Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 139 of 172
Found at i:45850681 original size:103 final size:103
Alignment explanation
Indices: 45850536--45850742 Score: 387
Period size: 103 Copynumber: 2.0 Consensus size: 103
45850526 AACATTGTCG
45850536 ATAATAAACTTGTTATGTGAACAAAGCTAACACTTCTTCCTGCTTCAATACAATTCAAGAGACAA
1 ATAATAAACTTGTTATGTGAACAAAGCTAACACTTCTTCCTGCTTCAATACAATTCAAGAGACAA
* *
45850601 ATCATTATACTTGTAGTAATAAGTTAAAACTGATCTGT
66 ATCATTATACTTGTAATAATAAGTTAAAACTAATCTGT
45850639 ATAATAAACTTGTTATGTGAACAAAGCTAACACTTCTTCCTGCTTCAATACAATTCAAGAGACAA
1 ATAATAAACTTGTTATGTGAACAAAGCTAACACTTCTTCCTGCTTCAATACAATTCAAGAGACAA
*
45850704 ATCATTATACTTGTAATAATAATTTAAAACTAATCTGT
66 ATCATTATACTTGTAATAATAAGTTAAAACTAATCTGT
45850742 A
1 A
45850743 ACACTTCGTA
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 101 1.00
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.33
Consensus pattern (103 bp):
ATAATAAACTTGTTATGTGAACAAAGCTAACACTTCTTCCTGCTTCAATACAATTCAAGAGACAA
ATCATTATACTTGTAATAATAAGTTAAAACTAATCTGT
Found at i:45854157 original size:132 final size:132
Alignment explanation
Indices: 45853812--45854202 Score: 434
Period size: 130 Copynumber: 3.0 Consensus size: 132
45853802 ATAATTATTC
** *
45853812 TTCTAAAAA-TCCTTTAAAACGAAGGCAATGTTCGATATTTGGCAATTCGCGGAATTGTGCCCTA
1 TTCTAAAAACT-C-TTAAAACGAAGGCAATGTTCGATATTTGGCAATTCAAGGAATCGTGCCCTA
* * * *
45853876 ACGTGTTGGGTTGCAATTTCTCGTTTGCTCAAAGTAATCGAAGGTCCATTTAGAATTTCACCCAT
64 ACGTGCTGGGTTGCAATTTCTCGTTTGCTCAAAATAATCGAAGGTCCCTTTAGAATTTCACTCAT
45853941 GTCT
129 GTCT
* * * * *
45853945 TT-TAAAATC-CTTTAAACGAAGGCGATGTTCGATATTTGACAATTCGCA-GAATCGTGCCCTAA
1 TTCTAAAAACTCTTAAAACGAAGGCAATGTTCGATATTTGGCAATTC-AAGGAATCGTGCCCTAA
* * * * *
45854007 CGTGCTGGGTTGTAATTTCTCGTTTGTTCAAAATAATCGAAGGTCCCTTTTGAAATTCACTTATG
65 CGTGCTGGGTTGCAATTTCTCGTTTGCTCAAAATAATCGAAGGTCCCTTTAGAATTTCACTCATG
45854072 T-T
130 TCT
* * * * *
45854074 TTCTAAAAACTCTTCAAAATGAAGGTAATATTCGATGTTTGGCAATTCAAGGAATCGTGCCCTAT
1 TTCTAAAAACTCTT-AAAACGAAGGCAATGTTCGATATTTGGCAATTCAAGGAATCGTGCCCTAA
* * * * * * *
45854139 CGTGCTGGGTAGCGATTTCTTGCTTGGC-CAAAATGATCGAAGATTCCTTTAGAATTTCACTCAT
65 CGTGCTGGGTTGCAATTTCTCG-TTTGCTCAAAATAATCGAAGGTCCCTTTAGAATTTCACTCAT
45854203 ACTCTCTAAA
Statistics
Matches: 213, Mismatches: 38, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
129 3 0.01
130 108 0.51
131 5 0.02
132 92 0.43
133 5 0.02
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (132 bp):
TTCTAAAAACTCTTAAAACGAAGGCAATGTTCGATATTTGGCAATTCAAGGAATCGTGCCCTAAC
GTGCTGGGTTGCAATTTCTCGTTTGCTCAAAATAATCGAAGGTCCCTTTAGAATTTCACTCATGT
CT
Found at i:45854211 original size:132 final size:128
Alignment explanation
Indices: 45853813--45854212 Score: 381
Period size: 132 Copynumber: 3.0 Consensus size: 128
45853803 TAATTATTCT
** *
45853813 TCTAAAAATCCTTTAAAACGAAGGCAATGTTCGATATTTGGCAATTCGCGGAATTGTGCCCTAAC
1 TCTAAAAATCC-TTAAAACGAAGGCAATGTTCGATATTTGGCAATTCAAGGAATCGTGCCCTAAC
* * * * * *
45853878 GTGTTGGGTTGCAATTTCTCGTTTGCTCAAAGTAATCGAAGGTCCATTTAGAATTTCACCCATGT
65 GTGCTGGGTTGCAATTTCTCGTTGGC-CAAAATAATCGAAGTTCC-TTTAGAATTTCACTCATCT
45853943 C
128 C
* * * * * *
45853944 TTTTAAAATCCTTTAAACGAAGGCGATGTTCGATATTTGACAATTCGCA-GAATCGTGCCCTAAC
1 TCTAAAAATCCTTAAAACGAAGGCAATGTTCGATATTTGGCAATTC-AAGGAATCGTGCCCTAAC
* ** * * * * *
45854008 GTGCTGGGTTGTAATTTCTCGTTTGTTCAAAATAATCGAAGGTCCCTTTTGAAATTCACTTATGT
65 GTGCTGGGTTGCAATTTCTCG-TTGGCCAAAATAATCGAA-GTTCCTTTAGAATTTCACTCAT-C
*
45854073 TT
127 TC
* * * * *
45854075 TCTAAAAA-CTCTTCAAAATGAAGGTAATATTCGATGTTTGGCAATTCAAGGAATCGTGCCCTAT
1 TCTAAAAATC-CTT-AAAACGAAGGCAATGTTCGATATTTGGCAATTCAAGGAATCGTGCCCTAA
* * * *
45854139 CGTGCTGGGTAGCGATTTCTTGCTTGGCCAAAATGATCGAAGATTCCTTTAGAATTTCACTCATA
64 CGTGCTGGGTTGCAATTTCTCG-TTGGCCAAAATAATCGAAG-TTCCTTTAGAATTTCACTCAT-
45854204 CTC
126 CTC
45854207 TCTAAA
1 TCTAAA
45854213 TTCTAAAATA
Statistics
Matches: 213, Mismatches: 48, Indels: 15
0.77 0.17 0.05
Matches are distributed among these distances:
130 91 0.43
131 26 0.12
132 96 0.45
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (128 bp):
TCTAAAAATCCTTAAAACGAAGGCAATGTTCGATATTTGGCAATTCAAGGAATCGTGCCCTAACG
TGCTGGGTTGCAATTTCTCGTTGGCCAAAATAATCGAAGTTCCTTTAGAATTTCACTCATCTC
Found at i:45856343 original size:20 final size:20
Alignment explanation
Indices: 45856306--45856362 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
45856296 ATTTATCATT
*
45856306 ATTATTATTCTATCAAATTATA
1 ATTATTA-T-TATTAAATTATA
*
45856328 ATT-TATATTATTAAATTATG
1 ATTAT-TATTATTAAATTATA
45856348 ATTATTATTATTAAA
1 ATTATTATTATTAAA
45856363 AATAAATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
20 23 0.74
21 3 0.10
22 5 0.16
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (20 bp):
ATTATTATTATTAAATTATA
Found at i:45856491 original size:18 final size:17
Alignment explanation
Indices: 45856468--45856508 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
45856458 TATTTAAGTA
**
45856468 AAAATATTTTATTATATT
1 AAAATATTAAATTATA-T
45856486 AAAATATTAAATTATAT
1 AAAATATTAAATTATAT
45856503 AAAATA
1 AAAATA
45856509 AATAAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAAATATTAAATTATAT
Found at i:45857498 original size:21 final size:21
Alignment explanation
Indices: 45857473--45857538 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
45857463 TTGTTTGGAA
45857473 TACTGCATTGAATTGTGAAGT
1 TACTGCATTGAATTGTGAAGT
* * *
45857494 TACTG-AAT--ATTGTTATGT
1 TACTGCATTGAATTGTGAAGT
* *
45857512 GTACTGCATTGAACTGTGAAAT
1 -TACTGCATTGAATTGTGAAGT
45857534 TACTG
1 TACTG
45857539 AAGTAATGAA
Statistics
Matches: 33, Mismatches: 8, Indels: 8
0.67 0.16 0.16
Matches are distributed among these distances:
18 8 0.24
19 5 0.15
20 4 0.12
21 10 0.30
22 6 0.18
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (21 bp):
TACTGCATTGAATTGTGAAGT
Found at i:45857505 original size:40 final size:40
Alignment explanation
Indices: 45857454--45857540 Score: 124
Period size: 40 Copynumber: 2.2 Consensus size: 40
45857444 AATTATGGAA
* *
45857454 TACTGAATATTGTT-TG-GAATACTGCATTGAATTGTGAAGT
1 TACTGAATATTGTTATGTG--TACTGCATTGAACTGTGAAAT
45857494 TACTGAATATTGTTATGTGTACTGCATTGAACTGTGAAAT
1 TACTGAATATTGTTATGTGTACTGCATTGAACTGTGAAAT
45857534 TACTGAA
1 TACTGAA
45857541 GTAATGAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
40 40 0.93
41 2 0.05
42 1 0.02
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39
Consensus pattern (40 bp):
TACTGAATATTGTTATGTGTACTGCATTGAACTGTGAAAT
Found at i:45857812 original size:45 final size:45
Alignment explanation
Indices: 45857744--45857844 Score: 141
Period size: 45 Copynumber: 2.2 Consensus size: 45
45857734 GCCGACTACT
* *
45857744 GTTACTGTTACCGATTCGACACTTTGTGTGTCGAATACTGTTACC
1 GTTACTGTTACAGATTCGACACTTTGTGAGTCGAATACTGTTACC
* *
45857789 GTTACTGTTACAGATTC-AGCACTTTGTGAGTTGAATACTGTTACT
1 GTTACTGTTACAGATTCGA-CACTTTGTGAGTCGAATACTGTTACC
*
45857834 GTTGCTGTTAC
1 GTTACTGTTAC
45857845 TGCTACCGTT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
44 1 0.02
45 49 0.98
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (45 bp):
GTTACTGTTACAGATTCGACACTTTGTGAGTCGAATACTGTTACC
Found at i:45857835 original size:6 final size:6
Alignment explanation
Indices: 45857824--45857867 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
45857814 GTGAGTTGAA
* * *
45857824 TACTGT TACTGT TGCTGT TACTGC TACCGT TACTGAT TACTGT T
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTGT T
45857868 TAGGTACTGT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.45
Consensus pattern (6 bp):
TACTGT
Found at i:45858615 original size:16 final size:17
Alignment explanation
Indices: 45858584--45858616 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
45858574 TTCATAAGTA
45858584 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
45858601 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
45858617 GCTCCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:45859055 original size:46 final size:46
Alignment explanation
Indices: 45858901--45859040 Score: 201
Period size: 46 Copynumber: 3.0 Consensus size: 46
45858891 TTTGACATGA
* * * * *
45858901 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TATCATGT
1 TGCCATAGTATCTTTCAACCATGGTCTTATTC-TTTTCATGTCACGT
* *
45858947 TGCCATGGTATCTTTCAACCATTGTCTTATTCTTTTCATGTCACGT
1 TGCCATAGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
45858993 TGCCATAGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATAGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
45859039 TG
1 TG
45859041 GTCTTATTCA
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
45 5 0.06
46 79 0.94
ACGTcount: A:0.19, C:0.23, G:0.14, T:0.45
Consensus pattern (46 bp):
TGCCATAGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
Found at i:45859062 original size:117 final size:117
Alignment explanation
Indices: 45858922--45859138 Score: 301
Period size: 117 Copynumber: 1.9 Consensus size: 117
45858912 CTTTCAACTA
* * * * ** * *
45858922 TGGTCTTACTCATTTTCTATCATGTTGCCATGGTATCTTTCAACCATTGTCTTATTCTTTTCATG
1 TGGTCTTACTCATTTTCTATCATGCTACCATGGCATCTTTCAACCATGGTCTTACACATTTCATA
*
45858987 TCACGTTGCCATAGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
66 TCACGTAGCCATAGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
* *
45859039 TGGTCTTATTCA-TTTCATGTCATGCTACCATGGCATCTTTCAACCATGGTCTTACACATTTCAT
1 TGGTCTTACTCATTTTC-TATCATGCTACCATGGCATCTTTCAACCATGGTCTTACACATTTCAT
* *
45859103 ATCATGTAGCCATGGTATCTTTCAACCATGGTCTTA
65 ATCACGTAGCCATAGTATCTTTCAACCATGGTCTTA
45859139 CACATTTTAT
Statistics
Matches: 86, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
116 4 0.05
117 82 0.95
ACGTcount: A:0.20, C:0.24, G:0.13, T:0.43
Consensus pattern (117 bp):
TGGTCTTACTCATTTTCTATCATGCTACCATGGCATCTTTCAACCATGGTCTTACACATTTCATA
TCACGTAGCCATAGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
Found at i:45859101 original size:71 final size:71
Alignment explanation
Indices: 45858970--45859102 Score: 185
Period size: 71 Copynumber: 1.9 Consensus size: 71
45858960 TTCAACCATT
* * * * ** *
45858970 GTCTTATTCTTTTCATGTCACGTTGCCATAGTATCTTTCAACCATGGTCTTATTCTTTTCATGTC
1 GTCTTATTCATTTCATGTCACGCTACCATAGCATCTTTCAACCATGGTCTTACACATTTCATGTC
45859035 ACGTTG
66 ACGTTG
* *
45859041 GTCTTATTCATTTCATGTCATGCTACCATGGCATCTTTCAACCATGGTCTTACACATTTCAT
1 GTCTTATTCATTTCATGTCACGCTACCATAGCATCTTTCAACCATGGTCTTACACATTTCAT
45859103 ATCATGTAGC
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
71 53 1.00
ACGTcount: A:0.20, C:0.24, G:0.13, T:0.44
Consensus pattern (71 bp):
GTCTTATTCATTTCATGTCACGCTACCATAGCATCTTTCAACCATGGTCTTACACATTTCATGTC
ACGTTG
Found at i:45859197 original size:46 final size:46
Alignment explanation
Indices: 45859039--45859198 Score: 239
Period size: 46 Copynumber: 3.5 Consensus size: 46
45859029 CATGTCACGT
** * * * *
45859039 TGGTCTTATTCATTTCATGTCATGCTACCATGGCATCTTTCAACCA
1 TGGTCTTACACATTTCATTTCATGTTGCCATGGTATCTTTCAACCA
* *
45859085 TGGTCTTACACATTTCATATCATGTAGCCATGGTATCTTTCAACCA
1 TGGTCTTACACATTTCATTTCATGTTGCCATGGTATCTTTCAACCA
*
45859131 TGGTCTTACACATTTTATTTCATGTTGCCATGGTATCTTTCAACCA
1 TGGTCTTACACATTTCATTTCATGTTGCCATGGTATCTTTCAACCA
45859177 TGGTCTTACACATTTCATTTCA
1 TGGTCTTACACATTTCATTTCA
45859199 GAAAGCACAT
Statistics
Matches: 103, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 103 1.00
ACGTcount: A:0.23, C:0.24, G:0.12, T:0.41
Consensus pattern (46 bp):
TGGTCTTACACATTTCATTTCATGTTGCCATGGTATCTTTCAACCA
Found at i:45863573 original size:17 final size:17
Alignment explanation
Indices: 45863551--45863595 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
45863541 ATTGTTAAAT
*
45863551 AGAGTTATTCTTGAACA
1 AGAGTTATTCTTAAACA
* *
45863568 AGAGTTGTTCTTAAATA
1 AGAGTTATTCTTAAACA
*
45863585 AGGGTTATTCT
1 AGAGTTATTCT
45863596 GACATGTTCC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (17 bp):
AGAGTTATTCTTAAACA
Found at i:45865550 original size:324 final size:324
Alignment explanation
Indices: 45864961--45865608 Score: 1296
Period size: 324 Copynumber: 2.0 Consensus size: 324
45864951 CTATCCTTTA
45864961 AAAAGGTGTAGATGCCATTGGCAGCTAAACATTAGACTATCCTACAAAGTATATCGGTTCTGTCC
1 AAAAGGTGTAGATGCCATTGGCAGCTAAACATTAGACTATCCTACAAAGTATATCGGTTCTGTCC
45865026 AGGCAGTTCAGGAAAACATGGCGATTAATCGTGTATGATGTCTTACTTCATGTCACATTGCTTCT
66 AGGCAGTTCAGGAAAACATGGCGATTAATCGTGTATGATGTCTTACTTCATGTCACATTGCTTCT
45865091 GTTATATCATCTGCTGATGAAGATCAGCTGCCTGCTGAGCCAACTCCACCACCATAGCCTCGTCA
131 GTTATATCATCTGCTGATGAAGATCAGCTGCCTGCTGAGCCAACTCCACCACCATAGCCTCGTCA
45865156 AAGAACTTGTTGATGCTCACATCTTCACTCATTCCCTGGAAAGTTCAACACAAATTTCACTCAAA
196 AAGAACTTGTTGATGCTCACATCTTCACTCATTCCCTGGAAAGTTCAACACAAATTTCACTCAAA
45865221 TCATTCCTGATTGGATTTTCTTTTTAAGGTTCTTTTGTCCATTTTCAGAAAGCAAATCCCTATT
261 TCATTCCTGATTGGATTTTCTTTTTAAGGTTCTTTTGTCCATTTTCAGAAAGCAAATCCCTATT
45865285 AAAAGGTGTAGATGCCATTGGCAGCTAAACATTAGACTATCCTACAAAGTATATCGGTTCTGTCC
1 AAAAGGTGTAGATGCCATTGGCAGCTAAACATTAGACTATCCTACAAAGTATATCGGTTCTGTCC
45865350 AGGCAGTTCAGGAAAACATGGCGATTAATCGTGTATGATGTCTTACTTCATGTCACATTGCTTCT
66 AGGCAGTTCAGGAAAACATGGCGATTAATCGTGTATGATGTCTTACTTCATGTCACATTGCTTCT
45865415 GTTATATCATCTGCTGATGAAGATCAGCTGCCTGCTGAGCCAACTCCACCACCATAGCCTCGTCA
131 GTTATATCATCTGCTGATGAAGATCAGCTGCCTGCTGAGCCAACTCCACCACCATAGCCTCGTCA
45865480 AAGAACTTGTTGATGCTCACATCTTCACTCATTCCCTGGAAAGTTCAACACAAATTTCACTCAAA
196 AAGAACTTGTTGATGCTCACATCTTCACTCATTCCCTGGAAAGTTCAACACAAATTTCACTCAAA
45865545 TCATTCCTGATTGGATTTTCTTTTTAAGGTTCTTTTGTCCATTTTCAGAAAGCAAATCCCTATT
261 TCATTCCTGATTGGATTTTCTTTTTAAGGTTCTTTTGTCCATTTTCAGAAAGCAAATCCCTATT
45865609 TGTGTGTGTG
Statistics
Matches: 324, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
324 324 1.00
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (324 bp):
AAAAGGTGTAGATGCCATTGGCAGCTAAACATTAGACTATCCTACAAAGTATATCGGTTCTGTCC
AGGCAGTTCAGGAAAACATGGCGATTAATCGTGTATGATGTCTTACTTCATGTCACATTGCTTCT
GTTATATCATCTGCTGATGAAGATCAGCTGCCTGCTGAGCCAACTCCACCACCATAGCCTCGTCA
AAGAACTTGTTGATGCTCACATCTTCACTCATTCCCTGGAAAGTTCAACACAAATTTCACTCAAA
TCATTCCTGATTGGATTTTCTTTTTAAGGTTCTTTTGTCCATTTTCAGAAAGCAAATCCCTATT
Found at i:45878662 original size:19 final size:19
Alignment explanation
Indices: 45878637--45878679 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
45878627 ATAATATAAT
*
45878637 AAAAGAAATAATA-AAAGA
1 AAAAGAAATAAAATAAAGA
45878655 ATAAAGAAATAAAATAAAGA
1 A-AAAGAAATAAAATAAAGA
45878675 AAAAG
1 AAAAG
45878680 GAAAGAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 15 0.68
20 6 0.27
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (19 bp):
AAAAGAAATAAAATAAAGA
Found at i:45883872 original size:40 final size:39
Alignment explanation
Indices: 45883810--45883889 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 39
45883800 TAACGACTTA
* *
45883810 TCGGCTAAAATGGCACTCAGTGTGTAGTTTGAAATAGCT
1 TCGGCTAAAATGGCACTCAGTGTGCAATTTGAAATAGCT
* *
45883849 TCGGCTAAAAGTGGCACTTAGTGTGCAATTTGAGATAGCT
1 TCGGCTAAAA-TGGCACTCAGTGTGCAATTTGAAATAGCT
45883889 T
1 T
45883890 TGACTATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 10 0.28
40 26 0.72
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (39 bp):
TCGGCTAAAATGGCACTCAGTGTGCAATTTGAAATAGCT
Found at i:45883969 original size:28 final size:28
Alignment explanation
Indices: 45883910--45883978 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 28
45883900 TATATAAATG
** ** * *
45883910 GCACTTAGTGTGCAAAGTATTGAGGATG
1 GCACTTAGTGTGCAAAACATCCAGAATA
45883938 GCACTTAGTGTGCAAAACATCCAGAATA
1 GCACTTAGTGTGCAAAACATCCAGAATA
*
45883966 GCACTTAGGGTGC
1 GCACTTAGTGTGC
45883979 GAGGTATCGA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (28 bp):
GCACTTAGTGTGCAAAACATCCAGAATA
Found at i:45885560 original size:18 final size:18
Alignment explanation
Indices: 45885537--45885573 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
45885527 TGACACAGCC
45885537 ATATGTCTCAGCTGTGTG
1 ATATGTCTCAGCTGTGTG
45885555 ATATGTCTCAGCTGTGTG
1 ATATGTCTCAGCTGTGTG
45885573 A
1 A
45885574 GGGACACGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.19, C:0.16, G:0.27, T:0.38
Consensus pattern (18 bp):
ATATGTCTCAGCTGTGTG
Found at i:45888126 original size:13 final size:13
Alignment explanation
Indices: 45888108--45888132 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45888098 TAATTGCTTA
45888108 ATTTTTTTATTTT
1 ATTTTTTTATTTT
45888121 ATTTTTTTATTT
1 ATTTTTTTATTT
45888133 CATATCTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
ATTTTTTTATTTT
Found at i:45903636 original size:30 final size:30
Alignment explanation
Indices: 45903600--45903714 Score: 194
Period size: 30 Copynumber: 3.8 Consensus size: 30
45903590 ACTTTTCTCA
*
45903600 ACTAGCCACTCCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
45903630 ACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
* *
45903660 ACTAGCCACTCTTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
*
45903690 ACTAGCCACACCTTTTTCACCACCA
1 ACTAGCCACACCTTTTCCACCACCA
45903715 CTTGTACCTA
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 79 1.00
ACGTcount: A:0.25, C:0.48, G:0.03, T:0.23
Consensus pattern (30 bp):
ACTAGCCACACCTTTTCCACCACCAACTCC
Found at i:45904332 original size:25 final size:24
Alignment explanation
Indices: 45904233--45904442 Score: 99
Period size: 25 Copynumber: 8.4 Consensus size: 24
45904223 TTGTTATTAT
*
45904233 TATATTTCTTAATATTATATTA--TA
1 TATATTT-TT-ATACTATATTATGTA
* *
45904257 TATATTCTTT-TAATATATTAGGTA
1 TATATT-TTTATACTATATTATGTA
** * *
45904281 TAT-TTTAAATTCTATATTACGTATA
1 TATATTTTTATACTATATTA--TGTA
*
45904306 TATATATTTTATACTATTTTATGTA
1 TATAT-TTTTATACTATATTATGTA
* * *
45904331 TATATCTTTAATATTATATTATTTA
1 TATAT-TTTTATACTATATTATGTA
* *
45904356 TATATTTTTTTTTACATGTTATCTTATGTA
1 TATA--TTTTTATAC----TATATTATGTA
*
45904386 TATA-TCTTA-ACTATATTATGTA
1 TATATTTTTATACTATATTATGTA
* *
45904408 TGTATTTTTAACACTATATTATGTA
1 TATATTTTT-ATACTATATTATGTA
*
45904433 CATATTTTTA
1 TATATTTTTA
45904443 ATATTATCAC
Statistics
Matches: 140, Mismatches: 29, Indels: 34
0.69 0.14 0.17
Matches are distributed among these distances:
22 23 0.16
23 13 0.09
24 15 0.11
25 53 0.38
26 8 0.06
27 15 0.11
30 13 0.09
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.57
Consensus pattern (24 bp):
TATATTTTTATACTATATTATGTA
Found at i:45904623 original size:16 final size:14
Alignment explanation
Indices: 45904604--45904637 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 14
45904594 TATTATTCTA
45904604 ATATTTTGATATTTT
1 ATATTTT-ATATTTT
45904619 GATATTTTATATTTT
1 -ATATTTTATATTTT
45904634 ATAT
1 ATAT
45904638 ATTTTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 7 0.39
16 7 0.39
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (14 bp):
ATATTTTATATTTT
Found at i:45904632 original size:7 final size:8
Alignment explanation
Indices: 45904604--45904637 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
45904594 TATTATTCTA
45904604 ATATTTTG
1 ATATTTTG
45904612 ATATTTTG
1 ATATTTTG
45904620 ATATTTT-
1 ATATTTTG
45904627 ATATTTT-
1 ATATTTTG
45904634 ATAT
1 ATAT
45904638 ATTTTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 11 0.42
8 15 0.58
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (8 bp):
ATATTTTG
Found at i:45904639 original size:16 final size:15
Alignment explanation
Indices: 45904604--45904644 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
45904594 TATTATTCTA
45904604 ATATTTTGATATTTTG
1 ATATTTT-ATATTTTG
*
45904620 ATATTTTATATTTTAT
1 ATATTTTATATTTT-G
45904636 ATATTTTAT
1 ATATTTTAT
45904645 TATTCACATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.30
16 16 0.70
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (15 bp):
ATATTTTATATTTTG
Found at i:45911470 original size:26 final size:27
Alignment explanation
Indices: 45911440--45911502 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 27
45911430 CTTTGTTAAA
*
45911440 TTTCTTGAAAGTTAACAAATCAGAAGC
1 TTTCTTCAAAGTTAACAAATCAGAAGC
* *
45911467 TTCTCTTTCAAATTTAACTAATCAGAAGC
1 TT-TC-TTCAAAGTTAACAAATCAGAAGC
45911496 TTCTCTT
1 TT-TCTT
45911503 TCAACTCCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 2 0.06
28 4 0.13
29 25 0.81
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (27 bp):
TTTCTTCAAAGTTAACAAATCAGAAGC
Found at i:45911483 original size:29 final size:29
Alignment explanation
Indices: 45911451--45911506 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
45911441 TTCTTGAAAG
45911451 TTAACAAATCAGAAGCTTCTCTTTCAAAT
1 TTAACAAATCAGAAGCTTCTCTTTCAAAT
*
45911480 TTAACTAATCAGAAGCTTCTCTTTCAA
1 TTAACAAATCAGAAGCTTCTCTTTCAA
45911507 CTCCTCAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (29 bp):
TTAACAAATCAGAAGCTTCTCTTTCAAAT
Found at i:45933338 original size:23 final size:22
Alignment explanation
Indices: 45933313--45933355 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
45933303 ATAAAAGTAA
*
45933313 AAAAATTA-AATATATATTTTAG
1 AAAAATTACAATAAAT-TTTTAG
45933335 AAAAATTACAATAAATTTTTA
1 AAAAATTACAATAAATTTTTA
45933356 ATTTTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
AAAAATTACAATAAATTTTTAG
Found at i:45933673 original size:15 final size:14
Alignment explanation
Indices: 45933653--45933684 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
45933643 GTTTAACTTT
45933653 TTTTTATATTTTATA
1 TTTTTATATTTTA-A
45933668 TTTTTATATTTTAA
1 TTTTTATATTTTAA
45933682 TTT
1 TTT
45933685 AAATAAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTTATATTTTAA
Found at i:45935480 original size:22 final size:22
Alignment explanation
Indices: 45935452--45935496 Score: 63
Period size: 25 Copynumber: 1.9 Consensus size: 22
45935442 AATTTACAGA
45935452 AGAAGAAGATAGAAAGAAAGAAAGG
1 AGAAGAAGA-A-AAA-AAAGAAAGG
45935477 AGAAGAAGAAAAAAAAGAAA
1 AGAAGAAGAAAAAAAAGAAA
45935497 AGGTAATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 7 0.35
23 3 0.15
24 1 0.05
25 9 0.45
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (22 bp):
AGAAGAAGAAAAAAAAGAAAGG
Found at i:45941873 original size:30 final size:29
Alignment explanation
Indices: 45941833--45941889 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
45941823 GGCTTTTTTT
*
45941833 ATTTTTATTTTCGGATTTTATTTTTTAAA
1 ATTTTTATTTTCAGATTTTATTTTTTAAA
*
45941862 ATTTATTATTTTCATATTTTATTTTTTA
1 ATTT-TTATTTTCAGATTTTATTTTTTA
45941890 TATTATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.68
Consensus pattern (29 bp):
ATTTTTATTTTCAGATTTTATTTTTTAAA
Found at i:45941892 original size:14 final size:14
Alignment explanation
Indices: 45941847--45941893 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
45941837 TTATTTTCGG
*
45941847 ATTTTATTTTTTAA
1 ATTTTATTTTTTAT
*
45941861 AATTTATTATTTTCAT
1 ATTTTATT-TTTT-AT
45941877 ATTTTATTTTTTAT
1 ATTTTATTTTTTAT
45941891 ATT
1 ATT
45941894 ATTTTAGTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
14 12 0.43
15 8 0.29
16 8 0.29
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (14 bp):
ATTTTATTTTTTAT
Found at i:45941914 original size:142 final size:143
Alignment explanation
Indices: 45941686--45942419 Score: 906
Period size: 142 Copynumber: 5.2 Consensus size: 143
45941676 TATTTTGGTA
* ** *
45941686 TTTA-TTTTATTTTTCAGATTTTAAAATTTTAAAATATACTATTTTCGTATTTTATTGTTTTATA
1 TTTATTTTTA-TTTTCGGATTTT-ATTTTTTAAAATATATTATTTTCGTATTTTATT-TTTTATA
45941750 TTATTTTAGTACATAATGTTTCAAATGTATTATTTTAG-TTTTTTATATTAATTTAGAAAAAAAC
63 TTATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTTTTTTTATATTAATTTAGAAAAAAAC
45941814 TCTGATTTTGGCTTTT
128 TCTGATTTTGGCTTTT
* *
45941830 TTTATTTTTATTTTCGGATTTTATTTTTTAAAATTTATTATTTTCATATTTTATTTTTTATATTA
1 TTTATTTTTATTTTCGGATTTTATTTTTTAAAATATATTATTTTCGTATTTTATTTTTTATATTA
*
45941895 TTTTAGTACATAATGTTTC--ATGTATTATTTTAGTTTTTTTATATTAATTTAGAAAAAAAACCC
66 TTTTAGTACATAATGTTTCAAATGTATTATTTTAGTTTTTTTATATTAATTTAG-AAAAAAACTC
**
45941958 TGATTTTGGCCCTT
130 TGATTTTGGCTTTT
* * *
45941972 TTTATTTTTATTTTTGGATTTTACTTTTTAAGATATATTATTTTCGTATTTTGA-TTTTTATATT
1 TTTATTTTTATTTTCGGATTTTATTTTTTAAAATATATTATTTTCGTATTTT-ATTTTTTATATT
* * *
45942036 ATTTTAGTACATAATG-TTC-AATGTATTATTTTTGTTTTTTTTATATTAATTTAGTAAAAATCT
65 ATTTTAGTACATAATGTTTCAAATGTATTATTTTAG-TTTTTTTATATTAATTTAGAAAAAAACT
*
45942099 GTGATTTTGGCCTTTT
129 CTGATTTTGG-CTTTT
* *
45942115 TTT-TATTTTGTTTTCGGA--TT-TTTTTAAAAATATATTATTTTCGTATTTTATTTTTTATATT
1 TTTAT-TTTTATTTTCGGATTTTATTTTTTAAAATATATTATTTTCGTATTTTATTTTTTATATT
* * * * ** *
45942176 ATTTTAGTATATAATGTTTCAAATG-AATAATTT-GTTTTTTTATATTAATTTAGTAAAAATTTT
65 ATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTTTTTTTATATTAATTTAGAAAAAAACTC
*
45942239 TGATTTTAGCCGTTTGT
130 TGATTTT-GGC-TTT-T
* ** *
45942256 TTTTTATTTTATTTTCGGATTTTATTTTCCAAAATATACTATTTTCGTATTTTATTTTTT-TATT
1 TTTAT-TTTTATTTTCGGATTTTATTTTTTAAAATATATTATTTTCGTATTTTATTTTTTATATT
* * * * *
45942320 ATTTTAGTACATAATGTTTCATATATATTATTTTAGTATATTTATATTAATTTAGTAAAAAACCT
65 ATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTTTTTTTATATTAATTTAG-AAAAAAACT
* *
45942385 CT-AATTTGGCCTTT
129 CTGATTTTGGCTTTT
45942399 TTTA-TTTTATTTTCGGATTTT
1 TTTATTTTTATTTTCGGATTTT
45942420 TTAAAATATA
Statistics
Matches: 518, Mismatches: 51, Indels: 45
0.84 0.08 0.07
Matches are distributed among these distances:
139 36 0.07
140 70 0.14
141 53 0.10
142 170 0.33
143 69 0.13
144 45 0.09
145 46 0.09
146 22 0.04
147 7 0.01
ACGTcount: A:0.27, C:0.06, G:0.08, T:0.59
Consensus pattern (143 bp):
TTTATTTTTATTTTCGGATTTTATTTTTTAAAATATATTATTTTCGTATTTTATTTTTTATATTA
TTTTAGTACATAATGTTTCAAATGTATTATTTTAGTTTTTTTATATTAATTTAGAAAAAAACTCT
GATTTTGGCTTTT
Found at i:45942179 original size:12 final size:13
Alignment explanation
Indices: 45942145--45942187 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
45942135 TTTTTAAAAA
45942145 TATATTATTTTCG
1 TATATTATTTTCG
* *
45942158 TATTTTATTTT-T
1 TATATTATTTTCG
*
45942170 TATATTATTTTAG
1 TATATTATTTTCG
45942183 TATAT
1 TATAT
45942188 AATGTTTCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (13 bp):
TATATTATTTTCG
Found at i:45942376 original size:285 final size:277
Alignment explanation
Indices: 45941686--45942435 Score: 935
Period size: 285 Copynumber: 2.6 Consensus size: 277
45941676 TATTTTGGTA
*
45941686 TTTATTTTATTTTTCAGATTTTAAAATTTTAAAATATACTATTTTCGTATTTTATTGTTTTATAT
1 TTTATTTTA-TTTTCGGATTTT---ATTTTAAAATATACTATTTTCGTATTTTATT-TTTT-TAT
*
45941751 TATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTTTTTTATATTAATTTAGAAAAAAACTC
60 TATTTTAGTACATAATGTTTC-AATGTATTATTTTAGTTTTTTATATTAATTTAGTAAAAAACTC
*
45941816 TGATTTTGG-CTTTTTTTATTTTTATTTTCGGATTTTATTTTTTAAAATTTATTATTTTCATATT
124 TGATTTTGGCCTTTTTTTA-TTTTATTTTCGGA---T-TTTTTTAAAATATATTATTTTCATATT
* *
45941880 TTATTTTTTATATTATTTTAGTACATAATGTTTCATGTATTATTTTAGTTTTTTTATATTAATTT
184 TTATTTTTTATATTATTTTAGTACATAATGTTTCATGTAATAATTTAGTTTTTTTATATTAATTT
*
45941945 AGAAAAAAAACCCTGATTTTGGCCCTTTT
249 AGAAAAAAAACCCTGATTTTAGCCCTTTT
* * * * *
45941974 TAT-TTTTATTTTTGGATTTTACTTTTTAAGATATATTATTTTCGTATTTTGATTTTTATATTAT
1 TTTATTTTATTTTCGGATTTTA--TTTTAAAATATACTATTTTCGTATTTT-ATTTTTTTATTAT
* * *
45942038 TTTAGTACATAATG-TTCAATGTATTATTTTTGTTTTTTTTATATTAATTTAGTAAAAATCTGTG
63 TTTAGTACATAATGTTTCAATGTATTATTTTAG--TTTTTTATATTAATTTAGTAAAAAACTCTG
* *
45942102 ATTTTGGCCTTTTTTTTATTTTGTTTTCGGATTTTTTTAAAAATATATTATTTTCGTATTTTATT
126 ATTTTGGCC-TTTTTTTATTTTATTTTCGGATTTTTTT-AAAATATATTATTTTCATATTTTATT
*
45942167 TTTTATATTATTTTAGTATATAATGTTTCAAATG-AATAATTT-GTTTTTTTATATTAATTTAG-
189 TTTTATATTATTTTAGTACATAATGTTTC--ATGTAATAATTTAGTTTTTTTATATTAATTTAGA
* **** *
45942229 TAAAAATTTTTGATTTTAGCCGTTTGTTT
252 AAAAAAACCCTGATTTTAGCC--CT-TTT
45942258 TTTATTTTATTTTCGGATTTTATTTTCCAAAATATACTATTTTCGTATTTTATTTTTTTATTATT
1 TTTATTTTATTTTCGGATTTTATTTT--AAAATATACTATTTTCGTATTTTATTTTTTTATTATT
* *
45942323 TTAGTACATAATGTTTCATATATATTATTTTAGTATATTTATATTAATTTAGTAAAAAACCTCT-
64 TTAGTACATAATGTTTCA-ATGTATTATTTTAGT-TTTTTATATTAATTTAGTAAAAAA-CTCTG
*
45942387 AATTTGGCC-TTTTTTATTTTATTTTCGGA-TTTTTTAAAATATATT-TTTT
126 ATTTTGGCCTTTTTTTATTTTATTTTCGGATTTTTTTAAAATATATTATTTT
45942436 AAAATATACT
Statistics
Matches: 407, Mismatches: 35, Indels: 48
0.83 0.07 0.10
Matches are distributed among these distances:
280 4 0.01
281 31 0.08
282 93 0.23
283 34 0.08
284 89 0.22
285 113 0.28
286 36 0.09
287 5 0.01
288 2 0.00
ACGTcount: A:0.28, C:0.06, G:0.08, T:0.59
Consensus pattern (277 bp):
TTTATTTTATTTTCGGATTTTATTTTAAAATATACTATTTTCGTATTTTATTTTTTTATTATTTT
AGTACATAATGTTTCAATGTATTATTTTAGTTTTTTATATTAATTTAGTAAAAAACTCTGATTTT
GGCCTTTTTTTATTTTATTTTCGGATTTTTTTAAAATATATTATTTTCATATTTTATTTTTTATA
TTATTTTAGTACATAATGTTTCATGTAATAATTTAGTTTTTTTATATTAATTTAGAAAAAAAACC
CTGATTTTAGCCCTTTT
Found at i:45942432 original size:14 final size:14
Alignment explanation
Indices: 45942415--45942443 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
45942405 TTATTTTCGG
45942415 ATTTTTTAAAATAT
1 ATTTTTTAAAATAT
45942429 ATTTTTTAAAATAT
1 ATTTTTTAAAATAT
45942443 A
1 A
45942444 CTATTAAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTTTTTAAAATAT
Found at i:45942892 original size:20 final size:20
Alignment explanation
Indices: 45942863--45942901 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
45942853 TTTTTTTTCT
*
45942863 TTCTCTTTCTCTTCTTCTTC
1 TTCTCCTTCTCTTCTTCTTC
*
45942883 TTCTCCTTCTCTTTTTCTT
1 TTCTCCTTCTCTTCTTCTT
45942902 TCTCTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (20 bp):
TTCTCCTTCTCTTCTTCTTC
Found at i:45942908 original size:12 final size:12
Alignment explanation
Indices: 45942856--45942927 Score: 67
Period size: 12 Copynumber: 5.8 Consensus size: 12
45942846 ATTACCTTTT
45942856 TTTTTCTTTCTC
1 TTTTTCTTTCTC
*
45942868 TTTCTC-TTCTTC
1 TTTTTCTTTC-TC
*
45942880 TTCTTCTCCTTCTC
1 TT-TT-TCTTTCTC
45942894 TTTTTCTTTCTC
1 TTTTTCTTTCTC
*
45942906 TTTTT-TTTTTC
1 TTTTTCTTTCTC
45942917 TTTTTTCTTTC
1 -TTTTTCTTTC
45942928 CCTCACCAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
11 8 0.16
12 26 0.53
13 6 0.12
14 6 0.12
15 3 0.06
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTCTTTCTC
Found at i:45942970 original size:22 final size:22
Alignment explanation
Indices: 45942944--45943009 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 22
45942934 CAATGCCGCC
45942944 TCTTCCTCCTCCTTCTTCTTCT
1 TCTTCCTCCTCCTTCTTCTTCT
* *
45942966 TCTTCTTCTTCTCTTC-TCTTCT
1 TCTTCCTCCTC-CTTCTTCTTCT
* *
45942988 CCTTCC-CC-CTTTCTTCTTCT
1 TCTTCCTCCTCCTTCTTCTTCT
45943008 TC
1 TC
45943010 ACTCACGCAC
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
19 3 0.09
20 8 0.23
21 1 0.03
22 19 0.54
23 4 0.11
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (22 bp):
TCTTCCTCCTCCTTCTTCTTCT
Found at i:45943009 original size:3 final size:3
Alignment explanation
Indices: 45942955--45942992 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
45942945 CTTCCTCCTC
*
45942955 CTT CTT CTT CTT CTT CTT CTT C-T CTT C-T CTT CTC CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
45942993 CCCCTTTCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (3 bp):
CTT
Found at i:45943103 original size:22 final size:22
Alignment explanation
Indices: 45943075--45943116 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
45943065 ACAAAAGCAA
*
45943075 TGGCAGTGAGGAGTCTCGTCTG
1 TGGCAGTGAGGAGTCCCGTCTG
*
45943097 TGGCAGTGCGGAGTCCCGTC
1 TGGCAGTGAGGAGTCCCGTC
45943117 GGTGCAGAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.24, G:0.40, T:0.24
Consensus pattern (22 bp):
TGGCAGTGAGGAGTCCCGTCTG
Found at i:45943175 original size:27 final size:27
Alignment explanation
Indices: 45943134--45943186 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
45943124 AGGAGTGACC
*
45943134 GGTGCCGCCTGTGGGGTACCCTCCACT
1 GGTGCCGCCTATGGGGTACCCTCCACT
45943161 GGTGCCGCCTATGGGGTACCCTCCAC
1 GGTGCCGCCTATGGGGTACCCTCCAC
45943187 CCCTATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.09, C:0.38, G:0.32, T:0.21
Consensus pattern (27 bp):
GGTGCCGCCTATGGGGTACCCTCCACT
Found at i:45944099 original size:16 final size:16
Alignment explanation
Indices: 45944080--45944110 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
45944070 ATATTAATTT
*
45944080 TATTTAATCTTAAAAA
1 TATTTAATATTAAAAA
45944096 TATTTAATATTAAAA
1 TATTTAATATTAAAA
45944111 CAATACAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
TATTTAATATTAAAAA
Found at i:45962000 original size:40 final size:38
Alignment explanation
Indices: 45961880--45962011 Score: 132
Period size: 35 Copynumber: 3.6 Consensus size: 38
45961870 TCCTCATTGA
* * *
45961880 AATACCATACCTACATTTTACAACTCGGTTTGG--GA-
1 AATACCATACCTACATTTCACAACTCAGTATGGATGAT
* * ** *
45961915 AATGCCATACCTATATTTCTTAACTGAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGA--TGAT
45961955 AATACCATACCTACATTTCACAACTCAGTATGGATG--
1 AATACCATACCTACATTTCACAACTCAGTATGGATGAT
45961991 -ATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
45962012 CTTTGCCATG
Statistics
Matches: 79, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
35 46 0.58
38 2 0.03
39 2 0.03
40 29 0.37
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.33
Consensus pattern (38 bp):
AATACCATACCTACATTTCACAACTCAGTATGGATGAT
Found at i:45966931 original size:34 final size:34
Alignment explanation
Indices: 45966882--45966948 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
45966872 CCCTGACGAT
* * *
45966882 GATCCTTAATTTATCATGGGCTAACTGGGTCCTC
1 GATCCTTAATCTATCATAGGCTAACTAGGTCCTC
*
45966916 GATCCTTGATCTATCATAGGCTAACTAGGTCCT
1 GATCCTTAATCTATCATAGGCTAACTAGGTCCT
45966949 TCTTCAAGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.34
Consensus pattern (34 bp):
GATCCTTAATCTATCATAGGCTAACTAGGTCCTC
Found at i:45970154 original size:13 final size:13
Alignment explanation
Indices: 45970136--45970161 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
45970126 GCATCTAACA
45970136 TTTTTATTTTTAT
1 TTTTTATTTTTAT
45970149 TTTTTATTTTTAT
1 TTTTTATTTTTAT
45970162 CACTTTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTATTTTTAT
Found at i:45974802 original size:6 final size:6
Alignment explanation
Indices: 45974791--45974822 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
45974781 TTAAATAATA
45974791 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT AT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT AT
45974823 CAAAACACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
ATTTAT
Found at i:45978621 original size:5 final size:6
Alignment explanation
Indices: 45978604--45978628 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
45978594 CATTTTACAG
45978604 ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA A
45978629 CTATATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:45979723 original size:3 final size:3
Alignment explanation
Indices: 45979708--45979744 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
45979698 ATATTGTGCT
* *
45979708 TTA TTA ATA TTA TTA TTA TCA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
45979745 AACTTGATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:45979943 original size:21 final size:20
Alignment explanation
Indices: 45979899--45979963 Score: 77
Period size: 19 Copynumber: 3.5 Consensus size: 20
45979889 TTTATGATGT
45979899 TATA-ATTTTTATATTTA-A
1 TATATATTTTTATATTTATA
*
45979917 -ATAT-TTTTATAAATTTATA
1 TATATATTTT-TATATTTATA
45979936 T-TATATTTTTATATTTATA
1 TATATATTTTTATATTTATA
45979955 TATATATTT
1 TATATATTT
45979964 CAAAATAACA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
17 7 0.18
18 7 0.18
19 14 0.36
20 11 0.28
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TATATATTTTTATATTTATA
Found at i:45980601 original size:29 final size:31
Alignment explanation
Indices: 45980542--45980602 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
45980532 AAAACACCCC
* *
45980542 TTTAAGACAAAAAAAAAAGTCCATGTTAACA
1 TTTAAGACAAAAAAAAAAGTCCAAGTCAACA
45980573 TTTAAGACAAAAAAAAAA-T-CAAGTCAACA
1 TTTAAGACAAAAAAAAAAGTCCAAGTCAACA
45980602 T
1 T
45980603 AATAGGTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 9 0.32
30 1 0.04
31 18 0.64
ACGTcount: A:0.57, C:0.13, G:0.08, T:0.21
Consensus pattern (31 bp):
TTTAAGACAAAAAAAAAAGTCCAAGTCAACA
Found at i:45988725 original size:27 final size:27
Alignment explanation
Indices: 45988695--45988749 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
45988685 TCAATTTTGT
45988695 ACTTGTATTTGAGCCTGAGGATAAATA
1 ACTTGTATTTGAGCCTGAGGATAAATA
45988722 ACTTGTATTTGAGCCTGAGGATAAATA
1 ACTTGTATTTGAGCCTGAGGATAAATA
45988749 A
1 A
45988750 TCGAGCATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.33
Consensus pattern (27 bp):
ACTTGTATTTGAGCCTGAGGATAAATA
Found at i:45990000 original size:64 final size:65
Alignment explanation
Indices: 45989876--45990000 Score: 175
Period size: 64 Copynumber: 1.9 Consensus size: 65
45989866 CAAACATAAA
45989876 CATGCAATCATCTAAAAAATAAGAAGAGACATAACAGCGAAAACTTAAAAAGACCATAAAAATCA
1 CATGCAATCATCTAAAAAATAAGAAGAGA-ATAACAGCGAAAACTTAAAAAGACCATAAAAATCA
45989941 G
65 G
* * *
45989942 CATGCAATTATCTAAAAAAATAAGAAGAG-ATAGA-AGTG-AAGCTTAAAAAGACCATAAAA
1 CATGCAATCATCT-AAAAAATAAGAAGAGAATA-ACAGCGAAAACTTAAAAAGACCATAAAA
45990001 TTAACATCTT
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
64 20 0.37
65 6 0.11
66 13 0.24
67 15 0.28
ACGTcount: A:0.56, C:0.14, G:0.14, T:0.17
Consensus pattern (65 bp):
CATGCAATCATCTAAAAAATAAGAAGAGAATAACAGCGAAAACTTAAAAAGACCATAAAAATCAG
Found at i:45990066 original size:79 final size:78
Alignment explanation
Indices: 45989958--45990107 Score: 212
Period size: 80 Copynumber: 1.9 Consensus size: 78
45989948 ATTATCTAAA
* ** *
45989958 AAAATAAGAAGAGATAGAAGTGAAGCTT-AAAAAGACCATAAAATTAACATCTTTCTCAAACACA
1 AAAATAAGAAGAGATAGAAGTGAAACTTAAAAAAGACCATAAAACCAACATCTTCCTCAAACACA
45990022 AACATGTAATCAG
66 AACATGTAATCAG
* *
45990035 AAAATAAGAAGAGACATAGAAGTGAAACTTAAAAAAGACCATAAAACCAGCATCTTCCTCGAACA
1 AAAATAAGAAGAG--ATAGAAGTGAAACTTAAAAAAGACCATAAAACCAACATCTTCCTCAAACA
*
45990100 CGAACATG
64 CAAACATG
45990108 CAATTATCTA
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
77 13 0.21
79 14 0.22
80 36 0.57
ACGTcount: A:0.51, C:0.17, G:0.14, T:0.18
Consensus pattern (78 bp):
AAAATAAGAAGAGATAGAAGTGAAACTTAAAAAAGACCATAAAACCAACATCTTCCTCAAACACA
AACATGTAATCAG
Found at i:45997493 original size:18 final size:18
Alignment explanation
Indices: 45997466--45997512 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
45997456 TGGGGTCGAT
45997466 AACAAAGAGGAAGCTGAG
1 AACAAAGAGGAAGCTGAG
* * *
45997484 AACGAAGAGGGAGTTGAG
1 AACAAAGAGGAAGCTGAG
45997502 AACAAAGAGGA
1 AACAAAGAGGA
45997513 TCTGAAAACA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.49, C:0.09, G:0.36, T:0.06
Consensus pattern (18 bp):
AACAAAGAGGAAGCTGAG
Found at i:45998162 original size:84 final size:85
Alignment explanation
Indices: 45998005--45998174 Score: 218
Period size: 84 Copynumber: 2.0 Consensus size: 85
45997995 AATGCTTCAC
* * *
45998005 ATACTTGTGTTGTTACAGGTATGTCACAAGATCATCCGAAATTGGATTCTAACCTGATTGCTGAC
1 ATACTTGTGTTGTTACAAGTATGTCACAAGATCATCCGAAACTAGATTCTAACCTGATTGCTGAC
* * *
45998070 GTTGTCTTACGTATGGTGAA
66 ATTATCTTACCTATGGTGAA
* * * * *
45998090 ATACTTGTGTTGTTGCAAGTATGTTAC-TGATCATCTGAAACTAGATTCTAACCTGATCT-TTGA
1 ATACTTGTGTTGTTACAAGTATGTCACAAGATCATCCGAAACTAGATTCTAACCTGAT-TGCTGA
45998153 CATTATCTTACCTATGGTGAA
65 CATTATCTTACCTATGGTGAA
45998174 A
1 A
45998175 ACAAGTCCTA
Statistics
Matches: 73, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
84 48 0.66
85 25 0.34
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.37
Consensus pattern (85 bp):
ATACTTGTGTTGTTACAAGTATGTCACAAGATCATCCGAAACTAGATTCTAACCTGATTGCTGAC
ATTATCTTACCTATGGTGAA
Found at i:45999517 original size:17 final size:18
Alignment explanation
Indices: 45999479--45999518 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
45999469 ACAGGATTAG
*
45999479 AATTTAGTTGAGAAAATT
1 AATTTAATTGAGAAAATT
45999497 -ATTTAATT-AGAAAATT
1 AATTTAATTGAGAAAATT
45999513 AATTTA
1 AATTTA
45999519 TCTAATTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.42
Consensus pattern (18 bp):
AATTTAATTGAGAAAATT
Found at i:46001422 original size:9 final size:8
Alignment explanation
Indices: 46001408--46001441 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
46001398 CTTTTCTCAA
46001408 TTTTTTTC
1 TTTTTTTC
*
46001416 TTCTTTTC
1 TTTTTTTC
46001424 TTTATTTTC
1 TTT-TTTTC
46001433 TTTTTTTC
1 TTTTTTTC
46001441 T
1 T
46001442 GTCTTTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTTTC
Found at i:46005388 original size:19 final size:18
Alignment explanation
Indices: 46005360--46005399 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
46005350 CACCATTTTG
46005360 TTTGCTAATCCATTTCCC
1 TTTGCTAATCCATTTCCC
*
46005378 TTTGTCTAATCCATTTTCC
1 TTTG-CTAATCCATTTCCC
46005397 TTT
1 TTT
46005400 TACGGGGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.15, C:0.28, G:0.05, T:0.53
Consensus pattern (18 bp):
TTTGCTAATCCATTTCCC
Found at i:46009195 original size:31 final size:31
Alignment explanation
Indices: 46009151--46009221 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
46009141 ATAGTCCCTA
** * *
46009151 AACTATTCGAAAGTT-TTCATTTAAGTTATTG
1 AACTATTAAAAAGTTGTT-ATTTAAATCATTG
46009182 AACTATTAAAAAGTTGTTATTTAAATCATTG
1 AACTATTAAAAAGTTGTTATTTAAATCATTG
*
46009213 AGCTATTAA
1 AACTATTAA
46009222 GTTTTTTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 32 0.94
32 2 0.06
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.42
Consensus pattern (31 bp):
AACTATTAAAAAGTTGTTATTTAAATCATTG
Found at i:46010396 original size:42 final size:42
Alignment explanation
Indices: 46010335--46010420 Score: 120
Period size: 42 Copynumber: 2.0 Consensus size: 42
46010325 GCTAATCTTG
* *
46010335 CAACAAATTCTGGTGTTAGATTGTATCAA-CAGTCTTATTTGA
1 CAACAAATTCTGGTATTAGATTGTAT-AAGCAGTCTTATTCGA
* *
46010377 CAACAGATTCTGGTATTAGATTGTATAAGTAGTCTTATTCGA
1 CAACAAATTCTGGTATTAGATTGTATAAGCAGTCTTATTCGA
46010419 CA
1 CA
46010421 GTCGATTTAG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 2 0.05
42 37 0.95
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.37
Consensus pattern (42 bp):
CAACAAATTCTGGTATTAGATTGTATAAGCAGTCTTATTCGA
Found at i:46014944 original size:9 final size:9
Alignment explanation
Indices: 46014930--46014955 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
46014920 TGAAGATGGG
46014930 GCATGAAAT
1 GCATGAAAT
46014939 GCATGAAAT
1 GCATGAAAT
46014948 GCATGAAA
1 GCATGAAA
46014956 AGGAAACCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.12, G:0.23, T:0.19
Consensus pattern (9 bp):
GCATGAAAT
Found at i:46027983 original size:17 final size:17
Alignment explanation
Indices: 46027963--46028004 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
46027953 ATTTGTGGTG
46027963 AATTTGAAATTGTGATT
1 AATTTGAAATTGTGATT
**
46027980 AATTTGTTATTGTGATT
1 AATTTGAAATTGTGATT
*
46027997 GATTTGAA
1 AATTTGAA
46028005 TTCGAATGAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (17 bp):
AATTTGAAATTGTGATT
Found at i:46030101 original size:20 final size:18
Alignment explanation
Indices: 46030063--46030106 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 18
46030053 AAACCCTAAT
46030063 TTTCCC-TTTTCTTTTTC
1 TTTCCCTTTTTCTTTTTC
46030080 TTTCCCTTTTTCCTTATTTC
1 TTTCCCTTTTT-CTT-TTTC
46030100 TTTCCCT
1 TTTCCCT
46030107 GCTCATTCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.25
18 4 0.17
19 3 0.12
20 11 0.46
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTCCCTTTTTCTTTTTC
Found at i:46030134 original size:9 final size:9
Alignment explanation
Indices: 46030120--46030155 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
46030110 CATTCGTGCC
46030120 TTTCTTTTT
1 TTTCTTTTT
46030129 TTTCTTTTT
1 TTTCTTTTT
*
46030138 CTTTGTTTTT
1 -TTTCTTTTT
46030148 TTTCTTTT
1 TTTCTTTT
46030156 ATTCATTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:46030146 original size:19 final size:19
Alignment explanation
Indices: 46030119--46030155 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
46030109 TCATTCGTGC
46030119 CTTTCTTTTTTTTCTTTTT
1 CTTTCTTTTTTTTCTTTTT
*
46030138 CTTTGTTTTTTTTCTTTT
1 CTTTCTTTTTTTTCTTTT
46030156 ATTCATTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.84
Consensus pattern (19 bp):
CTTTCTTTTTTTTCTTTTT
Found at i:46039369 original size:11 final size:12
Alignment explanation
Indices: 46039358--46039397 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
46039348 AAATTCAGTT
46039358 TTGGTTTGG-T-
1 TTGGTTTGGTTA
46039368 TTGGTTTGGTTA
1 TTGGTTTGGTTA
*
46039380 TT-ATTTGGTTA
1 TTGGTTTGGTTA
46039391 TTGGTTT
1 TTGGTTT
46039398 TATTATAGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 9 0.36
11 11 0.44
12 5 0.20
ACGTcount: A:0.07, C:0.00, G:0.30, T:0.62
Consensus pattern (12 bp):
TTGGTTTGGTTA
Found at i:46039935 original size:5 final size:5
Alignment explanation
Indices: 46039925--46039951 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
46039915 CCACAATCAG
46039925 ACATC ACATC ACATC ACATC ACATC AC
1 ACATC ACATC ACATC ACATC ACATC AC
46039952 TACCCCTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.41, G:0.00, T:0.19
Consensus pattern (5 bp):
ACATC
Found at i:46042998 original size:31 final size:31
Alignment explanation
Indices: 46042937--46042998 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
46042927 TCAGTCATGA
*
46042937 AATTATTAATAATTTTATAATTTAGTCACTC
1 AATTATTAATAAATTTATAATTTAGTCACTC
46042968 AATTATTAATAAATTTATAATTTAGTCACTC
1 AATTATTAATAAATTTATAATTTAGTCACTC
46042999 TCAACATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (31 bp):
AATTATTAATAAATTTATAATTTAGTCACTC
Found at i:46043396 original size:40 final size:40
Alignment explanation
Indices: 46043341--46043424 Score: 168
Period size: 40 Copynumber: 2.1 Consensus size: 40
46043331 AAAAATAACA
46043341 TGGCATATGACAGCGTACTTGGTGTCATTAATCATCCAGT
1 TGGCATATGACAGCGTACTTGGTGTCATTAATCATCCAGT
46043381 TGGCATATGACAGCGTACTTGGTGTCATTAATCATCCAGT
1 TGGCATATGACAGCGTACTTGGTGTCATTAATCATCCAGT
46043421 TGGC
1 TGGC
46043425 CGATTAGCAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (40 bp):
TGGCATATGACAGCGTACTTGGTGTCATTAATCATCCAGT
Found at i:46048054 original size:12 final size:10
Alignment explanation
Indices: 46048021--46048072 Score: 61
Period size: 10 Copynumber: 5.3 Consensus size: 10
46048011 ATCTTAATTC
46048021 TAAAAAAAT-
1 TAAAAAAATA
46048030 TAAAAAAATA
1 TAAAAAAATA
46048040 TAAAAAAATA
1 TAAAAAAATA
* * * *
46048050 CATAAATATT
1 TAAAAAAATA
46048060 TAAAAAAATA
1 TAAAAAAATA
46048070 TAA
1 TAA
46048073 TAAATTTTTA
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
9 9 0.26
10 25 0.74
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (10 bp):
TAAAAAAATA
Found at i:46048065 original size:21 final size:21
Alignment explanation
Indices: 46048021--46048087 Score: 77
Period size: 20 Copynumber: 3.3 Consensus size: 21
46048011 ATCTTAATTC
* *
46048021 TAAAAAAAT-TAA-AAAAATA
1 TAAAAAAATATAATAAATATT
*
46048040 TAAAAAAATA-CATAAATATT
1 TAAAAAAATATAATAAATATT
*
46048060 TAAAAAAATATAATAAATTTT
1 TAAAAAAATATAATAAATATT
46048081 TAAAAAA
1 TAAAAAA
46048088 TGTAAAATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 10 0.25
20 15 0.38
21 15 0.38
ACGTcount: A:0.70, C:0.01, G:0.00, T:0.28
Consensus pattern (21 bp):
TAAAAAAATATAATAAATATT
Found at i:46048096 original size:22 final size:21
Alignment explanation
Indices: 46048021--46048098 Score: 74
Period size: 21 Copynumber: 3.8 Consensus size: 21
46048011 ATCTTAATTC
46048021 TAAAAAAATTAAAA-AAATA--
1 TAAAAAAA-TAAAATAAATATT
*
46048040 TAAAAAAAT-ACATAAATATT
1 TAAAAAAATAAAATAAATATT
* *
46048060 TAAAAAAATATAATAAATTTT
1 TAAAAAAATAAAATAAATATT
*
46048081 TAAAAAATGTAAAATAAA
1 TAAAAAA-ATAAAATAAA
46048099 AAATGATTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
17 2 0.04
18 6 0.12
19 8 0.17
20 9 0.19
21 15 0.31
22 8 0.17
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.28
Consensus pattern (21 bp):
TAAAAAAATAAAATAAATATT
Found at i:46048135 original size:25 final size:24
Alignment explanation
Indices: 46048106--46048154 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 24
46048096 AAAAAATGAT
*
46048106 TTATATTAATATTAAATATAAATAA
1 TTATATTAATATCAAATA-AAATAA
46048131 TTATATTAATATCAAATAAAATAA
1 TTATATTAATATCAAATAAAATAA
46048155 AAATACCCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 6 0.26
25 17 0.74
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (24 bp):
TTATATTAATATCAAATAAAATAA
Found at i:46052890 original size:18 final size:18
Alignment explanation
Indices: 46052867--46052903 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
46052857 TAATTCTTCT
*
46052867 AATGAATTAGAAACTTAA
1 AATGAATTAAAAACTTAA
46052885 AATGAATTAAAAACTTAA
1 AATGAATTAAAAACTTAA
46052903 A
1 A
46052904 CTACCCCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.59, C:0.05, G:0.08, T:0.27
Consensus pattern (18 bp):
AATGAATTAAAAACTTAA
Found at i:46055996 original size:20 final size:20
Alignment explanation
Indices: 46055968--46056005 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
46055958 TTCCGTTTAG
46055968 CTCACATGAGCTTCAGTTAA
1 CTCACATGAGCTTCAGTTAA
* *
46055988 CTCATATGAGTTTCAGTT
1 CTCACATGAGCTTCAGTT
46056006 TAACACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (20 bp):
CTCACATGAGCTTCAGTTAA
Found at i:46056672 original size:21 final size:20
Alignment explanation
Indices: 46056648--46056687 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
46056638 TATGAGCTTT
*
46056648 AATGATTGATGGTAGATTATG
1 AATGATTGATGATAG-TTATG
*
46056669 AATGTTTGATGATAGTTAT
1 AATGATTGATGATAGTTAT
46056688 ACAAGTTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.00, G:0.25, T:0.42
Consensus pattern (20 bp):
AATGATTGATGATAGTTATG
Found at i:46062029 original size:26 final size:26
Alignment explanation
Indices: 46061993--46062076 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
46061983 CATGAAATTC
46061993 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
46062019 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
46062045 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
46062071 TTATCA
1 TTATCA
46062077 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:46068664 original size:31 final size:31
Alignment explanation
Indices: 46068626--46068685 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
46068616 TTGTGACACT
46068626 TATCAAAAACCTTCTAACTATTTTCAGGGCA
1 TATCAAAAACCTTCTAACTATTTTCAGGGCA
*
46068657 TATCAAAAGCCTTCTAACTATTTTCAGGG
1 TATCAAAAACCTTCTAACTATTTTCAGGG
46068686 TATTTTTGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (31 bp):
TATCAAAAACCTTCTAACTATTTTCAGGGCA
Found at i:46082581 original size:21 final size:22
Alignment explanation
Indices: 46082555--46082595 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
46082545 TTAATAAAAT
*
46082555 TGAATCAATA-AATTAAAATTA
1 TGAATCAATAGAATAAAAATTA
46082576 TGAATCAATAGAATAAAAAT
1 TGAATCAATAGAATAAAAAT
46082596 AACATCACCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.29
Consensus pattern (22 bp):
TGAATCAATAGAATAAAAATTA
Found at i:46084353 original size:25 final size:26
Alignment explanation
Indices: 46084313--46084364 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
46084303 TTTACAAAAG
*
46084313 TTATTTTTACACAATAATAAAATATT
1 TTATTTTTACAAAATAATAAAATATT
* *
46084339 TTATTTTTA-AAAATAATTATATATT
1 TTATTTTTACAAAATAATAAAATATT
46084364 T
1 T
46084365 ATTATTGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (26 bp):
TTATTTTTACAAAATAATAAAATATT
Found at i:46085755 original size:16 final size:17
Alignment explanation
Indices: 46085731--46085763 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
46085721 CTAGGTCTTC
46085731 TTTTGTGGTTTT-TTTT
1 TTTTGTGGTTTTGTTTT
*
46085747 TTTTTTGGTTTTGTTTT
1 TTTTGTGGTTTTGTTTT
46085764 GTTTCTCTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (17 bp):
TTTTGTGGTTTTGTTTT
Found at i:46085774 original size:2 final size:2
Alignment explanation
Indices: 46085767--46085791 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
46085757 TTGTTTTGTT
46085767 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
46085792 GAATGTTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:46086180 original size:25 final size:25
Alignment explanation
Indices: 46086162--46086209 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
46086152 TTAATTAATT
*
46086162 TAATTGATTTTAATATTAAAGAAGA
1 TAATTGATTTTAACATTAAAGAAGA
46086187 TAATTGATTTTAACATTAAAGAA
1 TAATTGATTTTAACATTAAAGAA
46086210 AAGTTTTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.48, C:0.02, G:0.10, T:0.40
Consensus pattern (25 bp):
TAATTGATTTTAACATTAAAGAAGA
Found at i:46088981 original size:3 final size:3
Alignment explanation
Indices: 46088968--46089042 Score: 141
Period size: 3 Copynumber: 24.7 Consensus size: 3
46088958 GTCCCTTCTT
46088968 TAC TCAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
1 TAC T-AC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
46089014 TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
46089043 TTGTTATTAT
Statistics
Matches: 71, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 68 0.96
4 3 0.04
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TAC
Found at i:46092376 original size:27 final size:29
Alignment explanation
Indices: 46092329--46092385 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 29
46092319 TTAATTTAGC
* *
46092329 ATTATTTACTATTATTATTGTTAT-TTTT
1 ATTATTTACTACTATTATTGTCATCTTTT
*
46092357 ATTA-TTACTACTATTTTTGTCATCTTTT
1 ATTATTTACTACTATTATTGTCATCTTTT
46092385 A
1 A
46092386 AACTGTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 16 0.64
28 9 0.36
ACGTcount: A:0.25, C:0.09, G:0.04, T:0.63
Consensus pattern (29 bp):
ATTATTTACTACTATTATTGTCATCTTTT
Found at i:46103711 original size:130 final size:129
Alignment explanation
Indices: 46103500--46103961 Score: 511
Period size: 130 Copynumber: 3.6 Consensus size: 129
46103490 TAATTATTTA
* ** ** * * * *
46103500 TTTAAAATTCTTTAAAACGAAGGCAATGTTTGATATTTGGCAATTCGCGGAATCGTGCCTTATCG
1 TTTAAAATTCTTCAAAAC-AAGATAATGTTCAATGTTTGGAAATTCG-AGAATCGTGCCCTATCG
* * * *
46103565 TGCTGGGTTGCAATTTCTCGTTTGCTCAAAATAATCGAATGTCCCTTTAGAATTTCACTCATGTT
64 TGCTGGGTTGCAATTTCTCGTTTGTTCAAAATAATCGAATATTCCTTTGGAATTTCACTCATGTT
46103630 T
129 T
* *
46103631 TTTAAAATTCTTCAAAATAAAGATAATGTTCAATGTTTGGCAATTCGAGAATCGTGCCCTATCGT
1 TTTAAAATTCTTCAAAA-CAAGATAATGTTCAATGTTTGGAAATTCGAGAATCGTGCCCTATCGT
* * *
46103696 GCTGGGTTGCGATTTCTCGTTTGTTCAAAACAATCAAATATTCCTTTGGAATTTCACTCAT-TTC
65 GCTGGGTTGCAATTTCTCGTTTGTTCAAAATAATCGAATATTCCTTTGGAATTTCACTCATGTT-
46103760 T
129 T
* * * * * *
46103761 TTAAAAATTCTTCAAAACGAGCATAATATTCGATGTTTGGAAATTCGGGGAATCATGCCCTATCG
1 TTTAAAATTCTTCAAAACAAG-ATAATGTTCAATGTTTGGAAATTC-GAGAATCGTGCCCTATCG
* *
46103826 TGCTGGGTTGCAATTTCCCGTTTGTTTAAAATAATCGAATATTCCTTTGGAA-TTCTACTCATGT
64 TGCTGGGTTGCAATTTCTCGTTTGTTCAAAATAATCGAATATTCCTTTGGAATTTC-ACTCATGT
46103890 TT
128 TT
* * * ** * * *
46103892 TCT-AAATGC-T-AAAGCAAGGCAATGTTCAATGTTTAGAAATTTGAGGAATCGTGCCCTACCGT
1 TTTAAAATTCTTCAAAACAAGATAATGTTCAATGTTTGGAAATTCGA-GAATCGTGCCCTATCGT
46103954 GCTGGGTT
65 GCTGGGTT
46103962 TCGATTTTTC
Statistics
Matches: 281, Mismatches: 43, Indels: 18
0.82 0.13 0.05
Matches are distributed among these distances:
126 1 0.00
127 41 0.15
128 6 0.02
129 5 0.02
130 116 0.41
131 110 0.39
132 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (129 bp):
TTTAAAATTCTTCAAAACAAGATAATGTTCAATGTTTGGAAATTCGAGAATCGTGCCCTATCGTG
CTGGGTTGCAATTTCTCGTTTGTTCAAAATAATCGAATATTCCTTTGGAATTTCACTCATGTTT
Found at i:46106542 original size:31 final size:31
Alignment explanation
Indices: 46106507--46106577 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
46106497 GTAATTAATT
* *
46106507 ATTTTTAAAAATTAGAAATTATTTTTTTATA
1 ATTTTTAAAAATTACAAATAATTTTTTTATA
* ** * *
46106538 ATTTTTATACTTTTCAAATAATTTTTTTTTA
1 ATTTTTAAAAATTACAAATAATTTTTTTATA
46106569 ATTTTTAAA
1 ATTTTTAAA
46106578 TACTAAAAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (31 bp):
ATTTTTAAAAATTACAAATAATTTTTTTATA
Found at i:46108041 original size:13 final size:13
Alignment explanation
Indices: 46108023--46108080 Score: 71
Period size: 13 Copynumber: 4.5 Consensus size: 13
46108013 AGTTCTTCAT
*
46108023 TGCTTTTGAAAAG
1 TGCTTTTGAGAAG
46108036 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
* * *
46108049 TTCTATGGAGAAG
1 TGCTTTTGAGAAG
*
46108062 TACTTTTGAGAAG
1 TGCTTTTGAGAAG
46108075 TGCTTT
1 TGCTTT
46108081 AAAAAAATTT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.40
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:46111782 original size:24 final size:24
Alignment explanation
Indices: 46111745--46111807 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
46111735 TCATGTACAC
*
46111745 ATTATT-TATATTATTTTCA-TGATT
1 ATTATTGTAT-TTATTTTCACT-ACT
* *
46111769 ATTATTGTGTTTATTTTTACTACT
1 ATTATTGTATTTATTTTCACTACT
46111793 ATTATTGTATTTATT
1 ATTATTGTATTTATT
46111808 ATTAGTATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 30 0.91
25 3 0.09
ACGTcount: A:0.25, C:0.05, G:0.06, T:0.63
Consensus pattern (24 bp):
ATTATTGTATTTATTTTCACTACT
Found at i:46111822 original size:24 final size:24
Alignment explanation
Indices: 46111766--46111822 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
46111756 TATTTTCATG
* *
46111766 ATTATTATTGTGTTTATTTTTACT
1 ATTATTATTGTATTTATTATTACT
* *
46111790 ACTATTATTGTATTTATTATTAGT
1 ATTATTATTGTATTTATTATTACT
*
46111814 ATTAGTATT
1 ATTATTATT
46111823 ATAATTACTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.61
Consensus pattern (24 bp):
ATTATTATTGTATTTATTATTACT
Found at i:46112070 original size:24 final size:23
Alignment explanation
Indices: 46112030--46112089 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 23
46112020 TTTTTAATAC
46112030 TATATTATGTATATATTATATTA
1 TATATTATGTATATATTATATTA
*
46112053 TATATATATGTATTTATTATA-T-
1 TATAT-TATGTATATATTATATTA
46112075 T-T-TTATGTATATATT
1 TATATTATGTATATATT
46112090 TTTAATATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 11 0.32
20 1 0.03
21 1 0.03
22 1 0.03
23 6 0.18
24 14 0.41
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (23 bp):
TATATTATGTATATATTATATTA
Found at i:46122195 original size:44 final size:44
Alignment explanation
Indices: 46122127--46122309 Score: 257
Period size: 44 Copynumber: 4.2 Consensus size: 44
46122117 GGTGAACAAA
* *
46122127 AACAAATTTGGCGTCTCTGTAGCGGGGGAGAGCAGATCGAAGAT
1 AACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGAT
*
46122171 AACAGATTTGGCGTCTCTATAGCGGCGGAGAGCAGATCGAAGAT
1 AACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGAT
** * *
46122215 ----GATTTGGCGTCTCTGTAGTAGTGGAGAGCAGATCAAAGAT
1 AACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGAT
* *
46122255 AACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGTAGGT
1 AACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGAT
46122299 AACAGATTTGG
1 AACAGATTTGG
46122310 TATCTACGGA
Statistics
Matches: 121, Mismatches: 14, Indels: 8
0.85 0.10 0.06
Matches are distributed among these distances:
40 35 0.29
44 86 0.71
ACGTcount: A:0.28, C:0.16, G:0.33, T:0.23
Consensus pattern (44 bp):
AACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGAAGAT
Found at i:46122278 original size:84 final size:84
Alignment explanation
Indices: 46122132--46122293 Score: 279
Period size: 84 Copynumber: 1.9 Consensus size: 84
46122122 ACAAAAACAA
* *
46122132 ATTTGGCGTCTCTGTAGCGGGGGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTATAGCGGC
1 ATTTGGCGTCTCTGTAGCAGGGGAGAGCAGATCAAAGATAACAGATTTGGCGTCTCTATAGCGGC
46122197 GGAGAGCAGATCGAAGATG
66 GGAGAGCAGATCGAAGATG
* * *
46122216 ATTTGGCGTCTCTGTAGTAGTGGAGAGCAGATCAAAGATAACAGATTTGGCGTCTCTGTAGCGGC
1 ATTTGGCGTCTCTGTAGCAGGGGAGAGCAGATCAAAGATAACAGATTTGGCGTCTCTATAGCGGC
46122281 GGAGAGCAGATCG
66 GGAGAGCAGATCG
46122294 TAGGTAACAG
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
84 73 1.00
ACGTcount: A:0.26, C:0.17, G:0.35, T:0.23
Consensus pattern (84 bp):
ATTTGGCGTCTCTGTAGCAGGGGAGAGCAGATCAAAGATAACAGATTTGGCGTCTCTATAGCGGC
GGAGAGCAGATCGAAGATG
Found at i:46124293 original size:44 final size:44
Alignment explanation
Indices: 46124185--46124579 Score: 490
Period size: 44 Copynumber: 9.2 Consensus size: 44
46124175 TCCTTGAAAC
* * *
46124185 AGATAACAGATTTGGCATTTCTGTAGCGGCGGAAAGCAGATCGA
1 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
* *
46124229 AGAT----GATTTGGCATCTCTGTAGCGGTGGAGAGCAGATCGA
1 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
*
46124269 AGATAACAGATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCGA
1 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
* * * *
46124313 AGATAACAAATTTGGCGTCTCTGTAGCAGCGGGGAGCAGATCAA
1 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
* *
46124357 AGAT----GATTTGGCATCTCTGTAGCGGGGGAGAGCAGATCGA
1 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
*
46124397 AGATAACAGATTTGGCGTCTCTATAGCGGCGGAGAGCAGATCGA
1 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
** * *
46124441 AGAT----GATTTGGCGTCTCTGTAGTAGTGGAGAGCAGATCAA
1 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
*
46124481 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGT
1 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
* ** * *
46124525 AGGTAACAGATTTGGTATCTCTATAGCGGCAGAGAGCAGATCGA
1 AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
*
46124569 AAATAACAGAT
1 AGATAACAGAT
46124580 CGGTGTTCCT
Statistics
Matches: 301, Mismatches: 38, Indels: 24
0.83 0.10 0.07
Matches are distributed among these distances:
40 106 0.35
44 195 0.65
ACGTcount: A:0.30, C:0.16, G:0.32, T:0.23
Consensus pattern (44 bp):
AGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCGA
Found at i:46124365 original size:84 final size:84
Alignment explanation
Indices: 46124193--46124579 Score: 451
Period size: 84 Copynumber: 4.6 Consensus size: 84
46124183 ACAGATAACA
* * *
46124193 GATTTGGCATTTCTGTAGCGGCGGAAAGCAGATCGAAGAT----GATTTGGCATCTCTGTAGCGG
1 GATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGG
* *
46124254 TGGAGAGCAGATCGAAGAT
66 CGGAGAGCAGATCAAAGAT
* * *
46124273 AACAGATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCGAAGATAACAAATTTGGCGTCTCTGTA
1 ----GATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTA
* *
46124338 GCAGCGGGGAGCAGATCAAAGAT
62 GCGGCGGAGAGCAGATCAAAGAT
* *
46124361 GATTTGGCATCTCTGTAGCGGGGGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTATAGCGG
1 GATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGG
*
46124426 CGGAGAGCAGATCGAAGAT
66 CGGAGAGCAGATCAAAGAT
* ** * *
46124445 GATTTGGCGTCTCTGTAGTAGTGGAGAGCAGATCAAAGATAACAGATTTGGCGTCTCTGTAGCGG
1 GATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGG
*
46124510 CGGAGAGCAGATCGTAGGTAACA-
66 CGGAGAGCAGATC--A---AAGAT
* * * *
46124533 GATTTGGTATCTCTATAGCGGCAGAGAGCAGATCGAAAATAACAGAT
1 GATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACAGAT
46124580 CGGTGTTCCT
Statistics
Matches: 259, Mismatches: 35, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
84 184 0.71
88 72 0.28
89 3 0.01
ACGTcount: A:0.29, C:0.16, G:0.32, T:0.23
Consensus pattern (84 bp):
GATTTGGCATCTCTGTAGCGGCGGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGG
CGGAGAGCAGATCAAAGAT
Found at i:46124413 original size:128 final size:128
Alignment explanation
Indices: 46124185--46124579 Score: 555
Period size: 128 Copynumber: 3.1 Consensus size: 128
46124175 TCCTTGAAAC
* * * * *
46124185 AGATAACAGATTTGGCATTTCTGTAGCGGCGGAAAGCAGATCGAAGATGATTTGGCATCTCTGTA
1 AGATAACAGATTTGGCGTCTCTGTAGCAGCGGAGAGCAGATCAAAGATGATTTGGCATCTCTGTA
* *
46124250 GCGGTGGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCGA
66 GCGGCGGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTATAGCGGCAGAGAGCAGATCGA
* *
46124313 AGATAACAAATTTGGCGTCTCTGTAGCAGCGGGGAGCAGATCAAAGATGATTTGGCATCTCTGTA
1 AGATAACAGATTTGGCGTCTCTGTAGCAGCGGAGAGCAGATCAAAGATGATTTGGCATCTCTGTA
* *
46124378 GCGGGGGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTATAGCGGCGGAGAGCAGATCGA
66 GCGGCGGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTATAGCGGCAGAGAGCAGATCGA
* * *
46124441 AGAT----GATTTGGCGTCTCTGTAGTAGTGGAGAGCAGATCAAAGATAACAGATTTGGCGTCTC
1 AGATAACAGATTTGGCGTCTCTGTAGCAGCGGAGAGCAGATCAAAGAT----GATTTGGCATCTC
* * **
46124502 TGTAGCGGCGGAGAGCAGATCGTAGGTAACAGATTTGGTATCTCTATAGCGGCAGAGAGCAGATC
62 TGTAGCGGCGGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTATAGCGGCAGAGAGCAGATC
46124567 GA
127 GA
*
46124569 AAATAACAGAT
1 AGATAACAGAT
46124580 CGGTGTTCCT
Statistics
Matches: 237, Mismatches: 22, Indels: 12
0.87 0.08 0.04
Matches are distributed among these distances:
124 36 0.15
128 198 0.84
132 3 0.01
ACGTcount: A:0.30, C:0.16, G:0.32, T:0.23
Consensus pattern (128 bp):
AGATAACAGATTTGGCGTCTCTGTAGCAGCGGAGAGCAGATCAAAGATGATTTGGCATCTCTGTA
GCGGCGGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTATAGCGGCAGAGAGCAGATCGA
Found at i:46128791 original size:3 final size:3
Alignment explanation
Indices: 46128785--46128870 Score: 50
Period size: 3 Copynumber: 28.7 Consensus size: 3
46128775 CTTATATCTT
* * * * *
46128785 TAA TAA TAA TAA TAA TAC TTA TAA TATT TAA TAA TCA T-A CAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
* * * * *
46128830 TAA TAC TTA TAA TATT TAA TAA TAA T-A CAA TAA TAA AAA TA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TA
46128871 TGTTTAACAA
Statistics
Matches: 60, Mismatches: 19, Indels: 8
0.69 0.22 0.09
Matches are distributed among these distances:
2 2 0.03
3 54 0.90
4 4 0.07
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:46128829 original size:33 final size:32
Alignment explanation
Indices: 46128765--46128865 Score: 140
Period size: 33 Copynumber: 3.2 Consensus size: 32
46128755 TATGTTGAAT
*
46128765 AATAATAATACTTAT-ATCTTTAAT-A-AT--
1 AATAATAATACTTATAATATTTAATAATATAC
46128792 AATAATAATACTTATAATATTTAATAATCATAC
1 AATAATAATACTTATAATATTTAATAAT-ATAC
46128825 AATAATAATACTTATAATATTTAATAATAATAC
1 AATAATAATACTTATAATATTTAATAAT-ATAC
46128858 AATAATAA
1 AATAATAA
46128866 AAATATGTTT
Statistics
Matches: 66, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
27 15 0.23
28 8 0.12
29 1 0.02
31 2 0.03
33 40 0.61
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (32 bp):
AATAATAATACTTATAATATTTAATAATATAC
Found at i:46128830 original size:11 final size:11
Alignment explanation
Indices: 46128792--46128865 Score: 53
Period size: 11 Copynumber: 6.7 Consensus size: 11
46128782 CTTTAATAAT
46128792 AATAATAATAC
1 AATAATAATAC
* **
46128803 TTATAAT-ATTT
1 -AATAATAATAC
*
46128814 AATAATCATAC
1 AATAATAATAC
46128825 AATAATAATAC
1 AATAATAATAC
* **
46128836 TTATAAT-ATTT
1 -AATAATAATAC
46128847 AATAATAATAC
1 AATAATAATAC
46128858 AATAATAA
1 AATAATAA
46128866 AAATATGTTT
Statistics
Matches: 46, Mismatches: 13, Indels: 7
0.70 0.20 0.11
Matches are distributed among these distances:
10 10 0.22
11 26 0.57
12 10 0.22
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (11 bp):
AATAATAATAC
Found at i:46130848 original size:48 final size:48
Alignment explanation
Indices: 46130796--46130946 Score: 162
Period size: 48 Copynumber: 3.2 Consensus size: 48
46130786 TCAGTAAAAT
*
46130796 TCAAAATCAGAGCCACGCGTCACGTATAAAACCGTGATTCAGTGAGAA
1 TCAAAATCAGAGCCACGCGTCACTTATAAAACCGTGATTCAGTGAGAA
* ** * * * * * * *
46130844 TCAAAATCAAAGTTA--TGTCACTTATGAAACTGTTATTCAATAAAAA
1 TCAAAATCAGAGCCACGCGTCACTTATAAAACCGTGATTCAGTGAGAA
* * *
46130890 TCGAAATCAGAGCCACGCGTCACTTACAAAATCGTGATTCAGTGAGAA
1 TCAAAATCAGAGCCACGCGTCACTTATAAAACCGTGATTCAGTGAGAA
46130938 TCAAAATCA
1 TCAAAATCA
46130947 AAACCACTCA
Statistics
Matches: 76, Mismatches: 25, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
46 34 0.45
48 42 0.55
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (48 bp):
TCAAAATCAGAGCCACGCGTCACTTATAAAACCGTGATTCAGTGAGAA
Found at i:46130933 original size:94 final size:94
Alignment explanation
Indices: 46130772--46130948 Score: 273
Period size: 94 Copynumber: 1.9 Consensus size: 94
46130762 ATACACCAAG
* * *
46130772 TATGAAACCGTCACTCAGTAAAATTCAAAATCAGAGCCACGCGTCACGTATAAAACCGTGATTCA
1 TATGAAACCGTCACTCAATAAAAATCAAAATCAGAGCCACGCGTCACGTACAAAACCGTGATTCA
46130837 GTGAGAATCAAAATCAAAGTTATGTCACT
66 GTGAGAATCAAAATCAAAGTTATGTCACT
* * * * * *
46130866 TATGAAACTGTTATTCAATAAAAATCGAAATCAGAGCCACGCGTCACTTACAAAATCGTGATTCA
1 TATGAAACCGTCACTCAATAAAAATCAAAATCAGAGCCACGCGTCACGTACAAAACCGTGATTCA
46130931 GTGAGAATCAAAATCAAA
66 GTGAGAATCAAAATCAAA
46130949 ACCACTCACT
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
94 74 1.00
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (94 bp):
TATGAAACCGTCACTCAATAAAAATCAAAATCAGAGCCACGCGTCACGTACAAAACCGTGATTCA
GTGAGAATCAAAATCAAAGTTATGTCACT
Found at i:46133265 original size:202 final size:202
Alignment explanation
Indices: 46132808--46133359 Score: 839
Period size: 205 Copynumber: 2.7 Consensus size: 202
46132798 AGCTGAAACT
* *
46132808 AAGTACATTGAAACTAGTCTCCTTTTTTCCTTCAATATTGAACAAAAAAATAATTCTGAAATTTG
1 AAGTACATTGAAACTAGTCTCC-TATTTCCTTCGATATTGAACAAAAAAATAATT-TGAAATTTG
*
46132873 AATTACAATATAATAATGCTTGGTGCAGTGTAATCAATGAATGGAGATTCCCAATGAAAATTTTG
64 AATTACAATATAATAATGCTTGGTGCAGTGTAATTAATGAATGGAGATTCCCAATGAAAATTTTG
* *
46132938 ATTACACGTTTCATTCACACACAAATAATACATTACTTCTGAAACTGTCACTCAGTGAGAGTCGA
129 ATTA-ACGTTTCATTCACACACAAATAATACATCACTTATGAAACTGTCACTCAGTGAGAGTCGA
*
46133003 AACCAAAGTC
193 AACCAAAGCC
*
46133013 AAGTACATTGAAACTAATCTCCTATTTCACTTCGATATTGAACAAAAAAATAATTTGGAAATTTG
1 AAGTACATTGAAACTAGTCTCCTATTTC-CTTCGATATTGAACAAAAAAATAATTT-GAAATTTG
*
46133078 AATTACAATATAATAATGCTTGGTGCAGTGTAATTAATGAATGGAGATTCCCAAT-AAAAATTTG
64 AATTACAATATAATAATGCTTGGTGCAGTGTAATTAATGAATGGAGATTCCCAATGAAAATTTTG
46133142 ATT-ACGTTTCATTCACACACAAATGAA-ACATCACTTATGAAACTGTCACTCAGTGAGAGTCGA
129 ATTAACGTTTCATTCACACACAAAT-AATACATCACTTATGAAACTGTCACTCAGTGAGAGTCGA
46133205 AACCAAAGCC
193 AACCAAAGCC
* * * *
46133215 AGGTACATCGAAACTAGTCTCCTATTTCCATCTGATATTG-A-AAAAAAA-AA-TTAAAATTTGA
1 AAGTACATTGAAACTAGTCTCCTATTTCCTTC-GATATTGAACAAAAAAATAATTTGAAATTTGA
** * *
46133276 ATTACAATATAATAATGCTTGGTGTGGTGTAATTAATGAATAGAGATTCTCAATGAAAATTTTGA
65 ATTACAATATAATAATGCTTGGTGCAGTGTAATTAATGAATGGAGATTCCCAATGAAAATTTTGA
46133341 TTACACGTTTCATTCACAC
130 TTA-ACGTTTCATTCACAC
46133360 TTATGAAACT
Statistics
Matches: 322, Mismatches: 18, Indels: 19
0.90 0.05 0.05
Matches are distributed among these distances:
197 58 0.18
198 13 0.04
199 2 0.01
200 22 0.07
201 4 0.01
202 96 0.30
203 2 0.01
204 17 0.05
205 108 0.34
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.32
Consensus pattern (202 bp):
AAGTACATTGAAACTAGTCTCCTATTTCCTTCGATATTGAACAAAAAAATAATTTGAAATTTGAA
TTACAATATAATAATGCTTGGTGCAGTGTAATTAATGAATGGAGATTCCCAATGAAAATTTTGAT
TAACGTTTCATTCACACACAAATAATACATCACTTATGAAACTGTCACTCAGTGAGAGTCGAAAC
CAAAGCC
Found at i:46137373 original size:995 final size:995
Alignment explanation
Indices: 46135443--46137432 Score: 3980
Period size: 995 Copynumber: 2.0 Consensus size: 995
46135433 AATCTTACTA
46135443 ACTTAATCATTAGAAAGCTTTTTAGAATACAAGCTTCACATCTTCATGAAATTCATTCAGATGAG
1 ACTTAATCATTAGAAAGCTTTTTAGAATACAAGCTTCACATCTTCATGAAATTCATTCAGATGAG
46135508 ATTTGATAGATTTCAGCTAAGCAATATAAATATTAAACTCACCCGACAAAAGAAGTCATTATACA
66 ATTTGATAGATTTCAGCTAAGCAATATAAATATTAAACTCACCCGACAAAAGAAGTCATTATACA
46135573 GTTCTTCCCGATAAAGCAGGTCTAGAGAGCAAGAGCTTGATAGGATTAAACCTGGATATCACAAT
131 GTTCTTCCCGATAAAGCAGGTCTAGAGAGCAAGAGCTTGATAGGATTAAACCTGGATATCACAAT
46135638 GAGTTTATAAGATAAGAAGAAAACCAAAAAAAGAGAATACTTATCCATTGATGAATAGTAGTCGT
196 GAGTTTATAAGATAAGAAGAAAACCAAAAAAAGAGAATACTTATCCATTGATGAATAGTAGTCGT
46135703 TCTTGTACCAAAAGTAAGGTGAAATAGAAGTTAAATTCAACATCTTTACTCATTAGCTTATCATC
261 TCTTGTACCAAAAGTAAGGTGAAATAGAAGTTAAATTCAACATCTTTACTCATTAGCTTATCATC
46135768 ATAAAAACCCCAGTATTCGTAAACCTTAAGTCCCTCCCGTCAACCTCCAAACTCGGTTATGCTCA
326 ATAAAAACCCCAGTATTCGTAAACCTTAAGTCCCTCCCGTCAACCTCCAAACTCGGTTATGCTCA
46135833 AAGGAGACTGTAAACACTTCTTACTATCAATTACTGTGAATTATTAATATAACTTTTGCAAAAGA
391 AAGGAGACTGTAAACACTTCTTACTATCAATTACTGTGAATTATTAATATAACTTTTGCAAAAGA
46135898 ACTTACACACGCACAGCTTCATTCGCGGCAACTTTGAACCAAAAGATGATTACAAAATTATTATG
456 ACTTACACACGCACAGCTTCATTCGCGGCAACTTTGAACCAAAAGATGATTACAAAATTATTATG
46135963 ATAATTGTTATTACCGGCCCAAAACCAGAATGGGTTTGGGTTGAATGCCATCAAGCTCGCATGAT
521 ATAATTGTTATTACCGGCCCAAAACCAGAATGGGTTTGGGTTGAATGCCATCAAGCTCGCATGAT
46136028 AATAATAGACTAAGCTCGCATAATAATAGGTGGTTGTAGGAGAGGTATTTATATTCTCATATGAA
586 AATAATAGACTAAGCTCGCATAATAATAGGTGGTTGTAGGAGAGGTATTTATATTCTCATATGAA
46136093 GTCACATATGAGATCGAGCATGAAACTTATAAACACGTGTTAAGTCTAGAGTAAGATATATGTTA
651 GTCACATATGAGATCGAGCATGAAACTTATAAACACGTGTTAAGTCTAGAGTAAGATATATGTTA
46136158 ATATGAATGAAACTTACCTAATATGTCATATTAGTGAACAATACCTCTATATAAATAGGGAAACA
716 ATATGAATGAAACTTACCTAATATGTCATATTAGTGAACAATACCTCTATATAAATAGGGAAACA
46136223 TACTCAACAAGAATAAGCAAAAATAATAATAATAACACGTTCTAGTATTAAAAAATTAATACAAA
781 TACTCAACAAGAATAAGCAAAAATAATAATAATAACACGTTCTAGTATTAAAAAATTAATACAAA
46136288 ATATGGTGTTAATACATAACATATCAAAATTTGTATGAATTAATAATATCTTAAACTCAACAAAA
846 ATATGGTGTTAATACATAACATATCAAAATTTGTATGAATTAATAATATCTTAAACTCAACAAAA
46136353 TTAACATGCAAAACTTTACGAATATAATAAGAATATACCAATGGTAATGTAGAGCACCTGACTTC
911 TTAACATGCAAAACTTTACGAATATAATAAGAATATACCAATGGTAATGTAGAGCACCTGACTTC
46136418 GTCAAAATGCCTAGTAGCTG
976 GTCAAAATGCCTAGTAGCTG
46136438 ACTTAATCATTAGAAAGCTTTTTAGAATACAAGCTTCACATCTTCATGAAATTCATTCAGATGAG
1 ACTTAATCATTAGAAAGCTTTTTAGAATACAAGCTTCACATCTTCATGAAATTCATTCAGATGAG
46136503 ATTTGATAGATTTCAGCTAAGCAATATAAATATTAAACTCACCCGACAAAAGAAGTCATTATACA
66 ATTTGATAGATTTCAGCTAAGCAATATAAATATTAAACTCACCCGACAAAAGAAGTCATTATACA
46136568 GTTCTTCCCGATAAAGCAGGTCTAGAGAGCAAGAGCTTGATAGGATTAAACCTGGATATCACAAT
131 GTTCTTCCCGATAAAGCAGGTCTAGAGAGCAAGAGCTTGATAGGATTAAACCTGGATATCACAAT
46136633 GAGTTTATAAGATAAGAAGAAAACCAAAAAAAGAGAATACTTATCCATTGATGAATAGTAGTCGT
196 GAGTTTATAAGATAAGAAGAAAACCAAAAAAAGAGAATACTTATCCATTGATGAATAGTAGTCGT
46136698 TCTTGTACCAAAAGTAAGGTGAAATAGAAGTTAAATTCAACATCTTTACTCATTAGCTTATCATC
261 TCTTGTACCAAAAGTAAGGTGAAATAGAAGTTAAATTCAACATCTTTACTCATTAGCTTATCATC
46136763 ATAAAAACCCCAGTATTCGTAAACCTTAAGTCCCTCCCGTCAACCTCCAAACTCGGTTATGCTCA
326 ATAAAAACCCCAGTATTCGTAAACCTTAAGTCCCTCCCGTCAACCTCCAAACTCGGTTATGCTCA
46136828 AAGGAGACTGTAAACACTTCTTACTATCAATTACTGTGAATTATTAATATAACTTTTGCAAAAGA
391 AAGGAGACTGTAAACACTTCTTACTATCAATTACTGTGAATTATTAATATAACTTTTGCAAAAGA
46136893 ACTTACACACGCACAGCTTCATTCGCGGCAACTTTGAACCAAAAGATGATTACAAAATTATTATG
456 ACTTACACACGCACAGCTTCATTCGCGGCAACTTTGAACCAAAAGATGATTACAAAATTATTATG
46136958 ATAATTGTTATTACCGGCCCAAAACCAGAATGGGTTTGGGTTGAATGCCATCAAGCTCGCATGAT
521 ATAATTGTTATTACCGGCCCAAAACCAGAATGGGTTTGGGTTGAATGCCATCAAGCTCGCATGAT
46137023 AATAATAGACTAAGCTCGCATAATAATAGGTGGTTGTAGGAGAGGTATTTATATTCTCATATGAA
586 AATAATAGACTAAGCTCGCATAATAATAGGTGGTTGTAGGAGAGGTATTTATATTCTCATATGAA
46137088 GTCACATATGAGATCGAGCATGAAACTTATAAACACGTGTTAAGTCTAGAGTAAGATATATGTTA
651 GTCACATATGAGATCGAGCATGAAACTTATAAACACGTGTTAAGTCTAGAGTAAGATATATGTTA
46137153 ATATGAATGAAACTTACCTAATATGTCATATTAGTGAACAATACCTCTATATAAATAGGGAAACA
716 ATATGAATGAAACTTACCTAATATGTCATATTAGTGAACAATACCTCTATATAAATAGGGAAACA
46137218 TACTCAACAAGAATAAGCAAAAATAATAATAATAACACGTTCTAGTATTAAAAAATTAATACAAA
781 TACTCAACAAGAATAAGCAAAAATAATAATAATAACACGTTCTAGTATTAAAAAATTAATACAAA
46137283 ATATGGTGTTAATACATAACATATCAAAATTTGTATGAATTAATAATATCTTAAACTCAACAAAA
846 ATATGGTGTTAATACATAACATATCAAAATTTGTATGAATTAATAATATCTTAAACTCAACAAAA
46137348 TTAACATGCAAAACTTTACGAATATAATAAGAATATACCAATGGTAATGTAGAGCACCTGACTTC
911 TTAACATGCAAAACTTTACGAATATAATAAGAATATACCAATGGTAATGTAGAGCACCTGACTTC
46137413 GTCAAAATGCCTAGTAGCTG
976 GTCAAAATGCCTAGTAGCTG
46137433 CTTCCCACGT
Statistics
Matches: 995, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
995 995 1.00
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (995 bp):
ACTTAATCATTAGAAAGCTTTTTAGAATACAAGCTTCACATCTTCATGAAATTCATTCAGATGAG
ATTTGATAGATTTCAGCTAAGCAATATAAATATTAAACTCACCCGACAAAAGAAGTCATTATACA
GTTCTTCCCGATAAAGCAGGTCTAGAGAGCAAGAGCTTGATAGGATTAAACCTGGATATCACAAT
GAGTTTATAAGATAAGAAGAAAACCAAAAAAAGAGAATACTTATCCATTGATGAATAGTAGTCGT
TCTTGTACCAAAAGTAAGGTGAAATAGAAGTTAAATTCAACATCTTTACTCATTAGCTTATCATC
ATAAAAACCCCAGTATTCGTAAACCTTAAGTCCCTCCCGTCAACCTCCAAACTCGGTTATGCTCA
AAGGAGACTGTAAACACTTCTTACTATCAATTACTGTGAATTATTAATATAACTTTTGCAAAAGA
ACTTACACACGCACAGCTTCATTCGCGGCAACTTTGAACCAAAAGATGATTACAAAATTATTATG
ATAATTGTTATTACCGGCCCAAAACCAGAATGGGTTTGGGTTGAATGCCATCAAGCTCGCATGAT
AATAATAGACTAAGCTCGCATAATAATAGGTGGTTGTAGGAGAGGTATTTATATTCTCATATGAA
GTCACATATGAGATCGAGCATGAAACTTATAAACACGTGTTAAGTCTAGAGTAAGATATATGTTA
ATATGAATGAAACTTACCTAATATGTCATATTAGTGAACAATACCTCTATATAAATAGGGAAACA
TACTCAACAAGAATAAGCAAAAATAATAATAATAACACGTTCTAGTATTAAAAAATTAATACAAA
ATATGGTGTTAATACATAACATATCAAAATTTGTATGAATTAATAATATCTTAAACTCAACAAAA
TTAACATGCAAAACTTTACGAATATAATAAGAATATACCAATGGTAATGTAGAGCACCTGACTTC
GTCAAAATGCCTAGTAGCTG
Found at i:46139097 original size:10 final size:10
Alignment explanation
Indices: 46139082--46139116 Score: 61
Period size: 10 Copynumber: 3.4 Consensus size: 10
46139072 TAATACAAGT
46139082 GTAAAATGCA
1 GTAAAATGCA
46139092 GTAAAAATGCA
1 GT-AAAATGCA
46139103 GTAAAATGCA
1 GTAAAATGCA
46139113 GTAA
1 GTAA
46139117 GTTTGTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 14 0.58
11 10 0.42
ACGTcount: A:0.51, C:0.09, G:0.20, T:0.20
Consensus pattern (10 bp):
GTAAAATGCA
Found at i:46139100 original size:11 final size:11
Alignment explanation
Indices: 46139084--46139116 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
46139074 ATACAAGTGT
46139084 AAAATGCAGTA
1 AAAATGCAGTA
46139095 AAAATGCAGT-
1 AAAATGCAGTA
46139105 AAAATGCAGTA
1 AAAATGCAGTA
46139116 A
1 A
46139117 GTTTGTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.55, C:0.09, G:0.18, T:0.18
Consensus pattern (11 bp):
AAAATGCAGTA
Found at i:46155427 original size:15 final size:15
Alignment explanation
Indices: 46155402--46155434 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
46155392 ATTTGGTTAT
46155402 TAATATAATTAAATAA
1 TAATATAATTAAA-AA
46155418 TAAT-TAATTAAAAA
1 TAATATAATTAAAAA
46155432 TAA
1 TAA
46155435 ATACTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 8 0.47
16 4 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TAATATAATTAAAAA
Found at i:46164437 original size:14 final size:15
Alignment explanation
Indices: 46164418--46164447 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
46164408 TTGTTGGAAT
46164418 AATTTT-AAATTTAA
1 AATTTTAAAATTTAA
46164432 AATTTTAAAATTTAA
1 AATTTTAAAATTTAA
46164447 A
1 A
46164448 TAAATTAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTTTAAAATTTAA
Found at i:46168064 original size:30 final size:30
Alignment explanation
Indices: 46168030--46168090 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
46168020 TTCCCAAGCC
46168030 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
* * * *
46168060 TAGGGGCAAAATTGTAATTTTTCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
46168090 T
1 T
46168091 GAGTTAAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.31
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAAATATGCAAAAGTT
Found at i:46176560 original size:25 final size:25
Alignment explanation
Indices: 46176525--46176572 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
46176515 CTTATATATA
46176525 TTGATACCTATGTATAAAATAAAAT
1 TTGATACCTATGTATAAAATAAAAT
* * *
46176550 TTGATATCTATTTATTAAATAAA
1 TTGATACCTATGTATAAAATAAA
46176573 TTCCAAGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (25 bp):
TTGATACCTATGTATAAAATAAAAT
Found at i:46183372 original size:6 final size:6
Alignment explanation
Indices: 46183363--46183407 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
46183353 CACTGTAAGG
*
46183363 GTAACA GTAACA GTAACA GTAACA ATAACA GTAACA GTAACA GTA
1 GTAACA GTAACA GTAACA GTAACA GTAACA GTAACA GTAACA GTA
46183408 GCGGTACACA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.51, C:0.16, G:0.16, T:0.18
Consensus pattern (6 bp):
GTAACA
Found at i:46185202 original size:39 final size:39
Alignment explanation
Indices: 46185158--46185278 Score: 206
Period size: 39 Copynumber: 3.1 Consensus size: 39
46185148 AATTATGTTA
*
46185158 CCAGCACAAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
* *
46185197 CCAGCACGAAGCCTGCGAGACTTTAGCCCAGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
*
46185236 CCAGCACGAAGCCTGCGGGTCTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
46185275 CCAG
1 CCAG
46185279 TGTCTTGCTT
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 76 1.00
ACGTcount: A:0.25, C:0.31, G:0.23, T:0.21
Consensus pattern (39 bp):
CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
Found at i:46187889 original size:15 final size:15
Alignment explanation
Indices: 46187853--46187894 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 15
46187843 TAATATAATA
*
46187853 ATTTAATAAATATCT
1 ATTTAATAAAAATCT
46187868 A-TT-ATAAAAATCT
1 ATTTAATAAAAATCT
46187881 ATTTAATAACAAAT
1 ATTTAATAA-AAAT
46187895 ATTCTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
13 10 0.43
14 4 0.17
15 5 0.22
16 4 0.17
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTTAATAAAAATCT
Found at i:46194521 original size:3 final size:3
Alignment explanation
Indices: 46194515--46194540 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
46194505 TAATAAGCAC
46194515 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
46194541 GGATATTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:46197708 original size:4 final size:4
Alignment explanation
Indices: 46197699--46197776 Score: 138
Period size: 4 Copynumber: 19.5 Consensus size: 4
46197689 AGTACAAGTG
* *
46197699 ATAC ATAC ATAC ATAC ATAC ACAC ATAC ACAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
46197747 ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
46197777 GCATGCATGC
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 70 1.00
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (4 bp):
ATAC
Found at i:46199675 original size:28 final size:24
Alignment explanation
Indices: 46199607--46199665 Score: 100
Period size: 24 Copynumber: 2.4 Consensus size: 24
46199597 TCGTTTAGCT
46199607 TTTAAATCATATATATATACAATTTG
1 TTTAAAT-A-ATATATATACAATTTG
46199633 TTTAAATAATATATATACAATTTG
1 TTTAAATAATATATATACAATTTG
46199657 TTTAAATAA
1 TTTAAATAA
46199666 GTATGCTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 25 0.76
25 1 0.03
26 7 0.21
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (24 bp):
TTTAAATAATATATATACAATTTG
Found at i:46200733 original size:15 final size:15
Alignment explanation
Indices: 46200713--46200764 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
46200703 ACTACAAAGC
46200713 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
46200728 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
46200747 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
46200762 ATT
1 ATT
46200765 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:46200825 original size:15 final size:16
Alignment explanation
Indices: 46200796--46200831 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
46200786 AGGTGAAGAA
*
46200796 TATTATTTAATATTAT
1 TATTATTTAAAATTAT
46200812 TATT-TTTAAAATTAT
1 TATTATTTAAAATTAT
46200827 TATTA
1 TATTA
46200832 AAATAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:46200850 original size:19 final size:17
Alignment explanation
Indices: 46200818--46200861 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 17
46200808 TTATTATTTT
46200818 TAAAATTATTATTAAAA
1 TAAAATTATTATTAAAA
46200835 TAAAATTAATTTATTAAAA
1 TAAAATT-A-TTATTAAAA
46200854 TAATAATT
1 TAA-AATT
46200862 TATATTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.29
18 1 0.04
19 12 0.50
20 4 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAAATTATTATTAAAA
Done.