Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr10
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: 57797951
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1092422 characters in sequence are not A, C, G, or T
File 138 of 187
Found at i:41485344 original size:10 final size:10
Alignment explanation
Indices: 41485331--41485358 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
41485321 CTAAATTTAT
41485331 TTAAATATAG
1 TTAAATATAG
41485341 TTAAATATAG
1 TTAAATATAG
41485351 TTAAATAT
1 TTAAATAT
41485359 TAATTACAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (10 bp):
TTAAATATAG
Found at i:41487901 original size:16 final size:18
Alignment explanation
Indices: 41487882--41487934 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 18
41487872 AAATTATTAA
41487882 AATAATTTATTAT-T-TT
1 AATAATTTATTATATATT
41487898 AATAAATTATATTTACTATATT
1 AAT-AATT-TA-TTA-TATATT
41487920 AATAATTTATTATAT
1 AATAATTTATTATAT
41487935 GACTACATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
16 3 0.10
17 4 0.13
18 5 0.16
19 6 0.19
20 3 0.10
21 5 0.16
22 5 0.16
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
AATAATTTATTATATATT
Found at i:41487911 original size:22 final size:22
Alignment explanation
Indices: 41487886--41487929 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
41487876 TATTAAAATA
* *
41487886 ATTTATTATTTTAATAAATTAT
1 ATTTACTATATTAATAAATTAT
*
41487908 ATTTACTATATTAATAATTTAT
1 ATTTACTATATTAATAAATTAT
41487930 TATATGACTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTACTATATTAATAAATTAT
Found at i:41493342 original size:30 final size:29
Alignment explanation
Indices: 41493306--41493585 Score: 137
Period size: 30 Copynumber: 9.4 Consensus size: 29
41493296 GGTTGTCACC
41493306 ATCCCTTTTCATAGTTCGATAGCTGAAGCT
1 ATCCCTTTTCATAGTTCGATAGCTGAA-CT
* * * *
41493336 ATCCCTTGTCATATTTCGAT-GGTCG-TCT
1 ATCCCTTTTCATAGTTCGATAGCT-GAACT
* * *
41493364 CCATCCCTTTTCATTGTT-GATAGTCAT-CACC
1 --ATCCCTTTTCATAGTTCGATAG-C-TGAACT
* *
41493395 ATCCGTTTTCATAATTCGATAGCTGAAGCT
1 ATCCCTTTTCATAGTTCGATAGCTGAA-CT
* * * * *
41493425 ATCCCTTTTCATATTTCAATGGTCAT-TACC
1 ATCCCTTTTCATAGTTCGATAG-C-TGAACT
* **
41493455 ATCCCTTTTCATAATTCGATAGCCAAAGCT
1 ATCCCTTTTCATAGTTCGATAGCTGAA-CT
* * *
41493485 ATCCCTTTTCATAGTTCGAT-GGTCGTCACC
1 ATCCCTTTTCATAGTTCGATAGCT-G-AACT
* * *
41493515 ATCCCTTTTCATGGTT-GAT-GGTCGTCACT
1 ATCCCTTTTCATAGTTCGATAGCT-G-AACT
41493544 ATCCCTTTTCATA-TTCTGATAGCTGAAGCT
1 ATCCCTTTTCATAGTTC-GATAGCTGAA-CT
*
41493574 ATCCTTTTTCAT
1 ATCCCTTTTCAT
41493586 TGGTTGATGA
Statistics
Matches: 191, Mismatches: 39, Indels: 40
0.71 0.14 0.15
Matches are distributed among these distances:
28 5 0.03
29 48 0.25
30 130 0.68
31 6 0.03
32 2 0.01
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.40
Consensus pattern (29 bp):
ATCCCTTTTCATAGTTCGATAGCTGAACT
Found at i:41493457 original size:89 final size:89
Alignment explanation
Indices: 41493301--41493466 Score: 271
Period size: 89 Copynumber: 1.9 Consensus size: 89
41493291 ACAATGGTTG
* * *
41493301 TCACCATCCCTTTTCATAGTTCGATAGCTGAAGCTATCCCTTGTCATATTTCGATGGTCGTCTCC
1 TCACCATCCCTTTTCATAATTCGATAGCTGAAGCTATCCCTTGTCATATTTCAATGGTCATCTCC
41493366 ATCCCTTTTCATTGTTGATAGTCA
66 ATCCCTTTTCATTGTTGATAGTCA
* *
41493390 TCACCATCCGTTTTCATAATTCGATAGCTGAAGCTATCCCTTTTCATATTTCAATGGTCAT-TAC
1 TCACCATCCCTTTTCATAATTCGATAGCTGAAGCTATCCCTTGTCATATTTCAATGGTCATCT-C
41493454 CATCCCTTTTCAT
65 CATCCCTTTTCAT
41493467 AATTCGATAG
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
88 1 0.01
89 70 0.99
ACGTcount: A:0.21, C:0.27, G:0.12, T:0.40
Consensus pattern (89 bp):
TCACCATCCCTTTTCATAATTCGATAGCTGAAGCTATCCCTTGTCATATTTCAATGGTCATCTCC
ATCCCTTTTCATTGTTGATAGTCA
Found at i:41493466 original size:60 final size:60
Alignment explanation
Indices: 41493366--41493526 Score: 225
Period size: 60 Copynumber: 2.7 Consensus size: 60
41493356 GGTCGTCTCC
* * * * **
41493366 ATCCCTTTTCATTGTT-GATAGTCATCACCATCCGTTTTCATAATTCGATAGCTGAAGCT
1 ATCCCTTTTCATAGTTCAATGGTCATCACCATCCCTTTTCATAATTCGATAGCCAAAGCT
* *
41493425 ATCCCTTTTCATATTTCAATGGTCATTACCATCCCTTTTCATAATTCGATAGCCAAAGCT
1 ATCCCTTTTCATAGTTCAATGGTCATCACCATCCCTTTTCATAATTCGATAGCCAAAGCT
* *
41493485 ATCCCTTTTCATAGTTCGATGGTCGTCACCATCCCTTTTCAT
1 ATCCCTTTTCATAGTTCAATGGTCATCACCATCCCTTTTCAT
41493527 GGTTGATGGT
Statistics
Matches: 89, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
59 14 0.16
60 75 0.84
ACGTcount: A:0.23, C:0.27, G:0.11, T:0.39
Consensus pattern (60 bp):
ATCCCTTTTCATAGTTCAATGGTCATCACCATCCCTTTTCATAATTCGATAGCCAAAGCT
Found at i:41493547 original size:29 final size:30
Alignment explanation
Indices: 41493294--41493556 Score: 180
Period size: 30 Copynumber: 8.8 Consensus size: 30
41493284 TAAAATTACA
* *
41493294 ATGGTTGTCACCATCCCTTTTCATAGTTCG
1 ATGGTCGTCACTATCCCTTTTCATAGTTCG
* * * *
41493324 ATAG-C-TGAAGCTATCCCTTGTCATATTTCG
1 ATGGTCGT-CA-CTATCCCTTTTCATAGTTCG
* * *
41493354 ATGGTCGTCTCCATCCCTTTTCATTGTT-G
1 ATGGTCGTCACTATCCCTTTTCATAGTTCG
* * * * *
41493383 ATAGTCATCACCATCCGTTTTCATAATTCG
1 ATGGTCGTCACTATCCCTTTTCATAGTTCG
* * * *
41493413 ATAG-C-TGAAGCTATCCCTTTTCATATTTCA
1 ATGGTCGT-CA-CTATCCCTTTTCATAGTTCG
* * * *
41493443 ATGGTCATTACCATCCCTTTTCATAATTCG
1 ATGGTCGTCACTATCCCTTTTCATAGTTCG
* ***
41493473 ATAG-CCAAAGCTATCCCTTTTCATAGTTCG
1 ATGGTCGTCA-CTATCCCTTTTCATAGTTCG
* *
41493503 ATGGTCGTCACCATCCCTTTTCATGGTT-G
1 ATGGTCGTCACTATCCCTTTTCATAGTTCG
41493532 ATGGTCGTCACTATCCCTTTTCATA
1 ATGGTCGTCACTATCCCTTTTCATA
41493557 TTCTGATAGC
Statistics
Matches: 179, Mismatches: 43, Indels: 23
0.73 0.18 0.09
Matches are distributed among these distances:
28 2 0.01
29 52 0.29
30 118 0.66
31 5 0.03
32 2 0.01
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.39
Consensus pattern (30 bp):
ATGGTCGTCACTATCCCTTTTCATAGTTCG
Found at i:41493565 original size:149 final size:149
Alignment explanation
Indices: 41493303--41493585 Score: 442
Period size: 149 Copynumber: 1.9 Consensus size: 149
41493293 AATGGTTGTC
* ** * *
41493303 ACCATCCCTTTTCATAGTTCGATAGCTGAAGCTATCCCTTGTCATATTTCGATGGTCGTCTCCAT
1 ACCATCCCTTTTCATAATTCGATAGCCAAAGCTATCCCTTGTCATAGTTCGATGGTCGTCACCAT
* *
41493368 CCCTTTTCATTGTTGATAGTCATCACCATCCGTTTTCATAATTCGATAGCTGAAGCTATCCCTTT
66 CCCTTTTCATGGTTGATAGTCATCACCATCCCTTTTCATAATTCGATAGCTGAAGCTATCCCTTT
41493433 TCATATTTCAATGGTCATT
131 TCATATTTCAATGGTCATT
*
41493452 ACCATCCCTTTTCATAATTCGATAGCCAAAGCTATCCCTTTTCATAGTTCGATGGTCGTCACCAT
1 ACCATCCCTTTTCATAATTCGATAGCCAAAGCTATCCCTTGTCATAGTTCGATGGTCGTCACCAT
* * * *
41493517 CCCTTTTCATGGTTGATGGTCGTCACTATCCCTTTTCAT-ATTCTGATAGCTGAAGCTATCCTTT
66 CCCTTTTCATGGTTGATAGTCATCACCATCCCTTTTCATAATTC-GATAGCTGAAGCTATCCCTT
41493581 TTCAT
130 TTCAT
41493586 TGGTTGATGA
Statistics
Matches: 121, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
148 4 0.03
149 117 0.97
ACGTcount: A:0.21, C:0.26, G:0.13, T:0.39
Consensus pattern (149 bp):
ACCATCCCTTTTCATAATTCGATAGCCAAAGCTATCCCTTGTCATAGTTCGATGGTCGTCACCAT
CCCTTTTCATGGTTGATAGTCATCACCATCCCTTTTCATAATTCGATAGCTGAAGCTATCCCTTT
TCATATTTCAATGGTCATT
Found at i:41497101 original size:18 final size:18
Alignment explanation
Indices: 41497078--41497112 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41497068 TCTTATTCCT
41497078 TCATTCATCATCCCTCAA
1 TCATTCATCATCCCTCAA
* *
41497096 TCATTCCTCATTCCTCA
1 TCATTCATCATCCCTCA
41497113 TTCTCTCTTT
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:0.40, G:0.00, T:0.37
Consensus pattern (18 bp):
TCATTCATCATCCCTCAA
Found at i:41502857 original size:60 final size:60
Alignment explanation
Indices: 41502790--41503040 Score: 183
Period size: 59 Copynumber: 4.2 Consensus size: 60
41502780 ACAATGGTTG
* * *
41502790 TCACCATCCCTTTTTATAGTTCGATAGTCGAAGCTATCCCTTTTCATATTTCGATGGTCA
1 TCACCATCCCTTTTCATAGTTCGATAGTCGAAGCCATCCCTTTTCATAGTTCGATGGTCA
* * * * * ***
41502850 TCACCATCCCTTTTCATTGTT-GATGGTC-ATAACCATCCCTTTTTATAATTCGATAACCGA
1 TCACCATCCCTTTTCATAGTTCGATAGTCGA-AGCCATCCCTTTTCATAGTTCGATGGTC-A
* * * * * * *
41502910 --AGCTATCCCTTTACATATTTTGATGGTCGTCA-CCATCCCTTTTCATGGTT-GATGGTCA
1 TCA-CCATCCCTTTTCATAGTTCGATAGTCG-AAGCCATCCCTTTTCATAGTTCGATGGTCA
* * * * * * *
41502968 TCA-CAGTCCCATTTCATAATTCGATAGCCAAAGCTATCCTTTTTCATAGTTCGATGGTCG
1 TCACCA-TCCCTTTTCATAGTTCGATAGTCGAAGCCATCCCTTTTCATAGTTCGATGGTCA
41503028 TCACCATCCCTTT
1 TCACCATCCCTTT
41503041 CCATGGTTGA
Statistics
Matches: 144, Mismatches: 35, Indels: 24
0.71 0.17 0.12
Matches are distributed among these distances:
58 5 0.03
59 77 0.53
60 59 0.41
61 3 0.02
ACGTcount: A:0.22, C:0.26, G:0.13, T:0.38
Consensus pattern (60 bp):
TCACCATCCCTTTTCATAGTTCGATAGTCGAAGCCATCCCTTTTCATAGTTCGATGGTCA
Found at i:41502884 original size:29 final size:29
Alignment explanation
Indices: 41502790--41503087 Score: 167
Period size: 30 Copynumber: 10.1 Consensus size: 29
41502780 ACAATGGTTG
* *
41502790 TCACCATCCCTTTTTATAGTTCGATAGTCGA
1 TCACCATCCCTTTTCATAGTT-GATGGTC-A
* *
41502821 --AGCTATCCCTTTTCATATTTCGATGGTCA
1 TCA-CCATCCCTTTTCATAGTT-GATGGTCA
*
41502850 TCACCATCCCTTTTCATTGTTGATGGTCA
1 TCACCATCCCTTTTCATAGTTGATGGTCA
* * * ***
41502879 TAACCATCCCTTTTTATAATTCGATAACCGA
1 TCACCATCCCTTTTCATAGTT-GATGGTC-A
* * * *
41502910 --AGCTATCCCTTTACATATTTTGATGGTCG
1 TCA-CCATCCCTTTTCATA-GTTGATGGTCA
*
41502939 TCACCATCCCTTTTCATGGTTGATGGTCA
1 TCACCATCCCTTTTCATAGTTGATGGTCA
* * * *
41502968 TCA-CAGTCCCATTTCATAATTCGATAGCCA
1 TCACCA-TCCCTTTTCATAGTT-GATGGTCA
* * * *
41502998 -AAGCTATCCTTTTTCATAGTTCGATGGTCG
1 TCA-CCATCCCTTTTCATAGTT-GATGGTCA
* *
41503028 TCACCATCCCTTTCCATGGTTGATGGTCA
1 TCACCATCCCTTTTCATAGTTGATGGTCA
* * ** *
41503057 TTACCGTCTATTTTCATGGTTGATGGTCA
1 TCACCATCCCTTTTCATAGTTGATGGTCA
41503086 TC
1 TC
41503088 CCTTTTCATT
Statistics
Matches: 201, Mismatches: 52, Indels: 30
0.71 0.18 0.11
Matches are distributed among these distances:
28 2 0.01
29 85 0.42
30 107 0.53
31 7 0.03
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.39
Consensus pattern (29 bp):
TCACCATCCCTTTTCATAGTTGATGGTCA
Found at i:41502935 original size:89 final size:89
Alignment explanation
Indices: 41502792--41503057 Score: 390
Period size: 89 Copynumber: 3.0 Consensus size: 89
41502782 AATGGTTGTC
* * *
41502792 ACCATCCCTTTTTATAGTTCGATAGTCGAAGCTATCCCTTTTCATATTTCGATGGTCATCACCAT
1 ACCATCCCTTTTTATAATTCGATAGCCGAAGCTATCCCTTTTCATATTTCGATGGTCGTCACCAT
*
41502857 CCCTTTTCATTGTTGATGGTCATA
66 CCCTTTTCATGGTTGATGGTCATA
* * *
41502881 ACCATCCCTTTTTATAATTCGATAACCGAAGCTATCCCTTTACATATTTTGATGGTCGTCACCAT
1 ACCATCCCTTTTTATAATTCGATAGCCGAAGCTATCCCTTTTCATATTTCGATGGTCGTCACCAT
*
41502946 CCCTTTTCATGGTTGATGGTCATC
66 CCCTTTTCATGGTTGATGGTCATA
* * * * *
41502970 A-CAGTCCCATTTCATAATTCGATAGCCAAAGCTATCCTTTTTCATAGTTCGATGGTCGTCACCA
1 ACCA-TCCCTTTTTATAATTCGATAGCCGAAGCTATCCCTTTTCATATTTCGATGGTCGTCACCA
*
41503034 TCCCTTTCCATGGTTGATGGTCAT
65 TCCCTTTTCATGGTTGATGGTCAT
41503058 TACCGTCTAT
Statistics
Matches: 159, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
88 2 0.01
89 157 0.99
ACGTcount: A:0.22, C:0.26, G:0.14, T:0.38
Consensus pattern (89 bp):
ACCATCCCTTTTTATAATTCGATAGCCGAAGCTATCCCTTTTCATATTTCGATGGTCGTCACCAT
CCCTTTTCATGGTTGATGGTCATA
Found at i:41513225 original size:17 final size:17
Alignment explanation
Indices: 41513205--41513247 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
41513195 CATATTATTG
*
41513205 TTGCATTTTTATTTTCA
1 TTGCATTTTTATTGTCA
41513222 TTGCATTTTTATTGTCA
1 TTGCATTTTTATTGTCA
41513239 TTGCATTTT
1 TTGCATTTT
41513248 AATGTTAGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.16, C:0.12, G:0.09, T:0.63
Consensus pattern (17 bp):
TTGCATTTTTATTGTCA
Found at i:41516853 original size:19 final size:19
Alignment explanation
Indices: 41516826--41516862 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
41516816 TGCACGCACG
* *
41516826 ATTCTACTAATCAAACACA
1 ATTCCACTAATAAAACACA
41516845 ATTCCACTAATAAAACAC
1 ATTCCACTAATAAAACAC
41516863 CATGAATGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (19 bp):
ATTCCACTAATAAAACACA
Found at i:41534489 original size:42 final size:42
Alignment explanation
Indices: 41534428--41534536 Score: 139
Period size: 42 Copynumber: 2.6 Consensus size: 42
41534418 ACGACCAAGC
*
41534428 CACACACCAATGTGCCAAGCTGTGTAACACTCGAAATGGCCT
1 CACACACCAATGTGCCAAGCCGTGTAACACTCGAAATGGCCT
** * *
41534470 CACACACCCGTGTGTCAAGCCGTGTAACACTTGAAATGGCCT
1 CACACACCAATGTGCCAAGCCGTGTAACACTCGAAATGGCCT
* *
41534512 CACACATCC-ACGTGCCAGGCCGTGT
1 CACACA-CCAATGTGCCAAGCCGTGT
41534537 GCTAGGCCGT
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
42 55 0.96
43 2 0.04
ACGTcount: A:0.27, C:0.33, G:0.21, T:0.19
Consensus pattern (42 bp):
CACACACCAATGTGCCAAGCCGTGTAACACTCGAAATGGCCT
Found at i:41536017 original size:50 final size:50
Alignment explanation
Indices: 41535941--41536132 Score: 233
Period size: 50 Copynumber: 3.9 Consensus size: 50
41535931 CATTTGGGTA
* * *
41535941 AAGAGGTCACATGTAAGACCAAGTCTGGGACATGGCGTTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
**
41535991 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
* * * * * *
41536041 GAGAGGTCCC-CGCAAGACCATGTTTGGGACATGGCATGGGCACCGATAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
* ** * *
41536090 GAGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
41536133 GTACAGAAAA
Statistics
Matches: 122, Mismatches: 19, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
49 40 0.33
50 82 0.67
ACGTcount: A:0.28, C:0.21, G:0.31, T:0.20
Consensus pattern (50 bp):
AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
Found at i:41541037 original size:47 final size:48
Alignment explanation
Indices: 41540962--41541116 Score: 179
Period size: 57 Copynumber: 3.1 Consensus size: 48
41540952 TGACAAGTGA
41540962 TAAGTGGTAGC-TTAGCTACACTTATCTGATCGGTGACAAGTGACAAG
1 TAAGTGGTAGCTTTAGCTACACTTATCTGATCGGTGACAAGTGACAAG
*
41541009 TAAGTGGTAGCTTTAGCTACAGTT-TCTGATCAGTGACAAGTGACAAGTGACAAGTG
1 TAAGTGGTAGCTTTAGCTACACTTATCTGATC---G----GTGACAAGTGACAA--G
* *
41541065 ATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGGCAAG
1 -TAAGTGGTAGCTTTAGCTACACTTATCTGATCGGTGACAAGTGACAAG
41541114 TAA
1 TAA
41541117 CAAGTGACAA
Statistics
Matches: 92, Mismatches: 4, Indels: 23
0.77 0.03 0.19
Matches are distributed among these distances:
47 18 0.20
48 14 0.15
49 1 0.01
50 1 0.01
51 13 0.14
54 14 0.15
56 1 0.01
57 23 0.25
58 7 0.08
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.28
Consensus pattern (48 bp):
TAAGTGGTAGCTTTAGCTACACTTATCTGATCGGTGACAAGTGACAAG
Found at i:41541052 original size:7 final size:7
Alignment explanation
Indices: 41541040--41541071 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
41541030 GTTTCTGATC
41541040 AGTGACA
1 AGTGACA
41541047 AGTGACA
1 AGTGACA
41541054 AGTGACA
1 AGTGACA
*
41541061 AGTGATA
1 AGTGACA
41541068 AGTG
1 AGTG
41541072 GTAGCTTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.41, C:0.09, G:0.31, T:0.19
Consensus pattern (7 bp):
AGTGACA
Found at i:41541113 original size:7 final size:7
Alignment explanation
Indices: 41541098--41541137 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
41541088 TTATCTGATC
41541098 AGTGACA
1 AGTGACA
*
41541105 AGTGGCA
1 AGTGACA
*
41541112 AGTAACA
1 AGTGACA
41541119 AGTGACA
1 AGTGACA
41541126 AGTGACA
1 AGTGACA
41541133 AGTGA
1 AGTGA
41541138 TAAATGTGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.42, C:0.12, G:0.30, T:0.15
Consensus pattern (7 bp):
AGTGACA
Found at i:41541114 original size:58 final size:57
Alignment explanation
Indices: 41540950--41541129 Score: 229
Period size: 58 Copynumber: 3.3 Consensus size: 57
41540940 ACTTCTGATC
41540950 AGTGACAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATC---G----GTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTT-TCTGATCAGTGACAAGTGACA
*
41541000 AGTGACAA--G-TAAGTGGTAGCTTTAGCTACAGTTTCTGATCAGTGACAAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTTCTGATCAGTGACAAGTGACA
*
41541054 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGGCA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTT-TCTGATCAGTGACAAGTGACA
* *
41541112 AGTAACAAGTGACAAGTG
1 AGTGACAAGTGATAAGTG
41541130 ACAAGTGATA
Statistics
Matches: 113, Mismatches: 5, Indels: 16
0.84 0.04 0.12
Matches are distributed among these distances:
47 18 0.16
48 12 0.11
50 9 0.08
54 14 0.12
56 1 0.01
57 23 0.20
58 36 0.32
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (57 bp):
AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTTCTGATCAGTGACAAGTGACA
Found at i:41546784 original size:50 final size:50
Alignment explanation
Indices: 41546709--41546950 Score: 249
Period size: 50 Copynumber: 4.9 Consensus size: 50
41546699 CATTTGGGTA
41546709 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
* **
41546759 AAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCGGCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
* * * * * *
41546809 GAGAGGTCCTC-CGTAAGACCATGTCTGGGACATGGCATGGGAACCGATAT
1 AAGAGGTCC-CATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
* ** * * * * *
41546859 GAGAACTCCCATGTAAGACCATATCTGGGATATGACTTTGGCAGTAC-AGA-
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA--CCGAGAT
** *
41546909 AA-ACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
41546951 TGTTATTATC
Statistics
Matches: 159, Mismatches: 29, Indels: 9
0.81 0.15 0.05
Matches are distributed among these distances:
49 36 0.23
50 119 0.75
51 3 0.02
52 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.21
Consensus pattern (50 bp):
AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
Found at i:41551902 original size:20 final size:20
Alignment explanation
Indices: 41551877--41551915 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
41551867 TACTTTCTTC
41551877 TTTACTTACT-GTCTTACTTG
1 TTTACTTACTCG-CTTACTTG
41551897 TTTACTTACTCGCTTACTT
1 TTTACTTACTCGCTTACTT
41551916 AAATAATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.15, C:0.23, G:0.08, T:0.54
Consensus pattern (20 bp):
TTTACTTACTCGCTTACTTG
Found at i:41552327 original size:56 final size:52
Alignment explanation
Indices: 41552213--41552354 Score: 162
Period size: 50 Copynumber: 2.7 Consensus size: 52
41552203 ATTTTATGGG
* * * * **
41552213 TGCCCATGCCATGTCCCAAACATAGTCTTACGGGGGACCTCTCATCTCGGTA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATCTCAATA
41552265 --CCAATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATAACCTCAATAA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCAT---CTCAAT-A
* *
41552319 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACGTGGG
41552355 GTCTCATCCC
Statistics
Matches: 76, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
50 39 0.51
53 4 0.05
54 1 0.01
56 32 0.42
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.25
Consensus pattern (52 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATCTCAATA
Found at i:41570192 original size:645 final size:647
Alignment explanation
Indices: 41568960--41570240 Score: 1789
Period size: 645 Copynumber: 2.0 Consensus size: 647
41568950 AATCGCCTAG
41568960 CAAAAGTGGTTTAACATAATTTCAAGCTTCATATTCTACCATAAAACACCAAAATAAACACATTT
1 CAAAAGTGGTTTAACATAATTTCAAGCTTCATATTCTACCATAAAACACCAAAATAAACACATTT
* * * *
41569025 CAACTATGGGTGTTTTTCCAAATATAAACCTTAACATGAATTAATGGTTGAATAAGCTAAATCGA
66 CAACTATGGGTATTTTTCCAAATATAAACCCTAACATGAATTAATGGTAGAATAAGCTAAACCGA
* * * * * * *
41569090 GCTACAATGACTCCAAAAACGTAAAAACCATTAAAAGCGGGGCTTGTATGTACTTACAATCAAGC
131 GCTACAATGACTCCAAAAACATAAAAACAATTAAAAACAGGGATTGGATGCACTTACAATCAAGC
** * *
41569155 TTGAAAGTGGCCAAAGCCCTAGCTATGGAGAACTTGTAAGTTTCCACTATGGTGGAAGAAATATG
196 TTGAAAGTGAACAAAGCCCTAGCTATGGAGAACTTGTAAGTTTCCACTATGATGGAAGAAAGATG
* * *
41569220 AGCACATTTTGGCTTTATTTTCCCTTTTAATTCATTTAATTACCAAATGACTAAAATGCCCCTAA
261 AGCACATGTTGCCTCTATTTTCCCTTTTAATTCATTTAATTACCAAATGACTAAAATGCCCCTAA
* * * * *
41569285 CTTAAAAATATCCTATTTCACCTATCTCTTGTCCATTTTTTTCTATGAAAATCTAATGGTCTAAT
326 CTTAAAAATATCCTATTTCACCTATCGCATGCCCATTTTTGTCCATGAAAATCTAATGGTCTAAT
*
41569350 TAACATTTAAGGACCTCTACTTCAATTATGCACTTCAATTAAATCCTTTATCATCTAAAACTCAT
391 TAACATTTAAGGACCTCTACTTCAATTACGCACTTCAATTAAATCCTTTATCATCTAAAACTCAT
*
41569415 ATTTACCCACTTTTGCAATTAAACCATAATATGCAATTCAGACATGCAATCGCTGAAATTTCTTA
456 ATTTACCCACTTTTGCAATTAAACCATAATATGCAATTCAGACATGCAATCGCTAAAATTTCTTA
* * * *
41569480 TCGGTATTCTAACACATGCATCCAATCAATTGGTAAATAATAAAAATTAATCACAATAAACTTTT
521 TCGATATTCTAACACATGCATCCAATAAATCGATAAATAATAAAAATTAATCACAATAAACTTTT
* *
41569545 CTATCTCAAATTCGTGGTTTCGCAACCACTATTTTGTTTAGGCCATATTTCGGGATGTTACA
586 CTATCTCAAATTCATGGTTTCGCAACCACTATTTCGTTTAGGCCATATTTCGGGATGTTACA
* **
41569607 CAAAAGTTGTTTAACATAATTTCAAGCTTCATATTCTACCATAAAACATTAAAATAAACACATTT
1 CAAAAGTGGTTTAACATAATTTCAAGCTTCATATTCTACCATAAAACACCAAAATAAACACATTT
** *
41569672 C-ACTTATGTTTATTTTTCCAAATATGAACCCTAACATGAATTAATGGTAGAATAAGCTAAACCG
66 CAAC-TATGGGTATTTTTCCAAATATAAACCCTAACATGAATTAATGGTAGAATAAGCTAAACCG
* *
41569736 AGCTACGAA-GACTCGAAAAACATAAAAA-AATTAAAAACAGGGATTGGATGCACTTACTAT-AA
130 AGCTAC-AATGACTCCAAAAACATAAAAACAATTAAAAACAGGGATTGGATGCACTTACAATCAA
* **
41569798 GCTTGAGAAAGTGAAGAAA-CCCTAGCTATGGAGTCCTT-TGAAGTTTTGGCC-CT-T-ATGGAA
194 GCTT--GAAAGTGAACAAAGCCCTAGCTATGGAGAACTTGT-AAG-TTT--CCACTATGATGGAA
* *
41569858 G-AAGATGAGCACATGTTGCCATCT-TTTTCCCTTTTAATT-ATTTTTATTACCAAATGACTATA
253 GAAAGATGAGCACATGTTGCC-TCTATTTTCCCTTTTAATTCA-TTTAATTACCAAATGACTAAA
* * * * * ** *
41569920 ATGCTCTTCA-TTAAAACTTTAGTTATTTTTACCTAT-GCATGCCCATTTTTGTCCATGAAAATC
316 ATGCCCCTAACTTAAAAATAT-CCTA-TTTCACCTATCGCATGCCCATTTTTGTCCATGAAAATC
* *
41569983 TACTGGTCTAATTATCATTTAAGGACCTCTACTTCAATTACGCACTTCAATTAAATCCTTTATCA
379 TAATGGTCTAATTAACATTTAAGGACCTCTACTTCAATTACGCACTTCAATTAAATCCTTTATCA
* *
41570048 TCTAAAACTCATATTTACCCACTTTTGTAATTAAACCCTAATATGCAATTCAGACATGCAATCGC
444 TCTAAAACTCATATTTACCCACTTTTGCAATTAAACCATAATATGCAATTCAGACATGCAATCGC
* ** *
41570113 TAAAATTTCTTATTGATATTCTAACGTATGCATCCAATAAATCGATAAATTATAAAAATTAATCA
509 TAAAATTTCTTATCGATATTCTAACACATGCATCCAATAAATCGATAAATAATAAAAATTAATCA
* * *
41570178 CAATAAACTTTTCTATCTCAGATTCATGGTTTCGCAACCACTGTTTCGTTTAGGCCCTATTTC
574 CAATAAACTTTTCTATCTCAAATTCATGGTTTCGCAACCACTATTTCGTTTAGGCCATATTTC
41570241 AAGATTTTAC
Statistics
Matches: 559, Mismatches: 63, Indels: 26
0.86 0.10 0.04
Matches are distributed among these distances:
644 9 0.02
645 327 0.58
646 64 0.11
647 153 0.27
648 4 0.01
649 2 0.00
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (647 bp):
CAAAAGTGGTTTAACATAATTTCAAGCTTCATATTCTACCATAAAACACCAAAATAAACACATTT
CAACTATGGGTATTTTTCCAAATATAAACCCTAACATGAATTAATGGTAGAATAAGCTAAACCGA
GCTACAATGACTCCAAAAACATAAAAACAATTAAAAACAGGGATTGGATGCACTTACAATCAAGC
TTGAAAGTGAACAAAGCCCTAGCTATGGAGAACTTGTAAGTTTCCACTATGATGGAAGAAAGATG
AGCACATGTTGCCTCTATTTTCCCTTTTAATTCATTTAATTACCAAATGACTAAAATGCCCCTAA
CTTAAAAATATCCTATTTCACCTATCGCATGCCCATTTTTGTCCATGAAAATCTAATGGTCTAAT
TAACATTTAAGGACCTCTACTTCAATTACGCACTTCAATTAAATCCTTTATCATCTAAAACTCAT
ATTTACCCACTTTTGCAATTAAACCATAATATGCAATTCAGACATGCAATCGCTAAAATTTCTTA
TCGATATTCTAACACATGCATCCAATAAATCGATAAATAATAAAAATTAATCACAATAAACTTTT
CTATCTCAAATTCATGGTTTCGCAACCACTATTTCGTTTAGGCCATATTTCGGGATGTTACA
Found at i:41571543 original size:41 final size:41
Alignment explanation
Indices: 41571484--41571588 Score: 115
Period size: 39 Copynumber: 2.6 Consensus size: 41
41571474 GAGTGTAAAA
* * * * *
41571484 AGGGGCACATATGCGCAATTTAGGGGTACCGAAGTAGAAAC
1 AGGGGCACGTATGTGCAATTCAGGGGTACCAAAGTACAAAC
* * * *
41571525 AGGGGCATGTATGTGCAATTCA-AGGTACTAAAGTACAAAT
1 AGGGGCACGTATGTGCAATTCAGGGGTACCAAAGTACAAAC
41571565 A-GGGCACGTATGTGCAATTCAGGG
1 AGGGGCACGTATGTGCAATTCAGGG
41571589 TATAAGAGTT
Statistics
Matches: 52, Mismatches: 11, Indels: 3
0.79 0.17 0.05
Matches are distributed among these distances:
39 19 0.37
40 15 0.29
41 18 0.35
ACGTcount: A:0.33, C:0.15, G:0.30, T:0.21
Consensus pattern (41 bp):
AGGGGCACGTATGTGCAATTCAGGGGTACCAAAGTACAAAC
Found at i:41574220 original size:35 final size:35
Alignment explanation
Indices: 41574161--41574229 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
41574151 TTGGTTGGAT
*
41574161 AAATAGTCTACTAGCACTACGTAGTGGCATCATGA
1 AAATAGTCTACTAGCACTAAGTAGTGGCATCATGA
* * *
41574196 AAATAGTCTATTGGCTCTAAGTAGTGGCATCATG
1 AAATAGTCTACTAGCACTAAGTAGTGGCATCATG
41574230 GAGTGATCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (35 bp):
AAATAGTCTACTAGCACTAAGTAGTGGCATCATGA
Found at i:41574780 original size:27 final size:28
Alignment explanation
Indices: 41574748--41574811 Score: 87
Period size: 27 Copynumber: 2.3 Consensus size: 28
41574738 TATACCAAGG
41574748 ACTATCTTATGATGGAA-GTCT-CCAAAA
1 ACTATCTTATG-TGGAATGTCTGCCAAAA
**
41574775 ACTATCTTATGTGGAATGTCTGCCAAGG
1 ACTATCTTATGTGGAATGTCTGCCAAAA
41574803 ACTATCTTA
1 ACTATCTTA
41574812 AATACAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 5 0.15
27 15 0.45
28 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (28 bp):
ACTATCTTATGTGGAATGTCTGCCAAAA
Found at i:41574809 original size:28 final size:27
Alignment explanation
Indices: 41574716--41574811 Score: 97
Period size: 28 Copynumber: 3.5 Consensus size: 27
41574706 GAAGCCTACT
* * *
41574716 AAGGACTATCTTATG-CGAGCTGTATACC
1 AAGGACTATCTTATGTGGA-ATGTCT-CC
41574744 AAGGACTATCTTATGATGGAA-GTCTCC
1 AAGGACTATCTTATG-TGGAATGTCTCC
**
41574771 AAAAACTATCTTATGTGGAATGTCTGCC
1 AAGGACTATCTTATGTGGAATGTCT-CC
41574799 AAGGACTATCTTA
1 AAGGACTATCTTA
41574812 AATACAAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
26 5 0.09
27 19 0.33
28 31 0.54
30 2 0.04
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (27 bp):
AAGGACTATCTTATGTGGAATGTCTCC
Found at i:41578425 original size:27 final size:28
Alignment explanation
Indices: 41578354--41578428 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 28
41578344 AATCAGGGTA
* *
41578354 TGCCACAAAGGCA-GTCTATTTAGAGTT
1 TGCCACAAAGGCATTTCTATTCAGAGTT
* **
41578381 TTCCACAAA-GTTTATTCT-TTCAGAGTT
1 TGCCACAAAGGCAT-TTCTATTCAGAGTT
41578408 TGCCACAAAGGCATTTCTATT
1 TGCCACAAAGGCATTTCTATT
41578429 GTCAGGTTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 7
0.71 0.16 0.14
Matches are distributed among these distances:
26 1 0.03
27 28 0.78
28 7 0.19
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (28 bp):
TGCCACAAAGGCATTTCTATTCAGAGTT
Found at i:41585493 original size:12 final size:12
Alignment explanation
Indices: 41585468--41585506 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
41585458 ACTCGCTTCT
* *
41585468 TTACTTACTCAC
1 TTACTTGCTTAC
*
41585480 TTACTTGTTTAC
1 TTACTTGCTTAC
41585492 TTACTTGCTTAC
1 TTACTTGCTTAC
41585504 TTA
1 TTA
41585507 AATAACTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:41585940 original size:50 final size:50
Alignment explanation
Indices: 41585768--41585942 Score: 176
Period size: 50 Copynumber: 3.5 Consensus size: 50
41585758 CAATGTCATA
* * ** * * * *
41585768 TCCCAGATATGGTCTTACATGAGAGTTCTCATATCGGTGCCCA-TACAATG
1 TCCCAGACATGGTCTTACATGGGACCTCTTATCTCGGTGCCAACT-CCATG
* * * *
41585818 TCCCAGACATGGTCTTGCGAT-GGATCT-TTCATCTCAGTGCCAACGCCATG
1 TCCCAGACATGGTCTTAC-ATGGGACCTCTT-ATCTCGGTGCCAACTCCATG
* *
41585868 TCCCAAACATAGTCTTACATGGGACCTCTTATCTCGGTGCCAACTCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTTATCTCGGTGCCAACTCCATG
41585918 TCCCAGACATGGTCTTACATGGGAC
1 TCCCAGACATGGTCTTACATGGGAC
41585943 ATCATTCCCT
Statistics
Matches: 101, Mismatches: 19, Indels: 10
0.78 0.15 0.08
Matches are distributed among these distances:
49 3 0.03
50 94 0.93
51 4 0.04
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (50 bp):
TCCCAGACATGGTCTTACATGGGACCTCTTATCTCGGTGCCAACTCCATG
Found at i:41589417 original size:9 final size:9
Alignment explanation
Indices: 41589403--41589437 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
41589393 TTATTTATTC
*
41589403 AATTAATTT
1 AATTAATTA
41589412 AATTAATTA
1 AATTAATTA
*
41589421 AATTAACTA
1 AATTAATTA
41589430 AATTAATT
1 AATTAATT
41589438 CCTAATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (9 bp):
AATTAATTA
Found at i:41594412 original size:28 final size:28
Alignment explanation
Indices: 41594378--41594432 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
41594368 TTGTACTGCA
*
41594378 ACTGTATTAGGCTAAGGCCCACACTGTT
1 ACTGTATCAGGCTAAGGCCCACACTGTT
* **
41594406 ACTGTATCGGGCTAAGGTTCACACTGT
1 ACTGTATCAGGCTAAGGCCCACACTGT
41594433 ACTATTACTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (28 bp):
ACTGTATCAGGCTAAGGCCCACACTGTT
Found at i:41601483 original size:27 final size:27
Alignment explanation
Indices: 41601445--41601641 Score: 189
Period size: 27 Copynumber: 7.0 Consensus size: 27
41601435 CACGAATGGC
* *
41601445 CGAAATACCCTCTAAGGGTAAAATAAT
1 CGAAATACCCTCAAAGGGTAAAATGAT
* *
41601472 CGAAATACCCTCGAAGGGTAAAATGAC
1 CGAAATACCCTCAAAGGGTAAAATGAT
* *
41601499 CAAAATACCGTCAAAGGGTAAAATGACCGAAAT
1 CGAAATACCCTCAAAGGGTAAAAT----G--AT
*
41601532 AACTGAAATACCCTCGAAGGGTAAAATGA-
1 --C-GAAATACCCTCAAAGGGTAAAATGAT
* * *
41601561 CTGAAATACCGTCAAAAGGTAAAATGAC
1 C-GAAATACCCTCAAAGGGTAAAATGAT
*
41601589 CGAAATACCCTCAAAGGGTTAAATGAT
1 CGAAATACCCTCAAAGGGTAAAATGAT
*
41601616 CGAAATACCCTCCAAGGGTAAAATGA
1 CGAAATACCCTCAAAGGGTAAAATGA
41601642 CCGATTTGCT
Statistics
Matches: 141, Mismatches: 19, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
27 115 0.82
28 1 0.01
30 1 0.01
31 1 0.01
32 1 0.01
33 1 0.01
35 1 0.01
36 20 0.14
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.18
Consensus pattern (27 bp):
CGAAATACCCTCAAAGGGTAAAATGAT
Found at i:41601530 original size:54 final size:54
Alignment explanation
Indices: 41601439--41601645 Score: 216
Period size: 54 Copynumber: 3.7 Consensus size: 54
41601429 ATGTGCCACG
* * * *
41601439 AATGGCCGAAATACCCTCTAAGGGTAAAATAATCGAAATACCCTCGAAGGGTAA
1 AATGACCGAAATACCCTCAAAGGGTAAAATGACCGAAATACCCTCGAAGGGTAA
* *
41601493 AATGACCAAAATACCGTCAAAGGGTAAAATGACCGAAATAACTGAAATACCCTCGAAGGGTAA
1 AATGACCGAAATACCCTCAAAGGGTAAAATGA-C-------C-GAAATACCCTCGAAGGGTAA
* * * * *
41601556 AATGACTGAAATACCGTCAAAAGGTAAAATGACCGAAATACCCTCAAAGGGTTA
1 AATGACCGAAATACCCTCAAAGGGTAAAATGACCGAAATACCCTCGAAGGGTAA
* *
41601610 AATGATCGAAATACCCTCCAAGGGTAAAATGACCGA
1 AATGACCGAAATACCCTCAAAGGGTAAAATGACCGA
41601646 TTTGCTCTAT
Statistics
Matches: 128, Mismatches: 16, Indels: 18
0.79 0.10 0.11
Matches are distributed among these distances:
54 76 0.59
55 1 0.01
62 2 0.02
63 49 0.38
ACGTcount: A:0.43, C:0.20, G:0.19, T:0.17
Consensus pattern (54 bp):
AATGACCGAAATACCCTCAAAGGGTAAAATGACCGAAATACCCTCGAAGGGTAA
Found at i:41601568 original size:63 final size:63
Alignment explanation
Indices: 41601465--41601595 Score: 219
Period size: 63 Copynumber: 2.1 Consensus size: 63
41601455 TCTAAGGGTA
*
41601465 AAATAATCGAAATACCCTCGAAGGGTAAAATGACCAAAATACCGTCAAAGGGTAAAATGACCG
1 AAATAATCGAAATACCCTCGAAGGGTAAAATGACCAAAATACCGTCAAAAGGTAAAATGACCG
**
41601528 AAATAA-CTGAAATACCCTCGAAGGGTAAAATGACTGAAATACCGTCAAAAGGTAAAATGACCG
1 AAATAATC-GAAATACCCTCGAAGGGTAAAATGACCAAAATACCGTCAAAAGGTAAAATGACCG
41601591 AAATA
1 AAATA
41601596 CCCTCAAAGG
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
62 1 0.02
63 63 0.98
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.17
Consensus pattern (63 bp):
AAATAATCGAAATACCCTCGAAGGGTAAAATGACCAAAATACCGTCAAAAGGTAAAATGACCG
Found at i:41601603 original size:90 final size:90
Alignment explanation
Indices: 41601446--41601622 Score: 257
Period size: 90 Copynumber: 2.0 Consensus size: 90
41601436 ACGAATGGCC
* * * *
41601446 GAAATACCCTCTAAGGGTAAAATAATCGAAATACCCTCGAAGGGTAAAATGACCAAAATACCGTC
1 GAAATACCCTCGAAGGGTAAAATAATCGAAATACCCTCAAAAGGTAAAATGACCAAAATACCCTC
41601511 AAAGGGTAAAATGACCGAAATAACT
66 AAAGGGTAAAATGACCGAAATAACT
* * *
41601536 GAAATACCCTCGAAGGGTAAAATGA-CTGAAATACCGTCAAAAGGTAAAATGACCGAAATACCCT
1 GAAATACCCTCGAAGGGTAAAATAATC-GAAATACCCTCAAAAGGTAAAATGACCAAAATACCCT
* *
41601600 CAAAGGGTTAAATGATCGAAATA
65 CAAAGGGTAAAATGACCGAAATA
41601623 CCCTCCAAGG
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
89 1 0.01
90 76 0.99
ACGTcount: A:0.45, C:0.18, G:0.19, T:0.18
Consensus pattern (90 bp):
GAAATACCCTCGAAGGGTAAAATAATCGAAATACCCTCAAAAGGTAAAATGACCAAAATACCCTC
AAAGGGTAAAATGACCGAAATAACT
Found at i:41605485 original size:29 final size:28
Alignment explanation
Indices: 41605442--41605519 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 28
41605432 TCATGAGATT
41605442 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
* *
41605472 -GCACTAAGTGTGCGAGTTTACAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
41605499 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
41605520 GATTATTAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
27 5 0.12
29 34 0.81
30 3 0.07
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:41605773 original size:174 final size:174
Alignment explanation
Indices: 41605474--41605799 Score: 510
Period size: 174 Copynumber: 1.9 Consensus size: 174
41605464 ATTGTACAGC
* * * *
41605474 ACTAAGTGTGCGAGTTTACAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATGTG
1 ACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGGTGATTACTAAACACTATGTG
* ** *
41605539 TGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGATT
66 TGCGAACCCAATATATATTTTCCATAAATTATTTACACGAAGGGTGCGACTTTACCGAGTCAATT
41605604 TTGGACAGCGGAAAAAGGTAAGTGTGCGAACTTGAAATGCATGGT
131 TTGGACAGCGG-AAAAGGTAAGTGTGCGAACTTGAAATGCATGGT
* * * * *
41605649 ACTAAGTGTGTGAGTTTAAAGTGCATGGCACTGAGTGTGCGTGGGTGATTACTAAACATTATGTG
1 ACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGGTGATTACTAAACACTATGTG
*
41605714 TGC-AACCCAATATATATTTTCCATAAATTATTTACACGAAGGGTGCGGCTTTACCGAGTCAATT
66 TGCGAACCCAATATATATTTTCCATAAATTATTTACACGAAGGGTGCGACTTTACCGAGTCAATT
41605778 TTGGACAGCGGAAAAGGTAAGT
131 TTGGACAGCGGAAAAGGTAAGT
41605800 ACCTTGAGTT
Statistics
Matches: 137, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
173 11 0.08
174 67 0.49
175 59 0.43
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (174 bp):
ACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGGTGATTACTAAACACTATGTG
TGCGAACCCAATATATATTTTCCATAAATTATTTACACGAAGGGTGCGACTTTACCGAGTCAATT
TTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATGGT
Found at i:41608214 original size:410 final size:409
Alignment explanation
Indices: 41607566--41608569 Score: 1134
Period size: 411 Copynumber: 2.4 Consensus size: 409
41607556 TTGGGAGGAG
* * * * * *
41607566 TCATCATAAGTGGTTGGGTTGACTCAAGAATAGAGGTGCCAACAATTGTAAAGTTAGGTTGAATT
1 TCATCATAAGTGGTTGGGCTAACTCAAGAACAGGGGTGTCAACAATTGTAAAGTTAGGTTGAATC
* * * * **
41607631 GAGGGAGAATCC-ATGGCTTTTTAGTTCAGTATTTTCCTAGATTGTGCCAATTGTTGATGTCTCT
66 GAGGGAGAA-CCTATGGC-TTTTAGTTCAATATTCTCATAAACAGTGCCAATTGTTGATGTCTCT
* * * *
41607695 TTCACTGGGCTTGGAGATTGGTTGAGCTAAACTTTATAGCTAGAAAATCTACAAAGTGTACTAGC
129 TTTATTGGGCTTGGAGATTAGTTGAGCT-AACTTTATAGCTAGAAAATCTACAAAGTATACTAGC
* *
41607760 AATATGGGTAGTCATGGTTGATGGTAGATATGATTGTGAGAACTTGTACTC-AATA-TTTGGTAA
193 AATATGGATAGTCATGGTTGATGGTAGAGATGATTGTGAGAACTTGTACTCAAATATTTTGGTAA
* * * *
41607823 TGATCTTATGGCAACCAATTA-TTTTTAGAAGTATCTCAGAAAAACATACAAATTAGTTGGAGCT
258 TGATCGTATGGAAACCAATTACTATTGA-AAGTATCT-A-AAAAACATACAAATTAGTTGGAGCT
* * * * *
41607887 GAGATTATTGGT-GGACTGGTCTTTCTGGAACTTGTCACCACGTAGGAAAATGTTTCGGCTCA-A
320 AAGATTATAGGTAGG-CTAGTCTTTCTGAAACTTGTAACCACGTAGGAAAATGTTTCGGCT-AGA
41607950 ACTCTCAATCAAAA-GCTTAAGAACAGC
383 ACTCTCAATCAAAAGGC-TAAGAACAGC
* * * *
41607977 -CATCATAAGTGGTTGGGCTAACTCAAGAACAGGGGCGTTAGCAATTGTAAAGTTAGCTTGAATC
1 TCATCATAAGTGGTTGGGCTAACTCAAGAACAGGGGTGTCAACAATTGTAAAGTTAGGTTGAATC
* *
41608041 GAGGGAGAACCTA-GAGCTTTTAGTTTAATATTCTCATAAACAGTGCCACTTGTTGATGTCTCTT
66 GAGGGAGAACCTATG-GCTTTTAGTTCAATATTCTCATAAACAGTGCCAATTGTTGATGTCTCTT
* * * * * *
41608105 TTATTGGGCTTAGAGACTAGTTGAGCTACACTTTATAGC-CGAACAATTTGCAAAGTATTCTAGC
130 TTATTGGGCTTGGAGATTAGTTGAGCTA-ACTTTATAGCTAGAA-AATCTACAAAGTATACTAGC
*
41608169 AATATGGATAGTCATGGTTGATGGTAGAGATGGTTGTGAAGAACTTGTACTCAAAATATTTTGGT
193 AATATGGATAGTCATGGTTGATGGTAGAGATGATTGTG-AGAACTTGTACTC-AAATATTTTGGT
* *** *
41608234 AATGATCGTATGGAAACCGATTACTATTGAAAGTATCTAAAAAACATATTGATTGGTTGGAGCTA
256 AATGATCGTATGGAAACCAATTACTATTGAAAGTATCTAAAAAACATACAAATTAGTTGGAGCTA
* * * ** * *
41608299 AGATTCTAGGTAGGTTAGTCTTTTTGAAACTTGTAACCACGTAGGGTAATGTTTGGGCTAGTACT
321 AGATTATAGGTAGGCTAGTCTTTCTGAAACTTGTAACCACGTAGGAAAATGTTTCGGCTAGAACT
* ** **
41608364 CTCTATCAAAAGGCTGGGAGGAGC
386 CTCAATCAAAAGGCTAAGAACAGC
* * * * * * ** * *
41608388 TGA-CGTAAGTAGATGGGCTAATTAAAGAACAGGGGTGTCAATTACTATAAAGTTAGGTTGAATC
1 TCATCATAAGTGGTTGGGCTAACTCAAGAACAGGGGTGTCAACAATTGTAAAGTTAGGTTGAATC
* *
41608452 GAGAGAGAACCTATGGCTTTTAGTTCAATATTCTCACAAACAGTGCCAATTGTTGATGTCTCTTT
66 GAGGGAGAACCTATGGCTTTTAGTTCAATATTCTCATAAACAGTGCCAATTGTTGATGTCTCTTT
*
41608517 TTTTGGGCTTGGATG-TTAGTTGAGCTAAGCTTTATAGCT-GAAAAATCTACAAA
131 TATTGGGCTTGGA-GATTAGTTGAGCTAA-CTTTATAGCTAG-AAAATCTACAAA
41608570 AAAAAAAAAG
Statistics
Matches: 495, Mismatches: 80, Indels: 36
0.81 0.13 0.06
Matches are distributed among these distances:
408 4 0.01
409 125 0.25
410 81 0.16
411 233 0.47
412 14 0.03
413 34 0.07
414 4 0.01
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (409 bp):
TCATCATAAGTGGTTGGGCTAACTCAAGAACAGGGGTGTCAACAATTGTAAAGTTAGGTTGAATC
GAGGGAGAACCTATGGCTTTTAGTTCAATATTCTCATAAACAGTGCCAATTGTTGATGTCTCTTT
TATTGGGCTTGGAGATTAGTTGAGCTAACTTTATAGCTAGAAAATCTACAAAGTATACTAGCAAT
ATGGATAGTCATGGTTGATGGTAGAGATGATTGTGAGAACTTGTACTCAAATATTTTGGTAATGA
TCGTATGGAAACCAATTACTATTGAAAGTATCTAAAAAACATACAAATTAGTTGGAGCTAAGATT
ATAGGTAGGCTAGTCTTTCTGAAACTTGTAACCACGTAGGAAAATGTTTCGGCTAGAACTCTCAA
TCAAAAGGCTAAGAACAGC
Found at i:41610504 original size:21 final size:21
Alignment explanation
Indices: 41610478--41610549 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
41610468 TCATATGAGT
41610478 TTTCGTTCAGCTCTTACGAGC
1 TTTCGTTCAGCTCTTACGAGC
* * * *
41610499 TTTCGTTCAACCCTTATG-GG
1 TTTCGTTCAGCTCTTACGAGC
41610519 TTTCCGTTCAGCTCTTACGAGC
1 TTT-CGTTCAGCTCTTACGAGC
*
41610541 TTCCGTTCA
1 TTTCGTTCA
41610550 ACCCTTATGG
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
20 4 0.10
21 33 0.82
22 3 0.08
ACGTcount: A:0.14, C:0.29, G:0.18, T:0.39
Consensus pattern (21 bp):
TTTCGTTCAGCTCTTACGAGC
Found at i:41610564 original size:42 final size:42
Alignment explanation
Indices: 41610439--41610564 Score: 162
Period size: 42 Copynumber: 3.0 Consensus size: 42
41610429 GTTTACTTTT
* * ** * * * * *
41610439 CGTTTAGCTCTCACGAGCTTCTATTTAACTCATATGAGTTTT
1 CGTTCAGCTCTTACGAGCTTCCGTTCAACCCTTATGGGTTTC
*
41610481 CGTTCAGCTCTTACGAGCTTTCGTTCAACCCTTATGGGTTTC
1 CGTTCAGCTCTTACGAGCTTCCGTTCAACCCTTATGGGTTTC
41610523 CGTTCAGCTCTTACGAGCTTCCGTTCAACCCTTATGGGTTTC
1 CGTTCAGCTCTTACGAGCTTCCGTTCAACCCTTATGGGTTTC
41610565 TGTTTAGTTC
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 73 1.00
ACGTcount: A:0.17, C:0.27, G:0.17, T:0.39
Consensus pattern (42 bp):
CGTTCAGCTCTTACGAGCTTCCGTTCAACCCTTATGGGTTTC
Found at i:41610583 original size:42 final size:42
Alignment explanation
Indices: 41610439--41610583 Score: 155
Period size: 42 Copynumber: 3.5 Consensus size: 42
41610429 GTTTACTTTT
* ** * * * * *
41610439 CGTTTAGCTCTCACGAGCTTCTATTTAACTCATATGAGTTTT
1 CGTTCAGCTCTCACGAGCTTCCGTTCAACCCTTATGGGTTTC
* *
41610481 CGTTCAGCTCTTACGAGCTTTCGTTCAACCCTTATGGGTTTC
1 CGTTCAGCTCTCACGAGCTTCCGTTCAACCCTTATGGGTTTC
*
41610523 CGTTCAGCTCTTACGAGCTTCCGTTCAACCCTTATGGGTTTC
1 CGTTCAGCTCTCACGAGCTTCCGTTCAACCCTTATGGGTTTC
* * * *
41610565 TGTTTAGTTCTCATGAGCT
1 CGTTCAGCTCTCACGAGCT
41610584 ACTATTCAGC
Statistics
Matches: 87, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 87 1.00
ACGTcount: A:0.17, C:0.26, G:0.18, T:0.40
Consensus pattern (42 bp):
CGTTCAGCTCTCACGAGCTTCCGTTCAACCCTTATGGGTTTC
Found at i:41614280 original size:21 final size:21
Alignment explanation
Indices: 41614256--41614318 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
41614246 GACGAGCTTT
41614256 CGTTCAACCTTTATGGGTTTC
1 CGTTCAACCTTTATGGGTTTC
* *** *
41614277 CGTTC-AGCTCTTACAAGCTTC
1 CGTTCAACCT-TTATGGGTTTC
*
41614298 CGTTCAACCCTTATGGGTTTC
1 CGTTCAACCTTTATGGGTTTC
41614319 TGTTTAGCTC
Statistics
Matches: 29, Mismatches: 11, Indels: 4
0.66 0.25 0.09
Matches are distributed among these distances:
20 3 0.10
21 24 0.83
22 2 0.07
ACGTcount: A:0.16, C:0.29, G:0.17, T:0.38
Consensus pattern (21 bp):
CGTTCAACCTTTATGGGTTTC
Found at i:41614281 original size:42 final size:42
Alignment explanation
Indices: 41614193--41614339 Score: 150
Period size: 42 Copynumber: 3.5 Consensus size: 42
41614183 GTTTACTTTT
* ** * * * * *
41614193 CGTTTAGCTCTCACGAGCTTCTATTTAACTCATATGAGTTTT
1 CGTTCAGCTCTCACGAGCTTCCGTTCAACCCTTATGGGTTTC
* * *
41614235 CGTTCAGCTCTGACGAGCTTTCGTTCAACCTTTATGGGTTTC
1 CGTTCAGCTCTCACGAGCTTCCGTTCAACCCTTATGGGTTTC
* *
41614277 CGTTCAGCTCTTACAAGCTTCCGTTCAACCCTTATGGGTTTC
1 CGTTCAGCTCTCACGAGCTTCCGTTCAACCCTTATGGGTTTC
* * *
41614319 TGTTTAGCTCTCATGAGCTTC
1 CGTTCAGCTCTCACGAGCTTC
41614340 TATTCAGCCT
Statistics
Matches: 85, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 85 1.00
ACGTcount: A:0.17, C:0.26, G:0.18, T:0.39
Consensus pattern (42 bp):
CGTTCAGCTCTCACGAGCTTCCGTTCAACCCTTATGGGTTTC
Found at i:41616003 original size:24 final size:24
Alignment explanation
Indices: 41615974--41616047 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
41615964 AATAGTTGTG
41615974 ATAATTATACATTTAAAAATAATT
1 ATAATTATACATTTAAAAATAATT
* ** *
41615998 ATAATT-TA-A--TAAAAGTTGTG
1 ATAATTATACATTTAAAAATAATT
*
41616018 ATAATTACACATTTAAAAATAATT
1 ATAATTATACATTTAAAAATAATT
*
41616042 AGAATT
1 ATAATT
41616048 CAAATTCAAA
Statistics
Matches: 36, Mismatches: 10, Indels: 8
0.67 0.19 0.15
Matches are distributed among these distances:
20 13 0.36
21 1 0.03
22 2 0.06
23 2 0.06
24 18 0.50
ACGTcount: A:0.51, C:0.04, G:0.05, T:0.39
Consensus pattern (24 bp):
ATAATTATACATTTAAAAATAATT
Found at i:41616017 original size:44 final size:47
Alignment explanation
Indices: 41615953--41616047 Score: 151
Period size: 44 Copynumber: 2.1 Consensus size: 47
41615943 TTAGTTAAAA
* *
41615953 AATTTAAGTAAAATAGTTGTGATAATTATACATTTAAAAATAATTAT
1 AATTTAAGTAAAATAGTTGTGATAATTACACATTTAAAAATAATTAG
41616000 AATTTAA-T-AAA-AGTTGTGATAATTACACATTTAAAAATAATTAG
1 AATTTAAGTAAAATAGTTGTGATAATTACACATTTAAAAATAATTAG
41616044 AATT
1 AATT
41616048 CAAATTCAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
44 35 0.76
45 3 0.07
46 1 0.02
47 7 0.15
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.39
Consensus pattern (47 bp):
AATTTAAGTAAAATAGTTGTGATAATTACACATTTAAAAATAATTAG
Found at i:41625303 original size:98 final size:96
Alignment explanation
Indices: 41625191--41625370 Score: 254
Period size: 98 Copynumber: 1.9 Consensus size: 96
41625181 TTAAAAAATA
* * *
41625191 AAATATATTTAACATAACGATAAATGTAAAAATAATTTT-ATTATATAATTGCATATTTATATTA
1 AAATATATTTAACATAACAATAAATATAAAAAT-ATTTTCATTATATAATTACATA-TT-TATTA
41625255 ATTTATTTATATAAATAAATGAGTTACTAATTAT
63 ATTTATTTATATAAATAAATGAGTTACTAATTAT
* * * * *
41625289 AAATATTTTTAACATAATAATATATATAAATATATTTTCATTATATAATTACATATTTATTATTT
1 AAATATATTTAACATAACAATAAATATAAAAATATTTTCATTATATAATTACATATTTATTAATT
41625354 TATTTATATAAATAAAT
66 TATTTATATAAATAAAT
41625371 AAAATTATTA
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
96 24 0.33
97 7 0.10
98 42 0.58
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (96 bp):
AAATATATTTAACATAACAATAAATATAAAAATATTTTCATTATATAATTACATATTTATTAATT
TATTTATATAAATAAATGAGTTACTAATTAT
Found at i:41625458 original size:14 final size:13
Alignment explanation
Indices: 41625425--41625463 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
41625415 CAACATATTT
41625425 ATTAATTAAAAAC
1 ATTAATTAAAAAC
*
41625438 ATTAATTAAAAAT
1 ATTAATTAAAAAC
*
41625451 TTTAAATTAAAAA
1 ATT-AATTAAAAA
41625464 AAAACAACCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 14 0.61
14 9 0.39
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (13 bp):
ATTAATTAAAAAC
Found at i:41630725 original size:39 final size:39
Alignment explanation
Indices: 41630682--41630798 Score: 180
Period size: 39 Copynumber: 3.0 Consensus size: 39
41630672 CCATATTAAA
* * * *
41630682 CATATAACCACATAACCTTTAAGAATATATCACAATACT
1 CATATAATCACATAACATTCAAGCATATATCACAATACT
*
41630721 CATATAATTACATAACATTCAAGCATATATCACAATACT
1 CATATAATCACATAACATTCAAGCATATATCACAATACT
*
41630760 CATATAATCACATAACATTCAAGCATACATCACAATACT
1 CATATAATCACATAACATTCAAGCATATATCACAATACT
41630799 AAAAAACATG
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 71 1.00
ACGTcount: A:0.46, C:0.23, G:0.03, T:0.28
Consensus pattern (39 bp):
CATATAATCACATAACATTCAAGCATATATCACAATACT
Found at i:41635891 original size:10 final size:10
Alignment explanation
Indices: 41635876--41635909 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
41635866 TATAACTCAA
41635876 CCATTTTAAT
1 CCATTTTAAT
41635886 CCATTTTAAT
1 CCATTTTAAT
*
41635896 CCATTTTGAT
1 CCATTTTAAT
41635906 CCAT
1 CCAT
41635910 GTGGAGACGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.26, C:0.24, G:0.03, T:0.47
Consensus pattern (10 bp):
CCATTTTAAT
Found at i:41638066 original size:56 final size:56
Alignment explanation
Indices: 41637980--41638092 Score: 156
Period size: 56 Copynumber: 2.0 Consensus size: 56
41637970 ACAAATTGCG
* * * *
41637980 ACCAAAACTGAAGAACCTAGGGAGTTTTACTTTTCCTTGCTCAA-TTGGAATCATT
1 ACCAAAACTGAAGAACCTAGAGAGTTTTACTATTCCTTGCTAAATTTGAAATCATT
* *
41638035 NACCAAAATTGAAGGACCTAGAGAGTTTTACTATTCCTTGCTAAATTTGAAATCATT
1 -ACCAAAACTGAAGAACCTAGAGAGTTTTACTATTCCTTGCTAAATTTGAAATCATT
41638092 A
1 A
41638093 TGTAGGGAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
56 40 0.80
57 10 0.20
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (56 bp):
ACCAAAACTGAAGAACCTAGAGAGTTTTACTATTCCTTGCTAAATTTGAAATCATT
Found at i:41639038 original size:16 final size:16
Alignment explanation
Indices: 41639017--41639048 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
41639007 GTTTTGTTGC
*
41639017 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
41639033 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
41639049 CTTCCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:41639228 original size:46 final size:43
Alignment explanation
Indices: 41639163--41639270 Score: 121
Period size: 46 Copynumber: 2.4 Consensus size: 43
41639153 ACACTTTGGA
41639163 ATAAT-AATAGATACACGGT-GGATTCAGCACACAGCAACCACCCTTT
1 ATAATCAAT-GATAC-CGGTGGGA-TCAGCACACAGCAACCA-CC-TT
* *
41639209 GTAATCAATGATATCCGGTGGGATCAGCACATAGCAACCACCTT
1 ATAATCAATGATA-CCGGTGGGATCAGCACACAGCAACCACCTT
*
41639253 ATAATTAATGATACCGGT
1 ATAATCAATGATACCGGT
41639271 TCACATAGTA
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
43 5 0.09
44 13 0.24
45 2 0.04
46 28 0.51
47 7 0.13
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (43 bp):
ATAATCAATGATACCGGTGGGATCAGCACACAGCAACCACCTT
Found at i:41639332 original size:51 final size:50
Alignment explanation
Indices: 41639272--41639464 Score: 205
Period size: 51 Copynumber: 3.8 Consensus size: 50
41639262 GATACCGGTT
* * * *
41639272 CACATAGTAGCCCGCGCATAGTCCTACACATGTGACCATCACTATCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACTAT-CGATA
* *
41639323 CACATAGTAGCCTGCACATAGTAGTACACACGTGATCGA--AGCTATTCGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTA-TCGATA
* * * * *
41639374 CGCATAGTAGCTTGCACATAGTACTACACATGCGACCTATCA-T-TCTAGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTATCGA-TA
41639424 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATCA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATCA
41639465 GTTTCACTTT
Statistics
Matches: 118, Mismatches: 17, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
49 7 0.06
50 37 0.31
51 70 0.59
52 3 0.03
53 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (50 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCGATA
Found at i:41639482 original size:101 final size:102
Alignment explanation
Indices: 41639270--41639458 Score: 249
Period size: 101 Copynumber: 1.9 Consensus size: 102
41639260 ATGATACCGG
* * * *
41639270 TTCACATAGTAGCCCGCGCATAGTCCTACACATGTGACCATCACTATCCGATACACATAGTAGCC
1 TTCACATAGTAGCCCGCACATAGTACTACACATGCGACCATCACTATCAGATACACATAGTAGCC
* *
41639335 TGCACATAGTAGTACACACGTGATCGAAGCTATTCGA
66 TGCACATAGTACTACACACGTGATCCAAGCTATTCGA
* * **
41639372 TACGCATAGTAGCTTGCACATAGTACTACACATGCGACCTATCA-T-TCTAG-TACACATAGTAG
1 TTCACATAGTAGCCCGCACATAGTACTACACATGCGACC-ATCACTATC-AGATACACATAGTAG
41639434 CCTGCACATAGTACTACACACGTGA
64 CCTGCACATAGTACTACACACGTGA
41639459 CCATCAGTTT
Statistics
Matches: 76, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
101 38 0.50
102 34 0.45
103 4 0.05
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (102 bp):
TTCACATAGTAGCCCGCACATAGTACTACACATGCGACCATCACTATCAGATACACATAGTAGCC
TGCACATAGTACTACACACGTGATCCAAGCTATTCGA
Found at i:41670009 original size:28 final size:28
Alignment explanation
Indices: 41669971--41670028 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
41669961 TTACCCTTGT
*
41669971 TCTCCGGTCCTCACTTCTCTTTCCAATC
1 TCTCCAGTCCTCACTTCTCTTTCCAATC
*
41669999 TCTCCAGTCCTCACTTCTCTTTCTAATC
1 TCTCCAGTCCTCACTTCTCTTTCCAATC
41670027 TC
1 TC
41670029 AATATTCCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.12, C:0.41, G:0.05, T:0.41
Consensus pattern (28 bp):
TCTCCAGTCCTCACTTCTCTTTCCAATC
Found at i:41675971 original size:16 final size:16
Alignment explanation
Indices: 41675950--41676017 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
41675940 TTTGGTTCGC
41675950 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
41675966 TGTATTGGATTAGAAG
1 TGTATTGGATTAGAGG
41675982 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
41675998 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
41676014 TGTA
1 TGTA
41676018 ATAGCAAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.26, C:0.00, G:0.35, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:41676274 original size:18 final size:17
Alignment explanation
Indices: 41676253--41676287 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
41676243 TTATTATTAA
*
41676253 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
41676271 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
41676288 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:41676353 original size:157 final size:157
Alignment explanation
Indices: 41676140--41676424 Score: 525
Period size: 157 Copynumber: 1.8 Consensus size: 157
41676130 TAGAATACCC
41676140 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* * *
41676205 TTATCAATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
41676270 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
*
41676297 TTAGCATAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
*
41676362 ATATCAATAATAAATAATTTAATCATATTTAAATATAATTATTATTAAATATATTATAATTAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAA
41676425 TAAGGAACCA
Statistics
Matches: 123, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
157 123 1.00
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (157 bp):
TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:41676423 original size:15 final size:16
Alignment explanation
Indices: 41676390--41676424 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
41676380 TTAATCATAT
*
41676390 TTAAATATAATTATTA
1 TTAAATATAATTATAA
41676406 TTAAATAT-ATTATAA
1 TTAAATATAATTATAA
41676421 TTAA
1 TTAA
41676425 TAAGGAACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTAAATATAATTATAA
Found at i:41679672 original size:28 final size:28
Alignment explanation
Indices: 41679641--41679695 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
41679631 GCAAACCGGT
*
41679641 AGAAAAGAAAAGAAAATAAACAGAGGGC
1 AGAAAAGAAAAGAAAAGAAACAGAGGGC
*
41679669 AGAAAAGAAAAGAAAAGAAACGGAGGG
1 AGAAAAGAAAAGAAAAGAAACAGAGGG
41679696 AGCAAATCGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.64, C:0.05, G:0.29, T:0.02
Consensus pattern (28 bp):
AGAAAAGAAAAGAAAAGAAACAGAGGGC
Found at i:41684475 original size:22 final size:22
Alignment explanation
Indices: 41684447--41684492 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
41684437 ACACATGAAA
41684447 GTTGTCTTCTCTTGGTTTTTAG
1 GTTGTCTTCTCTTGGTTTTTAG
41684469 GTTGTCTTCTCTTGGTTTTTAG
1 GTTGTCTTCTCTTGGTTTTTAG
41684491 GT
1 GT
41684493 GCTATAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.04, C:0.13, G:0.24, T:0.59
Consensus pattern (22 bp):
GTTGTCTTCTCTTGGTTTTTAG
Found at i:41690055 original size:176 final size:176
Alignment explanation
Indices: 41689761--41690111 Score: 558
Period size: 176 Copynumber: 2.0 Consensus size: 176
41689751 ATCTAGATTG
* * *
41689761 GGTTGGGGAGGTTACACCAGAGGAGAAAGGCAAACTAACATTGACCAAAACACTAAGAGGTTTAG
1 GGTTGGGGAGGTTACACCAGAGGAGAAAGGCAAACTAACACTAACCAAAACAATAAGAGGTTTAG
* *
41689826 AAACTAACCAAAGATGTTGATTGAGTCTTAACTCAATTGGCATCAGCATTGTTGCCAATGCAAGA
66 AAACTAACCAAAGATATTGATTGAGTCTTAACTCAATTGGCATCAACATTGTTGCCAATGCAAGA
41689891 GGACATGGGTTTGAGTGTGCTGAACCACATTATCCTCTTATTTAAA
131 GGACATGGGTTTGAGTGTGCTGAACCACATTATCCTCTTATTTAAA
* * * * *
41689937 GGTTGGGGAGGTTACACTAGAGGAGAAAGGCAAATTAACACTAACCACAACAATAGGATGTTTAG
1 GGTTGGGGAGGTTACACCAGAGGAGAAAGGCAAACTAACACTAACCAAAACAATAAGAGGTTTAG
* * *
41690002 AAACTAACCAAATATATTGATTGAGTCTTAGCTCAATTGGCATCAACATTGTTGCCAATGTAAGA
66 AAACTAACCAAAGATATTGATTGAGTCTTAACTCAATTGGCATCAACATTGTTGCCAATGCAAGA
* * *
41690067 GGACGTGGGTTTGAGTGTGCTGAAGCGCATTATCCTCTTATTTAA
131 GGACATGGGTTTGAGTGTGCTGAACCACATTATCCTCTTATTTAA
41690112 GGCTTGGAAA
Statistics
Matches: 159, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
176 159 1.00
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (176 bp):
GGTTGGGGAGGTTACACCAGAGGAGAAAGGCAAACTAACACTAACCAAAACAATAAGAGGTTTAG
AAACTAACCAAAGATATTGATTGAGTCTTAACTCAATTGGCATCAACATTGTTGCCAATGCAAGA
GGACATGGGTTTGAGTGTGCTGAACCACATTATCCTCTTATTTAAA
Found at i:41694799 original size:92 final size:92
Alignment explanation
Indices: 41694642--41694825 Score: 368
Period size: 92 Copynumber: 2.0 Consensus size: 92
41694632 TATATATTTT
41694642 TTAAATTATTAAAAATCATATATATCTAATATATAACATTCATATATATTCTAAGTTAGTTTAAG
1 TTAAATTATTAAAAATCATATATATCTAATATATAACATTCATATATATTCTAAGTTAGTTTAAG
41694707 TTTTAATATATATTTAATTCTATTTAA
66 TTTTAATATATATTTAATTCTATTTAA
41694734 TTAAATTATTAAAAATCATATATATCTAATATATAACATTCATATATATTCTAAGTTAGTTTAAG
1 TTAAATTATTAAAAATCATATATATCTAATATATAACATTCATATATATTCTAAGTTAGTTTAAG
41694799 TTTTAATATATATTTAATTCTATTTAA
66 TTTTAATATATATTTAATTCTATTTAA
41694826 AATTGATCCC
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 92 1.00
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.48
Consensus pattern (92 bp):
TTAAATTATTAAAAATCATATATATCTAATATATAACATTCATATATATTCTAAGTTAGTTTAAG
TTTTAATATATATTTAATTCTATTTAA
Found at i:41696929 original size:125 final size:123
Alignment explanation
Indices: 41696736--41697082 Score: 568
Period size: 123 Copynumber: 2.8 Consensus size: 123
41696726 TTTCAAGTTG
* * *
41696736 ACGTTTCTAATCAAATAGTATAAAATCGCTTTTAGCTGAATGCTATTTGAGAAGAATTTGTGAAA
1 ACGTTTCTAAGCAAATAGTATAAAATCGCTTCTAGCTGGATGCTATTTGAGAAGAATTTGTGAAA
*
41696801 TCGCGCCCTTGTGGACGCGCTTTTGCTACAGTAGGTCATGGAAGAAATAATTTTTTTTTC
66 TCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGGAAG-AAT-ATTTTTTTTTC
* *
41696861 ACGTTTCTAAGGAAATAGTATAAAATCGCTTCTAGTTGGATGCTATTTGAGAAGAATTTGTGAAA
1 ACGTTTCTAAGCAAATAGTATAAAATCGCTTCTAGCTGGATGCTATTTGAGAAGAATTTGTGAAA
* * *
41696926 TCGCGCCCTCGTGGACGCGCTTTTGCTACAATAGGTCATGGAAGAATTTTTTTTTTTG
66 TCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGGAAGAATATTTTTTTTTC
* *
41696984 ACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAA
1 ACGTTTCTAAGCAAATAGTATAAAATCGCTTCTAGCTGGATGCTATTTGAGAAGAATTTGTGAAA
*
41697049 TCACGCCCTCGTGGACGCGCTTTTGCTACAGTAG
66 TCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
41697083 TATGTTTGGG
Statistics
Matches: 207, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
123 102 0.49
124 3 0.01
125 102 0.49
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (123 bp):
ACGTTTCTAAGCAAATAGTATAAAATCGCTTCTAGCTGGATGCTATTTGAGAAGAATTTGTGAAA
TCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGGAAGAATATTTTTTTTTC
Found at i:41697058 original size:123 final size:125
Alignment explanation
Indices: 41696733--41697078 Score: 570
Period size: 125 Copynumber: 2.8 Consensus size: 125
41696723 TAATTTCAAG
* * *
41696733 TTGACGTTTCTAATCAAATAGTATAAAATCGCTTTTAGCTGAATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTAAGCAAATAGTATAAAATCGCTTCTAGCTGGATGCTATTTGAGAAGAATTTGTG
* *
41696798 AAATCGCGCCCTTGTGGACGCGCTTTTGCTACAGTAGGTCATGGAAGAAATAATTTTTTT
66 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAATAGGTCATGGAAGAAATAATTTTTTT
* * *
41696858 TTCACGTTTCTAAGGAAATAGTATAAAATCGCTTCTAGTTGGATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTAAGCAAATAGTATAAAATCGCTTCTAGCTGGATGCTATTTGAGAAGAATTTGTG
*
41696923 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAATAGGTCATGGAAG-AAT-TTTTTTTT
66 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAATAGGTCATGGAAGAAATAATTTTTTT
* *
41696981 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTAAGCAAATAGTATAAAATCGCTTCTAGCTGGATGCTATTTGAGAAGAATTTGTG
*
41697046 AAATCACGCCCTCGTGGACGCGCTTTTGCTACA
66 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACA
41697079 GTAGTATGTT
Statistics
Matches: 206, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
123 99 0.48
124 3 0.01
125 104 0.50
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (125 bp):
TTGACGTTTCTAAGCAAATAGTATAAAATCGCTTCTAGCTGGATGCTATTTGAGAAGAATTTGTG
AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAATAGGTCATGGAAGAAATAATTTTTTT
Found at i:41701253 original size:22 final size:22
Alignment explanation
Indices: 41701225--41701277 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
41701215 TAATAGGGGA
*
41701225 TAAAATATAAATTTTATGTGGC
1 TAAAATATAAATATTATGTGGC
* *
41701247 TAAAATACAAAATATTATGTGGT
1 TAAAATA-TAAATATTATGTGGC
*
41701270 TGAAATAT
1 TAAAATAT
41701278 GAAAATGACT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.45, C:0.04, G:0.13, T:0.38
Consensus pattern (22 bp):
TAAAATATAAATATTATGTGGC
Found at i:41701276 original size:23 final size:23
Alignment explanation
Indices: 41701225--41701268 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
41701215 TAATAGGGGA
* *
41701225 TAAAATA-TAAATTTTATGTGGC
1 TAAAATACAAAATATTATGTGGC
41701247 TAAAATACAAAATATTATGTGG
1 TAAAATACAAAATATTATGTGG
41701269 TTGAAATATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.45, C:0.05, G:0.14, T:0.36
Consensus pattern (23 bp):
TAAAATACAAAATATTATGTGGC
Found at i:41702705 original size:27 final size:27
Alignment explanation
Indices: 41702675--41702787 Score: 111
Period size: 27 Copynumber: 4.2 Consensus size: 27
41702665 AACTGTGAAC
* *
41702675 TGTCCCGTAGACACCTATATTGCGGAA
1 TGTCCTGTAGACACCTATATTGCAGAA
* **
41702702 TGTCCTGTGGACACCTATATTGTGGAA
1 TGTCCTGTAGACACCTATATTGCAGAA
* * * *
41702729 GGTCTTGCA-ATCACCTATGTTGCAGAA
1 TGTCCTGTAGA-CACCTATATTGCAGAA
* *
41702756 TGTCCTGCAGACACCTATATTGTAGAA
1 TGTCCTGTAGACACCTATATTGCAGAA
41702783 TGTCC
1 TGTCC
41702788 CATAGACATT
Statistics
Matches: 70, Mismatches: 14, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
26 1 0.01
27 68 0.97
28 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (27 bp):
TGTCCTGTAGACACCTATATTGCAGAA
Found at i:41709038 original size:11 final size:11
Alignment explanation
Indices: 41709022--41709067 Score: 58
Period size: 11 Copynumber: 4.0 Consensus size: 11
41709012 GTCCAACAAT
41709022 TTAAAAATTAA
1 TTAAAAATTAA
41709033 TTAAAAATATATTA
1 TTAAAAAT-TA--A
41709047 TTAAAAA-TAA
1 TTAAAAATTAA
41709057 TTAAAAATTAA
1 TTAAAAATTAA
41709068 AAACGTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
10 8 0.26
11 11 0.35
12 4 0.13
14 8 0.26
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
TTAAAAATTAA
Found at i:41712474 original size:16 final size:16
Alignment explanation
Indices: 41712455--41712499 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
41712445 TCCATTCCAC
41712455 ATCCTTAATGTATAAT
1 ATCCTTAATGTATAAT
41712471 ATCCTTAATGTATAAT
1 ATCCTTAATGTATAAT
*
41712487 ATGCTTATATGTA
1 ATCCTTA-ATGTA
41712500 ACATTATCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
16 22 0.81
17 5 0.19
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (16 bp):
ATCCTTAATGTATAAT
Found at i:41721902 original size:27 final size:27
Alignment explanation
Indices: 41721863--41721916 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
41721853 ATTGTAAAGA
*
41721863 AAGGAAAACTTCTTTCTTTTCCTCTCT
1 AAGGAAAAATTCTTTCTTTTCCTCTCT
41721890 AAGGAAAAATTCTTTCTTTTCCTCTCT
1 AAGGAAAAATTCTTTCTTTTCCTCTCT
41721917 TCTCACGTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.24, C:0.24, G:0.07, T:0.44
Consensus pattern (27 bp):
AAGGAAAAATTCTTTCTTTTCCTCTCT
Found at i:41725478 original size:20 final size:20
Alignment explanation
Indices: 41725453--41725495 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
41725443 AGCATTAAAA
*
41725453 TGCTAACAGAGGCACCGAAG
1 TGCTAACAGAGGCACCAAAG
*
41725473 TGCTAACATAGGCACCAAAG
1 TGCTAACAGAGGCACCAAAG
41725493 TGC
1 TGC
41725496 AATCCCGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.26, G:0.26, T:0.14
Consensus pattern (20 bp):
TGCTAACAGAGGCACCAAAG
Found at i:41727219 original size:47 final size:48
Alignment explanation
Indices: 41727166--41727276 Score: 113
Period size: 47 Copynumber: 2.4 Consensus size: 48
41727156 AAGGTGGAAC
* * *
41727166 TATGTGGTAGTTTATC-AC-ATTAAT-GTGACATTGTTCATGATTTTGAT
1 TATGTGGTAGTTTATCTACAATT-ATGGTGAC-TTGTCCATGATATTAAT
* * * *
41727213 TATGTGGCAGTATATCTACAATTTTGGTGGCTTGTCCATGATATTAAT
1 TATGTGGTAGTTTATCTACAATTATGGTGACTTGTCCATGATATTAAT
41727261 TAT-TGGTAGTTTATCT
1 TATGTGGTAGTTTATCT
41727277 GTGATTTTGA
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
47 25 0.48
48 20 0.38
49 7 0.13
ACGTcount: A:0.24, C:0.10, G:0.20, T:0.46
Consensus pattern (48 bp):
TATGTGGTAGTTTATCTACAATTATGGTGACTTGTCCATGATATTAAT
Found at i:41730562 original size:17 final size:15
Alignment explanation
Indices: 41730520--41730586 Score: 64
Period size: 14 Copynumber: 4.3 Consensus size: 15
41730510 GTAAGTAATC
41730520 TAGATGTGAAAA-TA
1 TAGATGTGAAAACTA
*
41730534 TAGATTTGAAAACTA
1 TAGATGTGAAAACTA
*
41730549 TAGAACTGTGAAAAACTC
1 TAG-A-TGTG-AAAACTA
*
41730567 TAGATTGTGAAAACAA
1 TAGA-TGTGAAAACTA
41730583 TAGA
1 TAGA
41730587 AACTTTAGAT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
14 11 0.26
15 5 0.12
16 10 0.23
17 8 0.19
18 9 0.21
ACGTcount: A:0.48, C:0.07, G:0.18, T:0.27
Consensus pattern (15 bp):
TAGATGTGAAAACTA
Found at i:41738582 original size:25 final size:25
Alignment explanation
Indices: 41738553--41738619 Score: 93
Period size: 25 Copynumber: 2.7 Consensus size: 25
41738543 TCCTATACAT
41738553 GTATGCTCATACGAGCTATAAATCG
1 GTATGCTCATACGAGCTATAAATCG
41738578 GTATGCTTTCAT--GAGCTATAAATCG
1 GTATGC--TCATACGAGCTATAAATCG
*
41738603 GTAAGCTCATACGAGCT
1 GTATGCTCATACGAGCT
41738620 GAGAATCGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
23 4 0.11
25 29 0.78
27 4 0.11
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (25 bp):
GTATGCTCATACGAGCTATAAATCG
Found at i:41745401 original size:23 final size:22
Alignment explanation
Indices: 41745349--41745402 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
41745339 GATTTATCAG
*
41745349 TATGGATATGTGTGGTATTGAAT
1 TATGG-TATGTCTGGTATTGAAT
*
41745372 TAAGGTATGTCTGAGTA-TGAATT
1 TATGGTATGTCTG-GTATTGAA-T
41745395 TATGGTAT
1 TATGGTAT
41745403 TATATTCTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 11 0.42
23 15 0.58
ACGTcount: A:0.28, C:0.02, G:0.28, T:0.43
Consensus pattern (22 bp):
TATGGTATGTCTGGTATTGAAT
Found at i:41747095 original size:50 final size:50
Alignment explanation
Indices: 41746992--41747184 Score: 215
Period size: 50 Copynumber: 3.7 Consensus size: 50
41746982 GGGAATGAGA
*
41746992 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGG
* *
41747048 TCCCATGTAAGACCATGCCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
*** * * **
41747098 TCCCCCATAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * *
41747148 TCCCATGTAAGACCATATCTGGGATATGACATTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
41747185 GTACAGAAAA
Statistics
Matches: 118, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
50 79 0.67
53 3 0.03
55 1 0.01
56 35 0.30
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.22
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:41747183 original size:100 final size:103
Alignment explanation
Indices: 41746999--41747184 Score: 243
Period size: 100 Copynumber: 1.8 Consensus size: 103
41746989 AGATCCCATG
* **
41746999 TAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCCCATGTAAGACCAT
1 TAAGACCATGTCTGGGACATGGCATGGGCATC--T-AGATTATGAGAACTCCCATGTAAGACCAT
* * *
41747064 GCCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCA
63 ACCTGGGACATGACATTGGCACCGAGATGAGAGGTCCCCCA
* *
41747105 TAAGACCATGTCTGGGACATGGCATGGGCA-C-CGA-TATGAGAACTCCCATGTAAGACCATATC
1 TAAGACCATGTCTGGGACATGGCATGGGCATCTAGATTATGAGAACTCCCATGTAAGACCATACC
*
41747167 TGGGATATGACATTGGCA
66 TGGGACATGACATTGGCA
41747185 GTACAGAAAA
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
100 39 0.55
101 2 0.03
105 1 0.01
106 29 0.41
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.22
Consensus pattern (103 bp):
TAAGACCATGTCTGGGACATGGCATGGGCATCTAGATTATGAGAACTCCCATGTAAGACCATACC
TGGGACATGACATTGGCACCGAGATGAGAGGTCCCCCA
Found at i:41747450 original size:12 final size:12
Alignment explanation
Indices: 41747433--41747471 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
41747423 ATGAGTTATT
41747433 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
41747445 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
41747457 TAAGTGAGTAAG
1 TAAGTAAGCAAG
41747469 TAA
1 TAA
41747472 AAAAGCGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:41797665 original size:30 final size:31
Alignment explanation
Indices: 41797620--41797683 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 31
41797610 GATGAAAAAT
* * *
41797620 TAAAATATAAACTAAT-TAAATTAATTATCC
1 TAAAAAATAAACTAATGGAAATTAATTAACC
* *
41797650 TAAAAAATAACCTAATGGAATTTAATTAACC
1 TAAAAAATAAACTAATGGAAATTAATTAACC
41797681 TAA
1 TAA
41797684 GATATCCAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 14 0.50
31 14 0.50
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.33
Consensus pattern (31 bp):
TAAAAAATAAACTAATGGAAATTAATTAACC
Found at i:41803029 original size:19 final size:19
Alignment explanation
Indices: 41803005--41803046 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
41802995 TTTAACTAGG
41803005 ATTAGGTGGGGCGACAACC
1 ATTAGGTGGGGCGACAACC
41803024 ATTAGGTGGGGCGACAACC
1 ATTAGGTGGGGCGACAACC
41803043 -TTAG
1 ATTAG
41803047 TTAAATAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.26, C:0.19, G:0.36, T:0.19
Consensus pattern (19 bp):
ATTAGGTGGGGCGACAACC
Found at i:41807745 original size:17 final size:17
Alignment explanation
Indices: 41807723--41807758 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
41807713 TATCTAACAT
*
41807723 CCTTCTTTTACGAATAC
1 CCTTCTTTTACGAAAAC
41807740 CCTTCTTTTACGAAAAC
1 CCTTCTTTTACGAAAAC
41807757 CC
1 CC
41807759 ATTTACTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.25, C:0.33, G:0.06, T:0.36
Consensus pattern (17 bp):
CCTTCTTTTACGAAAAC
Found at i:41808695 original size:35 final size:35
Alignment explanation
Indices: 41808580--41808696 Score: 119
Period size: 35 Copynumber: 3.3 Consensus size: 35
41808570 GTAGCTTTGT
* * *
41808580 AGAGCCTGTAGATCGTTTACACGGTGTCGCTCCAA
1 AGAGCCTGTAGACCATTTACATGGTGTCGCTCCAA
* * * ** *
41808615 AGAACTTGCA-AGCCATTTACATGGTGTCATTCCGA
1 AGAGCCTGTAGA-CCATTTACATGGTGTCGCTCCAA
*
41808650 AGAGCCTGTAGACCATTTACATGGTGTCGCTCTAA
1 AGAGCCTGTAGACCATTTACATGGTGTCGCTCCAA
*
41808685 AGAGCTTGTAGA
1 AGAGCCTGTAGA
41808697 TAACATTTCC
Statistics
Matches: 63, Mismatches: 17, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
34 1 0.02
35 61 0.97
36 1 0.02
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.27
Consensus pattern (35 bp):
AGAGCCTGTAGACCATTTACATGGTGTCGCTCCAA
Found at i:41811495 original size:50 final size:49
Alignment explanation
Indices: 41811420--41811521 Score: 150
Period size: 50 Copynumber: 2.1 Consensus size: 49
41811410 AAACTTGGTA
* * *
41811420 GTTATCATTCTTTTTGGAAAGAATATAACGTTTTTTAATACTTTCCATAT
1 GTTATAATTATTTTTGGAAAGAATATAACG-TGTTTAATACTTTCCATAT
* *
41811470 GTTATAATTATTTTTGGAAAGAATATAACGTGTTTAATACTTTTCATGT
1 GTTATAATTATTTTTGGAAAGAATATAACGTGTTTAATACTTTCCATAT
41811519 GTT
1 GTT
41811522 CTCTATAAGA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
49 19 0.40
50 28 0.60
ACGTcount: A:0.30, C:0.09, G:0.13, T:0.48
Consensus pattern (49 bp):
GTTATAATTATTTTTGGAAAGAATATAACGTGTTTAATACTTTCCATAT
Found at i:41815507 original size:18 final size:18
Alignment explanation
Indices: 41815486--41815521 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
41815476 TCTTCTCTTT
41815486 CTTTCTCTTCTTCAACAA
1 CTTTCTCTTCTTCAACAA
*
41815504 CTTTTTCTTCTTCAACAA
1 CTTTCTCTTCTTCAACAA
41815522 TGATTTCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.31, G:0.00, T:0.47
Consensus pattern (18 bp):
CTTTCTCTTCTTCAACAA
Found at i:41815528 original size:18 final size:18
Alignment explanation
Indices: 41815491--41815534 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
41815481 TCTTTCTTTC
*
41815491 TCTTCTTCAACAACTTTT
1 TCTTCTTCAACAACTATT
41815509 TCTTCTTCAACAA-TGATT
1 TCTTCTTCAACAACT-ATT
*
41815527 TCCTCTTC
1 TCTTCTTC
41815535 TATAGCAGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 1 0.04
18 22 0.96
ACGTcount: A:0.20, C:0.30, G:0.02, T:0.48
Consensus pattern (18 bp):
TCTTCTTCAACAACTATT
Found at i:41828546 original size:49 final size:49
Alignment explanation
Indices: 41828484--41828678 Score: 178
Period size: 49 Copynumber: 3.8 Consensus size: 49
41828474 TAACAACATG
** * *
41828484 CCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATGTAC-TA
1 CCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGTA
* ** *
41828533 CCAATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTG
1 CCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTC-GTA
* *
41828583 CCAACGCCATGTCCCAGACATGGTCTTACATTGGACCTCTCATGATCTCAAGGATA
1 CCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC---G-TA
* *
41828639 -CAAATGTCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 CCAAA-GCCATGTCCCAGACATGGTCTTACATGGGACCTCT
41828679 TTACCCAAAT
Statistics
Matches: 120, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
48 1 0.01
49 38 0.32
50 38 0.32
53 5 0.04
55 5 0.04
56 33 0.28
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (49 bp):
CCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGTA
Found at i:41828619 original size:50 final size:49
Alignment explanation
Indices: 41828482--41828625 Score: 173
Period size: 50 Copynumber: 2.9 Consensus size: 49
41828472 GATAACAACA
** * *
41828482 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATGTAC
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAC
* * **
41828531 TACCAATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCT-C
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAC
* *
41828579 GGTGCCAACGCCATGTCCCAGACATGGTCTTACATTGGACCTCTCAT
1 --TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT
41828626 GATCTCAAGG
Statistics
Matches: 80, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
48 1 0.01
49 39 0.49
50 40 0.50
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26
Consensus pattern (49 bp):
TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAC
Found at i:41836071 original size:600 final size:600
Alignment explanation
Indices: 41834926--41836093 Score: 1969
Period size: 600 Copynumber: 1.9 Consensus size: 600
41834916 ATCCATCAGC
* *
41834926 ATTATGCCTTGACACGTAGGACTAGAAAAAGGACAAACTATCCACATATAAGTTAAAAATCGGAT
1 ATTATGCCTTGACACGGAGGACCAGAAAAAGGACAAACTATCCACATATAAGTTAAAAATCGGAT
* * * *
41834991 AACTAATCAATACAAAAGAAGGTACTAGGACAAAGGAAGAGATAGATATAACTTTTTGAGTTGGC
66 AACTAATCAATAAAAAAGAAAGTACTACGACAAAGGAAGAGATAGATATAACTTTTTGAGTTAGC
*
41835056 AAATTATAGTGTGAGATTGTTTAGTACTATAATTCAAGGGGTTAGTATTTAAAGTACATACTTTG
131 AAATTATAGAGTGAGATTGTTTAGTACTATAATTCAAGGGGTTAGTATTTAAAGTACATACTTTG
* *
41835121 GGAGGGAACTATAATTTGAGGAATATACCTAAATTCTAATGTCAGAAATGTCGAGGAAAAGGCCA
196 GGAGGGAACTATAATTGGAGGAATATAACTAAATTCTAATGTCAGAAATGTCGAGGAAAAGGCCA
* *
41835186 CAGCCATATGCAATTCTACCTTTGTAGAGAGATTATGATAACATTCCTGTGGAATCAAGAACATA
261 CAGCCATATGCAACTCTACCTTTGTACAGAGATTATGATAACATTCCTGTGGAATCAAGAACATA
* *
41835251 AATTTTCTAGATGTTTATGTTTTAGAGTAATTTGTGTGAAACAAAACTCAGCAAGAAAATTTCAG
326 AATTTTCTAGATGTTTATGTTTTAGAGTAAATTGGGTGAAACAAAACTCAGCAAGAAAATTTCAG
* *
41835316 AAAGGAGGATTACATTGAGATCAGAATTATTGGATGCTGGTACTGCTGGACCGTAATTGGGTCCC
391 AAAGGAGGATTACATTGAGATCAGAATTATTGGATGCTGGTACTGCCGGACCATAATTGGGTCCC
* *
41835381 TTTATAAGACGTGGAACAAATTTCATTCTATAAGGAAGACATCCACTACTGAAAAAAGGTCAAAG
456 TTTATAAGACGAGGAACAAATTTCATTCTAGAAGGAAGACATCCACTACTGAAAAAAGGTCAAAG
* *
41835446 ATGATGCTACAAACAAATACAGATAATAAAAATGGGAAGTGTTAAAGGGTAACTTATTCACATAT
521 ATGATGCTACAAACAAATACAGATAATAAAAATGGGAAGCGTGAAAGGGTAACTTATTCACATAT
41835511 AAGTTATCTCACACT
586 AAGTTATCTCACACT
* * * *
41835526 ATTATGCCTTGACATGGAGGACCAGAAAAAGGGCAAACTATCCACATATAAGTTAAAAATTGGGT
1 ATTATGCCTTGACACGGAGGACCAGAAAAAGGACAAACTATCCACATATAAGTTAAAAATCGGAT
*
41835591 AACTAATCAATAAAAAAGAAAGTACTACGACAAAGGAAGAGATAGAATATAACTTTTTGGGTTAG
66 AACTAATCAATAAAAAAGAAAGTACTACGACAAAGGAAGAGATAG-ATATAACTTTTTGAGTTAG
* *
41835656 CAATTTATAGAGTGAGATTGTTTAGTACTAT-ATTCAAGGGGTTAGTATTTAAAGTACATTCTTT
130 CAAATTATAGAGTGAGATTGTTTAGTACTATAATTCAAGGGGTTAGTATTTAAAGTACATACTTT
*
41835720 GGGAGGGAACTATAATTGGAGGAATGTAACTAAATTCTAATGTCAGAAATGTCGAGGAAAAGGCC
195 GGGAGGGAACTATAATTGGAGGAATATAACTAAATTCTAATGTCAGAAATGTCGAGGAAAAGGCC
* * * *
41835785 ACAGCTATATGCAACTCTATCTTTGTACAGAGATTATGATAACATTCCTGTGGGATCGAGAACAT
260 ACAGCCATATGCAACTCTACCTTTGTACAGAGATTATGATAACATTCCTGTGGAATCAAGAACAT
* *
41835850 AAATTTTCTAGATGTTTATGTTTTAGATTAAATTGGGTGAAACAAACCTCAGCAAGAAAATTTCA
325 AAATTTTCTAGATGTTTATGTTTTAGAGTAAATTGGGTGAAACAAAACTCAGCAAGAAAATTTCA
*
41835915 GAAAGTAGGATTACATTGAGATCAGAATTATTGGATGCTGGTACTGCCGGACCATAATTGGGTCC
390 GAAAGGAGGATTACATTGAGATCAGAATTATTGGATGCTGGTACTGCCGGACCATAATTGGGTCC
* * * *
41835980 CTTTATAAGACGAGGAACAAATTTCATTCTAGAAGGCAGACATCCACTATTGACAAAAGGTTAAA
455 CTTTATAAGACGAGGAACAAATTTCATTCTAGAAGGAAGACATCCACTACTGAAAAAAGGTCAAA
*
41836045 GATGATGCTACAAACAAATGCAGATAATAAAAATGGGAAGCGTGAAAGG
520 GATGATGCTACAAACAAATACAGATAATAAAAATGGGAAGCGTGAAAGG
41836094 AAGGGTAACT
Statistics
Matches: 528, Mismatches: 39, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
600 482 0.91
601 46 0.09
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (600 bp):
ATTATGCCTTGACACGGAGGACCAGAAAAAGGACAAACTATCCACATATAAGTTAAAAATCGGAT
AACTAATCAATAAAAAAGAAAGTACTACGACAAAGGAAGAGATAGATATAACTTTTTGAGTTAGC
AAATTATAGAGTGAGATTGTTTAGTACTATAATTCAAGGGGTTAGTATTTAAAGTACATACTTTG
GGAGGGAACTATAATTGGAGGAATATAACTAAATTCTAATGTCAGAAATGTCGAGGAAAAGGCCA
CAGCCATATGCAACTCTACCTTTGTACAGAGATTATGATAACATTCCTGTGGAATCAAGAACATA
AATTTTCTAGATGTTTATGTTTTAGAGTAAATTGGGTGAAACAAAACTCAGCAAGAAAATTTCAG
AAAGGAGGATTACATTGAGATCAGAATTATTGGATGCTGGTACTGCCGGACCATAATTGGGTCCC
TTTATAAGACGAGGAACAAATTTCATTCTAGAAGGAAGACATCCACTACTGAAAAAAGGTCAAAG
ATGATGCTACAAACAAATACAGATAATAAAAATGGGAAGCGTGAAAGGGTAACTTATTCACATAT
AAGTTATCTCACACT
Found at i:41836699 original size:2 final size:2
Alignment explanation
Indices: 41836694--41836724 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
41836684 CATATATATC
41836694 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
41836725 AAAGAGAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:41838231 original size:12 final size:12
Alignment explanation
Indices: 41838214--41838238 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41838204 GGCGTGCATT
41838214 CGGTTAACCGAC
1 CGGTTAACCGAC
41838226 CGGTTAACCGAC
1 CGGTTAACCGAC
41838238 C
1 C
41838239 CGAATTAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:41838411 original size:9 final size:9
Alignment explanation
Indices: 41838397--41838489 Score: 107
Period size: 9 Copynumber: 10.4 Consensus size: 9
41838387 TTGTTAAAAA
41838397 TTAACCGAT
1 TTAACCGAT
*
41838406 TTAACCTAT
1 TTAACCGAT
41838415 TTAACCGA-
1 TTAACCGAT
* *
41838423 TTAACTGAC
1 TTAACCGAT
41838432 TTAACCGAT
1 TTAACCGAT
*
41838441 TTAACCGAC
1 TTAACCGAT
*
41838450 TTAACCGAC
1 TTAACCGAT
41838459 TTAACCGAT
1 TTAACCGAT
* *
41838468 TTAACCAAC
1 TTAACCGAT
*
41838477 TTAATCGAT
1 TTAACCGAT
41838486 TTAA
1 TTAA
41838490 ATCACTATAT
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
8 7 0.10
9 64 0.90
ACGTcount: A:0.35, C:0.24, G:0.09, T:0.32
Consensus pattern (9 bp):
TTAACCGAT
Found at i:41838461 original size:27 final size:27
Alignment explanation
Indices: 41838397--41838489 Score: 125
Period size: 27 Copynumber: 3.5 Consensus size: 27
41838387 TTGTTAAAAA
* *
41838397 TTAACCGATTTAACCTATTTAACCGA-
1 TTAACCGACTTAACCGATTTAACCGAC
*
41838423 TTAACTGACTTAACCGATTTAACCGAC
1 TTAACCGACTTAACCGATTTAACCGAC
*
41838450 TTAACCGACTTAACCGATTTAACCAAC
1 TTAACCGACTTAACCGATTTAACCGAC
* *
41838477 TTAATCGATTTAA
1 TTAACCGACTTAA
41838490 ATCACTATAT
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
26 23 0.39
27 36 0.61
ACGTcount: A:0.35, C:0.24, G:0.09, T:0.32
Consensus pattern (27 bp):
TTAACCGACTTAACCGATTTAACCGAC
Found at i:41838531 original size:37 final size:37
Alignment explanation
Indices: 41838489--41838561 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
41838479 AATCGATTTA
* *
41838489 AATCACTATATAATTTAAAAA-ATTACATAAGTCTTTG
1 AATCACTACATAA-CTAAAAACATTACATAAGTCTTTG
41838526 AATCACTACATAACTAAAAACATTACATAAGTCTTT
1 AATCACTACATAACTAAAAACATTACATAAGTCTTT
41838562 AACACATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 6 0.18
37 27 0.82
ACGTcount: A:0.47, C:0.15, G:0.04, T:0.34
Consensus pattern (37 bp):
AATCACTACATAACTAAAAACATTACATAAGTCTTTG
Found at i:41838743 original size:7 final size:7
Alignment explanation
Indices: 41838731--41838755 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
41838721 TGCAGTATTG
41838731 CATGAAA
1 CATGAAA
41838738 CATGAAA
1 CATGAAA
41838745 CATGAAA
1 CATGAAA
41838752 CATG
1 CATG
41838756 CAGTATAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (7 bp):
CATGAAA
Found at i:41838823 original size:7 final size:7
Alignment explanation
Indices: 41838811--41838869 Score: 73
Period size: 7 Copynumber: 8.3 Consensus size: 7
41838801 GTACAGAAGA
41838811 AAACATG
1 AAACATG
41838818 AAACATG
1 AAACATG
* **
41838825 CAGTATG
1 AAACATG
41838832 AAACATG
1 AAACATG
*
41838839 AAATCGTG
1 AAA-CATG
41838847 AAACATG
1 AAACATG
41838854 AAACATG
1 AAACATG
41838861 AAACATG
1 AAACATG
41838868 AA
1 AA
41838870 TTGTTCTTGG
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
7 37 0.86
8 6 0.14
ACGTcount: A:0.53, C:0.14, G:0.17, T:0.17
Consensus pattern (7 bp):
AAACATG
Found at i:41838890 original size:13 final size:13
Alignment explanation
Indices: 41838872--41838898 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41838862 AACATGAATT
41838872 GTTCTTGGGCTTA
1 GTTCTTGGGCTTA
41838885 GTTCTTGGGCTTA
1 GTTCTTGGGCTTA
41838898 G
1 G
41838899 AGCCTGGAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.15, G:0.33, T:0.44
Consensus pattern (13 bp):
GTTCTTGGGCTTA
Found at i:41839122 original size:18 final size:19
Alignment explanation
Indices: 41839087--41839138 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
41839077 AATCGACCGA
**
41839087 TTAACCGAATTCGGTCGG-
1 TTAACCGAATTTTGTCGGT
*
41839105 TTAACCGAATTTTTTCGGTT
1 TTAACCGAATTTTGTCGG-T
41839125 TTAACCGAATTTTG
1 TTAACCGAATTTTG
41839139 CACACCCCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 15 0.54
20 13 0.46
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.40
Consensus pattern (19 bp):
TTAACCGAATTTTGTCGGT
Found at i:41840379 original size:279 final size:279
Alignment explanation
Indices: 41839869--41840429 Score: 777
Period size: 279 Copynumber: 2.0 Consensus size: 279
41839859 ATGTTGAAAA
* * *
41839869 AATCTCAGTTTGAAAATGGTTTTCTTACACAACGAAAAATTAAAATTTTGAAAATCGATCCGGTT
1 AATCCCAGTTTGAAAATGGTTTTCTTACACAACGAAAAATTAAAATTTTGAAAATCCAACCGGTT
** * * ** *
41839934 TGTGATATTTATAGCAATAAACCTTAATTGAATTCGTACATGTGTTTTTGACTTAGTAGACGTTC
66 TGTGATATTTATAGCAATAAACCTTAACCGAATTCATACATATGTTTTCAACTTAGTAGACATTC
* * * * ** *
41839999 GTTGTTCTTGACTTTCAACCAAACGATCTTCTCCGCTTTTCTTGTACCACGAACTGCTTCGAGTG
131 ATTGTTCCTGAATTTCAACCAAACGATCTTCTCCGCTATTCTCATACCACGAACTACTTCGAGTG
* * * *
41840064 TGGGCTCGAATCAATTAAACCAAAACACAAAACTAGAAAAAGTTTTCTCT-CTATTTTGGGTGAA
196 TGGGCCCAAACCAATTAAACCAAAACACAAAACTAGAAAAAGTTTTCTCTCCT-TTTGGGGTGAA
*
41840128 AACGAAAATT-TTGTCTTTTT
260 AACAAAAATTCTT-TCTTTTT
* * *
41840148 AATCCCAGTTTGAAAATGGTTTTCTTGCACAGCGAAAATTTAAAATTTTGAAAA-CCAACCTGGT
1 AATCCCAGTTTGAAAATGGTTTTCTTACACAACGAAAAATTAAAATTTTGAAAATCCAACC-GGT
* *
41840212 TTGTGATATTTATAGCAATAAACCTTAACCGAATTCATACTTATGTTTTCAACTTAGTGGACATT
65 TTGTGATATTTATAGCAATAAACCTTAACCGAATTCATACATATGTTTTCAACTTAGTAGACATT
* *
41840277 CATTGTTCCTGAATTTCAACCAAACGATCTTCTCTGCTATTCTCATACTACGAACTACTTCGAGT
130 CATTGTTCCTGAATTTCAACCAAACGATCTTCTCCGCTATTCTCATACCACGAACTACTTCGAGT
* * * *
41840342 GTGGGCCCAAACCAATTGAATCGAAACACAGAACTAGAAAAAGTTTTCTCTCCTTTTGGGGTGAA
195 GTGGGCCCAAACCAATTAAACCAAAACACAAAACTAGAAAAAGTTTTCTCTCCTTTTGGGGTGAA
41840407 AACAAAAATTCTTTCTTTTT
260 AACAAAAATTCTTTCTTTTT
41840427 AAT
1 AAT
41840430 AGAAATCGGT
Statistics
Matches: 246, Mismatches: 33, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
278 4 0.02
279 238 0.97
280 4 0.02
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (279 bp):
AATCCCAGTTTGAAAATGGTTTTCTTACACAACGAAAAATTAAAATTTTGAAAATCCAACCGGTT
TGTGATATTTATAGCAATAAACCTTAACCGAATTCATACATATGTTTTCAACTTAGTAGACATTC
ATTGTTCCTGAATTTCAACCAAACGATCTTCTCCGCTATTCTCATACCACGAACTACTTCGAGTG
TGGGCCCAAACCAATTAAACCAAAACACAAAACTAGAAAAAGTTTTCTCTCCTTTTGGGGTGAAA
ACAAAAATTCTTTCTTTTT
Found at i:41842095 original size:8 final size:8
Alignment explanation
Indices: 41842084--41842117 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
41842074 AAGGTATAAG
41842084 TATGTATA
1 TATGTATA
41842092 TATGTATA
1 TATGTATA
* *
41842100 TGTATATA
1 TATGTATA
41842108 TATGTATA
1 TATGTATA
41842116 TA
1 TA
41842118 ATGCTCGAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (8 bp):
TATGTATA
Found at i:41842487 original size:75 final size:75
Alignment explanation
Indices: 41842388--41842528 Score: 167
Period size: 75 Copynumber: 1.9 Consensus size: 75
41842378 GCTTACATAT
* ** * * * * *
41842388 ATGTATATGTTCTTTTGTTGAATTTAGGAAGGACATTTATATAAGTTTATGTG-AGATTCGATTA
1 ATGTATATGTTCTTGTAATAAATTTAAGAAGGAAATTTACATAAGTATATG-GAAGATTCGATTA
41842452 TGCAGGTATAC
65 TGCAGGTATAC
* * *
41842463 ATGTATATGTTCTTGTAATAAATTTAAGTATGAAATTTACATATGTATATGGAAGATTCGATTAT
1 ATGTATATGTTCTTGTAATAAATTTAAGAAGGAAATTTACATAAGTATATGGAAGATTCGATTAT
41842528 G
66 G
41842529 TATATATATT
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
74 1 0.02
75 53 0.98
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.43
Consensus pattern (75 bp):
ATGTATATGTTCTTGTAATAAATTTAAGAAGGAAATTTACATAAGTATATGGAAGATTCGATTAT
GCAGGTATAC
Found at i:41842669 original size:41 final size:41
Alignment explanation
Indices: 41842610--41842689 Score: 106
Period size: 41 Copynumber: 2.0 Consensus size: 41
41842600 TGATCGAATG
* * *
41842610 TTTCAGACTTTACGTCTAGCAGGTTTGATACCGGTGAAATA
1 TTTCAGACTTTACATCTAGCAGGCTTAATACCGGTGAAATA
* * *
41842651 TTTCAGGCTTTATATCTAGCAGGCTTAATGCCGGTGAAA
1 TTTCAGACTTTACATCTAGCAGGCTTAATACCGGTGAAA
41842690 CAATTCGGAC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (41 bp):
TTTCAGACTTTACATCTAGCAGGCTTAATACCGGTGAAATA
Found at i:41842924 original size:33 final size:34
Alignment explanation
Indices: 41842877--41842950 Score: 105
Period size: 33 Copynumber: 2.2 Consensus size: 34
41842867 GTTAGGCATA
**
41842877 TGTATATATGCATTCAGCTATTCATG-TTTAAAG
1 TGTATATACACATTCAGCTATTCATGTTTTAAAG
* *
41842910 TGTATATACACATTCGGCTATTCATGTTTTAAAT
1 TGTATATACACATTCAGCTATTCATGTTTTAAAG
41842944 TGTATAT
1 TGTATAT
41842951 GCATTCGGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 23 0.64
34 13 0.36
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.45
Consensus pattern (34 bp):
TGTATATACACATTCAGCTATTCATGTTTTAAAG
Found at i:41845506 original size:10 final size:10
Alignment explanation
Indices: 41845491--41845515 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
41845481 TCAAATAAGC
41845491 ATGTATATAT
1 ATGTATATAT
41845501 ATGTATATAT
1 ATGTATATAT
41845511 ATGTA
1 ATGTA
41845516 AATTTCTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (10 bp):
ATGTATATAT
Found at i:41845635 original size:6 final size:6
Alignment explanation
Indices: 41845626--41846500 Score: 1750
Period size: 6 Copynumber: 145.8 Consensus size: 6
41845616 TGAGTATGTA
41845626 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
41845674 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
41845722 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
41845770 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
41845818 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
41845866 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
41845914 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
41845962 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
41846010 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
41846058 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
41846106 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
41846154 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
41846202 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
41846250 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
41846298 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
41846346 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
41846394 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
41846442 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
41846490 TATATG TATAT
1 TATATG TATAT
41846501 AATGCTCGAA
Statistics
Matches: 869, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 869 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
TATATG
Found at i:41847046 original size:40 final size:41
Alignment explanation
Indices: 41846996--41847074 Score: 106
Period size: 41 Copynumber: 2.0 Consensus size: 41
41846986 TGATCGAATG
* * * *
41846996 TTTCAGACTTT-CGTCTAGCTGGTTTGATGCCGGTGAAATA
1 TTTCAAACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATA
*
41847036 TTTCAAACTTTATGTCTAGCAGGCTTAATGCCGGTGAAA
1 TTTCAAACTTTACGTCTAGCAGGCTTAATGCCGGTGAAA
41847075 CAATTCGGAC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
40 10 0.30
41 23 0.70
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (41 bp):
TTTCAAACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATA
Found at i:41847094 original size:41 final size:41
Alignment explanation
Indices: 41847008--41847099 Score: 103
Period size: 41 Copynumber: 2.2 Consensus size: 41
41846998 TCAGACTTTC
* * * * * * *
41847008 GTCTAGCTGGTTTGATGCCGGTGAAATATTTCAAACTTTAT
1 GTCTAGCAGGCTTAATGCCGGTGAAACAATTCAAACTATAA
**
41847049 GTCTAGCAGGCTTAATGCCGGTGAAACAATTCGGACTATAA
1 GTCTAGCAGGCTTAATGCCGGTGAAACAATTCAAACTATAA
41847090 GTCTAGCAGG
1 GTCTAGCAGG
41847100 GTAAAAGCCG
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (41 bp):
GTCTAGCAGGCTTAATGCCGGTGAAACAATTCAAACTATAA
Found at i:41847306 original size:69 final size:71
Alignment explanation
Indices: 41847226--41847379 Score: 186
Period size: 69 Copynumber: 2.2 Consensus size: 71
41847216 TTGAAGAACA
* * ** **
41847226 TGTATATACATTCGGTGATAATACTTGTTAGGCA-TATGTATATATGCATTCAGCTATTCATG-T
1 TGTATATACATTCGATGATAATACTTGTTAAGCACTATCCATATACACATTCAGCTATTCATGTT
41847289 TTAAAG
66 TTAAAG
* * *
41847295 TGTATATACATTTGATGATAATATTTGTTAAGCATCTATCCATATACACATTCGGCTATTCATGT
1 TGTATATACATTCGATGATAATACTTGTTAAGCA-CTATCCATATACACATTCAGCTATTCATGT
*
41847360 TTTAAAT
65 TTTAAAG
*
41847367 TGTATATGCATTC
1 TGTATATACATTC
41847380 AGTTTTAAGT
Statistics
Matches: 70, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
69 30 0.43
71 23 0.33
72 17 0.24
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.42
Consensus pattern (71 bp):
TGTATATACATTCGATGATAATACTTGTTAAGCACTATCCATATACACATTCAGCTATTCATGTT
TTAAAG
Found at i:41850571 original size:16 final size:16
Alignment explanation
Indices: 41850529--41850574 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
41850519 ATCATCTCAT
* *
41850529 ATATATATATATATCAC
1 ATAT-TATAAATATTAC
41850546 A-ATTAT-AATATTAC
1 ATATTATAAATATTAC
41850560 ATATTATAAATATTA
1 ATATTATAAATATTA
41850575 TAAACAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
14 7 0.28
15 8 0.32
16 9 0.36
17 1 0.04
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAAATATTAC
Found at i:41852071 original size:21 final size:21
Alignment explanation
Indices: 41852047--41852089 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
41852037 TCTCACAATG
*
41852047 TAAACGTTCTTACAGTGTCAC
1 TAAACGTTCTTACAGTGCCAC
41852068 TAAACGTTCTTACAGTGCCAC
1 TAAACGTTCTTACAGTGCCAC
41852089 T
1 T
41852090 TATCATCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (21 bp):
TAAACGTTCTTACAGTGCCAC
Found at i:41853222 original size:49 final size:50
Alignment explanation
Indices: 41853152--41853280 Score: 161
Period size: 56 Copynumber: 2.5 Consensus size: 50
41853142 TGATTTATTC
* * *
41853152 TATTAATTTAAAAACAGAAAATG-GTAAATTATAGCTTTAAGTTATCTTT
1 TATTAATTTTAAAACAAAAAATGTATAAATTATAGCTTTAAGTTATCTTT
*
41853201 TATTAATTTTAAAACAAAAAATGTTATTATATAAATTATAGTTTTAAGTTATCTTT
1 TATTAATTTTAAAACAAAAAATG------TATAAATTATAGCTTTAAGTTATCTTT
41853257 TATTAATTTTAAAACAAAAAATGT
1 TATTAATTTTAAAACAAAAAATGT
41853281 TATATATAAT
Statistics
Matches: 69, Mismatches: 4, Indels: 13
0.80 0.05 0.15
Matches are distributed among these distances:
49 21 0.30
50 1 0.01
56 47 0.68
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (50 bp):
TATTAATTTTAAAACAAAAAATGTATAAATTATAGCTTTAAGTTATCTTT
Found at i:41853236 original size:56 final size:55
Alignment explanation
Indices: 41853176--41853289 Score: 210
Period size: 56 Copynumber: 2.1 Consensus size: 55
41853166 CAGAAAATGG
41853176 TAAATTATAGCTTTAAGTTATCTTTTATTAATTTTAAAACAAAAAATGTTATTATA
1 TAAATTATAGCTTTAAGTTATCTTTTATTAATTTTAAAACAAAAAATGTTA-TATA
*
41853232 TAAATTATAGTTTTAAGTTATCTTTTATTAATTTTAAAACAAAAAATGTTATATA
1 TAAATTATAGCTTTAAGTTATCTTTTATTAATTTTAAAACAAAAAATGTTATATA
41853287 TAA
1 TAA
41853290 TAGAGTTGCT
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
55 7 0.12
56 50 0.88
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.46
Consensus pattern (55 bp):
TAAATTATAGCTTTAAGTTATCTTTTATTAATTTTAAAACAAAAAATGTTATATA
Found at i:41853954 original size:14 final size:14
Alignment explanation
Indices: 41853935--41853972 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
41853925 AGCTCGATCG
*
41853935 TATTAATTTTTTTA
1 TATTAATTTTTTAA
*
41853949 TATTAATATTTTAA
1 TATTAATTTTTTAA
41853963 TA-TAATTTTT
1 TATTAATTTTT
41853973 AAAAATATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 7 0.33
14 14 0.67
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TATTAATTTTTTAA
Found at i:41854844 original size:106 final size:106
Alignment explanation
Indices: 41854723--41854932 Score: 393
Period size: 106 Copynumber: 2.0 Consensus size: 106
41854713 TATTTAAAGT
41854723 GGATCTTGTTTTTAAGTTAAGTTTTAAATTTAATTTTTTTACCATTGATAATAACAGTAATAATA
1 GGATCTTGTTTTTAAGTTAAGTTTTAAATTTAATTTTTTTACCATTGATAATAACAGTAATAATA
*
41854788 ATTATAATAATAAATTTGTAAATAATAAATAATTTTAAACA
66 ATCATAATAATAAATTTGTAAATAATAAATAATTTTAAACA
* *
41854829 GGATCTTGTTTTTAAGTTAAGTTTTAAATTTATTTTTTTTAGCATTGATAATAACAGTAATAATA
1 GGATCTTGTTTTTAAGTTAAGTTTTAAATTTAATTTTTTTACCATTGATAATAACAGTAATAATA
41854894 ATCATAATAATAAATTTGTAAATAATAAATAATTTTAAA
66 ATCATAATAATAAATTTGTAAATAATAAATAATTTTAAA
41854933 TGTCATGCAT
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
106 101 1.00
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (106 bp):
GGATCTTGTTTTTAAGTTAAGTTTTAAATTTAATTTTTTTACCATTGATAATAACAGTAATAATA
ATCATAATAATAAATTTGTAAATAATAAATAATTTTAAACA
Found at i:41854965 original size:6 final size:6
Alignment explanation
Indices: 41854944--41854979 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
41854934 GTCATGCATT
*
41854944 AAATTA TAATTAA AAATTA AAATTA AAATTA AAATT
1 AAATTA AAATT-A AAATTA AAATTA AAATTA AAATT
41854980 TCAATAGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 22 0.81
7 5 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
AAATTA
Found at i:41855441 original size:6 final size:6
Alignment explanation
Indices: 41855420--41855455 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
41855410 ATCATGCATT
*
41855420 AAATTA TAATTAA AAATTA AAATTA AAATTA AAATT
1 AAATTA AAATT-A AAATTA AAATTA AAATTA AAATT
41855456 TCAATAGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 22 0.81
7 5 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
AAATTA
Found at i:41856197 original size:31 final size:30
Alignment explanation
Indices: 41856162--41856239 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 30
41856152 TTAACTTTAT
* *
41856162 TTAATTACATCATATAATATTTTAATTTAAC
1 TTAATTACATAATATAATA-ATTAATTTAAC
* * *
41856193 TTAATCACATTATATAATAATTAATTTAAT
1 TTAATTACATAATATAATAATTAATTTAAC
41856223 TTAATTACCATAATATA
1 TTAATTA-CATAATATA
41856240 CACCTCACTA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
30 15 0.38
31 25 0.62
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.46
Consensus pattern (30 bp):
TTAATTACATAATATAATAATTAATTTAAC
Found at i:41856412 original size:5 final size:5
Alignment explanation
Indices: 41856402--41856435 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
41856392 CATATATACA
*
41856402 CATAT CATAT CATAT CATAT TATAT CATAT -ATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT
41856436 AATAAAATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (5 bp):
CATAT
Done.