Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008420.1 Hibiscus syriacus cultivar Beakdansim tig00111200_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1020524
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 6
Found at i:528975 original size:3 final size:3
Alignment explanation
Indices: 528967--529013 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
528957 ATTAATTATT
*
528967 TAA TAA TAA TAA T-A TAA T-A TAA TAA TAA -AA CAA -AA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
529011 TAA
1 TAA
529014 ATAAAACAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 8 0.20
3 32 0.80
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:528990 original size:13 final size:13
Alignment explanation
Indices: 528967--529017 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
528957 ATTAATTATT
528967 TAATAATAATAATA
1 TAAT-ATAATAATA
528981 TAATATAATAATA
1 TAATATAATAATA
* * *
528994 AAACAAAATAATAA
1 TAATATAATAAT-A
529008 TAATA-AATAA
1 TAATATAATAA
529018 AACAAATGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
13 23 0.74
14 8 0.26
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (13 bp):
TAATATAATAATA
Found at i:528990 original size:16 final size:15
Alignment explanation
Indices: 528969--529016 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
528959 TAATTATTTA
528969 ATAATAATAATATAAT
1 ATAATAATAATA-AAT
* *
528985 ATAATAATAAAACAAA
1 ATAATAATAATA-AAT
529001 ATAATAATAATAAAT
1 ATAATAATAATAAAT
529016 A
1 A
529017 AAACAAATGA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 3 0.11
16 24 0.89
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (15 bp):
ATAATAATAATAAAT
Found at i:529584 original size:113 final size:113
Alignment explanation
Indices: 529323--530229 Score: 1081
Period size: 113 Copynumber: 7.9 Consensus size: 113
529313 ATCTCCTTCT
** * *
529323 GTGATAGAA-TCAAAC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCATTATTCA
1 GTGAT-GAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
* * **
529386 GACGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAATTGATGTTGATCTATGTCCTTCT
65 GATGAGTTCTTCTCATTATGAACTTTCTCTGG---AA---ATGTTGATCCA--T-C--AA
* *** **
529446 GTGAT-AGAGTCATGTAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
1 GTGATGA-ATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
* * **
529510 GATGAGTTCTTCTCATTATGAACTTTCTCTGAAAAAGTTGATCCATTGA
65 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCATCAA
* * *
529559 GTGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAA
1 GTGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
* * * *
529624 ACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAATGCTGATCCATCAA
66 ATGAGTTCTTCTCATTATGAACT-TTCTCTGGAAATGTTGATCCATCAA
* *
529672 ATGATGAATTCAAACAAAAGGTTGAACAAATTCTTTTCATTATGAACTTCTTCTTCCTTCTTCAG
1 GTGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
529737 ATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCATCAA
66 ATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCATCAA
* ** * ** *
529785 GTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTTTTCAG
1 GTGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
* **
529850 ATGAGTTCTTCTCATTATGAAC-TCCTTCTGGAAATGTTGATCCATTGA
66 ATGAGTTCTTCTCATTATGAACTTTC-TCTGGAAATGTTGATCCATCAA
* ** *
529898 GTGATTAATTCAAACAAAAAATTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAG
1 GTGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
* * * *
529963 ACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAATGTTGATCAATCAA
66 ATGAGTTCTTCTCATTATGAACT-TTCTCTGGAAATGTTGATCCATCAA
* * * *
530011 ATGATGAATTCAAACAAAAGCTTGGACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAA
1 GTGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
* *
530076 ATGACTTCTTCTCATTTTGAACTTTCTCTGGAAATGTTGATCCATCAA
66 ATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCATCAA
* ** * ** *
530124 GTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAG
1 GTGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
*
530189 ATGAGTTCTTCTCATTATGAAC-TCCTTCTGGAAATGTTGAT
66 ATGAGTTCTTCTCATTATGAACTTTC-TCTGGAAATGTTGAT
530230 TCATTATGAT
Statistics
Matches: 679, Mismatches: 94, Indels: 32
0.84 0.12 0.04
Matches are distributed among these distances:
112 8 0.01
113 568 0.84
114 3 0.00
115 2 0.00
116 1 0.00
118 9 0.01
121 3 0.00
122 1 0.00
123 8 0.01
124 76 0.11
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (113 bp):
GTGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
ATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCATCAA
Found at i:529865 original size:339 final size:340
Alignment explanation
Indices: 529324--530234 Score: 1377
Period size: 339 Copynumber: 2.7 Consensus size: 340
529314 TCTCCTTCTG
** * *
529324 TGATAGAA-TCAAAC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCATTATTCAG
1 TGAT-GAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
* * ** *
529387 ACGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAATTGATGTTGATCTATGTCCTTCTGTGATA
65 ATGAGTTCTTCTCATTATGAACTTTCTCTGG---AA---ATGTTGATCCA--T-C--AAGTGATG
* * * *
529452 GA-GTCATGTAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
119 GATTTGA-GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTTTTCAGATGAG
* *
529516 TTCTTCTCATTATGAACTTTC-TCTGAAAAAGTTGATCCATTGAGTGATGAATTCAAACAAAAAG
183 TTCTTCTCATTATGAACTTCCTTCTGAAAAAGTTGATCCATTGAGTGATGAATTCAAACAAAAAA
529580 TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAAACGAGTTCTTCTCATTATGAA
248 TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAAACGAGTTCTTCTCATTATGAA
*
529645 CTCTACCTGGCAATGCTGATCCATCAAA
313 CTCTACCTGGCAATGCTGATCAATCAAA
*
529673 TGATGAATTCAAACAAAAGGTTGAACAAATTCTTTTCATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
529738 TGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGGATTTGAGCAAA
66 TGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGGATTTGAGCAAA
529803 AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTTTTCAGATGAGTTCTTCTCATTAT
131 AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTTTTCAGATGAGTTCTTCTCATTAT
* * *
529868 GAAC-TCCTTCTGGAAATGTTGATCCATTGAGTGATTAATTCAAACAAAAAATTGAACAAATTCT
196 GAACTTCCTTCTGAAAAAGTTGATCCATTGAGTGATGAATTCAAACAAAAAATTGAACAAATTCT
*
529932 TCTCATTATGAATTTCTTCTTCCTTCTTCAGACGAGTTCTTCTCATTATGAACTCTACCTGGCAA
261 TCTCATTATGAATTTCTTCTTCCTTCTTCAAACGAGTTCTTCTCATTATGAACTCTACCTGGCAA
*
529997 TGTTGATCAATCAAA
326 TGCTGATCAATCAAA
* * *
530012 TGATGAATTCAAACAAAAGCTTGGACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAA
1 TGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
* *
530077 TGACTTCTTCTCATTTTGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGGATTTGAGCAAA
66 TGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGGATTTGAGCAAA
530142 AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTT-AGATGAGTTCTTCTCATTA
131 AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTT-TTTCAGATGAGTTCTTCTCATTA
* * *
530206 TGAAC-TCCTTCTGGAAATGTTGATTCATT
195 TGAACTTCCTTCTGAAAAAGTTGATCCATT
530235 ATGATAGATT
Statistics
Matches: 528, Mismatches: 29, Indels: 20
0.92 0.05 0.03
Matches are distributed among these distances:
338 2 0.00
339 420 0.80
340 5 0.01
341 1 0.00
342 1 0.00
344 10 0.02
347 2 0.00
348 3 0.01
349 10 0.02
350 74 0.14
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (340 bp):
TGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
TGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGGATTTGAGCAAA
AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTTTTCAGATGAGTTCTTCTCATTAT
GAACTTCCTTCTGAAAAAGTTGATCCATTGAGTGATGAATTCAAACAAAAAATTGAACAAATTCT
TCTCATTATGAATTTCTTCTTCCTTCTTCAAACGAGTTCTTCTCATTATGAACTCTACCTGGCAA
TGCTGATCAATCAAA
Found at i:531109 original size:54 final size:54
Alignment explanation
Indices: 531006--531155 Score: 138
Period size: 54 Copynumber: 2.9 Consensus size: 54
530996 TGACTGGTTC
* * ** *
531006 GTAAAACATTTGTCAATACATTCATCATCTCATGTGGTTTATGCTCAGATGCTA
1 GTAAAACATTTGACAACACATTCATCATCTCATGTGACTTATGCACAGATGCTA
* * *
531060 GTAAAACATTTGACAACACATTCATCCTTTTC-TGTGACTTCTGCACAGATGC--
1 GTAAAACATTTGACAACACATTCAT-CATCTCATGTGACTTATGCACAGATGCTA
* *
531112 -T-----ATTTGATAACACATTCATCATTTCATGTGACTTATGCACAGAT
1 GTAAAACATTTGACAACACATTCATCATCTCATGTGACTTATGCACAGAT
531156 TTCTGGTCAT
Statistics
Matches: 83, Mismatches: 11, Indels: 12
0.78 0.10 0.11
Matches are distributed among these distances:
45 5 0.06
46 34 0.41
51 1 0.01
54 39 0.47
55 4 0.05
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (54 bp):
GTAAAACATTTGACAACACATTCATCATCTCATGTGACTTATGCACAGATGCTA
Found at i:531142 original size:46 final size:46
Alignment explanation
Indices: 531067--531155 Score: 135
Period size: 46 Copynumber: 1.9 Consensus size: 46
531057 CTAGTAAAAC
* *
531067 ATTTGACAACACATTCATCCTTTTCTGTGACTTCTGCACAGATGCT
1 ATTTGACAACACATTCATCCATTTCTGTGACTTATGCACAGATGCT
*
531113 ATTTGATAACACATTCAT-CATTTCATGTGACTTATGCACAGAT
1 ATTTGACAACACATTCATCCATTTC-TGTGACTTATGCACAGAT
531156 TTCTGGTCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
45 5 0.13
46 34 0.87
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.37
Consensus pattern (46 bp):
ATTTGACAACACATTCATCCATTTCTGTGACTTATGCACAGATGCT
Found at i:535728 original size:7 final size:7
Alignment explanation
Indices: 535716--535769 Score: 76
Period size: 7 Copynumber: 7.7 Consensus size: 7
535706 TGATTCAAAT
535716 TTTTTCC
1 TTTTTCC
535723 TTTTTCC
1 TTTTTCC
535730 TTTTTCC
1 TTTTTCC
535737 TTTTT--
1 TTTTTCC
535742 TTTCTTCC
1 TTT-TTCC
535750 TTTTTTCC
1 -TTTTTCC
535758 TTTTTCC
1 TTTTTCC
535765 TTTTT
1 TTTTT
535770 TTTATTTTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
5 3 0.07
6 2 0.05
7 31 0.72
8 4 0.09
9 3 0.07
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTCC
Found at i:535759 original size:28 final size:26
Alignment explanation
Indices: 535715--535772 Score: 98
Period size: 28 Copynumber: 2.2 Consensus size: 26
535705 TTGATTCAAA
535715 TTTTTTCCTTTTTCCTTTTTCCTTTT
1 TTTTTTCCTTTTTCCTTTTTCCTTTT
535741 TTTTCTTCCTTTTTTCCTTTTTCCTTTT
1 TTTT-TTCC-TTTTTCCTTTTTCCTTTT
535769 TTTT
1 TTTT
535773 ATTTTTATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 4 0.13
27 4 0.13
28 22 0.73
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (26 bp):
TTTTTTCCTTTTTCCTTTTTCCTTTT
Found at i:538368 original size:36 final size:34
Alignment explanation
Indices: 538316--538384 Score: 93
Period size: 36 Copynumber: 2.0 Consensus size: 34
538306 CAAAGATGGA
*
538316 AATGCAAAAATGAAAATGTAAATACAAACGTAAG
1 AATGCAAAAATGAAAATGCAAATACAAACGTAAG
* *
538350 AATGCAAAAAATGCAAAATGCAAATGCAAATGTAA
1 AATGC-AAAAATG-AAAATGCAAATACAAACGTAA
538385 ATGTAAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 5 0.17
35 7 0.23
36 18 0.60
ACGTcount: A:0.58, C:0.10, G:0.14, T:0.17
Consensus pattern (34 bp):
AATGCAAAAATGAAAATGCAAATACAAACGTAAG
Found at i:538476 original size:15 final size:14
Alignment explanation
Indices: 538443--538480 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
538433 ATAAAAGTAT
538443 AAATGCAAAATGAA
1 AAATGCAAAATGAA
*
538457 AAATGCAAAGATGCA
1 AAATGCAAA-ATGAA
538472 AAATGCAAA
1 AAATGCAAA
538481 TATACAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.61, C:0.11, G:0.16, T:0.13
Consensus pattern (14 bp):
AAATGCAAAATGAA
Found at i:541262 original size:29 final size:30
Alignment explanation
Indices: 541208--541266 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
541198 ATTGCAATTA
541208 AATAGTGACTAAAACATATAAAATTAAAAT
1 AATAGTGACTAAAACATATAAAATTAAAAT
* *
541238 AATAG-GATTAAAATATA-AAATATTAAAAT
1 AATAGTGACTAAAACATATAAA-ATTAAAAT
541267 TTACAACCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 3 0.12
29 18 0.69
30 5 0.19
ACGTcount: A:0.61, C:0.03, G:0.07, T:0.29
Consensus pattern (30 bp):
AATAGTGACTAAAACATATAAAATTAAAAT
Found at i:542603 original size:3 final size:3
Alignment explanation
Indices: 542595--542640 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
542585 ATTAGTTATT
*
542595 TAA TAA TAA TAA T-A TAA T-A TAA TAA TAA -ACA AAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA
542638 TAA
1 TAA
542641 ATAAAACAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
2 5 0.13
3 32 0.84
4 1 0.03
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:542647 original size:23 final size:20
Alignment explanation
Indices: 542595--542650 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 20
542585 ATTAGTTATT
* *
542595 TAATAAT-AATAATATAATA
1 TAATAATAAACAAAATAATA
542614 TAATAATAAACAAAATAATAA
1 TAATAATAAACAAAATAAT-A
542635 TAATAAATAAAACAAA
1 TAAT-AAT-AAACAAA
542651 TGGAATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 7 0.23
20 9 0.29
21 5 0.16
22 3 0.10
23 7 0.23
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.27
Consensus pattern (20 bp):
TAATAATAAACAAAATAATA
Found at i:547695 original size:20 final size:19
Alignment explanation
Indices: 547655--547702 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
547645 CTAGTGGCAT
547655 AATTTAAATTATAAATCAA
1 AATTTAAATTATAAATCAA
* *
547674 AATTTAATATTATAATTGAA
1 AATTTAA-ATTATAAATCAA
547694 AATATTAAA
1 AAT-TTAAA
547703 AATTCAATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 7 0.28
20 14 0.56
21 4 0.16
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (19 bp):
AATTTAAATTATAAATCAA
Found at i:551460 original size:16 final size:18
Alignment explanation
Indices: 551441--551473 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
551431 TTAATATTTA
551441 TAAT-ATTT-TTATTTTT
1 TAATAATTTATTATTTTT
551457 TAATAATTTATTATTTT
1 TAATAATTTATTATTTT
551474 ATAGCTTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 4 0.27
18 7 0.47
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TAATAATTTATTATTTTT
Found at i:551586 original size:16 final size:16
Alignment explanation
Indices: 551533--551598 Score: 57
Period size: 16 Copynumber: 4.3 Consensus size: 16
551523 TTTTAAATTC
*
551533 TTTTAATAATTTAAT-
1 TTTTAATATTTTAATA
*
551548 TTTT-A-ATTTTAGTA
1 TTTTAATATTTTAATA
**
551562 TTTGCATATTTTAATA
1 TTTTAATATTTTAATA
*
551578 TTTTAATATTTAAATA
1 TTTTAATATTTTAATA
*
551594 ATTTA
1 TTTTA
551599 TACTTAAAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
13 6 0.15
14 4 0.10
15 5 0.12
16 25 0.62
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (16 bp):
TTTTAATATTTTAATA
Found at i:556316 original size:29 final size:29
Alignment explanation
Indices: 556276--556332 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
556266 GAAATTAAGG
* *
556276 TTTTAAAGTTTT-AGGGTTTTTTTAAATT
1 TTTTAAAGTTTTGAGGGGTTTTTAAAATT
*
556304 TTTTGAAATTTTTGAGGGGTTTTTAAAAT
1 TTTT-AAAGTTTTGAGGGGTTTTTAAAAT
556333 AAAATTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 4 0.17
29 7 0.29
30 13 0.54
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.56
Consensus pattern (29 bp):
TTTTAAAGTTTTGAGGGGTTTTTAAAATT
Found at i:556558 original size:15 final size:15
Alignment explanation
Indices: 556538--556568 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
556528 CTTCACAATG
556538 ATATTAGTGATAAAA
1 ATATTAGTGATAAAA
*
556553 ATATTATTGATAAAA
1 ATATTAGTGATAAAA
556568 A
1 A
556569 GAAATGTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (15 bp):
ATATTAGTGATAAAA
Found at i:557844 original size:20 final size:21
Alignment explanation
Indices: 557809--557858 Score: 84
Period size: 20 Copynumber: 2.4 Consensus size: 21
557799 CAAAAGTTCT
*
557809 AGAATAAACTTTTGTTGAATG
1 AGAATAAGCTTTTGTTGAATG
557830 AGAATAAGC-TTTGTTGAATG
1 AGAATAAGCTTTTGTTGAATG
557850 AGAATAAGC
1 AGAATAAGC
557859 GACCTATGGC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 20 0.71
21 8 0.29
ACGTcount: A:0.40, C:0.06, G:0.22, T:0.32
Consensus pattern (21 bp):
AGAATAAGCTTTTGTTGAATG
Found at i:560613 original size:21 final size:21
Alignment explanation
Indices: 560587--560626 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
560577 TTCTTACACA
560587 ACTTATCTAATAT-CCTTTTAT
1 ACTTAT-TAATATACCTTTTAT
*
560608 ACTTATTTATATACCTTTT
1 ACTTATTAATATACCTTTT
560627 TCCTCAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.28, C:0.17, G:0.00, T:0.55
Consensus pattern (21 bp):
ACTTATTAATATACCTTTTAT
Found at i:561054 original size:18 final size:18
Alignment explanation
Indices: 561031--561083 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
561021 ACTGTATATT
*
561031 TGTCCCGAAAGACCACTA
1 TGTCCCGAAGGACCACTA
561049 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
561067 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
561084 CCTTAAGAGC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.28, C:0.34, G:0.21, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:569718 original size:2 final size:2
Alignment explanation
Indices: 569713--569738 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
569703 TTTTTAAATA
569713 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
569739 TATTTAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:572295 original size:3 final size:3
Alignment explanation
Indices: 572289--572343 Score: 67
Period size: 3 Copynumber: 18.0 Consensus size: 3
572279 CATTTAAATT
* *
572289 TTA TTA TTA TTA TTA -AA TTTA TTA TTA CTAA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA -TTA TTA TTA TTA TTA TTA
572335 TTA TTA TTA
1 TTA TTA TTA
572344 ATATATATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 1 0.02
3 41 0.91
4 3 0.07
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:572322 original size:25 final size:25
Alignment explanation
Indices: 572294--572345 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
572284 AAATTTTATT
572294 ATTATTATTAA-ATTTATTATTACTA
1 ATTATTATTAATA-TTATTATTACTA
* *
572319 ATTATTATTATTATTATTATTATTA
1 ATTATTATTAATATTATTATTACTA
572344 AT
1 AT
572346 ATATATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 23 0.96
26 1 0.04
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (25 bp):
ATTATTATTAATATTATTATTACTA
Found at i:572351 original size:2 final size:2
Alignment explanation
Indices: 572344--572399 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
572334 ATTATTATTA
572344 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
572386 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
572400 TACAAGCCCA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:573862 original size:11 final size:11
Alignment explanation
Indices: 573787--573862 Score: 50
Period size: 11 Copynumber: 6.5 Consensus size: 11
573777 TTTCATTTTA
573787 ATTATTATTATT
1 ATTATT-TTATT
573799 -TTATTTTATT
1 ATTATTTTATT
573809 ATTACTTTTGA-T
1 ATTA-TTTT-ATT
573821 A-TATGTTTAAATT
1 ATTAT-TTT--ATT
* *
573834 ATTATCTTCATG
1 ATTAT-TTTATT
573846 ATTATTTTATT
1 ATTATTTTATT
573857 ATTATT
1 ATTATT
573863 ATTAAGTTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
10 6 0.12
11 23 0.45
12 14 0.27
13 3 0.06
14 5 0.10
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (11 bp):
ATTATTTTATT
Found at i:574694 original size:20 final size:21
Alignment explanation
Indices: 574671--574722 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
574661 AGAAATTAAA
574671 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTAAATTTTT
* *
574691 AATTCTTTTCTTTCAAATTTTT
1 AATTCATTTATTT-AAATTTTT
574713 -ATT-ATTTATT
1 AATTCATTTATT
574723 ATTTTTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 16 0.62
21 3 0.12
22 7 0.27
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (21 bp):
AATTCATTTATTTAAATTTTT
Found at i:576835 original size:14 final size:14
Alignment explanation
Indices: 576799--576837 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
576789 TTCATACATG
576799 CATTTT-CATTTTA
1 CATTTTGCATTTTA
*
576812 CATCTTTGCATTTTT
1 CAT-TTTGCATTTTA
576827 CATTTTGCATT
1 CATTTTGCATT
576838 CATACTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 3 0.13
14 11 0.48
15 9 0.39
ACGTcount: A:0.18, C:0.18, G:0.05, T:0.59
Consensus pattern (14 bp):
CATTTTGCATTTTA
Found at i:581707 original size:93 final size:94
Alignment explanation
Indices: 581588--581773 Score: 322
Period size: 93 Copynumber: 2.0 Consensus size: 94
581578 CCAATCATTG
581588 GATTTGAAAGATGAATTTGCTCATAGTAGAAAATAAGGA-ACTCAATAGCATCTTCTGG-GTGTT
1 GATTTGAAAGATGAATTTGCTCATAGTAG-AAATAAGGAGACTCAATAGCATCTTCTGGAGTGTT
*
581651 TTTTGAGTTATCTGATCTGGTTTGGTATTT
65 CTTTGAGTTATCTGATCTGGTTTGGTATTT
*
581681 GATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACTCAATATCATCTTCTGGAAGTGTT
1 GATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACTCAATAGCATCTTCTGG-AGTGTT
581746 CTTTGAGTTATCTGATCTGGTTTGGTAT
65 CTTTGAGTTATCTGATCTGGTTTGGTAT
581774 GAAACCACAG
Statistics
Matches: 88, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
92 9 0.10
93 47 0.53
95 32 0.36
ACGTcount: A:0.28, C:0.10, G:0.23, T:0.39
Consensus pattern (94 bp):
GATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACTCAATAGCATCTTCTGGAGTGTTC
TTTGAGTTATCTGATCTGGTTTGGTATTT
Found at i:581880 original size:115 final size:115
Alignment explanation
Indices: 581681--582154 Score: 860
Period size: 115 Copynumber: 4.1 Consensus size: 115
581671 TTTGGTATTT
*
581681 GATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACTCAATATCATCTTCTGGAAGTGTT
1 GATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACTCAATAGCATCTTCTGGAAGTGTT
581746 CTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAATCATTG
66 CTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAATCATTG
581796 GATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACTCAATAGCATCTTCTGGAAGTGTT
1 GATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACTCAATAGCATCTTCTGGAAGTGTT
*
581861 TTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAATCATTG
66 CTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAATCATTG
581911 GATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACTCAATAGCATCTTCTGGAAGTGTT
1 GATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACTCAATAGCATCTTCTGGAAGTGTT
581976 CTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAATCATTG
66 CTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAATCATTG
* *
582026 GATTTGAAAGATGAATTTGTTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTT
1 GATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACTCAATAGCATCTTCTGGAAGTGTT
* * *
582091 CTTTGAGTTATCTGATCTGGTTCGGTATGAATCC-TAGAACCAATCATTG
66 CTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAATCATTG
* *
582140 GAATTGAAAGGTGAA
1 GATTTGAAAGATGAA
582155 CTACATGATT
Statistics
Matches: 349, Mismatches: 10, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
114 27 0.08
115 322 0.92
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.32
Consensus pattern (115 bp):
GATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACTCAATAGCATCTTCTGGAAGTGTT
CTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAATCATTG
Found at i:584363 original size:54 final size:54
Alignment explanation
Indices: 584274--584479 Score: 228
Period size: 54 Copynumber: 3.9 Consensus size: 54
584264 AGAAATCTTG
* * * *
584274 GCAGAAGCCAC-AGAAAAGGATGAATGTGTTGTCAAACGCTTTATGAACGTCTGA
1 GCAGAAACCACAAG-AAAGGATGAATGTGTTGTCAAATGTTTTATGAACATCTGA
* **
584328 GCAAAAACCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTACAAACATCTGA
1 GCAGAAACCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTATGAACATCTGA
* *
584382 GCAGAAGCCAC-AGAAAAGGATGAATGTGTTGTCAAGTG-TTT-T--ACATCTCGA
1 GCAGAAACCACAAG-AAAGGATGAATGTGTTGTCAAATGTTTTATGAACATCT-GA
* * *
584433 -CAGAAACCACAGGAAAAGATGAATGTATTGTCAAATGTTTTATGAAC
1 GCAGAAACCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTATGAAC
584480 CAGTGATTAT
Statistics
Matches: 128, Mismatches: 16, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
50 36 0.28
51 6 0.05
52 1 0.01
53 5 0.04
54 78 0.61
55 2 0.02
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.24
Consensus pattern (54 bp):
GCAGAAACCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTATGAACATCTGA
Found at i:585646 original size:76 final size:76
Alignment explanation
Indices: 585546--586113 Score: 1055
Period size: 76 Copynumber: 7.5 Consensus size: 76
585536 ACTATTTCCC
*
585546 TCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
585611 AAACCTTAGGG
66 AAGCCTTAGGG
585622 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
585687 AAGCCTTCGGG
66 AAGCCTTAGGG
585698 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
585763 AAGCCTTAGGG
66 AAGCCTTAGGG
585774 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
585839 AAGCCTCAGGG
66 AAGCCTTAGGG
*
585850 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTTATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
585915 AAGCCTTAGGG
66 AAGCCTTAGGG
585926 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
585991 AAGCCTTAGGG
66 AAGCCTTAGGG
*
586002 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
586067 AAGCCTTCGGG
66 AAGCCTTAGGG
* *
586078 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAA
586114 CATTTCCATC
Statistics
Matches: 480, Mismatches: 12, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 480 1.00
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.35
Consensus pattern (76 bp):
TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
AAGCCTTAGGG
Found at i:586248 original size:3 final size:3
Alignment explanation
Indices: 586240--586306 Score: 75
Period size: 3 Copynumber: 22.3 Consensus size: 3
586230 CATTTAAATT
* * *
586240 TTA TTA TTA TTA TTA -AA TTTA TTA TTA CTAA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA -TTA TTA TTA TTA TTA TTA
586286 TTA TTA TTA TTA TTA -TA TTA T
1 TTA TTA TTA TTA TTA TTA TTA T
586307 ATATATATAT
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 3 0.06
3 48 0.89
4 3 0.06
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:586311 original size:2 final size:2
Alignment explanation
Indices: 586299--586339 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
586289 TTATTATTAT
586299 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
586340 CAAGCCCAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:586394 original size:21 final size:21
Alignment explanation
Indices: 586356--586395 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
586346 CAAAGGACCC
*
586356 GGAGGCCCGTTTTACAAATAT
1 GGAGGCCCGTTATACAAATAT
586377 GGAGGCCCGGTTAT-CAAAT
1 GGAGGCCC-GTTATACAAAT
586396 CCCAAACCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.25
Consensus pattern (21 bp):
GGAGGCCCGTTATACAAATAT
Found at i:587807 original size:20 final size:22
Alignment explanation
Indices: 587719--587807 Score: 73
Period size: 20 Copynumber: 4.0 Consensus size: 22
587709 GTTTTCTTTC
587719 ATTTTAATTATTA-TTATT-TT
1 ATTTTAATTATTACTTATTATT
587739 ATTTT-ATTATTACTT-TTGATAT
1 ATTTTAATTATTACTTATT-AT-T
*
587761 ATGTTTAAATTATTATCTTCATGATT
1 AT-TTT-AATTATTA-CTT-ATTATT
587787 ATTTT-ATTATTA-TTATTATT
1 ATTTTAATTATTACTTATTATT
587807 A
1 A
587808 AGTTATATAA
Statistics
Matches: 57, Mismatches: 2, Indels: 20
0.72 0.03 0.25
Matches are distributed among these distances:
19 9 0.16
20 13 0.23
21 3 0.05
22 3 0.05
23 10 0.18
25 10 0.18
26 6 0.11
27 2 0.04
28 1 0.02
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.63
Consensus pattern (22 bp):
ATTTTAATTATTACTTATTATT
Found at i:589944 original size:39 final size:39
Alignment explanation
Indices: 589894--590023 Score: 163
Period size: 39 Copynumber: 3.3 Consensus size: 39
589884 AGGGGGTGCA
*
589894 CCATTGGCCCCATCGATAGCAACAGTGGTAGGATCGGTG
1 CCATTGGCCCCATCGATAGCAACAGTGGTAGCATCGGTG
* * * *
589933 CCATTGGCCCCAACAATAGCAGCAGTGGTAGCATCGGCG
1 CCATTGGCCCCATCGATAGCAACAGTGGTAGCATCGGTG
* * *
589972 CCATTGGCCCCATTGGTAGCAGA-AGTGGTAGCATCGGTA
1 CCATTGGCCCCATCGATAGCA-ACAGTGGTAGCATCGGTG
*
590011 CCACTGGCCCCAT
1 CCATTGGCCCCAT
590024 TGGTAGCATC
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
39 77 1.00
ACGTcount: A:0.23, C:0.29, G:0.28, T:0.19
Consensus pattern (39 bp):
CCATTGGCCCCATCGATAGCAACAGTGGTAGCATCGGTG
Found at i:598225 original size:3 final size:3
Alignment explanation
Indices: 598217--598284 Score: 118
Period size: 3 Copynumber: 22.7 Consensus size: 3
598207 TTTTTACCCA
598217 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
598265 TAT CAT TAA TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
598285 AATATATATT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:599728 original size:13 final size:13
Alignment explanation
Indices: 599712--599758 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
599702 ATATAATAAA
599712 TAAATATTTATTT
1 TAAATATTTATTT
*
599725 TAAATAAATTATTT
1 TAAAT-ATTTATTT
599739 T-AATATTTAGTTT
1 TAAATATTTA-TTT
*
599752 TCAATAT
1 TAAATAT
599759 CAAAGAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 4 0.14
13 12 0.41
14 13 0.45
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:611095 original size:14 final size:14
Alignment explanation
Indices: 611076--611106 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
611066 ATGCTTGAAG
611076 AAAAGAAAGAAAAA
1 AAAAGAAAGAAAAA
*
611090 AAAAGAGAGAAAAA
1 AAAAGAAAGAAAAA
611104 AAA
1 AAA
611107 GGAGGGTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAGAAAGAAAAA
Found at i:612383 original size:83 final size:83
Alignment explanation
Indices: 612244--612550 Score: 596
Period size: 83 Copynumber: 3.7 Consensus size: 83
612234 CATTAACTAA
612244 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGA
1 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGA
612309 ACCAATCATTGAATTTAG
66 ACCAATCATTGAATTTAG
612327 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGA
1 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGA
612392 ACCAATCATTGAATTTAG
66 ACCAATCATTGAATTTAG
* *
612410 AAGATGAATGTGCTCATATCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGGTTAGACAGA
1 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGA
612475 ACCAATCATTGAATTTAG
66 ACCAATCATTGAATTTAG
612493 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
1 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
612551 TGGTAGGAAC
Statistics
Matches: 220, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 220 1.00
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (83 bp):
AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGA
ACCAATCATTGAATTTAG
Found at i:613482 original size:113 final size:113
Alignment explanation
Indices: 613286--614188 Score: 1632
Period size: 113 Copynumber: 8.0 Consensus size: 113
613276 AAACTATTAT
** * *
613286 TTGATGGATTGACATTT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAATAAGGAAGAAG
1 TTGATGGATT-ATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
* * *
613350 AAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-ACTTGAATCCATCAT
65 AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTC-TGAATTCATCAC
* * *
613399 TTGATGGATCATCATTT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 TTGATGGATTAT-TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
**
613463 AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAC
65 AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCAC
613512 TTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
613577 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCAC
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCAC
613625 TTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
613690 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCAC
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCAC
613738 TTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
613803 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCAC
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCAC
613851 TTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
613916 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCAC
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCAC
*
613964 TTGATGGATTATTTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
614029 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCAC
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCAC
*
614077 CTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
614142 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCA
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCA
614189 TCTAAAGAAA
Statistics
Matches: 773, Mismatches: 14, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
112 4 0.01
113 768 0.99
114 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (113 bp):
TTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCAC
Found at i:614484 original size:3 final size:3
Alignment explanation
Indices: 614476--614521 Score: 74
Period size: 3 Copynumber: 15.0 Consensus size: 3
614466 TTTTACCCAT
*
614476 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
614522 AATATATATT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:615965 original size:13 final size:13
Alignment explanation
Indices: 615949--615995 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
615939 ATATAATAAA
615949 TAAATATTTATTT
1 TAAATATTTATTT
*
615962 TAAATAAATTATTT
1 TAAAT-ATTTATTT
615976 T-AATATTTAGTTT
1 TAAATATTTA-TTT
*
615989 TCAATAT
1 TAAATAT
615996 CAAAGAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 4 0.14
13 12 0.41
14 13 0.45
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:627306 original size:15 final size:15
Alignment explanation
Indices: 627286--627316 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
627276 ATGCTTGAAG
627286 AAAAGAAAGAAAAAA
1 AAAAGAAAGAAAAAA
*
627301 AAAAGAGAGAAAAAA
1 AAAAGAAAGAAAAAA
627316 A
1 A
627317 GAAAAAGGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAAGAAAGAAAAAA
Found at i:628593 original size:83 final size:83
Alignment explanation
Indices: 628454--628763 Score: 611
Period size: 83 Copynumber: 3.7 Consensus size: 83
628444 AAACATTAAC
628454 TAGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAC
1 TAGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAC
628519 AGAACCAATCATTGAATT
66 AGAACCAATCATTGAATT
628537 TAGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAC
1 TAGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAC
628602 AGAACCAATCATTGAATT
66 AGAACCAATCATTGAATT
*
628620 TAGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGGTTAGAC
1 TAGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAC
628685 AGAACCAATCATTGAATT
66 AGAACCAATCATTGAATT
628703 TAGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
1 TAGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
628764 TGGTAGGAAC
Statistics
Matches: 225, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 225 1.00
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (83 bp):
TAGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAC
AGAACCAATCATTGAATT
Found at i:629697 original size:113 final size:113
Alignment explanation
Indices: 629501--630402 Score: 1623
Period size: 113 Copynumber: 8.0 Consensus size: 113
629491 AAACTATTAT
** *
629501 TTGATGGATTGACATTT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 TTGATGGATT-ATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
* * *
629565 AAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-ACTTGAATCCATCAT
65 AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTC-TGAATTCATCAC
* * *
629614 TTGATGGATCATCATTT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 TTGATGGATTAT-TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
**
629678 AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAC
65 AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCAC
629727 TTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
629792 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCAC
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCAC
629840 TTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
629905 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCAC
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCAC
629953 TTGATGGATTA-TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
630017 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCAC
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCAC
*
630065 TTGATGGATTAGTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
630130 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCAC
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCAC
630178 TTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
*
630243 AGTTCATAATGAGAAGAATTTGTTTAACCTTTTGTCTGAATTCATCAC
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCAC
*
630291 CTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
630356 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCA
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCA
630403 TCTAAAGAAA
Statistics
Matches: 771, Mismatches: 14, Indels: 8
0.97 0.02 0.01
Matches are distributed among these distances:
112 116 0.15
113 654 0.85
114 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (113 bp):
TTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCAC
Found at i:630360 original size:451 final size:451
Alignment explanation
Indices: 629501--630402 Score: 1632
Period size: 451 Copynumber: 2.0 Consensus size: 451
629491 AAACTATTAT
629501 TTGATGGATTGACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATTGACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
*
629566 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCATCATTTGATGGATCATCATTT
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCATCACTTGATGGATCAT-ATTT
629631 CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
130 CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
629696 ATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAA
195 ATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAA
629761 TGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
260 TGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
*
629826 TCTGAATTCATCACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTG
325 TCTGAATTCATCACCTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTG
629891 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCAC
390 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCAC
* *
629953 TTGATGGATT-A-TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 TTGATGGATTGACATTT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
* * *
630016 AAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-GTCTGAATTCATCACTTGATGGATTAGT-T
65 AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACT-TGAATCCATCACTTGATGGATCA-TAT
*
630079 TTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
128 TT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
**
630144 AGAATTTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTATTTTTGCCAGAGAAGGTTCA
192 AGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTATTTTTGCCAGAGAAGGTTCA
*
630209 TAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTT
257 TAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTT
630274 TTGTCTGAATTCATCACCTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCAT
322 TTGTCTGAATTCATCACCTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCAT
630339 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCA
387 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCA
630403 TCTAAAGAAA
Statistics
Matches: 435, Mismatches: 11, Indels: 9
0.96 0.02 0.02
Matches are distributed among these distances:
450 7 0.02
451 417 0.96
452 11 0.03
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (451 bp):
TTGATGGATTGACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCATCACTTGATGGATCATATTTC
CAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
TTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAAT
GAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT
CTGAATTCATCACCTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCAC
Found at i:630697 original size:3 final size:3
Alignment explanation
Indices: 630689--630783 Score: 172
Period size: 3 Copynumber: 31.7 Consensus size: 3
630679 TTTTTACCCA
630689 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
630737 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAA TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
630784 AATATATATT
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 88 1.00
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:639423 original size:15 final size:15
Alignment explanation
Indices: 639405--639434 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
639395 GGCCAAACAT
639405 TAAAAGAGAGTAACC
1 TAAAAGAGAGTAACC
639420 TAAAAGAGAGTAACC
1 TAAAAGAGAGTAACC
639435 GTTGGGGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.13, G:0.20, T:0.13
Consensus pattern (15 bp):
TAAAAGAGAGTAACC
Found at i:639942 original size:20 final size:22
Alignment explanation
Indices: 639919--639963 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
639909 TTTAAATGTT
639919 ATAA-TAAA-ATATTAATTATG
1 ATAATTAAATATATTAATTATG
639939 ATAATTAAATTATATTAATTATG
1 ATAATTAAA-TATATTAATTATG
639962 AT
1 AT
639964 TCTTATGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.18
21 4 0.18
23 14 0.64
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (22 bp):
ATAATTAAATATATTAATTATG
Found at i:640159 original size:18 final size:18
Alignment explanation
Indices: 640138--640206 Score: 74
Period size: 18 Copynumber: 4.0 Consensus size: 18
640128 TATACCGTTT
640138 ATATATACTATATAGTTA
1 ATATATACTATATAGTTA
640156 ATATATACTA-AT-G--A
1 ATATATACTATATAGTTA
* *
640170 ACTATATAATATATAGTTT
1 A-TATATACTATATAGTTA
*
640189 ATATATACTATTTAGTTA
1 ATATATACTATATAGTTA
640207 GAGTAAATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
14 2 0.05
15 8 0.20
16 3 0.07
17 3 0.07
18 24 0.59
19 1 0.02
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (18 bp):
ATATATACTATATAGTTA
Found at i:641893 original size:30 final size:30
Alignment explanation
Indices: 641837--641893 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
641827 GCACAAACTT
*
641837 AAACATAAAGTACTAAAATAATAAAAATAG
1 AAACATAAAGTACTAAAATAACAAAAATAG
*
641867 AAAC-TAAAGTGACTAAAATGACAAAAA
1 AAACATAAAGT-ACTAAAATAACAAAAA
641894 AACTTAGGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 6 0.25
30 18 0.75
ACGTcount: A:0.65, C:0.09, G:0.09, T:0.18
Consensus pattern (30 bp):
AAACATAAAGTACTAAAATAACAAAAATAG
Found at i:641949 original size:31 final size:30
Alignment explanation
Indices: 641890--641948 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
641880 TAAAATGACA
641890 AAAAAACTTAGGGACTAAAATAGTAAAAAC
1 AAAAAACTTAGGGACTAAAATAGTAAAAAC
* *
641920 AAAAAAC-TAGAGGATTAAAATGGTAAAAA
1 AAAAAACTTAG-GGACTAAAATAGTAAAAA
641949 ATAGAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.61, C:0.07, G:0.15, T:0.17
Consensus pattern (30 bp):
AAAAAACTTAGGGACTAAAATAGTAAAAAC
Found at i:642047 original size:30 final size:29
Alignment explanation
Indices: 641995--642073 Score: 106
Period size: 30 Copynumber: 2.7 Consensus size: 29
641985 TTAAAGGGCT
* *
641995 AAAATAGA-AGAAAGAAAATTTAGGGACC
1 AAAATAGAGAAAAAGAAACTTTAGGGACC
642023 AAAATAGAGAAAATAGAAACTTTAGGGACC
1 AAAATAGAGAAAA-AGAAACTTTAGGGACC
*
642053 AAAATAGATGAAACAGAAACT
1 AAAATAGA-GAAAAAGAAACT
642074 AAAGGGAATA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
28 8 0.18
29 3 0.07
30 30 0.67
31 4 0.09
ACGTcount: A:0.57, C:0.09, G:0.19, T:0.15
Consensus pattern (29 bp):
AAAATAGAGAAAAAGAAACTTTAGGGACC
Found at i:642080 original size:30 final size:30
Alignment explanation
Indices: 642016--642103 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 30
642006 AAGAAAATTT
* **
642016 AGGGACCAAAATAGA-GAAAATAGAAACTTT
1 AGGGACCAAAATAGATG-AAACAGAAACTAA
642046 AGGGACCAAAATAGATGAAACAGAAACTAA
1 AGGGACCAAAATAGATGAAACAGAAACTAA
** * * *
642076 AGGGAATAAAATGGATAAAACATAAACT
1 AGGGACCAAAATAGATGAAACAGAAACT
642104 TAGGGGGCTA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
30 48 0.98
31 1 0.02
ACGTcount: A:0.56, C:0.10, G:0.19, T:0.15
Consensus pattern (30 bp):
AGGGACCAAAATAGATGAAACAGAAACTAA
Found at i:642990 original size:24 final size:24
Alignment explanation
Indices: 642945--642994 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
642935 TGGTGGTTGG
642945 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATGTTTAAACTTTATT
*
642969 TTTAATGGTATGTTT-AAGTTTATT
1 TTTAATGG-ATGTTTAAACTTTATT
642993 TT
1 TT
642995 GGTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (24 bp):
TTTAATGGATGTTTAAACTTTATT
Found at i:648596 original size:24 final size:24
Alignment explanation
Indices: 648551--648600 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
648541 TGGTGGTTGG
648551 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATGTTTAAACTTTATT
*
648575 TTTAATGGTATGTTT-AAGTTTATT
1 TTTAATGG-ATGTTTAAACTTTATT
648599 TT
1 TT
648601 GGTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (24 bp):
TTTAATGGATGTTTAAACTTTATT
Found at i:650416 original size:3 final size:3
Alignment explanation
Indices: 650392--650450 Score: 59
Period size: 3 Copynumber: 19.7 Consensus size: 3
650382 TGGCATTCAA
* * *
650392 AAT AAT -AT AAT -GT AAT ATAT AAT AAT AAT AATT AAT AAG CAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AA-T AAT AAT AAT AAT
650437 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
650451 AAAGAAAGAC
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 3 0.07
3 37 0.80
4 6 0.13
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:651114 original size:66 final size:64
Alignment explanation
Indices: 650964--651116 Score: 157
Period size: 66 Copynumber: 2.4 Consensus size: 64
650954 GATGATATTT
* * * *
650964 GTTTCAAGGGAAACGA-CTCAAAGATGACGTTTAAAGGAAACTGTCTCAAGCGAGGCAAATTTT
1 GTTTCAAGGGAAACGATCTCAAAGATGACGTTTAAAGGAAACTATCTCAAACGAGGCAAAATTC
* * * ** * *
651027 GTTTTTAAGGGAAACGTTCTCAAAGATCGATGTTTCATGGGAAACTATCTCAAATG-GGATAAAA
1 G-TTTCAAGGGAAACGATCTCAAAGAT-GACGTTT-AAAGGAAACTATCTCAAACGAGG-CAAAA
651091 TTC
62 TTC
651094 GTTTCAAGGGAAACGATCTCAAA
1 GTTTCAAGGGAAACGATCTCAAA
651117 TATGTTTGTT
Statistics
Matches: 72, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
63 1 0.01
64 13 0.18
65 9 0.12
66 28 0.39
67 21 0.29
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (64 bp):
GTTTCAAGGGAAACGATCTCAAAGATGACGTTTAAAGGAAACTATCTCAAACGAGGCAAAATTC
Found at i:651654 original size:35 final size:35
Alignment explanation
Indices: 651606--651674 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
651596 GAGAAAAAAA
*
651606 TGTCTCAAGCGAGACGAAA-TTTCTTTTAGAGAAAT
1 TGTCTCAAACGAGAC-AAAGTTTCTTTTAGAGAAAT
* *
651641 TGTCTCAAACGAGACAAAGTTTGTTTTTGAGAAA
1 TGTCTCAAACGAGACAAAGTTTCTTTTAGAGAAA
651675 ACGATCTCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 3 0.10
35 27 0.90
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (35 bp):
TGTCTCAAACGAGACAAAGTTTCTTTTAGAGAAAT
Found at i:652946 original size:14 final size:13
Alignment explanation
Indices: 652928--652973 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 13
652918 TCTGTGCTTC
652928 TTTTCTCTTTGTT
1 TTTTCTCTTTGTT
652941 TGTTTCTCTTTGCTT
1 T-TTTCTCTTTG-TT
*
652956 CTTTTATCTTTGTT
1 -TTTTCTCTTTGTT
652970 TTTT
1 TTTT
652974 TATTTTATCT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
13 5 0.17
14 12 0.41
15 11 0.38
16 1 0.03
ACGTcount: A:0.02, C:0.15, G:0.09, T:0.74
Consensus pattern (13 bp):
TTTTCTCTTTGTT
Found at i:653011 original size:21 final size:24
Alignment explanation
Indices: 652977--653030 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
652967 GTTTTTTTAT
652977 TTTATCTTTATTTGC-T-TTTTCTC
1 TTTAT-TTTATTTGCTTATTTTCTC
653000 TTTATTTT-TTTGCTTATTTTCTC
1 TTTATTTTATTTGCTTATTTTCTC
*
653023 TTTGTTTT
1 TTTATTTT
653031 GATTGGATCT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 5 0.18
22 4 0.14
23 19 0.68
ACGTcount: A:0.07, C:0.13, G:0.06, T:0.74
Consensus pattern (24 bp):
TTTATTTTATTTGCTTATTTTCTC
Found at i:661266 original size:30 final size:30
Alignment explanation
Indices: 661222--661344 Score: 92
Period size: 30 Copynumber: 4.1 Consensus size: 30
661212 GCACAAACTT
*
661222 AAACATAAAT-GACTAAAATAATAAAAACAG
1 AAAC-TAAATGGACTAAAATAATAAAAATAG
** *
661252 AAACTAAATGGACTAAAACT-GCAAAAATAA
1 AAACTAAATGGACTAAAA-TAATAAAAATAG
* * *
661282 AAACT-TAGGGACTAAAACAATAAAAATAG
1 AAACTAAATGGACTAAAATAATAAAAATAG
* **
661311 AAACCTAGA-GGACTAAAATGGTAAACAATAG
1 AAA-CTAAATGGACTAAAATAATAAA-AATAG
661342 AAA
1 AAA
661345 TTTAAGGACC
Statistics
Matches: 73, Mismatches: 14, Indels: 11
0.74 0.14 0.11
Matches are distributed among these distances:
29 25 0.34
30 38 0.52
31 10 0.14
ACGTcount: A:0.60, C:0.11, G:0.12, T:0.16
Consensus pattern (30 bp):
AAACTAAATGGACTAAAATAATAAAAATAG
Found at i:661294 original size:29 final size:30
Alignment explanation
Indices: 661261--661328 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
661251 GAAACTAAAT
** *
661261 GGACTAAAACTGCAAAAATAAAAACTTAG-
1 GGACTAAAACAACAAAAATAAAAACCTAGA
* *
661290 GGACTAAAACAATAAAAATAGAAACCTAGA
1 GGACTAAAACAACAAAAATAAAAACCTAGA
661320 GGACTAAAA
1 GGACTAAAA
661329 TGGTAAACAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
29 24 0.73
30 9 0.27
ACGTcount: A:0.57, C:0.13, G:0.15, T:0.15
Consensus pattern (30 bp):
GGACTAAAACAACAAAAATAAAAACCTAGA
Found at i:661298 original size:59 final size:57
Alignment explanation
Indices: 661236--661445 Score: 176
Period size: 59 Copynumber: 3.6 Consensus size: 57
661226 ATAAATGACT
* *
661236 AAAATAATAAAAACAGAAACTAAATGGACTAAAACT-GCAAAAATAAAAACTTAGGGACT
1 AAAATAATAAAAACAGAAACTAAA-GGACTAAAA-TAG-AAAAATAAAAATTTAGGGACC
* * * * * *
661295 AAAACAATAAAAATAGAAACCTAGAGGACTAAAATGGTAAACAATAGAAATTTAAGGACC
1 AAAATAATAAAAACAGAAA-CTAAAGGACTAAAATAG-AAA-AATAAAAATTTAGGGACC
* * * * *
661355 AAAAT-ACAAATACAGAAGCTTAAAGGGCTAAAATAGAAGAA-AAAAATTTAGGGACC
1 AAAATAATAAAAACAGAAAC-TAAAGGACTAAAATAGAAAAATAAAAATTTAGGGACC
* *
661411 AAAATAGA-GAAAACAGAAACTAAAGCGAATAAAAT
1 AAAATA-ATAAAAACAGAAACTAAAG-GACTAAAAT
661446 GGATAAAGCA
Statistics
Matches: 120, Mismatches: 24, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
56 23 0.19
57 18 0.15
58 5 0.04
59 52 0.43
60 22 0.18
ACGTcount: A:0.59, C:0.11, G:0.15, T:0.16
Consensus pattern (57 bp):
AAAATAATAAAAACAGAAACTAAAGGACTAAAATAGAAAAATAAAAATTTAGGGACC
Found at i:661353 original size:30 final size:30
Alignment explanation
Indices: 661302--661359 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
661292 ACTAAAACAA
*
661302 TAAAAATAGAAACCTAGAGGACTAAAATGG
1 TAAAAATAGAAACCTAGAGGACCAAAATGG
**
661332 TAAACAATAGAAATTTA-AGGACCAAAAT
1 TAAA-AATAGAAACCTAGAGGACCAAAAT
661360 ACAAATACAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 14 0.58
31 10 0.42
ACGTcount: A:0.55, C:0.10, G:0.16, T:0.19
Consensus pattern (30 bp):
TAAAAATAGAAACCTAGAGGACCAAAATGG
Found at i:662710 original size:3 final size:3
Alignment explanation
Indices: 662681--662745 Score: 55
Period size: 3 Copynumber: 21.7 Consensus size: 3
662671 TGGCCTGTAA
* * *
662681 AAT AAT -AT AAT -GT AAT ATAT CAAT AAT AAT AATT AAT AAG CAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT -AAT AAT AAT AA-T AAT AAT AAT AAT
662727 AAT AAT AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AA
662746 AAAGAAATAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
2 5 0.10
3 37 0.74
4 7 0.14
5 1 0.02
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:663685 original size:2 final size:2
Alignment explanation
Indices: 663678--663707 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
663668 AAATAAAACC
663678 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
663708 TAAAATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:663921 original size:18 final size:18
Alignment explanation
Indices: 663898--664076 Score: 162
Period size: 18 Copynumber: 10.4 Consensus size: 18
663888 ATTATTAATT
663898 TATACTATATAGTTTATA
1 TATACTATATAGTTTATA
*
663916 TATACTA-AT-G--AACTA
1 TATACTATATAGTTTA-TA
663931 TATACTATATAGTTTATA
1 TATACTATATAGTTTATA
*
663949 TATACTATATAGTTTTTA
1 TATACTATATAGTTTATA
*
663967 TATACTA-AT-G--AACTA
1 TATACTATATAGTTTA-TA
* *
663982 TATAATATATAATTTATA
1 TATACTATATAGTTTATA
* * *
664000 TACACCATATAGTTTATG
1 TATACTATATAGTTTATA
* *
664018 TATACTATATAATTTATG
1 TATACTATATAGTTTATA
*
664036 CA-A-TATATAGTTTATA
1 TATACTATATAGTTTATA
*
664052 TATACCATATAGTTTATA
1 TATACTATATAGTTTATA
664070 TATACTA
1 TATACTA
664077 ATGAACTATA
Statistics
Matches: 127, Mismatches: 22, Indels: 24
0.73 0.13 0.14
Matches are distributed among these distances:
14 1 0.01
15 17 0.13
16 18 0.14
17 7 0.06
18 82 0.65
19 2 0.02
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (18 bp):
TATACTATATAGTTTATA
Found at i:663969 original size:51 final size:51
Alignment explanation
Indices: 663898--664088 Score: 269
Period size: 51 Copynumber: 3.7 Consensus size: 51
663888 ATTATTAATT
* *
663898 TATACTATATAGTTTATATATACTAATGAACTATATACTATATAGTTTATA
1 TATACCATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATA
* * *
663949 TATACTATATAGTTTTTATATACTAATGAACTATATAATATATAATTTATA
1 TATACCATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATA
* * *
664000 TACACCATATAGTTTATGTATACTATAT-AA-TTTATGCAATATATAGTTTATA
1 TATACCATATAGTTTATATATACTA-ATGAACTATAT--AATATATAGTTTATA
664052 TATACCATATAGTTTATATATACTAATGAACTATATA
1 TATACCATATAGTTTATATATACTAATGAACTATATA
664089 GTTTATATAT
Statistics
Matches: 123, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
50 4 0.03
51 74 0.60
52 41 0.33
53 4 0.03
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (51 bp):
TATACCATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATA
Found at i:664120 original size:33 final size:33
Alignment explanation
Indices: 664083--664204 Score: 120
Period size: 33 Copynumber: 3.5 Consensus size: 33
664073 ACTAATGAAC
*
664083 TATATAGTTTATATATATTAATGAACTACATAA
1 TATATAGTTTATATATATTAATGAACTATATAA
* * * *
664116 TATATAATTTATATATACTAATGAACTTTACAA
1 TATATAGTTTATATATATTAATGAACTATATAA
*
664149 TATGTAGTTTATTAATATAATTATATGAACTATATAAA
1 TATATAGTTTA-T-ATAT-ATTA-ATGAACTATAT-AA
*
664187 CTATATA-TATATATATAT
1 -TATATAGTTTATATATAT
664205 ATATATATAT
Statistics
Matches: 71, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
33 37 0.52
34 1 0.01
35 6 0.08
36 7 0.10
37 10 0.14
38 5 0.07
39 5 0.07
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (33 bp):
TATATAGTTTATATATATTAATGAACTATATAA
Found at i:664121 original size:26 final size:26
Alignment explanation
Indices: 664066--664121 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
664056 CCATATAGTT
* * *
664066 TATATATACTAATGAACTATATAGTT
1 TATATATACTAATGAACTACATAATA
*
664092 TATATATATTAATGAACTACATAATA
1 TATATATACTAATGAACTACATAATA
664118 TATA
1 TATA
664122 ATTTATATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.41
Consensus pattern (26 bp):
TATATATACTAATGAACTACATAATA
Found at i:664193 original size:2 final size:2
Alignment explanation
Indices: 664188--664348 Score: 59
Period size: 2 Copynumber: 80.5 Consensus size: 2
664178 CTATATAAAC
* * *
664188 TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA CGA TA TA -A TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * * * *
664230 TA TA TA GT- TCG TA TA TA CA CTA CA TA GTT TA TA TA CA -A TA TA
1 TA TA TA -TA T-A TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA
* * * **
664272 TA -A AA CTA TA AA TA TA AA CTA TA TA GC T- TA TA TA T- TA TA T-
1 TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* *
664312 TA -A TA TA CA CTT 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 TA TA TA TA T
664349 TTTTTTTAAT
Statistics
Matches: 118, Mismatches: 25, Indels: 32
0.67 0.14 0.18
Matches are distributed among these distances:
1 8 0.07
2 103 0.87
3 7 0.06
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (2 bp):
TA
Found at i:665647 original size:50 final size:50
Alignment explanation
Indices: 665572--665672 Score: 166
Period size: 50 Copynumber: 2.0 Consensus size: 50
665562 TGTCTTGTCT
665572 ACATAAAGAATGAAGCTGATTTATCTCACTCTTAATCATTCCTGCATGAA
1 ACATAAAGAATGAAGCTGATTTATCTCACTCTTAATCATTCCTGCATGAA
* * * *
665622 ACATAATGAATGATGCTGATTTATCTTACTTTTAATCATTCCTGCATGAA
1 ACATAAAGAATGAAGCTGATTTATCTCACTCTTAATCATTCCTGCATGAA
665672 A
1 A
665673 ATCATTGCTG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.36
Consensus pattern (50 bp):
ACATAAAGAATGAAGCTGATTTATCTCACTCTTAATCATTCCTGCATGAA
Found at i:668463 original size:11 final size:11
Alignment explanation
Indices: 668429--668457 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
668419 TAAATATTAG
668429 TTATAAAACTT
1 TTATAAAACTT
668440 TTATAAAACTT
1 TTATAAAACTT
668451 TTATAAA
1 TTATAAA
668458 TATTTTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (11 bp):
TTATAAAACTT
Found at i:671600 original size:12 final size:12
Alignment explanation
Indices: 671583--671609 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
671573 ACGTGGACGG
671583 TTTTACATTTTA
1 TTTTACATTTTA
671595 TTTTACATTTTA
1 TTTTACATTTTA
671607 TTT
1 TTT
671610 AATGTGAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTTACATTTTA
Found at i:675106 original size:15 final size:15
Alignment explanation
Indices: 675086--675115 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
675076 TTGTGTTTCT
675086 GGCCTGCTCCATCTC
1 GGCCTGCTCCATCTC
675101 GGCCTGCTCCATCTC
1 GGCCTGCTCCATCTC
675116 ATCAGGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.47, G:0.20, T:0.27
Consensus pattern (15 bp):
GGCCTGCTCCATCTC
Found at i:683441 original size:45 final size:45
Alignment explanation
Indices: 683404--683609 Score: 324
Period size: 45 Copynumber: 4.6 Consensus size: 45
683394 TCACTTAGGG
*
683404 CATCCTTTCATGCCTTTAATGCACCGTTGTGCATTTCATTTATTG-
1 CATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTA-TGA
* *
683449 CATCATTTCATGCCTTTAATGCACCGTTATGCGTTTCATTTATGA
1 CATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGA
* * * *
683494 CATCTTTTCATGCCTTTAGTACACCGTTATACATTTCATTTATGA
1 CATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGA
683539 CATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGA
1 CATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGA
*
683584 CATCCTTTCATGCATTTAATGCACCG
1 CATCCTTTCATGCCTTTAATGCACCG
683610 ATAGGCCTTT
Statistics
Matches: 147, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
44 2 0.01
45 145 0.99
ACGTcount: A:0.22, C:0.24, G:0.12, T:0.42
Consensus pattern (45 bp):
CATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGA
Found at i:683511 original size:21 final size:21
Alignment explanation
Indices: 683487--683556 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
683477 ATGCGTTTCA
683487 TTTATGACATCTTTTCATGCC
1 TTTATGACATCTTTTCATGCC
* * * *
683508 TTTA-GTACACCGTTATACATTTCA
1 TTTATG-ACATC-TT-TTCA-TGCC
*
683532 TTTATGACATCCTTTCATGCC
1 TTTATGACATCTTTTCATGCC
683553 TTTA
1 TTTA
683557 ATGCACCGTT
Statistics
Matches: 35, Mismatches: 9, Indels: 10
0.65 0.17 0.19
Matches are distributed among these distances:
20 1 0.03
21 14 0.40
22 5 0.14
23 4 0.11
24 10 0.29
25 1 0.03
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.46
Consensus pattern (21 bp):
TTTATGACATCTTTTCATGCC
Found at i:683890 original size:56 final size:56
Alignment explanation
Indices: 683703--683880 Score: 266
Period size: 56 Copynumber: 3.2 Consensus size: 56
683693 AACTTTATAG
*
683703 TTTGCACACATAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTT
1 TTTGCACACACAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTT
* * * *
683759 TTTGTACACACAGTGCCCATACGAAAATTCATAAATTTATTATAAATTTCTTAGTT
1 TTTGCACACACAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTT
* * * **
683815 TTTGCATACACAGCGTCCATACGGAAATTCATAAACCCATTATGAATTTCTTAGTT
1 TTTGCACACACAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTT
683871 TTTGCACACA
1 TTTGCACACA
683881 AAGTATCCAT
Statistics
Matches: 107, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 107 1.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (56 bp):
TTTGCACACACAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTT
Found at i:684347 original size:19 final size:19
Alignment explanation
Indices: 684305--684353 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
684295 GTAATCAATG
684305 GTATCGATACATTCTCCATA
1 GTATCGATACA-TCTCCATA
*
684325 GTATCGATAC-TCTCCTCTA
1 GTATCGATACATCTCC-ATA
684344 GTATCGATAC
1 GTATCGATAC
684354 CAATTGCATC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 5 0.19
19 12 0.44
20 10 0.37
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (19 bp):
GTATCGATACATCTCCATA
Found at i:687326 original size:11 final size:11
Alignment explanation
Indices: 687302--687349 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
687292 CCCTAAAAAA
687302 TTTTAAATTATT
1 TTTTAAATT-TT
*
687314 TTTTATATTTT
1 TTTTAAATTTT
*
687325 TTATAAATTTT
1 TTTTAAATTTT
* *
687336 ATTTATATTTT
1 TTTTAAATTTT
687347 TTT
1 TTT
687350 GTTGAAAACT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
11 21 0.72
12 8 0.28
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTTAAATTTT
Found at i:687349 original size:23 final size:23
Alignment explanation
Indices: 687305--687348 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
687295 TAAAAAATTT
*
687305 TAAATTATTTTTTATATTTTTTA
1 TAAATTATTATTTATATTTTTTA
687328 TAAATT-TTATTTATATTTTTT
1 TAAATTATTATTTATATTTTTT
687349 TGTTGAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
TAAATTATTATTTATATTTTTTA
Found at i:688260 original size:14 final size:14
Alignment explanation
Indices: 688233--688266 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
688223 TTTCAATCAC
688233 TTAATAAATATATAT
1 TTAA-AAATATATAT
*
688248 TTAAAAATTTATAT
1 TTAAAAATATATAT
688262 TTAAA
1 TTAAA
688267 CACTGTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TTAAAAATATATAT
Found at i:694224 original size:24 final size:24
Alignment explanation
Indices: 694197--694247 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
694187 AAAGATATAT
* *
694197 AAATATTTACAATTAAATAATTAA
1 AAATATTTAAAATTAAATAATCAA
* *
694221 AAATCTTTAAAATTGAATAATCAA
1 AAATATTTAAAATTAAATAATCAA
694245 AAA
1 AAA
694248 AAGAATTGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATATTTAAAATTAAATAATCAA
Found at i:710717 original size:23 final size:23
Alignment explanation
Indices: 710699--710759 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
710689 CTCATATAAA
*
710699 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
710722 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
710745 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
710760 TATAATAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:710946 original size:103 final size:103
Alignment explanation
Indices: 710775--710992 Score: 427
Period size: 103 Copynumber: 2.1 Consensus size: 103
710765 TAATGTCCAT
710775 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
710840 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
710878 AAGGACCACATATCATTCCTTAAGAATCTTATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
710943 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
710981 AAGGACCACATA
1 AAGGACCACATA
710993 GACCCTCAAC
Statistics
Matches: 114, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 114 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:712216 original size:21 final size:21
Alignment explanation
Indices: 712192--712236 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
712182 TCTGGTTAGT
* * *
712192 TTGAGGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
712213 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
712234 TTG
1 TTG
712237 CTCAGAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.13, C:0.24, G:0.31, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:713972 original size:2 final size:2
Alignment explanation
Indices: 713965--714019 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
713955 TGAATTTTTC
713965 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
714007 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
714020 ATAAAGATAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:715194 original size:3 final size:3
Alignment explanation
Indices: 715186--715228 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
715176 TATATTTATT
* *
715186 TAA TAA TAA TAT TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
715229 TTTAAGATGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:715474 original size:86 final size:86
Alignment explanation
Indices: 715372--716513 Score: 1319
Period size: 86 Copynumber: 13.2 Consensus size: 86
715362 ATTATGTTCA
* *
715372 GAGGTCTTA-AGAATGACCCGAAAGATTTAACATCTTGCACTAGAGGTCTTACAGATGACCCGAA
1 GAGGTCTTATAG-ATGACCCGAAGGATTTAACATCTTGCACTGGAGGTCTTACAGATGACCCGAA
715436 GGATTTTAAACATCCTGCACTG
65 GGATTTTAAACATCCTGCACTG
* * * * ** ** *
715458 GAGGTCTTACAGATGACCCAAAGGATTTTAAACATCCTGCACTAGAGGTCTTATGGATGACTTGG
1 GAGGTCTTATAGATGACCCGAAGGA-TTT-AACATCTTGCACTGGAGGTCTTACAGATGACCCGA
*
715523 AGGA-TTT-AACATCTTGCACTG
64 AGGATTTTAAACATCCTGCACTG
* * * ** *
715544 GAGGTCTTACAGATGACCAGAAGGATTTTAAACATCCTGCACTGGAGGTCTTATGGATGACCCGG
1 GAGGTCTTATAGATGACCCGAAGGA-TTT-AACATCTTGCACTGGAGGTCTTACAGATGACCCGA
*
715609 AGGA-TTT-AACATCTTGCACTG
64 AGGATTTTAAACATCCTGCACTG
* * * * **
715630 GAGGTCATACAGATGACCCGAAGGATTTTAAACATCCTT-TACTGGAGGCCTTATGGATGACCCG
1 GAGGTCTTATAGATGACCCGAAGGA-TTT-AACAT-CTTGCACTGGAGGTCTTACAGATGACCCG
* * *
715694 GAGGA-TTT-AACATCTTGCACCG
63 AAGGATTTTAAACATCCTGCACTG
* * * *
715716 GAGGTCTTACAGATGACCCGAAGGATTTTAAACAACCTACACTGGAGGTCTTACAGATGACCCGA
1 GAGGTCTTATAGATGACCCGAAGGA-TTT-AACATCTTGCACTGGAGGTCTTACAGATGACCCGA
715781 AGGATTTTAAACATCCTGCACTG
64 AGGATTTTAAACATCCTGCACTG
715804 GAGGTCTTATAGATGACCC-AGAGGATTTAACATCTTGCACTGGAGGTCTTACAGATGACCCGAA
1 GAGGTCTTATAGATGACCCGA-AGGATTTAACATCTTGCACTGGAGGTCTTACAGATGACCCGAA
715868 GGATTTTAAACATCCTGCACTG
65 GGATTTTAAACATCCTGCACTG
* *
715890 GAGGTCTTATAGATGA-CCTAGAGGATTTAACATCTTGCACTGGAGGTCATACAGATGACCCGAA
1 GAGGTCTTATAGATGACCCGA-AGGATTTAACATCTTGCACTGGAGGTCTTACAGATGACCCGAA
* **
715954 GGATTTTAAATATCCTTTACTG
65 GGATTTTAAACATCCTGCACTG
* * *
715976 GAGATCTTATGGATGACCCGAAGGATTTAACATCTTGCACCGGAGGTCTTACAGATGACCCGAAG
1 GAGGTCTTATAGATGACCCGAAGGATTTAACATCTTGCACTGGAGGTCTTACAGATGACCCGAAG
*
716041 GATTTTAAACATCCTGCACTA
66 GATTTTAAACATCCTGCACTG
* *
716062 GAGGTCTTATAGATGACCCGAAGGATTTAACATCTTGCACTAGAGGTCTTA-ATAATGACCCGAA
1 GAGGTCTTATAGATGACCCGAAGGATTTAACATCTTGCACTGGAGGTCTTACA-GATGACCCGAA
716126 GGATTTTAAACATCCTGCACTG
65 GGATTTTAAACATCCTGCACTG
*
716148 GAGGTCTTATGGATGACCC-AGAGGATTTAACATCTTGCACTGGAGGTCTTACAGATGACCCGAA
1 GAGGTCTTATAGATGACCCGA-AGGATTTAACATCTTGCACTGGAGGTCTTACAGATGACCCGAA
* *
716212 TGATTTTAAACATCCTGCATTG
65 GGATTTTAAACATCCTGCACTG
* * * *
716234 GAGGTCTTATGGATGACCCGGAGGATATAACATCTTGCATTGGAGGTCTTACAGATGACCCGAAG
1 GAGGTCTTATAGATGACCCGAAGGATTTAACATCTTGCACTGGAGGTCTTACAGATGACCCGAAG
*
716299 GA-TTT-AACATCTTGCACTG
66 GATTTTAAACATCCTGCACTG
* * * * *
716318 GAGGTCTTACAAATGACCCGAAGGATTTTAAAAACATCATGCACTGAAAGTCTTACAGATGACCC
1 GAGGTCTTATAGATGACCCGAAGGA-TTT---AACATCTTGCACTGGAGGTCTTACAGATGACCC
*
716383 GAAGG-TTTTAAAAACATCCTACACTG
62 GAAGGATTTT--AAACATCCTGCACTG
* * * * * **
716409 TAGGTCTTATGGATGACCC-AATGGTTTTGAAAACATCATGCACTGTAGGTCTTATGGATGACCC
1 GAGGTCTTATAGATGACCCGAA-GGATTT---AACATCTTGCACTGGAGGTCTTACAGATGACCC
* *
716473 GAATG-TTTTGAAAACATCATGCACTG
62 GAAGGATTTT--AAACATCCTGCACTG
* *
716499 AAGGTCTTACAGATG
1 GAGGTCTTATAGATG
716514 TGGGAAATAG
Statistics
Matches: 941, Mismatches: 92, Indels: 42
0.88 0.09 0.04
Matches are distributed among these distances:
84 33 0.04
85 11 0.01
86 673 0.72
87 21 0.02
88 104 0.11
90 70 0.07
91 29 0.03
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (86 bp):
GAGGTCTTATAGATGACCCGAAGGATTTAACATCTTGCACTGGAGGTCTTACAGATGACCCGAAG
GATTTTAAACATCCTGCACTG
Found at i:715930 original size:302 final size:302
Alignment explanation
Indices: 715372--716513 Score: 1463
Period size: 302 Copynumber: 3.8 Consensus size: 302
715362 ATTATGTTCA
* * * **
715372 GAGGTCTTAAGAATGACCCGAAAGATTTAACATCTTGCACTAGAGGTCTTACAGATGACCCGAAG
1 GAGGTCTTATGGATGACCCGAAGGATTTAACATCTTGCACCGGAGGTCTTACAGATGACCCGAAG
* *
715437 GATTTTAAACATCCTGCACTGGAGGTCTTACAGATGACCCAAAGGATTTTAAACATCCTGCACTA
66 GATTTTAAACAACCTGCACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAACATCCTGCACTA
* *** *
715502 GAGGTCTTATGGATGACTTGGAGGATTT-AACATCTTGCACTGGAGGTCTTACAGATGACCAGAA
131 GAGGTCTTATAGATGACCCAGAGGATTTAAACATCTTGCACTGGAGGTCTTACAGATGACCCGAA
** *
715566 GGATTTTAAACATCCTGCACTGGAGGTCTTATGGATGACCCGGAGGATTTAACATCTTGCACTGG
196 GGATTTTAAACATCCTGCACTGGAGGTCTTACAGATGA-CCAGAGGATTTAACATCTTGCACTGG
715631 AGGTCATACAGATGACCCGAAGGATTTTAAACATCCTTTACTG
260 AGGTCATACAGATGACCCGAAGGATTTTAAACATCCTTTACTG
* *
715674 GAGGCCTTATGGATGACCCGGAGGATTTAACATCTTGCACCGGAGGTCTTACAGATGACCCGAAG
1 GAGGTCTTATGGATGACCCGAAGGATTTAACATCTTGCACCGGAGGTCTTACAGATGACCCGAAG
* *
715739 GATTTTAAACAACCTACACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAACATCCTGCACTG
66 GATTTTAAACAACCTGCACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAACATCCTGCACTA
715804 GAGGTCTTATAGATGACCCAGAGGATTT-AACATCTTGCACTGGAGGTCTTACAGATGACCCGAA
131 GAGGTCTTATAGATGACCCAGAGGATTTAAACATCTTGCACTGGAGGTCTTACAGATGACCCGAA
*
715868 GGATTTTAAACATCCTGCACTGGAGGTCTTATAGATGACCTAGAGGATTTAACATCTTGCACTGG
196 GGATTTTAAACATCCTGCACTGGAGGTCTTACAGATGACC-AGAGGATTTAACATCTTGCACTGG
*
715933 AGGTCATACAGATGACCCGAAGGATTTTAAATATCCTTTACTG
260 AGGTCATACAGATGACCCGAAGGATTTTAAACATCCTTTACTG
*
715976 GAGATCTTATGGATGACCCGAAGGATTTAACATCTTGCACCGGAGGTCTTACAGATGACCCGAAG
1 GAGGTCTTATGGATGACCCGAAGGATTTAACATCTTGCACCGGAGGTCTTACAGATGACCCGAAG
* * * *
716041 GATTTTAAACATCCTGCACTAGAGGTCTTATAGATGACCCGAAGGA-TTT-AACATCTTGCACTA
66 GATTTTAAACAACCTGCACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAACATCCTGCACTA
* **
716104 GAGGTCTTAATA-ATGACCC-GAAGGATTTTAAACATCCTGCACTGGAGGTCTTATGGATGACCC
131 GAGGTCTT-ATAGATGACCCAG-AGGA-TTTAAACATCTTGCACTGGAGGTCTTACAGATGACCC
* * * *
716167 -AGAGGA-TTT-AACATCTTGCACTGGAGGTCTTACAGATGACCCGAATGATTTTAAACATCCTG
193 GA-AGGATTTTAAACATCCTGCACTGGAGGTCTTACAGATGACCAG-AGGA-TTT-AACATCTTG
* * ** * * * *
716229 CATTGGAGGTCTTATGGATGACCCGGAGGA-TAT-AACAT-CTTGCATTG
254 CACTGGAGGTCATACAGATGACCCGAAGGATTTTAAACATCCTT-TACTG
** * *
716276 GAGGTCTTACAGATGACCCGAAGGATTTAACATCTTGCACTGGAGGTCTTACAAATGACCCGAAG
1 GAGGTCTTATGGATGACCCGAAGGATTTAACATCTTGCACCGGAGGTCTTACAGATGACCCGAAG
* * *
716341 GATTTTAAA-AACATCATGCACTGAAAGTCTTACAGATGACCCGAAGG-TTTTAAAAACATCCTA
66 GATTTTAAACAAC--C-TGCACTGGAGGTCTTACAGATGACCCGAAGGATTTT--AAACATCCTG
* * * * **
716404 CACT-GTAGGTCTTATGGATGACCCA-ATGGTTTTGAAAACATCATGCACTGTAGGTCTTATGGA
126 CACTAG-AGGTCTTATAGATGACCCAGA-GGATTT--AAACATCTTGCACTGGAGGTCTTACAGA
* * *
716467 TGACCCGAATG-TTTTGAAAACATCATGCACTGAAGGTCTTACAGATG
187 TGACCCGAAGGATTTT--AAACATCCTGCACTGGAGGTCTTACAGATG
716514 TGGGAAATAG
Statistics
Matches: 748, Mismatches: 64, Indels: 49
0.87 0.07 0.06
Matches are distributed among these distances:
299 7 0.01
300 140 0.19
301 21 0.03
302 481 0.64
304 7 0.01
305 27 0.04
306 37 0.05
307 1 0.00
309 27 0.04
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (302 bp):
GAGGTCTTATGGATGACCCGAAGGATTTAACATCTTGCACCGGAGGTCTTACAGATGACCCGAAG
GATTTTAAACAACCTGCACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAACATCCTGCACTA
GAGGTCTTATAGATGACCCAGAGGATTTAAACATCTTGCACTGGAGGTCTTACAGATGACCCGAA
GGATTTTAAACATCCTGCACTGGAGGTCTTACAGATGACCAGAGGATTTAACATCTTGCACTGGA
GGTCATACAGATGACCCGAAGGATTTTAAACATCCTTTACTG
Found at i:717192 original size:22 final size:22
Alignment explanation
Indices: 717157--717275 Score: 138
Period size: 22 Copynumber: 5.5 Consensus size: 22
717147 TAAAGCTTTT
* *
717157 ATCTTTAAAAAGAGAATCAATC
1 ATCTTTAAAGAGAGAATCTATC
*
717179 ATCTTTGAAGAGAGAATCTATC
1 ATCTTTAAAGAGAGAATCTATC
*
717201 ATCTTTAAAGAGAGGATCTATC
1 ATCTTTAAAGAGAGAATCTATC
717223 ATCTTTAAAGAGATG-AT-TATC
1 ATCTTTAAAGAGA-GAATCTATC
*
717244 ATCTTTGAAGA-ATGAA-CTATC
1 ATCTTTAAAGAGA-GAATCTATC
*
717265 ATCTTTGAAGA
1 ATCTTTAAAGA
717276 ATGTAGATGT
Statistics
Matches: 88, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
20 3 0.03
21 30 0.34
22 54 0.61
23 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (22 bp):
ATCTTTAAAGAGAGAATCTATC
Found at i:717708 original size:54 final size:54
Alignment explanation
Indices: 717639--717804 Score: 215
Period size: 54 Copynumber: 3.1 Consensus size: 54
717629 ATAATCACTG
* * * * ** * **
717639 GTTCATAAAACATTTGGCAACATATTCATCCTTTTATATGGCTTCTGCTTAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCCCAGAT
* * *
717693 GTTCGTAAAACATTTGACAACACATTCATCATTTCCTGTAGCTTCTACCCATAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCCCAGAT
*
717747 GTTCGTAAATCATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCCCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCCCAGAT
717801 GTTC
1 GTTC
717805 ACTAGTGAAG
Statistics
Matches: 96, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 96 1.00
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCCCAGAT
Found at i:719584 original size:8 final size:8
Alignment explanation
Indices: 719571--719652 Score: 75
Period size: 7 Copynumber: 10.5 Consensus size: 8
719561 TTTAATTTCT
719571 TTTTCTTC
1 TTTTCTTC
719579 TTTTCTTTC
1 TTTTC-TTC
719588 TTTTCTTC
1 TTTTCTTC
719596 -TTTCTTC
1 TTTTCTTC
719603 -TTTCTTC
1 TTTTCTTC
*
719610 TTTT-TTT
1 TTTTCTTC
*
719617 TTTTCTTT
1 TTTTCTTC
*
719625 TTTTCCTTT
1 TTTT-CTTC
719634 TTTTC-TC
1 TTTTCTTC
719641 TATTT-TTC
1 T-TTTCTTC
719649 TTTT
1 TTTT
719653 TTCCGATGAA
Statistics
Matches: 66, Mismatches: 2, Indels: 13
0.81 0.02 0.16
Matches are distributed among these distances:
7 25 0.38
8 25 0.38
9 16 0.24
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTCTTC
Found at i:719622 original size:34 final size:33
Alignment explanation
Indices: 719566--719655 Score: 94
Period size: 34 Copynumber: 2.7 Consensus size: 33
719556 CTTGATTTAA
* * *
719566 TTTCTTT-TTCTTCTTTTCTTTCTTTTCTTCTT
1 TTTCTTTCTTCTTTTTTTTTTTCTTTTCTTCCT
*
719598 TCTTCTTTCTTCTTTTTTTTTTTCTTTTTTTCCT
1 T-TTCTTTCTTCTTTTTTTTTTTCTTTTCTTCCT
*
719632 TTT-TTTCTCTATTTTTCTTTTTTC
1 TTTCTTTCT-TCTTTTT-TTTTTTC
719656 CGATGAACGA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
32 6 0.12
33 14 0.29
34 29 0.59
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (33 bp):
TTTCTTTCTTCTTTTTTTTTTTCTTTTCTTCCT
Found at i:719634 original size:19 final size:18
Alignment explanation
Indices: 719579--719654 Score: 73
Period size: 19 Copynumber: 4.1 Consensus size: 18
719569 CTTTTTCTTC
*
719579 TTTTCTTTCTTTTCTTCTT
1 TTTTCTTT-TTTTCTTTTT
*
719598 TCTTCTTTCTTCTT-TTTTT
1 TTTTCTTT-TT-TTCTTTTT
719617 TTTTCTTTTTTTCCTTTTT
1 TTTTCTTTTTTT-CTTTTT
* *
719636 TTCTCTATTTTTCTTTTT
1 TTTTCTTTTTTTCTTTTT
719654 T
1 T
719655 CCGATGAACG
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
17 2 0.04
18 9 0.18
19 36 0.73
20 2 0.04
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTCTTTTTTTCTTTTT
Found at i:722111 original size:12 final size:12
Alignment explanation
Indices: 722090--722124 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
722080 ATGCAAATAT
*
722090 AAAATGAAAATG
1 AAAATAAAAATG
722102 AAAATAAAAATG
1 AAAATAAAAATG
722114 AAAATATAAAA
1 AAAATA-AAAA
722125 ATGCAAATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 17 0.81
13 4 0.19
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (12 bp):
AAAATAAAAATG
Found at i:722124 original size:14 final size:13
Alignment explanation
Indices: 722096--722133 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
722086 ATATAAAATG
722096 AAAATGAAA-ATA
1 AAAATGAAATATA
722108 AAAATGAAAATATA
1 AAAATG-AAATATA
722122 AAAATGCAAATA
1 AAAATG-AAATA
722134 CAAACATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 6 0.26
13 3 0.13
14 14 0.61
ACGTcount: A:0.71, C:0.03, G:0.08, T:0.18
Consensus pattern (13 bp):
AAAATGAAATATA
Found at i:734596 original size:15 final size:15
Alignment explanation
Indices: 734576--734745 Score: 159
Period size: 15 Copynumber: 10.8 Consensus size: 15
734566 TAATAAGGTT
734576 ATTTATTTAAAAATA
1 ATTTATTTAAAAATA
*
734591 ATTTATTTTAAAATA
1 ATTTATTTAAAAATA
734606 ATTTA-TTATAAAATA
1 ATTTATTTA-AAAATA
*
734621 ATTTATTTTAAAATA
1 ATTTATTTAAAAATA
734636 ATTTA-TTATAAAATA
1 ATTTATTTA-AAAATA
734651 ATTTA-TTATAAAATA
1 ATTTATTTA-AAAATA
734666 ATTTA-TTATAAAATA
1 ATTTATTTA-AAAATA
*
734681 ATTTATTTTAAAATA
1 ATTTATTTAAAAATA
*
734696 AATTATTATAAAATATGGA
1 ATTTATT-TAAAA-AT--A
*
734715 TTGATTTATTTTAAAATA
1 ---ATTTATTTAAAAATA
734733 ATTTAGTTTAAAA
1 ATTTA-TTTAAAA
734746 TATGGATTGA
Statistics
Matches: 133, Mismatches: 10, Indels: 23
0.80 0.06 0.14
Matches are distributed among these distances:
14 4 0.03
15 99 0.74
16 14 0.11
17 2 0.02
18 1 0.01
19 1 0.01
20 2 0.02
21 4 0.03
22 6 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.48
Consensus pattern (15 bp):
ATTTATTTAAAAATA
Found at i:734612 original size:30 final size:31
Alignment explanation
Indices: 734576--734801 Score: 223
Period size: 30 Copynumber: 7.0 Consensus size: 31
734566 TAATAAGGTT
734576 ATTTATTTA-AAAATAATTTATTTTAAAATA
1 ATTTATTTATAAAATAATTTATTTTAAAATA
734606 ATTTA-TTATAAAATAATTTATTTTAAAATA
1 ATTTATTTATAAAATAATTTATTTTAAAATA
*
734636 ATTTA-TTATAAAATAATTTATTATAAAATA
1 ATTTATTTATAAAATAATTTATTTTAAAATA
734666 ATTTA-TTATAAAATAATTTATTTTAAAATA
1 ATTTATTTATAAAATAATTTATTTTAAAATA
*
734696 AATTA-TTATAAAATATGGATTGATTTATTTTAAAATA
1 ATTTATTTAT-AAA-AT--A---ATTTATTTTAAAATA
734733 ATTTAGTTTA-AAATATGGATTGATTTATTTT-AAATA
1 ATTTA-TTTATAAA-AT--A---ATTTATTTTAAAATA
* *
734769 ATTTATTAGTATAGATTAATTTATTTTAAAATA
1 ATTTATT--TATAAAATAATTTATTTTAAAATA
734802 TGGATTGGTT
Statistics
Matches: 176, Mismatches: 6, Indels: 25
0.85 0.03 0.12
Matches are distributed among these distances:
29 3 0.02
30 92 0.52
31 3 0.02
32 11 0.06
33 5 0.03
34 1 0.01
35 3 0.02
36 10 0.06
37 43 0.24
38 2 0.01
39 3 0.02
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (31 bp):
ATTTATTTATAAAATAATTTATTTTAAAATA
Found at i:734634 original size:45 final size:45
Alignment explanation
Indices: 734576--734747 Score: 236
Period size: 45 Copynumber: 3.7 Consensus size: 45
734566 TAATAAGGTT
*
734576 ATTTATTTAAAAATAATTTATTTTAAAATAATTTATTATAAAATA
1 ATTTATTTTAAAATAATTTATTTTAAAATAATTTATTATAAAATA
*
734621 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTATAAAATA
1 ATTTATTTTAAAATAATTTATTTTAAAATAATTTATTATAAAATA
* *
734666 ATTTATTATAAAATAATTTATTTTAAAATAAATTATTATAAAATATGGA
1 ATTTATTTTAAAATAATTTATTTTAAAATAATTTATTAT-AAA-AT--A
*
734715 TTGATTTATTTTAAAATAATTTAGTTTAAAATA
1 ---ATTTATTTTAAAATAATTTATTTTAAAATA
734748 TGGATTGATT
Statistics
Matches: 113, Mismatches: 7, Indels: 7
0.89 0.06 0.06
Matches are distributed among these distances:
45 79 0.70
46 3 0.03
47 2 0.02
49 1 0.01
52 28 0.25
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.48
Consensus pattern (45 bp):
ATTTATTTTAAAATAATTTATTTTAAAATAATTTATTATAAAATA
Found at i:734722 original size:37 final size:37
Alignment explanation
Indices: 734681--734776 Score: 160
Period size: 37 Copynumber: 2.6 Consensus size: 37
734671 TTATAAAATA
*
734681 ATTTATTTTAAAATAAATTATTATAAAATATGGATTG
1 ATTTATTTTAAAATAATTTATTATAAAATATGGATTG
734718 ATTTATTTTAAAATAATTTAGTT-TAAAATATGGATTG
1 ATTTATTTTAAAATAATTTA-TTATAAAATATGGATTG
734755 ATTTATTTT-AAATAATTTATTA
1 ATTTATTTTAAAATAATTTATTA
734777 GTATAGATTA
Statistics
Matches: 56, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
35 2 0.04
36 10 0.18
37 42 0.75
38 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (37 bp):
ATTTATTTTAAAATAATTTATTATAAAATATGGATTG
Found at i:734796 original size:32 final size:32
Alignment explanation
Indices: 734589--734964 Score: 204
Period size: 32 Copynumber: 11.4 Consensus size: 32
734579 TATTTAAAAA
*
734589 TAATTTATTTTAAAATAATTTATTA-TA-A-AA
1 TAATTTATTTT-AAATAATTTATTAGTATAGAT
*
734619 TAATTTATTTTAAAATAATTTATTA-TA-A-AA
1 TAATTTATTTT-AAATAATTTATTAGTATAGAT
* *
734649 TAATTTATTATAAAATAATTTATTA-TA-A-AA
1 TAATTTATT-TTAAATAATTTATTAGTATAGAT
*
734679 TAATTTATTTTAAAATAAATTATTA-TAAAATATGGAT
1 TAATTTATTTT-AAATAATTTATTAGT---ATA--GAT
* * *
734716 TGATTTATTTTAAAATAATTTAGTTTAAAATATGGAT
1 TAATTTATTTT-AAATAATTTA--TT--AGTATAGAT
*
734753 TGATTTATTTTAAATAATTTATTAGTATAGAT
1 TAATTTATTTTAAATAATTTATTAGTATAGAT
** * * **
734785 TAATTTATTTTAAA-ATATGGATTGGTTTATTT
1 TAATTTATTTTAAATA-ATTTATTAGTATAGAT
* * * * *
734817 TAAAATATGGATTGATT-TATTATTGCAGTT-GTATGGAT
1 T--AAT-T-TATT--TTAAATAATT-TA-TTAGTATAGAT
*
734855 TGATTTATTTTAAATAATTTATTAGTAT-GAAT
1 TAATTTATTTTAAATAATTTATTAGTATAG-AT
* *
734887 TGATTTATTTTAAATAATTTATTAGTATGGAT
1 TAATTTATTTTAAATAATTTATTAGTATAGAT
* *
734919 TGATTTATTTTAAATAATTTATTAGTATGGAT
1 TAATTTATTTTAAATAATTTATTAGTATAGAT
*
734951 TGATTTATTTTAAA
1 TAATTTATTTTAAA
734965 ACATGGATTG
Statistics
Matches: 288, Mismatches: 30, Indels: 54
0.77 0.08 0.15
Matches are distributed among these distances:
29 1 0.00
30 79 0.27
31 5 0.02
32 116 0.40
33 7 0.02
34 9 0.03
35 2 0.01
36 15 0.05
37 38 0.13
38 8 0.03
39 6 0.02
41 1 0.00
42 1 0.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (32 bp):
TAATTTATTTTAAATAATTTATTAGTATAGAT
Found at i:734807 original size:22 final size:22
Alignment explanation
Indices: 734782--734837 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
734772 TATTAGTATA
*
734782 GATTAATTTATTTTAAAATATG
1 GATTGATTTATTTTAAAATATG
*
734804 GATTGGTTTATTTTAAAATATG
1 GATTGATTTATTTTAAAATATG
734826 GATTGATTTATT
1 GATTGATTTATT
734838 ATTGCAGTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (22 bp):
GATTGATTTATTTTAAAATATG
Found at i:734876 original size:14 final size:14
Alignment explanation
Indices: 734857--734941 Score: 53
Period size: 14 Copynumber: 5.5 Consensus size: 14
734847 GTATGGATTG
734857 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
734871 ATTTATTAGTATGAATTG
1 ATTTATT--T-T-AAATA
734889 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* * *
734903 ATTTATTAGTATGGATTG
1 ATTTATT--T-T-AAATA
734921 ATTTATTTTAAATA
1 ATTTATTTTAAATA
734935 ATTTATT
1 ATTTATT
734942 AGTATGGATT
Statistics
Matches: 53, Mismatches: 10, Indels: 16
0.67 0.13 0.20
Matches are distributed among these distances:
14 26 0.49
15 2 0.04
16 4 0.08
17 2 0.04
18 19 0.36
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.55
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:734894 original size:18 final size:18
Alignment explanation
Indices: 734871--734959 Score: 68
Period size: 18 Copynumber: 5.4 Consensus size: 18
734861 ATTTTAAATA
734871 ATTTATTAGTATGAATTG
1 ATTTATTAGTATGAATTG
* *
734889 ATTTATT--T-T-AAATA
1 ATTTATTAGTATGAATTG
*
734903 ATTTATTAGTATGGATTG
1 ATTTATTAGTATGAATTG
* *
734921 ATTTATT--T-T-AAATA
1 ATTTATTAGTATGAATTG
*
734935 ATTTATTAGTATGGATTG
1 ATTTATTAGTATGAATTG
734953 ATTTATT
1 ATTTATT
734960 TTAAAACATG
Statistics
Matches: 52, Mismatches: 11, Indels: 16
0.66 0.14 0.20
Matches are distributed among these distances:
14 19 0.37
15 2 0.04
16 4 0.08
17 2 0.04
18 25 0.48
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.54
Consensus pattern (18 bp):
ATTTATTAGTATGAATTG
Found at i:734970 original size:22 final size:22
Alignment explanation
Indices: 734945--734986 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
734935 ATTTATTAGT
734945 ATGGATTGATTTATTTTAAAAC
1 ATGGATTGATTTATTTTAAAAC
734967 ATGGATTGATTTATTTTAAA
1 ATGGATTGATTTATTTTAAA
734987 TAATTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.48
Consensus pattern (22 bp):
ATGGATTGATTTATTTTAAAAC
Found at i:735516 original size:15 final size:15
Alignment explanation
Indices: 735492--735532 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
735482 AGAAATTCAT
*
735492 ATTAAATTTATTTAA
1 ATTAATTTTATTTAA
*
735507 ATTAATTTTATTTGA
1 ATTAATTTTATTTAA
735522 ATTAAATTTTA
1 ATT-AATTTTA
735533 ACCAAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
ATTAATTTTATTTAA
Found at i:736756 original size:23 final size:23
Alignment explanation
Indices: 736713--736756 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
736703 TTAGTGTAAA
* *
736713 TAATAAAATTAATAAGTTATTGG
1 TAATAAAATAAATAAGATATTGG
736736 TAATAAAATAAAATAA-ATATT
1 TAATAAAAT-AAATAAGATATT
736757 AGTATTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (23 bp):
TAATAAAATAAATAAGATATTGG
Found at i:739204 original size:92 final size:92
Alignment explanation
Indices: 739087--739262 Score: 282
Period size: 92 Copynumber: 1.9 Consensus size: 92
739077 GTGATAGATC
*
739087 GAACAAGCTCTTCTCATTATGAACTTATTC-TCTCTCTTTCGGATGAGTTCTTCTCATTATGAAC
1 GAACAAGCTCTTCTCATTATGAACTTATTCTTC-CTCTGTCGGATGAGTTCTTCTCATTATGAAC
739151 TCTCCATTGAAAATGTTGATGCGAAGTT
65 TCTCCATTGAAAATGTTGATGCGAAGTT
* * *
739179 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTGTCGGATGAGTTCTTCTCATTATGAGCT
1 GAACAAGCTCTTCTCATTATGAACTTATTCTTCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
* *
739244 CTTCATTGGAAATGTTGAT
66 CTCCATTGAAAATGTTGAT
739263 CCCTCAAGCG
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
92 75 0.97
93 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.40
Consensus pattern (92 bp):
GAACAAGCTCTTCTCATTATGAACTTATTCTTCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
CTCCATTGAAAATGTTGATGCGAAGTT
Found at i:739304 original size:228 final size:221
Alignment explanation
Indices: 738957--739392 Score: 631
Period size: 228 Copynumber: 1.9 Consensus size: 221
738947 GGACTTGAAA
* * *
738957 TGAACAAGTTCTTTTCATTATGGACTTTCTCCTTTAAGACGAGTTATTCTTATTATGAACTCTTT
1 TGAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAAGACGAGTTATTCTCATTATGAACTCTTT
*
739022 TGGAAATGTCAATCCCTCTAACGAGGCGTCACTGATTCGAAATGTCGTGAATCGAGTGATAGATC
66 TGGAAATGTCAATCCCTCTAACGAGGCGTCACTGATTCGAAATGTCATGAATCGAGTGATAGATC
* *
739087 GAACAAGCTCTTCTCATTATGAACTTATTCTCTCTCTTTCGGATGAGTTCTTCTCATTATGAACT
131 GAACAAGCTCTTCTCATTATGAACTTATTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
739152 CTCCATTGAAAATGTTGATGCGAAGT
196 CTCCATTGAAAATGTTGATGCGAAGT
** * * *
739178 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTGTCGGATGAGTTCTTCTCATTATGAGC
1 TGAACAAGTTCTTCTCATTATGAAC-T-TTC-TCCT-T-TAAGACGAGTTATTCTCATTATGAAC
** * *
739243 TCTTCATTGGAAATGTTGATCCCTC-AAGCGAGGTGTCACTGATTCGAAATGTTATGAATCGAGT
61 TCTT--TTGGAAATGTCAATCCCTCTAA-CGAGGCGTCACTGATTCGAAATGTCATGAATCGAGT
* *
739307 GATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCAT
123 GATAGATCGAACAAGCTCTTCTCATTATGAACTTATTCTCCCTCTGTCGGATGAGTTCTTCTCAT
*
739372 TATGAACTCTCCATTGGAAAT
188 TATGAACTCTCCATTGAAAAT
739393 ACTGATCCTT
Statistics
Matches: 189, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
221 23 0.12
222 1 0.01
223 3 0.02
224 4 0.02
225 1 0.01
226 24 0.13
227 2 0.01
228 131 0.69
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.37
Consensus pattern (221 bp):
TGAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAAGACGAGTTATTCTCATTATGAACTCTTT
TGGAAATGTCAATCCCTCTAACGAGGCGTCACTGATTCGAAATGTCATGAATCGAGTGATAGATC
GAACAAGCTCTTCTCATTATGAACTTATTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
CTCCATTGAAAATGTTGATGCGAAGT
Found at i:739344 original size:136 final size:136
Alignment explanation
Indices: 739179--739532 Score: 609
Period size: 136 Copynumber: 2.6 Consensus size: 136
739169 ATGCGAAGTT
* * *
739179 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTGTCGGATGAGTTCTTCTCATTATGAGCT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
* * * * *
739244 CTTCATTGGAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTTATGAATCGAGTGA
66 CTCCATTGGAAATGCTGATCCCTCAAGCAAGGTGTCACTGATTCAAAATGTCATGAATCGAGTGA
739309 TAGGTC
131 TAGGTC
739315 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
* * *
739380 CTCCATTGGAAATACTGATCCTTCAAGCAAGGTGTCACTGATTCAAAATGTCGTGAATCGAGTGA
66 CTCCATTGGAAATGCTGATCCCTCAAGCAAGGTGTCACTGATTCAAAATGTCATGAATCGAGTGA
739445 TAGGTC
131 TAGGTC
739451 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
739516 CTCCATTGGAAATGCTG
66 CTCCATTGGAAATGCTG
739533 GTTCACCTCC
Statistics
Matches: 206, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
136 206 1.00
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (136 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
CTCCATTGGAAATGCTGATCCCTCAAGCAAGGTGTCACTGATTCAAAATGTCATGAATCGAGTGA
TAGGTC
Found at i:740431 original size:25 final size:24
Alignment explanation
Indices: 740410--740503 Score: 77
Period size: 24 Copynumber: 3.8 Consensus size: 24
740400 CCTTTTTCTC
740410 TTTTT-ATTTTTTCATTTCTTTTTTCA
1 TTTTTCATTTTTT--TTTC-TTTTTCA
740436 TTTTTCATTTTTTTTTCTTTTTCA
1 TTTTTCATTTTTTTTTCTTTTTCA
**
740460 TTTTTTTCA-TTTTTCATCTTTTT-A
1 --TTTTTCATTTTTTTTTCTTTTTCA
**
740484 TTTGTTCCCTTTTTTTTCTT
1 TTT-TTCATTTTTTTTTCTT
740504 CAAGCATAGT
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
22 3 0.05
23 3 0.05
24 17 0.29
25 16 0.28
26 12 0.21
27 7 0.12
ACGTcount: A:0.09, C:0.14, G:0.01, T:0.77
Consensus pattern (24 bp):
TTTTTCATTTTTTTTTCTTTTTCA
Found at i:740431 original size:26 final size:25
Alignment explanation
Indices: 740403--740473 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 25
740393 AAACCCTCCT
740403 TTTTCTCTTTTT-ATTTTTTCATTTCT
1 TTTTCTCTTTTTCATTTTTT--TTTCT
740429 TTTT-TCATTTTTCATTTTTTTTTCT
1 TTTTCTC-TTTTTCATTTTTTTTTCT
*
740454 TTTTCATTTTTTTCATTTTT
1 TTTTC-TCTTTTTCATTTTT
740474 CATCTTTTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
25 11 0.28
26 21 0.52
27 8 0.20
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (25 bp):
TTTTCTCTTTTTCATTTTTTTTTCT
Found at i:740433 original size:20 final size:19
Alignment explanation
Indices: 740404--740476 Score: 86
Period size: 19 Copynumber: 4.1 Consensus size: 19
740394 AACCCTCCTT
740404 TTTCTCTTTTT-ATTTTTTCA
1 TTTCT-TTTTTCA-TTTTTCA
740424 TTTCTTTTTTCATTTTTCA
1 TTTCTTTTTTCATTTTTCA
740443 TTT-TTTTTTC-TTTTTCA
1 TTTCTTTTTTCATTTTTCA
740460 --T-TTTTTTCATTTTTCA
1 TTTCTTTTTTCATTTTTCA
740476 T
1 T
740477 CTTTTTATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 9
0.85 0.00 0.15
Matches are distributed among these distances:
15 8 0.16
16 7 0.14
17 7 0.14
18 7 0.14
19 15 0.30
20 6 0.12
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTCTTTTTTCATTTTTCA
Found at i:740449 original size:16 final size:16
Alignment explanation
Indices: 740428--740486 Score: 77
Period size: 16 Copynumber: 3.7 Consensus size: 16
740418 TTTTCATTTC
740428 TTTTTTCATTTTTCATTT
1 TTTTTTCATTTTTCA--T
740446 TTTTTTC-TTTTTCAT
1 TTTTTTCATTTTTCAT
740461 TTTTTTCATTTTTCAT
1 TTTTTTCATTTTTCAT
*
740477 CTTTTT-ATTT
1 TTTTTTCATTT
740487 GTTCCCTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
15 12 0.31
16 13 0.33
17 7 0.18
18 7 0.18
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTTCATTTTTCAT
Found at i:740497 original size:33 final size:33
Alignment explanation
Indices: 740402--740499 Score: 103
Period size: 33 Copynumber: 2.9 Consensus size: 33
740392 CAAACCCTCC
740402 TTTTTC-TCTTTTTATTTTTT-CATTTCTTTTTTCA
1 TTTTTCATCTTTTTATTTTTTCCA--T-TTTTTTCA
* *
740436 TTTTTCAT-TTTTTTTTCTTTTTCATTTTTTTCA
1 TTTTTCATCTTTTTATT-TTTTCCATTTTTTTCA
* *
740469 TTTTTCATCTTTTTATTTGTTCCCTTTTTTT
1 TTTTTCATCTTTTTATTTTTTCCATTTTTTT
740500 TCTTCAAGCA
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
33 27 0.49
34 21 0.38
35 5 0.09
36 2 0.04
ACGTcount: A:0.08, C:0.14, G:0.01, T:0.77
Consensus pattern (33 bp):
TTTTTCATCTTTTTATTTTTTCCATTTTTTTCA
Done.