Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008546.1 Hibiscus syriacus cultivar Beakdansim tig00111435_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: 125781
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:8303 original size:24 final size:23
Alignment explanation
Indices: 8267--8313 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
8257 GCCGATACAA
*
8267 TAATAATTTTAAATTGTGTTATTT
1 TAATAATTGTAAA-TGTGTTATTT
* *
8291 TAATTATTGTAAATGTTTTATTT
1 TAATAATTGTAAATGTGTTATTT
8314 ATTTATTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.60
Consensus pattern (23 bp):
TAATAATTGTAAATGTGTTATTT
Found at i:10643 original size:23 final size:22
Alignment explanation
Indices: 10617--10691 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 22
10607 TGACATATGA
10617 ATATGCAATACGTGATACATGTG
1 ATATG-AATACGTGATACATGTG
* ** *
10640 ATATG-ATATGAAATGACATATG
1 ATATGAATACGTGAT-ACATGTG
10662 AATATGTAATACGTGATACATGTG
1 -ATATG-AATACGTGATACATGTG
10686 ATATGA
1 ATATGA
10692 TATGAAATAC
Statistics
Matches: 40, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
21 6 0.15
22 7 0.17
23 15 0.38
24 6 0.15
25 6 0.15
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (22 bp):
ATATGAATACGTGATACATGTG
Found at i:10649 original size:46 final size:46
Alignment explanation
Indices: 10599--10703 Score: 194
Period size: 46 Copynumber: 2.3 Consensus size: 46
10589 CTATGTGACT
10599 ATATGAAATGACATATGAATATGCAATACGTGATACATGTGATATG
1 ATATGAAATGACATATGAATATGCAATACGTGATACATGTGATATG
*
10645 ATATGAAATGACATATGAATATGTAATACGTGATACATGTGATATG
1 ATATGAAATGACATATGAATATGCAATACGTGATACATGTGATATG
10691 ATATGAAAT-ACAT
1 ATATGAAATGACAT
10704 GGTTACACAT
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
45 4 0.07
46 54 0.93
ACGTcount: A:0.43, C:0.08, G:0.18, T:0.31
Consensus pattern (46 bp):
ATATGAAATGACATATGAATATGCAATACGTGATACATGTGATATG
Found at i:10890 original size:21 final size:21
Alignment explanation
Indices: 10865--10911 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
10855 ATAGGTCCCA
*
10865 CGGGACACAGATTACATCCTT
1 CGGGACACAGATGACATCCTT
* *
10886 TGGGACACAGATGATATCCTT
1 CGGGACACAGATGACATCCTT
10907 CGGGA
1 CGGGA
10912 TGATAGGTCC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (21 bp):
CGGGACACAGATGACATCCTT
Found at i:10915 original size:15 final size:16
Alignment explanation
Indices: 10895--10928 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
10885 TTGGGACACA
10895 GATGATA-TCCTTCGG
1 GATGATAGTCCTTCGG
10910 GATGATAGGTCCTTCGG
1 GATGATA-GTCCTTCGG
10927 GA
1 GA
10929 CATTTGTACG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
17 10 0.59
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (16 bp):
GATGATAGTCCTTCGG
Found at i:17383 original size:46 final size:46
Alignment explanation
Indices: 17327--17419 Score: 141
Period size: 46 Copynumber: 2.0 Consensus size: 46
17317 CTATGTGACT
* * * *
17327 ATATGAAATGATATATGAATATGCAATACGTGATATATGTGATATG
1 ATATGAAATGACATATGAATATGCAATACGAGATACATATGATATG
*
17373 ATATGAAATGACATATGAATATGTAATACGAGATACATATGATATG
1 ATATGAAATGACATATGAATATGCAATACGAGATACATATGATATG
17419 A
1 A
17420 AATACATGGT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.44, C:0.05, G:0.18, T:0.32
Consensus pattern (46 bp):
ATATGAAATGACATATGAATATGCAATACGAGATACATATGATATG
Found at i:17424 original size:23 final size:23
Alignment explanation
Indices: 17339--17420 Score: 71
Period size: 23 Copynumber: 3.6 Consensus size: 23
17329 ATGAAATGAT
* *
17339 ATATGAATATGCAATACGTGATAT
1 ATATGAATATG-AATACGAGATAC
* * *
17363 ATGTG-ATATG-ATATGAAATGAC
1 ATATGAATATGAATACGAGAT-AC
17385 ATATGAATATGTAATACGAGATAC
1 ATATGAATATG-AATACGAGATAC
17409 ATATG-ATATGAA
1 ATATGAATATGAA
17421 ATACATGGTT
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
21 6 0.13
22 7 0.15
23 15 0.33
24 11 0.24
25 7 0.15
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (23 bp):
ATATGAATATGAATACGAGATAC
Found at i:17607 original size:21 final size:21
Alignment explanation
Indices: 17583--17634 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
17573 ATATGATAGG
* *
17583 TCCTACGGGACACAGATTACA
1 TCCTTCGGGACACAGATGACA
17604 TCCTTCGGGACACAGATGACA
1 TCCTTCGGGACACAGATGACA
17625 TCCTTCGGGA
1 TCCTTCGGGA
17635 TGATAGGTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.27, C:0.29, G:0.23, T:0.21
Consensus pattern (21 bp):
TCCTTCGGGACACAGATGACA
Found at i:18845 original size:21 final size:21
Alignment explanation
Indices: 18767--18867 Score: 103
Period size: 21 Copynumber: 4.8 Consensus size: 21
18757 GCATCGTAGC
* * *
18767 CATTTCATATGGCACCGCATT
1 CATTTCAGATGGCACCACAGT
* * **
18788 CGTTTCAGATGGCACAACAAC
1 CATTTCAGATGGCACCACAGT
18809 CATTTCAGATGGCACCACAGT
1 CATTTCAGATGGCACCACAGT
* *
18830 CATTTCAGATGCCACCGCAGT
1 CATTTCAGATGGCACCACAGT
* *
18851 CAGTTCAGATGCCACCA
1 CATTTCAGATGGCACCA
18868 TTGCAGGATT
Statistics
Matches: 66, Mismatches: 14, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
21 66 1.00
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.24
Consensus pattern (21 bp):
CATTTCAGATGGCACCACAGT
Found at i:22111 original size:31 final size:30
Alignment explanation
Indices: 22076--22167 Score: 73
Period size: 31 Copynumber: 3.0 Consensus size: 30
22066 TTAATATTTC
22076 AATTTCATCCCTAAATTATGACTCTCATTCT
1 AATTTCATCCCTAAATTATGAC-CTCATTCT
* * *
22107 AATTT-AGTCCTTAAACTTTTGA--ACATTCT
1 AATTTCA-TCCCTAAA-TTATGACCTCATTCT
* * *
22136 AATTCCATCCCTAAACTATGACCCTCTTTCT
1 AATTTCATCCCTAAATTATGA-CCTCATTCT
22167 A
1 A
22168 CATCCCCAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
28 4 0.09
29 17 0.37
30 2 0.04
31 18 0.39
32 5 0.11
ACGTcount: A:0.29, C:0.26, G:0.04, T:0.40
Consensus pattern (30 bp):
AATTTCATCCCTAAATTATGACCTCATTCT
Found at i:22118 original size:60 final size:60
Alignment explanation
Indices: 22028--22167 Score: 160
Period size: 60 Copynumber: 2.3 Consensus size: 60
22018 ATATGTCTTC
* * * * *
22028 AAACTATAACCCTCATTTTAAATT-GTTCCTTAAACTTCTT-AATATT-TCAATTTCATCCCT
1 AAACTATGACCCTCATTCTAATTTAG-TCCTTAAACTT-TTGAACATTCT-AATTCCATCCCT
* *
22088 AAATTATGACTCTCATTCTAATTTAGTCCTTAAACTTTTGAACATTCTAATTCCATCCCT
1 AAACTATGACCCTCATTCTAATTTAGTCCTTAAACTTTTGAACATTCTAATTCCATCCCT
*
22148 AAACTATGACCCTCTTTCTA
1 AAACTATGACCCTCATTCTA
22168 CATCCCCAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
59 2 0.03
60 63 0.94
61 2 0.03
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.41
Consensus pattern (60 bp):
AAACTATGACCCTCATTCTAATTTAGTCCTTAAACTTTTGAACATTCTAATTCCATCCCT
Found at i:28903 original size:3 final size:3
Alignment explanation
Indices: 28895--29010 Score: 146
Period size: 3 Copynumber: 39.0 Consensus size: 3
28885 TTATTTATTA
*
28895 AAT AAT AAT AAT -AT AAT ATT AAT AAT AAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
* * * *
28940 AAT AAT AAT TAT AAT AAT AAT -AT ACT AAT ACT AAT AAT AAT ACT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
28987 AAT AAT AAT TTT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT
29011 TTTAAATGAA
Statistics
Matches: 96, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
2 4 0.04
3 89 0.93
4 3 0.03
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:29457 original size:76 final size:76
Alignment explanation
Indices: 29142--29705 Score: 1022
Period size: 76 Copynumber: 7.4 Consensus size: 76
29132 GAAACGTTGA
*
29142 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAATATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
29207 AGGCTTTTTGG
66 AGGCTTTTTGG
*
29218 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTG-AAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
*
29282 CGGCTTTTTGG
66 AGGCTTTTTGG
*
29293 AAACATCATGCACTGGAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-TTTTGAAAACATCAAAAAGCTCCCG
29358 AAGGCTTTTTGG
65 AAGGCTTTTTGG
*
29370 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
29435 AGGCTTTTTGG
66 AGGCTTTTTGG
*
29446 AAACATCATGCACTGGAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-TTTTGAAAACATCAAAAAGCTCCCG
29511 AAGGCTTTTTGG
65 AAGGCTTTTTGG
*
29523 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
29588 AGGCTTTTTGG
66 AGGCTTTTTGG
*
29599 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
29664 AGGCTTTTTGG
66 AGGCTTTTTGG
*
29675 AAACATCATGCACTGGAGGACTTACAGATGA
1 AAACATCATGCACTGAAGGACTTACAGATGA
29706 GGGAAATAGA
Statistics
Matches: 470, Mismatches: 15, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
75 67 0.14
76 262 0.56
77 141 0.30
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:29493 original size:153 final size:152
Alignment explanation
Indices: 29142--29705 Score: 1031
Period size: 153 Copynumber: 3.7 Consensus size: 152
29132 GAAACGTTGA
*
29142 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAATATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
29207 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTG-AAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
*
29271 AAAGCTCCCGACGGCTTTTTGG
131 AAAGCTCCCGAAGGCTTTTTGG
*
29293 AAACATCATGCACTGGAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-TTTTGAAAACATCAAAAAGCTCCCG
29358 AAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCA
65 AAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCA
29423 AAAAGCTCCCGAAGGCTTTTTGG
130 AAAAGCTCCCGAAGGCTTTTTGG
*
29446 AAACATCATGCACTGGAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-TTTTGAAAACATCAAAAAGCTCCCG
* *
29511 AAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCA
65 AAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCA
29576 AAAAGCTCCCGAAGGCTTTTTGG
130 AAAAGCTCCCGAAGGCTTTTTGG
*
29599 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
*
29664 AGGCTTTTTGGAAACATCATGCACTGGAGGACTTACAGATGA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
29706 GGGAAATAGA
Statistics
Matches: 402, Mismatches: 9, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
151 38 0.09
152 145 0.36
153 219 0.54
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (152 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
AAAGCTCCCGAAGGCTTTTTGG
Found at i:30399 original size:22 final size:22
Alignment explanation
Indices: 30371--30425 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
30361 CATAAAATTT
* **
30371 TCATCTTTGGAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCCA
*
30393 TCATCTTTAAAAAGAGAATCCA
1 TCATCTTTGAAAAGAGAATCCA
30415 TCATCTTTGAA
1 TCATCTTTGAA
30426 GAGTGTAGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCCA
Found at i:30871 original size:54 final size:54
Alignment explanation
Indices: 30789--30961 Score: 226
Period size: 54 Copynumber: 3.3 Consensus size: 54
30779 AGAATAGCAG
* ***
30789 GTTCGTAAAACATTTGATAGTGCATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
* * *
30843 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTTAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
* **
30897 GTTCGTAAAACATTTGACAACATATTCAT--TTTTTTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
*
30949 GTTC-TCAAACATT
1 GTTCGTAAAACATT
30962 GAATCTCTTT
Statistics
Matches: 105, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
51 8 0.08
52 22 0.21
54 75 0.71
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
Found at i:32569 original size:92 final size:92
Alignment explanation
Indices: 32401--32684 Score: 473
Period size: 92 Copynumber: 3.1 Consensus size: 92
32391 CTTATTTCTA
*
32401 CTATGAGCAAAATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAG
1 CTATGAGC-ACATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAG
*
32466 ATAACTCAAAGAACACTTCCAAAAGATG
65 ATAACTCAAAGAACACTTCCAGAAGATG
32494 CTATGAGCACATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGA
1 CTATGAGCACATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGA
32559 TAACTCAAAGAACACTTCCAGAAGATG
66 TAACTCAAAGAACACTTCCAGAAGATG
** * *
32586 CTATGAGCACATTCATCTTTCAAATTTAATGATT-AGTTCTGTG-GTTCATACCAAACCAGATCA
1 CTATGAGCACATTCATCTTTCAAATCCAATGATTGA-TTTTG-GAGTTCATACCAAATCAGATCA
32649 GATAACTCAAAGAACACTTCCAGAAGATG
64 GATAACTCAAAGAACACTTCCAGAAGATG
32678 CTATGAG
1 CTATGAG
32685 TATATTGCAT
Statistics
Matches: 183, Mismatches: 6, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
91 1 0.01
92 173 0.95
93 9 0.05
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (92 bp):
CTATGAGCACATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGA
TAACTCAAAGAACACTTCCAGAAGATG
Found at i:34757 original size:8 final size:8
Alignment explanation
Indices: 34744--34809 Score: 57
Period size: 8 Copynumber: 8.4 Consensus size: 8
34734 TTGATTCAAT
34744 TTTTTTTC
1 TTTTTTTC
34752 -TTTTTTC
1 TTTTTTTC
*
34759 TTTTTTTG
1 TTTTTTTC
34767 TTTTGTTT-
1 TTTT-TTTC
* *
34775 TGTTTTTG
1 TTTTTTTC
34783 TTTTTTGT-
1 TTTTTT-TC
34791 TTTTTTTC
1 TTTTTTTC
*
34799 TTTCTTTC
1 TTTTTTTC
34807 TTT
1 TTT
34810 GCTGGATGAG
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
7 11 0.22
8 34 0.69
9 4 0.08
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.85
Consensus pattern (8 bp):
TTTTTTTC
Found at i:35109 original size:2 final size:2
Alignment explanation
Indices: 35102--35147 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
35092 ATAACAAAGG
35102 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
35144 AT AT
1 AT AT
35148 TAAAGGATAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41702 original size:3 final size:3
Alignment explanation
Indices: 41694--41805 Score: 152
Period size: 3 Copynumber: 37.0 Consensus size: 3
41684 TTATTTATTA
*
41694 AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
41740 AAT TAT AAT AAT AAT AAT ACT AAT ACT AAT AAT AAT ACT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
41788 AAT TTT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT
41806 TTTAAATGAA
Statistics
Matches: 94, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
3 91 0.97
4 3 0.03
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:48293 original size:17 final size:16
Alignment explanation
Indices: 48271--48304 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
48261 TGCAAGATGG
48271 TTTTATTAAAAATAATA
1 TTTTATTAAAAA-AATA
*
48288 TTTTATTATAAAAATA
1 TTTTATTAAAAAAATA
48304 T
1 T
48305 GCATATGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTTATTAAAAAAATA
Found at i:62460 original size:65 final size:64
Alignment explanation
Indices: 62341--62550 Score: 216
Period size: 65 Copynumber: 3.2 Consensus size: 64
62331 TTTTTCAGAG
* *
62341 TGATGCA-CTGATGCACCAATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATG
1 TGATGCATC-GATGCACCAA-CCATGCACCGATGCACTCAGGATATT---TTGAAACATCGAATG
62402 CATT
61 CATT
* * *
62406 TCATGCATCGATGC-TCATACCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCA
1 TGATGCATCGATGCACCA-ACCATGCACCGATGCACTCAGGATATTT-TG-AAACATCGAATGCA
62469 TT
63 TT
* * * * *
62471 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCACCAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
62535 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
62551 TCTTAGTGCA
Statistics
Matches: 123, Mismatches: 13, Indels: 19
0.79 0.08 0.12
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 48 0.39
65 66 0.54
66 6 0.05
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (64 bp):
TGATGCATCGATGCACCAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:62550 original size:17 final size:19
Alignment explanation
Indices: 62522--62570 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
62512 TATTTTGAAA
62522 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
62540 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
62559 CACCGATGCACT
1 CATCGATGCACT
62571 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:62566 original size:64 final size:64
Alignment explanation
Indices: 62391--62570 Score: 190
Period size: 65 Copynumber: 2.8 Consensus size: 64
62381 AATTAAATTG
* * * *
62391 AACATCGAATGCATTTCATGCATCGATGCTCATACCA-TGCACCGATGCACTGAGGATTTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCAC-T-CTAGTGCACCGATGCACTCAGGATTTTATGA
62455 A
64 A
* * *
62456 AACATCGAATGCATTTGATGCATCGATGCAC-C-AGCCATGCATCGATGCACTCTGGCTATTT-T
1 AACATCGAATGCATTTGATGCATCGATGCACTCTAG---TGCACCGATGCACTCAGGAT-TTTAT
62518 G-A
62 GAA
*
62520 AACATCGAATGCACTTGATGCATCGATGCACTCTTAGTGCACCGATGCACT
1 AACATCGAATGCATTTGATGCATCGATGCACTC-TAGTGCACCGATGCACT
62571 AAGGGTCCAA
Statistics
Matches: 99, Mismatches: 8, Indels: 17
0.80 0.06 0.14
Matches are distributed among these distances:
61 1 0.01
62 1 0.01
64 44 0.44
65 48 0.48
66 3 0.03
67 2 0.02
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCGATGCACTCTAGTGCACCGATGCACTCAGGATTTTATGAA
Found at i:75682 original size:46 final size:45
Alignment explanation
Indices: 75626--75732 Score: 144
Period size: 45 Copynumber: 2.4 Consensus size: 45
75616 TGCACATACC
* * *
75626 ATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCATTTG
1 ATGCATCGATGCACTCAGGATATTT-TG-AAACATCGAATGCACTTG
* *
75672 ATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTG
1 ATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCACTTG
75717 ATGCATCGATGCACTC
1 ATGCATCGATGCACTC
75733 TTAGTGCACT
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
45 33 0.60
46 19 0.35
47 3 0.05
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (45 bp):
ATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCACTTG
Found at i:78956 original size:67 final size:66
Alignment explanation
Indices: 78823--78956 Score: 259
Period size: 67 Copynumber: 2.0 Consensus size: 66
78813 GTTCTTGTGT
78823 TGGTACACCCCAGCAAAATGGGTAGATAAGAAAAAAACATAAACATTTGTTAAAGGTCGCTCGTG
1 TGGTACACCCCAGCAAAATGGGTAGATAAGAAAAAAACATAAACATTTGTTAAAGGTCGCTCGTG
78888 C
66 C
78889 TGGTACACCCCAGCAAAATGGGTAGATAAGAAAAAAAACATAAACATTTGTTAAAGGTCGCTCGT
1 TGGTACACCCCAGCAAAATGGGTAGATAAG-AAAAAAACATAAACATTTGTTAAAGGTCGCTCGT
78954 GC
65 GC
78956 T
1 T
78957 TAACATTTTC
Statistics
Matches: 67, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
66 30 0.45
67 37 0.55
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.22
Consensus pattern (66 bp):
TGGTACACCCCAGCAAAATGGGTAGATAAGAAAAAAACATAAACATTTGTTAAAGGTCGCTCGTG
C
Found at i:88314 original size:13 final size:13
Alignment explanation
Indices: 88298--88322 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
88288 CGAATTGTCA
88298 CCCACAATTGATT
1 CCCACAATTGATT
88311 CCCACAATTGAT
1 CCCACAATTGAT
88323 ATATTTTATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.32, G:0.08, T:0.28
Consensus pattern (13 bp):
CCCACAATTGATT
Found at i:91870 original size:20 final size:21
Alignment explanation
Indices: 91847--92240 Score: 341
Period size: 21 Copynumber: 19.3 Consensus size: 21
91837 GATTCTGACT
91847 ATCGCATTGCGA-TTACGTAA
1 ATCGCATTGCGATTTACGTAA
* * * *
91867 ATCGCAATGCGAATTAGGAAA
1 ATCGCATTGCGATTTACGTAA
*
91888 ATCGCAATGCGA-TTACGTAA
1 ATCGCATTGCGATTTACGTAA
* * * *
91908 ATCGCAATGCGAATTAGGAAA
1 ATCGCATTGCGATTTACGTAA
*
91929 ATCGCAATGCGA-TTACGT-A
1 ATCGCATTGCGATTTACGTAA
* * *
91948 TTCGCATTGCGATTTTCCTAA
1 ATCGCATTGCGATTTACGTAA
*
91969 TTCGCATTGCGATTTACGT-A
1 ATCGCATTGCGATTTACGTAA
* *
91989 ATCGCATTGCGATTTTCCT-A
1 ATCGCATTGCGATTTACGTAA
92009 ATACGCATTGCGATTTACGT-A
1 AT-CGCATTGCGATTTACGTAA
* * * *
92030 ATCTCATTGCGATTTTCCTGA
1 ATCGCATTGCGATTTACGTAA
* * * *
92051 TTCGCATTGCGATTTTCCTGA
1 ATCGCATTGCGATTTACGTAA
* *
92072 TTCGCATTGCGATTTTTC-TAA
1 ATCGCATTGCGA-TTTACGTAA
*
92093 TTCGCATTGCGATTTACGT-A
1 ATCGCATTGCGATTTACGTAA
*
92113 ACCGCATTGCGATTTACGT-A
1 ATCGCATTGCGATTTACGTAA
*
92133 ATCGCATTGCGATTTTAC-TAT
1 ATCGCATTGCGA-TTTACGTAA
*
92154 TTCGCATTGCGATTTACGT-A
1 ATCGCATTGCGATTTACGTAA
* * *
92174 ATCGCATTACGATTTTCCTAA
1 ATCGCATTGCGATTTACGTAA
*
92195 TTCGCACTT-CGATTTACGT-A
1 ATCGCA-TTGCGATTTACGTAA
92215 ATCGCATTGCGATTTA-GTAA
1 ATCGCATTGCGATTTACGTAA
92235 ATCGCA
1 ATCGCA
92241 ACGAGATTCT
Statistics
Matches: 318, Mismatches: 41, Indels: 30
0.82 0.11 0.08
Matches are distributed among these distances:
19 15 0.05
20 146 0.46
21 150 0.47
22 7 0.02
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (21 bp):
ATCGCATTGCGATTTACGTAA
Found at i:91893 original size:41 final size:40
Alignment explanation
Indices: 91847--92000 Score: 182
Period size: 41 Copynumber: 3.8 Consensus size: 40
91837 GATTCTGACT
*
91847 ATCGCATTGCGATTACGTAAATCGCAATGCGAATTAGGAAA
1 ATCGCAATGCGATTACGT-AATCGCAATGCGAATTAGGAAA
91888 ATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGAAA
1 ATCGCAATGCGATTACGT-AATCGCAATGCGAATTAGGAAA
* * * ****
91929 ATCGCAATGCGATTACGTATTCGCATTGCGATTTTCCTAA
1 ATCGCAATGCGATTACGTAATCGCAATGCGAATTAGGAAA
* * *
91969 TTCGCATTGCGATTTACGTAATCGCATTGCGA
1 ATCGCAATGCGA-TTACGTAATCGCAATGCGA
92001 TTTTCCTAAT
Statistics
Matches: 101, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
40 25 0.25
41 76 0.75
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (40 bp):
ATCGCAATGCGATTACGTAATCGCAATGCGAATTAGGAAA
Found at i:92001 original size:41 final size:41
Alignment explanation
Indices: 91930--92240 Score: 339
Period size: 41 Copynumber: 7.6 Consensus size: 41
91920 ATTAGGAAAA
* *
91930 TCGCAATGCGA-TTACGTATTCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
91970 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
* * *
92011 ACGCATTGCGATTTACGTAATCTCATTGCGATTTTCCTGAT
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
* * * *
92052 TCGCATTGCGATTTTCCTGATTCGCATTGCGATTTTTCTAAT
1 TCGCATTGCGATTTACGT-AATCGCATTGCGATTTTCCTAAT
* * *
92094 TCGCATTGCGATTTACGTAACCGCATTGCGATTTACGTAA-
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
* * *
92134 TCGCATTGCGATTTTAC-TATTTCGCATTGCGATTTACGTAA-
1 TCGCATTGCGA-TTTACGTA-ATCGCATTGCGATTTTCCTAAT
* * * * *
92175 TCGCATTACGATTTTCCTAATTCGCACTT-CGATTTACGTAA-
1 TCGCATTGCGATTTACGTAA-TCGCA-TTGCGATTTTCCTAAT
92216 TCGCATTGCGATTTA-GTAAATCGCA
1 TCGCATTGCGATTTACGT-AATCGCA
92241 ACGAGATTCT
Statistics
Matches: 236, Mismatches: 27, Indels: 16
0.85 0.10 0.06
Matches are distributed among these distances:
40 33 0.14
41 166 0.70
42 37 0.16
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.39
Consensus pattern (41 bp):
TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
Found at i:92048 original size:82 final size:81
Alignment explanation
Indices: 91847--92240 Score: 352
Period size: 82 Copynumber: 4.8 Consensus size: 81
91837 GATTCTGACT
* * *** *
91847 ATCGCATTGCGA-TTACGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGA-TTACGTAAAT
1 ATCGCATTGCGATTTACGT-AATCGCATTGCGATTTA-CCTAATCGCATTGCGATTTACGTAAAT
* *****
91910 CGCAATGCGAATTAGGAAA
64 CGCATTGCG-ATTTTCCTA
* * *
91929 ATCGCAATGCGA-TTACGTATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGT-AATC
1 ATCGCATTGCGATTTACGTAATCGCATTGCGATTTACCTAA-TCGCATTGCGATTTACGTAAATC
91992 GCATTGCGATTTTCCTA
65 GCATTGCGATTTTCCTA
* * * * * * *
92009 ATACGCATTGCGATTTACGTAATCTCATTGCGATTTTCCTGATTCGCATTGCGATTTTCCTGATT
1 AT-CGCATTGCGATTTACGTAATCGCATTGCGATTTACCT-AATCGCATTGCGATTTACGTAAAT
*
92074 CGCATTGCGATTTTTCTA
64 CGCATTGCGATTTTCCTA
* * **
92092 ATTCGCATTGCGATTTACGTAACCGCATTGCGATTTACGTAATCGCATTGCGATTTTAC-TATTT
1 A-TCGCATTGCGATTTACGTAATCGCATTGCGATTTACCTAATCGCATTGCGA-TTTACGTAAAT
* *
92156 CGCATTGCGATTTACGTA
64 CGCATTGCGATTTTCCTA
* * * *
92174 ATCGCATTACGATTTTCCTAATTCGCACTT-CGATTTACGTAATCGCATTGCGATTTA-GTAAAT
1 ATCGCATTGCGATTTACGTAA-TCGCA-TTGCGATTTACCTAATCGCATTGCGATTTACGTAAAT
92237 CGCA
64 CGCA
92241 ACGAGATTCT
Statistics
Matches: 261, Mismatches: 40, Indels: 23
0.81 0.12 0.07
Matches are distributed among these distances:
80 8 0.03
81 71 0.27
82 121 0.46
83 60 0.23
84 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (81 bp):
ATCGCATTGCGATTTACGTAATCGCATTGCGATTTACCTAATCGCATTGCGATTTACGTAAATCG
CATTGCGATTTTCCTA
Found at i:93155 original size:24 final size:24
Alignment explanation
Indices: 93104--93157 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
93094 GTATTCGACA
*
93104 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
93128 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
93152 TTTGAT
1 TTTGAT
93158 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:95712 original size:19 final size:20
Alignment explanation
Indices: 95669--95723 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
95659 CAATCATCTT
*
95669 AATGTCTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
*
95689 AATGACTATCGCAATGCG-A
1 AATGACTATCGCAACGCGAA
**
95708 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
95724 AGAGAATCGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.18
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:95733 original size:14 final size:14
Alignment explanation
Indices: 95714--95801 Score: 59
Period size: 14 Copynumber: 5.6 Consensus size: 14
95704 GCGAAATGAA
95714 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
95728 AATCGCAATACGAAATGAA
1 AATCGC-A-ACG--A-GAG
95747 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
95761 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
95780 AATCGCAACGAGGG
1 AATCGCAACGAGAG
95794 AATCGCAA
1 AATCGCAA
95802 AAACGAAATG
Statistics
Matches: 59, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
14 25 0.42
15 3 0.05
16 5 0.08
17 5 0.08
18 3 0.05
19 18 0.31
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:95742 original size:33 final size:33
Alignment explanation
Indices: 95696--95823 Score: 211
Period size: 33 Copynumber: 3.8 Consensus size: 33
95686 GAAAATGACT
*
95696 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATACGAAATGAAAATCGCAACGAGAGA
95729 ATCGCAATACGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATACGAAATGAAAATCGCAACGAGAGA
* *
95762 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATACGAAATGAAAATCGCAACGAGAGA
*
95795 ATCGCAAAAACGAAATGAAAATCGCAACG
1 ATCGC-AATACGAAATGAAAATCGCAACG
95824 CAAATTTAGT
Statistics
Matches: 89, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
33 68 0.76
34 21 0.24
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.12
Consensus pattern (33 bp):
ATCGCAATACGAAATGAAAATCGCAACGAGAGA
Found at i:95752 original size:19 final size:19
Alignment explanation
Indices: 95696--95787 Score: 78
Period size: 19 Copynumber: 5.4 Consensus size: 19
95686 GAAAATGACT
*
95696 ATCGCAATGCGAAATGAAA
1 ATCGCAATACGAAATGAAA
*
95715 ATCGC-A-ACG--A-GAGA
1 ATCGCAATACGAAATGAAA
95729 ATCGCAATACGAAATGAAA
1 ATCGCAATACGAAATGAAA
*
95748 ATCGC-A-ACG--A-GAGA
1 ATCGCAATACGAAATGAAA
*
95762 ATCGCAATGCGAAATGAAA
1 ATCGCAATACGAAATGAAA
95781 ATCGCAA
1 ATCGCAA
95788 CGAGGGAATC
Statistics
Matches: 57, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 16 0.28
15 4 0.07
16 5 0.09
17 5 0.09
18 4 0.07
19 23 0.40
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
ATCGCAATACGAAATGAAA
Found at i:95852 original size:19 final size:19
Alignment explanation
Indices: 95828--95903 Score: 93
Period size: 19 Copynumber: 4.0 Consensus size: 19
95818 GCAACGCAAA
* *
95828 TTTAGTTTCGAGTGGCGAT
1 TTTAGTTTCGCGTTGCGAT
95847 TTTAGTTTCGCGTTGCGAT
1 TTTAGTTTCGCGTTGCGAT
95866 TTTCA-TTTCGCGTTGCGAT
1 TTT-AGTTTCGCGTTGCGAT
*
95885 TTTCA-TTTCGCATTGCGAT
1 TTT-AGTTTCGCGTTGCGAT
95904 AGTCATTTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
19 52 0.98
20 1 0.02
ACGTcount: A:0.13, C:0.17, G:0.24, T:0.46
Consensus pattern (19 bp):
TTTAGTTTCGCGTTGCGAT
Found at i:95910 original size:38 final size:38
Alignment explanation
Indices: 95833--95911 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 38
95823 GCAAATTTAG
* **
95833 TTTCGAGTGGCGATTTTAGTTTCGCGTTGCGATTTTCA
1 TTTCGAGTGGCGATTTTAGTTTCGCATTGCGATAGTCA
* *
95871 TTTCGCGTTGCGATTTTCA-TTTCGCATTGCGATAGTCA
1 TTTCGAGTGGCGATTTT-AGTTTCGCATTGCGATAGTCA
95909 TTT
1 TTT
95912 TTGCCTTCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
38 34 0.97
39 1 0.03
ACGTcount: A:0.14, C:0.18, G:0.23, T:0.46
Consensus pattern (38 bp):
TTTCGAGTGGCGATTTTAGTTTCGCATTGCGATAGTCA
Found at i:95911 original size:19 final size:19
Alignment explanation
Indices: 95842--95903 Score: 99
Period size: 19 Copynumber: 3.3 Consensus size: 19
95832 GTTTCGAGTG
95842 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCA-TTTCGCGTT
95861 GCGATTTTCATTTCGCGTT
1 GCGATTTTCATTTCGCGTT
*
95880 GCGATTTTCATTTCGCATT
1 GCGATTTTCATTTCGCGTT
95899 GCGAT
1 GCGAT
95904 AGTCATTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
19 40 0.98
20 1 0.02
ACGTcount: A:0.13, C:0.19, G:0.23, T:0.45
Consensus pattern (19 bp):
GCGATTTTCATTTCGCGTT
Found at i:96030 original size:14 final size:14
Alignment explanation
Indices: 96011--96047 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
96001 CATCAATTAA
96011 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
96025 ACAAATCATCTTTT
1 ACAAATCAACTTTT
96039 ACAAATCAA
1 ACAAATCAA
96048 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:97942 original size:19 final size:19
Alignment explanation
Indices: 97918--97978 Score: 78
Period size: 19 Copynumber: 3.5 Consensus size: 19
97908 AAAAAAGACT
97918 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
97937 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
97951 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
97970 ATCGCAACG
1 ATCGCAACG
97979 ACAAAATCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 19 0.54
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.10
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:97960 original size:33 final size:33
Alignment explanation
Indices: 97918--97997 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
97908 AAAAAAGACT
* *
97918 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
97951 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
97984 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
97998 CCAAAAATCG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.46, C:0.24, G:0.21, T:0.09
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:98050 original size:20 final size:20
Alignment explanation
Indices: 98021--98058 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
98011 TGCGATTATA
*
98021 GTTTCGCGTTGCGATTTTTG
1 GTTTCACGTTGCGATTTTTG
98041 GTTTCACGTTGCGATTTT
1 GTTTCACGTTGCGATTTT
98059 GTCGTTGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.16, G:0.26, T:0.50
Consensus pattern (20 bp):
GTTTCACGTTGCGATTTTTG
Found at i:98087 original size:33 final size:36
Alignment explanation
Indices: 98042--98131 Score: 105
Period size: 33 Copynumber: 2.5 Consensus size: 36
98032 CGATTTTTGG
98042 TTTCACGTTGCGATTTT-G-T-CGTTGCGAATTTCA
1 TTTCACGTTGCGATTTTCGTTCCGTTGCGAATTTCA
* *
98075 TTTCGCGTTGCGATTTTCGTTTCGCGTTGCGATTTTCA
1 TTTCACGTTGCGATTTTCG-TTC-CGTTGCGAATTTCA
*
98113 TTCTCTCGTTGCGATTTTC
1 TT-TCACGTTGCGATTTTC
98132 ATTTCAACCA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
33 16 0.33
34 1 0.02
36 1 0.02
38 15 0.31
39 15 0.31
ACGTcount: A:0.10, C:0.21, G:0.21, T:0.48
Consensus pattern (36 bp):
TTTCACGTTGCGATTTTCGTTCCGTTGCGAATTTCA
Found at i:98110 original size:19 final size:19
Alignment explanation
Indices: 98011--98136 Score: 118
Period size: 19 Copynumber: 6.8 Consensus size: 19
98001 AAAATCGCAA
* *
98011 TGCGATTATAGTTTCGCGT
1 TGCGATTTTCGTTTCGCGT
* *
98030 TGCGATTTTTGGTTTCACGT
1 TGCGA-TTTTCGTTTCGCGT
98050 TGCGATTTT-G--T--CGT
1 TGCGATTTTCGTTTCGCGT
* *
98064 TGCGAATTTCATTTCGCGT
1 TGCGATTTTCGTTTCGCGT
98083 TGCGATTTTCGTTTCGCGT
1 TGCGATTTTCGTTTCGCGT
* *
98102 TGCGATTTTCATTCTCTCGT
1 TGCGATTTTCGTT-TCGCGT
*
98122 TGCGATTTTCATTTC
1 TGCGATTTTCGTTTC
98137 AACCAAAAGA
Statistics
Matches: 91, Mismatches: 9, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
14 11 0.12
16 1 0.01
17 1 0.01
18 1 0.01
19 43 0.47
20 34 0.37
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.48
Consensus pattern (19 bp):
TGCGATTTTCGTTTCGCGT
Found at i:98349 original size:93 final size:93
Alignment explanation
Indices: 98225--98595 Score: 562
Period size: 93 Copynumber: 4.1 Consensus size: 93
98215 ATGGATTGCA
* * *
98225 TTAC-TTCAACCAAAA-CAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACA-TT
1 TTACTTTCAACCAAAAGAAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
*
98287 TAGCAGAATTGGCAGCAAACGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
98315 TTACTTTCAACCAAAAGATAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGA-AAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
98380 TTAGCAGAATTGGCAGCAACCGAACAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
98409 TTACTTTCAACCAAAAGACAAACAAAGACAAATACTAACTTCACAGTGTTAAAG-ATACACAGTT
1 TTACTTTCAACCAAAAGAAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
*
98473 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
* *
98501 TTAC-TTCAACCAAAAGACAAAAAAAAAGACAAATACTAACTTCACAGTGTT----AATAAACAG
1 TTACTTTCAACCAAAAG--AAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
98561 TTTAGCAGTATTGGCAGCAACCGAATAAAT
64 TTTAGCAGAATTGGCAGCAACCGAACAAAT
98591 TTACT
1 TTACT
98596 AAGCAATCTA
Statistics
Matches: 263, Mismatches: 10, Indels: 15
0.91 0.03 0.05
Matches are distributed among these distances:
90 44 0.17
91 23 0.09
92 41 0.16
93 108 0.41
94 47 0.18
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGAAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:100338 original size:19 final size:19
Alignment explanation
Indices: 100274--100391 Score: 173
Period size: 19 Copynumber: 6.1 Consensus size: 19
100264 TCTTTTGGTT
*
100274 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
100293 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
100313 AGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
100333 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
100352 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
* *
100371 GAAATGAAAATTGCAATGC
1 GAAATGAAAATCGCAACGC
100390 GA
1 GA
100392 TTTTGGTTTC
Statistics
Matches: 90, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
19 57 0.63
20 31 0.34
21 2 0.02
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:101017 original size:20 final size:20
Alignment explanation
Indices: 100994--101204 Score: 259
Period size: 20 Copynumber: 10.7 Consensus size: 20
100984 CGATAGTCAG
100994 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
101014 ATTCGCATTGCGATTT---T
1 ATTCGCATTGCGATTTACGT
*
101031 A-TCGCTTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
101050 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
101070 AATTCGCATTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGT
*
101091 AATCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
101111 AATCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * *
101131 ATTCGCATTGCAATTTTCCT
1 ATTCGCATTGCGATTTACGT
* *
101151 AATTCGTATTGTGATTTACGT
1 -ATTCGCATTGCGATTTACGT
* * *
101172 AATCGCGTTACGATTTACGT
1 ATTCGCATTGCGATTTACGT
101192 ATTCGCATTGCGA
1 ATTCGCATTGCGA
101205 ATTAGGAAAA
Statistics
Matches: 161, Mismatches: 24, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
16 13 0.08
17 2 0.01
19 2 0.01
20 111 0.69
21 33 0.20
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:101108 original size:61 final size:58
Alignment explanation
Indices: 100996--101204 Score: 269
Period size: 61 Copynumber: 3.5 Consensus size: 58
100986 ATAGTCAGAT
* *
100996 TCGCATTGCGATTTACGTATTCGCATTGCGATTT-T-ATCGCTTTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTATTCGCATTGCGATTTCTAATCGCATTGCGATTTACGTAA
* *
101052 TCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGT-ATTCGCATTGCGATTT-C-TAATCGCATTGCGATTTACGTAA
* * *
101113 TCGCATTGCGATTTACGTATTCGCATTGCAATTTTCCTAATTCGTATTGTGATTTACGTAA
1 TCGCATTGCGATTTACGTATTCGCATTGCGA-TTT-CTAA-TCGCATTGCGATTTACGTAA
* *
101174 TCGCGTTACGATTTACGTATTCGCATTGCGA
1 TCGCATTGCGATTTACGTATTCGCATTGCGA
101205 ATTAGGAAAA
Statistics
Matches: 133, Mismatches: 13, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
56 16 0.12
57 16 0.12
60 16 0.12
61 85 0.64
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.40
Consensus pattern (58 bp):
TCGCATTGCGATTTACGTATTCGCATTGCGATTTCTAATCGCATTGCGATTTACGTAA
Found at i:101148 original size:81 final size:81
Alignment explanation
Indices: 100994--101204 Score: 322
Period size: 81 Copynumber: 2.7 Consensus size: 81
100984 CGATAGTCAG
* *
100994 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTT---T-ATCGCTTTGCGATTTACGTATTCG
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTATTCG
*
101055 CATTGCGATTTTCCTA
66 CATTGCAATTTTCCTA
101071 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTATTCG
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTATTCG
101136 CATTGCAATTTTCCTA
66 CATTGCAATTTTCCTA
* * * * *
101152 ATTCGTATTGTGATTTACGTAATCGCGTTACGATTTACGTATTCGCATTGCGA
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTAATCGCATTGCGA
101205 ATTAGGAAAA
Statistics
Matches: 122, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
77 35 0.29
80 1 0.01
81 86 0.70
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.40
Consensus pattern (81 bp):
ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTATTCG
CATTGCAATTTTCCTA
Found at i:101225 original size:21 final size:21
Alignment explanation
Indices: 101201--101246 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
101191 TATTCGCATT
101201 GCGAATTAG-GAAAATCGCAAC
1 GCGAATTAGTG-AAATCGCAAC
* *
101222 GCGAATTTGTGAAATCGCAAT
1 GCGAATTAGTGAAATCGCAAC
101243 GCGA
1 GCGA
101247 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (21 bp):
GCGAATTAGTGAAATCGCAAC
Found at i:104612 original size:27 final size:28
Alignment explanation
Indices: 104582--104635 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
104572 AAGAATGGTT
104582 CACTAT-TTCAACAT-AAAAAAAAAGAAA
1 CACTATGTTCAA-ATGAAAAAAAAAGAAA
* *
104609 CACTTTGTTCAAATGAAAAAAGAAGAA
1 CACTATGTTCAAATGAAAAAAAAAGAA
104636 GAAGGAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.57, C:0.13, G:0.09, T:0.20
Consensus pattern (28 bp):
CACTATGTTCAAATGAAAAAAAAAGAAA
Found at i:105766 original size:21 final size:22
Alignment explanation
Indices: 105740--105781 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
105730 GTTTTTAATA
*
105740 AAAGTT-TTTCTTTTCTTTTTC
1 AAAGTTCTTTCTTTTATTTTTC
*
105761 AAAGTTCTTTGTTTTATTTTT
1 AAAGTTCTTTCTTTTATTTTT
105782 ATTTTCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.17, C:0.10, G:0.07, T:0.67
Consensus pattern (22 bp):
AAAGTTCTTTCTTTTATTTTTC
Found at i:110386 original size:64 final size:64
Alignment explanation
Indices: 110311--110443 Score: 248
Period size: 64 Copynumber: 2.1 Consensus size: 64
110301 GTGTACCTCC
* *
110311 TTCATTAATTATTTGGGGTAAATTATTGAATTAATCATTTTTCTTTTATATTTGTATACTTTTG
1 TTCATTAATTATTTGGGGTAAACTATTGAATTAATCATTTTTCTTTTATATTTGTATACTCTTG
110375 TTCATTAATTATTTGGGGTAAACTATTGAATTAATCATTTTTCTTTTATATTTGTATACTCTTG
1 TTCATTAATTATTTGGGGTAAACTATTGAATTAATCATTTTTCTTTTATATTTGTATACTCTTG
110439 TTCAT
1 TTCAT
110444 CAAATTCAAG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 67 1.00
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (64 bp):
TTCATTAATTATTTGGGGTAAACTATTGAATTAATCATTTTTCTTTTATATTTGTATACTCTTG
Done.