Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 121 of 186
Found at i:40068311 original size:96 final size:94
Alignment explanation
Indices: 40068145--40068464 Score: 349
Period size: 96 Copynumber: 3.3 Consensus size: 94
40068135 GTAAAATGTT
** * * *
40068145 GATGCCATGTCCCGGATATGGTCTTACATTGGCTCTCATACATCAGTGCCGATGCCATGTCCCAG
1 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATA-ATGAG-GCCGATGCCATGTCCCAG
*
40068210 ACATGGTCTTACATTGACACATATAACAATGCC
64 ACATGGTCTTACATTGACACATAT-ACAACG-C
* * *
40068243 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCAT-ATATTGAGGCTGATGCCATGTCCCAGA
1 GATGCCATGTCCCAAACATGGTCTTACACTGGCTC-TCATAATGAGGCCGATGCCATGTCCCAGA
* * ** *
40068307 CATGGTCTTACATTGGCTCGCATAT-TGAGGTC
65 CATGGTCTTACATT-G-ACACATATACAACG-C
* * *
40068339 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCCATGTCCCAAAC
1 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAATGAGGCCGATGCCATGTCCCAGAC
*
40068404 ATGGTCTTACACTAGCACACATAT-CAACGC
66 ATGGTCTTACA-TTG-ACACATATACAACGC
*
40068434 TAGTGCCATGTCCCAAACATGGTCTTACACT
1 GA-TGCCATGTCCCAAACATGGTCTTACACT
40068465 AGCACACATA
Statistics
Matches: 188, Mismatches: 28, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
95 3 0.02
96 140 0.74
97 5 0.03
98 39 0.21
99 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.28
Consensus pattern (94 bp):
GATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAATGAGGCCGATGCCATGTCCCAGAC
ATGGTCTTACATTGACACATATACAACGC
Found at i:40068406 original size:144 final size:146
Alignment explanation
Indices: 40068144--40068462 Score: 405
Period size: 144 Copynumber: 2.2 Consensus size: 146
40068134 GGTAAAATGT
* * *
40068144 TGATGCCATGTCCCGGATATGGTCTTACATTGGCTCTCATACATCAGTGCCGATGCCATGTCCCA
1 TGATGCCATGTCCCAGACATGGTCTTACATTGGCTCGCATACATCAGTGCCGATGCCATGTCCCA
* * *
40068209 GACATGGTCTTACATTGACACATATAACAATGCCGATGCCATGTTCCAAACATGGTCTTACACTG
66 GACATGGTCTTACACTGACACATATAACAATGCCGATGCCATGTCCCAAACATGGTCTTACACTA
* * ** *
40068274 GCTCATATATTGAGGC
131 GCACACATATCAACGC
* * *
40068290 TGATGCCATGTCCCAGACATGGTCTTACATTGGCTCGCATA-TTGAG-GTCGATGCCATGTCCCA
1 TGATGCCATGTCCCAGACATGGTCTTACATTGGCTCGCATACATCAGTGCCGATGCCATGTCCCA
* * **
40068353 GACATGGTCTTACACTGGCTC-TCATAA-TGTGGCCGATGCCATGTCCCAAACATGGTCTTACAC
66 GACATGGTCTTACACTGACACAT-ATAACAAT-GCCGATGCCATGTCCCAAACATGGTCTTACAC
40068416 TAGCACACATATCAACGC
129 TAGCACACATATCAACGC
*
40068434 T-AGTGCCATGTCCCAAACATGGTCTTACA
1 TGA-TGCCATGTCCCAGACATGGTCTTACA
40068463 CTAGCACACA
Statistics
Matches: 151, Mismatches: 19, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
143 3 0.02
144 107 0.71
145 3 0.02
146 38 0.25
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (146 bp):
TGATGCCATGTCCCAGACATGGTCTTACATTGGCTCGCATACATCAGTGCCGATGCCATGTCCCA
GACATGGTCTTACACTGACACATATAACAATGCCGATGCCATGTCCCAAACATGGTCTTACACTA
GCACACATATCAACGC
Found at i:40068463 original size:48 final size:49
Alignment explanation
Indices: 40068145--40068477 Score: 286
Period size: 48 Copynumber: 6.9 Consensus size: 49
40068135 GTAAAATGTT
** * * * *
40068145 GATGCCATGTCCCGGATATGGTCTTACATTGGCTCTCATA-CATCAGTGC-C
1 GATGCCATGTCCCAAACATGGTCTTACACTGGCACACATATCA--AG-GCTC
* * * * * *
40068195 GATGCCATGTCCCAGACATGGTCTTACATTGACACATATAACAATGC-C
1 GATGCCATGTCCCAAACATGGTCTTACACTGGCACACATATCAAGGCTC
* * * **
40068243 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCATATATTGAGGCT-
1 GATGCCATGTCCCAAACATGGTCTTACACTGGCACACATATCAAGGCTC
* * * * **
40068291 GATGCCATGTCCCAGACATGGTCTTACATTGGCTCGCATATTGAGG-TC
1 GATGCCATGTCCCAAACATGGTCTTACACTGGCACACATATCAAGGCTC
* * * **
40068339 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GTGGC-C
1 GATGCCATGTCCCAAACATGGTCTTACACTGGCACACAT-ATCAAGGCTC
* * *
40068387 GATGCCATGTCCCAAACATGGTCTTACACTAGCACACATATCAACGCTA
1 GATGCCATGTCCCAAACATGGTCTTACACTGGCACACATATCAAGGCTC
*
40068436 G-TGCCATGTCCCAAACATGGTCTTACACTAGCACACATATCA
1 GATGCCATGTCCCAAACATGGTCTTACACTGGCACACATATCA
40068478 TCCAAATGTC
Statistics
Matches: 244, Mismatches: 32, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
47 3 0.01
48 201 0.82
49 4 0.02
50 34 0.14
51 2 0.01
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.27
Consensus pattern (49 bp):
GATGCCATGTCCCAAACATGGTCTTACACTGGCACACATATCAAGGCTC
Found at i:40070969 original size:17 final size:18
Alignment explanation
Indices: 40070947--40070980 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
40070937 CAATCTGGGC
40070947 GTGTGGGCC-ACACGAGT
1 GTGTGGGCCTACACGAGT
40070964 GTGTGGGCCTACACGAG
1 GTGTGGGCCTACACGAG
40070981 CAAGCCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.18, C:0.24, G:0.41, T:0.18
Consensus pattern (18 bp):
GTGTGGGCCTACACGAGT
Found at i:40078266 original size:20 final size:20
Alignment explanation
Indices: 40078243--40078299 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
40078233 GTGCAGAAAG
40078243 AGGCACAAATGTGCAATCAA
1 AGGCACAAATGTGCAATCAA
* * *
40078263 AGGCATCGAA-GTGCAAACAG
1 AGGCA-CAAATGTGCAATCAA
*
40078283 AGGCAAAAATGTGCAAT
1 AGGCACAAATGTGCAAT
40078300 TTGAGGCAGC
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
19 2 0.07
20 24 0.83
21 3 0.10
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.14
Consensus pattern (20 bp):
AGGCACAAATGTGCAATCAA
Found at i:40078267 original size:40 final size:40
Alignment explanation
Indices: 40078223--40078323 Score: 123
Period size: 40 Copynumber: 2.5 Consensus size: 40
40078213 TGCATAACAG
*
40078223 AGGCACCGAAGTGCAGAA-AGAGGCACAAATGTGCAATCAA
1 AGGCACCGAAGTGCA-AACAGAGGCAAAAATGTGCAATCAA
* ***
40078263 AGGCATCGAAGTGCAAACAGAGGCAAAAATGTGCAATTTG
1 AGGCACCGAAGTGCAAACAGAGGCAAAAATGTGCAATCAA
* *
40078303 AGGCAGCAAAGTGCAAACAGA
1 AGGCACCGAAGTGCAAACAGA
40078324 AGCACTGTAC
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
39 2 0.04
40 51 0.96
ACGTcount: A:0.43, C:0.18, G:0.28, T:0.12
Consensus pattern (40 bp):
AGGCACCGAAGTGCAAACAGAGGCAAAAATGTGCAATCAA
Found at i:40083292 original size:21 final size:20
Alignment explanation
Indices: 40083268--40083306 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
40083258 AAACTTGTAT
40083268 ATCTATCAACAAGCATTCACA
1 ATCTATCAACAAGC-TTCACA
*
40083289 ATCTATCAAGAAGCTTCA
1 ATCTATCAACAAGCTTCA
40083307 AAATACACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.26
Consensus pattern (20 bp):
ATCTATCAACAAGCTTCACA
Found at i:40088561 original size:79 final size:81
Alignment explanation
Indices: 40088393--40088577 Score: 207
Period size: 79 Copynumber: 2.3 Consensus size: 81
40088383 GCTACTCGTT
* * * *
40088393 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTTGCACAAATGCCTTCGGGGCTTAACCCA
1 CAAA-GCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGAGCTTAACCCA
* *
40088457 GATTTAGTAACTCGCAC
65 GATATAGTAACTAGCAC
* * ** *
40088474 CAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAAGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGAGCTTAACCCAG
* *
40088537 ATATGGTCACTTAGCA-
66 ATATAGTAAC-TAGCAC
40088553 CAAAGCCTTCGGGACTTAGCCCGGA
1 CAAAGCCTTCGGGACTTAGCCCGGA
40088578 CATCATTCGA
Statistics
Matches: 87, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
79 59 0.68
80 25 0.29
81 3 0.03
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
CAAAGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGAGCTTAACCCAG
ATATAGTAACTAGCAC
Found at i:40088577 original size:40 final size:40
Alignment explanation
Indices: 40088374--40088577 Score: 211
Period size: 40 Copynumber: 5.1 Consensus size: 40
40088364 CGGAATTTAA
** *
40088374 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * * *
40088414 CCGGTTATAGTAACTTGCACAAATGCCTTCGGGGCTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
40088454 CCAGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
40088493 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
40088533 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
40088573 CCGGA
1 CCGGA
40088578 CATCATTCGA
Statistics
Matches: 136, Mismatches: 21, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.24
40 90 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:40093047 original size:28 final size:28
Alignment explanation
Indices: 40093004--40093062 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
40092994 TGAATATTTG
*
40093004 AAAACACTGTTGCACCTTTCAACTGATC
1 AAAACACTGTTACACCTTTCAACTGATC
40093032 AAAACACTGTTACACCTTTCAACTGATC
1 AAAACACTGTTACACCTTTCAACTGATC
40093060 AAA
1 AAA
40093063 CAAATCGTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.37, C:0.27, G:0.08, T:0.27
Consensus pattern (28 bp):
AAAACACTGTTACACCTTTCAACTGATC
Found at i:40098137 original size:46 final size:46
Alignment explanation
Indices: 40098084--40098207 Score: 153
Period size: 46 Copynumber: 2.7 Consensus size: 46
40098074 TATGTGTGCT
* *
40098084 AGTGTAAGACATGTCTGGGACATGCATCGGCCATATTATA-AGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCAT-TGAGACAGAGCC
* * *
40098130 AGTGTAAGACATGTCTGGGACATACATTGG-CATTGAGACGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCATTGAGAC-AGAGCC
* *
40098176 AGTGTAAAACATGTTTGGGACATGCATCGGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCC
40098208 TCGAGATATA
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
44 3 0.05
45 3 0.05
46 59 0.89
47 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCATTGAGACAGAGCC
Found at i:40098355 original size:49 final size:49
Alignment explanation
Indices: 40098267--40098374 Score: 110
Period size: 49 Copynumber: 2.2 Consensus size: 49
40098257 TGTTGTGTGT
* * * * *
40098267 CAGTGTAAGACCTGTCCGGGACATGGCATCGGCACCGATAGATGAGAGC
1 CAGTGTAAGACCTATCCGGGACACGACATCAGCACCGATAGATGAAAGC
** * *
40098316 CAGTGTAAGACCTATTTGGGACACGACATCAGC-CTCGATATATGAAAGT
1 CAGTGTAAGACCTATCCGGGACACGACATCAGCAC-CGATAGATGAAAGC
*
40098365 CAATGTAAGA
1 CAGTGTAAGA
40098375 TTTGTCTGTG
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
48 1 0.02
49 47 0.98
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.20
Consensus pattern (49 bp):
CAGTGTAAGACCTATCCGGGACACGACATCAGCACCGATAGATGAAAGC
Found at i:40103750 original size:20 final size:19
Alignment explanation
Indices: 40103714--40103764 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
40103704 AAGGGCTATT
*
40103714 TTGTAAA-GTTGTAAAATAA
1 TTGTAAATG-TGTGAAATAA
40103733 GTTGTAAATGTGTGAAATAA
1 -TTGTAAATGTGTGAAATAA
40103753 TTG-AAAT-TGTGA
1 TTGTAAATGTGTGA
40103765 GTTGCTATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.17
18 4 0.14
19 3 0.10
20 16 0.55
21 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (19 bp):
TTGTAAATGTGTGAAATAA
Found at i:40104464 original size:46 final size:46
Alignment explanation
Indices: 40104396--40104522 Score: 170
Period size: 46 Copynumber: 2.8 Consensus size: 46
40104386 TGATATGTGT
40104396 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATT-ACGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCC-CATTGACGAGA
*
40104442 GCTAGTGTAAGACATGTTTGGGACATGCATCGG--CATTGAGACGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCCATT--GACGAGA
* * *
40104488 GCTAGAGCAAAACATGTCTGGGACATGCATCGGCC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCC
40104523 TTGAGATATA
Statistics
Matches: 71, Mismatches: 5, Indels: 8
0.85 0.06 0.10
Matches are distributed among these distances:
43 4 0.06
46 67 0.94
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.21
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCCATTGACGAGA
Found at i:40104642 original size:49 final size:49
Alignment explanation
Indices: 40104583--40104707 Score: 153
Period size: 49 Copynumber: 2.6 Consensus size: 49
40104573 GTTGTGTGTT
* *
40104583 AGTGTAAGACCTGTCTGGGACATGGTATCGACAC-CGATAGATGAGAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGAC-CTCGATAGATGAAAGCC
* * * * *
40104632 AGTGTAAGACCTGTCTAGGACACGGCATCGGCCTCGATATATGAAAGTC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATGAAAGCC
* *
40104681 AGTGTAAGAGCTTTCTGGGACATGGCA
1 AGTGTAAGACCTGTCTGGGACATGGCA
40104708 CCAACTTTGA
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
48 1 0.02
49 63 0.98
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (49 bp):
AGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATGAAAGCC
Found at i:40114832 original size:40 final size:40
Alignment explanation
Indices: 40114667--40114852 Score: 193
Period size: 40 Copynumber: 4.7 Consensus size: 40
40114657 TTGAATGATG
* * *
40114667 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAGGTGAGC-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGA-GTTA-CTAAA
* * *
40114707 TCCGGACTAAGAT-CCGATGGCATTTGTACGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
40114747 TCTGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
40114787 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
40114828 -CCGGGCCATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
40114853 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
39 2 0.02
40 114 0.90
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:40120309 original size:26 final size:26
Alignment explanation
Indices: 40120273--40120327 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
40120263 TGGATGTTAA
40120273 GATCAAATCTCGCGAACTTCCCAATG
1 GATCAAATCTCGCGAACTTCCCAATG
40120299 GATCAAATCTCGCGAACTTCCCAATG
1 GATCAAATCTCGCGAACTTCCCAATG
40120325 GAT
1 GAT
40120328 GCCTCTACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (26 bp):
GATCAAATCTCGCGAACTTCCCAATG
Found at i:40121769 original size:10 final size:10
Alignment explanation
Indices: 40121754--40121784 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
40121744 GTTGTTGTTG
40121754 TTTCTTTTTT
1 TTTCTTTTTT
40121764 TTTC-TTTTT
1 TTTCTTTTTT
40121773 TTTCTTTTTT
1 TTTCTTTTTT
40121783 TT
1 TT
40121785 AAGAATAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:40121773 original size:8 final size:9
Alignment explanation
Indices: 40121754--40121784 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
40121744 GTTGTTGTTG
40121754 TTTCTTTTTT
1 TTTC-TTTTT
40121764 TTTCTTTTT
1 TTTCTTTTT
40121773 TTTCTTTTT
1 TTTCTTTTT
40121782 TTT
1 TTT
40121785 AAGAATAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 17 0.81
10 4 0.19
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:40131896 original size:30 final size:30
Alignment explanation
Indices: 40131860--40131920 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
40131850 GTCCTTAATC
40131860 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
40131890 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
40131920 A
1 A
40131921 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:40138019 original size:40 final size:39
Alignment explanation
Indices: 40137954--40138085 Score: 126
Period size: 40 Copynumber: 3.4 Consensus size: 39
40137944 AGTTTGGCAC
*
40137954 CCAGTGCCTCATCGGATAATTCGAAGTAATAATTTGACA
1 CCAGTGCCTCATCGGATAATCCGAAGTAATAATTTGACA
* * * *
40137993 CCGAGTGTCTCATCGGCTAAACCGAAGT-A-AATTGGTAC-
1 CC-AGTGCCTCATCGGATAATCCGAAGTAATAATTTG-ACA
* * *
40138031 CCAGTGCCTCATCGAATTAATCCGAAGTAGTAAATTGACA
1 CCAGTGCCTCATCGGA-TAATCCGAAGTAATAATTTGACA
*
40138071 CCTAGTGTCTCATCG
1 CC-AGTGCCTCATCG
40138086 ACTCGAAGTT
Statistics
Matches: 73, Mismatches: 13, Indels: 12
0.74 0.13 0.12
Matches are distributed among these distances:
37 11 0.15
38 17 0.23
39 7 0.10
40 27 0.37
41 11 0.15
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (39 bp):
CCAGTGCCTCATCGGATAATCCGAAGTAATAATTTGACA
Found at i:40139914 original size:20 final size:20
Alignment explanation
Indices: 40139881--40139919 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
40139871 TTGTACAGGG
* *
40139881 TTAATAAATTTATTTAAAAT
1 TTAATAAATATATTGAAAAT
*
40139901 TTAATTAATATATTGAAAA
1 TTAATAAATATATTGAAAA
40139920 ACTAATGTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (20 bp):
TTAATAAATATATTGAAAAT
Found at i:40140407 original size:15 final size:16
Alignment explanation
Indices: 40140374--40140408 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
40140364 TAAGCTTAAT
*
40140374 AATTTAATAATTATTA
1 AATTTAATAATTATAA
40140390 AATTTAAT-ATTATAA
1 AATTTAATAATTATAA
40140405 AATT
1 AATT
40140409 AAAAGTTAAT
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):
AATTTAATAATTATAA
Found at i:40154957 original size:20 final size:20
Alignment explanation
Indices: 40154920--40154958 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
40154910 TTCAACCATA
* *
40154920 TATTTTTACATTCGTTTATT
1 TATTTTTAAATTCATTTATT
*
40154940 TATTTTTAAATTTATTTAT
1 TATTTTTAAATTCATTTAT
40154959 GGGAATTTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.67
Consensus pattern (20 bp):
TATTTTTAAATTCATTTATT
Found at i:40157908 original size:78 final size:78
Alignment explanation
Indices: 40157774--40157931 Score: 298
Period size: 78 Copynumber: 2.0 Consensus size: 78
40157764 CCCTCAAACG
40157774 TAAACACAAAATTCTCTGAATGTGTTATGAGTTCTAATCTAATGGGTGTCTATTTAATTCTAAGA
1 TAAACACAAAATTCTCTGAATGTGTTATGAGTTCTAATCTAATGGGTGTCTATTTAATTCTAAGA
40157839 TTGTAAAGGAGCC
66 TTGTAAAGGAGCC
* *
40157852 TAAATACAAAATTCTCTGAATGTGTTATGAGTTCTAATCTAATGGGTGTCTCTTTAATTCTAAGA
1 TAAACACAAAATTCTCTGAATGTGTTATGAGTTCTAATCTAATGGGTGTCTATTTAATTCTAAGA
40157917 TTGTAAAGGAGCC
66 TTGTAAAGGAGCC
40157930 TA
1 TA
40157932 TTTATAGGCT
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.37
Consensus pattern (78 bp):
TAAACACAAAATTCTCTGAATGTGTTATGAGTTCTAATCTAATGGGTGTCTATTTAATTCTAAGA
TTGTAAAGGAGCC
Found at i:40157982 original size:24 final size:24
Alignment explanation
Indices: 40157955--40158006 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
40157945 TTAGTAAGTC
*
40157955 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
40157979 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
40158003 AAAT
1 AAAT
40158007 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:40165041 original size:32 final size:32
Alignment explanation
Indices: 40165003--40165067 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
40164993 ATTAATCAAT
* *
40165003 ATGAGTTATCAAATTAAATTAATTAATTTATA
1 ATGAGTTATCAAATTAAAGTAATCAATTTATA
** *
40165035 ATGAGTTATTGAATTCAAGTAATCAATTTATA
1 ATGAGTTATCAAATTAAAGTAATCAATTTATA
40165067 A
1 A
40165068 GTTTATGATG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.42
Consensus pattern (32 bp):
ATGAGTTATCAAATTAAAGTAATCAATTTATA
Found at i:40165186 original size:32 final size:32
Alignment explanation
Indices: 40165148--40165212 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
40165138 ATTAATCAAT
* *
40165148 ATGAGTTATCAAATTAAATTAATTAATTTATA
1 ATGAGTTATCAAATTAAAGTAATCAATTTATA
** *
40165180 ATGAGTTATTGAATTCAAGTAATCAATTTATA
1 ATGAGTTATCAAATTAAAGTAATCAATTTATA
40165212 A
1 A
40165213 GTTTATGATG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.42
Consensus pattern (32 bp):
ATGAGTTATCAAATTAAAGTAATCAATTTATA
Found at i:40165239 original size:145 final size:145
Alignment explanation
Indices: 40164976--40165577 Score: 1132
Period size: 145 Copynumber: 4.2 Consensus size: 145
40164966 ATAAAGTTCA
* *
40164976 TAAATCTAACAAGCTCAATTAATCAATATGAGTTATCAAATTAAATTAATTAATTTATAATGAGT
1 TAAATCTAGCAGGCTCAATTAATCAATATGAGTTATCAAATTAAATTAATTAATTTATAATGAGT
40165041 TATTGAATTCAAGTAATCAATTTATAAGTTTATGATGTTCCGAATTCATAGTAGAATACATTCTT
66 TATTGAATTCAAGTAATCAATTTATAAGTTTATGATGTTCCGAATTCATAGTAGAATACATTCTT
40165106 ACACATGATTAATCC
131 ACACATGATTAATCC
40165121 TAAATCTAGCAGGCTCAATTAATCAATATGAGTTATCAAATTAAATTAATTAATTTATAATGAGT
1 TAAATCTAGCAGGCTCAATTAATCAATATGAGTTATCAAATTAAATTAATTAATTTATAATGAGT
40165186 TATTGAATTCAAGTAATCAATTTATAAGTTTATGATGTTCCGAATTCATAGTAGAATACATTCTT
66 TATTGAATTCAAGTAATCAATTTATAAGTTTATGATGTTCCGAATTCATAGTAGAATACATTCTT
40165251 ACACATGATTAATCC
131 ACACATGATTAATCC
40165266 TAAATCTAGCAGGCTCAATTAATCAATATGAGTTATCAAATTAAATTAATTAATTTATAATGAGT
1 TAAATCTAGCAGGCTCAATTAATCAATATGAGTTATCAAATTAAATTAATTAATTTATAATGAGT
* *
40165331 TATTGAATTCAAGTAATCAATTTATAAGTTTATAATGTTCCGAATCCATAGTAGAATACATTCTT
66 TATTGAATTCAAGTAATCAATTTATAAGTTTATGATGTTCCGAATTCATAGTAGAATACATTCTT
* *
40165396 ACACATGATCAATCA
131 ACACATGATTAATCC
* *
40165411 TAAATCTAACAGGCTCAATTAATCAGTATGAGTTATCAAATTAAATTAATTAATTTATAATGAGT
1 TAAATCTAGCAGGCTCAATTAATCAATATGAGTTATCAAATTAAATTAATTAATTTATAATGAGT
40165476 TATTGAATTCAAGTAATCAATTTATAAGTTTATGATGTTCCGAATTCATAGTAGAATACATTCTT
66 TATTGAATTCAAGTAATCAATTTATAAGTTTATGATGTTCCGAATTCATAGTAGAATACATTCTT
40165541 ACACATGATTAATCC
131 ACACATGATTAATCC
40165556 TAAATCTAGCAGGCTCAATTAA
1 TAAATCTAGCAGGCTCAATTAA
40165578 CCAAATTCAT
Statistics
Matches: 444, Mismatches: 13, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
145 444 1.00
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.37
Consensus pattern (145 bp):
TAAATCTAGCAGGCTCAATTAATCAATATGAGTTATCAAATTAAATTAATTAATTTATAATGAGT
TATTGAATTCAAGTAATCAATTTATAAGTTTATGATGTTCCGAATTCATAGTAGAATACATTCTT
ACACATGATTAATCC
Found at i:40165331 original size:32 final size:32
Alignment explanation
Indices: 40165293--40165357 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
40165283 ATTAATCAAT
* *
40165293 ATGAGTTATCAAATTAAATTAATTAATTTATA
1 ATGAGTTATCAAATTAAAGTAATCAATTTATA
** *
40165325 ATGAGTTATTGAATTCAAGTAATCAATTTATA
1 ATGAGTTATCAAATTAAAGTAATCAATTTATA
40165357 A
1 A
40165358 GTTTATAATG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.42
Consensus pattern (32 bp):
ATGAGTTATCAAATTAAAGTAATCAATTTATA
Found at i:40165476 original size:32 final size:32
Alignment explanation
Indices: 40165438--40165502 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
40165428 ATTAATCAGT
* *
40165438 ATGAGTTATCAAATTAAATTAATTAATTTATA
1 ATGAGTTATCAAATTAAAGTAATCAATTTATA
** *
40165470 ATGAGTTATTGAATTCAAGTAATCAATTTATA
1 ATGAGTTATCAAATTAAAGTAATCAATTTATA
40165502 A
1 A
40165503 GTTTATGATG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.42
Consensus pattern (32 bp):
ATGAGTTATCAAATTAAAGTAATCAATTTATA
Found at i:40170982 original size:49 final size:49
Alignment explanation
Indices: 40170913--40171041 Score: 145
Period size: 49 Copynumber: 2.6 Consensus size: 49
40170903 ATCAAAGTCG
* * * * *
40170913 ATGCCATGTCCTAGACAGGTCGTACACTGACTTTCATATATCGAG-G-CTG
1 ATGCCATGTCCCAGATAGGTCTTACACTGACTCTCATATATCG-GTGTC-A
* * * *
40170962 ATGTCGTGTCCCAGATAGGTCTTACACTGGCTCTCATCTATCGGTGTCA
1 ATGCCATGTCCCAGATAGGTCTTACACTGACTCTCATATATCGGTGTCA
40171011 ATGCCATGTCCCAGATAGGTCTTACACTGAC
1 ATGCCATGTCCCAGATAGGTCTTACACTGAC
40171042 ACACAATAAG
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
48 1 0.02
49 64 0.97
50 1 0.02
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.29
Consensus pattern (49 bp):
ATGCCATGTCCCAGATAGGTCTTACACTGACTCTCATATATCGGTGTCA
Found at i:40171125 original size:48 final size:46
Alignment explanation
Indices: 40171059--40171179 Score: 143
Period size: 46 Copynumber: 2.6 Consensus size: 46
40171049 AAGCTGACGC
* * ** *
40171059 CATGTCCCAAACAAGTCTTACACTAGCTTGTATATCTCGAGGCTGATG
1 CATGTCCCAGACATGTCTTACACTAGC-CCT-TATCTCAAGGCTGATG
* * * *
40171107 CATGTCCTAGACATGTCTTACACTGGCCCTTGTCTCAATGCTGATG
1 CATGTCCCAGACATGTCTTACACTAGCCCTTATCTCAAGGCTGATG
40171153 CATGTCCCAGACATGTCTTACACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
40171180 ACACATATCA
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
46 38 0.61
47 1 0.02
48 23 0.37
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.30
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTAGCCCTTATCTCAAGGCTGATG
Found at i:40174748 original size:29 final size:29
Alignment explanation
Indices: 40174695--40174965 Score: 165
Period size: 29 Copynumber: 9.4 Consensus size: 29
40174685 AAGGCGTATC
* *
40174695 GACGATCATCGATCAATGAAAAGGGATGGAT
1 GACGACCATCGA-CTATGAAAAGGGATGG-T
** *
40174726 -TTGACCATCGACTATGAAAAGGGATAGT
1 GACGACCATCGACTATGAAAAGGGATGGT
*** ** *
40174754 TTTGATTAT--ATTATGAAAAGGGATGGT
1 GACGACCATCGACTATGAAAAGGGATGGT
* **
40174781 GACAACCATCGTA-TATGAAAAGGGATAAT
1 GACGACCATCG-ACTATGAAAAGGGATGGT
*** * * *
40174810 TTTGACTATCAACTATGAAAAGGGATAGT
1 GACGACCATCGACTATGAAAAGGGATGGT
** * * * * * *
40174839 TTCGACTATCAAATATCAAAATGGATGAT
1 GACGACCATCGACTATGAAAAGGGATGGT
* *
40174868 GACGACCGTCAACTATG-AAAGGGATGGT
1 GACGACCATCGACTATGAAAAGGGATGGT
*
40174896 GACGACCATCGATTAATGAAAAGGGATGGT
1 GACGACCATCGACT-ATGAAAAGGGATGGT
* *
40174926 GACAACCATCGAATATGAAAAGGGATGGT
1 GACGACCATCGACTATGAAAAGGGATGGT
*
40174955 TACGACCATCG
1 GACGACCATCG
40174966 TTAGCACACT
Statistics
Matches: 188, Mismatches: 45, Indels: 16
0.76 0.18 0.06
Matches are distributed among these distances:
27 19 0.10
28 22 0.12
29 115 0.61
30 32 0.17
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.24
Consensus pattern (29 bp):
GACGACCATCGACTATGAAAAGGGATGGT
Found at i:40174921 original size:30 final size:29
Alignment explanation
Indices: 40174765--40174965 Score: 174
Period size: 29 Copynumber: 6.9 Consensus size: 29
40174755 TTGATTATAT
* *
40174765 TATGAAAAGGGATGGTGACAACCATCGTA
1 TATGAAAAGGGATGGTGACGACCATCGAA
** *** *
40174794 TATGAAAAGGGATAATTTTGACTATC-AA
1 TATGAAAAGGGATGGTGACGACCATCGAA
* ** * *
40174822 CTATGAAAAGGGATAGTTTCGACTATCAAA
1 -TATGAAAAGGGATGGTGACGACCATCGAA
* * * *
40174852 TATCAAAATGGATGATGACGACCGTC-AA
1 TATGAAAAGGGATGGTGACGACCATCGAA
*
40174880 CTATG-AAAGGGATGGTGACGACCATCGAT
1 -TATGAAAAGGGATGGTGACGACCATCGAA
*
40174909 TAATGAAAAGGGATGGTGACAACCATCGAA
1 T-ATGAAAAGGGATGGTGACGACCATCGAA
*
40174939 TATGAAAAGGGATGGTTACGACCATCG
1 TATGAAAAGGGATGGTGACGACCATCG
40174966 TTAGCACACT
Statistics
Matches: 139, Mismatches: 27, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
28 22 0.16
29 92 0.66
30 25 0.18
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.23
Consensus pattern (29 bp):
TATGAAAAGGGATGGTGACGACCATCGAA
Found at i:40185037 original size:29 final size:29
Alignment explanation
Indices: 40184995--40185262 Score: 214
Period size: 29 Copynumber: 9.2 Consensus size: 29
40184985 AGATGGATTT
* * * *
40184995 GACCATTGACTATGAAAATGGATAGTTTC
1 GACCATCGACTATGAAAAGGGATGGTTAC
* * **
40185024 GACTATCGATTATGAAAAGGGATGGCAAC
1 GACCATCGACTATGAAAAGGGATGGTTAC
* * * * *
40185053 GACCATCAACTATGAAAACGAATGGTGAT
1 GACCATCGACTATGAAAAGGGATGGTTAC
* * * **
40185082 GACCATCAACAATGAAAAGGAATGGTGCC
1 GACCATCGACTATGAAAAGGGATGGTTAC
* *
40185111 GACCATCGTA-TATGAAAAGGGATAGTTTC
1 GACCATCG-ACTATGAAAAGGGATGGTTAC
* * * * *
40185140 AACTATCGACTATGAAAAGGAATAGTTTC
1 GACCATCGACTATGAAAAGGGATGGTTAC
* * * * *
40185169 GACTATCAAATATGAAAAGGGATAGTGAC
1 GACCATCGACTATGAAAAGGGATGGTTAC
* *
40185198 GACCATCGATTAATGAAAAGGGATGGTGAC
1 GACCATCGACT-ATGAAAAGGGATGGTTAC
*
40185228 GACCATCGAATATGAAAAGGGATGGTTAC
1 GACCATCGACTATGAAAAGGGATGGTTAC
40185257 GACCAT
1 GACCAT
40185263 TGTTAGCACA
Statistics
Matches: 195, Mismatches: 41, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
28 1 0.01
29 166 0.85
30 28 0.14
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (29 bp):
GACCATCGACTATGAAAAGGGATGGTTAC
Found at i:40187129 original size:52 final size:49
Alignment explanation
Indices: 40186960--40187186 Score: 276
Period size: 49 Copynumber: 4.5 Consensus size: 49
40186950 ACTAGTGACT
*
40186960 CAAGTGTGGTACTATATGAAGGCCACTTTGAGAAGAGATAGCTTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGAGAAGAGATAGCTTGGTCA
*
40187009 CAATTGTGGTACTATGTGAAGGCCACTTTGAGAAGAGATAGCTTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGAGAAGAGATAGCTTGGTCA
**
40187058 CAAGCATGGTACTATGTGAAGGCCACTTGGTGAAGAA-AGATAGCTTTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTT--TG-AGAAGAGATAGC-TTGGTCA
* * * * *
40187110 CAAGTGTGGTATTATGTGAAGGCCACTTTGTGAAGAAGGTAGCTTTGACTA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGAGAAG-AGATAGCTTGGTC-A
* * * *
40187161 AAAGGGTGGTAATATGTGCAGGCCAC
1 CAAGTGTGGTACTATGTGAAGGCCAC
40187187 CGGGTACCCG
Statistics
Matches: 155, Mismatches: 16, Indels: 12
0.85 0.09 0.07
Matches are distributed among these distances:
49 75 0.48
50 6 0.04
51 38 0.25
52 36 0.23
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.27
Consensus pattern (49 bp):
CAAGTGTGGTACTATGTGAAGGCCACTTTGAGAAGAGATAGCTTGGTCA
Found at i:40187138 original size:101 final size:99
Alignment explanation
Indices: 40186966--40187154 Score: 283
Period size: 101 Copynumber: 1.9 Consensus size: 99
40186956 GACTCAAGTG
*
40186966 TGGTACTATATGAAGGCCACTTTGAGAAGAGATAGCTTGGTCACAATTGTGGTACTATGTGAAGG
1 TGGTACTATATGAAGGCCACTTTGAGAAGAGATAGCTTGGTCACAAGTGTGGTACTATGTGAAGG
40187031 CCACTTTGAGAAG-AGATAGCTTGGTCACAAGCA
66 CCACTTTGAGAAGAAGATAGCTTGGTCACAAGCA
* *
40187064 TGGTACTATGTGAAGGCCACTTGGTGAAGAA-AGATAGCTTTGGTCACAAGTGTGGTATTATGTG
1 TGGTACTATATGAAGGCCACTT--TG-AGAAGAGATAGC-TTGGTCACAAGTGTGGTACTATGTG
* *
40187128 AAGGCCACTTTGTGAAGAAGGTAGCTT
62 AAGGCCACTTTGAGAAGAAGATAGCTT
40187155 TGACTAAAAG
Statistics
Matches: 81, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
98 21 0.26
100 9 0.11
101 43 0.53
102 8 0.10
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (99 bp):
TGGTACTATATGAAGGCCACTTTGAGAAGAGATAGCTTGGTCACAAGTGTGGTACTATGTGAAGG
CCACTTTGAGAAGAAGATAGCTTGGTCACAAGCA
Found at i:40192232 original size:9 final size:10
Alignment explanation
Indices: 40192206--40192231 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
40192196 AAAAGTATTG
40192206 TTTTTTTAAA
1 TTTTTTTAAA
40192216 TTTTTTTAAA
1 TTTTTTTAAA
40192226 TTTTTT
1 TTTTTT
40192232 ATCAATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTTTTAAA
Found at i:40195625 original size:26 final size:24
Alignment explanation
Indices: 40195544--40195626 Score: 71
Period size: 24 Copynumber: 3.4 Consensus size: 24
40195534 AGCTGATGGA
* *
40195544 CAGTAAGCTCTAATGAGCTGAAA-
1 CAGTAAGCTCTTACGAGCTGAAAT
* * * *
40195567 CGGTAAACTCTGACGATCTGAAAAT
1 CAGTAAGCTCTTACGAGCTG-AAAT
40195592 -AGTAAGCTCTTACGAGCTGATATAT
1 CAGTAAGCTCTTACGAGCTGA-A-AT
40195617 CAGTAAGCTC
1 CAGTAAGCTC
40195627 ACACAAGCTG
Statistics
Matches: 46, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
23 16 0.35
24 19 0.41
25 2 0.04
26 9 0.20
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.25
Consensus pattern (24 bp):
CAGTAAGCTCTTACGAGCTGAAAT
Found at i:40204205 original size:16 final size:16
Alignment explanation
Indices: 40204184--40204230 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
40204174 CCTAATTTTT
40204184 TTATTTAAATTAAATA
1 TTATTTAAATTAAATA
**
40204200 TTATTTTTATATAAATA
1 TTATTTAAAT-TAAATA
40204217 TT-TTTATAATTAAA
1 TTATTTA-AATTAAA
40204231 ATATATAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTATTTAAATTAAATA
Found at i:40204232 original size:17 final size:17
Alignment explanation
Indices: 40204187--40204234 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 17
40204177 AATTTTTTTA
40204187 TTTA-AATTAAATATTATT
1 TTTATAATTAAA-A-TATT
40204205 TTTAT-A-T-AAATATT
1 TTTATAATTAAAATATT
40204219 TTTATAATTAAAATAT
1 TTTATAATTAAAATAT
40204235 ATAAAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
14 9 0.35
15 2 0.08
16 3 0.12
17 7 0.27
18 5 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTATAATTAAAATATT
Found at i:40205987 original size:37 final size:36
Alignment explanation
Indices: 40205946--40206020 Score: 132
Period size: 37 Copynumber: 2.1 Consensus size: 36
40205936 GAACTTGAAA
40205946 AATTTTCGTCCCATAAGTCTGTGTACGATGATTTTAT
1 AATTTTCGTCCCATAAGTCTGTGTACGATGA-TTTAT
*
40205983 AATTTTCGTCCCATAAGTCTGTGTACGGTGATTTAT
1 AATTTTCGTCCCATAAGTCTGTGTACGATGATTTAT
40206019 AA
1 AA
40206021 AATCATCGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 7 0.19
37 30 0.81
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.41
Consensus pattern (36 bp):
AATTTTCGTCCCATAAGTCTGTGTACGATGATTTAT
Found at i:40209922 original size:5 final size:5
Alignment explanation
Indices: 40209912--40209938 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
40209902 AAGAAAATAT
40209912 TATTA TATTA TATTA TATTA TATTA TA
1 TATTA TATTA TATTA TATTA TATTA TA
40209939 AAATAAATAA
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:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATTA
Found at i:40210911 original size:16 final size:15
Alignment explanation
Indices: 40210860--40210912 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
40210850 GTTATATACT
40210860 CATGAATTGAGTATGG
1 CATGAATTGAGTAT-G
* * *
40210876 TATGAAATGATGTATT
1 CATGAATTGA-GTATG
40210892 CATGAATTGAGTACTG
1 CATGAATTGAGTA-TG
40210908 CATGA
1 CATGA
40210913 CTGATGCCAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 3 0.10
16 22 0.76
17 4 0.14
ACGTcount: A:0.34, C:0.08, G:0.25, T:0.34
Consensus pattern (15 bp):
CATGAATTGAGTATG
Found at i:40218102 original size:5 final size:5
Alignment explanation
Indices: 40218092--40218123 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
40218082 ATGAAAATAT
40218092 TATTA TATTA TATTA TATTA TATTA TATTA TA
1 TATTA TATTA TATTA TATTA TATTA TATTA TA
40218124 ATTAAAGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATTA
Found at i:40218359 original size:13 final size:13
Alignment explanation
Indices: 40218341--40218382 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
40218331 AAACAAGGGG
40218341 AAAGAAAGAAGAA
1 AAAGAAAGAAGAA
40218354 AAAGAAAGAAAGAA
1 AAAGAAAG-AAGAA
* *
40218368 AAAAAAAGGAGAA
1 AAAGAAAGAAGAA
40218381 AA
1 AA
40218383 TTTAGGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 14 0.54
14 12 0.46
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAGAA
Found at i:40218381 original size:17 final size:17
Alignment explanation
Indices: 40218340--40218372 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
40218330 GAAACAAGGG
40218340 GAAAGAAAGAAGAAAAA
1 GAAAGAAAGAAGAAAAA
40218357 GAAAGAAAGAA-AAAAA
1 GAAAGAAAGAAGAAAAA
40218373 AAGGAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
GAAAGAAAGAAGAAAAA
Found at i:40226548 original size:42 final size:42
Alignment explanation
Indices: 40226489--40226685 Score: 216
Period size: 42 Copynumber: 4.7 Consensus size: 42
40226479 TCGAAATCTT
* * * *
40226489 AACAGAATCTTATAAGAGCTAAACAGAAACCCATAAGGGTTG
1 AACAGAAGCTCATAAGAGCTAAACAGAAACTCATAAGAGTTG
* * * * *
40226531 AATAGAAGCTCATAAGAGCTGAAA-AAAAACTCGTATGAGTTA
1 AACAGAAGCTCATAAGAGCT-AAACAGAAACTCATAAGAGTTG
*
40226573 AACAGAAGCTCATAAGAGCTGAACAGAAACTCATAAGAGTTG
1 AACAGAAGCTCATAAGAGCTAAACAGAAACTCATAAGAGTTG
* ** *
40226615 AACAGAAGCTCATAAGAGCTGAACAGAAACTCATATCAGTTA
1 AACAGAAGCTCATAAGAGCTAAACAGAAACTCATAAGAGTTG
* * * *
40226657 AACAGAAGTTCGTAAGAGTTAAACGGAAA
1 AACAGAAGCTCATAAGAGCTAAACAGAAA
40226686 GAAAAACACG
Statistics
Matches: 130, Mismatches: 23, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
41 2 0.02
42 125 0.96
43 3 0.02
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.19
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTAAACAGAAACTCATAAGAGTTG
Found at i:40226630 original size:84 final size:84
Alignment explanation
Indices: 40226489--40226685 Score: 268
Period size: 84 Copynumber: 2.3 Consensus size: 84
40226479 TCGAAATCTT
* * * *
40226489 AACAGAATCTTATAAGAGCTAAACAGAAACCCATAAGGGTTGAATAGAAGCTCATAAGAGCTGAA
1 AACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGAGTTGAACAGAAGCTCATAAGAGCTGAA
* *
40226554 AAAAAACTCGTATGAGTTA
66 AAAAAACTCATATCAGTTA
* *
40226573 AACAGAAGCTCATAAGAGCTGAACAGAAACTCATAAGAGTTGAACAGAAGCTCATAAGAGCTGAA
1 AACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGAGTTGAACAGAAGCTCATAAGAGCTGAA
* *
40226638 CAGAAACTCATATCAGTTA
66 AAAAAACTCATATCAGTTA
* * * *
40226657 AACAGAAGTTCGTAAGAGTTAAACGGAAA
1 AACAGAAGCTCATAAGAGCTAAACAGAAA
40226686 GAAAAACACG
Statistics
Matches: 98, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
84 98 1.00
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.19
Consensus pattern (84 bp):
AACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGAGTTGAACAGAAGCTCATAAGAGCTGAA
AAAAAACTCATATCAGTTA
Found at i:40226660 original size:21 final size:21
Alignment explanation
Indices: 40226489--40226663 Score: 161
Period size: 21 Copynumber: 8.3 Consensus size: 21
40226479 TCGAAATCTT
* * * *
40226489 AACAGAATCTTATAAGAGCTA
1 AACAGAAACTCATAAGAGTTG
* *
40226510 AACAGAAACCCATAAGGGTTG
1 AACAGAAACTCATAAGAGTTG
* * *
40226531 AATAGAAGCTCATAAGAGCTG
1 AACAGAAACTCATAAGAGTTG
* * * * *
40226552 AAAAAAAACTCGTATGAGTTA
1 AACAGAAACTCATAAGAGTTG
* *
40226573 AACAGAAGCTCATAAGAGCTG
1 AACAGAAACTCATAAGAGTTG
40226594 AACAGAAACTCATAAGAGTTG
1 AACAGAAACTCATAAGAGTTG
* *
40226615 AACAGAAGCTCATAAGAGCTG
1 AACAGAAACTCATAAGAGTTG
** *
40226636 AACAGAAACTCATATCAGTTA
1 AACAGAAACTCATAAGAGTTG
40226657 AACAGAA
1 AACAGAA
40226664 GTTCGTAAGA
Statistics
Matches: 120, Mismatches: 34, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 120 1.00
ACGTcount: A:0.47, C:0.16, G:0.19, T:0.18
Consensus pattern (21 bp):
AACAGAAACTCATAAGAGTTG
Found at i:40232780 original size:21 final size:21
Alignment explanation
Indices: 40232704--40232782 Score: 63
Period size: 21 Copynumber: 3.9 Consensus size: 21
40232694 GTAAATCGTT
40232704 AACAGAAGCTTG-AA-AGTTG
1 AACAGAAGCTTGTAAGAGTTG
* * * *
40232723 AACAGAAGCTCGTGAGAGCTA
1 AACAGAAGCTTGTAAGAGTTG
* * * * *
40232744 AATAGAAACCTATAAGGGTTG
1 AACAGAAGCTTGTAAGAGTTG
40232765 AACAGAAGCTTGTAAGAG
1 AACAGAAGCTTGTAAGAG
40232783 CTAAAAAAAT
Statistics
Matches: 40, Mismatches: 18, Indels: 2
0.67 0.30 0.03
Matches are distributed among these distances:
19 11 0.28
20 1 0.03
21 28 0.70
ACGTcount: A:0.42, C:0.13, G:0.27, T:0.19
Consensus pattern (21 bp):
AACAGAAGCTTGTAAGAGTTG
Found at i:40232831 original size:21 final size:21
Alignment explanation
Indices: 40232721--40232907 Score: 71
Period size: 21 Copynumber: 9.0 Consensus size: 21
40232711 GCTTGAAAGT
* *
40232721 TGAACAGAAGCTCGTGAGAGC
1 TGAACAGAAGCTCATAAGAGC
* * * * *
40232742 TAAATAGAAAC-CTATAAGGGT
1 TGAACAGAAGCTC-ATAAGAGC
**
40232763 TGAACAGAAGCTTGTAAGAGC
1 TGAACAGAAGCTCATAAGAGC
** * *
40232784 T-AA-A-AAAATCATATGAGT
1 TGAACAGAAGCTCATAAGAGC
* *
40232802 TAAATAGAAGCTCATAAGAGC
1 TGAACAGAAGCTCATAAGAGC
* **
40232823 TGAACAGAAACTCATAAGATT
1 TGAACAGAAGCTCATAAGAGC
* *
40232844 TGAACAGAAGCTTGA-AAAAGC
1 TGAACAGAAGC-TCATAAGAGC
* * *
40232865 TGAAC-GAAAACTCATATGAGT
1 TGAACAG-AAGCTCATAAGAGC
* * *
40232886 TAAACAAAAGCTCGTAAGAGC
1 TGAACAGAAGCTCATAAGAGC
40232907 T
1 T
40232908 AAACGAAAAG
Statistics
Matches: 112, Mismatches: 45, Indels: 18
0.64 0.26 0.10
Matches are distributed among these distances:
18 9 0.08
19 3 0.03
20 7 0.06
21 91 0.81
22 2 0.02
ACGTcount: A:0.45, C:0.14, G:0.21, T:0.20
Consensus pattern (21 bp):
TGAACAGAAGCTCATAAGAGC
Found at i:40232916 original size:42 final size:42
Alignment explanation
Indices: 40232718--40232916 Score: 183
Period size: 42 Copynumber: 4.8 Consensus size: 42
40232708 GAAGCTTGAA
* * *
40232718 AGTTGAACAGAAGCTCGTGAGAGCTAAATAGAAACCT-ATAAG
1 AGTTGAACAGAAGCTCGTAAGAGCTAAA-CGAAAACTCATAAG
* * *
40232760 GGTTGAACAGAAGCTTGTAAGAGCTAAA--AAAA-TCATATG
1 AGTTGAACAGAAGCTCGTAAGAGCTAAACGAAAACTCATAAG
* * * *
40232799 AGTTAAATAGAAGCTCATAAGAGCTGAAC-AGAAACTCATAAG
1 AGTTGAACAGAAGCTCGTAAGAGCTAAACGA-AAACTCATAAG
* * * * * *
40232841 ATTTGAACAGAAGCTTGAAAAAGCTGAACGAAAACTCATATG
1 AGTTGAACAGAAGCTCGTAAGAGCTAAACGAAAACTCATAAG
* *
40232883 AGTTAAACAAAAGCTCGTAAGAGCTAAACGAAAA
1 AGTTGAACAGAAGCTCGTAAGAGCTAAACGAAAA
40232917 GTAAAACACG
Statistics
Matches: 125, Mismatches: 27, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
38 1 0.01
39 29 0.23
40 1 0.01
41 3 0.02
42 90 0.72
43 1 0.01
ACGTcount: A:0.46, C:0.14, G:0.21, T:0.20
Consensus pattern (42 bp):
AGTTGAACAGAAGCTCGTAAGAGCTAAACGAAAACTCATAAG
Found at i:40234644 original size:53 final size:53
Alignment explanation
Indices: 40234554--40234761 Score: 276
Period size: 53 Copynumber: 3.9 Consensus size: 53
40234544 TCCTTAGATT
*
40234554 TTCCCATATGATGCCATAACCCACCAATTATGATCTTACACGATATGGTCTTC
1 TTCCCATATGATGCCATAACCCACCAATTACGATCTTACACGATATGGTCTTC
* * *
40234607 TTCCTATATGATGCCATAACCCA-CAAGTTACGGTCTTACACGTTATGGTCTTC
1 TTCCCATATGATGCCATAACCCACCAA-TTACGATCTTACACGATATGGTCTTC
* * * * *
40234660 TTCCCATATAATGTCATAACCCACCAATTACGGTCTTACACAATATGGTCTTT
1 TTCCCATATGATGCCATAACCCACCAATTACGATCTTACACGATATGGTCTTC
* * * *
40234713 TTTCCATATTAT-CCACAACCCACCAGTTACGATCTTACACGATATGGTC
1 TTCCCATATGATGCCATAACCCACCAATTACGATCTTACACGATATGGTC
40234762 CTTTAATGTT
Statistics
Matches: 136, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
52 35 0.26
53 98 0.72
54 3 0.02
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.33
Consensus pattern (53 bp):
TTCCCATATGATGCCATAACCCACCAATTACGATCTTACACGATATGGTCTTC
Found at i:40235712 original size:17 final size:16
Alignment explanation
Indices: 40235692--40235755 Score: 53
Period size: 17 Copynumber: 4.0 Consensus size: 16
40235682 TATATATTTA
40235692 TAATAAATATATAAAAT
1 TAATAAATAT-TAAAAT
*
40235709 TAATAATTATTAAAA-
1 TAATAAATATTAAAAT
* *
40235724 T-ATAAAAATTAAATT
1 TAATAAATATTAAAAT
40235739 TAATGATAATA-TAAAAT
1 TAAT-A-AATATTAAAAT
40235756 ATAGAATGAC
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
14 10 0.27
15 2 0.05
16 7 0.19
17 15 0.41
18 3 0.08
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (16 bp):
TAATAAATATTAAAAT
Found at i:40235931 original size:32 final size:32
Alignment explanation
Indices: 40235895--40235960 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
40235885 AGTTTCTCTC
40235895 TTTTTTATGATTTGGGAATGTAGGTTTTACTT
1 TTTTTTATGATTTGGGAATGTAGGTTTTACTT
* * *
40235927 TTTTTTATGATTTGGTAATTTATGTTTTACTT
1 TTTTTTATGATTTGGGAATGTAGGTTTTACTT
40235959 TT
1 TT
40235961 AAATTTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.18, C:0.03, G:0.17, T:0.62
Consensus pattern (32 bp):
TTTTTTATGATTTGGGAATGTAGGTTTTACTT
Found at i:40238208 original size:17 final size:19
Alignment explanation
Indices: 40238166--40238209 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
40238156 ACGAAATTTT
*
40238166 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
40238185 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
40238203 AA-TATTA
1 AATTATTA
40238210 CTGCATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:40247361 original size:15 final size:13
Alignment explanation
Indices: 40247341--40247385 Score: 54
Period size: 15 Copynumber: 3.2 Consensus size: 13
40247331 GTTCTTGTTG
40247341 TTTTTACTTTCTTTA
1 TTTTTAC-TT-TTTA
40247356 TTTTTACTTTTTA
1 TTTTTACTTTTTA
40247369 TTTTTAGCATTTTTA
1 TTTTTA-C-TTTTTA
40247384 TT
1 TT
40247386 GTCATTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 10 0.36
14 3 0.11
15 15 0.54
ACGTcount: A:0.16, C:0.09, G:0.02, T:0.73
Consensus pattern (13 bp):
TTTTTACTTTTTA
Found at i:40250005 original size:136 final size:136
Alignment explanation
Indices: 40249761--40250031 Score: 461
Period size: 136 Copynumber: 2.0 Consensus size: 136
40249751 AATATAGAAC
* *
40249761 TCCTTTGCTTTCTATATTTCTTTTATATGAAAATAGACTCATTAAGATTTAATTTGATATCTCAT
1 TCCTTTGCTTGCTATATTTCTTTTATATGAAAATAGACTCATTAAGATTTAATTTGATACCTCAT
* * *
40249826 TCAGTCTCTGATTCAATTTATACTATTTTTGGTGATTTTTCAAAATCACGTCACTGCTACTGTCC
66 TAAGTCTCTGATTCAATTTATACTATTTTTGGTGATTTTTCAAAATCACATCACTGATACTGTCC
40249891 AAAACT
131 AAAACT
* *
40249897 TCCTTTTCTTGCTATGTTTCTTTTATATGAAAATAGACTCATTAAGATTTAATTTGATACCTCAT
1 TCCTTTGCTTGCTATATTTCTTTTATATGAAAATAGACTCATTAAGATTTAATTTGATACCTCAT
* *
40249962 TAAGTCTCTGATTCAATTTCTACTATTTTTTGTGATTTTTCAAAATCACATCACTGATACTGTCC
66 TAAGTCTCTGATTCAATTTATACTATTTTTGGTGATTTTTCAAAATCACATCACTGATACTGTCC
40250027 AAAAC
131 AAAAC
40250032 AGTTTTATTG
Statistics
Matches: 126, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
136 126 1.00
ACGTcount: A:0.28, C:0.18, G:0.09, T:0.45
Consensus pattern (136 bp):
TCCTTTGCTTGCTATATTTCTTTTATATGAAAATAGACTCATTAAGATTTAATTTGATACCTCAT
TAAGTCTCTGATTCAATTTATACTATTTTTGGTGATTTTTCAAAATCACATCACTGATACTGTCC
AAAACT
Found at i:40251204 original size:30 final size:30
Alignment explanation
Indices: 40251170--40251230 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
40251160 TCCTTAACTC
40251170 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
40251200 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
40251230 A
1 A
40251231 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:40254001 original size:25 final size:25
Alignment explanation
Indices: 40253967--40254014 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
40253957 TAAACAAGTT
40253967 AGATAGATATCACTCTTAATTTGTA
1 AGATAGATATCACTCTTAATTTGTA
*
40253992 AGATAGATATGACTCTTAATTTG
1 AGATAGATATCACTCTTAATTTG
40254015 AGTGTGAGGT
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:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (25 bp):
AGATAGATATCACTCTTAATTTGTA
Found at i:40256961 original size:16 final size:17
Alignment explanation
Indices: 40256931--40256963 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
40256921 TTCATAAGTA
40256931 TATATCAATTATTTCAT
1 TATATCAATTATTTCAT
40256948 TATATCAA-TATTTCAT
1 TATATCAATTATTTCAT
40256964 GCTCCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (17 bp):
TATATCAATTATTTCAT
Found at i:40257310 original size:46 final size:46
Alignment explanation
Indices: 40257250--40257517 Score: 288
Period size: 46 Copynumber: 5.8 Consensus size: 46
40257240 TTTGACATGA
* * * ** *
40257250 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTTTGTTAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTTATGT
* ** *
40257296 TGCCATGGTATCTTTCGACCATGGTCTTGTTCATTTCATGTTATAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTTATGT
* ** *
40257342 TGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTCCCGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTTATGT
* * * * * *
40257387 TGCCATTGTATCTTTCAACCATGGTCTTACACATTTTATATTCTAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTTATGT
* *
40257433 TGCCATGGTATCTTTCAACCATGGTCTTA-TACATTTCATATCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACT-CATTTCATGTTATGT
* * *
40257479 TGCCATGGTGTCGTTCAACCATGGTCTTACACATTTCAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCAT
40257518 ATCATGTTTT
Statistics
Matches: 184, Mismatches: 35, Indels: 6
0.82 0.16 0.03
Matches are distributed among these distances:
45 38 0.21
46 146 0.79
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.43
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTTATGT
Found at i:40257409 original size:91 final size:92
Alignment explanation
Indices: 40257294--40257519 Score: 319
Period size: 91 Copynumber: 2.5 Consensus size: 92
40257284 TTTTTGTTAG
* *** *
40257294 GTTGCCATGGTATCTTTCGACCATGGTCTTGTTCATTTCATGTTATATTGCCATGGTATCTTTCA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATTATATTGCCATGGTATCTTTCA
* * *
40257359 ACCATGGTCTTATTCA-TTCCCGTCAT
66 ACCATGGTCTTATACATTTCACATCAT
* * *
40257385 GTTGCCATTGTATCTTTCAACCATGGTCTTACACATTTTATATTCTATTGCCATGGTATCTTTCA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATTATATTGCCATGGTATCTTTCA
*
40257450 ACCATGGTCTTATACATTTCATATCAT
66 ACCATGGTCTTATACATTTCACATCAT
* *
40257477 GTTGCCATGGTGTCGTTCAACCATGGTCTTACACATTTCATAT
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
40257520 CATGTTTTCA
Statistics
Matches: 118, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
91 72 0.61
92 46 0.39
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.42
Consensus pattern (92 bp):
GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATTATATTGCCATGGTATCTTTCA
ACCATGGTCTTATACATTTCACATCAT
Found at i:40257482 original size:137 final size:137
Alignment explanation
Indices: 40257245--40257507 Score: 364
Period size: 137 Copynumber: 1.9 Consensus size: 137
40257235 TTATCTTTGA
* * * * * *
40257245 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTTTGTTAGGTTGCCATGGTATCTT
1 CATGATGCCATAGTATCTTTCAACCATGGTCTTACACATTTTATATTAGATTGCCATGGTATCTT
* * * * * *
40257310 TCGACCATGGTCTTGTTCATTTCATGTTATATTGCCATGGTATCTTTCAACCATGGTCTTATTCA
66 TCAACCATGGTCTTATACATTTCATATCATATTGCCATGGTATCGTTCAACCATGGTCTTATTCA
40257375 TTCCCGT
131 TTCCCGT
* * **
40257382 CATGTTGCCATTGTATCTTTCAACCATGGTCTTACACATTTTATATTCTATTGCCATGGTATCTT
1 CATGATGCCATAGTATCTTTCAACCATGGTCTTACACATTTTATATTAGATTGCCATGGTATCTT
* *
40257447 TCAACCATGGTCTTATACATTTCATATCATGTTGCCATGGTGTCGTTCAACCATGGTCTTA
66 TCAACCATGGTCTTATACATTTCATATCATATTGCCATGGTATCGTTCAACCATGGTCTTA
40257508 CACATTTCAT
Statistics
Matches: 108, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
137 108 1.00
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.43
Consensus pattern (137 bp):
CATGATGCCATAGTATCTTTCAACCATGGTCTTACACATTTTATATTAGATTGCCATGGTATCTT
TCAACCATGGTCTTATACATTTCATATCATATTGCCATGGTATCGTTCAACCATGGTCTTATTCA
TTCCCGT
Found at i:40269184 original size:18 final size:18
Alignment explanation
Indices: 40269142--40269184 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
40269132 GCCCATTCCG
* *
40269142 AAGTATATATATATACAT
1 AAGTATGTATATATACAC
40269160 ATA-TATGTATATATACAC
1 A-AGTATGTATATATACAC
40269178 AAGTATG
1 AAGTATG
40269185 CCCATTCGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 1 0.05
18 19 0.90
19 1 0.05
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (18 bp):
AAGTATGTATATATACAC
Found at i:40269712 original size:28 final size:27
Alignment explanation
Indices: 40269654--40269763 Score: 143
Period size: 27 Copynumber: 4.0 Consensus size: 27
40269644 TAAATTGTGC
* * *
40269654 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAGTTGATTATAT
40269681 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAG-TTGATTATAT
40269709 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGATTATAT
*
40269736 AGCACTGAA-TGTGCGGACTT-ATTATAT
1 AGCACT-AAGTGTGC-GAGTTGATTATAT
40269763 A
1 A
40269764 TTTTTGAAAC
Statistics
Matches: 76, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
27 45 0.59
28 31 0.41
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGATTATAT
Found at i:40276420 original size:7 final size:7
Alignment explanation
Indices: 40276408--40276433 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
40276398 TATATATGCA
40276408 AATGTCG
1 AATGTCG
40276415 AATGTCG
1 AATGTCG
40276422 AATGTCG
1 AATGTCG
40276429 AATGT
1 AATGT
40276434 ATACAAGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.31
Consensus pattern (7 bp):
AATGTCG
Found at i:40286101 original size:62 final size:62
Alignment explanation
Indices: 40286024--40286147 Score: 212
Period size: 62 Copynumber: 2.0 Consensus size: 62
40286014 AACCACCTAA
* *
40286024 GAAATGGACAGCCCAAAACCGTCCCAAGAGCTGACCCAAATCAGCTTATTAATTGATTATTT
1 GAAATGAACAGCCCAAAACCGTCCCAAGAGCTGACCCAAATCAGCTTATTAACTGATTATTT
* *
40286086 GAAATGAACAGCCCAAAACCGTCCCAAGAGCTTACCCAAATCAGCTTATTAGCTGATTATTT
1 GAAATGAACAGCCCAAAACCGTCCCAAGAGCTGACCCAAATCAGCTTATTAACTGATTATTT
40286148 AAGCTTGTAA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.24
Consensus pattern (62 bp):
GAAATGAACAGCCCAAAACCGTCCCAAGAGCTGACCCAAATCAGCTTATTAACTGATTATTT
Found at i:40294158 original size:48 final size:48
Alignment explanation
Indices: 40294092--40294231 Score: 219
Period size: 48 Copynumber: 2.9 Consensus size: 48
40294082 GTTATGTGTA
* * *
40294092 ATCCCATGTAAGATCATGTTTGGGACATGGCATTGGCATCGATATGTG
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATATGTG
40294140 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATATGTG
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATATGTG
* * *
40294188 ATCCCATGTAAGACCATATCT-GGATATGGCATTGGCATCTATAT
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATAT
40294232 CAGACATCGT
Statistics
Matches: 86, Mismatches: 6, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
47 21 0.24
48 65 0.76
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (48 bp):
ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATATGTG
Found at i:40295353 original size:30 final size:30
Alignment explanation
Indices: 40295313--40295371 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
40295303 TAAGCACAGG
* *
40295313 GGCGTATGTCTAAACCGTGTGTGACACACA
1 GGCGTATGTCTAAACCATGTGTCACACACA
* *
40295343 GGCGTGTGTCTAGACCATGTGTCACACAC
1 GGCGTATGTCTAAACCATGTGTCACACAC
40295372 GGTCTGTACC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.24, C:0.25, G:0.27, T:0.24
Consensus pattern (30 bp):
GGCGTATGTCTAAACCATGTGTCACACACA
Found at i:40297923 original size:20 final size:20
Alignment explanation
Indices: 40297893--40297937 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
40297883 CTGTTTTGTT
40297893 ATGGG-CCAACTATATTAAA
1 ATGGGCCCAACTATATTAAA
* *
40297912 ATGGGCCCAACTATGTTAAT
1 ATGGGCCCAACTATATTAAA
40297932 ATGGGC
1 ATGGGC
40297938 AAGGCCTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (20 bp):
ATGGGCCCAACTATATTAAA
Found at i:40298003 original size:60 final size:60
Alignment explanation
Indices: 40297928--40298042 Score: 135
Period size: 60 Copynumber: 1.9 Consensus size: 60
40297918 CCAACTATGT
* *
40297928 TAATATGGGCAAGGCCTAATATA-TCTCA-ACTTGTAATAGGGCTATGGCCCAGATTGATAC
1 TAATATAGGCAAGGCCCAATATACTCTCATA-TTGTAA-AGGGCTATGGCCCAGATTGATAC
* * * * *
40297988 TAATATAGGCTAGGCCCAGTATACTCTGATATTGTAAGGGGCTATGGCCTAGATT
1 TAATATAGGCAAGGCCCAATATACTCTCATATTGTAAAGGGCTATGGCCCAGATT
40298043 AATATTGATG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
60 35 0.76
61 10 0.22
62 1 0.02
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (60 bp):
TAATATAGGCAAGGCCCAATATACTCTCATATTGTAAAGGGCTATGGCCCAGATTGATAC
Found at i:40303750 original size:16 final size:16
Alignment explanation
Indices: 40303726--40303759 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
40303716 GCAATGTAGC
*
40303726 TATGATATGAATGATA
1 TATGATATGAAAGATA
*
40303742 TATGCTATGAAAGATA
1 TATGATATGAAAGATA
40303758 TA
1 TA
40303760 CATATTTAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.03, G:0.18, T:0.35
Consensus pattern (16 bp):
TATGATATGAAAGATA
Found at i:40305217 original size:21 final size:22
Alignment explanation
Indices: 40305175--40305222 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
40305165 TTAATTGATG
*
40305175 TTTATGTCATTATTGTTATTTTA
1 TTTATGT-ATTATAGTTATTTTA
* *
40305198 TTTATGT-TTATAGTTTTTTTT
1 TTTATGTATTATAGTTATTTTA
40305219 TTTA
1 TTTA
40305223 GACAATTCAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 15 0.68
23 7 0.32
ACGTcount: A:0.19, C:0.02, G:0.08, T:0.71
Consensus pattern (22 bp):
TTTATGTATTATAGTTATTTTA
Found at i:40306412 original size:20 final size:20
Alignment explanation
Indices: 40306387--40306437 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
40306377 CTTAATAAAG
*
40306387 ACACATACACATACATGCAC
1 ACACATACACATACACGCAC
* *
40306407 ACACATACACGTGCACGCAC
1 ACACATACACATACACGCAC
*
40306427 ACACACACACA
1 ACACATACACA
40306438 CAGAGACACA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.43, C:0.39, G:0.08, T:0.10
Consensus pattern (20 bp):
ACACATACACATACACGCAC
Found at i:40311234 original size:23 final size:23
Alignment explanation
Indices: 40311207--40311261 Score: 56
Period size: 26 Copynumber: 2.3 Consensus size: 23
40311197 GTTGTAGATG
*
40311207 CTTAGAAGTTGTTAGATAGGACT
1 CTTAGAAGTTGCTAGATAGGACT
*
40311230 CTTAGGAGAAGTTGCTAGGTAGGACT
1 CTT---AGAAGTTGCTAGATAGGACT
*
40311256 CCTAGA
1 CTTAGA
40311262 GTAAAATAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
23 6 0.23
26 20 0.77
ACGTcount: A:0.29, C:0.13, G:0.29, T:0.29
Consensus pattern (23 bp):
CTTAGAAGTTGCTAGATAGGACT
Found at i:40323088 original size:116 final size:117
Alignment explanation
Indices: 40322884--40323120 Score: 458
Period size: 116 Copynumber: 2.0 Consensus size: 117
40322874 CTATACATAT
*
40322884 AAATTTAAGTCCCTAATTATTTTTATTCAATTTTTTATAATTTTTCATAGTCAGAACAGGGGAAC
1 AAATTTAAGTCCCTAATTATTTTTATTCAATTTTTTATAATTTTTCAAAGTCAGAACAGGGGAAC
40322949 CCGAATTCATTCTGACCTTGTCTCACAAAATTCATTATATATCAAAATTTA-
66 CCGAATTCATTCTGACCTTGTCTCACAAAATTCATTATATATCAAAATTTAC
40323000 AAATTTAAGTCCCTAATTATTTTTATTCAATTTTTTATAATTTTTCAAAGTCAGAACAGGGGAAC
1 AAATTTAAGTCCCTAATTATTTTTATTCAATTTTTTATAATTTTTCAAAGTCAGAACAGGGGAAC
40323065 CCGAATTCATTCTGACCTTGTCTCACAAAATTCATTATATATCAAAATTTAC
66 CCGAATTCATTCTGACCTTGTCTCACAAAATTCATTATATATCAAAATTTAC
40323117 AAAT
1 AAAT
40323121 CCATTGCTTA
Statistics
Matches: 119, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
116 115 0.97
117 4 0.03
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.40
Consensus pattern (117 bp):
AAATTTAAGTCCCTAATTATTTTTATTCAATTTTTTATAATTTTTCAAAGTCAGAACAGGGGAAC
CCGAATTCATTCTGACCTTGTCTCACAAAATTCATTATATATCAAAATTTAC
Found at i:40330617 original size:17 final size:17
Alignment explanation
Indices: 40330595--40330629 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
40330585 ACTTTTTTTA
40330595 TATTTTTAATAAA-ATTT
1 TATTTTTAA-AAAGATTT
40330612 TATTTTTAAAAAGATTT
1 TATTTTTAAAAAGATTT
40330629 T
1 T
40330630 TCATAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.18
17 14 0.82
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
TATTTTTAAAAAGATTT
Found at i:40331190 original size:30 final size:29
Alignment explanation
Indices: 40331131--40331249 Score: 109
Period size: 30 Copynumber: 4.0 Consensus size: 29
40331121 ATTGAATAAC
* *
40331131 AAAATAAAATCTTTTAATATAATTTAATAT
1 AAAATAAAATATTTTAA-ATATTTTAATAT
** *
40331161 AAAATATTAT-TTTTAAATTTTATTAAATAT
1 AAAATAAAATATTTTAAATATT-TT-AATAT
40331191 AAAAATAAAATATTTTAAATATTTTAATAT
1 -AAAATAAAATATTTTAAATATTTTAATAT
**
40331221 AAAAGTAAAA-A-TAAAAATATTTTAATAT
1 AAAA-TAAAATATTTTAAATATTTTAATAT
40331249 A
1 A
40331250 TATTTAAATA
Statistics
Matches: 75, Mismatches: 9, Indels: 12
0.78 0.09 0.12
Matches are distributed among these distances:
28 19 0.25
29 13 0.17
30 23 0.31
31 10 0.13
32 10 0.13
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (29 bp):
AAAATAAAATATTTTAAATATTTTAATAT
Found at i:40331294 original size:20 final size:21
Alignment explanation
Indices: 40331255--40331299 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
40331245 ATATATATTT
*
40331255 AAATATTATTCTTTTGATATA
1 AAATATTATTCTTTTAATATA
*
40331276 AAATATTATTC-TTTAATATT
1 AAATATTATTCTTTTAATATA
40331296 AAAT
1 AAAT
40331300 TGATGTGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.51
Consensus pattern (21 bp):
AAATATTATTCTTTTAATATA
Found at i:40331298 original size:21 final size:22
Alignment explanation
Indices: 40331249--40331298 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
40331239 ATTTTAATAT
* *
40331249 ATATTTAAATATTATTCTTTTG
1 ATATTAAAATATTATTCTTTTA
40331271 ATA-TAAAATATTATTC-TTTA
1 ATATTAAAATATTATTCTTTTA
40331291 ATATTAAA
1 ATATTAAA
40331299 TTGATGTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.24
21 16 0.64
22 3 0.12
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (22 bp):
ATATTAAAATATTATTCTTTTA
Found at i:40331624 original size:19 final size:19
Alignment explanation
Indices: 40331600--40331668 Score: 138
Period size: 19 Copynumber: 3.6 Consensus size: 19
40331590 AATCTTTAAG
40331600 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
40331619 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
40331638 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
40331657 GATATGCAATCT
1 GATATGCAATCT
40331669 ATTTTATATG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:40332340 original size:44 final size:44
Alignment explanation
Indices: 40332292--40332380 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 44
40332282 TGAAATAAAG
** *
40332292 TAGAAATTGTGATAATTATGCA-TTTTAAATAAATTTTAATTTAA
1 TAGAAATTGTGATAATTAAACATTTTTAAAT-AATTATAATTTAA
*
40332336 TAGAAGTTGTGATAATTAAACATTTTTAAATAATTATAATTTAA
1 TAGAAATTGTGATAATTAAACATTTTTAAATAATTATAATTTAA
40332380 T
1 T
40332381 TTATACTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 32 0.80
45 8 0.20
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (44 bp):
TAGAAATTGTGATAATTAAACATTTTTAAATAATTATAATTTAA
Found at i:40342573 original size:15 final size:15
Alignment explanation
Indices: 40342553--40342584 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
40342543 CATTTCACTG
40342553 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
40342568 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
40342583 TT
1 TT
40342585 TGCATGCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:40344214 original size:37 final size:36
Alignment explanation
Indices: 40344163--40344275 Score: 101
Period size: 37 Copynumber: 3.1 Consensus size: 36
40344153 ATTCGAAAAA
*
40344163 TAAT-ATTATTTTAATAGTTTAATATTAAATTTAATT
1 TAATGATTATCTTAATAGTTTAATATT-AATTTAATT
* *
40344199 TAAT-ACTTGTCTTAATAGTATT-TTATTAATTTAATAT
1 TAATGA-TTATCTTAATAGT-TTAATATTAATTTAAT-T
*
40344236 TAAAGTGATTATCTTAATAG-TAAAT-TTAATTTAATT
1 T-AA-TGATTATCTTAATAGTTTAATATTAATTTAATT
40344272 TAAT
1 TAAT
40344276 TTAATGTTTA
Statistics
Matches: 64, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
34 1 0.02
35 2 0.03
36 15 0.23
37 28 0.44
38 5 0.08
39 12 0.19
40 1 0.02
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (36 bp):
TAATGATTATCTTAATAGTTTAATATTAATTTAATT
Found at i:40346694 original size:47 final size:47
Alignment explanation
Indices: 40346625--40346726 Score: 125
Period size: 47 Copynumber: 2.2 Consensus size: 47
40346615 ACCAACACAC
* * * **
40346625 CAGTACGACACTCAGTGCCTCATTGGCTT-TGCCGAAGTAAACAGTAA
1 CAGTACGACACTCAGTACCTCATCGGATTAAACCGAAGT-AACAGTAA
* *
40346672 CAGTACGATACTTAGTACCTCATCGGATTAAACCGAAGTAACAGTAA
1 CAGTACGACACTCAGTACCTCATCGGATTAAACCGAAGTAACAGTAA
40346719 CAGTACGA
1 CAGTACGA
40346727 AACACAAGGT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
47 40 0.85
48 7 0.15
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.23
Consensus pattern (47 bp):
CAGTACGACACTCAGTACCTCATCGGATTAAACCGAAGTAACAGTAA
Found at i:40347676 original size:27 final size:27
Alignment explanation
Indices: 40347646--40347700 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
40347636 CGTTTGAATG
* *
40347646 ACTTCTGTT-GTTCTTTTTGTTTCTTTT
1 ACTTCTGTTCTTTC-TTTAGTTTCTTTT
*
40347673 ACTTCTTTTCTTTCTTTAGTTTCTTTT
1 ACTTCTGTTCTTTCTTTAGTTTCTTTT
40347700 A
1 A
40347701 TTTACTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 21 0.88
28 3 0.12
ACGTcount: A:0.07, C:0.16, G:0.07, T:0.69
Consensus pattern (27 bp):
ACTTCTGTTCTTTCTTTAGTTTCTTTT
Found at i:40348113 original size:3 final size:3
Alignment explanation
Indices: 40348105--40348137 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
40348095 TTAATTTATT
*
40348105 TAA TAA TAA TAA TAG TAA TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
40348138 TAATCTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:40353089 original size:67 final size:66
Alignment explanation
Indices: 40352976--40353105 Score: 233
Period size: 67 Copynumber: 2.0 Consensus size: 66
40352966 AGATAAAGTA
40352976 AGACCAGAAGGTAATCTTGTCACGCACCCGTTCGATAGTTCCATATTAACCAATGAGGTCGGAAG
1 AGACCAGAAGGTAATCTTGTCACGCACCCGTTCGATAGTTCCATATTAACCAATGAGGT-GGAAG
40353041 AT
65 AT
* *
40353043 AGACCAGAAGGTAATCTTGTCATGCACCCGTTCGATAGTTCTATATTAACCAATGAGGTGGAA
1 AGACCAGAAGGTAATCTTGTCACGCACCCGTTCGATAGTTCCATATTAACCAATGAGGTGGAA
40353106 AATAAGCTAG
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
66 4 0.07
67 57 0.93
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (66 bp):
AGACCAGAAGGTAATCTTGTCACGCACCCGTTCGATAGTTCCATATTAACCAATGAGGTGGAAGA
T
Found at i:40353745 original size:25 final size:25
Alignment explanation
Indices: 40353711--40353776 Score: 105
Period size: 25 Copynumber: 2.6 Consensus size: 25
40353701 CCCATTTCAC
*
40353711 AGCTCATGTGAGCATTTACAGTCAT
1 AGCTCGTGTGAGCATTTACAGTCAT
*
40353736 AGCTCGTGTGAGCATTTACTGTCAT
1 AGCTCGTGTGAGCATTTACAGTCAT
*
40353761 AGCTTGTGTGAGCATT
1 AGCTCGTGTGAGCATT
40353777 GTTCCCGTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (25 bp):
AGCTCGTGTGAGCATTTACAGTCAT
Found at i:40353866 original size:26 final size:27
Alignment explanation
Indices: 40353836--40353886 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
40353826 GAGTAAATGG
*
40353836 AAATGGTAATAT-GAAATGGATATACA
1 AAATGGTAATATGGAAATAGATATACA
* *
40353862 AAATGTTTATATGGAAATAGATATA
1 AAATGGTAATATGGAAATAGATATA
40353887 TGAAACGGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 10 0.48
27 11 0.52
ACGTcount: A:0.49, C:0.02, G:0.18, T:0.31
Consensus pattern (27 bp):
AAATGGTAATATGGAAATAGATATACA
Found at i:40353891 original size:13 final size:13
Alignment explanation
Indices: 40353868--40353944 Score: 55
Period size: 13 Copynumber: 5.8 Consensus size: 13
40353858 TACAAAATGT
40353868 TTATATGGAAATAG
1 TTATAT-GAAATAG
* **
40353882 ATATATGAAACGG
1 TTATATGAAATAG
* *
40353895 TTATATGAAGTAT
1 TTATATGAAATAG
* *
40353908 TTATACGAAATAT
1 TTATATGAAATAG
*
40353921 TTATAAGAATATAG
1 TTATATGAA-ATAG
*
40353935 ATATATGAAA
1 TTATATGAAA
40353945 AATGACATTT
Statistics
Matches: 48, Mismatches: 14, Indels: 3
0.74 0.22 0.05
Matches are distributed among these distances:
13 33 0.69
14 15 0.31
ACGTcount: A:0.47, C:0.03, G:0.16, T:0.35
Consensus pattern (13 bp):
TTATATGAAATAG
Found at i:40353971 original size:13 final size:13
Alignment explanation
Indices: 40353953--40353977 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40353943 AAAATGACAT
40353953 TTGAAATGAATAC
1 TTGAAATGAATAC
40353966 TTGAAATGAATA
1 TTGAAATGAATA
40353978 TGTCAAATGT
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:0.48, C:0.04, G:0.16, T:0.32
Consensus pattern (13 bp):
TTGAAATGAATAC
Found at i:40358074 original size:40 final size:40
Alignment explanation
Indices: 40358019--40358236 Score: 334
Period size: 40 Copynumber: 5.5 Consensus size: 40
40358009 CGGATGATAA
* *
40358019 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
40358059 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
40358099 CCGAGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
40358139 CCGAGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
40358179 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TAGCTATGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
40358219 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
40358237 TACTTGGTTG
Statistics
Matches: 168, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
39 17 0.10
40 150 0.89
41 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:40360358 original size:3 final size:3
Alignment explanation
Indices: 40360350--40360377 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
40360340 TTTTATTTAT
40360350 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
40360378 AAGTGTTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:40361698 original size:3 final size:3
Alignment explanation
Indices: 40361690--40361830 Score: 51
Period size: 3 Copynumber: 47.3 Consensus size: 3
40361680 TAATATTTGC
* *
40361690 TAT TAT TAT TAT TAT TAT TAT TAT T-T TCAT TCT T-T TAT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT
* * ** * * * * *
40361734 TGT TGT TGC TAT T-T CTCT TGT TGT TTT TAT TAT T-T ATAT TAT TGT
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT
* * * * *
40361779 TAG TAT TAT TAT TCCT TAG T-T TAT TAT TAT T-T TAT CAT TAT TTT
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
40361823 CTAT TAT T
1 -TAT TAT T
40361831 GTTTATCATT
Statistics
Matches: 105, Mismatches: 22, Indels: 22
0.70 0.15 0.15
Matches are distributed among these distances:
2 9 0.09
3 88 0.84
4 8 0.08
ACGTcount: A:0.22, C:0.07, G:0.06, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:40361778 original size:21 final size:21
Alignment explanation
Indices: 40361754--40361840 Score: 63
Period size: 21 Copynumber: 4.1 Consensus size: 21
40361744 ATTTCTCTTG
*
40361754 TTGTTTTTATTATTTATATTA
1 TTGTTTTTATTATTTATATCA
** *
40361775 TTGTTAGTATTA-TTAT-TCC
1 TTGTTTTTATTATTTATATCA
40361794 TTAGTTTATTATTATTT-TATCA
1 TT-GTTT-TTATTATTTATATCA
* *
40361816 TTATTTTCTATTATTGTTTATCA
1 TTGTTTT-TATTATT-TATATCA
40361839 TT
1 TT
40361841 TTATATGATA
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
19 3 0.06
20 8 0.16
21 26 0.51
22 7 0.14
23 7 0.14
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.66
Consensus pattern (21 bp):
TTGTTTTTATTATTTATATCA
Found at i:40362037 original size:13 final size:12
Alignment explanation
Indices: 40362016--40362067 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 12
40362006 TTATACGCAA
40362016 TTTTAAATTATTC
1 TTTT-AATTATTC
*
40362029 TTTTGAATTATTA
1 TTTT-AATTATTC
40362042 TTTTAAGTTATTC
1 TTTTAA-TTATTC
40362055 TATTTATATTATT
1 T-TTTA-ATTATT
40362068 TTGTTATCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
12 2 0.06
13 21 0.64
14 9 0.27
15 1 0.03
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (12 bp):
TTTTAATTATTC
Found at i:40362711 original size:127 final size:127
Alignment explanation
Indices: 40362487--40362843 Score: 407
Period size: 127 Copynumber: 2.8 Consensus size: 127
40362477 AAAAGGTGAA
** * * *
40362487 GTTTGATGTTTAGAAATTCGAGGGCTTGTGCCCTAATGTGTTGGGTTTCGATCTTTCGTTTGTTT
1 GTTTGATGTTTAGAAATTCGAGGAATCGTGCCCTAATGTGTTGGGTTTCGATCTTTCATTTGTCT
* * * *
40362552 AAATAATCAAATTTCCCTTTAAAATTTTGTCCGCGTTT-TCTAAACCTTAAAACAAAGGCAAT
66 AAATAATCAAATTTCCCTTTAAAACTTCGTCCGCATTTAT-TAAACCTTAAAACAAAAGCAAT
*
40362614 GTTTGATGTTTAGAAATTCGAGGAATCGTGCCCTAATGTGCTGGGTTTCGATCTTTCATTTGTCT
1 GTTTGATGTTTAGAAATTCGAGGAATCGTGCCCTAATGTGTTGGGTTTCGATCTTTCATTTGTCT
* * * * *
40362679 AAATAATCAGATTTCCCTTTTACACTTCGTCCGCATTTATTAAACTTTAAAACAAAAGCGAT
66 AAATAATCAAATTTCCCTTTAAAACTTCGTCCGCATTTATTAAACCTTAAAACAAAAGCAAT
* * * * * ** *
40362741 GATTGATGTTTGGCAATTC-AGGAAATCGTACCCTAATGTGTTGGGTTTCAAT-TTCTTGTTTAT
1 GTTTGATGTTTAGAAATTCGAGG-AATCGTGCCCTAATGTGTTGGGTTTCGATCTT-TCATTTGT
* ** *
40362804 CCAAATAATCAAACATCCCTTTAAAA-TTCCGTCCACATTT
64 CTAAATAATCAAATTTCCCTTTAAAACTT-CGTCCGCATTT
40362844 TTCTTCAAAA
Statistics
Matches: 195, Mismatches: 31, Indels: 8
0.83 0.13 0.03
Matches are distributed among these distances:
126 7 0.04
127 187 0.96
128 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.39
Consensus pattern (127 bp):
GTTTGATGTTTAGAAATTCGAGGAATCGTGCCCTAATGTGTTGGGTTTCGATCTTTCATTTGTCT
AAATAATCAAATTTCCCTTTAAAACTTCGTCCGCATTTATTAAACCTTAAAACAAAAGCAAT
Found at i:40367186 original size:4 final size:4
Alignment explanation
Indices: 40367179--40367212 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
40367169 GCAGTAAAAA
*
40367179 AAAG AAAG AAAG AAAG AAAG AAA- AGAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
40367213 AAAACAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
3 2 0.07
4 25 0.93
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:40367196 original size:12 final size:11
Alignment explanation
Indices: 40367176--40367215 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
40367166 AATGCAGTAA
40367176 AAAAAAGAAAG
1 AAAAAAGAAAG
40367187 AAAGAAAGAAAG
1 AAA-AAAGAAAG
*
40367199 AAAAGAGAAAG
1 AAAAAAGAAAG
40367210 AAAAAA
1 AAAAAA
40367216 ACAAAAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 15 0.58
12 11 0.42
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:40367221 original size:19 final size:19
Alignment explanation
Indices: 40367185--40367221 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
40367175 AAAAAAAGAA
* *
40367185 AGAAAGAAAGAAAGAAAAG
1 AGAAAGAAAAAAACAAAAG
40367204 AGAAAGAAAAAAACAAAA
1 AGAAAGAAAAAAACAAAA
40367222 ACAACAAACT
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:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (19 bp):
AGAAAGAAAAAAACAAAAG
Found at i:40368896 original size:64 final size:64
Alignment explanation
Indices: 40368795--40368915 Score: 215
Period size: 64 Copynumber: 1.9 Consensus size: 64
40368785 TATATCATTC
* *
40368795 AGTTAGGAGCATTTGATTTATTTCGATCATAGCATCCTAATTATTTGACATAAGCATCACATCT
1 AGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATCATTTGACATAAGCATCACATCT
*
40368859 AGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATCATTTGGCATAAGCAT
1 AGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATCATTTGACATAAGCAT
40368916 AGATACATGA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 54 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (64 bp):
AGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATCATTTGACATAAGCATCACATCT
Found at i:40369341 original size:44 final size:44
Alignment explanation
Indices: 40369293--40369461 Score: 187
Period size: 44 Copynumber: 3.8 Consensus size: 44
40369283 AGCTATAAAC
** *
40369293 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAA-ATTTCAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATATCAA-T
* * * *
40369337 CTTATTTCTCTGAAGTTGTAGTGGAGCAGACTGAAGATACCAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATATCAAT
* * *
40369381 CTTATCTCCCCGAAGTTGCAGTGGGGCAGACTGAAGATAGTAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATA-TCAAT
* * * *
40369426 CTTATTTCCCTAAAGTTGCAGTGGAACAGATTGAAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG
40369462 CTAAATTACA
Statistics
Matches: 103, Mismatches: 20, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
44 65 0.63
45 38 0.37
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATATCAAT
Found at i:40371261 original size:3 final size:3
Alignment explanation
Indices: 40371019--40371243 Score: 81
Period size: 3 Copynumber: 75.3 Consensus size: 3
40371009 TAATATTTGC
* *
40371019 TAT TAT TAT TAT TAT TAT TAT TAT T-T TCAT TCT T-T TAT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT
* * ** * * * *
40371063 TGT TGT TGC TAT T-T CTCT TGT TGT TTT TAT TAT TAT T-T ATAT TAT
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
* * * * *
40371108 TGT TAG TAT TAT TAT TCCT TAG T-T TAT TAT TAT TAT T-T TAT CAT
1 TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * *
40371152 TAT TTT CTAT TAT TGT TAT TAT CAA TA- CAC TAT TAT TAT TCT TAT
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
40371197 TAAT GTAT TAT TAT TTT TGAC T-T TAT TTT TAT TA- TAT TAT TAC TAT
1 T-AT -TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT
40371243 T
1 T
40371244 GCTATCATCA
Statistics
Matches: 165, Mismatches: 40, Indels: 34
0.69 0.17 0.14
Matches are distributed among these distances:
2 13 0.08
3 138 0.84
4 13 0.08
5 1 0.01
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:40371498 original size:28 final size:28
Alignment explanation
Indices: 40371439--40371501 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
40371429 TATGTAGTAT
* * * *
40371439 TTATTTTGAAATTTTTATATGTATCTTT
1 TTATTTTGAAATTATTATATATATCATA
40371467 TTATTTT-AAATTATTATATATATACATA
1 TTATTTTGAAATTATTATATATAT-CATA
40371495 TTATTTT
1 TTATTTT
40371502 TTAAAAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 14 0.47
28 16 0.53
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (28 bp):
TTATTTTGAAATTATTATATATATCATA
Found at i:40371735 original size:13 final size:12
Alignment explanation
Indices: 40371714--40371765 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 12
40371704 TTATACGCAA
40371714 TTTTAAATTATTC
1 TTTT-AATTATTC
*
40371727 TTTTGAATTATTA
1 TTTT-AATTATTC
40371740 TTTTAAGTTATTC
1 TTTTAA-TTATTC
40371753 TATTTATATTATT
1 T-TTTA-ATTATT
40371766 TTCTTATCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
12 2 0.06
13 21 0.64
14 9 0.27
15 1 0.03
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (12 bp):
TTTTAATTATTC
Found at i:40372835 original size:18 final size:18
Alignment explanation
Indices: 40372812--40372854 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
40372802 CGTTCCTGGC
*
40372812 TTGATCAGTTCTTCTAGT
1 TTGATCAGTTCCTCTAGT
*
40372830 TTGATCAGTTCCTCTGGT
1 TTGATCAGTTCCTCTAGT
*
40372848 TCGATCA
1 TTGATCA
40372855 AATAAATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.44
Consensus pattern (18 bp):
TTGATCAGTTCCTCTAGT
Found at i:40376601 original size:19 final size:19
Alignment explanation
Indices: 40376564--40376601 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
40376554 CAAGTATCGA
*
40376564 TTTGGGTATCAATACATTT
1 TTTGGGTATCAATAAATTT
*
40376583 TTTGGGTATCGATAAATTT
1 TTTGGGTATCAATAAATTT
40376602 CTTCAAGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.08, G:0.18, T:0.47
Consensus pattern (19 bp):
TTTGGGTATCAATAAATTT
Found at i:40379774 original size:39 final size:39
Alignment explanation
Indices: 40379731--40380634 Score: 1754
Period size: 39 Copynumber: 23.2 Consensus size: 39
40379721 CGAAGTTTAG
* * * *
40379731 CTGAAGCACATAAGTGCTAAACGGAAGCCCGGAGGCTAA
1 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
*
40379770 CTGAAGCACAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
1 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
40379809 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
1 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
40379848 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
1 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
40379887 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
1 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
40379926 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
1 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
40379965 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
1 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
40380004 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
1 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
40380043 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
1 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
40380082 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
1 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
40380121 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
1 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
40380160 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
1 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
40380199 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
1 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
40380238 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
1 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
40380277 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
1 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
40380316 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
1 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
40380355 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
1 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
40380394 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
1 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
40380433 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
1 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
40380472 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
1 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
40380511 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
1 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
40380550 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
1 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
*
40380589 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTAA
1 CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
40380628 CTGAAGC
1 CTGAAGC
40380635 TCACCAGAGC
Statistics
Matches: 860, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
39 860 1.00
ACGTcount: A:0.36, C:0.21, G:0.31, T:0.13
Consensus pattern (39 bp):
CTGAAGCATAGAAGTGCTAAACGGAAGCCCGAAGGCTGA
Found at i:40390694 original size:17 final size:16
Alignment explanation
Indices: 40390671--40390718 Score: 78
Period size: 17 Copynumber: 2.9 Consensus size: 16
40390661 AAATTTTTTA
40390671 AAAATTAAAAAATATT
1 AAAATTAAAAAATATT
40390687 AAATATTAAAAATATATT
1 AAA-ATTAAAAA-ATATT
40390705 AAAATTAAAAAATA
1 AAAATTAAAAAATA
40390719 ATTCTTTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.20
17 16 0.53
18 8 0.27
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAATTAAAAAATATT
Found at i:40391551 original size:54 final size:54
Alignment explanation
Indices: 40391493--40391596 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 54
40391483 GGCATAGGTT
* * *
40391493 TATGATTCTTTTTTGTATTAAAGTA-TATGATAGGTTTAGATTTATTTGTTGAAA
1 TATGATTATTATTTGTATCAAAG-AGTATGATAGGTTTAGATTTATTTGTTGAAA
* * *
40391547 TATGATTATTATTTGTATCAAAGAGTATGGTAGGTTTGGATTTTTTTGTT
1 TATGATTATTATTTGTATCAAAGAGTATGATAGGTTTAGATTTATTTGTT
40391597 ATTGTCTATC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
53 1 0.02
54 42 0.98
ACGTcount: A:0.27, C:0.02, G:0.19, T:0.52
Consensus pattern (54 bp):
TATGATTATTATTTGTATCAAAGAGTATGATAGGTTTAGATTTATTTGTTGAAA
Found at i:40391783 original size:128 final size:128
Alignment explanation
Indices: 40391504--40392037 Score: 732
Period size: 128 Copynumber: 4.2 Consensus size: 128
40391494 ATGATTCTTT
* **
40391504 TTTGTATTAAAGTATATGATAGGTTT-AGATTTATTTGTTGAAATATGATTATTATTTGTATCAA
1 TTTGTATTAAAGTGTATGGCAGGTTTGA-ATTTATTTGTTGAAATATGATTATTATTTGTATCAA
* * * * * *
40391568 AGAGTATGGTAGGTTTGGATTTTTTTG-TTATTGTCTATCACGTGCATCACATAAATGGATTTG
65 AGAGTATGGCAAGTTTAGATTTCTTTGATTATTGTCTGTCATGTGCATCACATAAATGGATTTG
* *
40391631 TTTGTGTTAAAGTGTATGGCAGGTTTGAATTTATTTGTTAAAATATGATTATTATTTGTATCAAA
1 TTTGTATTAAAGTGTATGGCAGGTTTGAATTTATTTGTTGAAATATGATTATTATTTGTATCAAA
* * *
40391696 GAGTAAGGCAAGTTTAGATTTCTTTGATTATTGTCTGTCATGTGTATCAAATAAATGGATTTG
66 GAGTATGGCAAGTTTAGATTTCTTTGATTATTGTCTGTCATGTGCATCACATAAATGGATTTG
* *
40391759 TTTGTATTAAAGTGTATGGCAGGTTTGAATTTATTTGTTGAAATATGATTTTTTTTTGTATCAAA
1 TTTGTATTAAAGTGTATGGCAGGTTTGAATTTATTTGTTGAAATATGATTATTATTTGTATCAAA
* ** ** *
40391824 GAGTATGGCATGTTCGGATTTCTTTGGCTATTGTCTGTCATGTACATCACATAAATGGATTTG
66 GAGTATGGCAAGTTTAGATTTCTTTGATTATTGTCTGTCATGTGCATCACATAAATGGATTTG
** *
40391887 TTTGTATTAAAGTGTATGATAGGTTTGAATTTATTTGTTGAAATATGATTATTGTTTGTATCAAA
1 TTTGTATTAAAGTGTATGGCAGGTTTGAATTTATTTGTTGAAATATGATTATTATTTGTATCAAA
* * * *
40391952 GAGTATGACAAGTTTAGATTTCTTT-AGTTATTGTCTGTCATGTGTATCACATAAATAGATTTA
66 GAGTATGGCAAGTTTAGATTTCTTTGA-TTATTGTCTGTCATGTGCATCACATAAATGGATTTG
**
40392015 TTCATATTATAAAGTGTATGGCA
1 TTTGTA-T-TAAAGTGTATGGCA
40392038 TGTGCGTAAT
Statistics
Matches: 357, Mismatches: 45, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
127 79 0.22
128 265 0.74
129 1 0.00
130 12 0.03
ACGTcount: A:0.29, C:0.06, G:0.20, T:0.45
Consensus pattern (128 bp):
TTTGTATTAAAGTGTATGGCAGGTTTGAATTTATTTGTTGAAATATGATTATTATTTGTATCAAA
GAGTATGGCAAGTTTAGATTTCTTTGATTATTGTCTGTCATGTGCATCACATAAATGGATTTG
Found at i:40395962 original size:22 final size:22
Alignment explanation
Indices: 40395937--40395981 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
40395927 TTTAATAAAG
40395937 AAAATATCTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
* *
40395959 AAAATATTTACAGAATATTCCT
1 AAAATATCTACAAAATATTCCT
40395981 A
1 A
40395982 CACTCCCCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:40399735 original size:22 final size:22
Alignment explanation
Indices: 40399710--40399754 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
40399700 TTTAATAAAG
40399710 AAAATATCTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
* *
40399732 AAAATATTTACAGAATATTCCT
1 AAAATATCTACAAAATATTCCT
40399754 A
1 A
40399755 CATGATCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:40418432 original size:20 final size:20
Alignment explanation
Indices: 40418407--40418446 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
40418397 CTGTTTTTAC
40418407 ATATATTAATAAATTTATAT
1 ATATATTAATAAATTTATAT
40418427 ATATATTAATAAATTTATAT
1 ATATATTAATAAATTTATAT
40418447 TTTAAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATATTAATAAATTTATAT
Found at i:40418451 original size:16 final size:18
Alignment explanation
Indices: 40418402--40418446 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
40418392 AAAAGCTGTT
* *
40418402 TTTACATATATTAATAAA
1 TTTATATATTTTAATAAA
40418420 TTTATATATATATTAATAAA
1 TTTATATAT-T-TTAATAAA
40418440 TTTATAT
1 TTTATAT
40418447 TTTAAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 8 0.35
20 15 0.65
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTATATATTTTAATAAA
Found at i:40423850 original size:171 final size:170
Alignment explanation
Indices: 40423646--40423979 Score: 446
Period size: 171 Copynumber: 1.9 Consensus size: 170
40423636 AGATTTAAGT
* *
40423646 GAAACGAAACAACAGCCCTGAGAAGAGAAGATATGCGACAGACA-CTAAGG-AAAACGAAAA-TA
1 GAAACGAAACAACAGCCCTAAGAAGAGAAGATATGCGA-A-A-AGCTAAGGAAAAAAGAAAATTA
*
40423708 AAAGATGACCAACAGAAGAAGTAGAAGGAAAAAAGTTACCTAGATGAAGAAGAAGGAAGATGAAG
63 AAAGATGAACAACAGAAGAAGTAGAAGG---AAAG-TACCTAGATGAAGAAGAAGGAAGATGAAG
* * *
40423773 TAC-G-GCTA-GGAAAGATTGGTGAGAGTTGGAAAATGTTACAGAGC
124 AACAGCGCAAGGGAAAGATTAGTGAGAGTTGGAAAATGTTACAGAGC
*
40423817 GAAACGAAACAGCAGCCCTAAGAAGAGAAGATATGCGAAAAGCTAAGGAAAAAAGAAAATTAAAA
1 GAAACGAAACAACAGCCCTAAGAAGAGAAGATATGCGAAAAGCTAAGGAAAAAAGAAAATTAAAA
* * * *
40423882 GATGAAGAACAGAAGAAGTAGGAGGAAAGTACCTGGATGATGAAGAAGGAAGATGAAGAACAGCG
66 GATGAACAACAGAAGAAGTAGAAGGAAAGTACCTAGATGAAGAAGAAGGAAGATGAAGAACAGCG
40423947 CAAGGGGGAAAGATTAGTGAGAGTTGGAAAATG
131 CAA--GGGAAAGATTAGTGAGAGTTGGAAAATG
40423980 CCTTACAAAA
Statistics
Matches: 144, Mismatches: 11, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
167 29 0.20
168 6 0.04
169 10 0.07
170 10 0.07
171 63 0.44
172 26 0.18
ACGTcount: A:0.49, C:0.10, G:0.29, T:0.12
Consensus pattern (170 bp):
GAAACGAAACAACAGCCCTAAGAAGAGAAGATATGCGAAAAGCTAAGGAAAAAAGAAAATTAAAA
GATGAACAACAGAAGAAGTAGAAGGAAAGTACCTAGATGAAGAAGAAGGAAGATGAAGAACAGCG
CAAGGGAAAGATTAGTGAGAGTTGGAAAATGTTACAGAGC
Done.