumber: 2.7 Consensus size: 46
40868354 GGTTGAGCAT
* * *
40868364 CCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
40868410 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
*
40868456 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
40868489 GGGGCGGGTT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 75 1.00
ACGTcount: A:0.21, C:0.23, G:0.28, T:0.28
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Found at i:40872511 original size:8 final size:8
Alignment explanation
Indices: 40872498--40872534 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
40872488 AAACTTTTAA
40872498 CTTTTCGG
1 CTTTTCGG
*
40872506 CTTTTCAG
1 CTTTTCGG
40872514 CTTTTCGG
1 CTTTTCGG
*
40872522 CATTTCGG
1 CTTTTCGG
40872530 CTTTT
1 CTTTT
40872535 GCCGATCTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.05, C:0.24, G:0.19, T:0.51
Consensus pattern (8 bp):
CTTTTCGG
Found at i:40879387 original size:25 final size:25
Alignment explanation
Indices: 40879356--40879425 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 25
40879346 GCTGTAAACA
* *
40879356 GTAAGCTCCTCTGAGCTGAATAACG
1 GTAAGCTCATATGAGCTGAATAACG
* *
40879381 GTAAGCTCATATGAGCTGAGTATCG
1 GTAAGCTCATATGAGCTGAATAACG
* *
40879406 ATAAGCTCATAAGAGCTGAA
1 GTAAGCTCATATGAGCTGAA
40879426 ATCCGTAACC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (25 bp):
GTAAGCTCATATGAGCTGAATAACG
Found at i:40882038 original size:24 final size:22
Alignment explanation
Indices: 40882011--40882072 Score: 52
Period size: 24 Copynumber: 2.6 Consensus size: 22
40882001 ATTTTTCTTT
* *
40882011 TTTGAATTTTGAGTTCGAATCAA
1 TTTGAATTTTGAATTCAAAT-AA
**
40882034 GTTTGGTTTTTGAATTCAAATAA
1 -TTTGAATTTTGAATTCAAATAA
40882057 TTTGAATAATTTGAAT
1 TTTGAAT--TTTGAAT
40882073 AAACCGAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
22 5 0.17
23 2 0.07
24 23 0.77
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.47
Consensus pattern (22 bp):
TTTGAATTTTGAATTCAAATAA
Found at i:40882160 original size:19 final size:21
Alignment explanation
Indices: 40882116--40882160 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 21
40882106 TTACACAAAA
* *
40882116 CTCCCAAACTTCTTTACTTTC
1 CTCCCAAAATTCTTTACTTAC
40882137 C-CCCAAAATT-TTTAC-TAC
1 CTCCCAAAATTCTTTACTTAC
40882155 CTCCCA
1 CTCCCA
40882161 CTTTTCCCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
18 3 0.14
19 9 0.43
20 8 0.38
21 1 0.05
ACGTcount: A:0.24, C:0.40, G:0.00, T:0.36
Consensus pattern (21 bp):
CTCCCAAAATTCTTTACTTAC
Found at i:40889961 original size:30 final size:29
Alignment explanation
Indices: 40889927--40889987 Score: 104
Period size: 30 Copynumber: 2.1 Consensus size: 29
40889917 AAGCGGAAGT
40889927 TTTGGCACTAAGTGTGAGATTTAAACTAGC
1 TTTGGCACTAAGTGTGAGATTT-AACTAGC
*
40889957 TTTGGCACTAAGTGTGCGATTTAACTAGC
1 TTTGGCACTAAGTGTGAGATTTAACTAGC
40889986 TT
1 TT
40889988 CGGCTACTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 9 0.30
30 21 0.70
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (29 bp):
TTTGGCACTAAGTGTGAGATTTAACTAGC
Found at i:40897203 original size:30 final size:29
Alignment explanation
Indices: 40897167--40897227 Score: 95
Period size: 30 Copynumber: 2.1 Consensus size: 29
40897157 AAACGGAAGT
* *
40897167 TTTGGCACTAAGTGTGCTATTTAAACTAGC
1 TTTGGCACTAAGTGTGCGAGTT-AACTAGC
40897197 TTTGGCACTAAGTGTGCGAGTTAACTAGC
1 TTTGGCACTAAGTGTGCGAGTTAACTAGC
40897226 TT
1 TT
40897228 CGGCTACTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 9 0.31
30 20 0.69
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (29 bp):
TTTGGCACTAAGTGTGCGAGTTAACTAGC
Found at i:40903746 original size:49 final size:47
Alignment explanation
Indices: 40903686--40904236 Score: 861
Period size: 47 Copynumber: 11.6 Consensus size: 47
40903676 GATAATTGTG
* * *
40903686 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATAA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
40903733 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
40903780 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
40903829 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
40903878 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
40903925 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
40903972 ATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
40904021 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
40904070 ATGTGAAAGTGTATATATGTGATCAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
40904117 ATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * *
40904164 ATGTGAAAGTGTATATATGTGA-CAGAGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATGTGATAAG-GCCTAATGGCCGATGTGATGA
*
40904211 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
40904237 TCCCGAAGGG
Statistics
Matches: 477, Mismatches: 21, Indels: 11
0.94 0.04 0.02
Matches are distributed among these distances:
46 2 0.00
47 285 0.60
48 2 0.00
49 188 0.39
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:40903902 original size:192 final size:192
Alignment explanation
Indices: 40903686--40904236 Score: 941
Period size: 192 Copynumber: 2.9 Consensus size: 192
40903676 GATAATTGTG
* * *
40903686 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATAAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
*
40903751 GTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATG
66 GTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCGAATG
40903816 GCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
131 GCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
40903878 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
40903943 GTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCGAATG
66 GTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCGAATG
40904008 GCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
131 GCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
40904070 ATGTGAAAGTGTATATATGTGATCAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
* * * * *
40904135 GTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA-CAGAGCCGAGT
66 GTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAG-GCCGAAT
* * *
40904197 GGCCAACGTGATGGATGTGAAAGTGTATA-A-ATGTGATAAG
130 GGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
40904237 TCCCGAAGGG
Statistics
Matches: 345, Mismatches: 13, Indels: 6
0.95 0.04 0.02
Matches are distributed among these distances:
188 10 0.03
189 3 0.01
190 43 0.12
192 289 0.84
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.29
Consensus pattern (192 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
GTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCGAATG
GCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:40909261 original size:46 final size:45
Alignment explanation
Indices: 40909209--40909377 Score: 139
Period size: 46 Copynumber: 3.6 Consensus size: 45
40909199 ATTATATGCT
*
40909209 AGTGTAAGATATGTCTAGGACATGCATCGACCACATTACGAGAGCC
1 AGTGTAAGACATGTCTAGGACATGCATCGACCACATTACGA-AGCC
* * * *
40909255 AGTGTAAGACCATGTCTGGGACATGGCATCG---GCATTGAAACAACATCC
1 AGTGTAAGA-CATGTCTAGGACAT-GCATCGACCACATT---ACGA-AGCC
* * *
40909303 AGTGTAAGACATGTCTAGGACATGCATCGACCTCGA-GATGTAAGCC
1 AGTGTAAGACATGTCTAGGACATGCATCGACCAC-ATTACG-AAGCC
* *
40909349 AGTGTAAGACATGTCTAGAACATACATCG
1 AGTGTAAGACATGTCTAGGACATGCATCG
40909378 GCTACAAAAT
Statistics
Matches: 99, Mismatches: 14, Indels: 20
0.74 0.11 0.15
Matches are distributed among these distances:
45 4 0.04
46 46 0.46
47 26 0.26
48 21 0.21
49 1 0.01
50 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (45 bp):
AGTGTAAGACATGTCTAGGACATGCATCGACCACATTACGAAGCC
Found at i:40909451 original size:50 final size:48
Alignment explanation
Indices: 40909390--40909520 Score: 151
Period size: 50 Copynumber: 2.7 Consensus size: 48
40909380 TACAAAATGT
*
40909390 GTTAGTCTAAGACCATGTCTGGGACATGGCATCAGCAC-GGATATG-TGAG
1 GTTAGTGTAAGACCATGTCTGGGACATGGCATC-G-ACTGGATA-GCTGAG
* *
40909439 AGTTAGTGTAAGACCATGTCTAGGACATGGCATCGACTTGATAGCTGAG
1 -GTTAGTGTAAGACCATGTCTGGGACATGGCATCGACTGGATAGCTGAG
** *
40909488 CCTA-TGTAAGACCATGTCTGGGTCATGGCATCG
1 GTTAGTGTAAGACCATGTCTGGGACATGGCATCG
40909521 GCATTATACT
Statistics
Matches: 72, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
47 27 0.38
48 5 0.07
49 9 0.12
50 31 0.43
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (48 bp):
GTTAGTGTAAGACCATGTCTGGGACATGGCATCGACTGGATAGCTGAG
Found at i:40911667 original size:85 final size:85
Alignment explanation
Indices: 40911524--40911702 Score: 349
Period size: 85 Copynumber: 2.1 Consensus size: 85
40911514 GGCCGGCCAT
40911524 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
40911589 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
40911609 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
40911674 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
*
40911694 GGGCATGGG
1 GAGCATGGG
40911703 CAATAAAATA
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.37, C:0.08, G:0.28, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:40913047 original size:49 final size:49
Alignment explanation
Indices: 40912968--40913287 Score: 544
Period size: 49 Copynumber: 6.7 Consensus size: 49
40912958 TATTTGAATA
*
40912968 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
40913015 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
40913064 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
40913113 AATGTGAAAGTG--TATATATGTTATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
40913160 AATGTGAAAGTGTATATATGTGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
40913209 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
40913256 AATGTGAAAGTGTATATATATGTGATAAGGCC
1 AATGTGAAAGTGTATATATATGTGATAAGGCC
40913288 GAACCTTTAA
Statistics
Matches: 258, Mismatches: 9, Indels: 10
0.93 0.03 0.04
Matches are distributed among these distances:
47 101 0.39
49 157 0.61
ACGTcount: A:0.33, C:0.08, G:0.28, T:0.30
Consensus pattern (49 bp):
AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:40913076 original size:96 final size:95
Alignment explanation
Indices: 40912968--40913287 Score: 534
Period size: 96 Copynumber: 3.3 Consensus size: 95
40912958 TATTTGAATA
*
40912968 AATGTGAAAGTG-TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATAT
1 AATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TAT
40913032 ATATGTGATAAGGCCTAATGGCCGATGTGATG
64 ATATGTGATAAGGCCTAATGGCCGATGTGATG
*
40913064 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
*
40913129 TATGTTATAAGGCCTAATGGCCGATGTGATG
65 TATGTGATAAGGCCTAATGGCCGATGTGATG
*
40913160 AATGTGAAAGTGTATATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
* *
40913225 TATGTGATAAGGCCGAATGGCCAATGTGATG
65 TATGTGATAAGGCCTAATGGCCGATGTGATG
40913256 AATGTGAAAGTGTATATATATGTGATAAGGCC
1 AATGTGAAAGTG-ATATATATGTGATAAGGCC
40913288 GAACCTTTAA
Statistics
Matches: 213, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
96 168 0.79
98 45 0.21
ACGTcount: A:0.33, C:0.08, G:0.28, T:0.30
Consensus pattern (95 bp):
AATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
ATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:40913274 original size:145 final size:144
Alignment explanation
Indices: 40912968--40913287 Score: 552
Period size: 145 Copynumber: 2.2 Consensus size: 144
40912958 TATTTGAATA
40912968 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATA
*
40913033 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTA
66 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGGCCGA
*
40913098 ATAGCCGATGTGATG
130 ATAGCCAATGTGATG
* *
40913113 AATGTGAAAGTGTATATATGTTATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATA
*
40913178 TGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-TATATATGTGATAAGGCCGAA
66 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCGAA
*
40913242 TGGCCAATGTGATG
131 TAGCCAATGTGATG
40913256 AATGTGAAAGTGTATATATATGTGATAAGGCC
1 AATGTGAAAGTG--TATATATGTGATAAGGCC
40913288 GAACCTTTAA
Statistics
Matches: 166, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
143 44 0.27
145 122 0.73
ACGTcount: A:0.33, C:0.08, G:0.28, T:0.30
Consensus pattern (144 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATA
TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCGAA
TAGCCAATGTGATG
Found at i:40916915 original size:25 final size:25
Alignment explanation
Indices: 40916886--40916933 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
40916876 TTAAAACATG
** *
40916886 AAAATGACTGTTTTGCCCCTAGGTA
1 AAAATGACCATTTTACCCCTAGGTA
40916911 AAAATGACCATTTTACCCCTAGG
1 AAAATGACCATTTTACCCCTAGG
40916934 GTTTAATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (25 bp):
AAAATGACCATTTTACCCCTAGGTA
Found at i:40917099 original size:26 final size:25
Alignment explanation
Indices: 40917064--40917135 Score: 99
Period size: 26 Copynumber: 2.8 Consensus size: 25
40917054 GAGGAAGTGC
*
40917064 AAAAGGGCTTTGCCCTAGTTTACCGA
1 AAAAGGGCTTTGCCCTAGTTGACC-A
* *
40917090 AAAAGGGCTTTTGCCCCAGTTGATCA
1 AAAAGGGC-TTTGCCCTAGTTGACCA
40917116 AAAAGGGCTTTGCCCTAGTT
1 AAAAGGGCTTTGCCCTAGTT
40917136 ATTAAAAGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
25 11 0.27
26 17 0.41
27 13 0.32
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCTAGTTGACCA
Found at i:40927892 original size:25 final size:25
Alignment explanation
Indices: 40927863--40927910 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
40927853 TTATAACATG
* * *
40927863 AAAATGATTGTTTTGCCCCTAGGTA
1 AAAATGACTATTTTACCCCTAGGTA
40927888 AAAATGACTATTTTACCCCTAGG
1 AAAATGACTATTTTACCCCTAGG
40927911 GTTTAACTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (25 bp):
AAAATGACTATTTTACCCCTAGGTA
Found at i:40927998 original size:18 final size:19
Alignment explanation
Indices: 40927961--40927998 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
40927951 GATTTGATAC
40927961 GATATGCACATGTTATGTAT
1 GATATGCACATG-TATGTAT
40927981 GATATGCACATG-ATGTAT
1 GATATGCACATGTATGTAT
40927999 TCATTTATGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
20 12 0.67
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.37
Consensus pattern (19 bp):
GATATGCACATGTATGTAT
Found at i:40928086 original size:26 final size:24
Alignment explanation
Indices: 40928040--40928119 Score: 90
Period size: 25 Copynumber: 3.2 Consensus size: 24
40928030 GGAGGAAGTG
* *
40928040 CAAAACGGCTTTGCCCTAGTTTACT
1 CAAAAGGGCTTTGCCCCAGTTTA-T
*
40928065 GAAAAGGGCTTTTGCCCCAGTTTAT
1 CAAAAGGGC-TTTGCCCCAGTTTAT
40928090 CAAAACGGGCTTTGCCCCAG-TTAT
1 CAAAA-GGGCTTTGCCCCAGTTTAT
*
40928114 TAAAAG
1 CAAAAG
40928120 ATGCTAGGCC
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
23 1 0.02
24 8 0.17
25 22 0.46
26 17 0.35
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.29
Consensus pattern (24 bp):
CAAAAGGGCTTTGCCCCAGTTTAT
Found at i:40928368 original size:31 final size:31
Alignment explanation
Indices: 40928330--40928413 Score: 143
Period size: 31 Copynumber: 2.7 Consensus size: 31
40928320 TTGGTATAGT
*
40928330 AAAGGCTTCGGTCCAGTGATATGAATAATGA
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
*
40928361 AAAGGCTTCGGCCCAGTGATATGAATAATGT
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
40928392 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
40928414 CTGAGATTGA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
30 5 0.10
31 46 0.90
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGAATAATGA
Found at i:40936331 original size:43 final size:43
Alignment explanation
Indices: 40936228--40936331 Score: 147
Period size: 43 Copynumber: 2.4 Consensus size: 43
40936218 TAGCCCGGCT
* *
40936228 ATGGTCTTACACGA-AATCATATAACGATGCCAATGTCCCGGAC
1 ATGGTCTTACAC-ATAATCACATAACGATGCCAATGTCCCAGAC
* * *
40936271 ATAGTCTTACACGTAATCACATAATGATGCCAATGTCCCAGAC
1 ATGGTCTTACACATAATCACATAACGATGCCAATGTCCCAGAC
40936314 ATGGTCTTACACATAATC
1 ATGGTCTTACACATAATC
40936332 TCATCTCAGA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
43 53 1.00
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.26
Consensus pattern (43 bp):
ATGGTCTTACACATAATCACATAACGATGCCAATGTCCCAGAC
Found at i:40936869 original size:75 final size:75
Alignment explanation
Indices: 40936787--40936937 Score: 257
Period size: 75 Copynumber: 2.0 Consensus size: 75
40936777 CATTTTCCAT
* *
40936787 ATATTACTATCAGCCCATATTTCTAATTTATTTCACATTTTAACCACTAAACTTCCATATTTTAC
1 ATATTACTAACAGCCCATATTTCTAATTTATTTCACATTTTAACCACTAAACTTCCACATTTTAC
40936852 AATTTAGTCC
66 AATTTAGTCC
* * *
40936862 ATATTACTAACATCCCATATTTCTAATTTATTTCACATTTTAACCATTAAACTTCCACATTTTAT
1 ATATTACTAACAGCCCATATTTCTAATTTATTTCACATTTTAACCACTAAACTTCCACATTTTAC
40936927 AATTTAGTCC
66 AATTTAGTCC
40936937 A
1 A
40936938 AAATTGACAT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 71 1.00
ACGTcount: A:0.33, C:0.22, G:0.02, T:0.43
Consensus pattern (75 bp):
ATATTACTAACAGCCCATATTTCTAATTTATTTCACATTTTAACCACTAAACTTCCACATTTTAC
AATTTAGTCC
Found at i:40939975 original size:49 final size:50
Alignment explanation
Indices: 40939895--40940127 Score: 256
Period size: 49 Copynumber: 4.7 Consensus size: 50
40939885 ATCTATTGTG
40939895 AGGTCA-AGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 AGGTCACA-TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
* * * * *
40939945 -GGTCGCATGTGTAGTACTAAGTGTAGGCTACTATGCGTACCCGATAACTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-TT
* * ** * * **
40939995 CGATCATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
** * *
40940045 AGGTCATGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCGAATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
* *
40940095 -GGTCGCATGTGTAGTACTATGTGCAGGCTACTA
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTA
40940128 TGCGTACTAG
Statistics
Matches: 152, Mismatches: 28, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
49 69 0.45
50 47 0.31
51 36 0.24
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (50 bp):
AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
Found at i:40940104 original size:101 final size:98
Alignment explanation
Indices: 40939901--40940127 Score: 262
Period size: 100 Copynumber: 2.3 Consensus size: 98
40939891 TGTGAGGTCA
* *
40939901 AGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTACTAAG
1 AGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACATGTGTAGTACTAAG
* **
40939966 TGTAGGCTACTATGCGTACCCGATAACTTCGATC
66 TGCAGGCTACTACACGTACCCGATAACTTCGA-C
* ** **
40940000 ATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCATGTGTGTAGTACTA
1 A-GTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT-GGTCACATGTGTAGTACTA
* *
40940065 AGTGCAGGCTACTACATGTA-CCGAATAATTGGTCG-C
64 AGTGCAGGCTACTACACGTACCCG-ATAACT--TCGAC
*
40940101 A-TGTGTAGTACTATGTGCAGGCTACTA
1 AGTGTGTAGTACTAAGTGCAGGCTACTA
40940128 TGCGTACTAG
Statistics
Matches: 110, Mismatches: 13, Indels: 10
0.83 0.10 0.08
Matches are distributed among these distances:
99 26 0.24
100 42 0.38
101 39 0.35
103 3 0.03
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (98 bp):
AGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACATGTGTAGTACTAAG
TGCAGGCTACTACACGTACCCGATAACTTCGAC
Found at i:40948657 original size:15 final size:15
Alignment explanation
Indices: 40948637--40948697 Score: 63
Period size: 15 Copynumber: 4.1 Consensus size: 15
40948627 TTTGGGTTTT
40948637 TTTATTCTGGATTTC
1 TTTATTCTGGATTTC
*
40948652 TTTATTCTGGGTTTC
1 TTTATTCTGGATTTC
* *
40948667 TCTA-TCTTGGATTTA
1 TTTATTC-TGGATTTC
*
40948682 TTTATTC-GGTTTTC
1 TTTATTCTGGATTTC
40948696 TT
1 TT
40948698 GTTATCTTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
14 9 0.24
15 26 0.70
16 2 0.05
ACGTcount: A:0.11, C:0.13, G:0.15, T:0.61
Consensus pattern (15 bp):
TTTATTCTGGATTTC
Found at i:40960509 original size:19 final size:19
Alignment explanation
Indices: 40960485--40960524 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
40960475 TGAAAATGTG
40960485 TAAGTTATGCCTATAAATT
1 TAAGTTATGCCTATAAATT
*
40960504 TAAGTTATGCCTATGAATT
1 TAAGTTATGCCTATAAATT
40960523 TA
1 TA
40960525 TGATGACACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.42
Consensus pattern (19 bp):
TAAGTTATGCCTATAAATT
Found at i:40965793 original size:30 final size:30
Alignment explanation
Indices: 40965759--40965819 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
40965749 TCCTTAACTC
40965759 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
40965789 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
40965819 A
1 A
40965820 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Done.