Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007822.1 Hibiscus syriacus cultivar Beakdansim tig00110159_pilon, whole genome shotgun sequence
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: 1828853
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 10
Found at i:1448514 original size:31 final size:30
Alignment explanation
Indices: 1448476--1448541 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
1448466 AGGCAAATAC
**
1448476 ATTAAAATA-AAATTAATTTAAACTTTGAGTT
1 ATTAAAATATAAA-TAAAATAAA-TTTGAGTT
*
1448507 ATTAAAATATTAATAAAATAAATTTGAGTT
1 ATTAAAATATAAATAAAATAAATTTGAGTT
1448537 ATTAA
1 ATTAA
1448542 TAGATGTCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 13 0.42
31 16 0.52
32 2 0.06
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.41
Consensus pattern (30 bp):
ATTAAAATATAAATAAAATAAATTTGAGTT
Found at i:1453543 original size:12 final size:11
Alignment explanation
Indices: 1453521--1453568 Score: 78
Period size: 12 Copynumber: 4.2 Consensus size: 11
1453511 ATTTATCATT
1453521 TTAAAACACAC
1 TTAAAACACAC
1453532 TTAAACACACAC
1 TTAAA-ACACAC
1453544 TTAAACACACAC
1 TTAAA-ACACAC
1453556 TTAAAACACAC
1 TTAAAACACAC
1453567 TT
1 TT
1453569 CTCCCATTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.36
12 23 0.64
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (11 bp):
TTAAAACACAC
Found at i:1457120 original size:31 final size:31
Alignment explanation
Indices: 1456996--1457120 Score: 146
Period size: 31 Copynumber: 4.0 Consensus size: 31
1456986 AGTGAGGGTA
*
1456996 TACCTATGTTCTACGGAACATATGGACAGAAT
1 TACCTATGTTCTACGGAACATATGGACAG-TT
* *
1457028 TACCTATG-TCTTTC-GAGACATATGGACAGTA
1 TACCTATGTTC-TACGGA-ACATATGGACAGTT
*
1457059 TACCTATGTTCTAAGGAACATATGGACAGTT
1 TACCTATGTTCTACGGAACATATGGACAGTT
* * *
1457090 TACCTAGGTTCTTCGGAACCTATGGACAGTT
1 TACCTATGTTCTACGGAACATATGGACAGTT
1457121 GCCGAGGATC
Statistics
Matches: 79, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
31 53 0.67
32 26 0.33
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (31 bp):
TACCTATGTTCTACGGAACATATGGACAGTT
Found at i:1457169 original size:30 final size:30
Alignment explanation
Indices: 1457107--1457178 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
1457097 GTTCTTCGGA
* * * *
1457107 ACCTATGGACAGTTGCCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCCTTATG
* *
1457137 ACCTCTGGATAGTTACCGAGGTTCCTTGTG
1 ACCTCTGGATAGTTACCGAGGATCCTTATG
1457167 ACCTCTGGATAG
1 ACCTCTGGATAG
1457179 GTCCTTCGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.31
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCGAGGATCCTTATG
Found at i:1468375 original size:34 final size:33
Alignment explanation
Indices: 1468337--1468439 Score: 90
Period size: 34 Copynumber: 3.2 Consensus size: 33
1468327 TTAATAATAT
1468337 ATTTTAATTTGAAATATTCAAAAGATATATACAC
1 ATTTTAATTTGAAATATTCAAAA-ATATATACAC
* * * **
1468371 ATTTTATTATTCAAA-CTT-AAAAA-A-ATA-TT
1 ATTTTAAT-TTGAAATATTCAAAAATATATACAC
1468400 ATTTTAATTTGAAATATTCAAAATATATATACAC
1 ATTTTAATTTGAAATATTCAAAA-ATATATACAC
*
1468434 CTTTTA
1 ATTTTA
1468440 CTATTCAAAC
Statistics
Matches: 51, Mismatches: 11, Indels: 14
0.67 0.14 0.18
Matches are distributed among these distances:
28 5 0.10
29 9 0.18
30 7 0.14
31 2 0.04
32 2 0.04
33 7 0.14
34 14 0.27
35 5 0.10
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.43
Consensus pattern (33 bp):
ATTTTAATTTGAAATATTCAAAAATATATACAC
Found at i:1468416 original size:63 final size:62
Alignment explanation
Indices: 1468304--1468492 Score: 234
Period size: 63 Copynumber: 2.9 Consensus size: 62
1468294 ATCAAATATC
*
1468304 TTTTAATATTCAAATTTAAACAATTAATAATATATTTTAATTTGAAATATTCAAAAGATATATAC
1 TTTTAATATTCAAACTTAAA-AA--AAT-AT-TATTTTAATTTGAAATATTCAAAA-ATATATAC
1468369 ACA
60 ACA
* *
1468372 TTTTATTATTCAAACTTAAAAAAATATTATTTTAATTTGAAATATTCAAAATATATATACACC
1 TTTTAATATTCAAACTTAAAAAAATATTATTTTAATTTGAAATATTCAAAA-ATATATACACA
* * * ** *
1468435 TTTTACTATTCAAACTTTAAAAGATATTATTTTGCTTTAAAATATTCAAAAATATATA
1 TTTTAATATTCAAACTTAAAAAAATATTATTTTAATTTGAAATATTCAAAAATATATA
1468493 ATTATCTTTA
Statistics
Matches: 111, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
62 7 0.06
63 79 0.71
64 2 0.02
65 3 0.03
67 2 0.02
68 18 0.16
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (62 bp):
TTTTAATATTCAAACTTAAAAAAATATTATTTTAATTTGAAATATTCAAAAATATATACACA
Found at i:1468511 original size:63 final size:63
Alignment explanation
Indices: 1468305--1468517 Score: 200
Period size: 63 Copynumber: 3.3 Consensus size: 63
1468295 TCAAATATCT
* *
1468305 TTTAATATTCAAATTTAAACAATTAATAATATATTTTAATTTGAAATATTCAAAAGATATATACA
1 TTTAATATTCAAACTTAAA-AA--AAT-AT-TATTTTAATTTAAAATATTCAAAA-ATATATA-A
1468370 -CAT-
59 TCATC
* * *
1468373 TTTATTATTCAAACTTAAAAAAATATTATTTTAATTTGAAATATTC-AAAATATAT-ATACACC
1 TTTAATATTCAAACTTAAAAAAATATTATTTTAATTTAAAATATTCAAAAATATATAAT-CATC
* * * ** *
1468435 TTTTACTATTCAAACTTTAAAAGATATTATTTTGCTTTAAAATATTCAAAAATATATAATTATC
1 -TTTAATATTCAAACTTAAAAAAATATTATTTTAATTTAAAATATTCAAAAATATATAATCATC
* *
1468499 TTTAATAGTCAAAGTTAAA
1 TTTAATATTCAAACTTAAA
1468518 TAGATAATAA
Statistics
Matches: 124, Mismatches: 15, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
59 1 0.01
61 8 0.06
62 3 0.02
63 75 0.60
64 13 0.10
65 5 0.04
67 2 0.02
68 17 0.14
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.42
Consensus pattern (63 bp):
TTTAATATTCAAACTTAAAAAAATATTATTTTAATTTAAAATATTCAAAAATATATAATCATC
Found at i:1476109 original size:31 final size:31
Alignment explanation
Indices: 1476074--1476147 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
1476064 ATTTGTACAC
*
1476074 TTTTGATCATTTACGTTATCGTTTTATTAAG
1 TTTTGATCACTTACGTTATCGTTTTATTAAG
* *
1476105 TTTTGGTCACTTACGTTATTGTTTTATTAAG
1 TTTTGATCACTTACGTTATCGTTTTATTAAG
*
1476136 TTTTGGTCACTT
1 TTTTGATCACTT
1476148 GGAAATGAGG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.19, C:0.11, G:0.15, T:0.55
Consensus pattern (31 bp):
TTTTGATCACTTACGTTATCGTTTTATTAAG
Found at i:1476920 original size:31 final size:31
Alignment explanation
Indices: 1476885--1476974 Score: 135
Period size: 31 Copynumber: 2.9 Consensus size: 31
1476875 TTAACGTCCG
* * * *
1476885 AGTGACCAAAATTTAATAAAACGATCACGTA
1 AGTGACTAAAACTTAATAAAACGATAACGGA
1476916 AGTGACTAAAACTTAATAAAACGATAACGGA
1 AGTGACTAAAACTTAATAAAACGATAACGGA
*
1476947 AGTGACTAAAACTTAATAAAATGATAAC
1 AGTGACTAAAACTTAATAAAACGATAAC
1476975 ATAAATGAAC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 54 1.00
ACGTcount: A:0.51, C:0.13, G:0.13, T:0.22
Consensus pattern (31 bp):
AGTGACTAAAACTTAATAAAACGATAACGGA
Found at i:1483575 original size:3 final size:3
Alignment explanation
Indices: 1483567--1483591 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1483557 CTAAAGCTGC
1483567 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
1483592 AATCTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:1483648 original size:110 final size:110
Alignment explanation
Indices: 1483463--1483671 Score: 382
Period size: 110 Copynumber: 1.9 Consensus size: 110
1483453 ACATCGCTGC
1483463 TCTTCTTCTTCTTCTTCTTAATCTTTATATTTATTCTTCGTCTATCTCCACCGATCGGATTTTCG
1 TCTTCTTCTTCTTCTTCTTAATCTTTATATTTATTCTTCGTCTATCTCCACCGATCGGATTTTCG
1483528 AATCCATAATTTTTATTTTTGGAAAAATCCTAAAGCTGCTCTTCT
66 AATCCATAATTTTTATTTTTGGAAAAATCCTAAAGCTGCTCTTCT
* * *
1483573 TCTTCTTCTTCTTCTTCTTAATCTTTATTTTTATTCTTCGTCTCTCTTCACCGATCGGATTTTCG
1 TCTTCTTCTTCTTCTTCTTAATCTTTATATTTATTCTTCGTCTATCTCCACCGATCGGATTTTCG
*
1483638 AATCCCTAATTTTTATTTTTGGAAAAATCCTAAA
66 AATCCATAATTTTTATTTTTGGAAAAATCCTAAA
1483672 TTTGTGATTT
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
110 95 1.00
ACGTcount: A:0.21, C:0.22, G:0.08, T:0.49
Consensus pattern (110 bp):
TCTTCTTCTTCTTCTTCTTAATCTTTATATTTATTCTTCGTCTATCTCCACCGATCGGATTTTCG
AATCCATAATTTTTATTTTTGGAAAAATCCTAAAGCTGCTCTTCT
Found at i:1487228 original size:15 final size:15
Alignment explanation
Indices: 1487176--1487227 Score: 86
Period size: 15 Copynumber: 3.5 Consensus size: 15
1487166 ATATTTAACT
*
1487176 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
1487191 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
*
1487206 GGGCGGGTGGATGCG
1 GGGCGGGCGGATGCG
1487221 GGGCGGG
1 GGGCGGG
1487228 TAATGTCTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.06, C:0.15, G:0.69, T:0.10
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:1495244 original size:3 final size:3
Alignment explanation
Indices: 1495238--1495262 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1495228 AGCATTGTTG
1495238 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
1495263 ATATATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1498085 original size:21 final size:21
Alignment explanation
Indices: 1498048--1498087 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1498038 CTAAAATTTA
*
1498048 AATATTACAAATATTAAAAGT
1 AATATTACAAAAATTAAAAGT
1498069 AATATTA-AAAAACTTAAAA
1 AATATTACAAAAA-TTAAAA
1498088 TTAAATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (21 bp):
AATATTACAAAAATTAAAAGT
Found at i:1498131 original size:22 final size:27
Alignment explanation
Indices: 1498082--1498136 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
1498072 ATTAAAAAAC
1498082 TTAAAATTAAATATATATCAGAAGTTA
1 TTAAAATTAAATATATATCAGAAGTTA
*
1498109 -TAAAATTATATA-ATAT-A-AA-TTA
1 TTAAAATTAAATATATATCAGAAGTTA
1498131 TTAAAA
1 TTAAAA
1498137 AATTAAAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 3 0.12
23 7 0.27
24 1 0.04
25 4 0.15
26 11 0.42
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (27 bp):
TTAAAATTAAATATATATCAGAAGTTA
Found at i:1498595 original size:21 final size:20
Alignment explanation
Indices: 1498548--1498604 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
1498538 ATATATTAAA
*
1498548 TTTTTTAGTAATTTAATTTT
1 TTTTTTAGTATTTTAATTTT
*
1498568 TAATTTTAGTATTTTAATATATT
1 T-TTTTTAGTATTTTAAT-T-TT
*
1498591 TTTTTTAATATTTT
1 TTTTTTAGTATTTT
1498605 GCATTTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 1 0.03
21 14 0.47
22 12 0.40
23 3 0.10
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (20 bp):
TTTTTTAGTATTTTAATTTT
Found at i:1499948 original size:21 final size:21
Alignment explanation
Indices: 1499922--1499976 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
1499912 AAAAATGTGA
**
1499922 AGCAATATTGATATTTTTCAT
1 AGCAATATTGATATTGCTCAT
*
1499943 AGCAATATCGATATTGCTCAT
1 AGCAATATTGATATTGCTCAT
1499964 AG-AAGTATTGATA
1 AGCAA-TATTGATA
1499977 CTCGAGAGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 2 0.07
21 27 0.93
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (21 bp):
AGCAATATTGATATTGCTCAT
Found at i:1506368 original size:20 final size:19
Alignment explanation
Indices: 1506340--1506381 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1506330 ATCGTTGATA
* *
1506340 TTTTTTATTATCTTTTTCT
1 TTTTTTATTATATTTTTAT
1506359 TTTTTATATTATATTTTTAT
1 TTTTT-TATTATATTTTTAT
1506379 TTT
1 TTT
1506382 CTTTTATGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTTATTATATTTTTAT
Found at i:1507787 original size:2 final size:2
Alignment explanation
Indices: 1507780--1507818 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1507770 ATAAATTAAA
1507780 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1507819 CATCTGTATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1509691 original size:2 final size:2
Alignment explanation
Indices: 1509684--1509736 Score: 79
Period size: 2 Copynumber: 26.5 Consensus size: 2
1509674 GATTCATGTA
* * *
1509684 TG TG TG TG TA TG TG TG TG TA TG TG TG TG TG TG TA TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1509726 TG TG TG TG TG T
1 TG TG TG TG TG T
1509737 ATAAAGAACC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.06, C:0.00, G:0.43, T:0.51
Consensus pattern (2 bp):
TG
Found at i:1512654 original size:52 final size:52
Alignment explanation
Indices: 1512589--1512690 Score: 186
Period size: 52 Copynumber: 2.0 Consensus size: 52
1512579 AACATAAAAG
*
1512589 TAAAAAGTGTAGTTTTGATATTTTATACAAAGTTAATACTATATATCAATAA
1 TAAAAAATGTAGTTTTGATATTTTATACAAAGTTAATACTATATATCAATAA
*
1512641 TAAAAAATGTAGTTTTGATATTTTATATAAAGTTAATACTATATATCAAT
1 TAAAAAATGTAGTTTTGATATTTTATACAAAGTTAATACTATATATCAAT
1512691 CTCACAAGGT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (52 bp):
TAAAAAATGTAGTTTTGATATTTTATACAAAGTTAATACTATATATCAATAA
Found at i:1515261 original size:22 final size:21
Alignment explanation
Indices: 1515237--1515276 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1515227 GAGAAATTGT
1515237 TTTTAAAATACAAAAATGATA
1 TTTTAAAATACAAAAATGATA
**
1515258 TTTTAAAATTGAAAAATGA
1 TTTTAAAATACAAAAATGA
1515277 AAATAATCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.35
Consensus pattern (21 bp):
TTTTAAAATACAAAAATGATA
Found at i:1518430 original size:31 final size:31
Alignment explanation
Indices: 1518392--1518682 Score: 281
Period size: 31 Copynumber: 9.3 Consensus size: 31
1518382 GTCAAGGAAT
*
1518392 TACCTATGTCTTTTGGGACATATGGACAGTA
1 TACCTATGTCTTTCGGGACATATGGACAGTA
* * * *
1518423 TACCTATGT-TCTACGGAACATATGGATAGAA
1 TACCTATGTCT-TTCGGGACATATGGACAGTA
1518454 TTACCTATGTCTTTCGGGACATATGGACAGTA
1 -TACCTATGTCTTTCGGGACATATGGACAGTA
* *
1518486 TACCTATGT-TCTACGGAACATATGGACA-TAA
1 TACCTATGTCT-TTCGGGACATATGGACAGT-A
* *
1518517 TTGCCTATGTCTTTCGGGACATATGGACATTA
1 -TACCTATGTCTTTCGGGACATATGGACAGTA
* * *
1518549 TACCTATGT-TCTACTGAACATATGGACA-TAA
1 TACCTATGTCT-TTCGGGACATATGGACAGT-A
* *
1518580 TTACCTA-GTCTCTCGGGACATCTGGACAGTA
1 -TACCTATGTCTTTCGGGACATATGGACAGTA
* * *
1518611 TACCTATGT-TCTACGGAACATATGGACAGAA
1 TACCTATGTCT-TTCGGGACATATGGACAGTA
*
1518642 TTACCTATGTCTCTCGGGACATATGGACAGTA
1 -TACCTATGTCTTTCGGGACATATGGACAGTA
1518674 TACCTATGT
1 TACCTATGT
1518683 TCTAAGGAAC
Statistics
Matches: 211, Mismatches: 32, Indels: 34
0.76 0.12 0.12
Matches are distributed among these distances:
30 12 0.06
31 113 0.54
32 82 0.39
33 4 0.02
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (31 bp):
TACCTATGTCTTTCGGGACATATGGACAGTA
Found at i:1518466 original size:63 final size:63
Alignment explanation
Indices: 1518388--1518724 Score: 543
Period size: 63 Copynumber: 5.4 Consensus size: 63
1518378 AAGAGTCAAG
* *
1518388 GAATTACCTATGTCTTTTGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGATA
1 GAATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGACA
1518451 GAATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGACA
1 GAATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGACA
* * * *
1518514 TAATTGCCTATGTCTTTCGGGACATATGGACATTATACCTATGTTCTACTGAACATATGGACA
1 GAATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGACA
* * *
1518577 TAATTACCTA-GTCTCTCGGGACATCTGGACAGTATACCTATGTTCTACGGAACATATGGACA
1 GAATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGACA
* *
1518639 GAATTACCTATGTCTCTCGGGACATATGGACAGTATACCTATGTTCTAAGGAACATATGGACA
1 GAATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGACA
*
1518702 GAATTACCTAGGT-TCTTCGGGAC
1 GAATTACCTATGTCT-TTCGGGAC
1518725 CTATAAACAG
Statistics
Matches: 256, Mismatches: 16, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
62 58 0.23
63 198 0.77
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.31
Consensus pattern (63 bp):
GAATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGACA
Found at i:1518659 original size:125 final size:125
Alignment explanation
Indices: 1518388--1518712 Score: 542
Period size: 125 Copynumber: 2.6 Consensus size: 125
1518378 AAGAGTCAAG
* *
1518388 GAATTACCTATGTCTTTTGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGATAGA
1 GAATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGACAGA
*
1518453 ATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGACA
66 ATTACCTA-GTCTCTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGACA
* * * * *
1518514 TAATTGCCTATGTCTTTCGGGACATATGGACATTATACCTATGTTCTACTGAACATATGGACATA
1 GAATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGACAGA
*
1518579 ATTACCTAGTCTCTCGGGACATCTGGACAGTATACCTATGTTCTACGGAACATATGGACA
66 ATTACCTAGTCTCTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGACA
* *
1518639 GAATTACCTATGTCTCTCGGGACATATGGACAGTATACCTATGTTCTAAGGAACATATGGACAGA
1 GAATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGACAGA
1518704 ATTACCTAG
66 ATTACCTAG
1518713 GTTCTTCGGG
Statistics
Matches: 183, Mismatches: 16, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
125 117 0.64
126 66 0.36
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (125 bp):
GAATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGACAGA
ATTACCTAGTCTCTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGACA
Found at i:1520195 original size:44 final size:47
Alignment explanation
Indices: 1520100--1520199 Score: 161
Period size: 44 Copynumber: 2.2 Consensus size: 47
1520090 CTATGTGACT
1520100 ATATGAAATGATATATGAATATTGCAATACGTGATACATGTGATATG
1 ATATGAAATGATATATGAATATTGCAATACGTGATACATGTGATATG
* *
1520147 ATATGAAATGA-CTATGAATA-TGTAATACGTGATACA-GTGATATG
1 ATATGAAATGATATATGAATATTGCAATACGTGATACATGTGATATG
1520191 ATATGAAAT
1 ATATGAAAT
1520200 ACATGGTTAC
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
44 17 0.33
45 15 0.29
46 8 0.16
47 11 0.22
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (47 bp):
ATATGAAATGATATATGAATATTGCAATACGTGATACATGTGATATG
Found at i:1520405 original size:37 final size:37
Alignment explanation
Indices: 1520348--1520440 Score: 118
Period size: 37 Copynumber: 2.5 Consensus size: 37
1520338 TATAAGACAT
* * * *
1520348 ATGATAGGTCCTAC-GGACACAGATTACATCCTTCGGG
1 ATGACAGGTCCTTCGGGACACAGATGACATCCTTC-AG
1520385 ATG-CAGGTCCTTCGGGACACAGATGACATCCTTCAG
1 ATGACAGGTCCTTCGGGACACAGATGACATCCTTCAG
*
1520421 ATGATAGGTCCTTCGGGACA
1 ATGACAGGTCCTTCGGGACA
1520441 TTATACGAGC
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
36 12 0.24
37 37 0.76
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.24
Consensus pattern (37 bp):
ATGACAGGTCCTTCGGGACACAGATGACATCCTTCAG
Found at i:1526663 original size:22 final size:22
Alignment explanation
Indices: 1526638--1526709 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
1526628 CTATATGAAA
1526638 TGATATATGAATATGAAATACG
1 TGATATATGAATATGAAATACG
* ** ** **
1526660 TGATACATGTGTATGATAGGAAA
1 TGATATATGAATATGA-AATACG
* *
1526683 TGACATATGAATATGTAATACG
1 TGATATATGAATATGAAATACG
1526705 TGATA
1 TGATA
1526710 CATGTGATAT
Statistics
Matches: 32, Mismatches: 17, Indels: 2
0.63 0.33 0.04
Matches are distributed among these distances:
22 19 0.59
23 13 0.41
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.32
Consensus pattern (22 bp):
TGATATATGAATATGAAATACG
Found at i:1526683 original size:45 final size:46
Alignment explanation
Indices: 1526634--1526733 Score: 159
Period size: 45 Copynumber: 2.2 Consensus size: 46
1526624 GTGACTATAT
*
1526634 GAAATGATATATGAATATGAAATACGTGATACATGTG-TATGATAG
1 GAAATGACATATGAATATGAAATACGTGATACATGTGATATGATAG
* *
1526679 GAAATGACATATGAATATGTAATACGTGATACATGTGATATGATAT
1 GAAATGACATATGAATATGAAATACGTGATACATGTGATATGATAG
1526725 GAAAT-ACAT
1 GAAATGACAT
1526734 GGTTACACAT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
45 39 0.76
46 12 0.24
ACGTcount: A:0.43, C:0.06, G:0.20, T:0.31
Consensus pattern (46 bp):
GAAATGACATATGAATATGAAATACGTGATACATGTGATATGATAG
Found at i:1526732 original size:21 final size:21
Alignment explanation
Indices: 1526662--1526734 Score: 58
Period size: 21 Copynumber: 3.3 Consensus size: 21
1526652 GAAATACGTG
*
1526662 ATACATGTG-TATGATAGGAA
1 ATACATGTGATATGATACGAA
* **
1526682 ATGACATATGAATATGTAATACGTG
1 AT-ACATGTG-ATATG--ATACGAA
*
1526707 ATACATGTGATATGATATGAA
1 ATACATGTGATATGATACGAA
1526728 ATACATG
1 ATACATG
1526735 GTTACACATA
Statistics
Matches: 40, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
20 2 0.05
21 17 0.43
23 9 0.22
24 6 0.15
25 6 0.15
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.32
Consensus pattern (21 bp):
ATACATGTGATATGATACGAA
Found at i:1526938 original size:38 final size:37
Alignment explanation
Indices: 1526882--1526975 Score: 116
Period size: 38 Copynumber: 2.5 Consensus size: 37
1526872 TATAAGACAT
* *
1526882 ATGATAGGTCCTATGGGACACAGATTACATCATTCAGG
1 ATGATAGGTCCT-TGGGACACAAATGACATCATTCAGG
* * *
1526920 ATGACAGGTCCTTCGGGACACAAATGACATCCTTCGGG
1 ATGATAGGTCCTT-GGGACACAAATGACATCATTCAGG
1526958 ATGATAGGTCCTTTGGGA
1 ATGATAGGTCC-TTGGGA
1526976 TATTTATACG
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
37 1 0.02
38 45 0.94
39 2 0.04
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.26
Consensus pattern (37 bp):
ATGATAGGTCCTTGGGACACAAATGACATCATTCAGG
Found at i:1533839 original size:65 final size:64
Alignment explanation
Indices: 1533768--1533928 Score: 236
Period size: 65 Copynumber: 2.5 Consensus size: 64
1533758 TAAATAAATT
*
1533768 AAACATCGAATGCATTTTATGCATCGATGCACATA-CCATGCATCGATACACTC-CGATTTTTAT
1 AAACATCGAATGCATTTTATGCATCGATGCACA-AGCCATGCATCGATACACTCACGATTGTT-T
1533831 G
64 G
* * *
1533832 AAAACATCGAATGCATTTTATGCATCGATGCACAAGCCATGCATCGATGCACTCATGCTTGTTTG
1 -AAACATCGAATGCATTTTATGCATCGATGCACAAGCCATGCATCGATACACTCACGATTGTTTG
*
1533897 AAACATCAAATGCATTTTATGCATCGATGCAC
1 AAACATCGAATGCATTTTATGCATCGATGCAC
1533929 TATCAGTGTA
Statistics
Matches: 89, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
64 32 0.36
65 52 0.58
66 5 0.06
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.30
Consensus pattern (64 bp):
AAACATCGAATGCATTTTATGCATCGATGCACAAGCCATGCATCGATACACTCACGATTGTTTG
Found at i:1533944 original size:64 final size:64
Alignment explanation
Indices: 1533768--1533948 Score: 231
Period size: 65 Copynumber: 2.8 Consensus size: 64
1533758 TAAATAAATT
* *
1533768 AAACATCGAATGCATTTTATGCATCGATGCACATACCATGCATCGATACACTCCGATTTTTATGA
1 AAACATCGAATGCATTTTATGCATCGATGCAC-TACCATGCATCGATGCACTCCGATTGTTATGA
* * *
1533833 AAACATCGAATGCATTTTATGCATCGATGCACAAGCCATGCATCGATGCACTCATGCTTGTT-TG
1 AAACATCGAATGCATTTTATGCATCGATGCACTA-CCATGCATCGATGCACTC-CGATTGTTATG
1533897 -
64 A
* * * *
1533897 AAACATCAAATGCATTTTATGCATCGATGCACTATCAGTGTACCGATGCACT
1 AAACATCGAATGCATTTTATGCATCGATGCACTACCA-TGCATCGATGCACT
1533949 AAGGATCCAA
Statistics
Matches: 103, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
63 2 0.02
64 45 0.44
65 51 0.50
66 5 0.05
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (64 bp):
AAACATCGAATGCATTTTATGCATCGATGCACTACCATGCATCGATGCACTCCGATTGTTATGA
Found at i:1534737 original size:26 final size:26
Alignment explanation
Indices: 1534689--1534738 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
1534679 TTATATAAAC
*
1534689 AGTTAATCAAATCAATTTCTCAAATA
1 AGTTAATCAAATCAATTGCTCAAATA
* *
1534715 AGTTAATCAAATCAGTTGGTCAAA
1 AGTTAATCAAATCAATTGCTCAAA
1534739 CCAGCTACTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (26 bp):
AGTTAATCAAATCAATTGCTCAAATA
Found at i:1536500 original size:30 final size:29
Alignment explanation
Indices: 1536466--1536551 Score: 100
Period size: 30 Copynumber: 2.9 Consensus size: 29
1536456 ATTTTACATC
*
1536466 TTAACATTAAAAATATATTTTATTTTTATA
1 TTAAC-TTAAAAATATATTTTATTCTTATA
* * *
1536496 TTAACTTATTAAATATATTTTATTCTTGTT
1 TTAACTTA-AAAATATATTTTATTCTTATA
* *
1536526 TTAACCTAAAAATATATTTTAGTCTT
1 TTAACTTAAAAATATATTTTATTCTT
1536552 TAGGAAATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
29 19 0.40
30 29 0.60
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.53
Consensus pattern (29 bp):
TTAACTTAAAAATATATTTTATTCTTATA
Found at i:1537065 original size:31 final size:31
Alignment explanation
Indices: 1537028--1537088 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
1537018 CTAATTAGAG
*
1537028 ATTAAAATGAAAATT-AAGCATCACATTGAAC
1 ATTAAAAT-AAAATTCAAGCATCAAATTGAAC
* *
1537059 ATTAAAATCAAATTCAAGTATCAAATTGAA
1 ATTAAAATAAAATTCAAGCATCAAATTGAA
1537089 ACAAAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.52, C:0.11, G:0.08, T:0.28
Consensus pattern (31 bp):
ATTAAAATAAAATTCAAGCATCAAATTGAAC
Found at i:1539397 original size:24 final size:24
Alignment explanation
Indices: 1539363--1539409 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1539353 CTGAAACATC
1539363 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1539387 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1539410 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1540120 original size:20 final size:20
Alignment explanation
Indices: 1540092--1540361 Score: 281
Period size: 20 Copynumber: 13.5 Consensus size: 20
1540082 AAATTTCAGT
* *
1540092 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
1540112 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
1540132 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
1540152 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
1540172 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
1540192 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* *
1540212 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
1540232 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
1540252 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * * *
1540272 GTTGTGATATACGGATACAC
1 GTTGCGATTTACGGATTCTC
* *
1540292 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCTC
* *
1540312 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCTC
* ** *
1540332 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCTC
1540352 GTTGCGATTT
1 GTTGCGATTT
1540362 TGTAAAATCG
Statistics
Matches: 218, Mismatches: 30, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
20 217 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:1540378 original size:21 final size:21
Alignment explanation
Indices: 1540348--1540426 Score: 79
Period size: 21 Copynumber: 3.8 Consensus size: 21
1540338 ATTTTCATAT
*
1540348 TCGCGTTGCGATTTTGTAAAA
1 TCGCATTGCGATTTTGTAAAA
* * **
1540369 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGTAAAA
*
1540390 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGTAA-AA
*
1540411 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
1540427 GAAACTGATT
Statistics
Matches: 45, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
20 1 0.02
21 44 0.98
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.37
Consensus pattern (21 bp):
TCGCATTGCGATTTTGTAAAA
Found at i:1540421 original size:42 final size:43
Alignment explanation
Indices: 1540328--1540426 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
1540318 ATTTATGTGT
* *
1540328 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGTAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
1540369 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
1540411 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
1540427 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.38
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:1542353 original size:31 final size:30
Alignment explanation
Indices: 1542318--1542528 Score: 181
Period size: 31 Copynumber: 6.8 Consensus size: 30
1542308 GGCGAAGAAT
*
1542318 TACCTATGTCTCTCGGGACATATGGACATTA
1 TACCTATGT-TCTCGGGACATATGGACAGTA
* * *
1542349 TACCTATGTTCTATGGAACATATGGACAGAA
1 TACCTATGTTCT-CGGGACATATGGACAGTA
*
1542380 TTACCTATGTCTTTCGGGACATATGGACAGTA
1 -TACCTATGT-TCTCGGGACATATGGACAGTA
* * * *
1542412 TACATATGTTCTACGGAACATAGGGACA-AA
1 TACCTATGTTCT-CGGGACATATGGACAGTA
*
1542442 TTACCTATGTTTCTCGGGATATATGGACAGTA
1 -TACCTATG-TTCTCGGGACATATGGACAGTA
* * * * *
1542474 TACCTATATTCTAAGGAACATATGGATAGTT
1 TACCTATGTTCT-CGGGACATATGGACAGTA
* *
1542505 TACCTAAGTTCTTCGGGACCTATG
1 TACCTATGTTC-TCGGGACATATG
1542529 AACAATTTCC
Statistics
Matches: 142, Mismatches: 29, Indels: 18
0.75 0.15 0.10
Matches are distributed among these distances:
30 10 0.07
31 100 0.70
32 30 0.21
33 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (30 bp):
TACCTATGTTCTCGGGACATATGGACAGTA
Found at i:1542391 original size:63 final size:63
Alignment explanation
Indices: 1542313--1542499 Score: 286
Period size: 63 Copynumber: 3.0 Consensus size: 63
1542303 CAATAGGCGA
* *
1542313 AGAATTACCTATGTCTCTCGGGACATATGGACATTATACCTATGTTCTATGGAACATATGGAC
1 AGAATTACCTATGTCTCTCGGGACATATGGACAGTATACCTATGTTCTAAGGAACATATGGAC
* * * *
1542376 AGAATTACCTATGTCTTTCGGGACATATGGACAGTATACATATGTTCTACGGAACATAGGGAC
1 AGAATTACCTATGTCTCTCGGGACATATGGACAGTATACCTATGTTCTAAGGAACATATGGAC
* * *
1542439 A-AATTACCTATGTTTCTCGGGATATATGGACAGTATACCTATATTCTAAGGAACATATGGA
1 AGAATTACCTATGTCTCTCGGGACATATGGACAGTATACCTATGTTCTAAGGAACATATGGA
1542500 TAGTTTACCT
Statistics
Matches: 112, Mismatches: 12, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
62 53 0.47
63 59 0.53
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (63 bp):
AGAATTACCTATGTCTCTCGGGACATATGGACAGTATACCTATGTTCTAAGGAACATATGGAC
Found at i:1542508 original size:62 final size:62
Alignment explanation
Indices: 1542316--1542528 Score: 268
Period size: 62 Copynumber: 3.4 Consensus size: 62
1542306 TAGGCGAAGA
* * *
1542316 ATTACCTATGTCTCTCGGGACATATGGACATTATACCTATGTTCTATGGAACATATGGACAG
1 ATTACCTATGTTTCTCGGGACATATGGACAGTATACCTATGTTCTAAGGAACATATGGACAG
* * * *
1542378 AATTACCTATGTCTT-TCGGGACATATGGACAGTATACATATGTTCTACGGAACATAGGGACAA
1 -ATTACCTATGT-TTCTCGGGACATATGGACAGTATACCTATGTTCTAAGGAACATATGGACAG
* * *
1542441 ATTACCTATGTTTCTCGGGATATATGGACAGTATACCTATATTCTAAGGAACATATGGATAG
1 ATTACCTATGTTTCTCGGGACATATGGACAGTATACCTATGTTCTAAGGAACATATGGACAG
* * *
1542503 TTTACCTAAG-TTCTTCGGGACCTATG
1 ATTACCTATGTTTC-TCGGGACATATG
1542529 AACAATTTCC
Statistics
Matches: 130, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
61 5 0.04
62 70 0.54
63 54 0.42
64 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (62 bp):
ATTACCTATGTTTCTCGGGACATATGGACAGTATACCTATGTTCTAAGGAACATATGGACAG
Found at i:1544264 original size:30 final size:28
Alignment explanation
Indices: 1544134--1544348 Score: 116
Period size: 30 Copynumber: 7.3 Consensus size: 28
1544124 TCCATGGTCT
*
1544134 TTATCTTAATTTAAAAATATATATTTTATTC
1 TTATCTTAACTT--AAA-ATATATTTTATTC
* * *
1544165 TTATCTTCAA-TTATTACATAAATTATATTC
1 TTATCTT-AACTTA--AAATATATTTTATTC
* * * *
1544195 TTACCTTAAATTATTAAATATAATTAATTC
1 TTATCTTAACTTA--AAATATATTTTATTC
*
1544225 TTATTTTAACTTAAAGCATATATTTTATTC
1 TTATCTTAACTTAAA--ATATATTTTATTC
*
1544255 TTATCTTAACTTAAAAAAATATTTTTATT-
1 TTATCTTAACTT-AAAATATA-TTTTATTC
* * *
1544284 TTAAC-T-ACAT-AAATATATTTTATTT
1 TTATCTTAACTTAAAATATATTTTATTC
* * *
1544309 TTATCTTAACTACAAAAAATATATTATATTT
1 TTATCTTAACT---TAAAATATATTTTATTC
1544340 TTATCTTAA
1 TTATCTTAA
1544349 ATTTTAAATA
Statistics
Matches: 146, Mismatches: 23, Indels: 30
0.73 0.12 0.15
Matches are distributed among these distances:
24 7 0.05
25 10 0.07
26 1 0.01
27 5 0.03
28 3 0.02
29 11 0.08
30 71 0.49
31 36 0.25
32 2 0.01
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (28 bp):
TTATCTTAACTTAAAATATATTTTATTC
Found at i:1544284 original size:54 final size:54
Alignment explanation
Indices: 1544225--1544349 Score: 148
Period size: 54 Copynumber: 2.3 Consensus size: 54
1544215 TAATTAATTC
*
1544225 TTATTTTAACTTAAAGCATATATTTTATTCTTATCTTAACTTA-AAAAAATAT-TT
1 TTATTTTAACTTAAA-AATATATTTTATTCTTATCTTAAC-TACAAAAAATATATT
*
1544279 TTATTTTAAC-TACATAAATATATTTTATTTTTATCTTAACTACAAAAAATATATT
1 TTATTTTAACTTA-A-AAATATATTTTATTCTTATCTTAACTACAAAAAATATATT
* *
1544334 ATATTTTTATCTTAAA
1 TTA-TTTTAACTTAAA
1544350 TTTTAAATAT
Statistics
Matches: 61, Mismatches: 4, Indels: 11
0.80 0.05 0.14
Matches are distributed among these distances:
53 4 0.07
54 42 0.69
55 6 0.10
56 7 0.11
57 2 0.03
ACGTcount: A:0.40, C:0.09, G:0.01, T:0.50
Consensus pattern (54 bp):
TTATTTTAACTTAAAAATATATTTTATTCTTATCTTAACTACAAAAAATATATT
Found at i:1544332 original size:31 final size:30
Alignment explanation
Indices: 1544273--1544348 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 30
1544263 ACTTAAAAAA
* *
1544273 ATATTTTTATTTTAACTACATAAATATATT
1 ATATTTTTATCTTAACTACAAAAATATATT
*
1544303 TTATTTTTATCTTAACTACAAAAAATATATT
1 ATATTTTTATCTTAACTAC-AAAAATATATT
1544334 ATATTTTTATCTTAA
1 ATATTTTTATCTTAA
1544349 ATTTTAAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 17 0.41
31 24 0.59
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (30 bp):
ATATTTTTATCTTAACTACAAAAATATATT
Found at i:1544421 original size:30 final size:28
Alignment explanation
Indices: 1544387--1544499 Score: 118
Period size: 30 Copynumber: 3.8 Consensus size: 28
1544377 AATATTCAAG
1544387 TTAAGATAAGAATAAATTATATTTTTAAA
1 TTAAGATAAGAATAAA-TATATTTTTAAA
*
1544416 TTTAAGATAAGATTGAAATATATTTTTCAAA
1 -TTAAGATAAGAAT-AAATATATTTTT-AAA
* * *
1544447 TCAAAATAAGAATAAAATATATTTTTAAG
1 TTAAGATAAGAAT-AAATATATTTTTAAA
* *
1544476 TTATGAAAAGAATACAATATATTT
1 TTAAGATAAGAATA-AATATATTT
1544500 AATGAGTTAA
Statistics
Matches: 70, Mismatches: 10, Indels: 7
0.80 0.11 0.08
Matches are distributed among these distances:
28 1 0.01
29 20 0.29
30 43 0.61
31 6 0.09
ACGTcount: A:0.50, C:0.03, G:0.08, T:0.39
Consensus pattern (28 bp):
TTAAGATAAGAATAAATATATTTTTAAA
Found at i:1546176 original size:22 final size:21
Alignment explanation
Indices: 1546134--1546177 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
1546124 AGAAAAAAAT
*
1546134 AAAAATAACAAAATACGTAAA
1 AAAAATAACAAAATACATAAA
1546155 AAAAATAAACAAAATGA-ATAAA
1 AAAAAT-AACAAAAT-ACATAAA
1546177 A
1 A
1546178 TGTTAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 6 0.30
22 13 0.65
23 1 0.05
ACGTcount: A:0.75, C:0.07, G:0.05, T:0.14
Consensus pattern (21 bp):
AAAAATAACAAAATACATAAA
Found at i:1546384 original size:2 final size:2
Alignment explanation
Indices: 1546377--1546407 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1546367 TAAAGTAAAA
1546377 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1546408 AAACAAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1546437 original size:34 final size:38
Alignment explanation
Indices: 1546397--1546481 Score: 113
Period size: 39 Copynumber: 2.3 Consensus size: 38
1546387 ATATATATAT
1546397 ATATATATATAAAAC-A-AAAATAGAATATTAAGACAA
1 ATATATATATAAAACGATAAAATAGAATATTAAGACAA
*
1546433 ATATATATATAAAACGTATAAAATATAATATTAAGA-AA
1 ATATATATATAAAACG-ATAAAATAGAATATTAAGACAA
* *
1546471 AAATACATATA
1 ATATATATATA
1546482 CATAGTAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
36 15 0.35
38 12 0.28
39 16 0.37
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (38 bp):
ATATATATATAAAACGATAAAATAGAATATTAAGACAA
Found at i:1546545 original size:16 final size:15
Alignment explanation
Indices: 1546526--1546623 Score: 73
Period size: 16 Copynumber: 6.6 Consensus size: 15
1546516 ATATATATAT
*
1546526 ATATATATAATATAAG
1 ATATATATAATA-AAA
1546542 ATATATATAATAAAA
1 ATATATATAATAAAA
1546557 ATA-ATATAATAAAA
1 ATATATATAATAAAA
*
1546571 ATA-A-A-AA-AAGGA
1 ATATATATAATAA-AA
1546583 ATATAGTA-AATAAATA
1 ATATA-TATAATAAA-A
* *
1546599 AAAAATATAATTAAAA
1 ATATATATAA-TAAAA
1546615 ATATATATA
1 ATATATATA
1546624 TAGGGGACGA
Statistics
Matches: 67, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
11 2 0.03
12 6 0.09
13 2 0.03
14 15 0.22
15 10 0.15
16 28 0.42
17 4 0.06
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (15 bp):
ATATATATAATAAAA
Found at i:1546560 original size:20 final size:22
Alignment explanation
Indices: 1546520--1546560 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1546510 CTATACATAT
*
1546520 ATATATATATATATAATATAAG
1 ATATATATATATATAAAATAAG
1546542 ATATATATA-ATA-AAAATAA
1 ATATATATATATATAAAATAA
1546561 TATAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 3 0.17
22 9 0.50
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
ATATATATATATATAAAATAAG
Found at i:1546570 original size:14 final size:14
Alignment explanation
Indices: 1546530--1546574 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
1546520 ATATATATAT
*
1546530 ATATAATATAAGATA
1 ATATAATA-AAAATA
1546545 TATATAATAAAAATA
1 -ATATAATAAAAATA
1546560 ATATAATAAAAATA
1 ATATAATAAAAATA
1546574 A
1 A
1546575 AAAAAGGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
14 15 0.54
15 5 0.18
16 8 0.29
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (14 bp):
ATATAATAAAAATA
Found at i:1546579 original size:23 final size:22
Alignment explanation
Indices: 1546548--1546617 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 22
1546538 TAAGATATAT
*
1546548 ATAATAAAAATAATATAATAAAA
1 ATAA-AAAAAAAATATAATAAAA
* *
1546571 ATAAAAAAAGGAATATAGT--AA
1 ATAAAAAAA-AAATATAATAAAA
*
1546592 ATAAATAAAAAATATAATTAAAA
1 ATAAAAAAAAAATATAA-TAAAA
1546615 ATA
1 ATA
1546618 TATATATAGG
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
20 6 0.16
21 11 0.29
22 5 0.13
23 16 0.42
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.24
Consensus pattern (22 bp):
ATAAAAAAAAAATATAATAAAA
Found at i:1546608 original size:13 final size:14
Alignment explanation
Indices: 1546526--1546621 Score: 52
Period size: 14 Copynumber: 6.5 Consensus size: 14
1546516 ATATATATAT
*
1546526 ATATATATAATATAAG
1 ATATATA-AATA-AAA
1546542 ATATATATAATAAAA
1 ATATATA-AATAAAA
1546557 ATA-ATATAATAAAA
1 ATATATA-AATAAAA
* * *
1546571 ATAAAAAAAGGAATATA
1 ATATATAAA-TAA-A-A
* *
1546588 GTAAATAAATAAAA
1 ATATATAAATAAAA
*
1546602 A-ATATAATTAAAA
1 ATATATAAATAAAA
1546615 ATATATA
1 ATATATA
1546622 TATAGGGGAC
Statistics
Matches: 66, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
13 11 0.17
14 22 0.33
15 10 0.15
16 15 0.23
17 8 0.12
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (14 bp):
ATATATAAATAAAA
Found at i:1546613 original size:21 final size:21
Alignment explanation
Indices: 1546548--1546613 Score: 55
Period size: 21 Copynumber: 3.0 Consensus size: 21
1546538 TAAGATATAT
* *
1546548 ATAATAAAAATAATATAATAAAA
1 ATAA-AAAAAGAATATAAT-TAA
*
1546571 ATAAAAAAAGGAATAT-AGTAA
1 ATAAAAAAA-GAATATAATTAA
1546592 ATAAATAAAA-AATATAATTAA
1 ATAAA-AAAAGAATATAATTAA
1546613 A
1 A
1546614 AATATATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
20 5 0.14
21 12 0.33
22 10 0.28
23 9 0.25
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (21 bp):
ATAAAAAAAGAATATAATTAA
Found at i:1546665 original size:12 final size:12
Alignment explanation
Indices: 1546642--1546694 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
1546632 GAAATTAATA
* *
1546642 TAAAAGTAAAAT
1 TAAAGGTAAATT
1546654 TAAAGGGTAAATT
1 TAAA-GGTAAATT
*
1546667 TCAAGGTAAATT
1 TAAAGGTAAATT
*
1546679 TCAAGGTAAA-T
1 TAAAGGTAAATT
1546690 TAAAG
1 TAAAG
1546695 ATTAAGATTG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
11 5 0.14
12 22 0.61
13 9 0.25
ACGTcount: A:0.51, C:0.04, G:0.17, T:0.28
Consensus pattern (12 bp):
TAAAGGTAAATT
Found at i:1546672 original size:13 final size:12
Alignment explanation
Indices: 1546659--1546690 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
1546649 AAAATTAAAG
1546659 GGTAAATTTCAA
1 GGTAAATTTCAA
1546671 GGTAAATTTCAA
1 GGTAAATTTCAA
1546683 GGTAAATT
1 GGTAAATT
1546691 AAAGATTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.34
Consensus pattern (12 bp):
GGTAAATTTCAA
Found at i:1549196 original size:16 final size:17
Alignment explanation
Indices: 1549175--1549215 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 17
1549165 ACCCACCTTA
1549175 TTTTTTGTTC-TTTCTC
1 TTTTTTGTTCTTTTCTC
1549191 TTTTTTGTTCTATTTTCTC
1 TTTTTTGTTC--TTTTCTC
1549210 TTTTTT
1 TTTTTT
1549216 AATTTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 10 0.45
19 12 0.55
ACGTcount: A:0.02, C:0.15, G:0.05, T:0.78
Consensus pattern (17 bp):
TTTTTTGTTCTTTTCTC
Found at i:1559693 original size:19 final size:19
Alignment explanation
Indices: 1559671--1559712 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1559661 AAAATACGTA
1559671 AAAAATAAAAAAAAAT-AAT
1 AAAAAT-AAAAAAAATGAAT
*
1559690 AAAAATAAACAAAATGAAT
1 AAAAATAAAAAAAATGAAT
1559709 AAAA
1 AAAA
1559713 TGTTAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.14
Consensus pattern (19 bp):
AAAAATAAAAAAAATGAAT
Found at i:1559788 original size:18 final size:17
Alignment explanation
Indices: 1559756--1559802 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
1559746 TATTAATGGA
1559756 GTAAAAAAATAAAAAAG
1 GTAAAAAAATAAAAAAG
* *
1559773 GTAAAAGAAATTAAAAAT
1 GTAAAA-AAATAAAAAAG
1559791 G-AATAAAAATAA
1 GTAA-AAAAATAA
1559803 TGTGTACATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.72, C:0.00, G:0.11, T:0.17
Consensus pattern (17 bp):
GTAAAAAAATAAAAAAG
Found at i:1559928 original size:15 final size:13
Alignment explanation
Indices: 1559900--1559924 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1559890 CATGATATTA
1559900 AGAAAAAAATAAT
1 AGAAAAAAATAAT
1559913 AGAAAAAAATAA
1 AGAAAAAAATAA
1559925 AATAAAGTAA
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:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (13 bp):
AGAAAAAAATAAT
Found at i:1559928 original size:18 final size:18
Alignment explanation
Indices: 1559905--1559942 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1559895 TATTAAGAAA
1559905 AAAATAATAG-AAAAAAAT
1 AAAATAA-AGTAAAAAAAT
*
1559923 AAAATAAAGTAAAAATAT
1 AAAATAAAGTAAAAAAAT
1559941 AA
1 AA
1559943 TATATATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.18
Consensus pattern (18 bp):
AAAATAAAGTAAAAAAAT
Found at i:1559998 original size:40 final size:39
Alignment explanation
Indices: 1559954--1560039 Score: 102
Period size: 39 Copynumber: 2.2 Consensus size: 39
1559944 ATATATATTT
1559954 ATATATAAATAAATAAA-AACAAAAATAGAATATTAAGAAA
1 ATATATAAATAAA-AAAGAA-AAAAATAGAATATTAAGAAA
* * * *
1559994 ATATATATATAAAAAAGTATAAAATATAATATTAAGAAA
1 ATATATAAATAAAAAAGAAAAAAATAGAATATTAAGAAA
*
1560033 AAATATA
1 ATATATA
1560040 TATACATAGT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
39 27 0.68
40 13 0.32
ACGTcount: A:0.67, C:0.01, G:0.05, T:0.27
Consensus pattern (39 bp):
ATATATAAATAAAAAAGAAAAAAATAGAATATTAAGAAA
Found at i:1560108 original size:25 final size:25
Alignment explanation
Indices: 1560078--1560128 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
1560068 GCTTCTATAC
*
1560078 ATATATATATATATATAATGATATAAG
1 ATATATATA-ATATA-AATAATATAAG
1560105 ATATATATAATATAAATAATATAA
1 ATATATATAATATAAATAATATAA
1560129 TATAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 9 0.39
26 5 0.22
27 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (25 bp):
ATATATATAATATAAATAATATAAG
Found at i:1560183 original size:36 final size:37
Alignment explanation
Indices: 1560104--1560185 Score: 91
Period size: 36 Copynumber: 2.3 Consensus size: 37
1560094 AATGATATAA
*
1560104 GATATATATAATATAAATAATATAATATAAAAAAAAG
1 GATATATATAATATAAATAATAAAATATAAAAAAAAG
*
1560141 GA-ATATAGTAA-ATAAATAA-AAAATATAATTAAAAA-
1 GATATATA-TAATATAAATAATAAAATATAA-AAAAAAG
*
1560176 TATATATATA
1 GATATATATA
1560186 GGGGACGAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
35 11 0.28
36 23 0.59
37 5 0.13
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (37 bp):
GATATATATAATATAAATAATAAAATATAAAAAAAAG
Found at i:1560889 original size:14 final size:13
Alignment explanation
Indices: 1560869--1560907 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
1560859 TTTAAATTAT
1560869 TAAAATAATTTAA
1 TAAAATAATTTAA
**
1560882 TAAAAATAATAAAA
1 T-AAAATAATTTAA
1560896 TAAAATAATTTA
1 TAAAATAATTTA
1560908 TCTTCAAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
TAAAATAATTTAA
Found at i:1561626 original size:18 final size:19
Alignment explanation
Indices: 1561600--1561635 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1561590 AAAAAAAAGA
1561600 AAACACAAAA-TTTGAAAT
1 AAACACAAAACTTTGAAAT
*
1561618 AAACTCAAAACTTTGAAA
1 AAACACAAAACTTTGAAA
1561636 ACCTTCATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.58, C:0.14, G:0.06, T:0.22
Consensus pattern (19 bp):
AAACACAAAACTTTGAAAT
Found at i:1563233 original size:19 final size:19
Alignment explanation
Indices: 1563209--1563259 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
1563199 TAAAAAAAAT
*
1563209 TTATTTTATATT-ATTCATG
1 TTATTTT-TATTAATACATG
1563228 TTATTTTTTAATTAATACATG
1 TTA-TTTTT-ATTAATACATG
1563249 TTATTTTTATT
1 TTATTTTTATT
1563260 TTTGTGGGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
19 7 0.25
20 12 0.43
21 9 0.32
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (19 bp):
TTATTTTTATTAATACATG
Found at i:1563241 original size:20 final size:22
Alignment explanation
Indices: 1563212--1563256 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
1563202 AAAAAATTTA
*
1563212 TTTTATATT-ATTCATGTTATT
1 TTTTATATTAATACATGTTATT
1563233 TTTTA-ATTAATACATGTTATT
1 TTTTATATTAATACATGTTATT
1563254 TTT
1 TTT
1563257 ATTTTTGTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.64
Consensus pattern (22 bp):
TTTTATATTAATACATGTTATT
Found at i:1565506 original size:4 final size:4
Alignment explanation
Indices: 1565491--1565615 Score: 55
Period size: 4 Copynumber: 31.5 Consensus size: 4
1565481 ATATTAGAAA
* * * * *
1565491 AAAT ACAT AAAT AAAT -AAG AAAT AAAAT AAAT AAAT -GAT AAAT CAAG
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT
*** * * *
1565538 AGGG AAA- AAAG AAA- AAAT AAAT AAAAA AAAT AAAT AAAT AAA- AAAG
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT
*
1565584 AAGA- AGAAG AAAT AAAT AAAAT AAAT AAAT AA
1 AA-AT A-AAT AAAT AAAT -AAAT AAAT AAAT AA
1565616 TAGGAAAAAA
Statistics
Matches: 94, Mismatches: 16, Indels: 22
0.71 0.12 0.17
Matches are distributed among these distances:
3 13 0.14
4 67 0.71
5 14 0.15
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.16
Consensus pattern (4 bp):
AAAT
Found at i:1565506 original size:24 final size:20
Alignment explanation
Indices: 1565486--1565526 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
1565476 CGAAAATATT
1565486 AGAAAAAATACATAAATAAATA
1 AGAAAAAA-A-ATAAATAAATA
*
1565508 AGAAATAAAATAAATAAAT
1 AGAAAAAAAATAAATAAAT
1565527 GATAAATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 1 0.06
22 7 0.39
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (20 bp):
AGAAAAAAAATAAATAAATA
Found at i:1565567 original size:13 final size:13
Alignment explanation
Indices: 1565549--1565615 Score: 73
Period size: 13 Copynumber: 5.0 Consensus size: 13
1565539 GGGAAAAAAG
1565549 AAAAAATAAATAA
1 AAAAAATAAATAA
1565562 AAAAAATAAATAA
1 AAAAAATAAATAA
*
1565575 ATAAAAA-AGAAGAA
1 A-AAAAATA-AATAA
*
1565589 GAAGAAATAAATAA
1 -AAAAAATAAATAA
*
1565603 AATAAATAAATAA
1 AAAAAATAAATAA
1565616 TAGGAAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
13 27 0.59
14 17 0.37
15 2 0.04
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (13 bp):
AAAAAATAAATAA
Found at i:1565597 original size:37 final size:35
Alignment explanation
Indices: 1565542--1565615 Score: 112
Period size: 37 Copynumber: 2.1 Consensus size: 35
1565532 ATCAAGAGGG
*
1565542 AAAAAAGAAAAAATAAATAAAAAAAATAAATAAAT
1 AAAAAAGAAAAAAGAAATAAAAAAAATAAATAAAT
*
1565577 AAAAAAGAAGAAGAAGAAATAAATAAAATAAATAAAT
1 AAAAAAGAA-AA-AAGAAATAAAAAAAATAAATAAAT
1565614 AA
1 AA
1565616 TAGGAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 9 0.26
36 2 0.06
37 24 0.69
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.14
Consensus pattern (35 bp):
AAAAAAGAAAAAAGAAATAAAAAAAATAAATAAAT
Found at i:1565599 original size:24 final size:21
Alignment explanation
Indices: 1565542--1565604 Score: 74
Period size: 24 Copynumber: 2.9 Consensus size: 21
1565532 ATCAAGAGGG
*
1565542 AAAAAAGAAA-AAATAAATAA
1 AAAAAAGAAATAAATAAAAAA
*
1565562 AAAAAATAAATAAATAAAAAA
1 AAAAAAGAAATAAATAAAAAA
1565583 GAAGAAGAAGAAATAAATAAAA
1 -AA-AA-AAGAAATAAATAAAA
1565605 TAAATAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 9 0.25
21 9 0.25
22 2 0.06
23 2 0.06
24 14 0.39
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.11
Consensus pattern (21 bp):
AAAAAAGAAATAAATAAAAAA
Found at i:1566730 original size:34 final size:34
Alignment explanation
Indices: 1566683--1566844 Score: 104
Period size: 34 Copynumber: 4.6 Consensus size: 34
1566673 TCCAAAAACC
1566683 TATATAATATATATTTTCAAAAAATATTTTAAAAT
1 TATAT-ATATATATTTTCAAAAAATATTTTAAAAT
* * *
1566718 TATATATATATATATATATATATTTTAAAAATGTTTTCAAA-
1 TATATATATATAT-T-T-T-CA----AAAAATATTTTAAAAT
* *
1566759 -AT-TATATAT-TTTTC-AAAAATGTTTTAAAAC
1 TATATATATATATTTTCAAAAAATATTTTAAAAT
* *
1566789 TATATATTATATGTTTTC--AAAATGATTTCAAAAT
1 TATATA-TATATATTTTCAAAAAAT-ATTTTAAAAT
1566823 TATATATTATATATTTTCAAAA
1 TATATA-TATATATTTTCAAAA
1566845 TGTTTTTAAA
Statistics
Matches: 102, Mismatches: 9, Indels: 31
0.72 0.06 0.22
Matches are distributed among these distances:
29 14 0.14
31 2 0.02
32 2 0.02
33 10 0.10
34 37 0.36
35 7 0.07
36 4 0.04
37 2 0.02
38 2 0.02
39 7 0.07
40 2 0.02
42 13 0.13
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (34 bp):
TATATATATATATTTTCAAAAAATATTTTAAAAT
Found at i:1566748 original size:43 final size:43
Alignment explanation
Indices: 1566683--1566767 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 43
1566673 TCCAAAAACC
1566683 TATATAATATATATTTTCAAAAAATATTTT-AAAATTATATATA
1 TATATAATATATATTTTC-AAAAATATTTTCAAAATTATATATA
*
1566726 TATATATATATATATTTT-AAAAATGTTTTCAAAATTATATAT
1 TATATA-ATATATATTTTCAAAAATATTTTCAAAATTATATAT
1566768 TTTTCAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
42 10 0.26
43 18 0.46
44 11 0.28
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (43 bp):
TATATAATATATATTTTCAAAAATATTTTCAAAATTATATATA
Found at i:1566765 original size:29 final size:29
Alignment explanation
Indices: 1566732--1566829 Score: 110
Period size: 29 Copynumber: 3.2 Consensus size: 29
1566722 TATATATATA
1566732 TATATATATTTTAAAAATGTTTTCAAAAT
1 TATATATATTTTAAAAATGTTTTCAAAAT
1566761 TATATAT-TTTTCAAAAATGTTTT-AAAACT
1 TATATATATTTT-AAAAATGTTTTCAAAA-T
* *
1566790 ATATATTATATGTTTTCAAAATGATTTCAAAAT
1 -TATA-TATA--TTTTAAAAATGTTTTCAAAAT
1566823 TATATAT
1 TATATAT
1566830 TATATATTTT
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
28 8 0.14
29 19 0.32
30 4 0.07
31 6 0.10
32 4 0.07
33 10 0.17
34 8 0.14
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (29 bp):
TATATATATTTTAAAAATGTTTTCAAAAT
Found at i:1566961 original size:24 final size:24
Alignment explanation
Indices: 1566921--1566979 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
1566911 TATTTTAAAA
1566921 ATGTTTTC-AAAACTATATAATAT
1 ATGTTTTCAAAAACTATATAATAT
*
1566944 ATGTTTTCAAAAACTATATATTAT
1 ATGTTTTCAAAAACTATATAATAT
*
1566968 ATATTTTCAAAA
1 ATGTTTTCAAAA
1566980 TATTTTCTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
23 8 0.24
24 25 0.76
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (24 bp):
ATGTTTTCAAAAACTATATAATAT
Found at i:1567003 original size:173 final size:168
Alignment explanation
Indices: 1566724--1567092 Score: 410
Period size: 173 Copynumber: 2.1 Consensus size: 168
1566714 AAATTATATA
*
1566724 TATATATATATATATATTTTAAAAATGTTTTCAAAATTATATATTTTTCAAAAATGTTTTAAAAC
1 TATATATATATATATATTTTAAAAATGTTTTCAAAACTATATA----T-AAAAATGTTTTAAAAC
* ** *
1566789 TATATATTATATGTTTTCAAAATGATTTCAAAATTATATATTATAT-ATTTTCAAAATGTTTTTA
61 TATATATTATATATTTTCAAAATGATTTCAAAACCATATATTATATAATTTTCAAAATG-ATTT-
* ** *
1566853 AAAACTATATAATGTATATGTTTTTCCAAAAAT-G-CTTTCAAAAAC
124 AAAACTATATAATATATACATTTTT-AAAAAATCGTCTTTC-AAAAC
* * *
1566898 TATATAT-TATATGTATTTTAAAAATGTTTTCAAAACTATATA-ATATATGTTTTCAAAAACTAT
1 TATATATATATATATATTTTAAAAATGTTTTCAAAACTATATATAAAAATGTTTT--AAAACTAT
1566961 ATATTATATATTTTCAAAAT-ATTTTCTCAAAAAACCATATATTATATAATTTTCAAAATGATTT
64 ATATTATATATTTTCAAAATGA--TT-TC--AAAACCATATATTATATAATTTTCAAAATGATTT
* *
1567025 CAAACTATATAATATATACATTTTTAAAAAATCGTTTTTCAAAAC
124 AAAACTATATAATATATACATTTTTAAAAAATCGTCTTTCAAAAC
*
1567070 TATATATAT-TATATATTTCAAAA
1 TATATATATATATATATTTTAAAA
1567093 TCATTTGCAA
Statistics
Matches: 168, Mismatches: 16, Indels: 24
0.81 0.08 0.12
Matches are distributed among these distances:
167 9 0.05
168 1 0.01
169 27 0.16
170 2 0.01
171 8 0.05
172 46 0.27
173 56 0.33
174 19 0.11
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.45
Consensus pattern (168 bp):
TATATATATATATATATTTTAAAAATGTTTTCAAAACTATATATAAAAATGTTTTAAAACTATAT
ATTATATATTTTCAAAATGATTTCAAAACCATATATTATATAATTTTCAAAATGATTTAAAACTA
TATAATATATACATTTTTAAAAAATCGTCTTTCAAAAC
Found at i:1567054 original size:98 final size:100
Alignment explanation
Indices: 1566847--1567054 Score: 250
Period size: 98 Copynumber: 2.1 Consensus size: 100
1566837 TTTCAAAATG
* * *
1566847 TTTTTAAAAACTATATAATGTATATGTTTTTCCAAAAATGCTTTCAAAAACTATATATTATATGT
1 TTTTTAAAAACTATATAATGTATATGATTTTCCAAAAATGCTTTCAAAAACCATATATTATATGA
* *
1566912 ATTTTAAAAATGTTTTCAAAACTATATAATATATG
66 ATTTTAAAAATGATTTCAAAACTATATAATATATA
* *
1566947 TTTTCAAAAACTATAT-AT-TATAT-ATTTT-CAAAATAT-TTTCTCAAAAAACCATATATTATA
1 TTTTTAAAAACTATATAATGTATATGATTTTCCAAAA-ATGCTT-TC-AAAAACCATATATTATA
*
1567007 T-AATTTTCAAAATGATTTC-AAACTATATAATATATACA
63 TGAATTTTAAAAATGATTTCAAAACTATATAATATAT--A
1567045 TTTTTAAAAA
1 TTTTTAAAAA
1567055 ATCGTTTTTC
Statistics
Matches: 94, Mismatches: 9, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
96 23 0.24
97 23 0.24
98 31 0.33
99 2 0.02
100 15 0.16
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.43
Consensus pattern (100 bp):
TTTTTAAAAACTATATAATGTATATGATTTTCCAAAAATGCTTTCAAAAACCATATATTATATGA
ATTTTAAAAATGATTTCAAAACTATATAATATATA
Found at i:1567781 original size:85 final size:86
Alignment explanation
Indices: 1567681--1568039 Score: 262
Period size: 84 Copynumber: 4.2 Consensus size: 86
1567671 CAAATAGCTT
* * * * * *
1567681 TTCTCGACTTAAGTTATACTGTAAATTTGACATGCCCTTGAGCTGAATGGAATTAAACTCAAATG
1 TTCTCGCCTTGAGTTATGCTGTAAATTGGACATGCCCTTGAGCTGAATGGAATCAAACTCAAAGG
1567746 T-ATTGGCTGACAGATAACCC
66 TCATTGGCTGACAGATAACCC
* * * *
1567766 TTCTCGCCTTGAGTTATGCTGTAAATTGGATATGCCTTTGAGCTGAATGTAATCAAACTCGAAGG
1 TTCTCGCCTTGAGTTATGCTGTAAATTGGACATGCCCTTGAGCTGAATGGAATCAAACTCAAAGG
* * * * *
1567831 TCTTTTGTTGGCAGGTAACCC
66 TCATTGGCTGACAGATAACCC
* * ** * * * * *
1567852 TTCTCGCCTTGAGCTATGCTGCAAATT--ATGTGTCTTTGAGCTGAGTGTAATCGAACT-AGAAG
1 TTCTCGCCTTGAGTTATGCTGTAAATTGGACATGCCCTTGAGCTGAATGGAATCAAACTCA-AAG
* * * * * *
1567914 GTCTTTTGTTGGCGGATATCCC
65 GTCATTGGCTGACAGATAACCC
* * ** * * * * *
1567936 TTCTCGCCTTGAGCTATGCTGCAAA-T-GATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
1 TTCTCGCCTTGAGTTATGCTGTAAATTGGACATGCCCTTGAGCTGAATGGAATCAAACTCAAAGG
* * * * *
1567999 TCTTTTGTTGGCAGATAAACC
66 TCATTGGCTGACAGATAACCC
*
1568020 TTCTAGCCTTGAGTTATGCT
1 TTCTCGCCTTGAGTTATGCT
1568040 ACAAATGATG
Statistics
Matches: 238, Mismatches: 32, Indels: 9
0.85 0.11 0.03
Matches are distributed among these distances:
83 1 0.00
84 142 0.60
85 56 0.24
86 39 0.16
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (86 bp):
TTCTCGCCTTGAGTTATGCTGTAAATTGGACATGCCCTTGAGCTGAATGGAATCAAACTCAAAGG
TCATTGGCTGACAGATAACCC
Found at i:1567922 original size:84 final size:84
Alignment explanation
Indices: 1567756--1569172 Score: 1584
Period size: 84 Copynumber: 16.8 Consensus size: 84
1567746 TATTGGCTGA
* * * ** * *
1567756 CAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTGGATATGCCTTTGAGCTGAATGTAATCA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAA-T-GATGTGCCTTTGAGCTGAGCGTAGTCG
1567821 AACTCGAAGGTCTTTTGTTGG
64 AACTCGAAGGTCTTTTGTTGG
* * * * * * *
1567842 CAGGTAACCCTTCTCGCCTTGAGCTATGCTGCAAATTATGTGTCTTTGAGCTGAGTGTAATCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAA
*
1567907 CTAGAAGGTCTTTTGTTGG
66 CTCGAAGGTCTTTTGTTGG
* * * * * *
1567926 CGGATATCCCTTCTCGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAA
1567991 CTCGAAGGTCTTTTGTTGG
66 CTCGAAGGTCTTTTGTTGG
* * * * *
1568010 CAGATAAACCTTCTAGCCTTGAGTTATGCTACAAATGATGTGCCTTGGAGCTGAGCGTAGCCAAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAA
1568075 CTCGAAGGTCTTTTGATT-G
66 CTCGAAGGTCTTTTG-TTGG
* * * * ** * * **
1568094 CAGATAACCTTTATAGCCTTGAGTTATACTGTAAATGATGTTACTTGGAGCTGAGCGTAATAAAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAA
*
1568159 TTCGAAGGTCTTTTGTTGG
66 CTCGAAGGTCTTTTGTTGG
* * * * * * *
1568178 TAAATAGCCCTTATTGCCTTGAGTTATGCTGCAAATGATATGCCTTTGAGTTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAA
*
1568243 CTCAAAGGTCTTTTGTTGG
66 CTCGAAGGTCTTTTGTTGG
* ** * * * * * *
1568262 CAAATAATTCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGTCTTGGAGCTGGGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAA
*
1568327 CTCGAAGGTCTTTGGTTGG
66 CTCGAAGGTCTTTTGTTGG
* * * *
1568346 CAAATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGTCTTTGAGCTAAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAA
* *
1568411 CTCGAAGGTATTTTATTGG
66 CTCGAAGGTCTTTTGTTGG
* * * * *
1568430 CAAATAGCCC-TCATTGCCTTGAGCTATG-TCGCAAATGATGTGCC-TTGAAACTGAGCGTAGTC
1 CAGATAACCCTTC-TAGCCTTGAGTTATGCT-GCAAATGATGTGCCTTTG-AGCTGAGCGTAGTC
*
1568492 GAACTCGAAGGTCTTTGGTTGG
63 GAACTCGAAGGTCTTTTGTTGG
* * * *
1568514 CAGATAACCCTTCTAGCATTGAGTTATCCTGTAAATGATATGCCTTTGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAA
* * *
1568579 CTCGAATGTCTTTTATTGT
66 CTCGAAGGTCTTTTGTTGG
* * * * ** * * * * * *
1568598 AAAATATCACTTCTTTCCTTGAGCTGTGTTGCAGATGATATGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAA
* *
1568663 CTCGAAGGTCTTTGGTTAG
66 CTCGAAGGTCTTTTGTTGG
*
1568682 CAGATAACCCTTCTAGCCTTGAGATT-TGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
1 CAGATAACCCTTCTAGCCTTGAG-TTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGA
*
1568746 ACTCGAAGGTCTTTTGGTGG
65 ACTCGAAGGTCTTTTGTTGG
* * * * * * *
1568766 CAGATAGCCCGTCTTGCCTTCAGCTATGCTGCAAATGATGTGCATTTAAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAA
* * *
1568831 CTCGAATGTATTTGGTTGG
66 CTCGAAGGTCTTTTGTTGG
* * *
1568850 AAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTTGAGCTGACCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAA
* *
1568915 CTCGAAGATATTTTGTTGG
66 CTCGAAGGTCTTTTGTTGG
* * * * * *
1568934 CAAATAGCCCTTCTTGCCTTGAGATATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAA
* *
1568999 CTCGAAGGTCTTTGGTTGA
66 CTCGAAGGTCTTTTGTTGG
* * * * * * *
1569018 CATATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATATGTCTTCGAGCTGAGCATAGTCAAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAA
*
1569083 CTCGAAGGTCTTTTGGTGG
66 CTCGAAGGTCTTTTGTTGG
* * * * * * *
1569102 CAGATAACCCTTCTTGCCTTGTGCTATGCAGCAAATGATGTGCCTTTGAGCTGAGTGTAATTGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAA
1569167 CTCGAA
66 CTCGAA
1569173 TATTCTGGCT
Statistics
Matches: 1119, Mismatches: 202, Indels: 22
0.83 0.15 0.02
Matches are distributed among these distances:
83 9 0.01
84 1068 0.95
85 10 0.01
86 32 0.03
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (84 bp):
CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAA
CTCGAAGGTCTTTTGTTGG
Found at i:1570537 original size:95 final size:95
Alignment explanation
Indices: 1570346--1570601 Score: 331
Period size: 95 Copynumber: 2.7 Consensus size: 95
1570336 AACTAGCTGA
* * *
1570346 ATCCATAAAGCCGGGGTGTTTAACCAATTGCTCTAGAGGGACAACATAA-TATCATTG--TA-TA
1 ATCCATAAAGCCGGGGTGTTTAACCAATTGCTCTAGAGGGACAACTTAAGTTTTATTGTATATTA
* *
1570407 TAATCACCTTTATCTGGTTAGCTGAATATT
66 TAATCACCTTTATCAGGCTAGCTGAATATT
* *
1570437 ATCCATAAAGACGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTTAAGTTTTATTGTATATTA
1 ATCCATAAAGCCGGGGTGTTTAACCAATTGCTCTAGAGGGACAACTTAAGTTTTATTGTATATTA
*
1570502 TAATCACCTTTATCAGGCTAGCTGAATCTT
66 TAATCACCTTTATCAGGCTAGCTGAATATT
* * * * * * * *
1570532 ATCCATAAAGCCAGAGTGTTTAACCAATTACTTTAGACGGACATCTCAAGCTTTATTGTATATAT
1 ATCCATAAAGCCGGGGTGTTTAACCAATTGCTCTAGAGGGACAACTTAAGTTTTATTGTATAT-T
1570597 ATAAT
65 ATAAT
1570602 ATTATAATAT
Statistics
Matches: 142, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
91 46 0.32
92 6 0.04
94 2 0.01
95 82 0.58
96 6 0.04
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (95 bp):
ATCCATAAAGCCGGGGTGTTTAACCAATTGCTCTAGAGGGACAACTTAAGTTTTATTGTATATTA
TAATCACCTTTATCAGGCTAGCTGAATATT
Found at i:1574338 original size:17 final size:17
Alignment explanation
Indices: 1574311--1574375 Score: 64
Period size: 16 Copynumber: 3.8 Consensus size: 17
1574301 TCAAGAGGGG
1574311 AAAAATAAAAATAAAATA
1 AAAAAT-AAAATAAAATA
1574329 AAAAATAAAAT-AAATA
1 AAAAATAAAATAAAATA
*
1574345 AAAACA-AAAA-AGAATA
1 AAAA-ATAAAATAAAATA
1574361 AAAGAATACAAATAA
1 AAA-AATA-AAATAA
1574376 TTAAATAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
16 21 0.54
17 8 0.21
18 9 0.23
19 1 0.03
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.14
Consensus pattern (17 bp):
AAAAATAAAATAAAATA
Found at i:1574353 original size:21 final size:20
Alignment explanation
Indices: 1574319--1574362 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
1574309 GGAAAAATAA
1574319 AAATAAAATAAAAAATAAAAT
1 AAATAAAATAAAAAA-AAAAT
*
1574340 AAATAAAA-ACAAAAAAGAAT
1 AAATAAAATA-AAAAAAAAAT
1574360 AAA
1 AAA
1574363 AGAATACAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.82, C:0.02, G:0.02, T:0.14
Consensus pattern (20 bp):
AAATAAAATAAAAAAAAAAT
Found at i:1574354 original size:33 final size:34
Alignment explanation
Indices: 1574311--1574380 Score: 90
Period size: 33 Copynumber: 2.1 Consensus size: 34
1574301 TCAAGAGGGG
*
1574311 AAAAATAAAAATAAAATAAAA-AATA-AAATAAAT
1 AAAAACAAAAA-AAAATAAAAGAATACAAATAAAT
* *
1574344 AAAAACAAAAAAGAATAAAAGAATACAAATAATT
1 AAAAACAAAAAAAAATAAAAGAATACAAATAAAT
1574378 AAA
1 AAA
1574381 TAATATTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 8 0.25
33 14 0.44
34 10 0.31
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.16
Consensus pattern (34 bp):
AAAAACAAAAAAAAATAAAAGAATACAAATAAAT
Found at i:1575573 original size:18 final size:18
Alignment explanation
Indices: 1575550--1575598 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
1575540 GGACTTGGAC
1575550 AATAAAACAAA-AAAAATT
1 AATAAAA-AAATAAAAATT
*
1575568 AATAAAAAAATAAAAATG
1 AATAAAAAAATAAAAATT
1575586 AA-AAAATAAATAA
1 AATAAAA-AAATAA
1575599 CCATAATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 7 0.25
18 21 0.75
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (18 bp):
AATAAAAAAATAAAAATT
Found at i:1575684 original size:34 final size:35
Alignment explanation
Indices: 1575647--1575830 Score: 128
Period size: 34 Copynumber: 5.2 Consensus size: 35
1575637 ACCTATATAA
1575647 TATATATTTTCAAAAATATTTTAAAATTATATTA-
1 TATATATTTTCAAAAATATTTTAAAATTATATTAT
* * * * * **
1575681 TATATA-TAT--ATATTTTTTTAAAAATGTTTTCAAAAT
1 TATATATTTTCAAAAATATTTT-AAAA--TTAT-ATTAT
* *
1575717 TATATAGTTTTCAAAAATGTTTTAAAACTATA-TAT
1 TATATA-TTTTCAAAAATATTTTAAAATTATATTAT
* * *
1575752 TATATGTTTTCAAAATTATTTCAAAATTATA-TAT
1 TATATATTTTCAAAAATATTTTAAAATTATATTAT
* *
1575786 TATATATTTTCAAAATGTTTTTTAAAATTATATATAT
1 TATATATTTTCAAAA-ATATTTTAAAATTATAT-TAT
1575823 ATATATAT
1 -TATATAT
1575831 ATGTGTGTGT
Statistics
Matches: 114, Mismatches: 23, Indels: 22
0.72 0.14 0.14
Matches are distributed among these distances:
31 7 0.06
32 4 0.04
33 2 0.02
34 47 0.41
35 22 0.19
36 7 0.06
37 5 0.04
38 9 0.08
39 4 0.04
40 7 0.06
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.51
Consensus pattern (35 bp):
TATATATTTTCAAAAATATTTTAAAATTATATTAT
Found at i:1575688 original size:43 final size:43
Alignment explanation
Indices: 1575640--1575721 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 43
1575630 TTCAAAAACC
1575640 TATATA-ATATATATTTTCAAAAATATTTT-AAAATTATATTA
1 TATATATATATATATTTTCAAAAATATTTTCAAAATTATATTA
* * *
1575681 TATATATATATATTTTTTTAAAAATGTTTTCAAAATTATAT
1 TATATATATATATATTTTCAAAAATATTTTCAAAATTATAT
1575722 AGTTTTCAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 6 0.17
42 20 0.56
43 10 0.28
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.51
Consensus pattern (43 bp):
TATATATATATATATTTTCAAAAATATTTTCAAAATTATATTA
Found at i:1575720 original size:28 final size:28
Alignment explanation
Indices: 1575695--1575750 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
1575685 TATATATATT
* *
1575695 TTTTTAAAAATGTTTTCAAAATTATATAG
1 TTTTCAAAAATGTTTT-AAAACTATATAG
1575724 TTTTCAAAAATGTTTTAAAACTATATA
1 TTTTCAAAAATGTTTTAAAACTATATA
1575751 TTATATGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 10 0.40
29 15 0.60
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.46
Consensus pattern (28 bp):
TTTTCAAAAATGTTTTAAAACTATATAG
Found at i:1575818 original size:35 final size:34
Alignment explanation
Indices: 1575715--1575828 Score: 142
Period size: 34 Copynumber: 3.3 Consensus size: 34
1575705 TGTTTTCAAA
*
1575715 ATTATATAGTTTTCAAAAATG-TTTTAAAACTATAT
1 ATTATATA-TTTTC-AAAATGTTTTTAAAATTATAT
* *
1575750 ATTATATGTTTTCAAAAT-TATTTCAAAATTATAT
1 ATTATATATTTTCAAAATGT-TTTTAAAATTATAT
1575784 ATTATATATTTTCAAAATGTTTTTTAAAATTATAT
1 ATTATATATTTTCAAAATG-TTTTTAAAATTATAT
1575819 ATATATATAT
1 AT-TATATAT
1575829 ATATGTGTGT
Statistics
Matches: 69, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
33 5 0.07
34 34 0.49
35 22 0.32
36 8 0.12
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (34 bp):
ATTATATATTTTCAAAATGTTTTTAAAATTATAT
Found at i:1575857 original size:90 final size:93
Alignment explanation
Indices: 1575756--1575923 Score: 229
Period size: 90 Copynumber: 1.8 Consensus size: 93
1575746 ATATATTATA
* * ** *
1575756 TGTTTTCAAAAT-TATTTCAAAATTATAT-AT-TATAT-ATTTTC-AAAATGTTTTTTAAAATTA
1 TGTTTTCAAAATGT-TTTCAAAACTATATAATGTATATGATTTTCAAAAATGCTTTCAAAAACTA
1575816 TATATATATATATATATGTGTGTGTGTGTG
65 TATAT-TATATATATATGTGTGTGTGTGTG
*
1575846 TGTTTTCAAAATGTTTTCAAAACTATATAATGTATATGTTTTTCAAAAATGCTTTCAAAAACTAT
1 TGTTTTCAAAATGTTTTCAAAACTATATAATGTATATGATTTTCAAAAATGCTTTCAAAAACTAT
1575911 ATATTATATATAT
66 ATATTATATATAT
1575924 TTTAAAAAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
90 25 0.37
91 3 0.04
92 5 0.07
93 14 0.21
94 20 0.30
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (93 bp):
TGTTTTCAAAATGTTTTCAAAACTATATAATGTATATGATTTTCAAAAATGCTTTCAAAAACTAT
ATATTATATATATATGTGTGTGTGTGTG
Found at i:1575987 original size:40 final size:39
Alignment explanation
Indices: 1575943--1576104 Score: 110
Period size: 36 Copynumber: 4.2 Consensus size: 39
1575933 AATTCAAAAC
1575943 TATATAATTATTTTCAAAAATGTTTTCAAAAACTATATA-
1 TATATAA-TATTTTCAAAAATGTTTTCAAAAACTATATAT
* *
1575982 T-TAT-ATATTTTCAAAAATATTTTCTTAAAAAAACCATATAT
1 TATATAATATTTTCAAAAATGTTTTC----AAAAACTATATAT
* *
1576023 TATAT-A-ATTTTC-AAAATGATTTC--AAACTATATAA
1 TATATAATATTTTCAAAAATGTTTTCAAAAACTATATAT
* *
1576057 TATATACAT-TTTTAAAAAATCATTTTTCAAAATTA-TATATAT
1 TATATA-ATATTTTCAAAAAT--GTTTTCAAAA--ACTATATAT
1576099 TATATA
1 TATATA
1576105 TTTCAAAATC
Statistics
Matches: 97, Mismatches: 10, Indels: 29
0.71 0.07 0.21
Matches are distributed among these distances:
34 14 0.14
36 23 0.24
37 6 0.06
38 3 0.03
39 5 0.05
40 20 0.21
41 9 0.09
42 16 0.16
43 1 0.01
ACGTcount: A:0.46, C:0.08, G:0.01, T:0.44
Consensus pattern (39 bp):
TATATAATATTTTCAAAAATGTTTTCAAAAACTATATAT
Found at i:1576013 original size:107 final size:105
Alignment explanation
Indices: 1575848--1576057 Score: 259
Period size: 107 Copynumber: 2.0 Consensus size: 105
1575838 TGTGTGTGTG
* * *
1575848 TTTTCAAAATGTTTTCAAAACTATATAATGTATATGTTTTTCAAAAATGCTTTC-AAAAACTATA
1 TTTTCAAAATGTTTTCAAAACTATATAATGTATATGATTTTCAAAAATACTTTCAAAAAACCATA
1575912 TATTATATATATTTT-AAAAAAAATTCAAAACTATATAATTA
66 TATTATATA-ATTTTCAAAAAAAATTC-AAACTATATAATTA
*
1575953 TTTTCAAAAATGTTTTCAAAAACTATAT-AT-TATAT-ATTTTCAAAAATATTTTCTTAAAAAAA
1 TTTTC-AAAATGTTTTC-AAAACTATATAATGTATATGATTTTCAAAAATACTTTC---AAAAAA
** *
1576015 CCATATATTATATAATTTTCAAAATGATTTCAAACTATATAAT
61 CCATATATTATATAATTTTCAAAAAAAATTCAAACTATATAAT
1576058 ATATACATTT
Statistics
Matches: 91, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
104 15 0.16
105 10 0.11
106 13 0.14
107 27 0.30
108 26 0.29
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (105 bp):
TTTTCAAAATGTTTTCAAAACTATATAATGTATATGATTTTCAAAAATACTTTCAAAAAACCATA
TATTATATAATTTTCAAAAAAAATTCAAACTATATAATTA
Found at i:1576068 original size:76 final size:75
Alignment explanation
Indices: 1575938--1576137 Score: 198
Period size: 75 Copynumber: 2.7 Consensus size: 75
1575928 AAAAAAATTC
* * * *
1575938 AAAAC-TATATAAT-TATTTTCAAAAATGTTTTCAAAAACTATAT-AT-TATATA-TTTTCAAAA
1 AAAACATATATTATATATTTTC-AAAATGATTTC--AAACTATATAATATATACATTTTTAAAAA
*
1575998 AT-ATTTTCTTAAA
63 ATCATTTT-TCAAA
1576011 AAAACCATATATTATATAATTTTCAAAATGATTTCAAACTATATAATATATACATTTTTAAAAAA
1 AAAA-CATATATTATAT-ATTTTCAAAATGATTTCAAACTATATAATATATACATTTTTAAAAAA
1576076 TCATTTTTCAAA
64 TCATTTTTCAAA
** * * *
1576088 ATTATATATATTATATA-TTTCAAAATCATTTGCAAACTGTATAATATATA
1 AAAACATATATTATATATTTTCAAAATGATTT-CAAACTATATAATATATA
1576138 TGTATTAATA
Statistics
Matches: 108, Mismatches: 10, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
73 4 0.04
74 23 0.21
75 27 0.25
76 27 0.25
77 22 0.20
78 5 0.05
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (75 bp):
AAAACATATATTATATATTTTCAAAATGATTTCAAACTATATAATATATACATTTTTAAAAAATC
ATTTTTCAAA
Found at i:1576831 original size:39 final size:39
Alignment explanation
Indices: 1576778--1576852 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
1576768 TATATGATTT
1576778 TTTTTGTTCCTAATGCTTTTGTTTATTTGCACAAACCAA
1 TTTTTGTTCCTAATGCTTTTGTTTATTTGCACAAACCAA
*
1576817 TTTTTG-TCCGTAATGTTTTTGTTTATTTGCACAAAC
1 TTTTTGTTCC-TAATGCTTTTGTTTATTTGCACAAAC
1576853 TAAACGACTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 3 0.09
39 31 0.91
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (39 bp):
TTTTTGTTCCTAATGCTTTTGTTTATTTGCACAAACCAA
Found at i:1578579 original size:21 final size:20
Alignment explanation
Indices: 1578512--1578586 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 20
1578502 CAGTTTCCAA
* * *
1578512 AATCGCAACGCGATTCTTTAC
1 AATCGCAATGCGATT-TTCAT
1578533 AATCGCAATGCGATTTTCAT
1 AATCGCAATGCGATTTTCAT
* *
1578553 ATTCGCATTGCGATTTTCCAT
1 AATCGCAATGCGATTTT-CAT
*
1578574 AATCGCAACGCGA
1 AATCGCAATGCGA
1578587 ATATGAAAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 18 0.40
21 27 0.60
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (20 bp):
AATCGCAATGCGATTTTCAT
Found at i:1578668 original size:20 final size:20
Alignment explanation
Indices: 1578574--1578725 Score: 198
Period size: 20 Copynumber: 7.6 Consensus size: 20
1578564 GATTTTCCAT
* ** *
1578574 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1578594 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1578614 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1578634 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1578654 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1578674 AATCACAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1578694 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1578714 AATCGCAACGCG
1 AATCGCAACGCG
1578726 ATTTTTAAAG
Statistics
Matches: 115, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
19 1 0.01
20 112 0.97
21 2 0.02
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1579144 original size:33 final size:33
Alignment explanation
Indices: 1579105--1579175 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1579095 TTCACTTAGA
1579105 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1579138 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1579171 TTTCA
1 TTTCA
1579176 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1579281 original size:21 final size:20
Alignment explanation
Indices: 1579255--1579327 Score: 83
Period size: 21 Copynumber: 3.5 Consensus size: 20
1579245 TGCAGAAGAG
1579255 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
1579276 TCGCAACGTGAAAATGTCTA
1 TCGCAACGAGAAAATGAAAA
1579296 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAG-AAAATGAAAA
1579318 TCGCAACGAG
1 TCGCAACGAG
1579328 CTGTTTATCC
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
20 8 0.19
21 25 0.60
22 9 0.21
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.16
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:1580080 original size:14 final size:14
Alignment explanation
Indices: 1580061--1580096 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1580051 ATTGTTTAAT
1580061 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1580075 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1580089 TGATTTGT
1 TGATTTGT
1580097 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1580211 original size:19 final size:19
Alignment explanation
Indices: 1580187--1580274 Score: 114
Period size: 19 Copynumber: 4.8 Consensus size: 19
1580177 GCATTATGTT
1580187 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
1580206 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAATGC
*
1580223 G--A-GAGAATCGCAATGC
1 GAAATGAAAATCGCAATGC
1580239 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
*
1580258 GGAAATGAAAATAGCAA
1 -GAAATGAAAATCGCAA
1580275 CGAGAGAATC
Statistics
Matches: 60, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
14 10 0.17
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 29 0.48
20 15 0.25
ACGTcount: A:0.49, C:0.15, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAATGC
Found at i:1580306 original size:53 final size:53
Alignment explanation
Indices: 1580187--1580293 Score: 198
Period size: 53 Copynumber: 2.0 Consensus size: 53
1580177 GCATTATGTT
*
1580187 GAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAATGCGGAAATGAAAATAGCAACGAGAGAATCGCAATGC
1580239 GAAATGAAAATCGCAATGCGGAAATGAAAATAGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAATGCGGAAATGAAAATAGCAACGAGAGAATCGCAATGC
1580292 GA
1 GA
1580294 TTTTCATTTC
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
52 19 0.36
53 34 0.64
ACGTcount: A:0.47, C:0.16, G:0.24, T:0.13
Consensus pattern (53 bp):
GAAATGAAAATCGCAATGCGGAAATGAAAATAGCAACGAGAGAATCGCAATGC
Found at i:1580370 original size:72 final size:69
Alignment explanation
Indices: 1580284--1580577 Score: 262
Period size: 72 Copynumber: 4.2 Consensus size: 69
1580274 ACGAGAGAAT
*
1580284 CGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATT
1 CGCATTGCGATTTTC-TTTCG--TTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATT
1580349 TTCATTT-
62 TTCATTTC
* * * * *
1580356 CGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCATTGCGA
1 CGCATTGCGATTTTC-TTTCG--TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGTTGCGA
1580418 TTTTCATTTC
60 TTTTCATTTC
* *
1580428 CGCATTGCGA--TTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
1 CGCATTGCGATTTTCTTTCGTTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGAT
1580491 TTTCATTTC
61 TTTCATTTC
* * * * *
1580500 CACATTGCGATTTTC-TT-GTTGGGATTTTCATTTCGCATTGTGATTCTCTCGTTGCGATTGTAA
1 CGCATTGCGATTTTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
1580563 TTTC
66 TTTC
**
1580567 CGTGTTGCGAT
1 CGCATTGCGAT
1580578 AGTCAAATGC
Statistics
Matches: 185, Mismatches: 23, Indels: 33
0.77 0.10 0.14
Matches are distributed among these distances:
65 9 0.05
66 3 0.02
67 30 0.16
68 2 0.01
69 8 0.04
70 8 0.04
71 18 0.10
72 93 0.50
73 7 0.04
74 7 0.04
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (69 bp):
CGCATTGCGATTTTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
TTTC
Found at i:1580424 original size:105 final size:108
Alignment explanation
Indices: 1580289--1580558 Score: 414
Period size: 105 Copynumber: 2.6 Consensus size: 108
1580279 AGAATCGCAA
1580289 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
* *
1580354 TTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-T-CTCGT
66 TTCGCATTGCGATTTTCATTTCGCATTGCGATTTCTTCCACAT
1580394 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1580459 TTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCACAT
66 TTCGCATTGCGATTTTCATTTCGCATTGCGA-TTTC--TTCCACAT
* *
1580505 TGCGATTTTC--TT-G--TTGGGATTTTCATTT-CGCATTGTGATTCTCTCGTTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATT
1580559 GTAATTTCCG
Statistics
Matches: 155, Mismatches: 4, Indels: 12
0.91 0.02 0.07
Matches are distributed among these distances:
105 121 0.78
106 14 0.09
107 3 0.02
108 1 0.01
109 2 0.01
110 1 0.01
111 13 0.08
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (108 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
TTCGCATTGCGATTTTCATTTCGCATTGCGATTTCTTCCACAT
Found at i:1580573 original size:53 final size:52
Alignment explanation
Indices: 1580289--1580558 Score: 397
Period size: 53 Copynumber: 5.1 Consensus size: 52
1580279 AGAATCGCAA
1580289 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
1580342 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1580394 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
* *
1580447 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCACAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC---T-CTCGT
* *
1580505 TGCGATTTTC--TT-G--TTGGGATTTTCATTTCGCATTGTGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1580552 TGCGATT
1 TGCGATT
1580559 GTAATTTCCG
Statistics
Matches: 204, Mismatches: 6, Indels: 20
0.89 0.03 0.09
Matches are distributed among these distances:
47 10 0.05
48 1 0.00
51 3 0.01
52 62 0.30
53 108 0.53
54 3 0.01
55 1 0.00
56 2 0.01
57 1 0.00
58 13 0.06
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:1582859 original size:12 final size:12
Alignment explanation
Indices: 1582842--1582866 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1582832 TCTTCGGGGA
1582842 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1582854 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1582866 C
1 C
1582867 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1583075 original size:24 final size:24
Alignment explanation
Indices: 1583041--1583087 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1583031 CTGAAACATC
1583041 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1583065 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1583088 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1583104 original size:24 final size:24
Alignment explanation
Indices: 1583054--1583104 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
1583044 AAAATCCGTG
* * *
1583054 TATTGACCAATATCAAAGTCCGGA
1 TATTGACCAAGACCAAAGTCCGAA
* *
1583078 TATTGACCAAGACCAAATTTCGAA
1 TATTGACCAAGACCAAAGTCCGAA
1583102 TAT
1 TAT
1583105 GACTAGTACT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (24 bp):
TATTGACCAAGACCAAAGTCCGAA
Found at i:1583807 original size:20 final size:20
Alignment explanation
Indices: 1583779--1584027 Score: 257
Period size: 20 Copynumber: 12.4 Consensus size: 20
1583769 AAATTTCAGT
* * *
1583779 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1583799 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1583819 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
* * *
1583839 GTTGCCATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1583859 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
1583879 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1583899 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
1583919 ATTACGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1583939 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
1583959 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
1583979 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
1583999 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
1584019 GTTGCGATT
1 GTTGCGATT
1584028 ATGGAAAATC
Statistics
Matches: 201, Mismatches: 26, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 200 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:1584045 original size:21 final size:20
Alignment explanation
Indices: 1584021--1584068 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1584011 ATATTCGCGT
1584021 TGCGATTATGGAAAATCGCAA
1 TGCGATTAT-GAAAATCGCAA
* *
1584042 TGCGAATATGAAAATCGCAT
1 TGCGATTATGAAAATCGCAA
1584062 TGCGATT
1 TGCGATT
1584069 GTCAAGAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (20 bp):
TGCGATTATGAAAATCGCAA
Found at i:1584068 original size:61 final size:60
Alignment explanation
Indices: 1583995--1584148 Score: 150
Period size: 61 Copynumber: 2.5 Consensus size: 60
1583985 ATTTATGTGT
1583995 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTATGGAAAATCGCA-ATGCGAATATGAAAA
1 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTATGGAAAAT-G-ATATGCGAATATGAAAA
* * * * * * * * * ***
1584056 TCGCATTGCGATTGTCAAGAATCGCGTTGTGATTTTGGAAACTGATTTGCGATTATGGGGA
1 TCGCGTTGCGATTTTC-ATATTCGCGTTGCGATTATGGAAAATGATATGCGAATATGAAAA
*
1584117 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATT
1 TCGCGTTGCGATTTTCATATTCGCGTTGCGATT
1584149 TTGTTGGTCA
Statistics
Matches: 73, Mismatches: 18, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
59 12 0.16
60 2 0.03
61 38 0.52
62 21 0.29
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.36
Consensus pattern (60 bp):
TCGCGTTGCGATTTTCATATTCGCGTTGCGATTATGGAAAATGATATGCGAATATGAAAA
Found at i:1584957 original size:7 final size:7
Alignment explanation
Indices: 1584941--1584988 Score: 78
Period size: 7 Copynumber: 6.9 Consensus size: 7
1584931 TCTTTGGTCT
1584941 AATTCCA
1 AATTCCA
*
1584948 AATTCTA
1 AATTCCA
1584955 AATTCCA
1 AATTCCA
1584962 AATTCCA
1 AATTCCA
1584969 AATTCCA
1 AATTCCA
*
1584976 AATTTCA
1 AATTCCA
1584983 AATTCC
1 AATTCC
1584989 GTTCCTATAC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.42, C:0.25, G:0.00, T:0.33
Consensus pattern (7 bp):
AATTCCA
Found at i:1587500 original size:34 final size:34
Alignment explanation
Indices: 1587439--1587507 Score: 95
Period size: 33 Copynumber: 2.0 Consensus size: 34
1587429 TTATTTCATT
*
1587439 AATTGGTTGGATTTATTTTAATTTATTTT-GTTA
1 AATTGGTTGGATTTATTTTAATGTATTTTGGTTA
* *
1587472 AATTTGTTGGATTTTTTGTTAATGTATTTTGGTTA
1 AATTGGTTGGATTTATT-TTAATGTATTTTGGTTA
1587507 A
1 A
1587508 TTTTATTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
33 15 0.48
34 11 0.35
35 5 0.16
ACGTcount: A:0.23, C:0.00, G:0.17, T:0.59
Consensus pattern (34 bp):
AATTGGTTGGATTTATTTTAATGTATTTTGGTTA
Found at i:1587510 original size:34 final size:32
Alignment explanation
Indices: 1587437--1587510 Score: 94
Period size: 34 Copynumber: 2.2 Consensus size: 32
1587427 CTTTATTTCA
* *
1587437 TTAATTGGTTGGATTTATTTTAATTTATTTTG
1 TTAATTTGTTGGATTTATTTTAATGTATTTTG
*
1587469 TTAAATTTGTTGGATTTTTTGTTAATGTATTTTGG
1 TT-AATTTGTTGGATTTATT-TTAATGTATTTT-G
1587504 TTAATTT
1 TTAATTT
1587511 TATTTATTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 2 0.06
33 15 0.42
34 16 0.44
35 3 0.08
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (32 bp):
TTAATTTGTTGGATTTATTTTAATGTATTTTG
Found at i:1603648 original size:22 final size:23
Alignment explanation
Indices: 1603606--1603648 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1603596 TGTTTGAAAA
*
1603606 TTATATGAAATGTATGGATTTTC
1 TTATATGAAATATATGGATTTTC
1603629 TTATATGAAATAT-TGGATTT
1 TTATATGAAATATATGGATTT
1603649 AATTATGGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (23 bp):
TTATATGAAATATATGGATTTTC
Found at i:1603654 original size:22 final size:23
Alignment explanation
Indices: 1603604--1603654 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
1603594 AGTGTTTGAA
*
1603604 AATTATATGAAATGTATGGATTT
1 AATTATATGAAATATATGGATTT
**
1603627 TCTTATATGAAATAT-TGGATTT
1 AATTATATGAAATATATGGATTT
1603649 AATTAT
1 AATTAT
1603655 GGGTCTAGTC
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.37, C:0.02, G:0.14, T:0.47
Consensus pattern (23 bp):
AATTATATGAAATATATGGATTT
Found at i:1610233 original size:30 final size:33
Alignment explanation
Indices: 1610197--1610260 Score: 89
Period size: 30 Copynumber: 2.0 Consensus size: 33
1610187 TTGACAGTAT
1610197 TATAAAAAATTAAA-TTAAT-GATT-TTTTAAA
1 TATAAAAAATTAAATTTAATAGATTCTTTTAAA
* *
1610227 TATAAAATATTAAATTTATTAGATTCTTTTAAA
1 TATAAAAAATTAAATTTAATAGATTCTTTTAAA
1610260 T
1 T
1610261 TAATAGAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 13 0.45
31 4 0.14
32 4 0.14
33 8 0.28
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (33 bp):
TATAAAAAATTAAATTTAATAGATTCTTTTAAA
Found at i:1617757 original size:14 final size:14
Alignment explanation
Indices: 1617738--1617789 Score: 79
Period size: 14 Copynumber: 3.7 Consensus size: 14
1617728 ATCCATTTTT
1617738 CATAACATATCACA
1 CATAACATATCACA
1617752 CATAACATATCACA
1 CATAACATATCACA
1617766 CATACACATATCACA
1 CATA-ACATATCACA
*
1617781 TAT-ACATAT
1 CATAACATAT
1617790 AATATATATT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
13 6 0.17
14 18 0.50
15 12 0.33
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.25
Consensus pattern (14 bp):
CATAACATATCACA
Done.