Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 44 of 228
Found at i:13393631 original size:24 final size:24
Alignment explanation
Indices: 13393604--13393649 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
13393594 GAATTGATGA
13393604 TGAAT-TAAAATGAAATTATGAAAT
1 TGAATGTAAAATGAAA-TATGAAAT
* *
13393628 TGAATGTGAAATGATATATGAA
1 TGAATGTAAAATGAAATATGAA
13393650 TTGGATTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (24 bp):
TGAATGTAAAATGAAATATGAAAT
Found at i:13404750 original size:18 final size:18
Alignment explanation
Indices: 13404723--13404762 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
13404713 AATACTTGAG
*
13404723 TAAATCAGAATTAAAAAT
1 TAAATCAGAAATAAAAAT
*
13404741 TAAATTAGAAATAAAAAT
1 TAAATCAGAAATAAAAAT
13404759 TAAA
1 TAAA
13404763 ATTTGATAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28
Consensus pattern (18 bp):
TAAATCAGAAATAAAAAT
Found at i:13407153 original size:22 final size:22
Alignment explanation
Indices: 13407106--13407159 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
13407096 ACAAATGGCT
* * *
13407106 TGTCTCGAGACAATTTGCTCTG
1 TGTCTCGAGACAATCTGATCTA
13407128 TGTCTCGAGACAATCT-ATCGTA
1 TGTCTCGAGACAATCTGATC-TA
13407150 TGTCTCGAGA
1 TGTCTCGAGA
13407160 TTAAGCTCTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 2 0.07
22 26 0.93
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (22 bp):
TGTCTCGAGACAATCTGATCTA
Found at i:13410599 original size:23 final size:23
Alignment explanation
Indices: 13410567--13410616 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
13410557 AATTCAAAGC
13410567 AAATAAATTATTAAAACAT-TAA
1 AAATAAATTATTAAAACATATAA
13410589 AAATAGAATTATTAAAACATATAA
1 AAATA-AATTATTAAAACATATAA
13410613 AAAT
1 AAAT
13410617 CGGTCCAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 5 0.19
23 14 0.54
24 7 0.27
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (23 bp):
AAATAAATTATTAAAACATATAA
Found at i:13413228 original size:24 final size:24
Alignment explanation
Indices: 13413181--13413228 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
13413171 AGTTTAAATG
****
13413181 TTAGTTTTTGAATATATGGGCTAA
1 TTAGTTTTTGAATATACAAACTAA
13413205 TTAGTTTTTGAATATACAAACTAA
1 TTAGTTTTTGAATATACAAACTAA
13413229 AGTATGAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (24 bp):
TTAGTTTTTGAATATACAAACTAA
Found at i:13413710 original size:71 final size:71
Alignment explanation
Indices: 13413592--13413728 Score: 188
Period size: 71 Copynumber: 1.9 Consensus size: 71
13413582 AGTACGAATC
* *
13413592 ATTCTTTATCGATGGCTAAGACGCAACATATGTTGCGGATTCGCGACAGCTTGAGTGAACAACAT
1 ATTCTTTATCGATGGCTAAGACGCAACATATATTGCAGATTCGCGACAGCTTGAGTGAACAACAT
13413657 CAAATT
66 CAAATT
* * * *
13413663 ATTCTTTATCGATGGTTGAGATC-CAACATATATTGCAGATGT-TCGACAGCTTGAGTGAGCAAC
1 ATTCTTTATCGATGGCTAAGA-CGCAACATATATTGCAGAT-TCGCGACAGCTTGAGTGAACAAC
13413726 ATC
64 ATC
13413729 GAATAAAACT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
71 56 0.97
72 2 0.03
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (71 bp):
ATTCTTTATCGATGGCTAAGACGCAACATATATTGCAGATTCGCGACAGCTTGAGTGAACAACAT
CAAATT
Found at i:13418562 original size:28 final size:27
Alignment explanation
Indices: 13418531--13418586 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
13418521 TTTTTCCTTC
*
13418531 ACATTACTTATCTTATACTTTTATATAT
1 ACATTACTTATCTTAT-CTTATATATAT
* *
13418559 ACATTATTTATTTTATCTTATATATAT
1 ACATTACTTATCTTATCTTATATATAT
13418586 A
1 A
13418587 TATATATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.55
Consensus pattern (27 bp):
ACATTACTTATCTTATCTTATATATAT
Found at i:13421351 original size:33 final size:32
Alignment explanation
Indices: 13421314--13421378 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 32
13421304 AAGAACATAA
13421314 ATAGTCCACTGGGACAATAAACACAGAATAGAG
1 ATAGTCCACTGGGACAATAAACACAG-ATAGAG
* *
13421347 ATAGTCCACTGGGACAGTAACCACAGATAGAG
1 ATAGTCCACTGGGACAATAAACACAGATAGAG
13421379 TATGTGGGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 6 0.20
33 24 0.80
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.15
Consensus pattern (32 bp):
ATAGTCCACTGGGACAATAAACACAGATAGAG
Found at i:13422000 original size:9 final size:9
Alignment explanation
Indices: 13421986--13422025 Score: 71
Period size: 9 Copynumber: 4.4 Consensus size: 9
13421976 TTTGGTTAAA
13421986 AATTAACCG
1 AATTAACCG
13421995 AATTAACCG
1 AATTAACCG
*
13422004 AATTACCCG
1 AATTAACCG
13422013 AATTAACCG
1 AATTAACCG
13422022 AATT
1 AATT
13422026 GAATCACTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:13422168 original size:18 final size:18
Alignment explanation
Indices: 13422128--13422171 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
13422118 AATTTTTATG
* **
13422128 ATTGAGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
13422146 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
13422164 CTTGGGTT
1 ATTGGGTT
13422172 TGGATTGGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.16, C:0.02, G:0.41, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:13432736 original size:49 final size:49
Alignment explanation
Indices: 13432664--13432757 Score: 152
Period size: 49 Copynumber: 1.9 Consensus size: 49
13432654 ATTCAAACAC
** *
13432664 CATTTTAAAGTTATGTACACTAAGGAGTGTCCTAGAAACAAGGTTTTTG
1 CATTTTAAAGCCATGTACACTAAGGAGTGTCCCAGAAACAAGGTTTTTG
*
13432713 CATTTTAAAGCCATGTACACTAAGGAGTGTCCCAGAAATAAGGTT
1 CATTTTAAAGCCATGTACACTAAGGAGTGTCCCAGAAACAAGGTT
13432758 CTTACATATG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (49 bp):
CATTTTAAAGCCATGTACACTAAGGAGTGTCCCAGAAACAAGGTTTTTG
Found at i:13437445 original size:31 final size:32
Alignment explanation
Indices: 13437387--13437450 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
13437377 AGAGATAGAG
* *
13437387 ATCCCATGTATATCCCTTGTTTTTTTATGCTT
1 ATCCCAGGTATATCCCATGTTTTTTTATGCTT
13437419 ATCCCAGGTATATCCCATG-TTTTTTATGCTT
1 ATCCCAGGTATATCCCATGTTTTTTTATGCTT
13437450 A
1 A
13437451 ATATAACTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.19, C:0.22, G:0.11, T:0.48
Consensus pattern (32 bp):
ATCCCAGGTATATCCCATGTTTTTTTATGCTT
Found at i:13439594 original size:28 final size:28
Alignment explanation
Indices: 13439540--13439595 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
13439530 AATTAGTATT
* * *
13439540 TTTATATTTTTAAAGATTTTTTTAAAAA
1 TTTATATATTTAAAGATTTTATGAAAAA
13439568 TTTATATATTTATAA-ATTTTATGAAAAA
1 TTTATATATTTA-AAGATTTTATGAAAAA
13439596 AATATCTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 22 0.92
29 2 0.08
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (28 bp):
TTTATATATTTAAAGATTTTATGAAAAA
Found at i:13445496 original size:6 final size:6
Alignment explanation
Indices: 13445485--13445518 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
13445475 ATTTCCACTA
13445485 TCATCT TCATCT TCATCT TCATCT TCATCT TCAT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCAT
13445519 GTCCACCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.32, G:0.00, T:0.50
Consensus pattern (6 bp):
TCATCT
Found at i:13448179 original size:46 final size:46
Alignment explanation
Indices: 13448122--13448214 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
13448112 TAATGTATGC
13448122 AAAATAATAATGTATGCAAAATAATAATAAATAATTAACTTGAAGT
1 AAAATAATAATGTATGCAAAATAATAATAAATAATTAACTTGAAGT
13448168 AAAATAATAATGTATGCAAAATAATAATAAATAATTAACTTGAAGT
1 AAAATAATAATGTATGCAAAATAATAATAAATAATTAACTTGAAGT
13448214 A
1 A
13448215 GTGTAATTTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.57, C:0.04, G:0.09, T:0.30
Consensus pattern (46 bp):
AAAATAATAATGTATGCAAAATAATAATAAATAATTAACTTGAAGT
Found at i:13448197 original size:20 final size:17
Alignment explanation
Indices: 13448104--13448149 Score: 92
Period size: 17 Copynumber: 2.7 Consensus size: 17
13448094 TTTTATAATT
13448104 CAAAATAATAATGTATG
1 CAAAATAATAATGTATG
13448121 CAAAATAATAATGTATG
1 CAAAATAATAATGTATG
13448138 CAAAATAATAAT
1 CAAAATAATAAT
13448150 AAATAATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.57, C:0.07, G:0.09, T:0.28
Consensus pattern (17 bp):
CAAAATAATAATGTATG
Found at i:13461223 original size:41 final size:41
Alignment explanation
Indices: 13461123--13461277 Score: 213
Period size: 41 Copynumber: 3.8 Consensus size: 41
13461113 TTGACTTTTT
* *
13461123 GGGCTTTAGCGGCATTTTTGGAGAAGCG-CGCTAATGCTCC
1 GGGCTTTAGCGGCATTTTTGGAAAAGCGCCGCTAATGCTCA
* *
13461163 GGGCTTTAGCGGCGTTTTTTGGAAAACCGCCGCTAATGCTCA
1 GGGCTTTAGCGGC-ATTTTTGGAAAAGCGCCGCTAATGCTCA
13461205 GGGCTTTAGCGGCATTTTTGGAAAAGCGCCGCTAATGCTCA
1 GGGCTTTAGCGGCATTTTTGGAAAAGCGCCGCTAATGCTCA
** * * *
13461246 ATGCTTTAGCGGCGTTTTTGAAAAAGCTCCGC
1 GGGCTTTAGCGGCATTTTTGGAAAAGCGCCGC
13461278 AAAAGCATTT
Statistics
Matches: 102, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
40 13 0.13
41 65 0.64
42 24 0.24
ACGTcount: A:0.20, C:0.23, G:0.29, T:0.28
Consensus pattern (41 bp):
GGGCTTTAGCGGCATTTTTGGAAAAGCGCCGCTAATGCTCA
Found at i:13461906 original size:79 final size:82
Alignment explanation
Indices: 13461790--13461940 Score: 227
Period size: 79 Copynumber: 1.9 Consensus size: 82
13461780 TCATTGTTAT
* *
13461790 GTTAGGATTTAGGGTTTAGATTAATTAGTGTGCTTTAA-TT-TATATTAAATAAGGTTTA-GGGT
1 GTTAGGATTTAGGGTTGAGATTAATTAGTATGCTTTAATTTATATATTAAATAAGGTTTAGGGGT
13461852 TAGGGGTAGGGATTCGA
66 TAGGGGTAGGGATTCGA
* * **
13461869 GTTAGGGTTTATGGTTGAGATTAATTAGTATTTTTTAATTTATATATTAAATAAGGTTTAGGGGT
1 GTTAGGATTTAGGGTTGAGATTAATTAGTATGCTTTAATTTATATATTAAATAAGGTTTAGGGGT
13461934 TAGGGGT
66 TAGGGGT
13461941 TTGTGATTAG
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
79 32 0.51
80 2 0.03
81 18 0.29
82 11 0.17
ACGTcount: A:0.28, C:0.01, G:0.28, T:0.43
Consensus pattern (82 bp):
GTTAGGATTTAGGGTTGAGATTAATTAGTATGCTTTAATTTATATATTAAATAAGGTTTAGGGGT
TAGGGGTAGGGATTCGA
Found at i:13462610 original size:15 final size:16
Alignment explanation
Indices: 13462590--13462620 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
13462580 TTAGTTAGCA
13462590 AAATAAAAT-ATTTTT
1 AAATAAAATAATTTTT
13462605 AAATAAAATAATTTTT
1 AAATAAAATAATTTTT
13462621 TTGTGGCGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATAAAATAATTTTT
Found at i:13463237 original size:15 final size:16
Alignment explanation
Indices: 13463218--13463254 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
13463208 TAGGTTTTTA
*
13463218 TTTTTATTTGGGGTTC
1 TTTTCATTTGGGGTTC
*
13463234 TTTTCTTTTGGGGTTC
1 TTTTCATTTGGGGTTC
13463250 TTTTC
1 TTTTC
13463255 TGGGTTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.03, C:0.11, G:0.22, T:0.65
Consensus pattern (16 bp):
TTTTCATTTGGGGTTC
Found at i:13463237 original size:16 final size:16
Alignment explanation
Indices: 13463224--13463255 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
13463214 TTTATTTTTA
13463224 TTTGGGGTTCTTTTCT
1 TTTGGGGTTCTTTTCT
13463240 TTTGGGGTTCTTTTCT
1 TTTGGGGTTCTTTTCT
13463256 GGGTTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.12, G:0.25, T:0.62
Consensus pattern (16 bp):
TTTGGGGTTCTTTTCT
Found at i:13467187 original size:43 final size:43
Alignment explanation
Indices: 13467082--13467263 Score: 206
Period size: 43 Copynumber: 4.3 Consensus size: 43
13467072 GATATGTTTT
* * * * * *
13467082 TAGCGGCGTTTTTGCAAGAAGCGTCGCTAAAGGT-TTGTTCTT
1 TAGCGGCGTTTGTGGAAAAAGCGTCGCTAAAGGTCATGGTCTA
*
13467124 TAGCGGCGTTTGT-GACAAAAGCATCGCTAAAGGTCATGGTCTA
1 TAGCGGCGTTTGTGGA-AAAAGCGTCGCTAAAGGTCATGGTCTA
* * * * *
13467167 TAGCAGCATTTGTGGGAAAAGCGTTGCTAAAGGTCATGGTCTT
1 TAGCGGCGTTTGTGGAAAAAGCGTCGCTAAAGGTCATGGTCTA
* * *
13467210 TAGCGGCGTTTGTGGAAAAAGTGCCGCTAAAGGTCGTGGTCTA
1 TAGCGGCGTTTGTGGAAAAAGCGTCGCTAAAGGTCATGGTCTA
13467253 TAGCGGCGTTT
1 TAGCGGCGTTT
13467264 TTTGCGGCGC
Statistics
Matches: 116, Mismatches: 21, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
41 1 0.01
42 28 0.24
43 86 0.74
44 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.31, T:0.30
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGAAAAAGCGTCGCTAAAGGTCATGGTCTA
Found at i:13475264 original size:108 final size:108
Alignment explanation
Indices: 13475070--13475388 Score: 485
Period size: 108 Copynumber: 3.0 Consensus size: 108
13475060 ATTGGTTGTG
* * * * *
13475070 GAACCATGAGAACTTTAAATAGATGACGCATGAACTTGAGTTGATGATTGGCATAACAGAGCATA
1 GAACCATGAGAACTTTAAATAGACGAAGCTTGAACTTGAGTTGATGATTGGCATGACAGAGCATG
*
13475135 GTGGTCATAATCACTATCGGAGACAATTTTTGCATTTTCCCTA
66 GTGGTCATAATCACTACCGGAGACAATTTTTGCATTTTCCCTA
* * * *
13475178 GAACCATGAGAGCTTTAAATGGACGAAGCTTGAACTTGAGTTGATGATTGGCATGACAAAGCACG
1 GAACCATGAGAACTTTAAATAGACGAAGCTTGAACTTGAGTTGATGATTGGCATGACAGAGCATG
* *
13475243 GTGGTCATACTCACTACCGGAGACAATTTTTGCATTTTCCCTG
66 GTGGTCATAATCACTACCGGAGACAATTTTTGCATTTTCCCTA
* * * *
13475286 GAACCATGAGAACTTTAAATAGACGAAACTTGAACTTGAATTGATGATTGGCATGATAGAGCTTG
1 GAACCATGAGAACTTTAAATAGACGAAGCTTGAACTTGAGTTGATGATTGGCATGACAGAGCATG
*
13475351 GTGGTCATAATCACTACTGGAGACAATTTTTGCATTTT
66 GTGGTCATAATCACTACCGGAGACAATTTTTGCATTTT
13475389 TTAAAAAGTA
Statistics
Matches: 189, Mismatches: 22, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
108 189 1.00
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.30
Consensus pattern (108 bp):
GAACCATGAGAACTTTAAATAGACGAAGCTTGAACTTGAGTTGATGATTGGCATGACAGAGCATG
GTGGTCATAATCACTACCGGAGACAATTTTTGCATTTTCCCTA
Found at i:13475542 original size:17 final size:17
Alignment explanation
Indices: 13475520--13475553 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
13475510 ATTTTGGTCA
13475520 TCAAAAAATAAAATTTG
1 TCAAAAAATAAAATTTG
13475537 TCAAAAAATAAAATTTG
1 TCAAAAAATAAAATTTG
13475554 AAACTAGGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.29
Consensus pattern (17 bp):
TCAAAAAATAAAATTTG
Found at i:13479132 original size:2 final size:2
Alignment explanation
Indices: 13479125--13479152 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
13479115 TTCTTATAAG
13479125 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
13479153 AATATACGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:13482758 original size:30 final size:30
Alignment explanation
Indices: 13482722--13482784 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
13482712 ACTTATTTTA
13482722 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
* *
13482752 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
13482782 TTG
1 TTG
13482785 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:13483106 original size:12 final size:12
Alignment explanation
Indices: 13483089--13483113 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13483079 ACCTCTAACC
13483089 TATTCTATGTAA
1 TATTCTATGTAA
13483101 TATTCTATGTAA
1 TATTCTATGTAA
13483113 T
1 T
13483114 TTTAGATTTA
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:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (12 bp):
TATTCTATGTAA
Found at i:13484890 original size:17 final size:18
Alignment explanation
Indices: 13484865--13484900 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
13484855 TACCCTCAAA
*
13484865 ATAATATAATT-TATTTT
1 ATAAAATAATTATATTTT
13484882 ATAAAATAATTATATTTT
1 ATAAAATAATTATATTTT
13484900 A
1 A
13484901 ATCATTACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATAAAATAATTATATTTT
Found at i:13485444 original size:3 final size:3
Alignment explanation
Indices: 13485431--13485483 Score: 70
Period size: 3 Copynumber: 17.3 Consensus size: 3
13485421 CAACCTAGCT
* * *
13485431 GAA GGA GAA GAA GAA GAA GAGA GAT GAA GGA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GA-A GAA GAA GAA GAA GAA GAA GAA GAA
13485477 GAA GAA G
1 GAA GAA G
13485484 GTGGTGCGGA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.58, C:0.00, G:0.40, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:13485755 original size:79 final size:81
Alignment explanation
Indices: 13485662--13485853 Score: 214
Period size: 82 Copynumber: 2.4 Consensus size: 81
13485652 TTTTAGTTAG
* * * * *
13485662 TATTATTATTGTTAGTTTTTAGGGTTTAGT-TA-TTAATAATTATTGTTACTTAGTATTATTATT
1 TATTATTATGGTTAGTTATTAGGGATTAGTAAACCTAATAATTATTGTTACTTAGTATTATT-TT
*
13485725 -AGTAAAAAATTAATAT
65 GAGTAAAAAACTAATAT
* *
13485741 TATTATTATGGTTAGTTATTA-GGATTAGTAAAACCCTAATTATTATTGTTAGTTAGTATTATTT
1 TATTATTATGGTTAGTTATTAGGGATTAGT-AAA-CCTAATAATTATTGTTACTTAGTATTATTT
*
13485805 TGAGTAAAAAACTATTAT
64 TGAGTAAAAAACTAATAT
*
13485823 TATTGTTATTGTGTTAGTTATTA-GGATTAGT
1 TATTATTA-TG-GTTAGTTATTAGGGATTAGT
13485854 GGTTAAACGT
Statistics
Matches: 96, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
78 7 0.07
79 19 0.20
80 1 0.01
81 2 0.02
82 46 0.48
83 2 0.02
84 19 0.20
ACGTcount: A:0.33, C:0.03, G:0.14, T:0.51
Consensus pattern (81 bp):
TATTATTATGGTTAGTTATTAGGGATTAGTAAACCTAATAATTATTGTTACTTAGTATTATTTTG
AGTAAAAAACTAATAT
Found at i:13485811 original size:82 final size:84
Alignment explanation
Indices: 13485695--13485853 Score: 243
Period size: 82 Copynumber: 1.9 Consensus size: 84
13485685 GTTTAGTTAT
*
13485695 TAATAATTATTGTTACTTAGTATTATTATTAGTAAAAAATTAATATTATTATTA-TG-GTTAGTT
1 TAATAATTATTGTTACTTAGTATTATTATTAGTAAAAAACTAATATTATTATTATTGTGTTAGTT
13485758 ATTAGGATTAGTAAAACCC
66 ATTAGGATTAGTAAAACCC
* * * *
13485777 TAATTATTATTGTTAGTTAGTATTATT-TTGAGTAAAAAACTATTATTATTGTTATTGTGTTAGT
1 TAATAATTATTGTTACTTAGTATTATTATT-AGTAAAAAACTAATATTATTATTATTGTGTTAGT
13485841 TATTAGGATTAGT
65 TATTAGGATTAGT
13485854 GGTTAAACGT
Statistics
Matches: 69, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
81 2 0.03
82 46 0.67
83 2 0.03
84 19 0.28
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.48
Consensus pattern (84 bp):
TAATAATTATTGTTACTTAGTATTATTATTAGTAAAAAACTAATATTATTATTATTGTGTTAGTT
ATTAGGATTAGTAAAACCC
Found at i:13491413 original size:158 final size:157
Alignment explanation
Indices: 13490965--13491874 Score: 1301
Period size: 158 Copynumber: 5.8 Consensus size: 157
13490955 ATTTAGTAAA
* *
13490965 AACCTTTATTTCGGCCCTTTGTTCGTATTTTTTCCCCG-ATTTTATTACTTT-AA-AAAAATAT-
1 AACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTCAATAAAAATATA
* *
13491026 TCTATTTTCTAATTTTCTAATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAG
66 T-TATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAG
* * **
13491091 TGTGTTTTTAAAATCAATTT-AAAAAAA
130 TGTGTTTTTTAAATAAATTTCAAAAATT
*
13491118 AACTCCTTATTTCGGCCCTTTGTTCGTA-TTTTTTCCCGGATTTTATTACTTTCAATAAAAATAT
1 AAC-CCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTCAATAAAAATAT
*
13491182 ATTATATTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAG
65 ATTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAG
*
13491247 TGTATTTTTTAAATAAATTTCAAAAATT
130 TGTGTTTTTTAAATAAATTTCAAAAATT
* *
13491275 AACCCTTATTTCGGCCATTTGTTCGTATTTTTCTTCTCGAATTTTATTACTTTCAATAAAAATAT
1 AACCCTTATTTCGGCCCTTTGTTCGTATTTTT-TTCCCGAATTTTATTACTTTCAATAAAAATAT
* *
13491340 ATTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAT
65 ATTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAG
13491405 TGTGTTTTTTAAATAAATTTCAAAAATT
130 TGTGTTTTTTAAATAAATTTCAAAAATT
*
13491433 AACCCTTATTTCGGCCATTTGTTCGTATTTTTCTTCCCGAATTTTATTACTTTCAATAAAAATAT
1 AACCCTTATTTCGGCCCTTTGTTCGTATTTTT-TTCCCGAATTTTATTACTTTCAATAAAAATAT
*
13491498 ATTATTTTATAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAG
65 ATTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAG
* *
13491563 TGT-TTTTTAAAATAAATTTTAAAAATT
130 TGTGTTTTTTAAATAAATTTCAAAAATT
* * *
13491590 AACCCTTATTTCGGCCCTTTGTTCGCATTTTTTTCTCAAATTTTATTACTTTCAATAAAAATATA
1 AACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTCAATAAAAATATA
* * *
13491655 TTATTTT-TGTATTTTATTATTTTACATTATTTCAGTACATTATATTTGAAATGTATTAATTTAG
66 TTATTTTCT-AATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAG
* *
13491719 TGTATTTTTTAAATAAATTTTGTAAAAA--
130 TGTGTTTTTTAAATAAA-TTT-CAAAAATT
* * ** * *
13491747 AACTCTTATTTCGGCCCTTTGTTCGTATTTTTTTACCGAAGCCTCATT-GTTTC-A-AAAAATAT
1 AACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAA-TTTTATTACTTTCAATAAAAATAT
* * *
13491809 ATTATTTTC-ATATTTTATCATTTTA-AGCTATTTTAGTACATTATGTTTGAAATGCATTAATTT
65 ATTATTTTCTA-ATTTTATTATTTTACA-TTATTTTAGTACATTATGTTTGAAATGTATTAATTT
13491872 AGT
128 AGT
13491875 AAAAAAACCC
Statistics
Matches: 695, Mismatches: 46, Indels: 30
0.90 0.06 0.04
Matches are distributed among these distances:
153 12 0.02
154 37 0.05
155 67 0.10
156 202 0.29
157 116 0.17
158 255 0.37
159 6 0.01
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.51
Consensus pattern (157 bp):
AACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTCAATAAAAATATA
TTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGT
GTGTTTTTTAAATAAATTTCAAAAATT
Found at i:13491634 original size:314 final size:311
Alignment explanation
Indices: 13490965--13491874 Score: 1304
Period size: 314 Copynumber: 2.9 Consensus size: 311
13490955 ATTTAGTAAA
* * **
13490965 AACCTTTATTTCGGCCCTTTGTTCGTA-TTTTTTCCCCGATTTTATTACTTT-AA-AAAAATAT-
1 AACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCTCAAATTTTATTACTTTCAATAAAAATATA
* *
13491026 TCTATTTTCTAATTTTCTAATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAG
66 T-TATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAG
* *
13491091 TGTGTTTTTAAAATCAATTTAAAAAAAAACTCCTTATTTCGGCCCTTTGTTCGTA-TTTTTTCCC
130 TGTGTTTTTTAAATAAATTT--AAAAAAAC-CCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCC
* * *
13491155 GGATTTTATTACTTTCAATAAAAATATATTATATTCTAATTTTATTATTTTACATTATTTTAGTA
192 GAATTTTATTACTTTCAATAAAAATATATTATTTTATAATTTTATTATTTTACATTATTTTAGTA
*
13491220 CATTATGTTTGAAATGTATTAATTTAGTGTATTTTTTAAATAAATTTCAAAAATT
257 CATTATGTTTGAAATGTATTAATTTAGTGTATTTTTAAAATAAATTTCAAAAATT
* *
13491275 AACCCTTATTTCGGCCATTTGTTCGTATTTTTCTTCTCGAATTTTATTACTTTCAATAAAAATAT
1 AACCCTTATTTCGGCCCTTTGTTCGTATTTTT-TTCTCAAATTTTATTACTTTCAATAAAAATAT
* *
13491340 ATTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAT
65 ATTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAG
*
13491405 TGTGTTTTTTAAATAAATTTCAAAAATTAACCCTTATTTCGGCCATTTGTTCGTATTTTTCTTCC
130 TGTGTTTTTTAAATAAATTT-AAAAA--AACCCTTATTTCGGCCCTTTGTTCGTATTTTT-TTCC
13491470 CGAATTTTATTACTTTCAATAAAAATATATTATTTTATAATTTTATTATTTTACATTATTTTAGT
191 CGAATTTTATTACTTTCAATAAAAATATATTATTTTATAATTTTATTATTTTACATTATTTTAGT
*
13491535 ACATTATGTTTGAAATGTATTAATTTAGTGT-TTTTTAAAATAAATTTTAAAAATT
256 ACATTATGTTTGAAATGTATTAATTTAGTGTATTTTTAAAATAAATTTCAAAAATT
*
13491590 AACCCTTATTTCGGCCCTTTGTTCGCATTTTTTTCTCAAATTTTATTACTTTCAATAAAAATATA
1 AACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCTCAAATTTTATTACTTTCAATAAAAATATA
* * *
13491655 TTATTTT-TGTATTTTATTATTTTACATTATTTCAGTACATTATATTTGAAATGTATTAATTTAG
66 TTATTTTCT-AATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAG
* * *
13491719 TGTATTTTTTAAATAAATTTTGTAAAAAAACTCTTATTTCGGCCCTTTGTTCGTATTTTTTTACC
130 TGTGTTTTTTAAATAAA--TT-TAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCC
** * * * *
13491784 GAAGCCTCATT-GTTTC-A-AAAAATATATTATTTTCAT-ATTTTATCATTTTA-AGCTATTTTA
192 GAA-TTTTATTACTTTCAATAAAAATATATTATTTT-ATAATTTTATTATTTTACA-TTATTTTA
*
13491844 GTACATTATGTTTGAAATGCATTAATTTAGT
254 GTACATTATGTTTGAAATGTATTAATTTAGT
13491875 AAAAAAACCC
Statistics
Matches: 547, Mismatches: 37, Indels: 31
0.89 0.06 0.05
Matches are distributed among these distances:
310 26 0.05
311 70 0.13
312 20 0.04
313 19 0.03
314 247 0.45
315 60 0.11
316 104 0.19
317 1 0.00
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.51
Consensus pattern (311 bp):
AACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCTCAAATTTTATTACTTTCAATAAAAATATA
TTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGT
GTGTTTTTTAAATAAATTTAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAAT
TTTATTACTTTCAATAAAAATATATTATTTTATAATTTTATTATTTTACATTATTTTAGTACATT
ATGTTTGAAATGTATTAATTTAGTGTATTTTTAAAATAAATTTCAAAAATT
Found at i:13491671 original size:472 final size:465
Alignment explanation
Indices: 13490965--13491872 Score: 1341
Period size: 472 Copynumber: 1.9 Consensus size: 465
13490955 ATTTAGTAAA
* *
13490965 AACCTTTATTTCGGCCCTTTGTTCGTATTTTTTCCCCGATTTTATTACTTTAAAAAAATATTCTA
1 AACCCTTATTTCGGCCATTTGTTCGTATTTTTTCCCCGATTTTATTACTTTAAAAAAATATTCTA
* *
13491030 TTTTCTAATTTTCTAATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTG
66 TTTTATAATTTTATAATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTG
* * **
13491095 TTTTTAAAATCAATTTAAAAAAAAACTCCTTATTTCGGCCCTTTGTTCGTATTTTTTCCCGGATT
131 TTTTTAAAATAAATTTAAAAAAAAACTCCTTATTTCGGCCCTTTGTTCGCATTTTTTCCCAAATT
*
13491160 TTATTACTTTCAATAAAAATATATTATATTCTAATTTTATTATTTTACATTATTTTAGTACATTA
196 TTATTACTTTCAATAAAAATATATTATATTCTAATTTTATTATTTTACATTATTTCAGTACATTA
*
13491225 TGTTTGAAATGTATTAATTTAGTGTATTTTTTAAATAAA-TTT-CAAAAATTAACCCTTATTTCG
261 TATTTGAAATGTATTAATTTAGTGTATTTTTTAAATAAATTTTGCAAAAA--AACCCTTATTTCG
** *
13491288 GCCATTTGTTCGTATTTTTCTT-CTCGAA-TTTTATTACTTTCAATAAAAATATATTATTTTC-T
324 GCCATTTGTTCGTATTTTT-TTAC-CGAAGCCTCATT-CTTTC-A-AAAAATATATTATTTTCAT
* * **
13491350 AATTTTATTATTTTACA-TTATTTTAGTACATTATGTTTGAAATTTATTAATTTATTGTGTTTTT
384 -ATTTTATCATTTTA-AGCTATTTTAGTACATTATGTTTGAAATGCATTAATTTATTGTGTTTTT
13491414 TAAATAAATTTCAAAAATT
447 TAAATAAATTTCAAAAATT
*
13491433 AACCCTTATTTCGGCCATTTGTTCGTATTTTTCTTCCCGAATTTTATTACTTTCAATAAAAATAT
1 AACCCTTATTTCGGCCATTTGTTCGTATTTTT-TCCCCG-ATTTTATTACTTT-AA-AAAAATAT
*
13491498 AT-TATTTTATAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTA
62 -TCTATTTTATAATTTTATAATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTA
**
13491562 GTGT-TTTTTAAAATAAATTTTAAAAATTAAC-CCTTATTTCGGCCCTTTGTTCGCATTTTTTTC
126 GTGTGTTTTTAAAATAAA-TTTAAAAAAAAACTCCTTATTTCGGCCCTTTGTTCGCA-TTTTTTC
* * *
13491625 TCAAATTTTATTACTTTCAATAAAAATATATTAT-TTTTGTATTTTATTATTTTACATTATTTCA
189 CCAAATTTTATTACTTTCAATAAAAATATATTATATTCT-AATTTTATTATTTTACATTATTTCA
* *
13491689 GTACATTATATTTGAAATGTATTAATTTAGTGTATTTTTTAAATAAATTTTGTAAAAAAACTCTT
253 GTACATTATATTTGAAATGTATTAATTTAGTGTATTTTTTAAATAAATTTTGCAAAAAAACCCTT
* *
13491754 ATTTCGGCCCTTTGTTCGTATTTTTTTACCGAAGCCTCATTGTTTCAAAAAATATATTATTTTCA
318 ATTTCGGCCATTTGTTCGTATTTTTTTACCGAAGCCTCATTCTTTCAAAAAATATATTATTTTCA
13491819 TATTTTATCATTTTAAGCTATTTTAGTACATTATGTTTGAAATGCATTAATTTA
383 TATTTTATCATTTTAAGCTATTTTAGTACATTATGTTTGAAATGCATTAATTTA
13491873 GTAAAAAAAC
Statistics
Matches: 398, Mismatches: 28, Indels: 27
0.88 0.06 0.06
Matches are distributed among these distances:
468 31 0.08
469 69 0.17
470 15 0.04
471 50 0.13
472 224 0.56
473 4 0.01
474 5 0.01
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.51
Consensus pattern (465 bp):
AACCCTTATTTCGGCCATTTGTTCGTATTTTTTCCCCGATTTTATTACTTTAAAAAAATATTCTA
TTTTATAATTTTATAATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTG
TTTTTAAAATAAATTTAAAAAAAAACTCCTTATTTCGGCCCTTTGTTCGCATTTTTTCCCAAATT
TTATTACTTTCAATAAAAATATATTATATTCTAATTTTATTATTTTACATTATTTCAGTACATTA
TATTTGAAATGTATTAATTTAGTGTATTTTTTAAATAAATTTTGCAAAAAAACCCTTATTTCGGC
CATTTGTTCGTATTTTTTTACCGAAGCCTCATTCTTTCAAAAAATATATTATTTTCATATTTTAT
CATTTTAAGCTATTTTAGTACATTATGTTTGAAATGCATTAATTTATTGTGTTTTTTAAATAAAT
TTCAAAAATT
Found at i:13492173 original size:26 final size:27
Alignment explanation
Indices: 13492118--13492173 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
13492108 TGGGTTTTTT
* * * *
13492118 TATGCTAAATAAATTTCATAAAATATA
1 TATGCTAAATAAATATAATAAAACACA
13492145 TATGCTAAATAAA-ATAATAAAACACA
1 TATGCTAAATAAATATAATAAAACACA
13492171 TAT
1 TAT
13492174 AATGCACATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 12 0.48
27 13 0.52
ACGTcount: A:0.55, C:0.09, G:0.04, T:0.32
Consensus pattern (27 bp):
TATGCTAAATAAATATAATAAAACACA
Found at i:13492229 original size:19 final size:19
Alignment explanation
Indices: 13492201--13492238 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
13492191 TTTTTTACAT
*
13492201 AAATATTACAAAAAAATTA
1 AAATAATACAAAAAAATTA
13492220 AAATAATACAAAAAAATTA
1 AAATAATACAAAAAAATTA
13492239 TCTTTACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (19 bp):
AAATAATACAAAAAAATTA
Found at i:13492265 original size:10 final size:10
Alignment explanation
Indices: 13492252--13492362 Score: 60
Period size: 10 Copynumber: 10.2 Consensus size: 10
13492242 TTACTTATTT
13492252 TTTTTCTTTC
1 TTTTTCTTTC
*
13492262 TTTTTCCTTC
1 TTTTTCTTTC
* *
13492272 TCTTCCTCTTC
1 TTTTTCT-TTC
13492283 TTCTTCTCCTTTC
1 TT-TT-T-CTTTC
*
13492296 CTTTTCTTTC
1 TTTTTCTTTC
*
13492306 TTTTCCTTTC
1 TTTTTCTTTC
*
13492316 TTCTCCTTTCCTTCC
1 -T-T--TTT-CTTTC
*
13492331 CTTTTCTTTC
1 TTTTTCTTTC
13492341 TTTTTCTTTC
1 TTTTTCTTTC
* *
13492351 TTCTCCTTTC
1 TTTTTCTTTC
13492361 TT
1 TT
13492363 CTCTCTAGTC
Statistics
Matches: 76, Mismatches: 16, Indels: 18
0.69 0.15 0.16
Matches are distributed among these distances:
10 49 0.64
11 9 0.12
12 5 0.07
13 5 0.07
14 4 0.05
15 4 0.05
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:13492328 original size:35 final size:35
Alignment explanation
Indices: 13492257--13492360 Score: 131
Period size: 35 Copynumber: 3.0 Consensus size: 35
13492247 TATTTTTTTT
* * * *
13492257 CTTTCTTTTTCCTTCTCTTCCTCTTCTTCT--TCTC
1 CTTTCCTTTTCTTTCTTTTCCT-TTCTTCTCCTTTC
13492291 CTTTCCTTTTCTTTCTTTTCCTTTCTTCTCCTTTC
1 CTTTCCTTTTCTTTCTTTTCCTTTCTTCTCCTTTC
* *
13492326 CTTCCCTTTTCTTTCTTTTTCTTTCTTCTCCTTTC
1 CTTTCCTTTTCTTTCTTTTCCTTTCTTCTCCTTTC
13492361 TTCTCTCTAG
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
33 7 0.11
34 19 0.31
35 36 0.58
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (35 bp):
CTTTCCTTTTCTTTCTTTTCCTTTCTTCTCCTTTC
Found at i:13492363 original size:10 final size:10
Alignment explanation
Indices: 13492283--13492365 Score: 65
Period size: 10 Copynumber: 8.8 Consensus size: 10
13492273 CTTCCTCTTC
13492283 TTCTTCTCCT
1 TTCTTCTCCT
*
13492293 TTCCTT-TTCT
1 TT-CTTCTCCT
*
13492303 TTCTTTTCCT
1 TTCTTCTCCT
13492313 TTCTTCTCCT
1 TTCTTCTCCT
13492323 TTCCTTC-CCTT
1 TT-CTTCTCC-T
13492334 TTCTT-T-C-
1 TTCTTCTCCT
13492341 TT-TT-T-CT
1 TTCTTCTCCT
13492348 TTCTTCTCCT
1 TTCTTCTCCT
13492358 TTCTTCTC
1 TTCTTCTC
13492366 TCTAGTCGAA
Statistics
Matches: 61, Mismatches: 3, Indels: 18
0.74 0.04 0.22
Matches are distributed among these distances:
6 4 0.07
7 4 0.07
8 2 0.03
9 5 0.08
10 36 0.59
11 10 0.16
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (10 bp):
TTCTTCTCCT
Found at i:13492687 original size:26 final size:26
Alignment explanation
Indices: 13492639--13492688 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
13492629 GTATTTTATT
*
13492639 TTTATTATTTTTAATTTTCTTTAAGG
1 TTTATTATTTTTAAATTTCTTTAAGG
13492665 TTTATTATTTTTATAATTT-TTTAA
1 TTTATTATTTTTA-AATTTCTTTAA
13492689 ATGATGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (26 bp):
TTTATTATTTTTAAATTTCTTTAAGG
Found at i:13496562 original size:30 final size:31
Alignment explanation
Indices: 13496502--13496559 Score: 102
Period size: 30 Copynumber: 1.9 Consensus size: 31
13496492 GGGTTGGGAG
13496502 GGGAAGGGAGTAAAAGTTTTGGAGGGAAAGT
1 GGGAAGGGAGTAAAAGTTTTGGAGGGAAAGT
13496533 GGGAA-GGAGTAAAAGTTTT-GAGGGAAA
1 GGGAAGGGAGTAAAAGTTTTGGAGGGAAA
13496560 AGTAAAAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 8 0.30
30 14 0.52
31 5 0.19
ACGTcount: A:0.38, C:0.00, G:0.43, T:0.19
Consensus pattern (31 bp):
GGGAAGGGAGTAAAAGTTTTGGAGGGAAAGT
Found at i:13496624 original size:9 final size:9
Alignment explanation
Indices: 13496610--13496673 Score: 101
Period size: 9 Copynumber: 7.1 Consensus size: 9
13496600 TATAGTTTGA
13496610 TATTCGAAT
1 TATTCGAAT
13496619 TATTCGAAT
1 TATTCGAAT
*
13496628 TATTCGAGT
1 TATTCGAAT
*
13496637 TATTTGAAT
1 TATTCGAAT
13496646 TATTCGAAT
1 TATTCGAAT
*
13496655 TATTCGAGT
1 TATTCGAAT
13496664 TATTCGAAT
1 TATTCGAAT
13496673 T
1 T
13496674 CGAAAACTCA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 49 1.00
ACGTcount: A:0.30, C:0.09, G:0.14, T:0.47
Consensus pattern (9 bp):
TATTCGAAT
Found at i:13496645 original size:27 final size:27
Alignment explanation
Indices: 13496610--13496673 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
13496600 TATAGTTTGA
13496610 TATTCGAATTATTCGAATTATTCGAGT
1 TATTCGAATTATTCGAATTATTCGAGT
*
13496637 TATTTGAATTATTCGAATTATTCGAGT
1 TATTCGAATTATTCGAATTATTCGAGT
13496664 TATTCGAATT
1 TATTCGAATT
13496674 CGAAAACTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.30, C:0.09, G:0.14, T:0.47
Consensus pattern (27 bp):
TATTCGAATTATTCGAATTATTCGAGT
Found at i:13497694 original size:23 final size:24
Alignment explanation
Indices: 13497668--13497718 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
13497658 AAAAATCAAA
* *
13497668 ATATGTAATATACA-AAATAATAT
1 ATATGTAATATAAATAAATAATAC
*
13497691 ATAT-TAATCTAAATAAATAATAC
1 ATATGTAATATAAATAAATAATAC
13497714 ATATG
1 ATATG
13497719 GAATGAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.35
Consensus pattern (24 bp):
ATATGTAATATAAATAAATAATAC
Found at i:13497872 original size:185 final size:185
Alignment explanation
Indices: 13497601--13497938 Score: 608
Period size: 185 Copynumber: 1.8 Consensus size: 185
13497591 ACAAATAATC
13497601 AATAAATACTATATGAAATGATAATATCAAAATGAATTTCAAAGTAAATATTGTATAAAAAATCA
1 AATAAATACTATATGAAATGATAATATCAAAATGAATTTCAAAGTAAATATTGTATAAAAAATCA
13497666 AAATATGTAATATACAAAATAATATATATTAATCTAAATAAATAATACATATGGAATGAAAAATT
66 AAATATGTAATATACAAAATAATATATATTAATCTAAATAAATAATACATATGGAATGAAAAATT
**
13497731 TGAAATAAATAA-A-TATATATACGAGTTTGAAATAGATAAAAAATGAAGATAAA
131 CCAAATAAATAATATTATATATACGAGTTTGAAATAGATAAAAAATGAAGATAAA
*
13497784 AATAAATACTATGTGAAATGATAATATCAAAATGAATTTTCAAAGTAAATATTGTATAAAAAAAT
1 AATAAATACTATATGAAATGATAATATCAAAATGAA-TTTCAAAGTAAATATTGTAT-AAAAAAT
13497849 CAAAATATGTAATATACAAAATAATATATATTAATCTAAATAAATAATACATATGGAATGAAAAA
64 CAAAATATGTAATATACAAAATAATATATATTAATCTAAATAAATAATACATATGGAATGAAAAA
*
13497914 TTCCAAATAGATAATATTATATATA
129 TTCCAAATAAATAATATTATATATA
13497939 TAAAGATATA
Statistics
Matches: 147, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
183 35 0.24
184 20 0.14
185 83 0.56
186 1 0.01
187 8 0.05
ACGTcount: A:0.56, C:0.05, G:0.08, T:0.31
Consensus pattern (185 bp):
AATAAATACTATATGAAATGATAATATCAAAATGAATTTCAAAGTAAATATTGTATAAAAAATCA
AAATATGTAATATACAAAATAATATATATTAATCTAAATAAATAATACATATGGAATGAAAAATT
CCAAATAAATAATATTATATATACGAGTTTGAAATAGATAAAAAATGAAGATAAA
Found at i:13497879 original size:23 final size:24
Alignment explanation
Indices: 13497853--13497903 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
13497843 AAAAATCAAA
* *
13497853 ATATGTAATATACA-AAATAATAT
1 ATATGTAATATAAATAAATAATAC
*
13497876 ATAT-TAATCTAAATAAATAATAC
1 ATATGTAATATAAATAAATAATAC
13497899 ATATG
1 ATATG
13497904 GAATGAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.35
Consensus pattern (24 bp):
ATATGTAATATAAATAAATAATAC
Found at i:13498184 original size:20 final size:18
Alignment explanation
Indices: 13498161--13498208 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 18
13498151 GAATTTGAAT
13498161 AATAATACATGAAAACTTAA
1 AATAATACA--AAAACTTAA
13498181 AATATATGAACAAAAACTTAA
1 AATA-AT--ACAAAAACTTAA
13498202 AATAATA
1 AATAATA
13498209 ATGTACGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
18 1 0.04
20 6 0.24
21 15 0.60
23 3 0.12
ACGTcount: A:0.62, C:0.08, G:0.04, T:0.25
Consensus pattern (18 bp):
AATAATACAAAAACTTAA
Found at i:13500204 original size:51 final size:51
Alignment explanation
Indices: 13500123--13500575 Score: 699
Period size: 51 Copynumber: 8.9 Consensus size: 51
13500113 CATAATTTGT
** * *
13500123 AGCTTTAATCTGTTCTGCTGTAACGTCAGGGAAATAAGATTCGCTGCCTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* * *
13500174 AGCTTTAATCTATTCCACTACAACGCCAGGGAAATAAGATTCGTTGCCTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
** * *
13500225 AGCTTTAATCTACTCCACTGCAACGCCAGAGAAATAAGATTCGCTGCCTTT
1 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* *
13500276 AGCTTTAATCTGTTCCACTGCAACGCCAGAGAAATAAAATTCGCTGCCTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* *
13500327 AGCTTTAATCTGCTCCACTGCAACGCCAGGGAAATAAGATTCGCTACCTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* * *
13500378 AACTTTAATCTATTCCACTACAACGCCAGGGAAATAAGATTCGCTGCCTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
*
13500429 AGCTTTAATCTGTTCCACTGCAACGCTAGGGAAATAAGATTCGCTGCCTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* * *
13500480 AGTTTTAATCTGTTCCACTGCAACTCTAGGGAAATAAGATTCGCTGCCTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
*
13500531 AGCTTTAATATGTTCCACTGCAACGCCAGGGAAATAAGATTCGCT
1 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCT
13500576 ATAATGACTT
Statistics
Matches: 367, Mismatches: 35, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 367 1.00
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (51 bp):
AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
Found at i:13500318 original size:153 final size:153
Alignment explanation
Indices: 13499971--13500575 Score: 716
Period size: 153 Copynumber: 4.0 Consensus size: 153
13499961 ATAATTTGTA
* *
13499971 GCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGCGAGGGAAATAAGATTCGCTG---T---CTT
1 GCTGCCTTTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTT
* * ** * * * * **
13500030 TAGTCTGCTCCACTGCAACTTCAGGGAGATAAG----GCTG--GT-GGCTTCAATCTGCTCCACT
66 TAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTATTCCACT
** *
13500088 GCAACTTCA-GGAAGATAAGATCC
131 GCAACGCCAGGGAA-ATAAGATTC
*** ** * *
13500111 GCCATAATTTGTAGCTTTAATCTGTTCTGCTGTAACGTCAGGGAAATAAGATTCGCTGCCTTCAG
1 G-C-TGCCTT-TAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAG
* * * *
13500176 CTTTAATCTATTCCACTACAACGCCAGGGAAATAAGATTCGTTGCCTTCAGCTTTAATCTACTCC
63 CTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTATTCC
*
13500241 ACTGCAACGCCAGAGAAATAAGATTC
128 ACTGCAACGCCAGGGAAATAAGATTC
* *
13500267 GCTGCCTTTAGCTTTAATCTGTTCCACTGCAACGCCAGAGAAATAAAATTCGCTGCCTTCAGCTT
1 GCTGCCTTTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTT
* * *
13500332 TAATCTGCTCCACTGCAACGCCAGGGAAATAAGATTCGCTACCTTCAACTTTAATCTATTCCACT
66 TAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTATTCCACT
*
13500397 ACAACGCCAGGGAAATAAGATTC
131 GCAACGCCAGGGAAATAAGATTC
* * *
13500420 GCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGCTAGGGAAATAAGATTCGCTGCCTTCAGTTT
1 GCTGCCTTTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTT
* * * *
13500485 TAATCTGTTCCACTGCAACTCTAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATATGTTCCACT
66 TAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTATTCCACT
13500550 GCAACGCCAGGGAAATAAGATTC
131 GCAACGCCAGGGAAATAAGATTC
13500573 GCT
1 GCT
13500576 ATAATGACTT
Statistics
Matches: 392, Mismatches: 56, Indels: 21
0.84 0.12 0.04
Matches are distributed among these distances:
140 1 0.00
141 1 0.00
142 3 0.01
143 41 0.10
146 1 0.00
149 29 0.07
153 276 0.70
154 3 0.01
155 2 0.01
156 32 0.08
157 3 0.01
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (153 bp):
GCTGCCTTTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTT
TAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTATTCCACT
GCAACGCCAGGGAAATAAGATTC
Found at i:13502501 original size:19 final size:20
Alignment explanation
Indices: 13502477--13502523 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
13502467 TGGTAGACTT
* *
13502477 TAATGCATATG-ATGTAATG
1 TAATGCAAATGCATGAAATG
13502496 TAATGCAAATGCATGAAATG
1 TAATGCAAATGCATGAAATG
13502516 -AATGCAAA
1 TAATGCAAA
13502524 AAGGTGTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.28
Consensus pattern (20 bp):
TAATGCAAATGCATGAAATG
Found at i:13504825 original size:20 final size:21
Alignment explanation
Indices: 13504776--13504825 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
13504766 TAAAAATATA
* *
13504776 TAAAATAATGCATGATGAATT
1 TAAAATAATGCATGATAAACT
13504797 TGAATAATAATGCATGA-AAACT
1 T-AA-AATAATGCATGATAAACT
13504819 TAAAATA
1 TAAAATA
13504826 TATGAACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
20 4 0.16
21 3 0.12
22 6 0.24
23 12 0.48
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.30
Consensus pattern (21 bp):
TAAAATAATGCATGATAAACT
Found at i:13505143 original size:22 final size:22
Alignment explanation
Indices: 13505118--13505179 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
13505108 CTCAATTTCA
13505118 TTCAAAAATTCTCTTAAATTCC
1 TTCAAAAATTCTCTTAAATTCC
* *
13505140 TTCAAAAATTCTCTCAATTTCC
1 TTCAAAAATTCTCTTAAATTCC
*
13505162 TTCCAAAATTCTCTTAAA
1 TTCAAAAATTCTCTTAAA
13505180 CTCTCAAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.40
Consensus pattern (22 bp):
TTCAAAAATTCTCTTAAATTCC
Found at i:13505210 original size:21 final size:21
Alignment explanation
Indices: 13505182--13505230 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 21
13505172 CTCTTAAACT
*
13505182 CTCAAA-TTCCTTCCAAAATC
1 CTCAAATTTCCTTCAAAAATC
13505202 CTCACAATTTCCTTCAAAAAATC
1 CTCA-AATTTCCTTC-AAAAATC
13505225 TCTCAA
1 -CTCAA
13505231 CTCCATATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 4 0.17
21 2 0.08
22 7 0.29
23 7 0.29
24 4 0.17
ACGTcount: A:0.37, C:0.33, G:0.00, T:0.31
Consensus pattern (21 bp):
CTCAAATTTCCTTCAAAAATC
Found at i:13505211 original size:52 final size:52
Alignment explanation
Indices: 13505128--13505227 Score: 146
Period size: 52 Copynumber: 1.9 Consensus size: 52
13505118 TTCAAAAATT
* * * * *
13505128 CTCTTAAATTCCTTCAAAAATTCTCTCAATTTCCTTCCAAAATTCTCTTAAA
1 CTCTCAAATTCCTTCAAAAATCCTCACAATTTCCTTCAAAAAATCTCTTAAA
*
13505180 CTCTCAAATTCCTTCCAAAATCCTCACAATTTCCTTCAAAAAATCTCT
1 CTCTCAAATTCCTTCAAAAATCCTCACAATTTCCTTCAAAAAATCTCT
13505228 CAACTCCATA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 42 1.00
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.37
Consensus pattern (52 bp):
CTCTCAAATTCCTTCAAAAATCCTCACAATTTCCTTCAAAAAATCTCTTAAA
Found at i:13505317 original size:28 final size:29
Alignment explanation
Indices: 13505265--13505320 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
13505255 TTCAATTTCA
13505265 TTTTTTAAGAAAATTTTAAATATTTTTAT
1 TTTTTTAAGAAAATTTTAAATATTTTTAT
13505294 TTTTTTAA-AATAATTTTAAA-ATTTTTA
1 TTTTTTAAGAA-AATTTTAAATATTTTTA
13505321 ATATTTTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 9 0.35
29 17 0.65
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (29 bp):
TTTTTTAAGAAAATTTTAAATATTTTTAT
Found at i:13505327 original size:29 final size:29
Alignment explanation
Indices: 13505266--13505327 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
13505256 TCAATTTCAT
*
13505266 TTTTTAAGAAAATTTTAAATATTTTTATT
1 TTTTTAAGAAAATTTTAAATATTTTTATA
13505295 TTTTTAA-AATAATTTTAAA-ATTTTTAATA
1 TTTTTAAGAA-AATTTTAAATATTTTT-ATA
13505324 TTTT
1 TTTT
13505328 CAACAATGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 8 0.27
29 22 0.73
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (29 bp):
TTTTTAAGAAAATTTTAAATATTTTTATA
Found at i:13505447 original size:14 final size:15
Alignment explanation
Indices: 13505418--13505451 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
13505408 AAATTTTAAA
13505418 TTTTATTTAAGATAT
1 TTTTATTTAAGATAT
*
13505433 TTTTATTTATG-TAT
1 TTTTATTTAAGATAT
13505447 TTTTA
1 TTTTA
13505452 GATAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTTAAGATAT
Found at i:13509977 original size:125 final size:125
Alignment explanation
Indices: 13509755--13510036 Score: 394
Period size: 125 Copynumber: 2.3 Consensus size: 125
13509745 CACGAGGGCA
* * * *
13509755 CGATTTGACACTATTTACTCAGAAACGTCAACAAATAATTATTTCCTACATGACCAACTGTAGCG
1 CGATTTTATACTATTTGCTCAGAAACGTCAACAAAAAATTATTTCCTACATGACCAACTGTAGCG
* * * **
13509820 AAATTGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAT-ATAGCATCCTGGTATCAG
66 AAATGGCGTCCACGAGGGCACAATTTCACAATTTCTTCTC-TGATAGCATCCTGGTAGAAG
13509880 CGATTTTATACTATTTGCTCAGAAAACGTCAA-AAAAAATTATTT-CTGACATGACCAACTGT-G
1 CGATTTTATACTATTTGCTCAG-AAACGTCAACAAAAAATTATTTCCT-ACATGACCAACTGTAG
*
13509942 CCGAAATGGCGTCCACGAGGGTACAATTTCACAATTTCTTCTCTGATAGCATCCTGGTAGAAG
64 -CGAAATGGCGTCCACGAGGGCACAATTTCACAATTTCTTCTCTGATAGCATCCTGGTAGAAG
13510005 CGATTTTATACTATTTGAC-CAGAAACGTCAAC
1 CGATTTTATACTATTTG-CTCAGAAACGTCAAC
13510037 TCGAAATAAT
Statistics
Matches: 141, Mismatches: 10, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
124 13 0.09
125 118 0.84
126 10 0.07
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (125 bp):
CGATTTTATACTATTTGCTCAGAAACGTCAACAAAAAATTATTTCCTACATGACCAACTGTAGCG
AAATGGCGTCCACGAGGGCACAATTTCACAATTTCTTCTCTGATAGCATCCTGGTAGAAG
Found at i:13510299 original size:29 final size:26
Alignment explanation
Indices: 13510249--13510307 Score: 64
Period size: 29 Copynumber: 2.2 Consensus size: 26
13510239 GATTTCGGGG
*
13510249 AAAATGGCCCATTCCGGTAAATAATTAA
1 AAAATGGCCCATTCCGG-AAA-ATTTAA
* *
13510277 AAAATCGGCCTATTTCGGAAAATTTAA
1 AAAAT-GGCCCATTCCGGAAAATTTAA
13510304 AAAA
1 AAAA
13510308 AGGGCTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 9 0.33
28 8 0.30
29 10 0.37
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (26 bp):
AAAATGGCCCATTCCGGAAAATTTAA
Found at i:13521693 original size:2 final size:2
Alignment explanation
Indices: 13521686--13521714 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
13521676 CAAGCACATT
13521686 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13521715 TTTCATGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13522101 original size:12 final size:14
Alignment explanation
Indices: 13522076--13522104 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
13522066 TATAAATATT
13522076 ATATATAAAGAAAA
1 ATATATAAAGAAAA
13522090 ATATATAAA-AAAA
1 ATATATAAAGAAAA
13522103 AT
1 AT
13522105 CAATTGATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.24
Consensus pattern (14 bp):
ATATATAAAGAAAA
Found at i:13530375 original size:18 final size:18
Alignment explanation
Indices: 13530352--13530386 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
13530342 CCCAGCCGTC
13530352 TTCTCATTTCTTTCTCAT
1 TTCTCATTTCTTTCTCAT
13530370 TTCTCATTTCTTTCTCA
1 TTCTCATTTCTTTCTCA
13530387 CGTCTGAAAC
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:0.11, C:0.29, G:0.00, T:0.60
Consensus pattern (18 bp):
TTCTCATTTCTTTCTCAT
Found at i:13532939 original size:61 final size:61
Alignment explanation
Indices: 13532866--13533059 Score: 182
Period size: 61 Copynumber: 3.2 Consensus size: 61
13532856 TTATACTATT
*
13532866 ATATATTATAATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATC
1 ATATATTATAATTTAAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATC
* * * * * * * * *
13532927 ATATATTTTAATTAAAATATATTTA-ATAATTATTATGTTAA-ATT-A-TATTTTA-TAGTATC
1 ATATATTATAATTTAAGTAAATTCATATAA-GAATAT-TTAATATTAAGAATTTTATTA-AATC
* * * * *
13532986 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATAATTTAAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATC
*
13533047 ATATATTTTAATT
1 ATATATTATAATT
13533060 AAAATATATT
Statistics
Matches: 99, Mismatches: 26, Indels: 16
0.70 0.18 0.11
Matches are distributed among these distances:
58 4 0.04
59 34 0.34
60 10 0.10
61 45 0.45
62 6 0.06
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (61 bp):
ATATATTATAATTTAAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATC
Found at i:13532992 original size:120 final size:120
Alignment explanation
Indices: 13532825--13533090 Score: 435
Period size: 120 Copynumber: 2.2 Consensus size: 120
13532815 AAAAATTGAT
* * *
13532825 TATATTTAATAATAATTATG-TATATTATATTTTATACTATTATATATTATAATTTTAGTAAATT
1 TATATTTAATAATAATTATGTTAAATTATATTTTATACTATCATATATTATAATTTGAGTAAATT
*
13532889 CATATAAGAATATTTAATATTAAGAATTTTATTAAATCATATATTTTAATTAAAA
66 CATATAAGAATATTGAATATTAAGAATTTTATTAAATCATATATTTTAATTAAAA
* * *
13532944 TATATTTAATAATTATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATT
1 TATATTTAATAATAATTATGTTAAATTATATTTTATACTATCATATATTATAATTTGAGTAAATT
* *
13533009 CATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAA
66 CATATAAGAATATTGAATATTAAGAATTTTATTAAATCATATATTTTAATTAAAA
13533064 TATATTTAATAATAATTATGTTTAAAT
1 TATATTTAATAATAATTATG-TTAAAT
13533091 ATGATTAAAT
Statistics
Matches: 135, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
119 19 0.14
120 110 0.81
121 6 0.04
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
TATATTTAATAATAATTATGTTAAATTATATTTTATACTATCATATATTATAATTTGAGTAAATT
CATATAAGAATATTGAATATTAAGAATTTTATTAAATCATATATTTTAATTAAAA
Found at i:13533050 original size:59 final size:57
Alignment explanation
Indices: 13532867--13533062 Score: 127
Period size: 57 Copynumber: 3.3 Consensus size: 57
13532857 TATACTATTA
* *
13532867 TATATTATAATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAAT
1 TATATTAT-ATTTAAGTAAATTCATATAAGAATA-TTATTATTAAGAATTTTATTAAAT
* * * * * * *
13532926 CATA-TAT-TTTAATTAAAATAT-ATTTAATAATTATTATGT-TAAATTATATTTTA-TAGTAT
1 TATATTATATTTAAGT-AAAT-TCATATAAGAA-TATTAT-TATTAA-GA-ATTTTATTA-AAT
*
13532985 CATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAAT
1 --TATATTAT-ATTTAAGTAAATTCATATAAGAATATT-ATTATTAAGAATTTTATTAAAT
*
13533046 TATA-TAT-TTTAATTAAA
1 TATATTATATTTAAGTAAA
13533063 ATATATTTAA
Statistics
Matches: 102, Mismatches: 19, Indels: 35
0.65 0.12 0.22
Matches are distributed among these distances:
56 13 0.13
57 17 0.17
58 13 0.13
59 15 0.15
61 11 0.11
62 12 0.12
63 16 0.16
64 5 0.05
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (57 bp):
TATATTATATTTAAGTAAATTCATATAAGAATATTATTATTAAGAATTTTATTAAAT
Found at i:13533062 original size:18 final size:17
Alignment explanation
Indices: 13533034--13533068 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
13533024 ATTATTAAGA
*
13533034 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
13533051 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
13533069 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:13533297 original size:44 final size:45
Alignment explanation
Indices: 13533232--13533322 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
13533222 ACCTCTATTC
* * *
13533232 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
13533276 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
13533321 CA
1 CA
13533323 CCTCTAATCC
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:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:13533324 original size:16 final size:16
Alignment explanation
Indices: 13533303--13533387 Score: 143
Period size: 16 Copynumber: 5.2 Consensus size: 16
13533293 GATTAGCTAT
13533303 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
13533319 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
13533335 TACACCTTTAATCCCAA
1 TACACCTCTAAT-CCAA
*
13533352 TACACCTCTAATCTAA
1 TACACCTCTAATCCAA
13533368 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
13533384 TACA
1 TACA
13533388 GCGAACCAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
16 49 0.77
17 15 0.23
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.27
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:13533357 original size:33 final size:32
Alignment explanation
Indices: 13533303--13533387 Score: 143
Period size: 33 Copynumber: 2.6 Consensus size: 32
13533293 GATTAGCTAT
13533303 TACACCTCTAATCCAATACACCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
* *
13533335 TACACCTTTAATCCCAATACACCTCTAATCTAA
1 TACACCTCTAAT-CCAATACACCTCTAATCCAA
13533368 TACACCTCTAATCCAATACA
1 TACACCTCTAATCCAATACA
13533388 GCGAACCAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
32 19 0.39
33 30 0.61
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.27
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:13533475 original size:31 final size:31
Alignment explanation
Indices: 13533440--13533503 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
13533430 TATAATTAAT
* *
13533440 TATATTAACAATTTTATTTA-AAATCAATCAC
1 TATATCAACAATTTTA-ATAGAAATCAATCAC
* *
13533471 TATATCAATAATTTTAATAGGAATCAATCAC
1 TATATCAACAATTTTAATAGAAATCAATCAC
13533502 TA
1 TA
13533504 AAAATTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 2 0.07
31 26 0.93
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.39
Consensus pattern (31 bp):
TATATCAACAATTTTAATAGAAATCAATCAC
Found at i:13534936 original size:125 final size:126
Alignment explanation
Indices: 13534721--13535254 Score: 720
Period size: 125 Copynumber: 4.3 Consensus size: 126
13534711 ATTTTTGCAG
* * * * *
13534721 TCGCGCCCACGT-GTACGCGCTTTTGTTATAGTAGGTCCTGGAA-AAATAATGTCAATTTGACGT
1 TCGCGCCCACGTAG-ACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGAGTTGACGT
* *
13534784 TTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTATATGCGAAGAATTTGTGAAA
65 TTCTGAGCAAATAGTATAAAAAACGCTTCAACCAGGATGCTATATGAGAAGAATTTGTGAAA
* * ** *
13534846 TCGCGCCCTCCTAGACGCGCTTTTGCTACAGTTTGTCCTGGAAGAAATAATTTCGAGTTAACGTT
1 TCGCGCCCACGTAGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGAGTTGACGTT
* * * * *
13534911 TCTGAGCAAATAGTAT-AAAATCGCTTCTACCAAGATACTTTATGAGAAGAATTTGTGAAA
66 TCTGAGCAAATAGTATAAAAAACGCTTCAACCAGGATGCTATATGAGAAGAATTTGTGAAA
* * * *
13534971 TCGCACCCACGTAGACGCGCTTTTGCTACAGTAGGTCCT-GAAAAAATTATTTCGAGCTGACGTT
1 TCGCGCCCACGTAGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGAGTTGACGTT
* * *
13535035 TCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTATTTGAGAAGAATTTCTGAAA
66 TCTGAGCAAATAGTATAAAAAACGCTTCAACCAGGATGCTATATGAGAAGAATTTGTGAAA
* * * *
13535096 TCGCGCCCTCGTGGACGCGCTTTTGCTACAGTTGGTCTTGGAAGAAATAATTTCGAGTTGACGTT
1 TCGCGCCCACGTAGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGAGTTGACGTT
* *
13535161 TCTGAGCAAATAGTAT-AAAATCGCTT-ATACCAGGATGCTTTATGAGAAGAATTTGTGAAA
66 TCTGAGCAAATAGTATAAAAAACGCTTCA-ACCAGGATGCTATATGAGAAGAATTTGTGAAA
* *
13535221 TCGCGCCCACGTGGATGCGCTTTTGCTACAGTAG
1 TCGCGCCCACGTAGACGCGCTTTTGCTACAGTAG
13535255 CATGTTTGTG
Statistics
Matches: 354, Mismatches: 50, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
124 38 0.11
125 244 0.69
126 72 0.20
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (126 bp):
TCGCGCCCACGTAGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGAGTTGACGTT
TCTGAGCAAATAGTATAAAAAACGCTTCAACCAGGATGCTATATGAGAAGAATTTGTGAAA
Found at i:13535167 original size:250 final size:249
Alignment explanation
Indices: 13534721--13535254 Score: 852
Period size: 250 Copynumber: 2.1 Consensus size: 249
13534711 ATTTTTGCAG
* * * **
13534721 TCGCGCCCACGTGTACGCGCTTTTGTTATAGTAGGTCCTGGAAAAATAATGTCAATTTGACGTTT
1 TCGCGCCCACGTG-ACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATGTCAAGCTGACGTTT
* *
13534786 CTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTATATGCGAAGAATTTGTGAAATCGCG
65 CTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTATATGAGAAGAATTTCTGAAATCGCG
*
13534851 CCCTCCTAGACGCGCTTTTGCTACAGTTTGTCCTGGAAGAAATAATTTCGAGTTAACGTTTCTGA
130 CCCTCCTAGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAATTTCGAGTTAACGTTTCTGA
*
13534916 GCAAATAGTATAAAATCGCTTCTACCAAGATACTTTATGAGAAGAATTTGTGAAA
195 GCAAATAGTATAAAATCGCTTATACCAAGATACTTTATGAGAAGAATTTGTGAAA
* * * *
13534971 TCGCACCCACGTAGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATTATTTCGAGCTGACGTTT
1 TCGCGCCCACGT-GACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATGTCAAGCTGACGTTT
*
13535036 CTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTATTTGAGAAGAATTTCTGAAATCGCG
65 CTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTATATGAGAAGAATTTCTGAAATCGCG
* * * *
13535101 CCCTCGTGGACGCGCTTTTGCTACAGTTGGTCTTGGAAGAAATAATTTCGAGTTGACGTTTCTGA
130 CCCTCCTAGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAATTTCGAGTTAACGTTTCTGA
* *
13535166 GCAAATAGTATAAAATCGCTTATACCAGGATGCTTTATGAGAAGAATTTGTGAAA
195 GCAAATAGTATAAAATCGCTTATACCAAGATACTTTATGAGAAGAATTTGTGAAA
*
13535221 TCGCGCCCACGTGGATGCGCTTTTGCTACAGTAG
1 TCGCGCCCACGT-GACGCGCTTTTGCTACAGTAG
13535255 CATGTTTGTG
Statistics
Matches: 260, Mismatches: 23, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
250 259 1.00
251 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (249 bp):
TCGCGCCCACGTGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATGTCAAGCTGACGTTTC
TGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTATATGAGAAGAATTTCTGAAATCGCGC
CCTCCTAGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAATTTCGAGTTAACGTTTCTGAG
CAAATAGTATAAAATCGCTTATACCAAGATACTTTATGAGAAGAATTTGTGAAA
Found at i:13538460 original size:15 final size:14
Alignment explanation
Indices: 13538422--13538474 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
13538412 AACTTAAGGG
13538422 TTAGGGTTTTAAAG-
1 TTAGGGTTTT-AAGT
* *
13538436 TTAAGGTTTTAGTGT
1 TTAGGGTTTTA-AGT
13538451 TTAGGGTTTTTAAGT
1 TTAGGG-TTTTAAGT
13538466 TTAGGGTTT
1 TTAGGGTTT
13538475 AGAAGTTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
13 1 0.03
14 13 0.41
15 13 0.41
16 5 0.16
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.51
Consensus pattern (14 bp):
TTAGGGTTTTAAGT
Found at i:13538468 original size:22 final size:21
Alignment explanation
Indices: 13538443--13538719 Score: 122
Period size: 21 Copynumber: 12.6 Consensus size: 21
13538433 AAGTTAAGGT
13538443 TTTAGTGTTTAGGGTTTTTAAG
1 TTTAG-GTTTAGGGTTTTTAAG
*
13538465 TTTAGGGTTTAGAAG-TTTT-AG
1 TTTA-GGTTTAG-GGTTTTTAAG
*
13538486 CTTTAGGGTTT-GTAGTTTTTAAG
1 -TTTA-GGTTTAG-GGTTTTTAAG
* *
13538509 TTTAAAGTTTAGTGTTTTTAAG
1 TTT-AGGTTTAGGGTTTTTAAG
13538531 TTTAAGGTTT-GAGGTTTTTAAG
1 TTT-AGGTTTAG-GGTTTTTAAG
* * *
13538553 TTAAGGGTTAGGGTTTTTAGG
1 TTTAGGTTTAGGGTTTTTAAG
* *
13538574 TTTAAGG-TAAGGGTTTTTAGG
1 TTT-AGGTTTAGGGTTTTTAAG
* *
13538595 TTTAGGGTTTTAGGTTTATGGTTTAGGG
1 TTTA-GG-TTTAGG-GT-T--TTTA-AG
*
13538623 TTTTAAGTTTAGGGTTTTTATA-
1 TTT-AGGTTTAGGGTTTTTA-AG
*
13538645 TTTAGGGCTT-GGAG-TTTTAAG
1 TTTA-GGTTTAGG-GTTTTTAAG
* * *
13538666 TTAAGGGTTAGCGTTTTTAA-
1 TTTAGGTTTAGGGTTTTTAAG
*
13538686 TTTAAGGGTTAGGGTTTTTAAG
1 TTT-AGGTTTAGGGTTTTTAAG
* *
13538708 TTAAGGGTTAGG
1 TTTAGGTTTAGG
13538720 ATTAGGGTTA
Statistics
Matches: 204, Mismatches: 25, Indels: 53
0.72 0.09 0.19
Matches are distributed among these distances:
20 9 0.04
21 83 0.41
22 77 0.38
23 14 0.07
24 1 0.00
25 2 0.01
26 1 0.00
27 10 0.05
28 6 0.03
29 1 0.00
ACGTcount: A:0.21, C:0.01, G:0.29, T:0.48
Consensus pattern (21 bp):
TTTAGGTTTAGGGTTTTTAAG
Found at i:13538480 original size:15 final size:15
Alignment explanation
Indices: 13538422--13538482 Score: 54
Period size: 15 Copynumber: 4.1 Consensus size: 15
13538412 AACTTAAGGG
13538422 TTAGGGTTTTA-AAGT
1 TTAGGG-TTTAGAAGT
* * *
13538437 TAAGGTTTTAG-TGT
1 TTAGGGTTTAGAAGT
**
13538451 TTAGGGTTTTTAAGT
1 TTAGGGTTTAGAAGT
13538466 TTAGGGTTTAGAAGT
1 TTAGGGTTTAGAAGT
13538481 TT
1 TT
13538483 TAGCTTTAGG
Statistics
Matches: 34, Mismatches: 10, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
14 13 0.38
15 21 0.62
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (15 bp):
TTAGGGTTTAGAAGT
Found at i:13538601 original size:15 final size:15
Alignment explanation
Indices: 13538583--13538618 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
13538573 GTTTAAGGTA
13538583 AGGGTTTTTAGGTTT
1 AGGGTTTTTAGGTTT
13538598 AGGG-TTTTAGGTTT
1 AGGGTTTTTAGGTTT
*
13538612 ATGGTTT
1 AGGGTTT
13538619 AGGGTTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.14, C:0.00, G:0.33, T:0.53
Consensus pattern (15 bp):
AGGGTTTTTAGGTTT
Found at i:13538612 original size:35 final size:35
Alignment explanation
Indices: 13538560--13538640 Score: 110
Period size: 35 Copynumber: 2.3 Consensus size: 35
13538550 AAGTTAAGGG
*
13538560 TTAGGGTTTTTAGGTTTAAGG-TAAGGGTTTTTAGGT
1 TTAGGG-TTTTAGGTTTAAGGTTAAGGG-TTTTAAGT
* *
13538596 TTAGGGTTTTAGGTTTATGGTTTAGGGTTTTAAGT
1 TTAGGGTTTTAGGTTTAAGGTTAAGGGTTTTAAGT
13538631 TTAGGGTTTT
1 TTAGGGTTTT
13538641 TATATTTAGG
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
35 30 0.73
36 11 0.27
ACGTcount: A:0.17, C:0.00, G:0.32, T:0.51
Consensus pattern (35 bp):
TTAGGGTTTTAGGTTTAAGGTTAAGGGTTTTAAGT
Found at i:13538617 original size:21 final size:20
Alignment explanation
Indices: 13538443--13539524 Score: 200
Period size: 22 Copynumber: 50.8 Consensus size: 20
13538433 AAGTTAAGGT
13538443 TTTAGTGTTTAGGGTTTTTAAG
1 TTTAG-GTTTAGGG-TTTTAAG
*
13538465 TTTAGGGTTTAGAAGTTTT-AG
1 TTTA-GGTTTAG-GGTTTTAAG
*
13538486 CTTTAGGGTTT-GTAGTTTTTAAG
1 -TTTA-GGTTTAG--GGTTTTAAG
* *
13538509 TTTAAAGTTTAGTGTTTTTAAG
1 TTT-AGGTTTAG-GGTTTTAAG
*
13538531 TTTAAGGTTTGAGGTTTTTAAG
1 TTT-AGGTTT-AGGGTTTTAAG
* * *
13538553 TTAAGGGTTAGGGTTTTTAGG
1 TTTAGGTTTAGGG-TTTTAAG
*
13538574 TTTAAGG-TAAGGG--TT---
1 TTT-AGGTTTAGGGTTTTAAG
*
13538589 TTTAGGTTTAGGGTTTTAGG
1 TTTAGGTTTAGGGTTTTAAG
13538609 TTTATGGTTTAGGGTTTTAAG
1 TTTA-GGTTTAGGGTTTTAAG
*
13538630 TTTA-G----GGTTTTTATA-
1 TTTAGGTTTAGGGTTTTA-AG
*
13538645 TTTAGGGCTT-GGAGTTTTAAG
1 TTTA-GGTTTAGG-GTTTTAAG
* * *
13538666 TTAAGGGTTAGCGTTTTTAA-
1 TTTAGGTTTAG-GGTTTTAAG
*
13538686 TTTAAGGGTTAGGGTTTTTAAG
1 TTT-AGGTTTAGGG-TTTTAAG
* * * *
13538708 TTAAGGGTTA-GG-ATTAGGG
1 TTTAGGTTTAGGGTTTTA-AG
** ** * *
13538727 TTATAATTTTAAAG-CTAAAG
1 TT-TAGGTTTAGGGTTTTAAG
* *
13538747 TTTTAGGGTTTATAGTTTTTAAG
1 -TTTA-GGTTTA-GGGTTTTAAG
*
13538770 TTTAGTGTTTAGGGTTGTTAGG
1 TTTAG-GTTTAGGGTT-TTAAG
13538792 TTTAGGGTTTAGGGTTTTAATTTTAAAG
1 TTTA-GGTTTAGGG------TTTT-AAG
*
13538820 TTTAGGGTTTATGGTTTTTAAG
1 TTTA-GGTTTA-GGGTTTTAAG
*
13538842 TTTAGGATTTAAGGTTTTTAAG
1 TTTAGG-TTT-AGGGTTTTAAG
* * *
13538864 -TTAGGGGTTAAGGTTTTTAGG
1 TTTA--GGTTTAGGGTTTTAAG
* * * *
13538885 TTAAGGGTTA-GG-ATTAGG
1 TTTAGGTTTAGGGTTTTAAG
**
13538903 TTTAGGGTTTTAAAG--TTAATG
1 TTTA-GG-TTTAGGGTTTTAA-G
13538924 TTTTAGGGTTTAGAGGTTTTAAG
1 -TTTA-GGTTTAG-GGTTTTAAG
* * * *
13538947 CTTAAGGTTCATGGTTTTTAGG
1 -TTTAGGTTTA-GGGTTTTAAG
*
13538969 TTTATGGTTTATGGTTTTTAAG
1 TTTA-GGTTTA-GGGTTTTAAG
* * * *
13538991 TTTAGGGTTTAATGCTGTTAGG
1 TTTA-GGTTT-AGGGTTTTAAG
*
13539013 TTTAGGGTTTAAGGTTTTTAAG
1 TTTA-GGTTT-AGGGTTTTAAG
* *
13539035 TTTAAGGTTTATGGTTTTTAGG
1 TTT-AGGTTTA-GGGTTTTAAG
13539057 TTTAGGGTTTAGGGTTTTAAG
1 TTTA-GGTTTAGGGTTTTAAG
* * *
13539078 TTTAAGGCTTAAGGTTTTTAGG
1 TTT-AGG-TTTAGGGTTTTAAG
*
13539100 TTTAGGGTTTCTA-GTTTTTAAG
1 TTTA-GG-TT-TAGGGTTTTAAG
* * * **
13539122 TTAAAGATTAGCATTTTTAA-
1 TTTAGGTTTAG-GGTTTTAAG
*
13539142 TTTAAGGGTTAGGGTTTTAAG
1 TTT-AGGTTTAGGGTTTTAAG
* * * *
13539163 TTAAGGGTTA-GG-ATTAGG
1 TTTAGGTTTAGGGTTTTAAG
* **
13539181 GTTAGGGTTTTAAAG--TTAAG
1 TTTA-GG-TTTAGGGTTTTAAG
13539201 TTTTTAGGGTTTAGGGTTTTAAG
1 --TTTA-GGTTTAGGGTTTTAAG
13539224 TTTAAGGTTTAGGGTTTTTAAG
1 TTT-AGGTTTAGGG-TTTTAAG
*
13539246 TTTGAGGTTTGGGGTTTGGGGTTTTAAG
1 TTT-A-------GGTTTAGGGTTTTAAG
* * *
13539274 TTAAGAG-TTAGTGTTTTTAG
1 TTTAG-GTTTAGGGTTTTAAG
* *
13539294 GTTAGGCTTTGAGGTTTTTAAG
1 TTTAGG-TTT-AGGGTTTTAAG
* * *
13539316 TTAAGG-GTAGGGTTTTTAGG
1 TTTAGGTTTAGGG-TTTTAAG
*
13539336 TTTAGGGTTTGAGGTTTTTAAG
1 TTTA-GGTTT-AGGGTTTTAAG
13539358 TTTAGGGTTTAGGGTTTTAAAG
1 TTTA-GGTTTAGGGTTTT-AAG
*
13539380 TTTAGTGTTT-GTGTTTTTAAG
1 TTTAG-GTTTAG-GGTTTTAAG
*
13539401 TTTAGGGTTTAAGGTTTTTAAG
1 TTTA-GGTTT-AGGGTTTTAAG
*
13539423 TTTATGGTTTGAGGTTTTTAAG
1 TTTA-GGTTT-AGGGTTTTAAG
* *
13539445 TTAAGAG-TTAGCGTTTTTAA-
1 TTTAG-GTTTAG-GGTTTTAAG
* *
13539465 TTTAAGGGTTAAGGTTTTTAAG
1 TTT-A-GGTTTAGGGTTTTAAG
* * *
13539487 TTAAGGGTTAGGGTTTTTAG
1 TTTAGGTTTAGGGTTTTAAG
*
13539507 TTTAAGGGTTTATGGTTT
1 TTT-A-GGTTTAGGGTTT
13539525 GTCAATTAAA
Statistics
Matches: 810, Mismatches: 137, Indels: 226
0.69 0.12 0.19
Matches are distributed among these distances:
14 3 0.00
15 19 0.02
16 1 0.00
17 3 0.00
18 19 0.02
19 17 0.02
20 101 0.12
21 211 0.26
22 358 0.44
23 37 0.05
24 4 0.00
27 3 0.00
28 24 0.03
29 10 0.01
ACGTcount: A:0.22, C:0.01, G:0.29, T:0.48
Consensus pattern (20 bp):
TTTAGGTTTAGGGTTTTAAG
Found at i:13538641 original size:15 final size:15
Alignment explanation
Indices: 13538609--13538651 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
13538599 GGGTTTTAGG
*
13538609 TTTATGGTTTAGGGT
1 TTTATAGTTTAGGGT
13538624 TTTA-AGTTTAGGGTT
1 TTTATAGTTTAGGG-T
13538639 TTTATA-TTTAGGG
1 TTTATAGTTTAGGG
13538652 CTTGGAGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 8 0.32
15 16 0.64
16 1 0.04
ACGTcount: A:0.19, C:0.00, G:0.28, T:0.53
Consensus pattern (15 bp):
TTTATAGTTTAGGGT
Found at i:13538796 original size:44 final size:44
Alignment explanation
Indices: 13538748--13539524 Score: 337
Period size: 43 Copynumber: 17.9 Consensus size: 44
13538738 AAGCTAAAGT
* * *
13538748 TTTAGGGTTTATAGTTTTTAAGTTTAGTGTTTAGGGTTGTTAGG
1 TTTAGGGTTTATAGTTTTTAAGTTTAGGGTTTAAGGTTTTTAGG
* * * *
13538792 TTTAGGGTTTAGGGTTTTAATTTTAAAGTTTAGGGTTTATGGTTTTTAAG
1 TTTAGGGTTTA------TAGTTTTTAAGTTTAGGGTTTAAGGTTTTTAGG
* *
13538842 TTTAGGATTTA-AGGTTTTTAAG-TTAGGGGTTAAGGTTTTTAGG
1 TTTAGGGTTTATA-GTTTTTAAGTTTAGGGTTTAAGGTTTTTAGG
* ** * * ** *
13538885 TTAAGGG--T-TAG-GATTAGGTTTAGGGTTTTAAAGTTAAT-GT
1 TTTAGGGTTTATAGTTTTTAAGTTTAGGG-TTTAAGGTTTTTAGG
* * * * * *
13538925 TTTAGGGTTTAGAGGTTTTAAGCTTAAGGTTCATGGTTTTTAGG
1 TTTAGGGTTTATAGTTTTTAAGTTTAGGGTTTAAGGTTTTTAGG
* * * * *
13538969 TTTATGGTTTATGGTTTTTAAGTTTAGGGTTTAATGCTGTTAGG
1 TTTAGGGTTTATAGTTTTTAAGTTTAGGGTTTAAGGTTTTTAGG
* *
13539013 TTTAGGGTTTA-AGGTTTTTAAGTTTAAGGTTTATGGTTTTTAGG
1 TTTAGGGTTTATA-GTTTTTAAGTTTAGGGTTTAAGGTTTTTAGG
* * * *
13539057 TTTAGGGTTTA-GGGTTTTAAGTTTAAGGCTTAAGGTTTTTAGG
1 TTTAGGGTTTATAGTTTTTAAGTTTAGGGTTTAAGGTTTTTAGG
* ** * * *
13539100 TTTAGGGTTTCTAGTTTTTAAG-TTAAAGATT-AGCATTTTTA-A
1 TTTAGGGTTTATAGTTTTTAAGTTTAGGGTTTAAG-GTTTTTAGG
* * * *
13539142 TTTAAGGG-TTA-GGGTTTTAAGTTAAGGG-TT-AGG--ATTAGG
1 TTT-AGGGTTTATAGTTTTTAAGTTTAGGGTTTAAGGTTTTTAGG
* * *
13539181 GTTAGGGTTTTAAAGTTAAGTTTTTAGGGTTTAGGGTTTTAA-G-TTTAAGG
1 TTTAGGG-TTT--A--T-AGTTTTTA-AGTTTAGGG-TTTAAGGTTTTTAGG
* * * * * * *
13539231 TTTAGGGTTTTTAAG-TTTGAGGTTTGGGGTTT-GGGGTTTTAAG
1 TTTAGGGTTTAT-AGTTTTTAAGTTTAGGGTTTAAGGTTTTTAGG
* * * * * *
13539274 TTAAGAG-TTAGT-GTTTTT-AGGTTAGGCTTTGAGGTTTTTAAG
1 TTTAGGGTTTA-TAGTTTTTAAGTTTAGGGTTTAAGGTTTTTAGG
* ** * * *
13539316 TTAAGGG--TAGGGTTTTTAGGTTTAGGGTTTGAGGTTTTTAAG
1 TTTAGGGTTTATAGTTTTTAAGTTTAGGGTTTAAGGTTTTTAGG
** * * *
13539358 TTTAGGGTTTAGGGTTTTAAAGTTTAGTGTTT--GTGTTTTTAAG
1 TTTAGGGTTTATAGTTTTTAAGTTTAGGGTTTAAG-GTTTTTAGG
* * *
13539401 TTTAGGGTTTA-AGGTTTTTAAGTTTATGGTTTGAGGTTTTTAAG
1 TTTAGGGTTTATA-GTTTTTAAGTTTAGGGTTTAAGGTTTTTAGG
* * ** *
13539445 TTAAGAG-TTAGCGTTTTTAA-TTTAAGGG-TTAAGGTTTTTAAG
1 TTTAGGGTTTATAGTTTTTAAGTTT-AGGGTTTAAGGTTTTTAGG
* ** *
13539487 TTAAGGG-TTAGGGTTTTT-AGTTTAAGGGTTTATGGTTT
1 TTTAGGGTTTATAGTTTTTAAGTTT-AGGGTTTAAGGTTT
13539525 GTCAATTAAA
Statistics
Matches: 564, Mismatches: 118, Indels: 103
0.72 0.15 0.13
Matches are distributed among these distances:
38 7 0.01
39 6 0.01
40 16 0.03
41 40 0.07
42 104 0.18
43 165 0.29
44 154 0.27
45 5 0.01
46 6 0.01
47 7 0.01
49 6 0.01
50 48 0.09
ACGTcount: A:0.22, C:0.01, G:0.29, T:0.48
Consensus pattern (44 bp):
TTTAGGGTTTATAGTTTTTAAGTTTAGGGTTTAAGGTTTTTAGG
Found at i:13538872 original size:72 final size:73
Alignment explanation
Indices: 13538742--13538882 Score: 189
Period size: 72 Copynumber: 1.9 Consensus size: 73
13538732 ATTTTAAAGC
* * *
13538742 TAAAGTTTTAGGGTTTATAGTTTTTAAGTTTAGTGTTTAGGGTTGTTAGGTTTAGGGTTTAGGGT
1 TAAAGTTTTAGGGTTTATAGTTTTTAAGTTTAGTGTTTAAGGTTGTTAAGTTTAGGGTTAAGGGT
13538807 TTTAATTT
66 TTTAATTT
* *
13538815 TAAAG-TTTAGGGTTTATGGTTTTTAAGTTTAG-GATTTAAGGTTTTTAAG-TTAGGGGTTAAGG
1 TAAAGTTTTAGGGTTTATAGTTTTTAAGTTTAGTG-TTTAAGGTTGTTAAGTTTA-GGGTTAAGG
*
13538877 TTTTTA
64 GTTTTA
13538883 GGTTAAGGGT
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
71 4 0.07
72 51 0.85
73 5 0.08
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (73 bp):
TAAAGTTTTAGGGTTTATAGTTTTTAAGTTTAGTGTTTAAGGTTGTTAAGTTTAGGGTTAAGGGT
TTTAATTT
Found at i:13538881 original size:177 final size:171
Alignment explanation
Indices: 13538678--13539065 Score: 456
Period size: 177 Copynumber: 2.2 Consensus size: 171
13538668 AAGGGTTAGC
* * * *
13538678 GTTTTTAATTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGATTAGGGTTATAATTTTAAAGCT
1 GTTTTTAAGTTAAGGGTTAAGGTTTTTAGGTTAAGGGTTAGGATTAGGGTTAGAATTTTAAAGCT
* * * *
13538743 AAAGTTTTAGGGTTTATAGTTTTTAAG-TTTAGTGTTTAGGGTTGTTAGGTTTAGGGTTTAGGGT
66 AAAGTTTTAGGGTTTAGAGGTTTTAAGCTTAAG-GTTCAGGGTTGTTAGGTTTAGGGTTTAGGG-
* *
13538807 TTTAATTTTAAAGTTTAGGGTTT-ATGGTTTTTAAGTTTAGGATTTAAG
129 --T--TTTT-AAGTTTAGGGTTTAAT-GCTGTTAAGTTTAGGATTTAAG
* * ** *
13538855 GTTTTTAAGTTAGGGGTTAAGGTTTTTAGGTTAAGGGTTAGGATTAGGTTTAGGGTTTTAAAGTT
1 GTTTTTAAGTTAAGGGTTAAGGTTTTTAGGTTAAGGGTTAGGATTAGGGTTAGAATTTTAAAGCT
* * * * *
13538920 AATGTTTTAGGGTTTAGAGGTTTTAAGCTTAAGGTTCATGGTTTTTAGGTTTATGGTTTATGGTT
66 AAAGTTTTAGGGTTTAGAGGTTTTAAGCTTAAGGTTCAGGGTTGTTAGGTTTAGGGTTTAGGGTT
* *
13538985 TTTAAGTTTAGGGTTTAATGCTGTTAGGTTTAGGGTTTAAG
131 TTTAAGTTTAGGGTTTAATGCTGTTAAGTTTAGGATTTAAG
* * *
13539026 GTTTTTAAGTTTAAGGTTTATGGTTTTTAGGTTTAGGGTT
1 GTTTTTAAG-TTAAGGGTTAAGGTTTTTAGGTTAAGGGTT
13539066 TAGGGTTTTA
Statistics
Matches: 182, Mismatches: 26, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
171 40 0.22
172 32 0.18
174 1 0.01
177 105 0.58
178 4 0.02
ACGTcount: A:0.23, C:0.01, G:0.28, T:0.48
Consensus pattern (171 bp):
GTTTTTAAGTTAAGGGTTAAGGTTTTTAGGTTAAGGGTTAGGATTAGGGTTAGAATTTTAAAGCT
AAAGTTTTAGGGTTTAGAGGTTTTAAGCTTAAGGTTCAGGGTTGTTAGGTTTAGGGTTTAGGGTT
TTTAAGTTTAGGGTTTAATGCTGTTAAGTTTAGGATTTAAG
Found at i:13539040 original size:6 final size:7
Alignment explanation
Indices: 13538789--13539109 Score: 76
Period size: 7 Copynumber: 44.9 Consensus size: 7
13538779 TAGGGTTGTT
13538789 AGGTTTA
1 AGGTTTA
*
13538796 GGGTTTA
1 AGGTTTA
*
13538803 GGGTTTTA
1 AGG-TTTA
*
13538811 A-TTTTA
1 AGGTTTA
*
13538817 AAGTTTA
1 AGGTTTA
*
13538824 GGGTTTA
1 AGGTTTA
*
13538831 TGGTTTTTA
1 AGG--TTTA
13538840 A-GTTT-
1 AGGTTTA
13538845 AGGATTTA
1 AGG-TTTA
13538853 AGGTTTTTA
1 AGG--TTTA
13538862 A-G-TTA
1 AGGTTTA
* *
13538867 GGGGTTA
1 AGGTTTA
*
13538874 AGGTTTTT
1 AGG-TTTA
13538882 AGG-TTA
1 AGGTTTA
*
13538888 AGGGTT-
1 AGGTTTA
*
13538894 AGGATT-
1 AGGTTTA
13538900 AGGTTTA
1 AGGTTTA
*
13538907 GGGTTTTA
1 AGG-TTTA
*
13538915 AAG-TTA
1 AGGTTTA
*
13538921 ATGTTTTA
1 A-GGTTTA
*
13538929 GGGTTTA
1 AGGTTTA
13538936 GAGGTTTTA
1 -AGG-TTTA
*
13538945 A-GCTTA
1 AGGTTTA
*
13538951 AGGTTCA
1 AGGTTTA
* *
13538958 TGGTTTTT
1 AGG-TTTA
13538966 AGGTTTA
1 AGGTTTA
*
13538973 TGGTTTA
1 AGGTTTA
*
13538980 TGGTTTTTA
1 AGG--TTTA
13538989 A-GTTTA
1 AGGTTTA
*
13538995 GGGTTTA
1 AGGTTTA
*
13539002 ATGCTGTT-
1 A-GGT-TTA
13539010 AGGTTTA
1 AGGTTTA
*
13539017 GGGTTTA
1 AGGTTTA
13539024 AGGTTTTTA
1 AGG--TTTA
13539033 A-GTTTA
1 AGGTTTA
13539039 AGGTTTA
1 AGGTTTA
* *
13539046 TGGTTTTT
1 AGG-TTTA
13539054 AGGTTTA
1 AGGTTTA
*
13539061 GGGTTTA
1 AGGTTTA
*
13539068 GGGTTTTA
1 AGG-TTTA
13539076 A-GTTTA
1 AGGTTTA
*
13539082 AGGCTTA
1 AGGTTTA
*
13539089 AGGTTTTT
1 AGG-TTTA
13539097 AGGTTTA
1 AGGTTTA
*
13539104 GGGTTT
1 AGGTTT
13539110 CTAGTTTTTA
Statistics
Matches: 230, Mismatches: 51, Indels: 66
0.66 0.15 0.19
Matches are distributed among these distances:
5 4 0.02
6 49 0.21
7 105 0.46
8 48 0.21
9 24 0.10
ACGTcount: A:0.21, C:0.01, G:0.29, T:0.48
Consensus pattern (7 bp):
AGGTTTA
Found at i:13539161 original size:20 final size:20
Alignment explanation
Indices: 13539028--13539516 Score: 148
Period size: 21 Copynumber: 22.8 Consensus size: 20
13539018 GGTTTAAGGT
* *
13539028 TTTTAAGTTTAAGGTTTATGGT
1 TTTTAAG-TTAAGGGTTA-GGG
* *
13539050 TTTTAGGTTTAGGGTTTAGGG
1 TTTTAAGTTAAGGG-TTAGGG
* *
13539071 TTTTAAGTTTAAGGCTTAAGGT
1 TTTTAAG-TTAAGGGTT-AGGG
* * *
13539093 TTTTAGGTTTAGGGTTTCTA-GT
1 TTTTAAGTTAAGGG--T-TAGGG
* * **
13539115 TTTTAAGTTAAAGATTAGCAT
1 TTTTAAGTTAAGGGTTAG-GG
*
13539136 TTTTAATTTAAGGGTTAGGG
1 TTTTAAGTTAAGGGTTAGGG
13539156 TTTTAAGTTAAGGGTTA-GG
1 TTTTAAGTTAAGGGTTAGGG
* * **
13539175 -ATTAGGGTT-AGGGTTTTAAAG
1 TTTTA-AGTTAAGGG--TTAGGG
*
13539196 --TTAAGTTTTTAGGGTTTAGGG
1 TTTTAAG--TTAAGGG-TTAGGG
*
13539217 TTTTAAGTTTAAGGTTTAGGG
1 TTTTAAG-TTAAGGGTTAGGG
* *
13539238 TTTTTAAGTTTGAGGTTTGGGGTTTGGGG
1 -TTTTAAG-TT-A-----AGGG-TTAGGG
* *
13539267 TTTTAAGTTAAGAGTTAGTGT
1 TTTTAAGTTAAGGGTTAG-GG
* * *
13539288 TTTTAGGTT-AGGCTTTGAGGT
1 TTTTAAGTTAAGG-GTT-AGGG
13539309 TTTTAAGTTAAGGG-TAGGG
1 TTTTAAGTTAAGGGTTAGGG
* * *
13539328 TTTTTAGGTTTAGGGTTTGAGGT
1 -TTTTAAGTTAAGGG-TT-AGGG
*
13539351 TTTTAAGTTTAGGGTTTAGGG
1 TTTTAAGTTAAGGG-TTAGGG
* * * *
13539372 TTTTAAAGTTTAGTGTTTGTGT
1 TTTT-AAGTTAAGGGTTAG-GG
* *
13539394 TTTTAAGTTTAGGGTTTAAGGT
1 TTTTAAGTTAAGGG-TT-AGGG
* * *
13539416 TTTTAAGTTTATGGTTTGAGGT
1 TTTTAAG-TTAAGGGTT-AGGG
* *
13539438 TTTTAAGTTAAGAGTTAGCGT
1 TTTTAAGTTAAGGGTTAG-GG
* *
13539459 TTTTAATTTAAGGGTTAAGGT
1 TTTTAAGTTAAGGGTT-AGGG
13539480 TTTTAAGTTAAGGGTTAGGG
1 TTTTAAGTTAAGGGTTAGGG
*
13539500 TTTTTAGTTTAAGGGTT
1 TTTTAAG-TTAAGGGTT
13539517 TATGGTTTGT
Statistics
Matches: 361, Mismatches: 65, Indels: 83
0.71 0.13 0.16
Matches are distributed among these distances:
18 7 0.02
19 11 0.03
20 52 0.14
21 140 0.39
22 117 0.32
23 16 0.04
24 1 0.00
26 1 0.00
27 2 0.01
28 9 0.02
29 5 0.01
ACGTcount: A:0.22, C:0.01, G:0.29, T:0.48
Consensus pattern (20 bp):
TTTTAAGTTAAGGGTTAGGG
Found at i:13539209 original size:28 final size:27
Alignment explanation
Indices: 13539176--13539275 Score: 86
Period size: 28 Copynumber: 3.8 Consensus size: 27
13539166 AGGGTTAGGA
*
13539176 TTAGGGTTAGGGTTTTAAAG-TTAAGTTT
1 TTAGGGTTAGGGTTTT-AAGTTTAAG-GT
13539204 TTAGGGTTTAGGGTTTTAAGTTTAAGGT
1 TTAGGG-TTAGGGTTTTAAGTTTAAGGT
*
13539232 TTAGGG-T----TTTTAAGTTTGAGGT
1 TTAGGGTTAGGGTTTTAAGTTTAAGGT
* *
13539254 TTGGGGTTTGGGGTTTTAAGTT
1 TTAGGG-TTAGGGTTTTAAGTT
13539276 AAGAGTTAGT
Statistics
Matches: 61, Mismatches: 3, Indels: 16
0.76 0.04 0.20
Matches are distributed among these distances:
22 19 0.31
24 1 0.02
26 1 0.02
28 25 0.41
29 15 0.25
ACGTcount: A:0.19, C:0.00, G:0.33, T:0.48
Consensus pattern (27 bp):
TTAGGGTTAGGGTTTTAAGTTTAAGGT
Found at i:13539504 original size:42 final size:41
Alignment explanation
Indices: 13539267--13539516 Score: 234
Period size: 42 Copynumber: 5.9 Consensus size: 41
13539257 GGGTTTGGGG
* * ** *
13539267 TTTTAAGTTAAGAGTTAGTGTTTTTAGGTTAGGCTTTGAGGT
1 TTTTAAGTTAAGGGTTAGGGTTTTTAATTTAGG-GTTGAGGT
*
13539309 TTTTAAGTTAAGGG-TAGGGTTTTTAGGTTTAGGGTTTGAGGT
1 TTTTAAGTTAAGGGTTAGGGTTTTTA-ATTTAGGG-TTGAGGT
* * * *
13539351 TTTTAAGTTTAGGGTTTAGGGTTTTAAAGTTTAGTGTTTG-TGT
1 TTTTAAGTTAAGGG-TTAGGGTTTTTAA-TTTAG-GGTTGAGGT
* * *
13539394 TTTTAAGTTTAGGGTTTAAGGTTTTTAAGTTTATGGTTTGAGGT
1 TTTTAAGTTAAGGG-TTAGGGTTTTTAA-TTTA-GGGTTGAGGT
* * *
13539438 TTTTAAGTTAAGAGTTAGCGTTTTTAATTTAAGGGTTAAGGT
1 TTTTAAGTTAAGGGTTAGGGTTTTTAATTT-AGGGTTGAGGT
*
13539480 TTTTAAGTTAAGGGTTAGGGTTTTTAGTTTAAGGGTT
1 TTTTAAGTTAAGGGTTAGGGTTTTTAATTT-AGGGTT
13539517 TATGGTTTGT
Statistics
Matches: 178, Mismatches: 21, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
41 10 0.06
42 84 0.47
43 50 0.28
44 33 0.19
45 1 0.01
ACGTcount: A:0.22, C:0.01, G:0.29, T:0.49
Consensus pattern (41 bp):
TTTTAAGTTAAGGGTTAGGGTTTTTAATTTAGGGTTGAGGT
Found at i:13540090 original size:18 final size:18
Alignment explanation
Indices: 13540067--13540106 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
13540057 GACTCGAAAA
* *
13540067 AGGATACATATAAGGGTT
1 AGGATACATAAAAGGGCT
*
13540085 AGGATATATAAAAGGGCT
1 AGGATACATAAAAGGGCT
13540103 AGGA
1 AGGA
13540107 AACGCACCTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.30, T:0.23
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:13542045 original size:12 final size:12
Alignment explanation
Indices: 13542004--13542047 Score: 65
Period size: 11 Copynumber: 3.8 Consensus size: 12
13541994 ATTAAAAATG
13542004 AATTTGAG-GGA
1 AATTTGAGAGGA
*
13542015 AATTTGAAAGGA
1 AATTTGAGAGGA
13542027 AA-TTGAGAGGA
1 AATTTGAGAGGA
13542038 AATTTGAGAG
1 AATTTGAGAG
13542048 AGGATTTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 17 0.59
12 12 0.41
ACGTcount: A:0.43, C:0.00, G:0.32, T:0.25
Consensus pattern (12 bp):
AATTTGAGAGGA
Found at i:13543949 original size:26 final size:26
Alignment explanation
Indices: 13543918--13543978 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 26
13543908 TTGAATTATG
*
13543918 AAATTGTTTTTGTGTGGTTGTAATTT
1 AAATTGTTTTTGTGTGGTTATAATTT
13543944 AAATTGTTTTTGTGTGGTTATAATTT
1 AAATTGTTTTTGTGTGGTTATAATTT
*
13543970 GAATTGTTT
1 AAATTGTTT
13543979 ACAATTTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.57
Consensus pattern (26 bp):
AAATTGTTTTTGTGTGGTTATAATTT
Found at i:13545229 original size:16 final size:16
Alignment explanation
Indices: 13545208--13545246 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
13545198 TTTTAATAAA
13545208 ATTAAAACTAATTATT
1 ATTAAAACTAATTATT
* *
13545224 ATTAAAATTAATTGTT
1 ATTAAAACTAATTATT
*
13545240 AGTAAAA
1 ATTAAAA
13545247 TCATCAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (16 bp):
ATTAAAACTAATTATT
Found at i:13545232 original size:22 final size:23
Alignment explanation
Indices: 13545179--13545234 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 23
13545169 CCCGTTTTTA
* *
13545179 ATTAAAATTAAAATTATATTTTT
1 ATTAAAATTAAAACTATATTATT
*
13545202 AATAAAATTAAAACTA-ATTATT
1 ATTAAAATTAAAACTATATTATT
13545224 ATTAAAATTAA
1 ATTAAAATTAA
13545235 TTGTTAGTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 15 0.52
23 14 0.48
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTATT
Found at i:13545762 original size:21 final size:22
Alignment explanation
Indices: 13545721--13545763 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
13545711 ATTAATTGTA
* *
13545721 TAAAACTAAAACTATTATATTT
1 TAAAAATAAAAATATTATATTT
13545743 TAAAAATAAAAATA-TATATTT
1 TAAAAATAAAAATATTATATTT
13545764 AATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAAAATAAAAATATTATATTT
Found at i:13546605 original size:19 final size:19
Alignment explanation
Indices: 13546581--13546634 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
13546571 AACCATATCT
13546581 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
13546600 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
13546619 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
13546635 CTTGAAGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:13550949 original size:11 final size:12
Alignment explanation
Indices: 13550909--13550951 Score: 70
Period size: 12 Copynumber: 3.6 Consensus size: 12
13550899 CCTATTTGAA
13550909 AAGTGATGCTTGG
1 AAGT-ATGCTTGG
13550922 AAGTATGCTTGG
1 AAGTATGCTTGG
13550934 AAGTATGCTT-G
1 AAGTATGCTTGG
13550945 AAGTATG
1 AAGTATG
13550952 TTTGTTTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 8 0.27
12 18 0.60
13 4 0.13
ACGTcount: A:0.28, C:0.07, G:0.33, T:0.33
Consensus pattern (12 bp):
AAGTATGCTTGG
Found at i:13552847 original size:24 final size:24
Alignment explanation
Indices: 13552820--13552934 Score: 83
Period size: 24 Copynumber: 4.7 Consensus size: 24
13552810 GTTGTATAAT
13552820 GGAAGCTCATAAGAGCCATAATCG
1 GGAAGCTCATAAGAGCCATAATCG
* *
13552844 GGAAGCTCATGCAAG-TCAATAAT-G
1 GGAAGCTCAT--AAGAGCCATAATCG
* *
13552868 GGTAGCTTC-GAAGAGCCATTAATCG
1 GGAAGC-TCATAAGAGCCA-TAATCG
* *
13552893 GGAAGCTCACGAAGAGCCATATAACG
1 GGAAGCTCA-TAAGAGCCATA-ATCG
* *
13552919 GGATGTTCATAAGAGC
1 GGAAGCTCATAAGAGC
13552935 TGCGGTGTGT
Statistics
Matches: 71, Mismatches: 11, Indels: 17
0.72 0.11 0.17
Matches are distributed among these distances:
22 3 0.04
23 2 0.03
24 22 0.31
25 22 0.31
26 22 0.31
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.19
Consensus pattern (24 bp):
GGAAGCTCATAAGAGCCATAATCG
Found at i:13556575 original size:25 final size:26
Alignment explanation
Indices: 13556528--13556576 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
13556518 AAGGCACCTT
13556528 ATAAATTCTTTAAGGGTTACAAGAGC
1 ATAAATTCTTTAAGGGTTACAAGAGC
*
13556554 ATAAATTC-TTAGGGGTTACAAGA
1 ATAAATTCTTTAAGGGTTACAAGA
13556577 CTTGTATGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (26 bp):
ATAAATTCTTTAAGGGTTACAAGAGC
Found at i:13564823 original size:221 final size:221
Alignment explanation
Indices: 13564440--13564882 Score: 859
Period size: 221 Copynumber: 2.0 Consensus size: 221
13564430 TAGTGCAAGA
*
13564440 TGGTTTACCAAGTTGGATTTGAAATCGGGGCACCATCAAGTTTGGGTAGTCGAGAGAGACGAGCC
1 TGGTTTACCAAGTTGGATTTGAAATCGGGGCACCATCAAGTTTGGGTAGTCGAGAGAAACGAGCC
13564505 AAAGACAGCTTATGTAACGTGGTATGGTTAGTATGAGTTCCTTGTGATGCATTTCGGACTCACGA
66 AAAGACAGCTTATGTAACGTGGTATGGTTAGTATGAGTTCCTTGTGATGCATTTCGGACTCACGA
13564570 ATGCCCTAACTACATTCTGTACCCTAATGAATAAAATACTTCAACTTTTCTTAGATTGTTTTGTG
131 ATGCCCTAACTACATTCTGTACCCTAATGAATAAAATACTTCAACTTTTCTTAGATTGTTTTGTG
13564635 GTTGTTTACCTTGATGATATTGTGGT
196 GTTGTTTACCTTGATGATATTGTGGT
* *
13564661 TGGTTTACCAAGTTGGATTTGAGATCGGGGCACCATCAAGTTTGGGTAGTCGAGAGAAATGAGCC
1 TGGTTTACCAAGTTGGATTTGAAATCGGGGCACCATCAAGTTTGGGTAGTCGAGAGAAACGAGCC
13564726 AAAGACAGCTTATGTAACGTGGTATGGTTAGTATGAGTTCCTTGTGATGCATTTCGGACTCACGA
66 AAAGACAGCTTATGTAACGTGGTATGGTTAGTATGAGTTCCTTGTGATGCATTTCGGACTCACGA
13564791 ATGCCCTAACTACATTCTGTACCCTAATGAATAAAATACTTCAACTTTTCTTAGATTGTTTTGTG
131 ATGCCCTAACTACATTCTGTACCCTAATGAATAAAATACTTCAACTTTTCTTAGATTGTTTTGTG
13564856 GTTGTTTACCTTGATGATATTGTGGT
196 GTTGTTTACCTTGATGATATTGTGGT
13564882 T
1 T
13564883 TATAGTAAGT
Statistics
Matches: 219, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
221 219 1.00
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (221 bp):
TGGTTTACCAAGTTGGATTTGAAATCGGGGCACCATCAAGTTTGGGTAGTCGAGAGAAACGAGCC
AAAGACAGCTTATGTAACGTGGTATGGTTAGTATGAGTTCCTTGTGATGCATTTCGGACTCACGA
ATGCCCTAACTACATTCTGTACCCTAATGAATAAAATACTTCAACTTTTCTTAGATTGTTTTGTG
GTTGTTTACCTTGATGATATTGTGGT
Found at i:13568466 original size:29 final size:29
Alignment explanation
Indices: 13568426--13568484 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
13568416 GAATATAAAC
*
13568426 TATATTTTTTATTTTTAAAATACACCACA
1 TATATTTTTTATTTTTAAAAAACACCACA
*
13568455 TATATTTTTTATTTTTAAAAAACACTACA
1 TATATTTTTTATTTTTAAAAAACACCACA
13568484 T
1 T
13568485 TTAAAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (29 bp):
TATATTTTTTATTTTTAAAAAACACCACA
Found at i:13575580 original size:17 final size:16
Alignment explanation
Indices: 13575558--13575589 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
13575548 GCCTCCTCCT
13575558 CGCGCGTGCTGCGCCTA
1 CGCGCGTG-TGCGCCTA
13575575 CGCGCGTGTGCGCCT
1 CGCGCGTGTGCGCCT
13575590 TTGTTCATCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.03, C:0.41, G:0.38, T:0.19
Consensus pattern (16 bp):
CGCGCGTGTGCGCCTA
Found at i:13576605 original size:3 final size:3
Alignment explanation
Indices: 13576597--13576634 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
13576587 ATGTTTCCAC
*
13576597 TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
13576635 GTTTTTTACT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:13580194 original size:51 final size:51
Alignment explanation
Indices: 13580133--13580235 Score: 190
Period size: 51 Copynumber: 2.0 Consensus size: 51
13580123 AAATTAAAAG
13580133 ATTATACATACACCAACAATGTTTTTTAGGGTA-AATAACATTAAACCAACA
1 ATTATACATACACCAACAATGTTTTTTAGGG-ACAATAACATTAAACCAACA
13580184 ATTATACATACACCAACAATGTTTTTTAGGGACAATAACATTAAACCAACA
1 ATTATACATACACCAACAATGTTTTTTAGGGACAATAACATTAAACCAACA
13580235 A
1 A
13580236 GTAATTTTAG
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
50 1 0.02
51 50 0.98
ACGTcount: A:0.46, C:0.18, G:0.08, T:0.28
Consensus pattern (51 bp):
ATTATACATACACCAACAATGTTTTTTAGGGACAATAACATTAAACCAACA
Found at i:13580244 original size:33 final size:34
Alignment explanation
Indices: 13580181--13580291 Score: 115
Period size: 33 Copynumber: 3.4 Consensus size: 34
13580171 CATTAAACCA
* *
13580181 ACAATTATACATACACCAACAATGT-TTTTTAGGG
1 ACAATTATACATAAACCAACAA-GTAATTTTAGGG
13580215 ACAA-TA-ACATTAAACCAACAAGTAATTTTA-GG
1 ACAATTATACA-TAAACCAACAAGTAATTTTAGGG
* * *
13580247 TCAATTATACATACACCAACAATTAATTTTA-GG
1 ACAATTATACATAAACCAACAAGTAATTTTAGGG
*
13580280 TCAATTATACAT
1 ACAATTATACAT
13580292 GCTTTATAAT
Statistics
Matches: 68, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
32 10 0.15
33 51 0.75
34 7 0.10
ACGTcount: A:0.43, C:0.17, G:0.08, T:0.32
Consensus pattern (34 bp):
ACAATTATACATAAACCAACAAGTAATTTTAGGG
Found at i:13583362 original size:29 final size:28
Alignment explanation
Indices: 13583329--13583415 Score: 83
Period size: 28 Copynumber: 3.1 Consensus size: 28
13583319 TCATAAGAAC
13583329 ATTTTATGAAATTATATTTAATAATAATT
1 ATTTTAT-AAATTATATTTAATAATAATT
* *
13583358 A-TTT-TAAATTATATTAAATCAT-A-T
1 ATTTTATAAATTATATTTAATAATAATT
* *
13583382 ATTTTAATTAAAATATATTTAATATTAATT
1 ATTTT-A-TAAATTATATTTAATAATAATT
13583412 ATTT
1 ATTT
13583416 CAAATTTTCA
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
24 2 0.04
25 4 0.09
26 15 0.33
27 1 0.02
28 17 0.37
29 2 0.04
30 5 0.11
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (28 bp):
ATTTTATAAATTATATTTAATAATAATT
Found at i:13583368 original size:26 final size:26
Alignment explanation
Indices: 13583337--13583421 Score: 91
Period size: 26 Copynumber: 3.2 Consensus size: 26
13583327 ACATTTTATG
13583337 AAATTATATTTAATAATAATTATTTT
1 AAATTATATTTAATAATAATTATTTT
* *
13583363 AAATTATATTAAATCATATATT-TTAATT
1 AAATTATATTTAATAATA-ATTATT--TT
* * *
13583391 AAAATATATTTAATATTAATTATTTC
1 AAATTATATTTAATAATAATTATTTT
13583417 AAATT
1 AAATT
13583422 TTCATTTAGT
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
26 23 0.49
27 6 0.13
28 18 0.38
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (26 bp):
AAATTATATTTAATAATAATTATTTT
Found at i:13583591 original size:67 final size:66
Alignment explanation
Indices: 13583516--13583728 Score: 150
Period size: 67 Copynumber: 3.2 Consensus size: 66
13583506 ATTGTAATGT
13583516 ATTT-AATAATAATTATGTTTAAATACGATTAAATTATTTATTATTGATATTAATAATCTTATTA
1 ATTTAAATAATAATTATGTTTAAATACGATTAAA-TATTTATTATTGATATTAATAATCTTATTA
13583580 AA
65 AA
* * ** * * * * * * *
13583582 ATTTAAATAACAATAACAAATTT--CTGCTAATTATAAGAATT-TTATT-AAATT-ATATATTTT
1 ATTTAAATAATAAT--TATGTTTAAATAC-GATTA-AATATTTATTATTGATATTAATA-ATCTT
13583642 AATTAAAA
61 -ATT-AAA
* * * *
13583650 TATATTTAATAATAATTATGTTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTAT
1 -AT-TTAAATAATAATTATGTTTAAATACGATT-AAATATTTATTATTGATATTAATAATCTTAT
13583715 TAAA
63 TAAA
13583719 ATTTAAATAA
1 ATTTAAATAA
13583729 CATTAACAAT
Statistics
Matches: 104, Mismatches: 27, Indels: 31
0.64 0.17 0.19
Matches are distributed among these distances:
65 3 0.03
66 12 0.12
67 25 0.24
68 16 0.15
69 19 0.18
70 19 0.18
71 7 0.07
72 3 0.03
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (66 bp):
ATTTAAATAATAATTATGTTTAAATACGATTAAATATTTATTATTGATATTAATAATCTTATTAA
A
Found at i:13583626 original size:137 final size:138
Alignment explanation
Indices: 13583472--13583893 Score: 418
Period size: 137 Copynumber: 2.9 Consensus size: 138
13583462 TAAGAATATG
** *
13583472 AATTATTAAGAATTTTATTAAATTATATACCAAAATTGTAATGTATTTAATAATAATTATGTTTA
1 AATTATTAAGAATTTTATTAAATTATATACCAAAATTAAAATATATTTAATAATAATTATGTTTA
* * *
13583537 AATACGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAAA
66 AATACGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAAA
13583602 TTTCTGCT
131 TTTCTGCT
****
13583610 AATTA-TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
1 AATTATTAAGAATTTTATTAAATTATATACCAAAATTAAAATATATTTAATAATAATTATGTTTA
* *
13583674 AATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACATTAACAAT
66 AATACGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAAC-A-
*
13583739 AATCATT-TACCAAAAT
129 AAT--TTCT-GC----T
** * ** * * ** * *
13583755 AATT-TTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATTAT
1 AATTATTAAG--AATTTTATTAA-ATTA-TATACCA-A-A-ATTAA----AATATATTTAATAAT
*
13583819 AATTATGTTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATA
55 AATTATGTTTAAATACGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATA
13583884 ACAATAACAA
120 ACAATAACAA
13583894 TAATCATTTA
Statistics
Matches: 238, Mismatches: 25, Indels: 26
0.82 0.09 0.09
Matches are distributed among these distances:
137 109 0.46
138 6 0.03
139 3 0.01
140 1 0.00
141 3 0.01
145 7 0.03
147 8 0.03
148 3 0.01
149 5 0.02
151 1 0.00
152 4 0.02
154 1 0.00
155 1 0.00
156 86 0.36
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (138 bp):
AATTATTAAGAATTTTATTAAATTATATACCAAAATTAAAATATATTTAATAATAATTATGTTTA
AATACGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAAA
TTTCTGCT
Found at i:13583648 original size:18 final size:17
Alignment explanation
Indices: 13583620--13583654 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
13583610 AATTATAAGA
*
13583620 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
13583637 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
13583655 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:13583726 original size:50 final size:51
Alignment explanation
Indices: 13583670--13583883 Score: 122
Period size: 50 Copynumber: 4.2 Consensus size: 51
13583660 AATAATTATG
13583670 TTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTT-ATTAAAA
1 TTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTAATTAAAA
** * * * * ** *
13583720 TTTAAATAACATTAACAATAATCATTTAC-CAAAATAATTTTCTGCTAATTATAA
1 TTTAAATATGATTAA-AATATTTA-TTACTGATAATAATAATCT--TAATTAAAA
* * * * * * *
13583774 ---GAATTTTATTAAATTATATATT-TTAATTAA-AATATAT-TTAATTATAATTA
1 TTTAAATATGATTAAAATATTTATTACTGA-TAATAATA-ATCTTAATTA-AA--A
13583824 TGTTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTT-ATTAAAA
1 --TTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTAATTAAAA
13583876 TTTAAATA
1 TTTAAATA
13583884 ACAATAACAA
Statistics
Matches: 115, Mismatches: 30, Indels: 38
0.63 0.16 0.21
Matches are distributed among these distances:
47 6 0.05
48 1 0.01
49 7 0.06
50 29 0.25
51 24 0.21
52 5 0.04
53 1 0.01
54 8 0.07
55 26 0.23
56 8 0.07
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (51 bp):
TTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTAATTAAAA
Found at i:13583778 original size:156 final size:156
Alignment explanation
Indices: 13583596--13583923 Score: 611
Period size: 156 Copynumber: 2.1 Consensus size: 156
13583586 AAATAACAAT
*
13583596 AACAAATTTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATA
1 AACAATTTTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATA
13583661 ATAATTATGTTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAA
66 ATAATTATGTTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAA
*
13583726 TAACATTAACAATAATCATTTACCAA
131 TAACAATAACAATAATCATTTACCAA
* *
13583752 AATAATTTTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATT
1 AACAATTTTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATA
13583817 ATAATTATGTTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAA
66 ATAATTATGTTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAA
13583882 TAACAATAACAATAATCATTTACCAA
131 TAACAATAACAATAATCATTTACCAA
*
13583908 AACAATTTTATGCTAA
1 AACAATTTTCTGCTAA
13583924 GGGTATTCTA
Statistics
Matches: 166, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
156 166 1.00
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.43
Consensus pattern (156 bp):
AACAATTTTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATA
ATAATTATGTTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAA
TAACAATAACAATAATCATTTACCAA
Found at i:13583804 original size:18 final size:18
Alignment explanation
Indices: 13583776--13583824 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 18
13583766 AATTATAAGA
13583776 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAATTATAT
13583793 ATTTTAATTAAA--ATAT
1 ATTTTAATTAAATTATAT
13583809 A-TTTAATTATAATTAT
1 ATTTTAATTA-AATTAT
13583825 GTTTAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 8 0.29
16 7 0.25
17 5 0.18
18 8 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTTAATTAAATTATAT
Found at i:13583810 original size:16 final size:16
Alignment explanation
Indices: 13583776--13583830 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
13583766 AATTATAAGA
13583776 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA--ATAT
13583793 ATTTTAATTAAAATAT
1 ATTTTAATTAAAATAT
*
13583809 A-TTTAATTATAAT-T
1 ATTTTAATTAAAATAT
13583823 ATGTTTAA
1 AT-TTTAA
13583831 ATATGATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 2 0.06
15 11 0.32
16 10 0.29
17 5 0.15
18 6 0.18
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
ATTTTAATTAAAATAT
Found at i:13584067 original size:16 final size:16
Alignment explanation
Indices: 13584046--13584113 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
13584036 GATTAGCTAT
13584046 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
13584062 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
13584078 TACACATCTAATCCAA
1 TACACCTCTAATCCAA
13584094 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
13584110 TACA
1 TACA
13584114 GTGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.40, C:0.35, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:13586538 original size:25 final size:25
Alignment explanation
Indices: 13586510--13586568 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
13586500 AAATATATTG
*
13586510 TATATTAT-TGTATATATTTTAGGAA
1 TATATTATATGAATATA-TTTAGGAA
13586535 TATATT-TATGAATATATTTAGGAA
1 TATATTATATGAATATATTTAGGAA
*
13586559 TATTTTATAT
1 TATATTATAT
13586569 ACCTTTCCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 14 0.47
25 16 0.53
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (25 bp):
TATATTATATGAATATATTTAGGAA
Found at i:13586542 original size:12 final size:12
Alignment explanation
Indices: 13586521--13586565 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
13586511 ATATTATTGT
13586521 ATATATTTTAGGA
1 ATATA-TTTAGGA
*
13586534 ATATATTTATGA
1 ATATATTTAGGA
13586546 ATATATTTAGGA
1 ATATATTTAGGA
13586558 ATAT-TTTA
1 ATATATTTA
13586566 TATACCTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 4 0.13
12 21 0.70
13 5 0.17
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (12 bp):
ATATATTTAGGA
Found at i:13586559 original size:24 final size:24
Alignment explanation
Indices: 13586521--13586566 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
13586511 ATATTATTGT
13586521 ATATATTTTAGGAATATATTTATGA
1 ATATATTTTAGGAATAT-TTTATGA
13586546 ATATA-TTTAGGAATATTTTAT
1 ATATATTTTAGGAATATTTTAT
13586567 ATACCTTTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 5 0.24
24 11 0.52
25 5 0.24
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (24 bp):
ATATATTTTAGGAATATTTTATGA
Found at i:13592311 original size:222 final size:222
Alignment explanation
Indices: 13591925--13592325 Score: 516
Period size: 222 Copynumber: 1.8 Consensus size: 222
13591915 GAACGACCTG
* *
13591925 TGCCCGTGTGGCCCACACGCCCAAATTGGCCTTGCCCGTATGCCCCACACGGCCTAACCCAAAGC
1 TGCCCGTGTGGCCCACACGCCCAAATTGGCCTTGCCCGTATGCCCCACACGACCTAACCCAAAAC
* * * * *
13591990 CCACACACCCAACTTGGCCTAGCCCGTGTGACCCATGCGATCACACTCACACTACCATATGACCG
66 CCACACACCCAACTTGGCCTAGCCCGTGTGACCCACGCGACCACACTCACACCACCACACGACCG
* ** * *
13592055 TGTCTTGCGTATGACCATGCTCTCGTCAACCACACAACCGTGTCTCACAAACGACCAGACATACA
131 TGTCTTACGTACAACCATGCCCTCATCAACCACACAACCGTGTCTCACAAACGACCAGACATACA
13592120 CCCGTGTTACAGAATTATTGTCCCACA
196 CCCGTGTTACAGAATTATTGTCCCACA
* * * * * * **
13592147 TGCCCGTGTGGCCCACACGTCTAGATTGGTCTTGCCCGTGTGGCCCACACGACCTGGCCCAAAAC
1 TGCCCGTGTGGCCCACACGCCCAAATTGGCCTTGCCCGTATGCCCCACACGACCTAACCCAAAAC
* * * * * * **
13592212 CCACACGCCCAACTTGGCTTAGCCCGTGT-AGCCCACGTGGCCACACTCATACCACTACACGGTC
66 CCACACACCCAACTTGGCCTAGCCCGTGTGA-CCCACGCGACCACACTCACACCACCACACGACC
**
13592276 GTGTCTTACGTACAACCATGCCCTCATCAACCACACAGTCGTGTCTCACA
130 GTGTCTTACGTACAACCATGCCCTCATCAACCACACAACCGTGTCTCACA
13592326 CACGGCCAAC
Statistics
Matches: 148, Mismatches: 30, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
221 1 0.01
222 147 0.99
ACGTcount: A:0.23, C:0.38, G:0.18, T:0.20
Consensus pattern (222 bp):
TGCCCGTGTGGCCCACACGCCCAAATTGGCCTTGCCCGTATGCCCCACACGACCTAACCCAAAAC
CCACACACCCAACTTGGCCTAGCCCGTGTGACCCACGCGACCACACTCACACCACCACACGACCG
TGTCTTACGTACAACCATGCCCTCATCAACCACACAACCGTGTCTCACAAACGACCAGACATACA
CCCGTGTTACAGAATTATTGTCCCACA
Found at i:13593361 original size:20 final size:21
Alignment explanation
Indices: 13593314--13593361 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
13593304 TACTGTAGTG
*
13593314 AAGAATATGAGAAGAGAGAAA
1 AAGAAAATGAGAAGAGAGAAA
* *
13593335 AA-TAAATGGGAAGA-AGAAA
1 AAGAAAATGAGAAGAGAGAAA
13593354 AAGAAAAT
1 AAGAAAAT
13593362 AAAGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
19 7 0.32
20 13 0.59
21 2 0.09
ACGTcount: A:0.65, C:0.00, G:0.25, T:0.10
Consensus pattern (21 bp):
AAGAAAATGAGAAGAGAGAAA
Found at i:13593375 original size:14 final size:14
Alignment explanation
Indices: 13593351--13593383 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
13593341 TGGGAAGAAG
13593351 AAAAA-GAAAATAA
1 AAAAATGAAAATAA
*
13593364 AGAAATGAAAATAA
1 AAAAATGAAAATAA
13593378 AAAAAT
1 AAAAAT
13593384 TCAAAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (14 bp):
AAAAATGAAAATAA
Found at i:13593856 original size:60 final size:61
Alignment explanation
Indices: 13593782--13593897 Score: 198
Period size: 60 Copynumber: 1.9 Consensus size: 61
13593772 AGTTTACCCC
* * *
13593782 AAAATATAAGAAAAATTATGATAAATTATGATTATAATTTAATTTAAATATTATTAATTGG
1 AAAATATAAGAAAAATTATGATAAAATATAATTATAATTTAATTTAAAAATTATTAATTGG
13593843 AAAATATAA-AAAAATTATGATAAAATATAATTATAATTTAATTTAAAAATTATTA
1 AAAATATAAGAAAAATTATGATAAAATATAATTATAATTTAATTTAAAAATTATTA
13593898 GTTAAAAAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
60 43 0.83
61 9 0.17
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (61 bp):
AAAATATAAGAAAAATTATGATAAAATATAATTATAATTTAATTTAAAAATTATTAATTGG
Found at i:13597198 original size:22 final size:22
Alignment explanation
Indices: 13597170--13597214 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
13597160 AAAAAAACAA
*
13597170 ATCCCTACAAACCAGTTCTATG
1 ATCCCTACAAACCAGCTCTATG
*
13597192 ATCCCTACAAATCAGCTCTATG
1 ATCCCTACAAACCAGCTCTATG
13597214 A
1 A
13597215 ATCAACATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.31, G:0.09, T:0.27
Consensus pattern (22 bp):
ATCCCTACAAACCAGCTCTATG
Done.