Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 30 of 97
Found at i:12632232 original size:36 final size:36
Alignment explanation
Indices: 12632172--12632241 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
12632162 CGAAGGCAAG
* ** *
12632172 GTAAGGGATGCTAGGTCTGTTGGTGGCCGGTTTGCT
1 GTAAGGGATGATAGGTCTACTGGTGACCGGTTTGCT
* *
12632208 GTAAGGGATGATGGGTCTACTGGTGACCTGTTTG
1 GTAAGGGATGATAGGTCTACTGGTGACCGGTTTG
12632242 AGGGGTCCGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.14, C:0.13, G:0.40, T:0.33
Consensus pattern (36 bp):
GTAAGGGATGATAGGTCTACTGGTGACCGGTTTGCT
Found at i:12635934 original size:2 final size:2
Alignment explanation
Indices: 12635919--12635971 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
12635909 GAAAACTAGC
12635919 AT AT A- AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12635959 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
12635972 AAAGCTTCAC
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 47 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12636389 original size:54 final size:54
Alignment explanation
Indices: 12636287--12636472 Score: 207
Period size: 54 Copynumber: 3.5 Consensus size: 54
12636277 TCGAACTTAG
* ** **
12636287 TCTTGATCACAAACT-TCACTT-A-ATCTTCGCTTCAAAAGTCTTGGCAACTTGA
1 TCTTGATCACCAACTAT-ACTTGATATCTTCGCTTCAAGGGTCTTCACAACTTGA
* * * * *
12636339 TCTTGATCACGAATTATATTTGATATCTTTGCTTCAAGGGTTTTCACAACTTGA
1 TCTTGATCACCAACTATACTTGATATCTTCGCTTCAAGGGTCTTCACAACTTGA
* * *
12636393 TCTTGATCACCAACTATGCTTGATATCTTCGCTTCAAGGGTCTTCACGACTTAA
1 TCTTGATCACCAACTATACTTGATATCTTCGCTTCAAGGGTCTTCACAACTTGA
**
12636447 TCTTGATCACCAACTACGCTTGATAT
1 TCTTGATCACCAACTATACTTGATAT
12636473 ATTGATAACT
Statistics
Matches: 113, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
52 16 0.14
53 2 0.02
54 95 0.84
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.37
Consensus pattern (54 bp):
TCTTGATCACCAACTATACTTGATATCTTCGCTTCAAGGGTCTTCACAACTTGA
Found at i:12636502 original size:25 final size:25
Alignment explanation
Indices: 12636474--12636521 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
12636464 GCTTGATATA
12636474 TTGATAACTTGATCACGAACTTCTC
1 TTGATAACTTGATCACGAACTTCTC
*
12636499 TTGATGACTTGATCACGAACTTC
1 TTGATAACTTGATCACGAACTTC
12636522 ATTGCCGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (25 bp):
TTGATAACTTGATCACGAACTTCTC
Found at i:12636626 original size:18 final size:18
Alignment explanation
Indices: 12636605--12636639 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12636595 TATCTGAAAT
* *
12636605 GCTCTCAATCTTTGAATG
1 GCTCCCAATCTTCGAATG
12636623 GCTCCCAATCTTCGAAT
1 GCTCCCAATCTTCGAAT
12636640 ACCTCCGAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.29, G:0.14, T:0.34
Consensus pattern (18 bp):
GCTCCCAATCTTCGAATG
Found at i:12636951 original size:57 final size:57
Alignment explanation
Indices: 12636837--12636951 Score: 137
Period size: 57 Copynumber: 2.0 Consensus size: 57
12636827 AAGTTAGATG
* * **
12636837 TTATCTCTAAATTATATTAATTTATTTAGAGATAAATTAAATAATCTTATTTGATTT
1 TTATCTCTAAATTATATTAATTTATTTAGAGATAAATTAAATAACCTAATTAAATTT
*
12636894 TTATCTCTAAATTAGTA-TAA-TTA-TTAGAGATAAATTAAATGACCAATAATTAAATTT
1 TTATCTCTAAATTA-TATTAATTTATTTAGAGATAAATTAAATAACC--TAATTAAATTT
12636951 T
1 T
12636952 GGTTGGTTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
55 19 0.38
56 3 0.06
57 26 0.52
58 2 0.04
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (57 bp):
TTATCTCTAAATTATATTAATTTATTTAGAGATAAATTAAATAACCTAATTAAATTT
Found at i:12637441 original size:28 final size:28
Alignment explanation
Indices: 12637401--12637567 Score: 165
Period size: 28 Copynumber: 5.6 Consensus size: 28
12637391 TATGACCTGA
* *
12637401 GAAGATGTATATTGTAATAAAAATATTT
1 GAAGAAGTATATTGCAATAAAAATATTT
12637429 GAAGAAGTATATTGCAATAAGACTGTAATA-TT
1 GAAGAAGTATATTGCAATAA-A----AATATTT
* *
12637461 GAAAGAAGTATATTACAATAAAACTATTT
1 G-AAGAAGTATATTGCAATAAAAATATTT
* *
12637490 GAAGAAATATATTGCAATCAAACTATAATTTT
1 GAAGAAGTATATTGCAAT-AAA-AAT-A-TTT
*
12637522 GGAAGAAGTATATTGCAATAAAACTATTT
1 -GAAGAAGTATATTGCAATAAAAATATTT
12637551 GAAGAAGTATATTGCAA
1 GAAGAAGTATATTGCAA
12637568 AAAGACTTAT
Statistics
Matches: 116, Mismatches: 11, Indels: 24
0.77 0.07 0.16
Matches are distributed among these distances:
28 53 0.46
29 10 0.09
30 2 0.02
31 2 0.02
32 10 0.09
33 39 0.34
ACGTcount: A:0.47, C:0.06, G:0.15, T:0.32
Consensus pattern (28 bp):
GAAGAAGTATATTGCAATAAAAATATTT
Found at i:12637459 original size:33 final size:31
Alignment explanation
Indices: 12637401--12637598 Score: 150
Period size: 28 Copynumber: 6.5 Consensus size: 31
12637391 TATGACCTGA
* *
12637401 GAAGATGTATATTGTAATAAA---AATATTT
1 GAAGAAGTATATTGCAATAAACTTAATATTT
12637429 GAAGAAGTATATTGCAATAAGACTGTAATA-TT
1 GAAGAAGTATATTGCAATAA-ACT-TAATATTT
* *
12637461 GAAAGAAGTATATTACAATAAA---ACTATTT
1 G-AAGAAGTATATTGCAATAAACTTAATATTT
*
12637490 GAAGAAATATATTGCAATCAAACTATAAT-TTT
1 GAAGAAGTATATTGCAAT-AAACT-TAATATTT
*
12637522 GGAAGAAGTATATTGCAATAAA---ACTATTT
1 -GAAGAAGTATATTGCAATAAACTTAATATTT
*
12637551 GAAGAAGTATATTGCAAAAAGACTT-ATAATCTT
1 GAAGAAGTATATTGCAATAA-ACTTAAT-AT-TT
*
12637584 GGAAGAAATATATTG
1 -GAAGAAGTATATTG
12637599 TAATTGGTAT
Statistics
Matches: 137, Mismatches: 12, Indels: 36
0.74 0.06 0.19
Matches are distributed among these distances:
28 57 0.42
29 11 0.08
31 1 0.01
32 12 0.09
33 43 0.31
34 13 0.09
ACGTcount: A:0.46, C:0.06, G:0.15, T:0.32
Consensus pattern (31 bp):
GAAGAAGTATATTGCAATAAACTTAATATTT
Found at i:12637502 original size:61 final size:61
Alignment explanation
Indices: 12637401--12637598 Score: 272
Period size: 61 Copynumber: 3.2 Consensus size: 61
12637391 TATGACCTGA
* * * *
12637401 GAAGATGTATATTGTAATAAAAATATTTGAAGAAGTATATTGCAATAAGACTGTAATATTG
1 GAAGAAGTATATTGCAATAAAACTATTTGAAGAAGTATATTGCAATAAGACTATAATATTG
* * * *
12637462 AAAGAAGTATATTACAATAAAACTATTTGAAGAAATATATTGCAATCAA-ACTATAATTTTG
1 GAAGAAGTATATTGCAATAAAACTATTTGAAGAAGTATATTGCAAT-AAGACTATAATATTG
* *
12637523 GAAGAAGTATATTGCAATAAAACTATTTGAAGAAGTATATTGCAAAAAGACTTATAATCTTG
1 GAAGAAGTATATTGCAATAAAACTATTTGAAGAAGTATATTGCAATAAGAC-TATAATATTG
*
12637585 GAAGAAATATATTG
1 GAAGAAGTATATTG
12637599 TAATTGGTAT
Statistics
Matches: 120, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
60 2 0.02
61 94 0.78
62 24 0.20
ACGTcount: A:0.46, C:0.06, G:0.15, T:0.32
Consensus pattern (61 bp):
GAAGAAGTATATTGCAATAAAACTATTTGAAGAAGTATATTGCAATAAGACTATAATATTG
Found at i:12638464 original size:35 final size:36
Alignment explanation
Indices: 12638385--12638473 Score: 135
Period size: 36 Copynumber: 2.5 Consensus size: 36
12638375 ATTTAAATGA
* *
12638385 TGCTCTTTATAATAGCACTTGTCGAGCTTTGGAGAG
1 TGCTATTTATAATAGCACTTGTCGAGCCTTGGAGAG
* *
12638421 TGCTATTTATAATAGCACTTGTTGATCCTTGG-GAG
1 TGCTATTTATAATAGCACTTGTCGAGCCTTGGAGAG
12638456 TGCTATTTATAATAGCAC
1 TGCTATTTATAATAGCAC
12638474 ACAATTTAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 21 0.43
36 28 0.57
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (36 bp):
TGCTATTTATAATAGCACTTGTCGAGCCTTGGAGAG
Found at i:12646539 original size:8 final size:8
Alignment explanation
Indices: 12646521--12646573 Score: 56
Period size: 8 Copynumber: 6.9 Consensus size: 8
12646511 AAGTTTTTGT
12646521 TGGGT-AA
1 TGGGTAAA
12646528 TGGGTAAA
1 TGGGTAAA
* *
12646536 TGGGTTAG
1 TGGGTAAA
* *
12646544 TGGCTAAG
1 TGGGTAAA
12646552 TGGGTAAA
1 TGGGTAAA
12646560 TGGGT-AA
1 TGGGTAAA
12646567 TGGGTAA
1 TGGGTAA
12646574 TGAGTAGTCC
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
7 12 0.32
8 26 0.68
ACGTcount: A:0.28, C:0.02, G:0.42, T:0.28
Consensus pattern (8 bp):
TGGGTAAA
Found at i:12646831 original size:12 final size:12
Alignment explanation
Indices: 12646816--12646853 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
12646806 TTGAAATTTG
12646816 TTTTATTTTAAT
1 TTTTATTTTAAT
12646828 TTTTATTTTAA-
1 TTTTATTTTAAT
*
12646839 -TTTATTTTTAT
1 TTTTATTTTAAT
12646850 TTTT
1 TTTT
12646854 TTAAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
10 9 0.39
12 14 0.61
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTATTTTAAT
Found at i:12656949 original size:2 final size:2
Alignment explanation
Indices: 12656942--12656980 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
12656932 ATGGAGAATA
*
12656942 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12656981 ATTGAATAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:12657419 original size:33 final size:35
Alignment explanation
Indices: 12657333--12657448 Score: 89
Period size: 34 Copynumber: 3.4 Consensus size: 35
12657323 AATCTTTGTG
* * *
12657333 GCTTTGGCTACTGATTTTTAAGGGAG-AATAGTGCA
1 GCTTTGGCTACTGATTTTTGATGGAGAAAT-GAGCA
* ** *
12657368 -ATTAAGCTGCTGATTTTTGA-GGAGAAATAGAGCA
1 GCTTTGGCTACTGATTTTTGATGGAGAAAT-GAGCA
** *
12657402 GC-TTGGCTACTGA-TTTTGATGTTGATATGAGCA
1 GCTTTGGCTACTGATTTTTGATGGAGAAATGAGCA
12657435 GCTTTGGCTACTGA
1 GCTTTGGCTACTGA
12657449 AAATTATTGG
Statistics
Matches: 64, Mismatches: 13, Indels: 9
0.74 0.15 0.10
Matches are distributed among these distances:
33 17 0.27
34 47 0.73
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (35 bp):
GCTTTGGCTACTGATTTTTGATGGAGAAATGAGCA
Found at i:12657610 original size:1 final size:1
Alignment explanation
Indices: 12657580--12657646 Score: 80
Period size: 1 Copynumber: 67.0 Consensus size: 1
12657570 ACGGTGAAAG
* * * * * *
12657580 AAAAGAAAAGAAAACAAAACAAAAAGAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
12657645 AA
1 AA
12657647 TGGGCATGGC
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.91, C:0.03, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:12660120 original size:54 final size:54
Alignment explanation
Indices: 12660040--12660251 Score: 255
Period size: 54 Copynumber: 3.9 Consensus size: 54
12660030 ACTTCACTTG
* * ***
12660040 ATCTTCGCTTCAAGAGTCTT-AGCGACTTGATCTTGATCACGAACTATATTTGAT
1 ATCTTCGCTTCAAGGGTCTTCA-CGACTTGATCTTGATCACCAACTACGCTTGAT
* *
12660094 ATCTTTGCTTTAAGGGTCTTCACGACTTGATCTTGATCACCAACTACGCTTGAT
1 ATCTTCGCTTCAAGGGTCTTCACGACTTGATCTTGATCACCAACTACGCTTGAT
* * * * *
12660148 ATCTTCGCGTAAAGTGTTTTCACGACTTGATCTTGATCACCAACTACGCTTAAT
1 ATCTTCGCTTCAAGGGTCTTCACGACTTGATCTTGATCACCAACTACGCTTGAT
* * * * *
12660202 ATCTTTGCTTCAAGGGTCTTCACGACTTAATCTTAATCACGAACTTCGCT
1 ATCTTCGCTTCAAGGGTCTTCACGACTTGATCTTGATCACCAACTACGCT
12660252 CGATGACTTA
Statistics
Matches: 135, Mismatches: 22, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
54 134 0.99
55 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.36
Consensus pattern (54 bp):
ATCTTCGCTTCAAGGGTCTTCACGACTTGATCTTGATCACCAACTACGCTTGAT
Found at i:12665207 original size:20 final size:20
Alignment explanation
Indices: 12665179--12665217 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12665169 TAAATTCAGA
* *
12665179 TTAGTTTTAGTTATAGTTTG
1 TTAGATTTAATTATAGTTTG
*
12665199 TTAGATTTAATTTTAGTTT
1 TTAGATTTAATTATAGTTT
12665218 TTAATAATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (20 bp):
TTAGATTTAATTATAGTTTG
Found at i:12668135 original size:42 final size:41
Alignment explanation
Indices: 12668089--12668234 Score: 202
Period size: 42 Copynumber: 3.5 Consensus size: 41
12668079 GTGCTAGTAA
*
12668089 GAGTGCACATAAGCCGTTGCTGACCTGGCTATGTGTGAGTGG
1 GAGTGCACATAAGCCGTTGCT-ACCTGACTATGTGTGAGTGG
*
12668131 GAGTGCACATAAGCCGTTGCTAGCTCGACTATGTGTGAGTGG
1 GAGTGCACATAAGCCGTTGCTACCT-GACTATGTGTGAGTGG
* *
12668173 GAGTGCACATAAGCCGTTGCTAACCCGACTATGTGCGAGTGG
1 GAGTGCACATAAGCCGTTGCT-ACCTGACTATGTGTGAGTGG
***
12668215 GAGTATGCATAAGCCGTTGC
1 GAGTGCACATAAGCCGTTGC
12668235 ATATGAGATG
Statistics
Matches: 94, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
41 3 0.03
42 89 0.95
43 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.33, T:0.25
Consensus pattern (41 bp):
GAGTGCACATAAGCCGTTGCTACCTGACTATGTGTGAGTGG
Found at i:12670087 original size:163 final size:163
Alignment explanation
Indices: 12669812--12670127 Score: 497
Period size: 163 Copynumber: 1.9 Consensus size: 163
12669802 GCATAAGGAT
* * *
12669812 TAATTAACTTAGGGGGAGGTTTCAATAAATTTTAAATGCAATATGCTCATATTTTTGTCATATCA
1 TAATTAACTCAGGGGGAGGTTTCAAGAAATTTTAAATGCAATATGCTCATATTTTTATCATATCA
* * *
12669877 AAAAGAGGGAGATTGTTAGCCTTGAGTTACATCATGTTTTCATTTGACAAAAATCACAAATTTTC
66 AAAAGAGGGAGATTGATAACCTTAAGTTACATCATGTTTTCATTTGACAAAAATCACAAATTTTC
*
12669942 TTGAACCTAATGTCATGCATTTGGCATAGAGAC
131 TTGAACCTAATGTCAAGCATTTGGCATAGAGAC
* * *
12669975 TAATTAAGTCAGGGGGAGGTTTCAAGAAATTTTAAATGCAATATGCTTATGTTTTTATCATATCA
1 TAATTAACTCAGGGGGAGGTTTCAAGAAATTTTAAATGCAATATGCTCATATTTTTATCATATCA
* * * * *
12670040 AAAAGGGGGAGATTGATAACGTTAAGTTACATTATGTTTTGATTTGACAAAAATCACATATTTTC
66 AAAAGAGGGAGATTGATAACCTTAAGTTACATCATGTTTTCATTTGACAAAAATCACAAATTTTC
12670105 TTGAACCTAATGTCAAGCATTTG
131 TTGAACCTAATGTCAAGCATTTG
12670128 AAAGTGTCTT
Statistics
Matches: 138, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
163 138 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (163 bp):
TAATTAACTCAGGGGGAGGTTTCAAGAAATTTTAAATGCAATATGCTCATATTTTTATCATATCA
AAAAGAGGGAGATTGATAACCTTAAGTTACATCATGTTTTCATTTGACAAAAATCACAAATTTTC
TTGAACCTAATGTCAAGCATTTGGCATAGAGAC
Found at i:12672711 original size:19 final size:20
Alignment explanation
Indices: 12672682--12672721 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
12672672 TCACTTCTAA
12672682 ACTTCAAATCATACTCCAAT
1 ACTTCAAATCATACTCCAAT
12672702 ACTT-AAATCATACTCCAAT
1 ACTTCAAATCATACTCCAAT
12672721 A
1 A
12672722 AGTCAAATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (20 bp):
ACTTCAAATCATACTCCAAT
Found at i:12672782 original size:26 final size:26
Alignment explanation
Indices: 12672760--12672822 Score: 119
Period size: 26 Copynumber: 2.5 Consensus size: 26
12672750 TAAAAATTTT
12672760 CATTTTGTCCCCAAGTGGCAAATGAC
1 CATTTTGTCCCCAAGTGGCAAATGAC
12672786 CATTTTGTCCCCAAGTGGCAAATGAC
1 CATTTTGTCCCCAAGTGGCAAATGAC
12672812 CATTTTG-CCCC
1 CATTTTGTCCCC
12672823 TAGATAGTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 4 0.11
26 33 0.89
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (26 bp):
CATTTTGTCCCCAAGTGGCAAATGAC
Found at i:12673692 original size:52 final size:53
Alignment explanation
Indices: 12673623--12673781 Score: 187
Period size: 52 Copynumber: 2.9 Consensus size: 53
12673613 AAAAAGCAAG
* **
12673623 AATCTCTTTGTGGATTGTGTAAGGGTTATTGCTTGATCTTATTAAAAAGTAC-A
1 AATCT-TTTGTGGATTGTGTAAGGGTTATCGCTTGATCCCATTAAAAAGTACAA
* **
12673676 AATCTTTTGTGGATTGTGTAAGGGTTATCGCTAGATCCCCATTAAAAAAAAACAA
1 AATCTTTTGTGGATTGTGTAAGGGTTATCGCTTGAT-CCCATT-AAAAAGTACAA
* *
12673731 AATTCTTTTATGGATTGTGTGAGGGTTATCGCTT-AGTCCCATTAAAAAGTA
1 AA-TCTTTTGTGGATTGTGTAAGGGTTATCGCTTGA-TCCCATTAAAAAGTA
12673782 AGAATTCTTG
Statistics
Matches: 90, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
52 29 0.32
53 9 0.10
54 13 0.14
55 10 0.11
56 29 0.32
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.37
Consensus pattern (53 bp):
AATCTTTTGTGGATTGTGTAAGGGTTATCGCTTGATCCCATTAAAAAGTACAA
Found at i:12673802 original size:55 final size:56
Alignment explanation
Indices: 12673633--12673778 Score: 151
Period size: 56 Copynumber: 2.7 Consensus size: 56
12673623 AATCTCTTTG
* * ** ** **
12673633 TGGATTGTGTAAGGGTTATTGCTTGAT-CTTATT-AAAAAGTAC-AAA-TCTTTTG
1 TGGATTGTGTAAGGGTTATCGCTAGATCCCCATTAAAAAAAAACAAAATTCTTTAA
*
12673685 TGGATTGTGTAAGGGTTATCGCTAGATCCCCATTAAAAAAAAACAAAATTCTTTTA
1 TGGATTGTGTAAGGGTTATCGCTAGATCCCCATTAAAAAAAAACAAAATTCTTTAA
*
12673741 TGGATTGTGTGAGGGTTATCGCTTAG-T-CCCATTAAAAA
1 TGGATTGTGTAAGGGTTATCGC-TAGATCCCCATTAAAAA
12673779 GTAAGAATTC
Statistics
Matches: 81, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
52 25 0.31
53 4 0.05
54 7 0.09
55 14 0.17
56 28 0.35
57 3 0.04
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.36
Consensus pattern (56 bp):
TGGATTGTGTAAGGGTTATCGCTAGATCCCCATTAAAAAAAAACAAAATTCTTTAA
Found at i:12676228 original size:2 final size:2
Alignment explanation
Indices: 12676221--12676268 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
12676211 NNNNNNNNNN
*
12676221 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12676263 TA TA TA
1 TA TA TA
12676269 CCCATCATCA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:12676388 original size:43 final size:43
Alignment explanation
Indices: 12676314--12676432 Score: 132
Period size: 43 Copynumber: 2.8 Consensus size: 43
12676304 TCACCAGCTC
* ** *
12676314 ATGCGCACTCCCTACTCACACATGGTTGGGTCA-TCACCGGGTT
1 ATGCGCACTCCCTACTCACACATAGCCGGGTCATTC-CCGGCTT
* * * *
12676357 ATGCGCACTTCCTACTCGCACATAACCGGGTCATTCTCGGCTT
1 ATGCGCACTCCCTACTCACACATAGCCGGGTCATTCCCGGCTT
* *
12676400 ATGCGCACCCCCTACTCACACATAGCCGAGTCA
1 ATGCGCACTCCCTACTCACACATAGCCGGGTCA
12676433 AAATAATTAC
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
43 60 0.97
44 2 0.03
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCACACATAGCCGGGTCATTCCCGGCTT
Found at i:12680025 original size:218 final size:214
Alignment explanation
Indices: 12679507--12680120 Score: 775
Period size: 211 Copynumber: 2.8 Consensus size: 214
12679497 GTATAGCTAA
*
12679507 TTTGATTCATATAAGGAAGTGTTGACGAAGCCGT--TCTCTTCATTTTGGAACTACTGTTTTTCT
1 TTTGATTCATATAAGGAAGTATTGACGAAGCCGTAGTCTCTTCATTTTGGAACTAC-----TT-T
*
12679570 TTTTTTTTTTGCTTTCATTGTTCATTGCTTTTGCCAGCATTTCGGCTCTGCAGATGCTTGTAAGT
60 TTTTTTTCTTG--TTCATTGTTC-TTGCTTTTGCCAGCATTTCGGCTCTGCAGATGCTTGTAAGT
* *
12679635 TTTAATAATTTTTGAAATGCTAAGCAGTGGAATGAGGAAGTTGGCATTGATTTAGGTGATGTTAG
122 TTTAATAATTTTTTAAATGCTAAGCAGTGG-ATGAGGAAGTTGGCATTGATTTAGGT-AAGTTAG
12679700 ACAGTCTTTTGTCACTTTTTCTATTTTTTTTGGCTT
185 ACAGTCTTTTGTCA-----TC-ATTTTTTTTGGCTT
* * *
12679736 TTTTATTCATATAAAGAAGTATTGACGAAGTCGTAGTCTCTTCATTTTGGAACTAC---TTTTTT
1 TTTGATTCATATAAGGAAGTATTGACGAAGCCGTAGTCTCTTCATTTTGGAACTACTTTTTTTTT
* *
12679798 TC-T-TTCATTGTTCGTTGCTTTTGCCAGCATTTGGGCTTTGCAGATGCTTGTAAGTTTTAATAA
66 TCTTGTTCATTGTTC-TTGCTTTTGCCAGCATTTCGGCTCTGCAGATGCTTGTAAGTTTTAATAA
*
12679861 TTTTTTAAATGCTAAGCAGTGGATGAGGAAGTTGGCATTGATTTAGGTACAGTTAGCCAGTCTTT
130 TTTTTTAAATGCTAAGCAGTGGATGAGGAAGTTGGCATTGATTTAGGTA-AGTTAGACAGTCTTT
12679926 TGTCA-C-TTTTTTTTGGCTT
194 TGTCATCATTTTTTTTGGCTT
* * * * *
12679945 TTTGATTCATATGAGGAGGTATTGATGAAGCCTTAGTCTCTTCATTTTGGAACTAC-ATTTTTTT
1 TTTGATTCATATAAGGAAGTATTGACGAAGCCGTAGTCTCTTCATTTTGGAACTACTTTTTTTTT
* * * * *
12680009 TC-T-ATCATTGTTCATTGCTTTTGCCACCATTTTGGCGCTGCAGATGCTTGTAATTTTTAATAA
66 TCTTGTTCATTGTTC-TTGCTTTTGCCAGCATTTCGGCTCTGCAGATGCTTGTAAGTTTTAATAA
*
12680072 TTTTTTAAATGCTAAGCAGTGGAAGAGGAAGTTGGCATTGATTTAGGTA
130 TTTTTTAAATGCTAAGCAGTGGATGAGGAAGTTGGCATTGATTTAGGTA
12680121 GGGATGAACA
Statistics
Matches: 354, Mismatches: 26, Indels: 28
0.87 0.06 0.07
Matches are distributed among these distances:
209 62 0.18
211 111 0.31
216 1 0.00
217 44 0.12
218 78 0.22
221 1 0.00
222 7 0.02
229 30 0.08
231 20 0.06
ACGTcount: A:0.22, C:0.13, G:0.20, T:0.44
Consensus pattern (214 bp):
TTTGATTCATATAAGGAAGTATTGACGAAGCCGTAGTCTCTTCATTTTGGAACTACTTTTTTTTT
TCTTGTTCATTGTTCTTGCTTTTGCCAGCATTTCGGCTCTGCAGATGCTTGTAAGTTTTAATAAT
TTTTTAAATGCTAAGCAGTGGATGAGGAAGTTGGCATTGATTTAGGTAAGTTAGACAGTCTTTTG
TCATCATTTTTTTTGGCTT
Found at i:12680071 original size:211 final size:211
Alignment explanation
Indices: 12679572--12680120 Score: 807
Period size: 211 Copynumber: 2.6 Consensus size: 211
12679562 GTTTTTCTTT
12679572 TTTTTTTTGCTTTCATTGTTCATTGCTTTTGCCAGCATTTCGGCTCTGCAGATGCTTGTAAGTTT
1 TTTTTTTT-CTTTCATTGTTCATTGCTTTTGCCAGCATTTCGGCTCTGCAGATGCTTGTAAGTTT
* *
12679637 TAATAATTTTTGAAATGCTAAGCAGTGGAATGAGGAAGTTGGCATTGATTTAGGTGATGTTAGAC
65 TAATAATTTTTTAAATGCTAAGCAGTGG-ATGAGGAAGTTGGCATTGATTTAGGT-AAGTTAGAC
* *
12679702 AGTCTTTTGTCACTTTTTCTATTTTTTTTGGCTTTTTTATTCATATAAAGAAGTATTGACGAAGT
128 AGTCTTTTGTCA-----TC-ATTTTTTTTGGCTTTTTGATTCATATAAAGAAGTATTGACGAAGC
12679767 CGTAGTCTCTTCATTTTGGAACTAC
187 CGTAGTCTCTTCATTTTGGAACTAC
* * *
12679792 -TTTTTTTCTTTCATTGTTCGTTGCTTTTGCCAGCATTTGGGCTTTGCAGATGCTTGTAAGTTTT
1 TTTTTTTTCTTTCATTGTTCATTGCTTTTGCCAGCATTTCGGCTCTGCAGATGCTTGTAAGTTTT
*
12679856 AATAATTTTTTAAATGCTAAGCAGTGGATGAGGAAGTTGGCATTGATTTAGGTACAGTTAGCCAG
66 AATAATTTTTTAAATGCTAAGCAGTGGATGAGGAAGTTGGCATTGATTTAGGTA-AGTTAGACAG
* * * * *
12679921 TCTTTTGTCA-C-TTTTTTTTGGCTTTTTGATTCATATGAGGAGGTATTGATGAAGCCTTAGTCT
130 TCTTTTGTCATCATTTTTTTTGGCTTTTTGATTCATATAAAGAAGTATTGACGAAGCCGTAGTCT
12679984 CTTCATTTTGGAACTAC
195 CTTCATTTTGGAACTAC
* * * * *
12680001 ATTTTTTTTCTATCATTGTTCATTGCTTTTGCCACCATTTTGGCGCTGCAGATGCTTGTAATTTT
1 -TTTTTTTTCTTTCATTGTTCATTGCTTTTGCCAGCATTTCGGCTCTGCAGATGCTTGTAAGTTT
*
12680066 TAATAATTTTTTAAATGCTAAGCAGTGGAAGAGGAAGTTGGCATTGATTTAGGTA
65 TAATAATTTTTTAAATGCTAAGCAGTGGATGAGGAAGTTGGCATTGATTTAGGTA
12680121 GGGATGAACA
Statistics
Matches: 305, Mismatches: 21, Indels: 15
0.89 0.06 0.04
Matches are distributed among these distances:
209 62 0.20
211 111 0.36
216 1 0.00
217 44 0.14
218 80 0.26
219 7 0.02
ACGTcount: A:0.22, C:0.13, G:0.20, T:0.44
Consensus pattern (211 bp):
TTTTTTTTCTTTCATTGTTCATTGCTTTTGCCAGCATTTCGGCTCTGCAGATGCTTGTAAGTTTT
AATAATTTTTTAAATGCTAAGCAGTGGATGAGGAAGTTGGCATTGATTTAGGTAAGTTAGACAGT
CTTTTGTCATCATTTTTTTTGGCTTTTTGATTCATATAAAGAAGTATTGACGAAGCCGTAGTCTC
TTCATTTTGGAACTAC
Found at i:12682728 original size:173 final size:174
Alignment explanation
Indices: 12682438--12682779 Score: 618
Period size: 173 Copynumber: 2.0 Consensus size: 174
12682428 TCGTTCTGTC
*
12682438 TAAGTGCATGTTTGGCCTAGTTTTTTTTCAGCTTATCTACCTCTTAAAAGCAAAAGTCATGCCAA
1 TAAGTGCATGTTTGGCCTAGTTTTTTTTCAGCTTATCTACCTCTTAAAAACAAAAGTCATGCCAA
12682503 ACATGATCTGTTGAGAAACTCTTAAAAAAAAAGTAACTTTTTTTTAAGAATAAAATTTTT-AAAA
66 ACATGATCTGTTGAGAAACTCTTAAAAAAAAAGTAACTTTTTTTTAAGAATAAAATTTTTAAAAA
12682567 AAGAGCTT-AAAAAAAAGCTCCAGGGAGGAGCTTTTTCTTNTATTT
131 AAGAG-TTAAAAAAAAAGCTCCAGGGAGGAGCTTTTTCTT-TATTT
*
12682612 TAAGTGCTTGTTTGGCCTAG-TTTTTTTCAGCTTATCTACCTCTTAAAAACAAAAGTCATGCCAA
1 TAAGTGCATGTTTGGCCTAGTTTTTTTTCAGCTTATCTACCTCTTAAAAACAAAAGTCATGCCAA
*
12682676 ACATGATCTTTTGAGAAACTCTTAAAAAAAAAGTAACTTTTTTTTAAGAATAAAATTTTTAAAAA
66 ACATGATCTGTTGAGAAACTCTTAAAAAAAAAGTAACTTTTTTTTAAGAATAAAATTTTTAAAAA
12682741 AAGAGTTAAAAAAAAAGCTCCAGGGAGGAGCTTTTTCTT
131 AAGAGTTAAAAAAAAAGCTCCAGGGAGGAGCTTTTTCTT
12682780 CTCTTCTTTT
Statistics
Matches: 163, Mismatches: 3, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
173 104 0.64
174 59 0.36
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (174 bp):
TAAGTGCATGTTTGGCCTAGTTTTTTTTCAGCTTATCTACCTCTTAAAAACAAAAGTCATGCCAA
ACATGATCTGTTGAGAAACTCTTAAAAAAAAAGTAACTTTTTTTTAAGAATAAAATTTTTAAAAA
AAGAGTTAAAAAAAAAGCTCCAGGGAGGAGCTTTTTCTTTATTT
Found at i:12686500 original size:124 final size:124
Alignment explanation
Indices: 12686340--12686587 Score: 496
Period size: 124 Copynumber: 2.0 Consensus size: 124
12686330 CTATGGTGTA
12686340 GAGAATAGCCTTATACTCCCTTATCGTCTCTTTCTTGGGGTTAGACTAGTAGACAAGTGTAATCT
1 GAGAATAGCCTTATACTCCCTTATCGTCTCTTTCTTGGGGTTAGACTAGTAGACAAGTGTAATCT
12686405 TTGTTGTTTAGTAGTAAATCAACCAAACGCTGAAATGCCCAGTATGATGTTGGGTTGGC
66 TTGTTGTTTAGTAGTAAATCAACCAAACGCTGAAATGCCCAGTATGATGTTGGGTTGGC
12686464 GAGAATAGCCTTATACTCCCTTATCGTCTCTTTCTTGGGGTTAGACTAGTAGACAAGTGTAATCT
1 GAGAATAGCCTTATACTCCCTTATCGTCTCTTTCTTGGGGTTAGACTAGTAGACAAGTGTAATCT
12686529 TTGTTGTTTAGTAGTAAATCAACCAAACGCTGAAATGCCCAGTATGATGTTGGGTTGGC
66 TTGTTGTTTAGTAGTAAATCAACCAAACGCTGAAATGCCCAGTATGATGTTGGGTTGGC
12686588 TTACTAATTG
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
124 124 1.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.34
Consensus pattern (124 bp):
GAGAATAGCCTTATACTCCCTTATCGTCTCTTTCTTGGGGTTAGACTAGTAGACAAGTGTAATCT
TTGTTGTTTAGTAGTAAATCAACCAAACGCTGAAATGCCCAGTATGATGTTGGGTTGGC
Found at i:12693324 original size:2 final size:2
Alignment explanation
Indices: 12693317--12693369 Score: 76
Period size: 2 Copynumber: 28.0 Consensus size: 2
12693307 AGTCCTTGTC
*
12693317 TA TA TA TA TA TA TA T- TA TA -A TA T- TG TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12693356 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
12693370 NNNNNNNNNN
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
1 3 0.06
2 44 0.94
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12693387 original size:2 final size:2
Alignment explanation
Indices: 12693382--12693445 Score: 98
Period size: 2 Copynumber: 33.5 Consensus size: 2
12693372 NNNNNNNNNN
*
12693382 AT AT AT AT AT AT AT AT AT AT AT AT AT -T GT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12693423 AT AT AT AT AT AT AT A- AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
12693446 AAATAGTTTT
Statistics
Matches: 58, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
1 3 0.05
2 55 0.95
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12706966 original size:52 final size:52
Alignment explanation
Indices: 12706827--12707050 Score: 214
Period size: 59 Copynumber: 4.1 Consensus size: 52
12706817 AATTTCAATT
* * * * *
12706827 TTTTAAATCGAACCTATTATGAGATAGGTCAAGCCTAAATTAAGTTTAGGAATTTCA
1 TTTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTTT-GGGA----A
* * * *
12706884 TTTTTAAATCGAACCTGTTGTGAGAGAGGTCGAACTTAGATCAAGTTTGGGAA
1 -TTTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTTTGGGAA
* *
12706937 TTTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAA
1 TTTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGT-TTGG-----GAA
* *
12706995 TTTTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAA
1 -TTTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTTTGGGAA
12707048 TTT
1 TTT
12707051 CAATTTTTAN
Statistics
Matches: 140, Mismatches: 19, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
52 44 0.31
53 6 0.04
57 3 0.02
58 42 0.30
59 45 0.32
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (52 bp):
TTTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTTTGGGAA
Found at i:12707026 original size:59 final size:59
Alignment explanation
Indices: 12706937--12707059 Score: 246
Period size: 59 Copynumber: 2.1 Consensus size: 59
12706927 AGTTTGGGAA
12706937 TTTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAAT
1 TTTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAAT
12706996 TTTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAAT
1 TTTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAAT
12707055 TTTTA
1 TTTTA
12707060 NNNNNNNNNN
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 64 1.00
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (59 bp):
TTTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAAT
Found at i:12708600 original size:28 final size:29
Alignment explanation
Indices: 12708557--12708613 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
12708547 TTTACTTTTT
*
12708557 TAAATAATAATAATAAAAATTAAATAAAA
1 TAAATAATAATAATAAAAAGTAAATAAAA
* *
12708586 TAAAT-ATAGTAATAATAAGTAAATAAAA
1 TAAATAATAATAATAAAAAGTAAATAAAA
12708614 AATGAATGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 20 0.80
29 5 0.20
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (29 bp):
TAAATAATAATAATAAAAAGTAAATAAAA
Found at i:12710489 original size:79 final size:79
Alignment explanation
Indices: 12710358--12710513 Score: 260
Period size: 79 Copynumber: 2.0 Consensus size: 79
12710348 AATAACCCAT
12710358 CACAGTTTAGAATCACCACACCAATTGCTCCCAATGCTCATGCCATATTAGCAAAAGTAACCACA
1 CACAGTTTAGAATCACCACACCAATTGCTCCCAATGCTCATGCCATATTAGCAAAAGTAACCACA
*
12710423 TTCAGCAAACACAA
66 TCCAGCAAACACAA
* * *
12710437 CACAGTTTAGAA-CTAGCACACCAGTTGCTCCCAATGCTCATGCCATATTAGCACAAGTAACCAC
1 CACAGTTTAGAATC-ACCACACCAATTGCTCCCAATGCTCATGCCATATTAGCAAAAGTAACCAC
12710501 ATCCAGCAAACAC
65 ATCCAGCAAACAC
12710514 CAAAAACCTT
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
78 1 0.01
79 71 0.99
ACGTcount: A:0.37, C:0.31, G:0.12, T:0.20
Consensus pattern (79 bp):
CACAGTTTAGAATCACCACACCAATTGCTCCCAATGCTCATGCCATATTAGCAAAAGTAACCACA
TCCAGCAAACACAA
Found at i:12711748 original size:17 final size:17
Alignment explanation
Indices: 12711728--12711760 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12711718 CTTCCAAGTC
12711728 TTTAGTGCTTTAATTCT
1 TTTAGTGCTTTAATTCT
*
12711745 TTTAGTGCTTTCATTC
1 TTTAGTGCTTTAATTC
12711761 CTATCATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.15, G:0.12, T:0.58
Consensus pattern (17 bp):
TTTAGTGCTTTAATTCT
Found at i:12712670 original size:29 final size:27
Alignment explanation
Indices: 12712616--12712670 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
12712606 CAAGCACAAC
*
12712616 CTTTCTACCCTTTCAAGAAGGTATAAT
1 CTTTCTACCCTTTCAAGAAGCTATAAT
* *
12712643 CTTTCTACCTTTTGCTATGAAGCTATAA
1 CTTTCTACCCTTT-C-AAGAAGCTATAA
12712671 CCTCACAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 12 0.52
28 1 0.04
29 10 0.43
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.40
Consensus pattern (27 bp):
CTTTCTACCCTTTCAAGAAGCTATAAT
Found at i:12721798 original size:19 final size:20
Alignment explanation
Indices: 12721774--12721811 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
12721764 AGCTAAATAA
12721774 ATGTGTTTGACAAA-AAAAT
1 ATGTGTTTGACAAAGAAAAT
12721793 ATGTGTTTGACAAAGAAAA
1 ATGTGTTTGACAAAGAAAA
12721812 GGTAAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.47, C:0.05, G:0.18, T:0.29
Consensus pattern (20 bp):
ATGTGTTTGACAAAGAAAAT
Found at i:12728266 original size:35 final size:35
Alignment explanation
Indices: 12728240--12728392 Score: 153
Period size: 35 Copynumber: 4.3 Consensus size: 35
12728230 TTAATTGTTT
*
12728240 AATTTAATCAATTAGGCCCAATAACTTAATTAATC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
* ** * *
12728275 AATTTAATTAATTAATCCTAACAACTTAATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
* * *
12728310 AATTTTAATCAATTAGGCCCAATGACCTAATTAAAT
1 AA-TTTAATCAATTAGGCCCAATAACTTAATTAAAC
* * ** * *
12728346 AATTTAATTAATTAAGCTTAACAATTTAATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
12728381 AATTTTAATCAA
1 AA-TTTAATCAA
12728393 GTACTTGAGA
Statistics
Matches: 92, Mismatches: 24, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
35 57 0.62
36 35 0.38
ACGTcount: A:0.46, C:0.14, G:0.04, T:0.37
Consensus pattern (35 bp):
AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
Found at i:12728326 original size:71 final size:71
Alignment explanation
Indices: 12728242--12728392 Score: 241
Period size: 71 Copynumber: 2.1 Consensus size: 71
12728232 AATTGTTTAA
* *
12728242 TTTAATCAATTAGGCCCAATAACTTAATT-AATCAATTTAATTAATTAATCCTAACAACTTAATT
1 TTTAATCAATTAGGCCCAATAACCTAATTAAAT-AATTTAATTAATTAAGCCTAACAACTTAATT
12728306 AAACAAT
65 AAACAAT
* * *
12728313 TTTAATCAATTAGGCCCAATGACCTAATTAAATAATTTAATTAATTAAGCTTAACAATTTAATTA
1 TTTAATCAATTAGGCCCAATAACCTAATTAAATAATTTAATTAATTAAGCCTAACAACTTAATTA
12728378 AACAAT
66 AACAAT
12728384 TTTAATCAA
1 TTTAATCAA
12728393 GTACTTGAGA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
71 71 0.96
72 3 0.04
ACGTcount: A:0.45, C:0.14, G:0.04, T:0.37
Consensus pattern (71 bp):
TTTAATCAATTAGGCCCAATAACCTAATTAAATAATTTAATTAATTAAGCCTAACAACTTAATTA
AACAAT
Found at i:12730237 original size:2 final size:2
Alignment explanation
Indices: 12730230--12730258 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12730220 CATTTCTCAA
12730230 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12730259 ATAAAAAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12730294 original size:2 final size:2
Alignment explanation
Indices: 12730289--12730318 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12730279 CTANCTTTTT
12730289 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12730319 AAAAAAAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12732782 original size:35 final size:37
Alignment explanation
Indices: 12732684--12732788 Score: 108
Period size: 35 Copynumber: 2.8 Consensus size: 37
12732674 TTTACAAGCA
* *
12732684 ACTACCTTTTAAGAATCAAGTACAACCTCTTAACAAGTC
1 ACTACCTTTTAAGGATCAAGCACAACCTCTT-A-AAGTC
* *
12732723 ACTACCTTTTTCAA-GATCAGGCACAACCTCTT-TAGT-
1 ACTACC-TTTT-AAGGATCAAGCACAACCTCTTAAAGTC
*
12732759 ATTACCTTTTAAGGATCAAGCACAACCTCT
1 ACTACCTTTTAAGGATCAAGCACAACCTCT
12732789 CTATCTTTTC
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
34 2 0.04
35 20 0.35
36 5 0.09
37 3 0.05
39 6 0.11
40 19 0.33
41 2 0.04
ACGTcount: A:0.33, C:0.27, G:0.10, T:0.30
Consensus pattern (37 bp):
ACTACCTTTTAAGGATCAAGCACAACCTCTTAAAGTC
Found at i:12735150 original size:2 final size:2
Alignment explanation
Indices: 12735143--12735177 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
12735133 NNNNNNNNNN
*
12735143 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12735178 GGTATATGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:12740354 original size:2 final size:2
Alignment explanation
Indices: 12740347--12740382 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
12740337 NNNNNNNNNG
* *
12740347 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12740383 GGTATATGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:12742668 original size:22 final size:24
Alignment explanation
Indices: 12742643--12742690 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
12742633 ACATTCTATT
12742643 TTTTGAGA-ATCGA-TCTTTCCAC
1 TTTTGAGACATCGATTCTTTCCAC
*
12742665 TTTTGAGACATCGATTCTTTTCAC
1 TTTTGAGACATCGATTCTTTCCAC
12742689 TT
1 TT
12742691 CAATTTAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.35
23 5 0.22
24 10 0.43
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.46
Consensus pattern (24 bp):
TTTTGAGACATCGATTCTTTCCAC
Found at i:12742668 original size:23 final size:25
Alignment explanation
Indices: 12742642--12742690 Score: 68
Period size: 22 Copynumber: 2.1 Consensus size: 25
12742632 GACATTCTAT
12742642 TTTTTGAGA-ATCGA-TCTTTCCAC
1 TTTTTGAGACATCGATTCTTTCCAC
*
12742665 -TTTTGAGACATCGATTCTTTTCAC
1 TTTTTGAGACATCGATTCTTTCCAC
12742689 TT
1 TT
12742691 CAATTTAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 8 0.36
23 5 0.23
24 8 0.36
25 1 0.05
ACGTcount: A:0.20, C:0.20, G:0.12, T:0.47
Consensus pattern (25 bp):
TTTTTGAGACATCGATTCTTTCCAC
Found at i:12746786 original size:26 final size:27
Alignment explanation
Indices: 12746755--12746806 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
12746745 TTGTATANTC
*
12746755 ATTTAAATATTAATAT-TTTATTTATA
1 ATTTAAATATTAATATGATTATTTATA
* *
12746781 ATTTAAATTTTATTATGATTATTTAT
1 ATTTAAATATTAATATGATTATTTAT
12746807 TTTTATTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (27 bp):
ATTTAAATATTAATATGATTATTTATA
Found at i:12746792 original size:18 final size:19
Alignment explanation
Indices: 12746755--12746892 Score: 62
Period size: 19 Copynumber: 7.3 Consensus size: 19
12746745 TTGTATANTC
12746755 ATTTAAATATTAATATTTT
1 ATTTAAATATTAATATTTT
12746774 ATTTATAAT-TTAA-ATTTT
1 ATTTA-AATATTAATATTTT
* * *
12746792 ATTATGATTATTTAT-TTTT
1 ATT-TAAATATTAATATTTT
*
12746811 ATTT-AAT-TT--TA-TCT
1 ATTTAAATATTAATATTTT
12746825 -TTTAAATATTAATAATTTAT
1 ATTTAAATATTAAT-ATTT-T
*
12746845 ATTTTTTAAATATTAATAATTGATC
1 A---TTTAAATATTAAT-ATT--TT
*
12746870 ATTTCAATATTAATA-TTT
1 ATTTAAATATTAATATTTT
12746888 ATTTA
1 ATTTA
12746893 TATTTTAAAA
Statistics
Matches: 91, Mismatches: 10, Indels: 37
0.66 0.07 0.27
Matches are distributed among these distances:
13 3 0.03
14 6 0.07
15 2 0.02
16 2 0.02
17 3 0.03
18 17 0.19
19 21 0.23
20 5 0.05
21 1 0.01
22 12 0.13
24 17 0.19
25 1 0.01
26 1 0.01
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (19 bp):
ATTTAAATATTAATATTTT
Found at i:12746856 original size:24 final size:24
Alignment explanation
Indices: 12746814--12746930 Score: 95
Period size: 24 Copynumber: 5.0 Consensus size: 24
12746804 TATTTTTATT
*
12746814 TAATTT-TATCTTTTAAATATTAA
1 TAATTTATATTTTTTAAATATTAA
12746837 TAATTTATATTTTTTAAATATTAA
1 TAATTTATATTTTTTAAATATTAA
* *
12746861 TAATTGATCA---TTTCAATATTAA
1 TAATTTAT-ATTTTTTAAATATTAA
*
12746883 T-ATTTATTTATATTTTAAAATATTAA
1 TAATTTA--TAT-TTTTTAAATATTAA
*
12746909 T-A-TTATATTTAATTAAATATTA
1 TAATTTATATTT-TTTAAATATTA
12746931 TGATGATTAA
Statistics
Matches: 77, Mismatches: 8, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
21 4 0.05
22 15 0.19
23 19 0.25
24 23 0.30
25 4 0.05
26 12 0.16
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.55
Consensus pattern (24 bp):
TAATTTATATTTTTTAAATATTAA
Found at i:12746946 original size:59 final size:62
Alignment explanation
Indices: 12746878--12746993 Score: 145
Period size: 60 Copynumber: 1.9 Consensus size: 62
12746868 TCATTTCAAT
12746878 ATTAATA-TTTA-TTTATATTTTAAAATATTAAT-ATT-A-TATTTA-ATTAAATATTATGATG
1 ATTAATATTTTATTTTAT-TTTTAAAA-ATTAATAATTGATTATTTATATTAAATATTATGATG
* *
12746936 ATTAATTATTTTATTTTATTTTTGAAAATTAATAATTGATTATTTATTTTAAATATTA
1 ATTAA-TATTTTATTTTATTTTTAAAAATTAATAATTGATTATTTATATTAAATATTA
12746994 ATAATAGATA
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
58 5 0.10
59 8 0.16
60 14 0.29
61 6 0.12
62 6 0.12
63 10 0.20
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (62 bp):
ATTAATATTTTATTTTATTTTTAAAAATTAATAATTGATTATTTATATTAAATATTATGATG
Found at i:12746993 original size:27 final size:27
Alignment explanation
Indices: 12746950--12747127 Score: 84
Period size: 27 Copynumber: 6.6 Consensus size: 27
12746940 ATTATTTTAT
12746950 TTTATTTTTGAAA-ATTAATAATTGATTA
1 TTTA-TTTT-AAATATTAATAATTGATTA
* *
12746978 TTTATTTTAAATATTAATAATAGATAA
1 TTTATTTTAAATATTAATAATTGATTA
* * *
12747005 TTTATATT-AATATT--TATTTAATTTA
1 TTTATTTTAAATATTAATAATTGA-TTA
** * ** *
12747030 AATATTATT--ATGATTACTTTTTTATT-
1 TTTATT-TTAAAT-ATTAATAATTGATTA
* * *
12747056 TTATTTTTTAAATATTAATAATTGGTAA
1 TT-TATTTTAAATATTAATAATTGATTA
* *
12747084 TTTATTTAAAATATTAATAATTGATGA
1 TTTATTTTAAATATTAATAATTGATTA
12747111 TTTAATTATT-AATATTA
1 TTT-ATT-TTAAATATTA
12747128 TTTATCTAAT
Statistics
Matches: 112, Mismatches: 26, Indels: 24
0.69 0.16 0.15
Matches are distributed among these distances:
24 4 0.04
25 7 0.06
26 16 0.14
27 61 0.54
28 23 0.21
29 1 0.01
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (27 bp):
TTTATTTTAAATATTAATAATTGATTA
Found at i:12747030 original size:43 final size:39
Alignment explanation
Indices: 12746975--12747092 Score: 118
Period size: 43 Copynumber: 2.9 Consensus size: 39
12746965 TAATAATTGA
12746975 TTATTTATTTTAAATATTAATAATAGATAATTTATATTAATAT
1 TTATTTA-TTTAAATATTAATAAT-GATAATTTAT-TTAAT-T
* *
12747018 TTATTTAATTTAAATATT-ATTATGATTACTTT-TTT-ATT
1 TTATTT-ATTTAAATATTAATAATGA-TAATTTATTTAATT
*
12747056 TTATTT-TTTAAATATTAATAATTGGTAATTTATTTAA
1 TTATTTATTTAAATATTAATAA-TGATAATTTATTTAA
12747093 AATATTAATA
Statistics
Matches: 64, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
36 10 0.16
37 8 0.12
38 12 0.19
39 3 0.05
40 2 0.03
41 3 0.05
42 9 0.14
43 16 0.25
44 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (39 bp):
TTATTTATTTAAATATTAATAATGATAATTTATTTAATT
Found at i:12747031 original size:106 final size:106
Alignment explanation
Indices: 12746901--12747131 Score: 333
Period size: 106 Copynumber: 2.2 Consensus size: 106
12746891 TATATTTTAA
12746901 AATATTAATATTATATTTAATTAAATATTATGATGATTAATTATTTTATTTTATTTTTGAAA-AT
1 AATATTAATATT-TATTTAATTAAATATTATGATGATTAATT-TTTTATTTTATTTTTGAAATAT
* *
12746965 TAATAATTGATTATTTATTTTAAATATTAATAATAGATAATTT
64 TAATAATTGATAATTTATTTAAAATATTAATAATAGATAATTT
* * *
12747008 -ATATTAATATTTATTTAATTTAAATATTATTATGATTACTTTTTTATTTTATTTTTTAAATATT
1 AATATTAATATTTATTTAA-TTAAATATTATGATGATTAATTTTTTATTTTATTTTTGAAATATT
* * *
12747072 AATAATTGGTAATTTATTTAAAATATTAATAATTGATGATTT
65 AATAATTGATAATTTATTTAAAATATTAATAATAGATAATTT
12747114 AATTATTAATA-TTATTTA
1 AA-TATTAATATTTATTTA
12747132 TCTAATTTAA
Statistics
Matches: 112, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
105 25 0.22
106 71 0.63
107 8 0.07
108 8 0.07
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (106 bp):
AATATTAATATTTATTTAATTAAATATTATGATGATTAATTTTTTATTTTATTTTTGAAATATTA
ATAATTGATAATTTATTTAAAATATTAATAATAGATAATTT
Found at i:12747180 original size:11 final size:11
Alignment explanation
Indices: 12747146--12747173 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
12747136 ATTTAAATGA
12747146 TATTTTTTATT
1 TATTTTTTATT
12747157 TATTTTTTATT
1 TATTTTTTATT
12747168 TATTTT
1 TATTTT
12747174 GTTTTTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (11 bp):
TATTTTTTATT
Found at i:12747265 original size:111 final size:113
Alignment explanation
Indices: 12746945--12747267 Score: 266
Period size: 111 Copynumber: 2.9 Consensus size: 113
12746935 GATTAATTAT
** * *
12746945 TTTATTTTA-TTTTTGAAA-ATTAATAATTGATTATTTATTTTAAATATTAATAATAGATAATTT
1 TTTATTTTAGTTTTT-AAATAGGAATAATTGATAATTTA-TTT--ATATTAATAATTGATAATTT
* * *
12747008 --ATATT-A-A-TATTTATTTAATTTAAAT-AT-TA--TTA-TGATTACTTT-
62 AAATATTAATATTATTTATATAATTTAAATGATATATTTTATTTATT-TTTTA
* ** * *
12747050 TTTATTTTATTTTTTAAATATTAATAATTGGTAATTTATTTAAAATATTAATAATTGATGATTTA
1 TTTATTTTAGTTTTTAAATAGGAATAATTGATAATTTATTT---ATATTAATAATTGATAATTTA
* * *
12747115 ATTATTAATATTATTTATCTAATTTAAATGATATTTTTTATTTATTTTTTA
63 AATATTAATATTATTTATATAATTTAAATGATATATTTTATTTATTTTTTA
*
12747166 TTTATTTT-GTTTTTAAATAGGAATAATTTATAATTTATTT-TATTAATAATTGATAATTTAAAT
1 TTTATTTTAGTTTTTAAATAGGAATAATTGATAATTTATTTATATTAATAATTGATAATTTAAAT
* * *
12747229 -TTAATAATTTTTTTTATAATTTAATATTA-ATATTTTATT
66 ATTAAT-ATTATTTATATAATTTAA-ATGATATATTTTATT
12747268 AAAAGTTGGA
Statistics
Matches: 181, Mismatches: 21, Indels: 26
0.79 0.09 0.11
Matches are distributed among these distances:
105 15 0.08
106 42 0.23
108 4 0.02
109 1 0.01
110 6 0.03
111 62 0.34
112 5 0.03
113 1 0.01
115 33 0.18
116 12 0.07
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (113 bp):
TTTATTTTAGTTTTTAAATAGGAATAATTGATAATTTATTTATATTAATAATTGATAATTTAAAT
ATTAATATTATTTATATAATTTAAATGATATATTTTATTTATTTTTTA
Found at i:12749059 original size:6 final size:6
Alignment explanation
Indices: 12749044--12749085 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
12749034 AAGGGGATTT
* *
12749044 GCTTTG GCTCTG GCTCTG GCTTTG GCTTTG GCTTTG GCTTTG
1 GCTTTG GCTTTG GCTTTG GCTTTG GCTTTG GCTTTG GCTTTG
12749086 CTTATTGGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.00, C:0.21, G:0.33, T:0.45
Consensus pattern (6 bp):
GCTTTG
Found at i:12754695 original size:21 final size:20
Alignment explanation
Indices: 12754671--12754717 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
12754661 TTTAATTAAA
*
12754671 TTTTTATGTAAAT-TTATTAGT
1 TTTTTATATAAATATT-TTA-T
*
12754692 TTTTAATATAAATATTTTAT
1 TTTTTATATAAATATTTTAT
12754712 TTTTTA
1 TTTTTA
12754718 AAAATATCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 6 0.27
21 14 0.64
22 2 0.09
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (20 bp):
TTTTTATATAAATATTTTAT
Found at i:12764381 original size:75 final size:74
Alignment explanation
Indices: 12764290--12764432 Score: 223
Period size: 75 Copynumber: 1.9 Consensus size: 74
12764280 AAACCTATAC
* * *
12764290 TTATAAATATGTATTCATTAAATGACGATCATTGAAATATTTTTTTAGTATAATTATTTGTAAGA
1 TTATAAATATGAATTCATCAAATGACGATCATTGAAATA-TTTTTTAGTATAATTATTAGTAAGA
12764355 TTTAAACCTA
65 TTTAAACCTA
* * *
12764365 TTATAAATGTGAATTCATCAAATGATGATCATTGAAATATTTTTTATTATAATTATTAGTAAGAT
1 TTATAAATATGAATTCATCAAATGACGATCATTGAAATATTTTTTAGTATAATTATTAGTAAGAT
12764430 TTA
66 TTA
12764433 TTCCATTTAT
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
74 27 0.44
75 35 0.56
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (74 bp):
TTATAAATATGAATTCATCAAATGACGATCATTGAAATATTTTTTAGTATAATTATTAGTAAGAT
TTAAACCTA
Found at i:12768777 original size:44 final size:44
Alignment explanation
Indices: 12768680--12768940 Score: 306
Period size: 44 Copynumber: 5.8 Consensus size: 44
12768670 ACCATAAGTG
* *
12768680 TAGTTGAGTTCAACTAGATGAACAAAATATATATAGAATCTAAATGAGTC
1 TAGTTGAGATCAACTAGAT-AAC-AAA-ATATAT---ACCTAAATGAGTC
* * *
12768730 TAGTTGTGATCAACTAGATAACGAAATATATACCTAAATGAGCC
1 TAGTTGAGATCAACTAGATAACAAAATATATACCTAAATGAGTC
* * ** *
12768774 TAGTTGAGATTAATTAGATAATGAAATATATACCTAAATGAGCC
1 TAGTTGAGATCAACTAGATAACAAAATATATACCTAAATGAGTC
*
12768818 TAGTTGAGATCAACTATAGATAACAAAATTTATACCTAAATGAGTC
1 TAGTTGAGATCAAC--TAGATAACAAAATATATACCTAAATGAGTC
* *
12768864 TAGTTGAGATCAACCAGATAACAAAATATGTACCTAAATGAGTC
1 TAGTTGAGATCAACTAGATAACAAAATATATACCTAAATGAGTC
* * *
12768908 AAGTTGAGTTCAACCAGATAACAAAATATATAC
1 TAGTTGAGATCAACTAGATAACAAAATATATAC
12768941 TTTATCTCAA
Statistics
Matches: 188, Mismatches: 21, Indels: 10
0.86 0.10 0.05
Matches are distributed among these distances:
44 120 0.64
46 40 0.21
47 6 0.03
48 2 0.01
49 3 0.02
50 17 0.09
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (44 bp):
TAGTTGAGATCAACTAGATAACAAAATATATACCTAAATGAGTC
Found at i:12768867 original size:90 final size:88
Alignment explanation
Indices: 12768719--12768940 Score: 300
Period size: 90 Copynumber: 2.5 Consensus size: 88
12768709 TATATAGAAT
* *
12768719 CTAAATGAGTCTAGTTGTGATCAACTAGATAACGAAATATATACCTAAATGAGCCTAGTTGAGAT
1 CTAAATGAGTCTAGTTGAGATCAACTAGATAACAAAATATATACCTAAATGAGCCTAGTTGAGAT
* ** **
12768784 TAATTAGATAATGAAATATATAC
66 CAACCAGATAACAAAATATATAC
* * *
12768807 CTAAATGAGCCTAGTTGAGATCAACTATAGATAACAAAATTTATACCTAAATGAGTCTAGTTGAG
1 CTAAATGAGTCTAGTTGAGATCAAC--TAGATAACAAAATATATACCTAAATGAGCCTAGTTGAG
*
12768872 ATCAACCAGATAACAAAATATGTAC
64 ATCAACCAGATAACAAAATATATAC
* * *
12768897 CTAAATGAGTCAAGTTGAGTTCAACCAGATAACAAAATATATAC
1 CTAAATGAGTCTAGTTGAGATCAACTAGATAACAAAATATATAC
12768941 TTTATCTCAA
Statistics
Matches: 116, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
88 40 0.34
90 76 0.66
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (88 bp):
CTAAATGAGTCTAGTTGAGATCAACTAGATAACAAAATATATACCTAAATGAGCCTAGTTGAGAT
CAACCAGATAACAAAATATATAC
Found at i:12774538 original size:19 final size:19
Alignment explanation
Indices: 12774516--12774562 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 19
12774506 AAAAAGAAGT
12774516 TGAAAAGCAAAA-ATGAAAA
1 TGAAAAG-AAAAGATGAAAA
12774535 TGAAAA-AAAATGATGAAAA
1 TGAAAAGAAAA-GATGAAAA
12774554 TGGAAAAGA
1 T-GAAAAGA
12774563 GAAACAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
17 4 0.17
19 14 0.58
20 5 0.21
21 1 0.04
ACGTcount: A:0.66, C:0.02, G:0.19, T:0.13
Consensus pattern (19 bp):
TGAAAAGAAAAGATGAAAA
Found at i:12775618 original size:11 final size:12
Alignment explanation
Indices: 12775602--12775636 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
12775592 CGAATTAAAT
12775602 TTTTGTCAC-AA
1 TTTTGTCACTAA
12775613 TTTTGTCACTAA
1 TTTTGTCACTAA
12775625 TTTTGTCACTAA
1 TTTTGTCACTAA
12775637 ACAAGCAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.49
Consensus pattern (12 bp):
TTTTGTCACTAA
Found at i:12778822 original size:108 final size:107
Alignment explanation
Indices: 12778633--12778945 Score: 491
Period size: 108 Copynumber: 2.9 Consensus size: 107
12778623 AAGAACAAGA
* * * *
12778633 AAAAAAAAGGTTCAAGGTGAAAACTTAAAAAGACAGTTTGAATCCAAAGGAAGCAACTAAGTTGA
1 AAAAAAAAGGTTCAAGGTGAAAACCTAAAAGGACAATTTGAATCCAAAGGAGGCAACTAAGTTGA
12778698 AAACCTGAAAAGGTGACTTATGTACAAAGATTGATAACATAGG
66 AAACCTGAAAAGGTGACTTATGTACAAAGATTGATAACATA-G
*
12778741 AAAAAAAAGGTTCAAGGTGAAAACCTAAAAGGACAATTTGAATCCAAGGGAGGCAACTAAGTTGA
1 AAAAAAAAGGTTCAAGGTGAAAACCTAAAAGGACAATTTGAATCCAAAGGAGGCAACTAAGTTGA
*
12778806 AAACCTGAAAAGGTGACTTATGTACAAAGATTGATACCATAG
66 AAACCTGAAAAGGTGACTTATGTACAAAGATTGATAACATAG
** ** *
12778848 AGAAAAAAAGGTTTGAGGTGAAAACCTAAAAGGACAATTCAAATCCAAAGGAGGCAACTAAGGTG
1 A-AAAAAAAGGTTCAAGGTGAAAACCTAAAAGGACAATTTGAATCCAAAGGAGGCAACTAAGTTG
* *
12778913 AAAACTTGAAAAGGTGACTTATGCACAAAGATT
65 AAAACCTGAAAAGGTGACTTATGTACAAAGATT
12778946 TATAGCATGG
Statistics
Matches: 190, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
107 2 0.01
108 188 0.99
ACGTcount: A:0.47, C:0.12, G:0.21, T:0.19
Consensus pattern (107 bp):
AAAAAAAAGGTTCAAGGTGAAAACCTAAAAGGACAATTTGAATCCAAAGGAGGCAACTAAGTTGA
AAACCTGAAAAGGTGACTTATGTACAAAGATTGATAACATAG
Found at i:12779693 original size:48 final size:48
Alignment explanation
Indices: 12779618--12779921 Score: 242
Period size: 48 Copynumber: 6.6 Consensus size: 48
12779608 AAAAGAAAAA
* **
12779618 TTTT-CAATCTTTTTAAAGTTATGTAGCCTCGTTTAGAGATGAGGAGC
1 TTTTCCAATCATTTTAAAGTTACATAGCCTCGTTTAGAGATGAGGAGC
* *
12779665 TTTTCCAATCATTTTAAAGTTACATAGCCTTGTTTAGAGATGATGAGC
1 TTTTCCAATCATTTTAAAGTTACATAGCCTCGTTTAGAGATGAGGAGC
** * * * * * *
12779713 TTTTTGAATTATTTTAAAGTTTCGTAGCCTCATTTAGAGATAAGGAGA
1 TTTTCCAATCATTTTAAAGTTACATAGCCTCGTTTAGAGATGAGGAGC
* * *
12779761 TGTTCAAATCATTTTAAAG-T---T-G--T--TTT-GAGATGAAGAGC
1 TTTTCCAATCATTTTAAAGTTACATAGCCTCGTTTAGAGATGAGGAGC
* * * *
12779799 TTTTCTAATCATTTT-AAGTTGCATAACCTCGTTTAGAGATAAGGAGC
1 TTTTCCAATCATTTTAAAGTTACATAGCCTCGTTTAGAGATGAGGAGC
** * * * * *
12779846 TTTTCCAATCGCTTTGAA-TTGCGTAGCTTCGTTTAGAGGTGAGGAG-
1 TTTTCCAATCATTTTAAAGTTACATAGCCTCGTTTAGAGATGAGGAGC
*
12779892 TTTTCCCTATCA-TTTAAAGTTACATAGCCT
1 TTTT-CCAATCATTTTAAAGTTACATAGCCT
12779922 TATTTAAAGA
Statistics
Matches: 202, Mismatches: 41, Indels: 28
0.75 0.15 0.10
Matches are distributed among these distances:
37 3 0.01
38 23 0.11
39 3 0.01
41 2 0.01
43 1 0.00
44 2 0.01
46 12 0.06
47 63 0.31
48 93 0.46
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (48 bp):
TTTTCCAATCATTTTAAAGTTACATAGCCTCGTTTAGAGATGAGGAGC
Found at i:12780112 original size:17 final size:17
Alignment explanation
Indices: 12780092--12780131 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
12780082 TAATAGGAAA
*
12780092 AATAGAAAAATATAAAT
1 AATAAAAAAATATAAAT
*
12780109 AATAAAAAAATCTAAAT
1 AATAAAAAAATATAAAT
12780126 AA-AAAA
1 AATAAAA
12780132 GAGAAAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.20
Consensus pattern (17 bp):
AATAAAAAAATATAAAT
Found at i:12781738 original size:73 final size:73
Alignment explanation
Indices: 12781564--12781821 Score: 295
Period size: 73 Copynumber: 3.5 Consensus size: 73
12781554 GTCAAATAAT
* * * * *
12781564 CTTAGTCGACTAAGAAGTATCGTTAGTCAACTAAGAACTTACTGTCAGAAATCTGGATTACGAGA
1 CTTAATCGACTAAGAAGTATTGTTAGTCAACTAAGAGCTTACTGCCAGAAAT-TGGGTT-C-AGA
* *
12781629 TAGAAAGA--A
63 GACAAAGACGA
* * * * *
12781638 CTTAATCGACAAAGAAGCATTGCTAGTCAACCAAGAGCTTACTGCCAAAAATTGGGTTCAGAGAC
1 CTTAATCGACTAAGAAGTATTGTTAGTCAACTAAGAGCTTACTGCCAGAAATTGGGTTCAGAGAC
12781703 AAAGACGA
66 AAAGACGA
* * *
12781711 CTTAATCGACTAAGAAGTATTGTTAGTCGACTAAGAGCTCACTGCCAGAAATTGGGTTTAGAGAC
1 CTTAATCGACTAAGAAGTATTGTTAGTCAACTAAGAGCTTACTGCCAGAAATTGGGTTCAGAGAC
12781776 AAAGACGA
66 AAAGACGA
* * * * *
12781784 CTTAATTGACTAAGAAGCATAGTTAATCGACTAAGAGC
1 CTTAATCGACTAAGAAGTATTGTTAGTCAACTAAGAGC
12781822 ATTCTGTTTG
Statistics
Matches: 158, Mismatches: 24, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
71 9 0.06
72 1 0.01
73 105 0.66
74 43 0.27
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (73 bp):
CTTAATCGACTAAGAAGTATTGTTAGTCAACTAAGAGCTTACTGCCAGAAATTGGGTTCAGAGAC
AAAGACGA
Found at i:12781809 original size:21 final size:20
Alignment explanation
Indices: 12781785--12781823 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
12781775 CAAAGACGAC
*
12781785 TTAATTGACTAAGAAGCATAG
1 TTAATCGACTAAG-AGCATAG
12781806 TTAATCGACTAAGAGCAT
1 TTAATCGACTAAGAGCAT
12781824 TCTGTTTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (20 bp):
TTAATCGACTAAGAGCATAG
Found at i:12782257 original size:35 final size:35
Alignment explanation
Indices: 12782211--12782318 Score: 120
Period size: 35 Copynumber: 3.2 Consensus size: 35
12782201 GTTAGTTTTG
12782211 GGTT-TTGGTTGATCCCTTGAAAAACCATTGTTAAA
1 GGTTGTTGGTTGAT-CCTTGAAAAACCATTGTTAAA
* * *
12782246 GGTTGTT-GTTGAGCCTTGGAAAAGCCATT-TT--G
1 GGTTGTTGGTTGATCCTT-GAAAAACCATTGTTAAA
12782278 GGTT-TTGGTTGATCCTGTGAAAAACCATTGTTAAA
1 GGTTGTTGGTTGATCCT-TGAAAAACCATTGTTAAA
12782313 GGTTGT
1 GGTTGT
12782319 GGCAGAGCTT
Statistics
Matches: 59, Mismatches: 6, Indels: 15
0.74 0.08 0.19
Matches are distributed among these distances:
31 2 0.03
32 22 0.37
33 3 0.05
34 6 0.10
35 23 0.39
36 3 0.05
ACGTcount: A:0.24, C:0.12, G:0.26, T:0.38
Consensus pattern (35 bp):
GGTTGTTGGTTGATCCTTGAAAAACCATTGTTAAA
Found at i:12782279 original size:67 final size:67
Alignment explanation
Indices: 12782206--12782341 Score: 213
Period size: 67 Copynumber: 2.0 Consensus size: 67
12782196 GAAAAGTTAG
* **
12782206 TTTTGGGTTTTGGTTGATCCCT-TGAAAAACCATTGTTAAAGGTTGTTGTTGAGCCTTG-GAAAA
1 TTTTGGGTTTTGGTTGAT-CCTGTGAAAAACCATTGTTAAAGGTTGTGGCAGAG-CTTGTGAAAA
12782269 GCCA
64 GCCA
12782273 TTTTGGGTTTTGGTTGATCCTGTGAAAAACCATTGTTAAAGGTTGTGGCAGAGCTTGTGAAAAGC
1 TTTTGGGTTTTGGTTGATCCTGTGAAAAACCATTGTTAAAGGTTGTGGCAGAGCTTGTGAAAAGC
12782338 CA
66 CA
12782340 TT
1 TT
12782342 GTAATAGCTT
Statistics
Matches: 64, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
66 7 0.11
67 57 0.89
ACGTcount: A:0.24, C:0.12, G:0.26, T:0.37
Consensus pattern (67 bp):
TTTTGGGTTTTGGTTGATCCTGTGAAAAACCATTGTTAAAGGTTGTGGCAGAGCTTGTGAAAAGC
CA
Found at i:12782300 original size:32 final size:31
Alignment explanation
Indices: 12782206--12782306 Score: 105
Period size: 32 Copynumber: 3.1 Consensus size: 31
12782196 GAAAAGTTAG
12782206 TTTTGGGTTTTGGTTGATCCCTTGAAAAACCA
1 TTTTGGGTTTTGGTTGAT-CCTTGAAAAACCA
* * *
12782238 TTGTTAAAGGTTGTT-GTTGAGCCTTGGAAAAGCCA
1 TT-TT--GGGTT-TTGGTTGATCCTT-GAAAAACCA
12782273 TTTTGGGTTTTGGTTGATCCTGTGAAAAACCA
1 TTTTGGGTTTTGGTTGATCCT-TGAAAAACCA
12782305 TT
1 TT
12782307 GTTAAAGGTT
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
31 2 0.04
32 24 0.43
33 3 0.05
34 6 0.11
35 19 0.34
36 2 0.04
ACGTcount: A:0.23, C:0.13, G:0.25, T:0.40
Consensus pattern (31 bp):
TTTTGGGTTTTGGTTGATCCTTGAAAAACCA
Found at i:12782332 original size:35 final size:35
Alignment explanation
Indices: 12782228--12782343 Score: 114
Period size: 35 Copynumber: 3.4 Consensus size: 35
12782218 GTTGATCCCT
*
12782228 TGAAAAACCATTGTTAAAGGTTGTTGTTGAGCCTTG
1 TGAAAAACCATTGTTAAAGGTTGTGGTTGAG-CTTG
* * * * *
12782264 -GAAAAGCCATT-TT--GGGTTTTGGTTGATCCTG
1 TGAAAAACCATTGTTAAAGGTTGTGGTTGAGCTTG
**
12782295 TGAAAAACCATTGTTAAAGGTTGTGGCAGAGCTTG
1 TGAAAAACCATTGTTAAAGGTTGTGGTTGAGCTTG
*
12782330 TGAAAAGCCATTGT
1 TGAAAAACCATTGT
12782344 AATAGCTTGG
Statistics
Matches: 62, Mismatches: 14, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
31 3 0.05
32 20 0.32
33 2 0.03
34 2 0.03
35 35 0.56
ACGTcount: A:0.28, C:0.12, G:0.27, T:0.34
Consensus pattern (35 bp):
TGAAAAACCATTGTTAAAGGTTGTGGTTGAGCTTG
Found at i:12785834 original size:14 final size:15
Alignment explanation
Indices: 12785796--12785837 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
12785786 TTTAGAATAA
12785796 AATAATATT-ATATT
1 AATAATATTAATATT
*
12785810 AATAA-AATAATATT
1 AATAATATTAATATT
12785824 AA-AATATTAATATT
1 AATAATATTAATATT
12785838 TTATTCAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 4 0.17
14 20 0.83
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATAATATTAATATT
Found at i:12787569 original size:44 final size:44
Alignment explanation
Indices: 12787505--12787744 Score: 208
Period size: 44 Copynumber: 5.8 Consensus size: 44
12787495 AGGGAGTGTG
* *
12787505 GATGATGAGAT-TGCCTATGTGCGCGATGTGGCGGTGCACATGAT
1 GATGATGATATATGCC-ATGTGCGCGATGTGGGGGTGCACATGAT
*
12787549 GATGATGATATATGCCATGTGCGCGATGTGGGGGGAGCACATGAT
1 GATGATGATATATGCCATGTGCGCGATGT-GGGGGTGCACATGAT
* * * *
12787594 G--G--CAT-TA-G--TTGTGTGCGATGTGGGGGTGCACACGAT
1 GATGATGATATATGCCATGTGCGCGATGTGGGGGTGCACATGAT
* * *
12787630 GATGATGATATATGCCATGTGCACAATGTGGGGG-G-AGCA-CAT
1 GATGATGATATATGCCATGTGCGCGATGTGGGGGTGCA-CATGAT
* ** *
12787672 GATG--G-CAT-TG-GTTGTGCACGATGTGGGGGTGCACATGAT
1 GATGATGATATATGCCATGTGCGCGATGTGGGGGTGCACATGAT
12787711 GATGATGATATATGCCATGTGCGCGATGTGGGGG
1 GATGATGATATATGCCATGTGCGCGATGTGGGGG
12787745 GAGAACATGA
Statistics
Matches: 154, Mismatches: 23, Indels: 38
0.72 0.11 0.18
Matches are distributed among these distances:
36 14 0.09
37 27 0.18
38 6 0.04
39 10 0.06
40 5 0.03
41 5 0.03
42 10 0.06
43 6 0.04
44 53 0.34
45 18 0.12
ACGTcount: A:0.22, C:0.14, G:0.38, T:0.26
Consensus pattern (44 bp):
GATGATGATATATGCCATGTGCGCGATGTGGGGGTGCACATGAT
Found at i:12787619 original size:37 final size:37
Alignment explanation
Indices: 12787566--12787781 Score: 141
Period size: 37 Copynumber: 5.5 Consensus size: 37
12787556 ATATATGCCA
12787566 TGTGCGCGATGTGGGGGGAGCACATGATGGCATTAGT
1 TGTGCGCGATGTGGGGGGAGCACATGATGGCATTAGT
* *
12787603 TGTGTGCGATGTGGGGGTGCA-CACGATGATGATG-ATATATGCCA
1 TGTGCGCGATGTGGGGG-G-AGCAC-ATGATG--GCAT-TA-G--T
* * *
12787647 TGTGCACAATGTGGGGGGAGCACATGATGGCATTGGT
1 TGTGCGCGATGTGGGGGGAGCACATGATGGCATTAGT
* * * *
12787684 TGTGCACGATGT-GGGGGTGCACATGATGATGATGATATATGCCA
1 TGTGCGCGATGTGGGGGGAGCACATGATG--G--CAT-TA-G--T
*
12787728 TGTGCGCGATGTGGGGGGAGAACATGATGGCATTAGT
1 TGTGCGCGATGTGGGGGGAGCACATGATGGCATTAGT
* **
12787765 TATGCTTGATGTGGGGG
1 TGTGCGCGATGTGGGGG
12787782 TTCACACGAT
Statistics
Matches: 139, Mismatches: 20, Indels: 40
0.70 0.10 0.20
Matches are distributed among these distances:
36 15 0.11
37 41 0.29
38 5 0.04
39 9 0.06
40 8 0.06
41 8 0.06
42 9 0.06
43 5 0.04
44 25 0.18
45 14 0.10
ACGTcount: A:0.21, C:0.12, G:0.40, T:0.26
Consensus pattern (37 bp):
TGTGCGCGATGTGGGGGGAGCACATGATGGCATTAGT
Found at i:12787622 original size:81 final size:81
Alignment explanation
Indices: 12787522--12787793 Score: 427
Period size: 81 Copynumber: 3.4 Consensus size: 81
12787512 AGATTGCCTA
* *
12787522 TGTGCGCGATGTGGCGGTGCACATGATGATGATGATATATGCCATGTGCGCGATGTGGGGGGAGC
1 TGTGCGCGATGTGGGGGTGCACACGATGATGATGATATATGCCATGTGCGCGATGTGGGGGGAGC
12787587 ACATGATGGCATTAGT
66 ACATGATGGCATTAGT
* * *
12787603 TGTGTGCGATGTGGGGGTGCACACGATGATGATGATATATGCCATGTGCACAATGTGGGGGGAGC
1 TGTGCGCGATGTGGGGGTGCACACGATGATGATGATATATGCCATGTGCGCGATGTGGGGGGAGC
*
12787668 ACATGATGGCATTGGT
66 ACATGATGGCATTAGT
* * *
12787684 TGTGCACGATGTGGGGGTGCACATGATGATGATGATATATGCCATGTGCGCGATGTGGGGGGAGA
1 TGTGCGCGATGTGGGGGTGCACACGATGATGATGATATATGCCATGTGCGCGATGTGGGGGGAGC
12787749 ACATGATGGCATTAGT
66 ACATGATGGCATTAGT
* ** *
12787765 TATGCTTGATGTGGGGGTTCACACGATGA
1 TGTGCGCGATGTGGGGGTGCACACGATGA
12787794 CTTCGGCTAT
Statistics
Matches: 173, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 173 1.00
ACGTcount: A:0.22, C:0.14, G:0.38, T:0.26
Consensus pattern (81 bp):
TGTGCGCGATGTGGGGGTGCACACGATGATGATGATATATGCCATGTGCGCGATGTGGGGGGAGC
ACATGATGGCATTAGT
Found at i:12790466 original size:2 final size:2
Alignment explanation
Indices: 12790459--12790501 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
12790449 TTTCTATAAC
12790459 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12790501 A
1 A
12790502 CATACATCAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12790604 original size:43 final size:43
Alignment explanation
Indices: 12790535--12790650 Score: 162
Period size: 43 Copynumber: 2.7 Consensus size: 43
12790525 TCGCCACACA
* *
12790535 CAGCTCATGTGCACTCCCTAC-TCGCACATAGCCGGGTCATCAT
1 CAGCTCATGTGCACTCCC-ACACCGCACATAGCCAGGTCATCAT
*
12790578 CAGCTCATGTGCACTCCCACACCGCACATAGCTAGGTCATCAT
1 CAGCTCATGTGCACTCCCACACCGCACATAGCCAGGTCATCAT
* * *
12790621 CAACTCATATGCACTCCCACACCGTACATA
1 CAGCTCATGTGCACTCCCACACCGCACATA
12790651 ATTGGGTCAT
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
42 2 0.03
43 64 0.97
ACGTcount: A:0.26, C:0.38, G:0.15, T:0.22
Consensus pattern (43 bp):
CAGCTCATGTGCACTCCCACACCGCACATAGCCAGGTCATCAT
Found at i:12793356 original size:23 final size:23
Alignment explanation
Indices: 12793286--12793875 Score: 349
Period size: 23 Copynumber: 25.5 Consensus size: 23
12793276 TGTAAGTACT
*
12793286 ATATTTGACAT-AGCATGGTGAGA
1 ATATGTGACATGA-CATGGTGAGA
* * * * *
12793309 ATATGTGAGACGACATAGAGGGA
1 ATATGTGACATGACATGGTGAGA
* *
12793332 ATATGTGACACGACATGTTGAGA
1 ATATGTGACATGACATGGTGAGA
* * * *
12793355 ATATGTAACATGCCATGGAGGGA
1 ATATGTGACATGACATGGTGAGA
*
12793378 ATATGTGACATGCCATGGTGAGA
1 ATATGTGACATGACATGGTGAGA
* * *
12793401 ATATGTGAGATGCCA-GG-AAGGA
1 ATATGTGACATGACATGGTGA-GA
*
12793423 ATATGTGACATGCCATGGTGAG-
1 ATATGTGACATGACATGGTGAGA
* * *
12793445 -TATGTGAGACGACATGGAGAGGGAGGGA
1 ATATGTGACATGACAT---G-GTGA--GA
* * *
12793473 ATATGAGACATGGCATGTTGAGA
1 ATATGTGACATGACATGGTGAGA
* *
12793496 ATATGTGACATGGCATTGTGAGA
1 ATATGTGACATGACATGGTGAGA
* ** *
12793519 ATATGTGACACGGTAGGGTGAGA
1 ATATGTGACATGACATGGTGAGA
* * *
12793542 ATATGTGACATGCCATGGAGGGA
1 ATATGTGACATGACATGGTGAGA
*
12793565 ATATGTGAGATGACATGGTGAGA
1 ATATGTGACATGACATGGTGAGA
* * * *
12793588 CTATGTGACATGCCAAAGGTGACA
1 ATATGTGACATGAC-ATGGTGAGA
* * * *
12793612 ATATATGACA-CACCATGGAGGGA
1 ATATGTGACATGA-CATGGTGAGA
* * *
12793635 ATAAGTGAGATGACATGGTGACA
1 ATATGTGACATGACATGGTGAGA
* * * *
12793658 ATATGTGACACGCCAAGGTGAGT
1 ATATGTGACATGACATGGTGAGA
* *
12793681 ATATGTGACA-CACCATAGATG-GA
1 ATATGTGACATGA-CAT-GGTGAGA
* *
12793704 ATATGTGGCATGCCATGGTGAGA
1 ATATGTGACATGACATGGTGAGA
* * *
12793727 ATATGTTACACGGCATGGTGAGA
1 ATATGTGACATGACATGGTGAGA
* * * * * *
12793750 ATATATGAGACGACATAGAGGGA
1 ATATGTGACATGACATGGTGAGA
*
12793773 ATATGTGACATGACATGGAGAGA
1 ATATGTGACATGACATGGTGAGA
* *
12793796 ATATGTG-CATGCCATGG-AAGGA
1 ATATGTGACATGACATGGTGA-GA
*
12793818 ATATGTGACATGCCATGGGTG-GA
1 ATATGTGACATGACAT-GGTGAGA
* * *
12793841 ATATGTGGCACGCCATGGATG-GA
1 ATATGTGACATGACATGG-TGAGA
12793864 ATATGTGACATG
1 ATATGTGACATG
12793876 GCATAAATGT
Statistics
Matches: 433, Mismatches: 110, Indels: 48
0.73 0.19 0.08
Matches are distributed among these distances:
21 14 0.03
22 41 0.09
23 335 0.77
24 25 0.06
25 5 0.01
26 1 0.00
27 1 0.00
29 11 0.03
ACGTcount: A:0.33, C:0.12, G:0.32, T:0.23
Consensus pattern (23 bp):
ATATGTGACATGACATGGTGAGA
Found at i:12793358 original size:46 final size:46
Alignment explanation
Indices: 12793286--12793875 Score: 384
Period size: 46 Copynumber: 12.8 Consensus size: 46
12793276 TGTAAGTACT
* * * * *
12793286 ATATTTGACAT-AGCATGGTGAGAATATGTGAGACGACATAGAGGGA
1 ATATGTGACATGA-CATGGTGAGAATATGTGACATGCCATGGAGGGA
* * *
12793332 ATATGTGACACGACATGTTGAGAATATGTAACATGCCATGGAGGGA
1 ATATGTGACATGACATGGTGAGAATATGTGACATGCCATGGAGGGA
* * *
12793378 ATATGTGACATGCCATGGTGAGAATATGTGAGATGCCA-GGAAGGA
1 ATATGTGACATGACATGGTGAGAATATGTGACATGCCATGGAGGGA
* * * * ** *
12793423 ATATGTGACATGCCATGGTGAGTATGTGAGACGACATGGAGAGGGAGGGA
1 ATATGTGACATGACATGGTGAGAATAT--G-TGACAT-GCCATGGAGGGA
* * * * * * *
12793473 ATATGAGACATGGCATGTTGAGAATATGTGACATGGCATTGTGAGA
1 ATATGTGACATGACATGGTGAGAATATGTGACATGCCATGGAGGGA
* ** *
12793519 ATATGTGACACGGTAGGGTGAGAATATGTGACATGCCATGGAGGGA
1 ATATGTGACATGACATGGTGAGAATATGTGACATGCCATGGAGGGA
* * * * **
12793565 ATATGTGAGATGACATGGTGAGACTATGTGACATGCCAAAGGTGACA
1 ATATGTGACATGACATGGTGAGAATATGTGACATGCC-ATGGAGGGA
* * * * * * * * **
12793612 ATATATGACA-CACCATGGAGGGAATAAGTGAGATGACATGGTGACA
1 ATATGTGACATGA-CATGGTGAGAATATGTGACATGCCATGGAGGGA
* * * * ** * *
12793658 ATATGTGACACGCCAAGGTGAGTATATGTGACACACCATAGATGGA
1 ATATGTGACATGACATGGTGAGAATATGTGACATGCCATGGAGGGA
* * * * * * *
12793704 ATATGTGGCATGCCATGGTGAGAATATGTTACACGGCATGGTGAGA
1 ATATGTGACATGACATGGTGAGAATATGTGACATGCCATGGAGGGA
* * * * * * * *
12793750 ATATATGAGACGACATAGAGGGAATATGTGACATGACATGGAGAGA
1 ATATGTGACATGACATGGTGAGAATATGTGACATGCCATGGAGGGA
* *
12793796 ATATGTG-CATGCCATGG-AAGGAATATGTGACATGCCATGG-GTGGA
1 ATATGTGACATGACATGGTGA-GAATATGTGACATGCCATGGAG-GGA
* * *
12793841 ATATGTGGCACGCCATGGATG-GAATATGTGACATG
1 ATATGTGACATGACATGG-TGAGAATATGTGACATG
12793876 GCATAAATGT
Statistics
Matches: 417, Mismatches: 113, Indels: 28
0.75 0.20 0.05
Matches are distributed among these distances:
44 1 0.00
45 65 0.16
46 278 0.67
47 38 0.09
48 5 0.01
49 2 0.00
50 28 0.07
ACGTcount: A:0.33, C:0.12, G:0.32, T:0.23
Consensus pattern (46 bp):
ATATGTGACATGACATGGTGAGAATATGTGACATGCCATGGAGGGA
Found at i:12793568 original size:69 final size:69
Alignment explanation
Indices: 12793286--12793873 Score: 427
Period size: 69 Copynumber: 8.5 Consensus size: 69
12793276 TGTAAGTACT
* * * ** * * * *
12793286 ATATTTGACATAG-CATGGTGAGAATATGTGAGACGACATAGAGGGAATATGTGACACGACATGT
1 ATATGTGACAT-GCCATGGTGAGAATATGTGACACGCCAGGGTGAGAATATGTGACACGCCATGG
* *
12793350 TGAGA
65 AGGGA
* * * * * * *
12793355 ATATGTAACATGCCATGGAGGGAATATGTGACATGCCATGGTGAGAATATGTGAGATGCCA-GGA
1 ATATGTGACATGCCATGGTGAGAATATGTGACACGCCAGGGTGAGAATATGTGACACGCCATGGA
*
12793419 AGGA
66 GGGA
* * * * * *
12793423 ATATGTGACATGCCATGGTGAG--TATGTGAGACGACATGGAGAGGGAGGGAATATGAGACATGG
1 ATATGTGACATGCCATGGTGAGAATATGTGACACGCCA--G-G-GTGA--GAATATGTGACACGC
** *
12793486 CATGTTGAGA
60 CATGGAGGGA
* * ** *
12793496 ATATGTGACATGGCATTGTGAGAATATGTGACACGGTAGGGTGAGAATATGTGACATGCCATGGA
1 ATATGTGACATGCCATGGTGAGAATATGTGACACGCCAGGGTGAGAATATGTGACACGCCATGGA
12793561 GGGA
66 GGGA
* * * * * * * *
12793565 ATATGTGAGATGACATGGTGAGACTATGTGACATGCCAAAGGTGACAATATATGACACACCATGG
1 ATATGTGACATGCCATGGTGAGAATATGTGACACGCC-AGGGTGAGAATATGTGACACGCCATGG
12793630 AGGGA
65 AGGGA
* * * * * * * *
12793635 ATAAGTGAGATGACATGGTGACAATATGTGACACGCCAAGGTGAGTATATGTGACACACCATAGA
1 ATATGTGACATGCCATGGTGAGAATATGTGACACGCCAGGGTGAGAATATGTGACACGCCATGGA
*
12793700 TGGA
66 GGGA
* * * * * * * *
12793704 ATATGTGGCATGCCATGGTGAGAATATGTTACACGGCATGGTGAGAATATATGAGACGACATAGA
1 ATATGTGACATGCCATGGTGAGAATATGTGACACGCCAGGGTGAGAATATGTGACACGCCATGGA
12793769 GGGA
66 GGGA
* * * * * *
12793773 ATATGTGACATGACATGGAGAGAATATGTG-CATGCCATGG-AAGGAATATGTGACATGCCATGG
1 ATATGTGACATGCCATGGTGAGAATATGTGACACGCCAGGGTGA-GAATATGTGACACGCCATGG
12793836 -GTGGA
65 AG-GGA
* *
12793841 ATATGTGGCACGCCATGGATG-GAATATGTGACA
1 ATATGTGACATGCCATGG-TGAGAATATGTGACA
12793874 TGGCATAAAT
Statistics
Matches: 410, Mismatches: 94, Indels: 30
0.77 0.18 0.06
Matches are distributed among these distances:
66 11 0.03
67 2 0.00
68 73 0.18
69 208 0.51
70 63 0.15
71 3 0.01
72 15 0.04
73 24 0.06
75 11 0.03
ACGTcount: A:0.34, C:0.12, G:0.32, T:0.23
Consensus pattern (69 bp):
ATATGTGACATGCCATGGTGAGAATATGTGACACGCCAGGGTGAGAATATGTGACACGCCATGGA
GGGA
Found at i:12793843 original size:91 final size:92
Alignment explanation
Indices: 12793702--12793875 Score: 221
Period size: 91 Copynumber: 1.9 Consensus size: 92
12793692 ACCATAGATG
* * *
12793702 GAATATGTGGCATGCCATGGTGAGAATATGTTACACGGCATGGTGAGAATATATGAG-ACGACAT
1 GAATATGTGGCATGCCATGGAGAGAATATGTGACACGCCATGGTGAGAATATATG-GCACGACAT
12793766 AGAGGGAATATGTGACATGACATGGAGA
65 AGAGGGAATATGTGACATGACATGGAGA
* * *
12793794 GAATATGT-GCATGCCATGGA-AGGAATATGTGACATGCCATGGGTG-GAATATGTGGCACGCCA
1 GAATATGTGGCATGCCATGGAGA-GAATATGTGACACGCCAT-GGTGAGAATATATGGCACGACA
* *
12793856 TGGATGGAATATGTGACATG
64 TAGAGGGAATATGTGACATG
12793876 GCATAAATGT
Statistics
Matches: 71, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
90 2 0.03
91 57 0.80
92 12 0.17
ACGTcount: A:0.32, C:0.12, G:0.32, T:0.24
Consensus pattern (92 bp):
GAATATGTGGCATGCCATGGAGAGAATATGTGACACGCCATGGTGAGAATATATGGCACGACATA
GAGGGAATATGTGACATGACATGGAGA
Found at i:12804290 original size:20 final size:20
Alignment explanation
Indices: 12804246--12804283 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12804236 ATAGTCTTTA
*
12804246 ATTACTCAATTTCTAAAATC
1 ATTATTCAATTTCTAAAATC
12804266 ATTATTCAATTTC-AAAAT
1 ATTATTCAATTTCTAAAAT
12804284 GATTTATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTATTCAATTTCTAAAATC
Found at i:12818084 original size:20 final size:20
Alignment explanation
Indices: 12818059--12818105 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
12818049 AATCATAACC
12818059 AAATTAAAAGGAA-TAACATA
1 AAATTAAAA-GAACTAACATA
* *
12818079 AAATTAAAATAACTAACTTA
1 AAATTAAAAGAACTAACATA
12818099 AAATTAA
1 AAATTAA
12818106 CCTAATTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26
Consensus pattern (20 bp):
AAATTAAAAGAACTAACATA
Found at i:12823332 original size:18 final size:16
Alignment explanation
Indices: 12823306--12823355 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 16
12823296 TGCAAGATTT
12823306 TTCTTCTTTTCTTTGGC
1 TTCTTCTTTTCTTT-GC
*
12823323 TTCTTTCTTTTCCTTTTC
1 TTC-TTCTTTT-CTTTGC
12823341 TTCTTCTTCTTCTTT
1 TTCTTCTT-TTCTTT
12823356 CAGTTCAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 12 0.41
18 13 0.45
19 4 0.14
ACGTcount: A:0.00, C:0.26, G:0.04, T:0.70
Consensus pattern (16 bp):
TTCTTCTTTTCTTTGC
Found at i:12826195 original size:42 final size:42
Alignment explanation
Indices: 12826136--12826220 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
12826126 GGCGTAAACA
12826136 ACATCTAACAAGCGTGGTGTGTAACAATATAATACTACAATG
1 ACATCTAACAAGCGTGGTGTGTAACAATATAATACTACAATG
*
12826178 ACATCTAACAAGCGTGGTGTGTAACAATATAATACTCCAATG
1 ACATCTAACAAGCGTGGTGTGTAACAATATAATACTACAATG
12826220 A
1 A
12826221 AATAGCGTGT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.26
Consensus pattern (42 bp):
ACATCTAACAAGCGTGGTGTGTAACAATATAATACTACAATG
Found at i:12826294 original size:71 final size:71
Alignment explanation
Indices: 12826177--12826376 Score: 226
Period size: 71 Copynumber: 2.8 Consensus size: 71
12826167 ATACTACAAT
*
12826177 GACATCTAACAAGCGTGG-TGTGTAACAATATAATACTCCAATGAAATAGCGTGTCACAACACGA
1 GACATCTAACAAGCGTGGCT-TGTAACAATATAATACTCCAATGAAATAGCATGTCACAACACGA
*
12826241 TGTGAAC
65 TGTAAAC
* * * * *
12826248 GACATCTATCAAGCGTGGCTTGTAACAATATAATATTGC-ATCGAAATGGCATGTCATAACACGA
1 GACATCTAACAAGCGTGGCTTGTAACAATATAATACTCCAAT-GAAATAGCATGTCACAACACGA
*
12826312 TGTAAAT
65 TGTAAAC
* * * * * *
12826319 GACATCTAACAAGCATGGCGTGTAACTATATGATACTTCAACGAAAT-GACATGTCACA
1 GACATCTAACAAGCGTGGCTTGTAACAATATAATACTCCAATGAAATAG-CATGTCACA
12826377 TCGTATAAGT
Statistics
Matches: 108, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
70 3 0.03
71 103 0.95
72 2 0.02
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (71 bp):
GACATCTAACAAGCGTGGCTTGTAACAATATAATACTCCAATGAAATAGCATGTCACAACACGAT
GTAAAC
Found at i:12829410 original size:36 final size:36
Alignment explanation
Indices: 12829363--12829435 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
12829353 TGTATGGCAT
12829363 TCCTTAATAGTGATGTACACTACCGAAACATTCCTC
1 TCCTTAATAGTGATGTACACTACCGAAACATTCCTC
12829399 TCCTTAATAGTGATGTACACTACCGAAACATTCCTC
1 TCCTTAATAGTGATGTACACTACCGAAACATTCCTC
12829435 T
1 T
12829436 ACTCTAGCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (36 bp):
TCCTTAATAGTGATGTACACTACCGAAACATTCCTC
Found at i:12829837 original size:25 final size:25
Alignment explanation
Indices: 12829780--12829871 Score: 112
Period size: 25 Copynumber: 3.6 Consensus size: 25
12829770 TGAAAACATG
* * *
12829780 TTGTTACATGCCATGTTGAAAAAATT
1 TTGTTACACGCCATGTTCAAAAAA-A
* *
12829806 TTCTTACACGCAATGTTCAAAAAAA
1 TTGTTACACGCCATGTTCAAAAAAA
12829831 TTGTTACACGCCATGTTCAAAAAAA
1 TTGTTACACGCCATGTTCAAAAAAA
* *
12829856 ATGTTACACTCCATGT
1 TTGTTACACGCCATGT
12829872 ACTAAAACAT
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
25 37 0.65
26 20 0.35
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (25 bp):
TTGTTACACGCCATGTTCAAAAAAA
Found at i:12830289 original size:9 final size:9
Alignment explanation
Indices: 12830271--12830310 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
12830261 AAGGGAGAGC
*
12830271 TGAGAGAGT
1 TGAGAAAGT
*
12830280 TTAGAAAGT
1 TGAGAAAGT
*
12830289 TGAGACAGT
1 TGAGAAAGT
12830298 TGAGAAAGT
1 TGAGAAAGT
12830307 TGAG
1 TGAG
12830311 GGGGTTGAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.38, C:0.03, G:0.35, T:0.25
Consensus pattern (9 bp):
TGAGAAAGT
Found at i:12830320 original size:18 final size:18
Alignment explanation
Indices: 12830271--12830310 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
12830261 AAGGGAGAGC
* *
12830271 TGAGAGAGTTTAGAAAGT
1 TGAGACAGTTGAGAAAGT
12830289 TGAGACAGTTGAGAAAGT
1 TGAGACAGTTGAGAAAGT
12830307 TGAG
1 TGAG
12830311 GGGGTTGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.03, G:0.35, T:0.25
Consensus pattern (18 bp):
TGAGACAGTTGAGAAAGT
Found at i:12839409 original size:26 final size:26
Alignment explanation
Indices: 12839378--12839436 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
12839368 TAAATATCTT
*
12839378 AAGTAAATGAAGAGTAAAAAGGAAAG
1 AAGTAAATGAAGAGTAAAAAGAAAAG
* * *
12839404 ACGTAAATGGAGAGTACAAAGAAAAG
1 AAGTAAATGAAGAGTAAAAAGAAAAG
12839430 AAGTAAA
1 AAGTAAA
12839437 ATGAGGATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.59, C:0.03, G:0.25, T:0.12
Consensus pattern (26 bp):
AAGTAAATGAAGAGTAAAAAGAAAAG
Found at i:12844828 original size:43 final size:43
Alignment explanation
Indices: 12844771--12844889 Score: 159
Period size: 43 Copynumber: 2.8 Consensus size: 43
12844761 GCAATTATGT
* *
12844771 TGACTCGGCTATGTGCGAGTAGGGAGTGTGCATAAACCGAG-GA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAAACCG-GTGA
* * *
12844814 TGACCCGGTTATGTGCGAGTAAGGAGTGCGCATAACCCGGTGA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAAACCGGTGA
* *
12844857 TGACCCGACCATGTGCGAGTAGGGAGTGCGCAT
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCAT
12844890 GAGCTGGTGA
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
42 1 0.02
43 65 0.98
ACGTcount: A:0.24, C:0.20, G:0.36, T:0.20
Consensus pattern (43 bp):
TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAAACCGGTGA
Found at i:12844905 original size:3 final size:3
Alignment explanation
Indices: 12844897--12844967 Score: 53
Period size: 3 Copynumber: 24.7 Consensus size: 3
12844887 CATGAGCTGG
* *
12844897 TGA TGA TGA TGA TG- TGA TGG TG- TGTA TGA TGA TGA TG- GGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TG-A TGA TGA TGA TGA TGA TGA
* *
12844940 TGA TG- GGA TGA TG- TGCA TGA TAA TGA TG
1 TGA TGA TGA TGA TGA TG-A TGA TGA TGA TG
12844968 GGTATACGTA
Statistics
Matches: 54, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
2 8 0.15
3 42 0.78
4 4 0.07
ACGTcount: A:0.27, C:0.01, G:0.38, T:0.34
Consensus pattern (3 bp):
TGA
Found at i:12844914 original size:11 final size:11
Alignment explanation
Indices: 12844900--12844952 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
12844890 GAGCTGGTGA
12844900 TGATGATGATG
1 TGATGATGATG
*
12844911 TGATGGTG-TG
1 TGATGATGATG
12844921 TATGATGATGATG
1 --TGATGATGATG
*
12844934 GGATGATGATG
1 TGATGATGATG
*
12844945 GGATGATG
1 TGATGATG
12844953 TGCATGATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
10 2 0.06
11 25 0.69
12 7 0.19
13 2 0.06
ACGTcount: A:0.25, C:0.00, G:0.42, T:0.34
Consensus pattern (11 bp):
TGATGATGATG
Found at i:12844939 original size:34 final size:34
Alignment explanation
Indices: 12844901--12844969 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
12844891 AGCTGGTGAT
* * * *
12844901 GATGATGATGTGATGGTGTGTATGATGATGATGG
1 GATGATGATGGGATGATGTGCATGATAATGATGG
12844935 GATGATGATGGGATGATGTGCATGATAATGATGG
1 GATGATGATGGGATGATGTGCATGATAATGATGG
12844969 G
1 G
12844970 TATACGTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.26, C:0.01, G:0.41, T:0.32
Consensus pattern (34 bp):
GATGATGATGGGATGATGTGCATGATAATGATGG
Found at i:12845331 original size:39 final size:39
Alignment explanation
Indices: 12845264--12845372 Score: 123
Period size: 39 Copynumber: 2.8 Consensus size: 39
12845254 CAGTGAAAAG
*
12845264 GAATCTCGCTGCAGCGAGAAA-CTCTCTGTTTCATCAGCT-
1 GAATTTCGCTGCAGCGAGAAACCT-TCTGTTTC-TCAGCTA
* * ** *
12845303 GAATTTCGTTGCAGCCAGAAACCTTCTGTTTCTGGGTTA
1 GAATTTCGCTGCAGCGAGAAACCTTCTGTTTCTCAGCTA
*
12845342 CAATTTCGCTGCAGCGAGAAACCTTCTGTTT
1 GAATTTCGCTGCAGCGAGAAACCTTCTGTTT
12845373 TGGTCTCCTA
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
38 3 0.05
39 54 0.92
40 2 0.03
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (39 bp):
GAATTTCGCTGCAGCGAGAAACCTTCTGTTTCTCAGCTA
Found at i:12849038 original size:80 final size:79
Alignment explanation
Indices: 12848940--12849162 Score: 304
Period size: 80 Copynumber: 2.8 Consensus size: 79
12848930 AACATGCATG
* * *
12848940 CCATGAGATGTATGTGTTGTGATAGTCATATAAATTATAAGCTAAGCATGTGAGAGATTTATGAG
1 CCATGAGATGTATGTGTTGAGATAGTCATATAAA-TATGAGCTAAGCATGTGAGTGATTTATGAG
*
12849005 GTTATGAAATATATC
65 GTTATGAAATACATC
* * * *
12849020 CCATGAGATGTATATGTTGAGATAGTCATATACAATATGGGTTAAGCATGTGAGTGATTTAAGAG
1 CCATGAGATGTATGTGTTGAGATAGTCATATA-AATATGAGCTAAGCATGTGAGTGATTTATGAG
* *
12849085 GTTATGAAATGCATG
65 GTTATGAAATACATC
*
12849100 CCATGAGATGTATGTGTTGAGATAGTCATATACACTATGAGCTAAGCATGATGA-TGATTTATG
1 CCATGAGATGTATGTGTTGAGATAGTCATATA-AATATGAGCTAAGCATG-TGAGTGATTTATG
12849163 GAAATGTTAT
Statistics
Matches: 126, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
80 121 0.96
81 5 0.04
ACGTcount: A:0.34, C:0.09, G:0.24, T:0.34
Consensus pattern (79 bp):
CCATGAGATGTATGTGTTGAGATAGTCATATAAATATGAGCTAAGCATGTGAGTGATTTATGAGG
TTATGAAATACATC
Found at i:12862663 original size:43 final size:43
Alignment explanation
Indices: 12862616--12862733 Score: 150
Period size: 43 Copynumber: 2.7 Consensus size: 43
12862606 CATAAGCTGA
* * * *
12862616 TGATGACCTGCTTATGTGCGAGTAGGAAGTGTGCAAAAATCGG
1 TGATGACCAGCTCATGTGCGAGTAGGGAGTGCGCAAAAATCGG
*
12862659 TGATGATGCAGC-CATGTGCGAGTAGGGAGTGCGCAAAAATCGG
1 TGATGA-CCAGCTCATGTGCGAGTAGGGAGTGCGCAAAAATCGG
*
12862702 TGATAACGCAG-TCATGTGCGAGTAGGGAGTGC
1 TGATGAC-CAGCTCATGTGCGAGTAGGGAGTGC
12862734 ACATGAGCTG
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
43 62 0.95
44 3 0.05
ACGTcount: A:0.27, C:0.15, G:0.36, T:0.22
Consensus pattern (43 bp):
TGATGACCAGCTCATGTGCGAGTAGGGAGTGCGCAAAAATCGG
Found at i:12862772 original size:23 final size:23
Alignment explanation
Indices: 12862742--12862800 Score: 109
Period size: 23 Copynumber: 2.6 Consensus size: 23
12862732 GCACATGAGC
12862742 TGATGATGATGGGATGGTGTGCA
1 TGATGATGATGGGATGGTGTGCA
*
12862765 TGATGATGATGGAATGGTGTGCA
1 TGATGATGATGGGATGGTGTGCA
12862788 TGATGATGATGGG
1 TGATGATGATGGG
12862801 TACNATATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.24, C:0.03, G:0.42, T:0.31
Consensus pattern (23 bp):
TGATGATGATGGGATGGTGTGCA
Found at i:12863125 original size:61 final size:61
Alignment explanation
Indices: 12863030--12863146 Score: 225
Period size: 61 Copynumber: 1.9 Consensus size: 61
12863020 TTCTTGCTGT
*
12863030 AGCGAGAAACATTCTGTTTTGGCAGTAGAAAACTTGCTGCAATGAAAATAAATCTCACTGC
1 AGCGAGAAACATTCTGTTTTGGCAGCAGAAAACTTGCTGCAATGAAAATAAATCTCACTGC
12863091 AGCGAGAAACATTCTGTTTTGGCAGCAGAAAACTTGCTGCAATGAAAATAAATCTC
1 AGCGAGAAACATTCTGTTTTGGCAGCAGAAAACTTGCTGCAATGAAAATAAATCTC
12863147 GCTACAATAA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.26
Consensus pattern (61 bp):
AGCGAGAAACATTCTGTTTTGGCAGCAGAAAACTTGCTGCAATGAAAATAAATCTCACTGC
Found at i:12863160 original size:61 final size:61
Alignment explanation
Indices: 12863034--12863161 Score: 202
Period size: 61 Copynumber: 2.1 Consensus size: 61
12863024 TGCTGTAGCG
* * * *
12863034 AGAAACATTCTGTTTTGGCAGTAGAAAACTTGCTGCAATGAAAATAAATCTCACTGCAGCG
1 AGAAACATTCTGTTTTGGCAGCAGAAAACTTGCTGCAATGAAAATAAATCTCACTACAACA
* *
12863095 AGAAACATTCTGTTTTGGCAGCAGAAAACTTGCTGCAATGAAAATAAATCTCGCTACAATA
1 AGAAACATTCTGTTTTGGCAGCAGAAAACTTGCTGCAATGAAAATAAATCTCACTACAACA
12863156 AGAAAC
1 AGAAAC
12863162 TCTTGGGTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (61 bp):
AGAAACATTCTGTTTTGGCAGCAGAAAACTTGCTGCAATGAAAATAAATCTCACTACAACA
Found at i:12868852 original size:29 final size:29
Alignment explanation
Indices: 12868815--12868900 Score: 154
Period size: 29 Copynumber: 3.0 Consensus size: 29
12868805 AAATATTTAT
12868815 AATATCTACAGTAGCTAAGCAAGATATAC
1 AATATCTACAGTAGCTAAGCAAGATATAC
12868844 AATATCTACAGTAGCTAAGCAAGATATAC
1 AATATCTACAGTAGCTAAGCAAGATATAC
* *
12868873 AATATCCACAATAGCTAAGCAAGATATA
1 AATATCTACAGTAGCTAAGCAAGATATA
12868901 TTAAACATCT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 55 1.00
ACGTcount: A:0.47, C:0.17, G:0.13, T:0.23
Consensus pattern (29 bp):
AATATCTACAGTAGCTAAGCAAGATATAC
Found at i:12877359 original size:34 final size:34
Alignment explanation
Indices: 12877297--12877361 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
12877287 AACCGTTCGT
*
12877297 GTGTGGTGTGGGAGTGCACATGACGATGATAGTG
1 GTGTGGTGTGGGAGTGCACATCACGATGATAGTG
* *
12877331 GTGTGTTGTGTGAGTGCACA-CACTGATGATA
1 GTGTGGTGTGGGAGTGCACATCAC-GATGATA
12877362 TATGCCATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 2 0.07
34 25 0.93
ACGTcount: A:0.22, C:0.11, G:0.38, T:0.29
Consensus pattern (34 bp):
GTGTGGTGTGGGAGTGCACATCACGATGATAGTG
Found at i:12877445 original size:33 final size:34
Alignment explanation
Indices: 12877408--12877485 Score: 95
Period size: 35 Copynumber: 2.3 Consensus size: 34
12877398 GCACACACTA
12877408 ATGAT-ATTTACCATGTGCGATGTGGGAGTGCAC
1 ATGATGATTTACCATGTGCGATGTGGGAGTGCAC
* * * *
12877441 ATGATGGTATTGCCTTGTGCGGTGTGGGAGTGCAC
1 ATGATGAT-TTACCATGTGCGATGTGGGAGTGCAC
*
12877476 AGGATGATTT
1 ATGATGATTT
12877486 TAGCTATGTG
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
33 5 0.14
34 3 0.08
35 29 0.78
ACGTcount: A:0.21, C:0.13, G:0.35, T:0.32
Consensus pattern (34 bp):
ATGATGATTTACCATGTGCGATGTGGGAGTGCAC
Found at i:12879012 original size:31 final size:29
Alignment explanation
Indices: 12878939--12879004 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
12878929 TTTGCAATAA
* * *
12878939 AATATTTATAATATCAATAGTAGCTAAAC
1 AATATATACAATATCCATAGTAGCTAAAC
* *
12878968 AATATATACAATATTCATAGTAGCTAAGC
1 AATATATACAATATCCATAGTAGCTAAAC
*
12878997 AAGATATA
1 AATATATA
12879005 TTGAATATCC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.32
Consensus pattern (29 bp):
AATATATACAATATCCATAGTAGCTAAAC
Found at i:12887422 original size:28 final size:27
Alignment explanation
Indices: 12887364--12887510 Score: 183
Period size: 26 Copynumber: 5.5 Consensus size: 27
12887354 GATTGCAATA
**
12887364 TTTTTTCAACATGATGTGTAACAAC-T
1 TTTTTTCAACATGACATGTAACAACTT
*
12887390 ATTTTTCAACATGACATGTAACAACTTT
1 TTTTTTCAACATGACATGTAACAAC-TT
*
12887418 TTTTTTCAACATGGCATGTAACAAC-T
1 TTTTTTCAACATGACATGTAACAACTT
* * *
12887444 TTGTTTCAACATGGCGTGTAACAACTTT
1 TTTTTTCAACATGACATGTAACAAC-TT
*
12887472 TTTTTTCAACATGACATGTAACAA-TG
1 TTTTTTCAACATGACATGTAACAACTT
12887498 TTTTTTCAACATG
1 TTTTTTCAACATG
12887511 GCGTGTAATA
Statistics
Matches: 106, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
26 60 0.57
28 46 0.43
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.41
Consensus pattern (27 bp):
TTTTTTCAACATGACATGTAACAACTT
Found at i:12887531 original size:54 final size:54
Alignment explanation
Indices: 12887364--12887518 Score: 231
Period size: 54 Copynumber: 2.9 Consensus size: 54
12887354 GATTGCAATA
** * * *
12887364 TTTTTTCAACATGATGTGTAACAACTATTTTTCAACATGACATGTAACAACTTT
1 TTTTTTCAACATGACATGTAACAACTTTTTTTCAACATGGCGTGTAACAACTTT
* *
12887418 TTTTTTCAACATGGCATGTAACAACTTTGTTTCAACATGGCGTGTAACAACTTT
1 TTTTTTCAACATGACATGTAACAACTTTTTTTCAACATGGCGTGTAACAACTTT
12887472 TTTTTTCAACATGACATGTAACAA-TGTTTTTTCAACATGGCGTGTAA
1 TTTTTTCAACATGACATGTAACAACT-TTTTTTCAACATGGCGTGTAA
12887519 TATAAATTTT
Statistics
Matches: 91, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
53 1 0.01
54 90 0.99
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (54 bp):
TTTTTTCAACATGACATGTAACAACTTTTTTTCAACATGGCGTGTAACAACTTT
Found at i:12890894 original size:19 final size:17
Alignment explanation
Indices: 12890870--12890905 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
12890860 CTTGATTTCC
12890870 TTTATTTAATCTTTATTTA
1 TTTATTT-ATCTTT-TTTA
12890889 TTTATTTATCTTTTTTA
1 TTTATTTATCTTTTTTA
12890906 GTAAGTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 6 0.35
19 7 0.41
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTATTTATCTTTTTTA
Found at i:12891091 original size:19 final size:19
Alignment explanation
Indices: 12891050--12891089 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
12891040 AAATGAAATT
12891050 AAATAAAAACAAAATAACA
1 AAATAAAAACAAAATAACA
*
12891069 AAATAAAACCAAAA-AACA
1 AAATAAAAACAAAATAACA
12891087 AAA
1 AAA
12891090 ATTTCTTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.80, C:0.12, G:0.00, T:0.07
Consensus pattern (19 bp):
AAATAAAAACAAAATAACA
Found at i:12891855 original size:17 final size:17
Alignment explanation
Indices: 12891833--12891865 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12891823 TTATGAATAC
12891833 TTTTATTTTGATATTTA
1 TTTTATTTTGATATTTA
*
12891850 TTTTATTTTTATATTT
1 TTTTATTTTGATATTT
12891866 TTCTTTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (17 bp):
TTTTATTTTGATATTTA
Found at i:12900717 original size:22 final size:20
Alignment explanation
Indices: 12900666--12900717 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
12900656 CTTAACTTAT
12900666 TTAGTTTTTAATTTATTTAA
1 TTAGTTTTTAATTTATTTAA
* *
12900686 TGTTGATTTTTAATTGTTTTTAA
1 T-TAG-TTTTTAATT-TATTTAA
12900709 TTAGTTTTT
1 TTAGTTTTT
12900718 CTTCAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 1 0.04
21 7 0.27
22 11 0.42
23 7 0.27
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (20 bp):
TTAGTTTTTAATTTATTTAA
Found at i:12903617 original size:20 final size:20
Alignment explanation
Indices: 12903576--12903618 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
12903566 GGCAGTGAGC
* *
12903576 TCTTAGTCGACTAATTTTCT
1 TCTTAGTCGACTAAGTTGCT
*
12903596 TCTTAGTCGATTAAGTTGCT
1 TCTTAGTCGACTAAGTTGCT
12903616 TCT
1 TCT
12903619 GTCTTGAAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.19, C:0.19, G:0.14, T:0.49
Consensus pattern (20 bp):
TCTTAGTCGACTAAGTTGCT
Found at i:12903655 original size:73 final size:73
Alignment explanation
Indices: 12903505--12903691 Score: 163
Period size: 73 Copynumber: 2.6 Consensus size: 73
12903495 CAAAATGATC
* *
12903505 TTTA-TCGACTAACTGTGTTCTTAGTCGACTAAGTTGTCTCTGTCTTCTGATCTCAGTTTTTGGC
1 TTTAGTCGACTAACTGTCTTCTTAGTCGACTAAGTTGTCTCTGTCTTCTGATCTCAGTTTCTGGC
12903569 AGTGAGCT
66 AGTGAGCT
* * * *
12903577 CTTAGTCGACTAATTTTCTTCTTAGTCGATTAAGTTG-CTTCTGTC-T-TGAAGTCT-AGATTTC
1 TTTAGTCGACTAACTGTCTTCTTAGTCGACTAAGTTGTC-TCTGTCTTCTG-A-TCTCAG-TTTC
12903638 TGGCAGT-AGGCT
62 TGGCAGTGA-GCT
** * * * *
12903650 TTTAGTTAACTGACT-TATTTCTTGGTCGACTAAGTTTTCTCT
1 TTTAGTCGACTAACTGT-CTTCTTAGTCGACTAAGTTGTCTCT
12903692 ATTTCTCAAG
Statistics
Matches: 92, Mismatches: 15, Indels: 15
0.75 0.12 0.12
Matches are distributed among these distances:
71 2 0.02
72 10 0.11
73 79 0.86
74 1 0.01
ACGTcount: A:0.18, C:0.18, G:0.19, T:0.44
Consensus pattern (73 bp):
TTTAGTCGACTAACTGTCTTCTTAGTCGACTAAGTTGTCTCTGTCTTCTGATCTCAGTTTCTGGC
AGTGAGCT
Found at i:12904064 original size:17 final size:17
Alignment explanation
Indices: 12904042--12904075 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12904032 GACATTTTCC
12904042 TCCCCCCAAGTGTGTGT
1 TCCCCCCAAGTGTGTGT
**
12904059 TCCCCCTTAGTGTGTGT
1 TCCCCCCAAGTGTGTGT
12904076 ATATTTTATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.32, G:0.24, T:0.35
Consensus pattern (17 bp):
TCCCCCCAAGTGTGTGT
Found at i:12909261 original size:15 final size:15
Alignment explanation
Indices: 12909243--12909272 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12909233 TAAAAAAGTT
*
12909243 TTCAAACTCATCTCC
1 TTCAAACTCACCTCC
12909258 TTCAAACTCACCTCC
1 TTCAAACTCACCTCC
12909273 ATGATCACTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.43, G:0.00, T:0.30
Consensus pattern (15 bp):
TTCAAACTCACCTCC
Found at i:12914233 original size:20 final size:20
Alignment explanation
Indices: 12914208--12914249 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
12914198 GCAACTAACT
12914208 TTGCTTTGTTCCTTACCACA
1 TTGCTTTGTTCCTTACCACA
*
12914228 TTGCTTTGTTCTTTACCACA
1 TTGCTTTGTTCCTTACCACA
12914248 TT
1 TT
12914250 ACCCAACTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.26, G:0.10, T:0.50
Consensus pattern (20 bp):
TTGCTTTGTTCCTTACCACA
Found at i:12916897 original size:25 final size:25
Alignment explanation
Indices: 12916869--12916918 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
12916859 TACTTCTTTG
12916869 CATACTGATTTTTTAAATCTCAAAA
1 CATACTGATTTTTTAAATCTCAAAA
*
12916894 CATACTGTTTTTTTAAATCTCAAAA
1 CATACTGATTTTTTAAATCTCAAAA
12916919 ACTTGTTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.42
Consensus pattern (25 bp):
CATACTGATTTTTTAAATCTCAAAA
Found at i:12932035 original size:19 final size:19
Alignment explanation
Indices: 12932011--12932048 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
12932001 TTCTCTACCT
*
12932011 TAATACTAGATATTAGGGA
1 TAATACTAGAAATTAGGGA
12932030 TAATACTAGAAATTAGGGA
1 TAATACTAGAAATTAGGGA
12932049 CATGATCAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.29
Consensus pattern (19 bp):
TAATACTAGAAATTAGGGA
Found at i:12933563 original size:21 final size:21
Alignment explanation
Indices: 12933539--12933614 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
12933529 CTGAAAAAAT
*
12933539 TGTATTGATACATTATGAACA
1 TGTATCGATACATTATGAACA
* * *
12933560 TGTATCCATACATGACT--ATA
1 TGTATCGATACATTA-TGAACA
*
12933580 TGCATCGATACATTATGAACA
1 TGTATCGATACATTATGAACA
12933601 TGTATCGATACATT
1 TGTATCGATACATT
12933615 TAAAATAGAA
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
19 1 0.02
20 14 0.33
21 27 0.63
22 1 0.02
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTATGAACA
Done.