Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 131 of 226
Found at i:43943623 original size:13 final size:13
Alignment explanation
Indices: 43943605--43943633 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
43943595 TAATTTTTCA
43943605 ACACTTGAGTGGT
1 ACACTTGAGTGGT
43943618 ACACTTGAGTGGT
1 ACACTTGAGTGGT
43943631 ACA
1 ACA
43943634 ATTGTGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (13 bp):
ACACTTGAGTGGT
Found at i:43944647 original size:20 final size:18
Alignment explanation
Indices: 43944600--43944648 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
43944590 CAAGAAAAAC
43944600 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
43944617 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
43944637 ATTAAATTAATA
1 ATTAAATTAATA
43944649 AAATAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:43945702 original size:21 final size:21
Alignment explanation
Indices: 43945643--43945707 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
43945633 CAAAAGCAGT
*
43945643 ATACGACACATAAAGTGCCTG
1 ATACGACACATATAGTGCCTG
* ** *
43945664 AAACGACACACGTGGTGCCT-
1 ATACGACACATATAGTGCCTG
43945684 ATTACGACACATATAGTGCCTG
1 A-TACGACACATATAGTGCCTG
43945706 AT
1 AT
43945708 CGGCAAAACC
Statistics
Matches: 33, Mismatches: 9, Indels: 4
0.72 0.20 0.09
Matches are distributed among these distances:
20 1 0.03
21 31 0.94
22 1 0.03
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.22
Consensus pattern (21 bp):
ATACGACACATATAGTGCCTG
Found at i:43946190 original size:17 final size:18
Alignment explanation
Indices: 43946156--43946191 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
43946146 GAATTTTTTA
43946156 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
43946174 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
43946191 T
1 T
43946192 AACTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:43946861 original size:29 final size:29
Alignment explanation
Indices: 43946824--43946898 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 29
43946814 TATAATATAA
43946824 TTAATTAATAAATAAATAAATATCT-TTTAC
1 TTAA-TAATAAAT-AATAAATATCTATTTAC
43946854 TTAATAATAAATAATAAATATCTATTTAC
1 TTAATAATAAATAATAAATATCTATTTAC
*
43946883 TTAAATAATAAGTAAT
1 TT-AATAATAAATAAT
43946899 TTAAATCCAT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 11 0.26
29 15 0.36
30 16 0.38
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.41
Consensus pattern (29 bp):
TTAATAATAAATAATAAATATCTATTTAC
Found at i:43947054 original size:13 final size:12
Alignment explanation
Indices: 43947000--43947055 Score: 51
Period size: 13 Copynumber: 4.5 Consensus size: 12
43946990 ATTTAATAAG
*
43947000 ATAATATCAATT
1 ATAATATTAATT
*
43947012 A-AATAATAATTT
1 ATAATATTAA-TT
43947024 ATAATATTATATT
1 ATAATATTA-ATT
*
43947037 CTAATATTAATT
1 ATAATATTAATT
43947049 AATAATA
1 -ATAATA
43947056 ACTTAAATCA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
11 6 0.17
12 7 0.20
13 21 0.60
14 1 0.03
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.45
Consensus pattern (12 bp):
ATAATATTAATT
Found at i:43952663 original size:20 final size:20
Alignment explanation
Indices: 43952636--43952687 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
43952626 TATGAACCAC
43952636 TCCATTTACTTACTTTCCAT
1 TCCATTTACTTACTTTCCAT
*
43952656 TTCATTTACTTACTTTCCAT
1 TCCATTTACTTACTTTCCAT
43952676 TCCATTTACTTA
1 TCCATTTACTTA
43952688 GCATAAACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.21, C:0.27, G:0.00, T:0.52
Consensus pattern (20 bp):
TCCATTTACTTACTTTCCAT
Found at i:43956101 original size:37 final size:38
Alignment explanation
Indices: 43956050--43956124 Score: 143
Period size: 37 Copynumber: 2.0 Consensus size: 38
43956040 TTATTTCAAG
43956050 ATAGGTACCTCGAATGTTGAAAGACCCGAGGAGTTTTA
1 ATAGGTACCTCGAATGTTGAAAGACCCGAGGAGTTTTA
43956088 ATAGG-ACCTCGAATGTTGAAAGACCCGAGGAGTTTTA
1 ATAGGTACCTCGAATGTTGAAAGACCCGAGGAGTTTTA
43956125 CTATTCCTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 32 0.86
38 5 0.14
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.25
Consensus pattern (38 bp):
ATAGGTACCTCGAATGTTGAAAGACCCGAGGAGTTTTA
Found at i:43967129 original size:12 final size:12
Alignment explanation
Indices: 43967112--43967137 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
43967102 AATGGAATTG
43967112 TAAATCGTGAGA
1 TAAATCGTGAGA
43967124 TAAATCGTGAGA
1 TAAATCGTGAGA
43967136 TA
1 TA
43967138 TAATAAGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.27
Consensus pattern (12 bp):
TAAATCGTGAGA
Found at i:43974735 original size:25 final size:24
Alignment explanation
Indices: 43974693--43974744 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
43974683 ACATACCGTA
43974693 GCTCTTTATGAACGTCCTGATATAG
1 GCTCTTTATGAACGTCCTGATAT-G
* * *
43974718 GCTCTTTGTGAGCTTCCTGATATG
1 GCTCTTTATGAACGTCCTGATATG
43974742 GCT
1 GCT
43974745 TGGTTGAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.38
Consensus pattern (24 bp):
GCTCTTTATGAACGTCCTGATATG
Found at i:43980177 original size:25 final size:25
Alignment explanation
Indices: 43980149--43980232 Score: 114
Period size: 25 Copynumber: 3.4 Consensus size: 25
43980139 AGCTATAAAT
43980149 GGTAAGCTCCTCCAAGTTGAATAAC
1 GGTAAGCTCCTCCAAGTTGAATAAC
* * *
43980174 GGTAAGCTCATCCAAGCTGAATAAT
1 GGTAAGCTCCTCCAAGTTGAATAAC
* *
43980199 GGTAAGCTCCTACGAGTTGAATAAC
1 GGTAAGCTCCTCCAAGTTGAATAAC
*
43980224 AGTAAGCTC
1 GGTAAGCTC
43980233 ATACGAGTTG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 50 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.24
Consensus pattern (25 bp):
GGTAAGCTCCTCCAAGTTGAATAAC
Found at i:43980237 original size:25 final size:25
Alignment explanation
Indices: 43980163--43980269 Score: 115
Period size: 25 Copynumber: 4.3 Consensus size: 25
43980153 AGCTCCTCCA
* * *
43980163 AGTTGAATAACGGTAAGCTCATCCA
1 AGTTGAATAACAGTAAGCTCATACG
* ** *
43980188 AGCTGAATAATGGTAAGCTCCTACG
1 AGTTGAATAACAGTAAGCTCATACG
43980213 AGTTGAATAACAGTAAGCTCATACG
1 AGTTGAATAACAGTAAGCTCATACG
* * *
43980238 AGTTGAGTACCAGTAAGCTCATAAG
1 AGTTGAATAACAGTAAGCTCATACG
*
43980263 AGCTGAA
1 AGTTGAA
43980270 ATCGGTAACC
Statistics
Matches: 68, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 68 1.00
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.23
Consensus pattern (25 bp):
AGTTGAATAACAGTAAGCTCATACG
Found at i:43980254 original size:50 final size:50
Alignment explanation
Indices: 43980150--43980257 Score: 126
Period size: 50 Copynumber: 2.2 Consensus size: 50
43980140 GCTATAAATG
* * * **
43980150 GTAAGCTCCTCCAAGTTGAATAACGGTAAGCTCATCCAAGCTGAATAATG
1 GTAAGCTCCTACAAGTTGAATAACAGTAAGCTCATACAAGCTGAATAACA
* * * * *
43980200 GTAAGCTCCTACGAGTTGAATAACAGTAAGCTCATACGAGTTGAGTACCA
1 GTAAGCTCCTACAAGTTGAATAACAGTAAGCTCATACAAGCTGAATAACA
43980250 GTAAGCTC
1 GTAAGCTC
43980258 ATAAGAGCTG
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.24
Consensus pattern (50 bp):
GTAAGCTCCTACAAGTTGAATAACAGTAAGCTCATACAAGCTGAATAACA
Found at i:43984054 original size:26 final size:25
Alignment explanation
Indices: 43983990--43984055 Score: 78
Period size: 26 Copynumber: 2.6 Consensus size: 25
43983980 AAGTGAGAAC
*
43983990 TAATGGGAAGCTCACAAAGAGCCTT
1 TAATGGGAAGCTCACAAAGAGCCTA
* *
43984015 TAATCAGGAAGCTCACGAAGAGCCATA
1 TAAT-GGGAAGCTCACAAAGAGCC-TA
*
43984042 TAATGGGACGCTCA
1 TAATGGGAAGCTCA
43984056 TAAGAGCTGA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
25 4 0.12
26 25 0.74
27 5 0.15
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.18
Consensus pattern (25 bp):
TAATGGGAAGCTCACAAAGAGCCTA
Found at i:43984529 original size:21 final size:21
Alignment explanation
Indices: 43984503--43984542 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
43984493 TATACGATTA
43984503 AATTTAACA-TCAATTTAATAC
1 AATTT-ACATTCAATTTAATAC
43984524 AATTTACATTCAATTTAAT
1 AATTTACATTCAATTTAAT
43984543 CCAAGTCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (21 bp):
AATTTACATTCAATTTAATAC
Found at i:43984553 original size:21 final size:21
Alignment explanation
Indices: 43984512--43984553 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
43984502 AAATTTAACA
* *
43984512 TCAATTTAATACAATTTACAT
1 TCAATTTAATACAAGTCACAT
*
43984533 TCAATTTAATCCAAGTCACAT
1 TCAATTTAATACAAGTCACAT
43984554 CTTAGGCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.38
Consensus pattern (21 bp):
TCAATTTAATACAAGTCACAT
Found at i:43984747 original size:29 final size:29
Alignment explanation
Indices: 43984687--43984740 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
43984677 AATAGCAGCA
*
43984687 CATGAATTCCAATAAATTTTAGAATTTTC
1 CATGAATTCCAATAAATTTTACAATTTTC
*
43984716 CATGAATT-CAATAACTTTT-CAATTT
1 CATGAATTCCAATAAATTTTACAATTT
43984741 AATCCATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 5 0.22
28 10 0.43
29 8 0.35
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.43
Consensus pattern (29 bp):
CATGAATTCCAATAAATTTTACAATTTTC
Found at i:43989789 original size:25 final size:25
Alignment explanation
Indices: 43989746--43989810 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
43989736 TGAGCACTTA
* *
43989746 AACAGGAAGCTCTTTTGAGTCATAT
1 AACAGGAAGCTCATGTGAGTCATAT
* *
43989771 AACAGGAAGCTGATGTGAGTCATGT
1 AACAGGAAGCTCATGTGAGTCATAT
*
43989796 AATAGGGAAGCTCAT
1 AACA-GGAAGCTCAT
43989811 AAGAGCTATA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 24 0.73
26 9 0.27
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.26
Consensus pattern (25 bp):
AACAGGAAGCTCATGTGAGTCATAT
Found at i:43991615 original size:12 final size:12
Alignment explanation
Indices: 43991598--43991622 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43991588 CGGAACTTCA
43991598 ACACAACAATTC
1 ACACAACAATTC
43991610 ACACAACAATTC
1 ACACAACAATTC
43991622 A
1 A
43991623 TTCAATAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (12 bp):
ACACAACAATTC
Found at i:43993511 original size:18 final size:18
Alignment explanation
Indices: 43993488--43993522 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
43993478 CATAAAATTT
43993488 CAAGAAAATCGATACCAC
1 CAAGAAAATCGATACCAC
43993506 CAAGAAAATCGATACCA
1 CAAGAAAATCGATACCA
43993523 ATCTAGCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.26, G:0.11, T:0.11
Consensus pattern (18 bp):
CAAGAAAATCGATACCAC
Found at i:43997487 original size:20 final size:20
Alignment explanation
Indices: 43997452--43997504 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
43997442 GAGTTACCGG
*
43997452 AGTATAACCA-GGGTACCAA
1 AGTATAAACAGGGGTACCAA
* *
43997471 GGTATAATCAGGGGTACCAA
1 AGTATAAACAGGGGTACCAA
*
43997491 AGTACAAACAGGGG
1 AGTATAAACAGGGG
43997505 CATGTAAGTG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 8 0.29
20 20 0.71
ACGTcount: A:0.40, C:0.17, G:0.28, T:0.15
Consensus pattern (20 bp):
AGTATAAACAGGGGTACCAA
Found at i:43997513 original size:20 final size:20
Alignment explanation
Indices: 43997490--43997553 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
43997480 AGGGGTACCA
43997490 AAGTACAAACAGGGGCATGT
1 AAGTACAAACAGGGGCATGT
* * *
43997510 AAGTGCAATCAGGGGTATCG-
1 AAGTACAAACAGGGGCAT-GT
*
43997530 AAGTACAAACAGGGGCACGT
1 AAGTACAAACAGGGGCATGT
43997550 AAGT
1 AAGT
43997554 GTAATAAGGG
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
19 1 0.03
20 33 0.94
21 1 0.03
ACGTcount: A:0.38, C:0.16, G:0.31, T:0.16
Consensus pattern (20 bp):
AAGTACAAACAGGGGCATGT
Found at i:43997520 original size:40 final size:40
Alignment explanation
Indices: 43997476--43997600 Score: 178
Period size: 40 Copynumber: 3.1 Consensus size: 40
43997466 ACCAAGGTAT
* *
43997476 AATCAGGGGTACCAAAGTACAAACAGGGGCATGTAAGTGC
1 AATCAGGGGTACCGAAGTACAAACAGGGGCACGTAAGTGC
* *
43997516 AATCAGGGGTATCGAAGTACAAACAGGGGCACGTAAGTGT
1 AATCAGGGGTACCGAAGTACAAACAGGGGCACGTAAGTGC
* * * *
43997556 AATAAGGGGTACCGAATTACAAATAGGGGCACATAAGTGC
1 AATCAGGGGTACCGAAGTACAAACAGGGGCACGTAAGTGC
43997596 AATCA
1 AATCA
43997601 TTCAATAATT
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 74 1.00
ACGTcount: A:0.38, C:0.16, G:0.29, T:0.17
Consensus pattern (40 bp):
AATCAGGGGTACCGAAGTACAAACAGGGGCACGTAAGTGC
Found at i:43999194 original size:37 final size:38
Alignment explanation
Indices: 43999140--43999212 Score: 112
Period size: 37 Copynumber: 1.9 Consensus size: 38
43999130 TTTTCATAAT
* *
43999140 TTCACTTTTTCACTTTCAA-TCACTATTCAATTCAAAA
1 TTCACTTTGTCACTTTCAAGTCAATATTCAATTCAAAA
*
43999177 TTCACTTTGTCATTTTCAAGTCAATATTCAATTCAA
1 TTCACTTTGTCACTTTCAAGTCAATATTCAATTCAA
43999213 TTCCACACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 17 0.53
38 15 0.47
ACGTcount: A:0.32, C:0.22, G:0.03, T:0.44
Consensus pattern (38 bp):
TTCACTTTGTCACTTTCAAGTCAATATTCAATTCAAAA
Found at i:43999243 original size:23 final size:22
Alignment explanation
Indices: 43999200--43999243 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
43999190 TTTCAAGTCA
43999200 ATATTCAATTCAATTCCACACAT
1 ATATTCAATTCAATT-CACACAT
43999223 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
43999244 TTAATCGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACAT
Found at i:43999475 original size:51 final size:51
Alignment explanation
Indices: 43999417--43999607 Score: 244
Period size: 51 Copynumber: 3.8 Consensus size: 51
43999407 CCGGTTCACA
* * *
43999417 TAGTAGCCTACACATAGTACTACACATGTGACCATCACTATCTGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCTGGTACACG
* * * * *
43999468 TAGTAGCCTGCACATAGTACTACACACGTGATCGA-AACTATCCGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATCACTATCTGGTACACG
* *
43999519 TAGTAGCCTGCACATAGTACTACACATGTGACC-T-ATCTTTCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCA-CTATCTGGTACACG
*
43999569 TAGTAGCCTGTACATAGTACTACACACGTGACCATCACT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
43999608 TTCACTTTCA
Statistics
Matches: 119, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
49 1 0.01
50 42 0.35
51 73 0.61
52 3 0.03
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCTGGTACACG
Found at i:43999533 original size:102 final size:101
Alignment explanation
Indices: 43999415--43999599 Score: 309
Period size: 101 Copynumber: 1.8 Consensus size: 101
43999405 TACCGGTTCA
43999415 CATAGTAGCCTACACATAGTACTACACATGTGACC-ATCACTATCTGATACACGTAGTAGCCTGC
1 CATAGTAGCCTACACATAGTACTACACATGTGACCTAT--CTATCTGATACACGTAGTAGCCTGC
43999479 ACATAGTACTACACACGTGATCGAAACTATCCGGTACG
64 ACATAGTACTACACACGTGATCGAAACTATCCGGTACG
* * * *
43999517 CATAGTAGCCTGCACATAGTACTACACATGTGACCTATCTTTCTGGTACACGTAGTAGCCTGTAC
1 CATAGTAGCCTACACATAGTACTACACATGTGACCTATCTATCTGATACACGTAGTAGCCTGCAC
43999582 ATAGTACTACACACGTGA
66 ATAGTACTACACACGTGA
43999600 CCATCACTTT
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
101 42 0.54
102 34 0.44
103 2 0.03
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.25
Consensus pattern (101 bp):
CATAGTAGCCTACACATAGTACTACACATGTGACCTATCTATCTGATACACGTAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAACTATCCGGTACG
Found at i:43999739 original size:9 final size:10
Alignment explanation
Indices: 43999709--43999742 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
43999699 CAACTGGGAA
43999709 TTTCTCACTT
1 TTTCTCACTT
*
43999719 TTTTTCACTT
1 TTTCTCACTT
43999729 TTTCTCA-TT
1 TTTCTCACTT
43999738 TTTCT
1 TTTCT
43999743 TTTTCACTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 7 0.32
10 15 0.68
ACGTcount: A:0.09, C:0.24, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTCTCACTT
Found at i:44001437 original size:44 final size:45
Alignment explanation
Indices: 44001374--44001464 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
44001364 TGCATGAAGA
44001374 AAATCAAAACCAAAGCTT-CCCCCCCTTTAATGGTGATTTCAGCC
1 AAATCAAAACCAAAGCTTCCCCCCCCTTTAATGGTGATTTCAGCC
44001418 AAATCAAAACCAAAGCTTCCCCCCCCTTTAATGGTGATTTCAGCC
1 AAATCAAAACCAAAGCTTCCCCCCCCTTTAATGGTGATTTCAGCC
44001463 AA
1 AA
44001465 GGAATAAGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 18 0.39
45 28 0.61
ACGTcount: A:0.33, C:0.32, G:0.11, T:0.24
Consensus pattern (45 bp):
AAATCAAAACCAAAGCTTCCCCCCCCTTTAATGGTGATTTCAGCC
Found at i:44001530 original size:16 final size:16
Alignment explanation
Indices: 44001509--44001555 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
44001499 CATCTTTTGT
44001509 TTAATTAACATTTAAC
1 TTAATTAACATTTAAC
* *
44001525 TTAATTATCAAATT-AC
1 TTAATTAAC-ATTTAAC
*
44001541 TTAATTAACCTTTAA
1 TTAATTAACATTTAA
44001556 AAATTGTTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
15 2 0.08
16 19 0.79
17 3 0.12
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAATTAACATTTAAC
Found at i:44002303 original size:33 final size:33
Alignment explanation
Indices: 44002257--44002363 Score: 115
Period size: 33 Copynumber: 3.5 Consensus size: 33
44002247 ACCGAGACAA
*
44002257 TAAACATGAAACAGAGTAAGTTCGTCGGGATAG
1 TAAACATGGAACAGAGTAAGTTCGTCGGGATAG
* *
44002290 TAAACATGGAACAGAG-ATAGTTTG-CTGG---G
1 TAAACATGGAACAGAGTA-AGTTCGTCGGGATAG
44002319 ---AC-TGGAACAGAGTAAGTTCGTCGGGATAG
1 TAAACATGGAACAGAGTAAGTTCGTCGGGATAG
44002348 TAAACATGGAACAGAG
1 TAAACATGGAACAGAG
44002364 ATAGTAAACA
Statistics
Matches: 59, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
25 15 0.25
26 6 0.10
29 2 0.03
32 6 0.10
33 30 0.51
ACGTcount: A:0.37, C:0.12, G:0.30, T:0.21
Consensus pattern (33 bp):
TAAACATGGAACAGAGTAAGTTCGTCGGGATAG
Found at i:44002379 original size:20 final size:20
Alignment explanation
Indices: 44002343--44002382 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
44002333 AGTTCGTCGG
**
44002343 GATAGTAAACATGGAACAGA
1 GATAGTAAACACAGAACAGA
44002363 GATAGTAAACACAGAACAGA
1 GATAGTAAACACAGAACAGA
44002383 TAAAGTCTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.12, G:0.23, T:0.12
Consensus pattern (20 bp):
GATAGTAAACACAGAACAGA
Found at i:44005424 original size:23 final size:22
Alignment explanation
Indices: 44005381--44005424 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
44005371 TTCTAAGTCG
44005381 ATATTCAATTCAATTCCACACAT
1 ATATTCAATTCAATT-CACACAT
44005404 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
44005425 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACAT
Found at i:44005533 original size:45 final size:45
Alignment explanation
Indices: 44005469--44005557 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
44005459 AACAGATACT
* * *
44005469 CGGTGGATTCAGCATATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
44005514 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
44005558 TTGATTCACA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.26
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:44005654 original size:17 final size:17
Alignment explanation
Indices: 44005632--44005667 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
44005622 TAGCCTGCAC
44005632 ATAGTACTACACACGTG
1 ATAGTACTACACACGTG
44005649 ATAGTACTACACACGTG
1 ATAGTACTACACACGTG
44005666 AT
1 AT
44005668 CGAAACTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (17 bp):
ATAGTACTACACACGTG
Found at i:44005657 original size:68 final size:68
Alignment explanation
Indices: 44005581--44005712 Score: 185
Period size: 68 Copynumber: 1.9 Consensus size: 68
44005571 TAACCTGCAC
* * *
44005581 ATAGTACTACACATGTGA-CCATTACCATCCGATACACGTAGTAGCCTGCACATAGTACTACACA
1 ATAGTACTACACACGTGATCCA-AACCATCCGATACACATAGTAGCCTGCACATAGTACTACACA
44005645 CGTG
65 CGTG
* * * *
44005649 ATAGTACTACACACGTGATCGAAACTATCCGGTACGCATAGTAGCCTGCACATAGTACTACACA
1 ATAGTACTACACACGTGATCCAAACCATCCGATACACATAGTAGCCTGCACATAGTACTACACA
44005713 TGCGACCTAT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
68 54 0.96
69 2 0.04
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (68 bp):
ATAGTACTACACACGTGATCCAAACCATCCGATACACATAGTAGCCTGCACATAGTACTACACAC
GTG
Found at i:44008192 original size:27 final size:27
Alignment explanation
Indices: 44008162--44008218 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
44008152 AATGAATTCT
44008162 GCTAAAGGTAAATAATGTTCCCAAATA
1 GCTAAAGGTAAATAATGTTCCCAAATA
*
44008189 GCTAAGGGTAAATAATGTTCCCAAATA
1 GCTAAAGGTAAATAATGTTCCCAAATA
44008216 GCT
1 GCT
44008219 TCAAACTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (27 bp):
GCTAAAGGTAAATAATGTTCCCAAATA
Found at i:44012023 original size:16 final size:16
Alignment explanation
Indices: 44011998--44012031 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
44011988 AAAATAATAT
* *
44011998 ATGTGTAAATGTGATA
1 ATGTGCAAATATGATA
44012014 ATGTGCAAATATGATA
1 ATGTGCAAATATGATA
44012030 AT
1 AT
44012032 TGGATATTGG
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:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (16 bp):
ATGTGCAAATATGATA
Found at i:44013347 original size:48 final size:48
Alignment explanation
Indices: 44013276--44013372 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
44013266 ACGGGTTGAA
*
44013276 TGACCCCTACAGTTGAATTTTTTAACTTTTTCCTCAAATTTTCAAATG
1 TGACCCCTACAGTTGAATTTTTTAACTTTTTCCTCAAATCTTCAAATG
44013324 TGACCCCTACAGTTGAATTTTTTAACTTTTTCCTCAAATCTTCAAATG
1 TGACCCCTACAGTTGAATTTTTTAACTTTTTCCTCAAATCTTCAAATG
44013372 T
1 T
44013373 TCCTGATTAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.27, C:0.22, G:0.08, T:0.43
Consensus pattern (48 bp):
TGACCCCTACAGTTGAATTTTTTAACTTTTTCCTCAAATCTTCAAATG
Found at i:44021221 original size:15 final size:15
Alignment explanation
Indices: 44021198--44021229 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
44021188 GTGGTAAGAA
44021198 TTTAATACTTAATTT
1 TTTAATACTTAATTT
*
44021213 TTTAGTACTTAATTT
1 TTTAATACTTAATTT
44021228 TT
1 TT
44021230 AATTGATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.62
Consensus pattern (15 bp):
TTTAATACTTAATTT
Found at i:44031852 original size:43 final size:43
Alignment explanation
Indices: 44031799--44032028 Score: 320
Period size: 43 Copynumber: 5.3 Consensus size: 43
44031789 GTTTTTAGAA
*
44031799 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTTCC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGACGCTTTTTCC
* *
44031842 ACAAACGCCGCTAAATACCAAGACCATTAGCGACGCTTTTTCC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGACGCTTTTTCC
* * * *
44031885 ACAAACGTCGCTAAAGACCCAGACCTTTAGCGACGATTTTCCC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGACGCTTTTTCC
*
44031928 ACAAACGCCGCTAAAGACCAGGACCTTTAGCGACGC-TTTTCTC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGACGCTTTTTC-C
* * *
44031971 ACAAACGCCGCTAAAGACCCAA-ACCTCTAGCGGCGCTTTTCCC
1 ACAAACGCCGCTAAAGA-CCAAGACCTTTAGCGACGCTTTTTCC
*
44032014 AGAAACGCCGCTAAA
1 ACAAACGCCGCTAAA
44032029 AATATATCTT
Statistics
Matches: 165, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
42 4 0.02
43 154 0.93
44 7 0.04
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.19
Consensus pattern (43 bp):
ACAAACGCCGCTAAAGACCAAGACCTTTAGCGACGCTTTTTCC
Found at i:44032184 original size:27 final size:27
Alignment explanation
Indices: 44032154--44032207 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
44032144 ACTTTAAAAC
*
44032154 TAAATATA-AATATAAAATTAATGAATT
1 TAAATATAGAATATAAAA-TAATAAATT
* *
44032181 TAAATTTAGAATTTAAAATAATAAATT
1 TAAATATAGAATATAAAATAATAAATT
44032208 AATAACACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (27 bp):
TAAATATAGAATATAAAATAATAAATT
Found at i:44032343 original size:43 final size:43
Alignment explanation
Indices: 44032295--44032385 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 43
44032285 ACATATGCAA
* * * * *
44032295 GGTAATAAAATATACAATGCATTTTCTTAATCAAGTAAATCTT
1 GGTAATAAAAGACACAATACATTTACTTAATCAAGGAAATCTT
* *
44032338 GGTAATAAAAGGCATAATACATTTACTTAATCAAGGAAATCTT
1 GGTAATAAAAGACACAATACATTTACTTAATCAAGGAAATCTT
44032381 -GTAAT
1 GGTAAT
44032386 GAACTCAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 5 0.12
43 36 0.88
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (43 bp):
GGTAATAAAAGACACAATACATTTACTTAATCAAGGAAATCTT
Found at i:44036694 original size:30 final size:31
Alignment explanation
Indices: 44036653--44036716 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
44036643 TTATAAAAAT
* *
44036653 AAAAGTTTAAAATCTTTTTAAATT-TTTTAA
1 AAAAATTTAAAATCTTTTAAAATTATTTTAA
44036683 AAAAATTTAAAATCTTTTAAAATTCATTTTAA
1 AAAAATTTAAAATCTTTTAAAATT-ATTTTAA
44036715 AA
1 AA
44036717 TTTCAAATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 22 0.73
32 8 0.27
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (31 bp):
AAAAATTTAAAATCTTTTAAAATTATTTTAA
Found at i:44036701 original size:10 final size:10
Alignment explanation
Indices: 44036658--44036717 Score: 57
Period size: 10 Copynumber: 5.8 Consensus size: 10
44036648 AAAATAAAAG
44036658 TTTAAAATCT
1 TTTAAAATCT
* *
44036668 TTTTAAATTT
1 TTTAAAATCT
***
44036678 TTTAAAAAAA
1 TTTAAAATCT
44036688 TTTAAAATCT
1 TTTAAAATCT
44036698 TTTAAAATTCAT
1 TTTAAAA-TC-T
44036710 TTTAAAAT
1 TTTAAAAT
44036718 TTCAAATCAC
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
10 28 0.72
11 3 0.08
12 8 0.21
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (10 bp):
TTTAAAATCT
Found at i:44036716 original size:29 final size:27
Alignment explanation
Indices: 44036652--44036725 Score: 76
Period size: 30 Copynumber: 2.5 Consensus size: 27
44036642 ATTATAAAAA
*
44036652 TAAAAGTTTAAAATCTTTTTAAATTTTT
1 TAAAA-TTTAAAATCTTTTAAAATTTTT
44036680 TAAAAAAATTTAAAATCTTTTAAAATTCATTT
1 T---AAAATTTAAAATCTTTTAAAATT--TTT
*
44036712 TAAAATTTCAAATC
1 TAAAATTTAAAATC
44036726 ACGAAAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
28 1 0.03
29 12 0.31
30 18 0.46
31 4 0.10
32 4 0.10
ACGTcount: A:0.46, C:0.07, G:0.01, T:0.46
Consensus pattern (27 bp):
TAAAATTTAAAATCTTTTAAAATTTTT
Found at i:44037181 original size:27 final size:27
Alignment explanation
Indices: 44037117--44037181 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
44037107 CTAAAATGTA
*
44037117 AACTCTAAACCTTAAACCCCAATCCCC
1 AACTCTAAACCTTAAACCCCAAACCCC
*
44037144 AAGCCCTAAACC-TAAACCCCAAACCCC
1 AA-CTCTAAACCTTAAACCCCAAACCCC
*
44037171 GAACTCAAAAC
1 -AACTCTAAAC
44037182 TGTAATCCTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 22 0.69
28 10 0.31
ACGTcount: A:0.42, C:0.43, G:0.03, T:0.12
Consensus pattern (27 bp):
AACTCTAAACCTTAAACCCCAAACCCC
Found at i:44038354 original size:41 final size:41
Alignment explanation
Indices: 44038296--44038483 Score: 286
Period size: 41 Copynumber: 4.6 Consensus size: 41
44038286 GCTAAAGTCA
**
44038296 AGCATTAGCGGCGCTTTTTCAAAAACGTCGCTAAAGGCCCG
1 AGCATTAGCGGCGCTTTTGAAAAAACGTCGCTAAAGGCCCG
* * *
44038337 AGCATTAGCGGCACTTTTGAAAAAACGCCGCTAAAGGACCG
1 AGCATTAGCGGCGCTTTTGAAAAAACGTCGCTAAAGGCCCG
* *
44038378 AGCATTAGCGGCGCTTTTGAAAAAACGCCGCTAAAGCCCCG
1 AGCATTAGCGGCGCTTTTGAAAAAACGTCGCTAAAGGCCCG
*
44038419 AGCATTAGCGGCGCTTTTGAAAAAACGTCGCTAAAGCCCCG
1 AGCATTAGCGGCGCTTTTGAAAAAACGTCGCTAAAGGCCCG
* *
44038460 AACATTAGCTGCGCTTTTGAAAAA
1 AGCATTAGCGGCGCTTTTGAAAAA
44038484 GCACGGCTAA
Statistics
Matches: 136, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 136 1.00
ACGTcount: A:0.31, C:0.26, G:0.23, T:0.20
Consensus pattern (41 bp):
AGCATTAGCGGCGCTTTTGAAAAAACGTCGCTAAAGGCCCG
Found at i:44038645 original size:40 final size:40
Alignment explanation
Indices: 44038542--44038686 Score: 145
Period size: 40 Copynumber: 3.6 Consensus size: 40
44038532 GGTTTTTTGC
* *
44038542 GGCGCTTTTTGGAAAA-CGCCGCTAATGCTT-ATTTTTAGC
1 GGCG-TTTTTGCAAAAGCGCCGCTAATGCTTGATTTTTAGT
* * *
44038581 AGCGTTTTT-CAATATGCGCCGCTAATGCTTGATCTTTAGT
1 GGCGTTTTTGCAA-AAGCGCCGCTAATGCTTGATTTTTAGT
* *
44038621 GGCGTTTTTGTAAAAGCGCTGCTAATGCTTGATTTTTAGT
1 GGCGTTTTTGCAAAAGCGCCGCTAATGCTTGATTTTTAGT
* *
44038661 GGCATTTTTTGTCCAAA-CGCCGCTAA
1 GGC-GTTTTTG-CAAAAGCGCCGCTAA
44038687 AAATGCCACT
Statistics
Matches: 86, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
37 2 0.02
38 6 0.07
39 17 0.20
40 42 0.49
41 16 0.19
42 3 0.03
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (40 bp):
GGCGTTTTTGCAAAAGCGCCGCTAATGCTTGATTTTTAGT
Found at i:44048837 original size:20 final size:21
Alignment explanation
Indices: 44048804--44048843 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
44048794 CAGCTTGTTG
44048804 AGCTCAATTGAGCTCATTTCT
1 AGCTCAATTGAGCTCATTTCT
*
44048825 AGCTCAA-TGAGCTCCTTTC
1 AGCTCAATTGAGCTCATTTC
44048844 CATCTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.35
Consensus pattern (21 bp):
AGCTCAATTGAGCTCATTTCT
Found at i:44051442 original size:20 final size:21
Alignment explanation
Indices: 44051409--44051450 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
44051399 CAGCTTGTTG
44051409 AGCTCAATTGAGCTCATTTCC
1 AGCTCAATTGAGCTCATTTCC
*
44051430 AGCTCAA-TGAGCTCGTTTCC
1 AGCTCAATTGAGCTCATTTCC
44051450 A
1 A
44051451 TCTTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.31
Consensus pattern (21 bp):
AGCTCAATTGAGCTCATTTCC
Found at i:44055107 original size:20 final size:20
Alignment explanation
Indices: 44055082--44055125 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
44055072 ATAACGATTC
44055082 AAAAGAAAAAAAATTGAGAG
1 AAAAGAAAAAAAATTGAGAG
* *
44055102 AAAAGAACAAAAATTGTGAG
1 AAAAGAAAAAAAATTGAGAG
44055122 AAAA
1 AAAA
44055126 ACAAGAGTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.68, C:0.02, G:0.18, T:0.11
Consensus pattern (20 bp):
AAAAGAAAAAAAATTGAGAG
Found at i:44055153 original size:21 final size:23
Alignment explanation
Indices: 44055120--44055164 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
44055110 AAAAATTGTG
*
44055120 AGAAAAACAAGAGTG-GAGAAAA
1 AGAAAAACAAGAGTGAAAGAAAA
*
44055142 AGAAAAA-GAGAGTGAAAGAAAA
1 AGAAAAACAAGAGTGAAAGAAAA
44055164 A
1 A
44055165 TGAATGAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.67, C:0.02, G:0.27, T:0.04
Consensus pattern (23 bp):
AGAAAAACAAGAGTGAAAGAAAA
Found at i:44055935 original size:42 final size:42
Alignment explanation
Indices: 44055876--44055961 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
44055866 CCTGGCCCAC
44055876 ATTACTCACTTAAATTAATTCACTCGTTTGATGAGACTTTGT
1 ATTACTCACTTAAATTAATTCACTCGTTTGATGAGACTTTGT
44055918 ATTACTCACTTAAATTAATTCACTCGTTTGATGAGACTTTGT
1 ATTACTCACTTAAATTAATTCACTCGTTTGATGAGACTTTGT
44055960 AT
1 AT
44055962 GGTGAAGGTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (42 bp):
ATTACTCACTTAAATTAATTCACTCGTTTGATGAGACTTTGT
Found at i:44056377 original size:20 final size:21
Alignment explanation
Indices: 44056344--44056385 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
44056334 TAGCTTGTTA
44056344 AGCTCAATTGAGCTCATTTCC
1 AGCTCAATTGAGCTCATTTCC
*
44056365 AGCTCAA-TGAGCTCGTTTCC
1 AGCTCAATTGAGCTCATTTCC
44056385 A
1 A
44056386 TCTTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.31
Consensus pattern (21 bp):
AGCTCAATTGAGCTCATTTCC
Found at i:44060218 original size:27 final size:27
Alignment explanation
Indices: 44060188--44060241 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
44060178 AGAACTCTTA
44060188 GCTTAGATATTACAACTCGACTTGTAT
1 GCTTAGATATTACAACTCGACTTGTAT
44060215 GCTTAGATATTACAACTCGACTTGTAT
1 GCTTAGATATTACAACTCGACTTGTAT
44060242 AGTAGCAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.37
Consensus pattern (27 bp):
GCTTAGATATTACAACTCGACTTGTAT
Found at i:44072363 original size:17 final size:17
Alignment explanation
Indices: 44072341--44072374 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
44072331 AAGTGAGAAA
44072341 CAAATGAAGGACTAAAG
1 CAAATGAAGGACTAAAG
* *
44072358 CAAATGAGGGGCTAAAG
1 CAAATGAAGGACTAAAG
44072375 GAAGGAGAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.12, G:0.29, T:0.12
Consensus pattern (17 bp):
CAAATGAAGGACTAAAG
Found at i:44074431 original size:13 final size:13
Alignment explanation
Indices: 44074413--44074437 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44074403 AAAATTTGAT
44074413 TTGATTATGTAAA
1 TTGATTATGTAAA
44074426 TTGATTATGTAA
1 TTGATTATGTAA
44074438 TCTTATAAAT
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:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (13 bp):
TTGATTATGTAAA
Found at i:44078905 original size:28 final size:28
Alignment explanation
Indices: 44078865--44078922 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
44078855 AATCATACAT
*
44078865 CAACAACTTCAAAAGAGAGGAAAAACAC
1 CAACAACATCAAAAGAGAGGAAAAACAC
44078893 CAACAACATCAAAAGAGAGGAAAAACAC
1 CAACAACATCAAAAGAGAGGAAAAACAC
44078921 CA
1 CA
44078923 GCTGGAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.59, C:0.22, G:0.14, T:0.05
Consensus pattern (28 bp):
CAACAACATCAAAAGAGAGGAAAAACAC
Found at i:44080513 original size:6 final size:6
Alignment explanation
Indices: 44080471--44080510 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
44080461 CAGTATTCTT
*
44080471 TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTTTCC TTTT
1 TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTTT
44080511 CCTCCTCTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.17, G:0.12, T:0.70
Consensus pattern (6 bp):
TTTTGC
Found at i:44081201 original size:28 final size:29
Alignment explanation
Indices: 44081169--44081223 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
44081159 AGCAAAGAAA
*
44081169 TAAAA-GATTATT-AAATTTTAAAAAAAAC
1 TAAAACGATT-TTAAAATTATAAAAAAAAC
44081197 TAAAACGATTTTAAAATTATAAAAAAA
1 TAAAACGATTTTAAAATTATAAAAAAA
44081224 CAAGTTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.31
Consensus pattern (29 bp):
TAAAACGATTTTAAAATTATAAAAAAAAC
Found at i:44081819 original size:6 final size:6
Alignment explanation
Indices: 44081808--44081834 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
44081798 TTTGTTCTTA
44081808 TTAATT TTAATT TTAATT TTAATT TTA
1 TTAATT TTAATT TTAATT TTAATT TTA
44081835 TAAAAATATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTAATT
Found at i:44082302 original size:30 final size:30
Alignment explanation
Indices: 44082262--44082341 Score: 76
Period size: 30 Copynumber: 2.7 Consensus size: 30
44082252 TTAAATTAAA
*
44082262 TAAAAAAATTTATTTAATTACATATTA--TT
1 TAAAATAATTTATTTAATTA-ATATTATGTT
* *
44082291 TATAAATAATTTTTTTAAGTTAATTTTATGTT
1 TA-AAATAATTTATTTAA-TTAATATTATGTT
*
44082323 TAAAATAA-ATATTTAATTA
1 TAAAATAATTTATTTAATTA
44082342 GATAAATATA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
29 5 0.12
30 24 0.57
31 9 0.21
32 4 0.10
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (30 bp):
TAAAATAATTTATTTAATTAATATTATGTT
Found at i:44082792 original size:23 final size:23
Alignment explanation
Indices: 44082766--44082809 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
44082756 ATTTTAACCT
44082766 ATTATAAAAATATGAATATTTTA
1 ATTATAAAAATATGAATATTTTA
* *
44082789 ATTATATAAATATGAGTATTT
1 ATTATAAAAATATGAATATTT
44082810 GTTTAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (23 bp):
ATTATAAAAATATGAATATTTTA
Found at i:44082917 original size:17 final size:17
Alignment explanation
Indices: 44082897--44082934 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
44082887 TTAAGTTTTA
44082897 ATTAAGTATAATTTATT
1 ATTAAGTATAATTTATT
* *
44082914 ATTAAGTATATTTTCTT
1 ATTAAGTATAATTTATT
44082931 ATTA
1 ATTA
44082935 TGAAATAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (17 bp):
ATTAAGTATAATTTATT
Found at i:44084236 original size:34 final size:35
Alignment explanation
Indices: 44084181--44084247 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
44084171 CAAACACCAG
*
44084181 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
44084216 AAAACATTTTCCCG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
44084248 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:44089972 original size:27 final size:27
Alignment explanation
Indices: 44089942--44090003 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 27
44089932 AACAATGTTT
44089942 CTGGCAATAAAATCCTGAACAGAGTTC
1 CTGGCAATAAAATCCTGAACAGAGTTC
* * * *
44089969 CTGG-AGATAAGATTCTTAATAGAGTTC
1 CTGGCA-ATAAAATCCTGAACAGAGTTC
*
44089996 CTGTCAAT
1 CTGGCAAT
44090004 CGCAACTCAC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
26 1 0.04
27 26 0.93
28 1 0.04
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (27 bp):
CTGGCAATAAAATCCTGAACAGAGTTC
Found at i:44090212 original size:35 final size:35
Alignment explanation
Indices: 44090131--44090255 Score: 146
Period size: 35 Copynumber: 3.6 Consensus size: 35
44090121 CACATGGTTA
* *
44090131 ACCATCCAACACACCAGATACTCATAAGAG-TCAGT
1 ACCATCCAGCACACCAGTTACTCATAAGAGCT-AGT
44090166 ACCATCCAGCACACCAGTTACTCATAAGAGCTAGT
1 ACCATCCAGCACACCAGTTACTCATAAGAGCTAGT
** * * * *
44090201 ACCATTTAGCACACCA-TTCGCTCATACGAACCAGT
1 ACCATCCAGCACACCAGTT-ACTCATAAGAGCTAGT
44090236 ACCATCCAGCACACCAGTTA
1 ACCATCCAGCACACCAGTTA
44090256 ACACTATAAA
Statistics
Matches: 76, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
34 2 0.03
35 71 0.93
36 3 0.04
ACGTcount: A:0.35, C:0.34, G:0.12, T:0.19
Consensus pattern (35 bp):
ACCATCCAGCACACCAGTTACTCATAAGAGCTAGT
Found at i:44092581 original size:25 final size:25
Alignment explanation
Indices: 44092553--44092607 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
44092543 AAATACGAAT
*
44092553 AAAAATTGTAATACAAAATTAATTAA
1 AAAAATT-TAATACAAAATTAATAAA
* **
44092579 AAAAACTTAATACAATTTTAATAAA
1 AAAAATTTAATACAAAATTAATAAA
44092604 AAAA
1 AAAA
44092608 TAAGAGTGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 19 0.76
26 6 0.24
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (25 bp):
AAAAATTTAATACAAAATTAATAAA
Found at i:44092636 original size:11 final size:11
Alignment explanation
Indices: 44092620--44092675 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
44092610 AGAGTGAACT
44092620 GAGAGAATTGA
1 GAGAGAATTGA
* *
44092631 GTGAGAATTAA
1 GAGAGAATTGA
*
44092642 GAGAGGATTGA
1 GAGAGAATTGA
44092653 GA-ATGAATTGA
1 GAGA-GAATTGA
* *
44092664 GAAAGAGTTGA
1 GAGAGAATTGA
44092675 G
1 G
44092676 TGAATTGAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
10 1 0.03
11 34 0.94
12 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.36, T:0.21
Consensus pattern (11 bp):
GAGAGAATTGA
Found at i:44097323 original size:115 final size:116
Alignment explanation
Indices: 44097186--44097428 Score: 373
Period size: 116 Copynumber: 2.1 Consensus size: 116
44097176 TAAGTTTGTG
* *
44097186 AAATTATTAATTGATAAATTGTATTAATGGTTAGTAAAAATTATCAAATTATATAAAATTATTAA
1 AAATTATTAATTGATAAATTGTATTAATGATTAGT-AAAATTATCAAATTATATAAAATAATTAA
* ** *
44097251 TTGTT-GTATCA-GTCAAAACATTTTTCAAAATCTAAAATTATGTGAATGTA
65 TTGTTAGTACCAGGAAAAAACATTTTTCAAAATCTAAAATTATGTGAAAGTA
44097301 AAATTATTAATTGATAAATTGTATTAATGATTAGTAAAATTATCAAATTATATAAAATAATTAAT
1 AAATTATTAATTGATAAATTGTATTAATGATTAGTAAAATTATCAAATTATATAAAATAATTAAT
* * * *
44097366 TGTTAGTACCAGGAAAAAATATTTTTCCAAATCTAACATTATTTGAAAGTA
66 TGTTAGTACCAGGAAAAAACATTTTTCAAAATCTAAAATTATGTGAAAGTA
44097417 AAATTATTAATT
1 AAATTATTAATT
44097429 TAGTTTAGGG
Statistics
Matches: 116, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
114 33 0.28
115 39 0.34
116 44 0.38
ACGTcount: A:0.46, C:0.05, G:0.09, T:0.40
Consensus pattern (116 bp):
AAATTATTAATTGATAAATTGTATTAATGATTAGTAAAATTATCAAATTATATAAAATAATTAAT
TGTTAGTACCAGGAAAAAACATTTTTCAAAATCTAAAATTATGTGAAAGTA
Found at i:44097463 original size:23 final size:22
Alignment explanation
Indices: 44097433--44098138 Score: 578
Period size: 23 Copynumber: 31.8 Consensus size: 22
44097423 TTAATTTAGT
44097433 TTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAATTTAA-TAGG
* * *
44097456 TTAAGGTTTTTAAGTTAA-GGG
1 TTAGGGTTTTTAATTTAATAGG
* * *
44097477 TTAGGATTTTTAAGTTAA-GGG
1 TTAGGGTTTTTAATTTAATAGG
* * *
44097498 TTTAGTGTTTTTAAGTTAA-GGG
1 -TTAGGGTTTTTAATTTAATAGG
* **
44097520 TTAGGGTTTTTAAGTTAAGGGG
1 TTAGGGTTTTTAATTTAATAGG
* **
44097542 TTAGGGTTTTTAA-GTAACGGG
1 TTAGGGTTTTTAATTTAATAGG
* *
44097563 TTAGGGTTTTTAACTAAATTAGG
1 TTAGGGTTTTTAATTTAA-TAGG
44097586 TTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAATTTAA-TAGG
*
44097609 TTAGGGTTTTTAAGTTAATTAGG
1 TTAGGGTTTTTAATTTAA-TAGG
* **
44097632 TTAGGGTTTTTAACTTAAGGGGG
1 TTAGGGTTTTTAATTTAA-TAGG
* *
44097655 TTAGGGTTTTTAAGTTAA-GGG
1 TTAGGGTTTTTAATTTAATAGG
* * **
44097676 TTATGGTTTTTAA-GTAACGGG
1 TTAGGGTTTTTAATTTAATAGG
* *
44097697 TTAGAGTTTTTAAGTTT-A-GGG
1 TTAGGGTTTTTAA-TTTAATAGG
*** *
44097718 TTTAAAATTTTTAATTAAATTAGG
1 -TTAGGGTTTTTAATTTAA-TAGG
* *
44097742 TTAGGGTTTTTAAGTTAA-GGG
1 TTAGGGTTTTTAATTTAATAGG
44097763 TTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAATTTAA-TAGG
**
44097786 TTAGGGTTTTTAATTTAAGGGGG
1 TTAGGGTTTTTAATTTAA-TAGG
* *
44097809 TTAGGGTTTTTAAGTTAA-AAG
1 TTAGGGTTTTTAATTTAATAGG
*
44097830 TTAGAGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAATTTAA-TAGG
* * *
44097853 TTAGAGTTTTTAAGTTAA-GGG
1 TTAGGGTTTTTAATTTAATAGG
44097874 TTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAATTTAA-TAGG
44097897 TTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAATTTAA-TAGG
* *
44097920 TTAGGGTTTTTAAGTTAA-GGG
1 TTAGGGTTTTTAATTTAATAGG
44097941 TTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAATTTAA-TAGG
44097964 TTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAATTTAA-TAGG
* * *
44097987 TTAGAGTTTTTAAGTTAA-GGG
1 TTAGGGTTTTTAATTTAATAGG
44098008 TTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAATTTAA-TAGG
* * *
44098031 TTAGAGTTTTTAAATTAA-GGG
1 TTAGGGTTTTTAATTTAATAGG
* * *
44098052 TTTAAGGTTTCTAATTAAATTAGG
1 -TTAGGGTTTTTAATTTAA-TAGG
* *
44098076 TTAGGGTTTTTAAGTTAA-GGG
1 TTAGGGTTTTTAATTTAATAGG
* * *
44098097 TTTAAGGTTTCTAATTAAATTAGG
1 -TTAGGGTTTTTAATTTAA-TAGG
*
44098121 TTAGGGTTTTTAAGTTAA
1 TTAGGGTTTTTAATTTAA
44098139 GGGTATTAAT
Statistics
Matches: 570, Mismatches: 86, Indels: 54
0.80 0.12 0.08
Matches are distributed among these distances:
20 3 0.01
21 186 0.33
22 77 0.14
23 298 0.52
24 6 0.01
ACGTcount: A:0.27, C:0.01, G:0.25, T:0.46
Consensus pattern (22 bp):
TTAGGGTTTTTAATTTAATAGG
Found at i:44097621 original size:67 final size:65
Alignment explanation
Indices: 44097433--44098142 Score: 731
Period size: 67 Copynumber: 10.7 Consensus size: 65
44097423 TTAATTTAGT
* * *
44097433 TTAGGGTTTTTAATTTAATTAGGTTAAGGTTTTTAAGTTAAGGGTTAGGATTTTTAAGTTAAGGG
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAAGG
* * *
44097498 TTTAGTGTTTTTAAGTTAA--GGGTTAGGGTTTTTAAGTTAAGGGGTTAGGGTTTTTAAG-TAAC
1 -TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA-GGGTTAGGGTTTTTAAGTTAA-
*
44097560 GGG
63 AGG
* * * *
44097563 TTAGGGTTTTTAACTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAT
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA--GGGTTAGGGTTTTTAAGTTAA-
44097628 TAGG
63 -AGG
* *** * *
44097632 TTAGGGTTTTTAACTTAAGGGGGTTAGGGTTTTTAAGTTAAGGGTTATGGTTTTTAAG-TAACGG
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAA-AG
44097696 G
65 G
* * *** *
44097697 TTAGAGTTTTTAAGTTT-A--GGGTTTAAAATTTTTAA-TTAAATTAGGTTAGGGTTTTTAAGTT
1 TTAGGGTTTTTAA-TTTAATTAGG-TTAGGGTTTTTAAGTT-AA--GGGTTAGGGTTTTTAAGTT
*
44097758 AAGGG
61 AAAGG
*
44097763 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAAGGGGGTTAGGGTTTTTAAGTTAAA
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA--GGGTTAGGGTTTTTAAGTTAAA
*
44097828 AG
64 GG
* * *
44097830 TTAGAGTTTTTAATTTAATTAGGTTAGAGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAATTA
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAA--A
44097895 GG
64 GG
*
44097897 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAATTA
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAA--A
44097962 GG
64 GG
* *
44097964 TTAGGGTTTTTAATTTAATTAGGTTAGAGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAATTA
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAA--A
44098029 GG
64 GG
* * * * * *
44098031 TTAGAGTTTTTAAATTAA--GGGTTTAAGGTTTCTAA-TTAAATTAGGTTAGGGTTTTTAAGTTA
1 TTAGGGTTTTTAATTTAATTAGG-TTAGGGTTTTTAAGTT-AA--GGGTTAGGGTTTTTAAGTTA
*
44098093 AGGG
62 AAGG
* * *
44098097 TTTAAGGTTTCTAATTAAATTAGGTTAGGGTTTTTAAGTTAAGGGT
1 -TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGT
44098143 ATTAATGGTT
Statistics
Matches: 551, Mismatches: 66, Indels: 54
0.82 0.10 0.08
Matches are distributed among these distances:
63 5 0.01
64 49 0.09
65 61 0.11
66 88 0.16
67 267 0.48
68 39 0.07
69 42 0.08
ACGTcount: A:0.27, C:0.01, G:0.26, T:0.46
Consensus pattern (65 bp):
TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAAGG
Found at i:44097788 original size:44 final size:44
Alignment explanation
Indices: 44097433--44098138 Score: 611
Period size: 44 Copynumber: 15.9 Consensus size: 44
44097423 TTAATTTAGT
* * *
44097433 TTAGGGTTTTTAATTTAATTAGGTTAAGGTTTTTAAGTTAA-GGG
1 TTAGGGTTTTTAAGTTAA-TAGGTTAGGGTTTTTAAGTTAATAGG
* * * *
44097477 TTAGGATTTTTAAGTTAA-GGGTTTAGTGTTTTTAAGTTAA-GGG
1 TTAGGGTTTTTAAGTTAATAGG-TTAGGGTTTTTAAGTTAATAGG
** **
44097520 TTAGGGTTTTTAAGTTAAGGGGTTAGGGTTTTTAAG-TAACGGG
1 TTAGGGTTTTTAAGTTAATAGGTTAGGGTTTTTAAGTTAATAGG
* * *
44097563 TTAGGGTTTTTAACTAAATTAGGTTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAAGTTAA-TAGGTTAGGGTTTTTAAGTTAA-TAGG
* **
44097609 TTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAACTTAAGGGGG
1 TTAGGGTTTTTAAGTTAA-TAGGTTAGGGTTTTTAAGTTAA-TAGG
* * **
44097655 TTAGGGTTTTTAAGTTAA-GGGTTATGGTTTTTAAG-TAACGGG
1 TTAGGGTTTTTAAGTTAATAGGTTAGGGTTTTTAAGTTAATAGG
* ***
44097697 TTAGAGTTTTTAAGTT--TAGGGTTTAAAATTTTTAA-TTAAATTAGG
1 TTAGGGTTTTTAAGTTAATA-GG-TTAGGGTTTTTAAGTT-AA-TAGG
* *
44097742 TTAGGGTTTTTAAGTTAA-GGGTTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAAGTTAATAGGTTAGGGTTTTTAAGTTAA-TAGG
* ** *
44097786 TTAGGGTTTTTAATTTAAGGGGGTTAGGGTTTTTAAGTTAA-AAG
1 TTAGGGTTTTTAAGTTAA-TAGGTTAGGGTTTTTAAGTTAATAGG
* * * *
44097830 TTAGAGTTTTTAATTTAATTAGGTTAGAGTTTTTAAGTTAA-GGG
1 TTAGGGTTTTTAAGTTAA-TAGGTTAGGGTTTTTAAGTTAATAGG
* *
44097874 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAAGTTAA-TAGGTTAGGGTTTTTAAGTTAA-TAGG
* *
44097920 TTAGGGTTTTTAAGTTAA-GGGTTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAAGTTAATAGGTTAGGGTTTTTAAGTTAA-TAGG
* * *
44097964 TTAGGGTTTTTAATTTAATTAGGTTAGAGTTTTTAAGTTAA-GGG
1 TTAGGGTTTTTAAGTTAA-TAGGTTAGGGTTTTTAAGTTAATAGG
* * * *
44098008 TTAGGGTTTTTAATTTAATTAGGTTAGAGTTTTTAAATTAA-GGG
1 TTAGGGTTTTTAAGTTAA-TAGGTTAGGGTTTTTAAGTTAATAGG
* * *
44098052 TTTAAGGTTTCTAA-TTAAATTAGGTTAGGGTTTTTAAGTTAA-GGG
1 -TTAGGGTTTTTAAGTT-AA-TAGGTTAGGGTTTTTAAGTTAATAGG
* *
44098097 TTTAAGGTTTCTAA-TTAAATTAGGTTAGGGTTTTTAAGTTAA
1 -TTAGGGTTTTTAAGTT-AA-TAGGTTAGGGTTTTTAAGTTAA
44098139 GGGTATTAAT
Statistics
Matches: 577, Mismatches: 62, Indels: 45
0.84 0.09 0.07
Matches are distributed among these distances:
42 25 0.04
43 82 0.14
44 250 0.43
45 103 0.18
46 117 0.20
ACGTcount: A:0.27, C:0.01, G:0.25, T:0.46
Consensus pattern (44 bp):
TTAGGGTTTTTAAGTTAATAGGTTAGGGTTTTTAAGTTAATAGG
Found at i:44098187 original size:9 final size:9
Alignment explanation
Indices: 44098169--44098209 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
44098159 ATTCTCAAAT
44098169 AATA-TCAA
1 AATATTCAA
44098177 AATATTCAA
1 AATATTCAA
44098186 AATATTCAA
1 AATATTCAA
44098195 AATATT-AA
1 AATATTCAA
*
44098203 AAAATTC
1 AATATTC
44098210 CTATTTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
8 11 0.37
9 19 0.63
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.32
Consensus pattern (9 bp):
AATATTCAA
Found at i:44098204 original size:17 final size:18
Alignment explanation
Indices: 44098169--44098209 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
44098159 ATTCTCAAAT
44098169 AATA-TCAAAATATTCAA
1 AATATTCAAAATATTCAA
44098186 AATATTCAAAATATT-AA
1 AATATTCAAAATATTCAA
*
44098203 AAAATTC
1 AATATTC
44098210 CTATTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.32
Consensus pattern (18 bp):
AATATTCAAAATATTCAA
Found at i:44098707 original size:18 final size:18
Alignment explanation
Indices: 44098684--44098723 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
44098674 GACTCGGAAA
*
44098684 AGGATACATATAAGGGTT
1 AGGATACATATAAGGGCT
44098702 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
44098720 AGGA
1 AGGA
44098724 AACGCACCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.07, G:0.30, T:0.23
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:44099368 original size:7 final size:7
Alignment explanation
Indices: 44099358--44099382 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
44099348 TTATATACAT
44099358 AATACTA
1 AATACTA
44099365 AATACTA
1 AATACTA
44099372 AATACTA
1 AATACTA
44099379 AATA
1 AATA
44099383 TCAATTGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:44099590 original size:20 final size:20
Alignment explanation
Indices: 44099553--44099590 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
44099543 TTTATTTTTA
*
44099553 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
44099573 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
44099591 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:44100508 original size:12 final size:12
Alignment explanation
Indices: 44100484--44100526 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 12
44100474 ATTTTTATGG
44100484 TTTAAAAAA-AT
1 TTTAAAAAATAT
44100495 TTTAAAAAATAT
1 TTTAAAAAATAT
* *
44100507 TTTTAAAATTA-
1 TTTAAAAAATAT
44100518 TTTAAAAAA
1 TTTAAAAAA
44100527 AAGGAGTTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TTTAAAAAATAT
Found at i:44102608 original size:38 final size:38
Alignment explanation
Indices: 44102561--44102645 Score: 109
Period size: 38 Copynumber: 2.2 Consensus size: 38
44102551 AAATAACATA
* **
44102561 AAAAATAATAAAAAATCATTAA-AATTATTAAAATTTAT
1 AAAAATAATAAAAAATAATTAATAACCA-TAAAATTTAT
* *
44102599 AAAATTAATAAAAATTAATTAATAACCATAAAATTTAT
1 AAAAATAATAAAAAATAATTAATAACCATAAAATTTAT
44102637 AAAAATAAT
1 AAAAATAAT
44102646 TGATTAGAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
38 37 0.93
39 3 0.08
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.33
Consensus pattern (38 bp):
AAAAATAATAAAAAATAATTAATAACCATAAAATTTAT
Found at i:44102878 original size:9 final size:9
Alignment explanation
Indices: 44102866--44102897 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
44102856 AAATTATTTT
44102866 TTTTATAAA
1 TTTTATAAA
44102875 TTTTATAAA
1 TTTTATAAA
44102884 TTTTATAAA
1 TTTTATAAA
44102893 TTTTA
1 TTTTA
44102898 ATTAATTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTTATAAA
Found at i:44102926 original size:23 final size:21
Alignment explanation
Indices: 44102870--44102929 Score: 72
Period size: 23 Copynumber: 2.9 Consensus size: 21
44102860 TATTTTTTTT
*
44102870 ATAAATTTT-ATAAATTT-T-
1 ATAAATTTTAATTAATTTCTA
44102888 ATAAATTTTAATTAATTTCTA
1 ATAAATTTTAATTAATTTCTA
44102909 ATAATATTTATAATTAATTTC
1 ATAA-ATTT-TAATTAATTTC
44102930 ATGACTTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
18 9 0.25
19 7 0.19
20 1 0.03
21 4 0.11
22 4 0.11
23 11 0.31
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (21 bp):
ATAAATTTTAATTAATTTCTA
Found at i:44103268 original size:61 final size:61
Alignment explanation
Indices: 44103188--44103311 Score: 187
Period size: 61 Copynumber: 2.0 Consensus size: 61
44103178 GCTTATTGGA
* * * *
44103188 AAAATAATCCTTAACTTTTAAGTT-AAAAGATTTGCAATTATCTAATTTTATTTTTAGGCTT
1 AAAATAAGCCTTAAATTTTAAGTTAAAAAGATTAGCAATTATCTAATTTT-TGTTTAGGCTT
*
44103249 AAAATAAGCCTTAAATTTTAAGTTAAAAAGATTAGCCATTATCTAATTTTTGTTTAGGCTT
1 AAAATAAGCCTTAAATTTTAAGTTAAAAAGATTAGCAATTATCTAATTTTTGTTTAGGCTT
44103310 AA
1 AA
44103312 TATGCACTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
61 34 0.60
62 23 0.40
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.43
Consensus pattern (61 bp):
AAAATAAGCCTTAAATTTTAAGTTAAAAAGATTAGCAATTATCTAATTTTTGTTTAGGCTT
Found at i:44103536 original size:7 final size:8
Alignment explanation
Indices: 44103525--44103587 Score: 60
Period size: 9 Copynumber: 7.8 Consensus size: 8
44103515 AAAAATTCTT
44103525 TAAAAATA
1 TAAAAATA
44103533 -AAAAATA
1 TAAAAATA
44103540 TAAAAAATA
1 T-AAAAATA
44103549 TTAAAAATTA
1 -TAAAAA-TA
*
44103559 TTAAAATTA
1 -TAAAAATA
44103568 TAAAAAT-
1 TAAAAATA
44103575 T-AAAATA
1 TAAAAATA
44103582 TAAAAA
1 TAAAAA
44103588 AATTTACTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
6 5 0.11
7 9 0.19
8 10 0.21
9 14 0.30
10 9 0.19
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (8 bp):
TAAAAATA
Found at i:44103544 original size:9 final size:9
Alignment explanation
Indices: 44103526--44103590 Score: 57
Period size: 8 Copynumber: 7.6 Consensus size: 9
44103516 AAAATTCTTT
44103526 AAAA-ATAA
1 AAAATATAA
44103534 AAAATATAA
1 AAAATATAA
44103543 AAAATATTAA
1 AAAATA-TAA
* *
44103553 AAATTATTA
1 AAAATATAA
*
44103562 AAATTAT-A
1 AAAATATAA
44103570 AAAAT-TAA
1 AAAATATAA
*
44103578 AATATA-AA
1 AAAATATAA
44103586 AAAAT
1 AAAAT
44103591 TTACTAAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
7 1 0.02
8 20 0.42
9 19 0.40
10 8 0.17
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (9 bp):
AAAATATAA
Found at i:44103553 original size:19 final size:18
Alignment explanation
Indices: 44103526--44103590 Score: 57
Period size: 19 Copynumber: 3.8 Consensus size: 18
44103516 AAAATTCTTT
44103526 AAAA-ATAAAAAATATAA
1 AAAATATAAAAAATATAA
* *
44103543 AAAATATTAAAAATTATTA
1 AAAATA-TAAAAAATATAA
*
44103562 AAATTAT-AAAAAT-TAA
1 AAAATATAAAAAATATAA
*
44103578 AATATA-AAAAAAT
1 AAAATATAAAAAAT
44103591 TTACTAAAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
16 12 0.32
17 9 0.24
18 2 0.05
19 15 0.39
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAATATAAAAAATATAA
Found at i:44103579 original size:35 final size:36
Alignment explanation
Indices: 44103512--44103611 Score: 107
Period size: 35 Copynumber: 2.8 Consensus size: 36
44103502 TAGAAAAGAA
* *
44103512 ATTAAAAATTCTTTAAAAATA-AAAAATATAAAAAAT
1 ATTAAAAATT-ATTAAAATTATAAAAATATAAAAAAT
*
44103548 ATTAAAAATTATTAAAATTATAAAAAT-TAAAATAT
1 ATTAAAAATTATTAAAATTATAAAAATATAAAAAAT
* * *
44103583 A-AAAAAATTTACTAAAATTTTAAAAATAT
1 ATTAAAAA-TTATTAAAATTATAAAAATAT
44103612 TAGATATTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
34 5 0.09
35 33 0.60
36 17 0.31
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (36 bp):
ATTAAAAATTATTAAAATTATAAAAATATAAAAAAT
Found at i:44103585 original size:14 final size:15
Alignment explanation
Indices: 44103558--44103587 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
44103548 ATTAAAAATT
44103558 ATTAAAATTATAAAA
1 ATTAAAATTATAAAA
44103573 ATTAAAA-TATAAAA
1 ATTAAAATTATAAAA
44103587 A
1 A
44103588 AATTTACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
ATTAAAATTATAAAA
Found at i:44103589 original size:43 final size:42
Alignment explanation
Indices: 44103525--44103607 Score: 107
Period size: 43 Copynumber: 1.9 Consensus size: 42
44103515 AAAAATTCTT
44103525 TAAAAATAAAAAATATAAAAAATATTA-AAAATTATTAAAATTA
1 TAAAAATAAAAAATATAAAAAAT-TTACAAAATT-TTAAAATTA
*
44103568 TAAAAAT-TAAAATATAAAAAAATTTACTAAAATTTTAAAA
1 TAAAAATAAAAAATAT-AAAAAATTTAC-AAAATTTTAAAA
44103608 ATATTAGATA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
42 10 0.28
43 20 0.56
44 6 0.17
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.31
Consensus pattern (42 bp):
TAAAAATAAAAAATATAAAAAATTTACAAAATTTTAAAATTA
Found at i:44108840 original size:12 final size:12
Alignment explanation
Indices: 44108823--44108849 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
44108813 TGGATTGGAA
44108823 GCAATATGAAGT
1 GCAATATGAAGT
44108835 GCAATATGAAGT
1 GCAATATGAAGT
44108847 GCA
1 GCA
44108850 GTTTGATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.11, G:0.26, T:0.22
Consensus pattern (12 bp):
GCAATATGAAGT
Found at i:44110623 original size:59 final size:59
Alignment explanation
Indices: 44110531--44110652 Score: 226
Period size: 59 Copynumber: 2.1 Consensus size: 59
44110521 ACCAAGACTT
* *
44110531 GGACAATAACTACGATACCCTTTTTGTACATGGGAATTTCTCCAAAACATACATTATAA
1 GGACAATAACTACGATACCCTTTTTGTACATGGGAATATCCCCAAAACATACATTATAA
44110590 GGACAATAACTACGATACCCTTTTTGTACATGGGAATATCCCCAAAACATACATTATAA
1 GGACAATAACTACGATACCCTTTTTGTACATGGGAATATCCCCAAAACATACATTATAA
44110649 GGAC
1 GGAC
44110653 TTAGGATCAA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (59 bp):
GGACAATAACTACGATACCCTTTTTGTACATGGGAATATCCCCAAAACATACATTATAA
Found at i:44134853 original size:22 final size:22
Alignment explanation
Indices: 44134825--44134870 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
44134815 CTACAAACAA
44134825 TTCACGTACTAAGCTCTCATGT
1 TTCACGTACTAAGCTCTCATGT
44134847 TTCACGTACTAAGCTCTCATGT
1 TTCACGTACTAAGCTCTCATGT
44134869 TT
1 TT
44134871 GAACAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.26, G:0.13, T:0.39
Consensus pattern (22 bp):
TTCACGTACTAAGCTCTCATGT
Found at i:44134952 original size:17 final size:16
Alignment explanation
Indices: 44134917--44134976 Score: 111
Period size: 16 Copynumber: 3.7 Consensus size: 16
44134907 GCCTCTAAGG
44134917 TTAGAGGTGTATTGGA
1 TTAGAGGTGTATTGGA
44134933 TTAGAGGTGTATTGGGA
1 TTAGAGGTGTATT-GGA
44134950 TTAGAGGTGTATTGGA
1 TTAGAGGTGTATTGGA
44134966 TTAGAGGTGTA
1 TTAGAGGTGTA
44134977 ATAGCTAATC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 27 0.63
17 16 0.37
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.37
Consensus pattern (16 bp):
TTAGAGGTGTATTGGA
Found at i:44135041 original size:44 final size:45
Alignment explanation
Indices: 44134957--44135047 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
44134947 GGATTAGAGG
* * *
44134957 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
44135002 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
44135046 TG
1 TG
44135048 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:44135229 original size:16 final size:16
Alignment explanation
Indices: 44135192--44135246 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
44135182 TTAATCATAT
*
44135192 TTAAACATA-ATTATAA
1 TTAAA-ATATATTTTAA
44135208 TT-AAATATATTTTAA
1 TTAAAATATATTTTAA
44135223 TTAAAATATATAATTTAA
1 TTAAAATATAT--TTTAA
44135241 -TAAAAT
1 TTAAAAT
44135247 TCTTATAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 3 0.09
15 10 0.29
16 10 0.29
17 6 0.18
18 5 0.15
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAAATATATTTTAA
Found at i:44135239 original size:18 final size:18
Alignment explanation
Indices: 44135198--44135246 Score: 61
Period size: 16 Copynumber: 2.9 Consensus size: 18
44135188 ATATTTAAAC
44135198 ATAATTATAATT-AAATAT
1 ATAATT-TAATTAAAATAT
44135216 AT--TTTAATTAAAATAT
1 ATAATTTAATTAAAATAT
44135232 ATAATTTAA-TAAAAT
1 ATAATTTAATTAAAAT
44135247 TCTTATAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 5 0.18
16 10 0.36
17 6 0.21
18 7 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATAATTTAATTAAAATAT
Found at i:44135383 original size:156 final size:156
Alignment explanation
Indices: 44135099--44135426 Score: 611
Period size: 156 Copynumber: 2.1 Consensus size: 156
44135089 TAGAATACCC
* *
44135099 TTAGCATAAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTAATGTTATTTAAATTTTAATAAGATTATTA
*
44135164 TTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATAATTAAATATATTTTAATTAAAA
66 TTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATAACTAAATATATTTTAATTAAAA
44135229 TATATAATTTAATAAAATTCTTATAA
131 TATATAATTTAATAAAATTCTTATAA
44135255 TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTAATGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTAATGTTATTTAAATTTTAATAAGATTATTA
*
44135320 TTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATTACTAAATATATTTTAATTAAAA
66 TTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATAACTAAATATATTTTAATTAAAA
44135385 TATATAATTTAATAAAATTCTTATAA
131 TATATAATTTAATAAAATTCTTATAA
*
44135411 TTAGCAGAAATTTGTT
1 TTAGCAGAAAATTGTT
44135427 ATTGTTATTT
Statistics
Matches: 167, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
156 167 1.00
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.47
Consensus pattern (156 bp):
TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTAATGTTATTTAAATTTTAATAAGATTATTA
TTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATAACTAAATATATTTTAATTAAAA
TATATAATTTAATAAAATTCTTATAA
Found at i:44135389 original size:18 final size:17
Alignment explanation
Indices: 44135368--44135402 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
44135358 TTATTACTAA
*
44135368 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
44135386 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
44135403 TCTTATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:44135393 original size:137 final size:137
Alignment explanation
Indices: 44135104--44135544 Score: 306
Period size: 156 Copynumber: 3.1 Consensus size: 137
44135094 TACCCTTAGC
*
44135104 ATAAAATTGTT-TTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTAT
1 ATAAAATTCTTATTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTAT
*
44135168 CAGTAATAAATATTTTAATCATATTTAAACATAATTATAATTAAATATATTTTAATTAAAATATA
66 CAGTAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATA
44135233 TAATTTA
131 TAATTTA
* * * * * *
44135240 ATAAAATTCTTATAATTAGCAGAAAATTG-TT-TTGGTAAATGATTATTGTTAATGTTATTTAA-
1 ATAAAATTC-T-T-ATT-G--GTAAA-TGATTATT-GTTATTG-TTATT-TAAATTTTA-ATAAG
* * * * ** *
44135302 ATT-TTA--ATAAGATTATTATTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATTA
55 ATTATTATTATCAG-TAATAAATAT-TTTAAT-CATA---T--T--T----AAACATAATTATTA
*
44135364 CTAAATATATTTTAATTAAAATATATAATTTA
106 TTAAATATATTTTAATTAAAATATATAATTTA
*** * * *
44135396 ATAAAATTCTTATAATTAGCA-GA-AATTTGTTATTGTTATTTAAATTTTAATAAGATTATTAAT
1 ATAAAATTCTTATTGGTA-AATGATTA-TTGTTATTGTTATTTAAATTTTAATAAGATTATTATT
* * * * ****
44135459 ATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATACATTATAATTTTGGTA
64 ATCAGTAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATA
44135524 TATAATTTA
129 TATAATTTA
44135533 ATAAAATTCTTA
1 ATAAAATTCTTA
44135545 ATAATTCATA
Statistics
Matches: 228, Mismatches: 43, Indels: 67
0.67 0.13 0.20
Matches are distributed among these distances:
136 8 0.04
137 52 0.23
138 1 0.00
140 2 0.01
141 2 0.01
142 6 0.03
143 19 0.08
144 14 0.06
145 14 0.06
146 3 0.01
147 3 0.01
148 14 0.06
149 13 0.06
150 13 0.06
151 6 0.03
152 1 0.00
153 2 0.01
154 1 0.00
155 1 0.00
156 53 0.23
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.47
Consensus pattern (137 bp):
ATAAAATTCTTATTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTAT
CAGTAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATA
TAATTTA
Found at i:44135502 original size:67 final size:67
Alignment explanation
Indices: 44135294--44135506 Score: 152
Period size: 67 Copynumber: 3.1 Consensus size: 67
44135284 ATTGTTAATG
* * *
44135294 TTATTTAAATTTTAATAAGATTATTATTATCAGTAATAAATATTTTAATCATATTTAAACATAAT
1 TTATTTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAACATAAT
44135359 TA
66 TA
* * * * ** ***
44135361 TTACTAAATATATTTTAATTAA-AATATATAAT-TTAAT-A-AAATTCTTATAAT--TAGCAGAA
1 TTA-T--TTAAATTTTAA-TAAGATTAT-TAATATCAATAATAAATAATT-TAATCATA-TTTAA
** * *
44135420 ATTTGTTATTG
59 A--CATAATTA
44135431 TTATTTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAACATAAT
1 TTATTTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAACATAAT
44135496 TA
66 TA
44135498 TTA-TTAAAT
1 TTATTTAAAT
44135507 ACATTATAAT
Statistics
Matches: 103, Mismatches: 28, Indels: 31
0.64 0.17 0.19
Matches are distributed among these distances:
66 13 0.13
67 29 0.28
68 15 0.15
69 15 0.15
70 25 0.24
71 6 0.06
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (67 bp):
TTATTTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAACATAAT
TA
Found at i:44135584 original size:137 final size:135
Alignment explanation
Indices: 44135306--44135584 Score: 330
Period size: 137 Copynumber: 2.0 Consensus size: 135
44135296 ATTTAAATTT
* * *
44135306 TAATAAGATTATTATTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATTACTAAATA
1 TAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTACTAAATA
* * * *
44135371 TATTTTAATTAAAATATATAATTTAATAAAATTCTTATAATTAGCAGAAATTTGTTATTGTTATT
66 CATTATAATTAAAATATATAATTTAATAAAATTCTTATAATTA-CA-AAATTTCTTATTGTTACT
* **
44135436 TAAATTT
129 CAAATCA
*
44135443 TAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATA
1 TAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTACTAAATA
**** *
44135508 CATTATAATTTTGGTATATAATTTAATAAAATTCTTAATAATT-C-ATA-TTCTTATATGAATTT
66 CATTATAATTAAAATATATAATTTAATAAAATTCTT-ATAATTACAAAATTTCTTAT-TG---TT
44135570 ACTCAAATCA
126 ACTCAAATCA
44135580 TAATA
1 TAATA
44135585 TATGATAAAT
Statistics
Matches: 121, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
133 6 0.05
134 4 0.03
136 1 0.01
137 104 0.86
138 6 0.05
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.45
Consensus pattern (135 bp):
TAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTACTAAATA
CATTATAATTAAAATATATAATTTAATAAAATTCTTATAATTACAAAATTTCTTATTGTTACTCA
AATCA
Found at i:44141701 original size:13 final size:13
Alignment explanation
Indices: 44141683--44141708 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44141673 TAGCTAAACT
44141683 GAAACAGAAGGAA
1 GAAACAGAAGGAA
44141696 GAAACAGAAGGAA
1 GAAACAGAAGGAA
44141709 CGGCAGCTAA
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:0.62, C:0.08, G:0.31, T:0.00
Consensus pattern (13 bp):
GAAACAGAAGGAA
Found at i:44143533 original size:15 final size:15
Alignment explanation
Indices: 44143515--44143557 Score: 54
Period size: 13 Copynumber: 3.0 Consensus size: 15
44143505 ATATCAATAA
44143515 AACACATAGCTAATT
1 AACACATAGCTAATT
**
44143530 AACACATAATTAA--
1 AACACATAGCTAATT
44143543 AACACATAGCTAATT
1 AACACATAGCTAATT
44143558 TAAACAAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
13 11 0.50
15 11 0.50
ACGTcount: A:0.51, C:0.19, G:0.05, T:0.26
Consensus pattern (15 bp):
AACACATAGCTAATT
Found at i:44144380 original size:99 final size:99
Alignment explanation
Indices: 44144271--44144455 Score: 307
Period size: 99 Copynumber: 1.9 Consensus size: 99
44144261 TGATTTGTAC
*
44144271 AAAAATGGACAGCATTTAAGCACTAATTTGGACAACATTAATATACTAAAAAATGGACAGCAATT
1 AAAAATGGACAGCATTTAAGCACTAATTTGGACAACATTAATATACTAAAAAATGGACAACAATT
* *
44144336 AAGCATCAATTTGGACAGCATTAATATGCTAAAA
66 AAACACCAATTTGGACAGCATTAATATGCTAAAA
* * * *
44144370 AAAAATGGACATCATTTAAGCACTAATTTGGACAGCATTAATATGCTCAAAAATGGACAACAATT
1 AAAAATGGACAGCATTTAAGCACTAATTTGGACAACATTAATATACTAAAAAATGGACAACAATT
44144435 AAACACCAATTTGGACAGCAT
66 AAACACCAATTTGGACAGCAT
44144456 CTTATCATCA
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
99 79 1.00
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.25
Consensus pattern (99 bp):
AAAAATGGACAGCATTTAAGCACTAATTTGGACAACATTAATATACTAAAAAATGGACAACAATT
AAACACCAATTTGGACAGCATTAATATGCTAAAA
Found at i:44144398 original size:51 final size:48
Alignment explanation
Indices: 44144271--44144455 Score: 246
Period size: 48 Copynumber: 3.8 Consensus size: 48
44144261 TGATTTGTAC
* * *
44144271 AAAAATGGACAGCATTTAAGCACTAATTTGGACAACATTAATATACTA
1 AAAAATGGACAGCAATTAAGCACTAATTTGGACAGCATTAATATGCTA
44144319 AAAAATGGACAGCAATTAAGCA-TCAATTTGGACAGCATTAATATGCTAAAA
1 AAAAATGGACAGCAATTAAGCACT-AATTTGGACAGCATTAATATGCT---A
* * *
44144370 AAAAATGGACATCATTTAAGCACTAATTTGGACAGCATTAATATGCTC
1 AAAAATGGACAGCAATTAAGCACTAATTTGGACAGCATTAATATGCTA
* * *
44144418 AAAAATGGACAACAATTAAACACCAATTTGGACAGCAT
1 AAAAATGGACAGCAATTAAGCACTAATTTGGACAGCAT
44144456 CTTATCATCA
Statistics
Matches: 122, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
47 1 0.01
48 76 0.62
51 44 0.36
52 1 0.01
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.25
Consensus pattern (48 bp):
AAAAATGGACAGCAATTAAGCACTAATTTGGACAGCATTAATATGCTA
Found at i:44146788 original size:19 final size:19
Alignment explanation
Indices: 44146764--44146804 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
44146754 CTTCCACGAA
44146764 GATACTTTCAAAAACACTC
1 GATACTTTCAAAAACACTC
44146783 GATACTTTCAAAAACACTC
1 GATACTTTCAAAAACACTC
44146802 GAT
1 GAT
44146805 CCCCAATCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.27
Consensus pattern (19 bp):
GATACTTTCAAAAACACTC
Found at i:44152208 original size:48 final size:47
Alignment explanation
Indices: 44152155--44152397 Score: 222
Period size: 48 Copynumber: 5.0 Consensus size: 47
44152145 ACATTCGAAT
* * * *
44152155 AACATTGATTTGTACAAAAATGGACAGCATTTAGGCACTAATTTGGAC
1 AACATTAATTTGTA-AAAAATGGACAACAATTAAGCACTAATTTGGAC
**
44152203 AACATTAATATACTAAAAAATGGACAACAATTAAGCA-TCAATTTGGAC
1 AACATTAAT-TTGTAAAAAATGGACAACAATTAAGCACT-AATTTGGAC
* **
44152251 AGCATTAATATACTAAAAAAT-GAGCAACAATTAAGC-CTCAATTTGGAC
1 AACATTAAT-TTGTAAAAAATGGA-CAACAATTAAGCACT-AATTTGGAC
* * * *
44152299 AACATTAATATGCTAAAAAAAATGGACATCATTTAAGAACTAATTTGGAC
1 AACATTAATTTG-T--AAAAAATGGACAACAATTAAGCACTAATTTGGAC
* * * *
44152349 AACATTAATATGCTCAATAATGGACAACAATTAAGCACCAATTTGGAC
1 AACATTAATTTG-TAAAAAATGGACAACAATTAAGCACTAATTTGGAC
44152397 A
1 A
44152398 GCATCTTATC
Statistics
Matches: 166, Mismatches: 20, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
47 3 0.02
48 117 0.70
49 3 0.02
50 39 0.23
51 4 0.02
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.26
Consensus pattern (47 bp):
AACATTAATTTGTAAAAAATGGACAACAATTAAGCACTAATTTGGAC
Found at i:44152217 original size:23 final size:23
Alignment explanation
Indices: 44152191--44152266 Score: 66
Period size: 23 Copynumber: 3.2 Consensus size: 23
44152181 GCATTTAGGC
44152191 ACTAATTTGGACAACATTAATAT
1 ACTAATTTGGACAACATTAATAT
** *
44152214 ACTAAAAAATGGACAACAATTAAGCAT
1 ACT--AATTTGGACAAC-ATTAA-TAT
*
44152241 -C-AATTTGGACAGCATTAATAT
1 ACTAATTTGGACAACATTAATAT
44152262 ACTAA
1 ACTAA
44152267 AAAATGAGCA
Statistics
Matches: 40, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
21 2 0.05
22 6 0.15
23 14 0.35
25 10 0.25
26 6 0.15
27 2 0.05
ACGTcount: A:0.47, C:0.14, G:0.11, T:0.28
Consensus pattern (23 bp):
ACTAATTTGGACAACATTAATAT
Found at i:44152358 original size:98 final size:96
Alignment explanation
Indices: 44152170--44152397 Score: 282
Period size: 98 Copynumber: 2.4 Consensus size: 96
44152160 TGATTTGTAC
* * * *
44152170 AAAAATGGACAGCATTTAGGCACTAATTTGGACAACATTAATATACTAAAAAATGGACAACAATT
1 AAAAATGGACAACAATTAAGCACCAATTTGGACAACATTAATATACTAAAAAATGGACAACAATT
* *
44152235 AAGCATCAATTTGGACAGCATTAATATACTA
66 AAGAATCAATTTGGACAACATTAATATACTA
* *
44152266 AAAAAT-GAGCAACAATTAAGC-CTCAATTTGGACAACATTAATATGCTAAAAAAAATGGACATC
1 AAAAATGGA-CAACAATTAAGCAC-CAATTTGGACAACATTAATATACT--AAAAAATGGACAAC
* * *
44152329 ATTTAAGAA-CTAATTTGGACAACATTAATATGCTC
62 AATTAAGAATC-AATTTGGACAACATTAATATACTA
*
44152364 AATAATGGACAACAATTAAGCACCAATTTGGACA
1 AAAAATGGACAACAATTAAGCACCAATTTGGACA
44152398 GCATCTTATC
Statistics
Matches: 113, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
95 3 0.03
96 37 0.33
97 1 0.01
98 69 0.61
99 3 0.03
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.25
Consensus pattern (96 bp):
AAAAATGGACAACAATTAAGCACCAATTTGGACAACATTAATATACTAAAAAATGGACAACAATT
AAGAATCAATTTGGACAACATTAATATACTA
Found at i:44152369 original size:27 final size:26
Alignment explanation
Indices: 44152290--44152382 Score: 63
Period size: 27 Copynumber: 3.7 Consensus size: 26
44152280 ATTAAGCCTC
*
44152290 AATTTGGACAACATTAATATGCTAAAA
1 AATTTGGACAACATTAATATGCT-AAT
** * *
44152317 AAAATGGACATCATT--TAAG--AACT
1 AATTTGGACAACATTAATATGCTAA-T
44152340 AATTTGGACAACATTAATATGCTCAAT
1 AATTTGGACAACATTAATATGCT-AAT
44152367 AA--TGGACAACAATTAA
1 AATTTGGACAAC-ATTAA
44152383 GCACCAATTT
Statistics
Matches: 50, Mismatches: 9, Indels: 15
0.68 0.12 0.20
Matches are distributed among these distances:
22 2 0.04
23 12 0.24
25 14 0.28
26 5 0.10
27 15 0.30
28 2 0.04
ACGTcount: A:0.47, C:0.13, G:0.12, T:0.28
Consensus pattern (26 bp):
AATTTGGACAACATTAATATGCTAAT
Found at i:44153044 original size:42 final size:43
Alignment explanation
Indices: 44152977--44153062 Score: 102
Period size: 42 Copynumber: 2.0 Consensus size: 43
44152967 ACATGTTATA
* ** * *
44152977 ATATATCGATGCCACTGTCTTAGACAAGGTCTTACACGAAATC
1 ATATATCGATGCCAATGTCCCAGACAAGGTCGTACACAAAATC
* *
44153020 ATATA-CGATGCCAATGTCCCAGACATGTTCGTACACAAAATC
1 ATATATCGATGCCAATGTCCCAGACAAGGTCGTACACAAAATC
44153062 A
1 A
44153063 CACCTCAGAA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 31 0.86
43 5 0.14
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (43 bp):
ATATATCGATGCCAATGTCCCAGACAAGGTCGTACACAAAATC
Found at i:44164468 original size:27 final size:27
Alignment explanation
Indices: 44164436--44164569 Score: 155
Period size: 27 Copynumber: 5.0 Consensus size: 27
44164426 AGACCCCAAA
*
44164436 ATAGGGTAAAATGACTGAAATACCCCT
1 ATAGGGTAAAATGACTGAAATACCCCC
*
44164463 GTAGGGTAAAATGA-TCGAAATACCCCC
1 ATAGGGTAAAATGACT-GAAATACCCCC
* *
44164490 GTAGGGTAAAATGA-TCGAAATACCTCC
1 ATAGGGTAAAATGACT-GAAATACCCCC
* *
44164517 ACAGGGTAAAATGACCGAAATACCCCC
1 ATAGGGTAAAATGACTGAAATACCCCC
* **
44164544 ATAGGATAAAATGACTGTTATACCCC
1 ATAGGGTAAAATGACTGAAATACCCC
44164570 TAGGAGATGA
Statistics
Matches: 93, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
26 1 0.01
27 92 0.99
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (27 bp):
ATAGGGTAAAATGACTGAAATACCCCC
Found at i:44164512 original size:54 final size:54
Alignment explanation
Indices: 44164436--44164560 Score: 173
Period size: 54 Copynumber: 2.3 Consensus size: 54
44164426 AGACCCCAAA
** *
44164436 ATAGGGTAAAATGACTGAAATACC-CCTGTAGGGTAAAATGATCGAAATACCCCC
1 ATAGGGTAAAATGACTGAAATACCTCC-ACAGGGTAAAATGACCGAAATACCCCC
*
44164490 GTAGGGTAAAATGA-TCGAAATACCTCCACAGGGTAAAATGACCGAAATACCCCC
1 ATAGGGTAAAATGACT-GAAATACCTCCACAGGGTAAAATGACCGAAATACCCCC
*
44164544 ATAGGATAAAATGACTG
1 ATAGGGTAAAATGACTG
44164561 TTATACCCCT
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
53 1 0.02
54 58 0.94
55 3 0.05
ACGTcount: A:0.40, C:0.20, G:0.21, T:0.19
Consensus pattern (54 bp):
ATAGGGTAAAATGACTGAAATACCTCCACAGGGTAAAATGACCGAAATACCCCC
Found at i:44164731 original size:26 final size:26
Alignment explanation
Indices: 44164702--44164782 Score: 108
Period size: 26 Copynumber: 3.1 Consensus size: 26
44164692 TGGAGGAAAT
*
44164702 ATACTGTTACTGGCAGCTTTGCTACG
1 ATACTGTTACTGGCAGCTTTGCTGCG
* * *
44164728 ATACTGTTATTGGCAACTTTGCTGCT
1 ATACTGTTACTGGCAGCTTTGCTGCG
* *
44164754 ATACTATTACTGGTAGCTTTGCTGCG
1 ATACTGTTACTGGCAGCTTTGCTGCG
44164780 ATA
1 ATA
44164783 TTAGTGTGTT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (26 bp):
ATACTGTTACTGGCAGCTTTGCTGCG
Found at i:44164964 original size:33 final size:34
Alignment explanation
Indices: 44164916--44164983 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 34
44164906 GGCCCACACC
* *
44164916 GTTACTGTATTGGGCTAAGGCCCACACTGT-ACT
1 GTTACTGAATAGGGCTAAGGCCCACACTGTCACT
* *
44164949 GTTACTGAATAGGGCTCAGGCCCAGACTGTCACT
1 GTTACTGAATAGGGCTAAGGCCCACACTGTCACT
44164983 G
1 G
44164984 CTTATTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 26 0.87
34 4 0.13
ACGTcount: A:0.22, C:0.25, G:0.26, T:0.26
Consensus pattern (34 bp):
GTTACTGAATAGGGCTAAGGCCCACACTGTCACT
Found at i:44178457 original size:70 final size:70
Alignment explanation
Indices: 44178343--44178483 Score: 273
Period size: 70 Copynumber: 2.0 Consensus size: 70
44178333 GGTTACCTCT
44178343 ATGGATAAAGGTTGAAACCTTCTACAACGATTTGAATCTCTCAAGTAGGCAGTTGATCGATGCAG
1 ATGGATAAAGGTTGAAACCTTCTACAACGATTTGAATCTCTCAAGTAGGCAGTTGATCGATGCAG
44178408 CAGCC
66 CAGCC
*
44178413 ATGGATAAAGGTTGAAACCTTCTACAACGATTTGAATCTTTCAAGTAGGCAGTTGATCGATGCAG
1 ATGGATAAAGGTTGAAACCTTCTACAACGATTTGAATCTCTCAAGTAGGCAGTTGATCGATGCAG
44178478 CAGCC
66 CAGCC
44178483 A
1 A
44178484 GTGGTACACT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (70 bp):
ATGGATAAAGGTTGAAACCTTCTACAACGATTTGAATCTCTCAAGTAGGCAGTTGATCGATGCAG
CAGCC
Found at i:44180063 original size:29 final size:28
Alignment explanation
Indices: 44180020--44180116 Score: 124
Period size: 29 Copynumber: 3.4 Consensus size: 28
44180010 CGACGTATTG
*
44180020 ACGACCATC-ACATATGAAAATGGATGTT
1 ACGACCATCGA-ATATGAAAAGGGATGTT
*
44180048 AACGACCATCGAATATGAAAAGGGATGGTG
1 -ACGACCATCGAATATGAAAAGGGAT-GTT
44180078 ACGACCATCGAATATGAAAAGGGATGGTT
1 ACGACCATCGAATATGAAAAGGGAT-GTT
*
44180107 TCGACCATCG
1 ACGACCATCG
44180117 TTTAAAGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
29 59 0.95
30 3 0.05
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.21
Consensus pattern (28 bp):
ACGACCATCGAATATGAAAAGGGATGTT
Found at i:44180112 original size:58 final size:59
Alignment explanation
Indices: 44180018--44180135 Score: 152
Period size: 58 Copynumber: 2.0 Consensus size: 59
44180008 AACGACGTAT
* *
44180018 TGACGACCATCACATATGAAAATGGATGTTAACGACCATCGAAT-ATGAAAAGGGATGG
1 TGACGACCATCACATATGAAAAGGGATGTTAACGACCATCGAATAAAGAAAAGGGATGG
* **
44180076 TGACGACCATCGA-ATATGAAAAGGGATGGTT-TCGACCATCGTTTAAAGAAAAGGGATGG
1 TGACGACCATC-ACATATGAAAAGGGAT-GTTAACGACCATCGAATAAAGAAAAGGGATGG
44180135 T
1 T
44180136 TTCAAAAATA
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
58 34 0.65
59 18 0.35
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.22
Consensus pattern (59 bp):
TGACGACCATCACATATGAAAAGGGATGTTAACGACCATCGAATAAAGAAAAGGGATGG
Found at i:44180129 original size:30 final size:29
Alignment explanation
Indices: 44180050--44180138 Score: 115
Period size: 29 Copynumber: 3.0 Consensus size: 29
44180040 TGGATGTTAA
* **
44180050 CGACCATCGAATATGAAAAGGGATGGTGA
1 CGACCATCGAATAAGAAAAGGGATGGTTT
*
44180079 CGACCATCGAATATGAAAAGGGATGGTTT
1 CGACCATCGAATAAGAAAAGGGATGGTTT
**
44180108 CGACCATCGTTTAAAGAAAAGGGATGGTTT
1 CGACCATCGAAT-AAGAAAAGGGATGGTTT
44180138 C
1 C
44180139 AAAAATATGA
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 37 0.69
30 17 0.31
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.22
Consensus pattern (29 bp):
CGACCATCGAATAAGAAAAGGGATGGTTT
Done.