Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000482.1 Hibiscus syriacus cultivar Beakdansim tig00000916_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: 2886609
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 16
Found at i:2038590 original size:60 final size:59
Alignment explanation
Indices: 2038479--2038616 Score: 147
Period size: 60 Copynumber: 2.3 Consensus size: 59
2038469 AGTGTATATG
** ** *
2038479 TATAA-TTTGGGATGAAATTGGAATTTCAAAAGTTTGGGGACTACTTTAGAAT-AAAAT
1 TATAATTTTGGGATGAAATTAAAATTTCAAAAGTTTAAGGACTAATTTAGAATGAAAAT
* *
2038536 TCATAGTTTTGGGATGAAATTAAAATGTT-AAAACGTTTAAGGACTAATTTAGAATGATAAT
1 T-ATAATTTTGGGATGAAATTAAAAT-TTCAAAA-GTTTAAGGACTAATTTAGAATGAAAAT
* *
2038597 TATAATTTAGGGATGTAATT
1 TATAATTTTGGGATGAAATT
2038617 GGAATATTTA
Statistics
Matches: 66, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
57 1 0.02
58 3 0.05
59 21 0.32
60 36 0.55
61 5 0.08
ACGTcount: A:0.39, C:0.04, G:0.20, T:0.37
Consensus pattern (59 bp):
TATAATTTTGGGATGAAATTAAAATTTCAAAAGTTTAAGGACTAATTTAGAATGAAAAT
Found at i:2040776 original size:16 final size:16
Alignment explanation
Indices: 2040755--2040789 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2040745 ATTTATTATT
2040755 TATTATTTATGTTACA
1 TATTATTTATGTTACA
* *
2040771 TATTATTTGTGTTATA
1 TATTATTTATGTTACA
2040787 TAT
1 TAT
2040790 AACTTAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.60
Consensus pattern (16 bp):
TATTATTTATGTTACA
Found at i:2045573 original size:2 final size:2
Alignment explanation
Indices: 2045560--2045589 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2045550 GGAAAAAGAA
*
2045560 AT AT AA 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
2045590 CAAAGTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2046572 original size:37 final size:37
Alignment explanation
Indices: 2046483--2046584 Score: 114
Period size: 37 Copynumber: 2.8 Consensus size: 37
2046473 GTGCTTGTGG
* * * * * *
2046483 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
* *
2046520 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
* *
2046557 ATCCTATTTTTAGGAGTCTGAATTCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
2046585 TAGGACGAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
Found at i:2047539 original size:109 final size:105
Alignment explanation
Indices: 2047137--2047704 Score: 521
Period size: 109 Copynumber: 5.4 Consensus size: 105
2047127 TCCGAGTCCA
* *** *
2047137 ATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAACCAGCCG
1 ATATCCTCCGTCGTGAAGTTGAAATCGGCTCT-GAAATTGAAAATTG-TTGTTGACAACCAGCCG
* * *
2047202 TCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTC-CA
64 TCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGGAGGCACG
* * * * * *
2047243 ATATCCTTCG-CTGTGAAGTTAAAATTGACTCTG-AA-TG-AAATT-TTGTTGACAAGCAGCGGT
1 ATATCCTCCGTC-GTGAAGTTGAAATCGGCTCTGAAATTGAAAATTGTTGTTGACAACCAGCCGT
* * * *
2047303 CCCTTCGTCGTGGAGTTGAACTTGCGTTGTCTGGAGTCTA--
65 CCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGGAGGC-ACG
* * * * * * *
2047343 ATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGT
1 ATATCCTCCGTCGTGAAGTTGAAATCGGCTCTGAAATTGA-AAATTGTTGTTGACAACCAGCCGT
* * *
2047408 CCCTTCGTCGTGAAGTTAAACTTGCGTTGTCTGGAATGGCACG
65 CCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGG-A-GGCACG
* ** *
2047451 ATATCCTCCGTCGTGGAGTTGAAATC-GCGGATGAAACTGAAAAGTTGTTCGTTGACAACCAGCC
1 ATATCCTCCGTCGTGAAGTTGAAATCGGC-TCTGAAATTGAAAA-TTGTT-GTTGACAACCAGCC
2047515 GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGG-GTAGCACG
63 GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT-GGAG--GCACG
* * *
2047560 ATATCCTCCGTCGTGGAGTTGAAATCGGCTCTGGAATTGGGAAATTGTTTGTTGACAACCAGCCG
1 ATATCCTCCGTCGTGAAGTTGAAATCGGCTCTGAAATT-GAAAATTG-TTGTTGACAACCAGCCG
* * * *
2047625 TCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTC-CA
64 TCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGGAGGCACG
* * * *
2047666 ATATCCTTCG-CTGTGAAGTTGAGATTGGCTCCGAAATTG
1 ATATCCTCCGTC-GTGAAGTTGAAATCGGCTCTGAAATTG
2047705 CTTGTCGACA
Statistics
Matches: 390, Mismatches: 48, Indels: 49
0.80 0.10 0.10
Matches are distributed among these distances:
100 78 0.20
101 2 0.01
102 7 0.02
103 1 0.00
104 5 0.01
105 54 0.14
106 60 0.15
107 8 0.02
108 35 0.09
109 130 0.33
110 10 0.03
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (105 bp):
ATATCCTCCGTCGTGAAGTTGAAATCGGCTCTGAAATTGAAAATTGTTGTTGACAACCAGCCGTC
CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGGAGGCACG
Found at i:2047769 original size:98 final size:98
Alignment explanation
Indices: 2047600--2047785 Score: 291
Period size: 98 Copynumber: 1.9 Consensus size: 98
2047590 CTGGAATTGG
* * * *
2047600 GAAATTGTTTGTTGACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCC
1 GAAATTGCTTGTCGACAACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCC
2047665 AATATCCTTCGCTGTGAAGTTGAGATTGGCTCC
66 AATATCCTTCGCTGTGAAGTTGAGATTGGCTCC
** * * *
2047698 GAAATTGCTTGTCGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCC
1 GAAATTGCTTGTCGACAACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCC
2047763 AATATCCTTCGCTGTGAAGTTGA
66 AATATCCTTCGCTGTGAAGTTGA
2047786 AACCGTGGAG
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
98 79 1.00
ACGTcount: A:0.18, C:0.23, G:0.26, T:0.33
Consensus pattern (98 bp):
GAAATTGCTTGTCGACAACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCC
AATATCCTTCGCTGTGAAGTTGAGATTGGCTCC
Found at i:2048119 original size:29 final size:28
Alignment explanation
Indices: 2048055--2048121 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 28
2048045 GCCTGTCTGG
* *
2048055 AATCTTGATTCTTGAATCTTCAAATTTTGA
1 AATC-TGA-TCTTGAATCTTCAAATGTTCA
**
2048085 TCTCTGATCTTGAATTCTTCAAATGTTCA
1 AATCTGATCTTGAA-TCTTCAAATGTTCA
2048114 AATCTGAT
1 AATCTGAT
2048122 GTGCACATTC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
28 7 0.23
29 21 0.70
30 2 0.07
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.45
Consensus pattern (28 bp):
AATCTGATCTTGAATCTTCAAATGTTCA
Found at i:2048267 original size:33 final size:33
Alignment explanation
Indices: 2048230--2048295 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
2048220 GTCTTGAAAG
*
2048230 AGATAGAAT-TTGTTTCAAGGGAAACGATCTCAA
1 AGATA-AATGTTGTTTCAAGAGAAACGATCTCAA
* * *
2048263 AGATATATGTTGTTTCATGAGAAACGGTCTCAA
1 AGATAAATGTTGTTTCAAGAGAAACGATCTCAA
2048296 GGGAAACAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 2 0.07
33 26 0.93
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.30
Consensus pattern (33 bp):
AGATAAATGTTGTTTCAAGAGAAACGATCTCAA
Found at i:2048565 original size:37 final size:36
Alignment explanation
Indices: 2048407--2048564 Score: 253
Period size: 36 Copynumber: 4.3 Consensus size: 36
2048397 AAATATTTTG
2048407 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTA
1 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTA
* *
2048443 TTTCAAGGGAAAATGTCTCAAGAGAGACAAAATTTA
1 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTA
* *
2048479 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTTG
1 TTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TTTA
*
2048516 TTTCAAGGGAAATTATCTCAAGAGAGACGAAAATTTA
1 TTTCAAGGGAAACTATCTCAAGAGAGAC-AAAATTTA
2048553 TTTCAAGGGAAA
1 TTTCAAGGGAAA
2048565 TGTTTTCAAT
Statistics
Matches: 113, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
36 65 0.58
37 44 0.39
38 4 0.04
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (36 bp):
TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTA
Found at i:2048630 original size:36 final size:36
Alignment explanation
Indices: 2048580--2048649 Score: 115
Period size: 36 Copynumber: 1.9 Consensus size: 36
2048570 TCAATGTTTA
2048580 TGTTTCAAGAGAAACTGTCTCAAG-GGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGG-GACAAAATT
*
2048616 TGTTTCAAGGGAAACTGTCTCAAGAGGGACAAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGGGACAAAA
2048650 CTCTTCTAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
36 30 0.94
37 2 0.06
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.23
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGGGACAAAATT
Found at i:2048699 original size:35 final size:35
Alignment explanation
Indices: 2048580--2048699 Score: 93
Period size: 35 Copynumber: 3.4 Consensus size: 35
2048570 TCAATGTTTA
*
2048580 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAT-T
1 TGTTTCAAGA-AAACTGTCTCAAGAGAGAC-AAATCT
* * *
2048616 TGTTTCAAGGGAAACTGTCTCAAGAGGGACAAAAC-
1 TGTTTCAA-GAAAACTGTCTCAAGAGAGACAAATCT
* * * *
2048651 T-CTTCTAGTGAAAACGGTCTCAAGCGAGACAAATCT
1 TGTTTC-A-AGAAAACTGTCTCAAGAGAGACAAATCT
*
2048687 TGTTTTAAGAAAA
1 TGTTTCAAGAAAA
2048700 ACAATCATGA
Statistics
Matches: 64, Mismatches: 14, Indels: 13
0.70 0.15 0.14
Matches are distributed among these distances:
34 3 0.05
35 31 0.48
36 27 0.42
37 3 0.05
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.25
Consensus pattern (35 bp):
TGTTTCAAGAAAACTGTCTCAAGAGAGACAAATCT
Found at i:2049156 original size:18 final size:18
Alignment explanation
Indices: 2049129--2049164 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2049119 TGTTGAATCC
* *
2049129 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
2049147 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
2049165 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:2049606 original size:22 final size:22
Alignment explanation
Indices: 2049580--2049628 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
2049570 TTGTGTTTGG
* *
2049580 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTGGATGC
2049602 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTGGATGC
2049624 TCAAA
1 TCAAA
2049629 AGATTGATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (22 bp):
TCAAAGGTTTGACATTGGATGC
Found at i:2049635 original size:22 final size:22
Alignment explanation
Indices: 2049592--2049635 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2049582 AAAGGTTTGG
* * *
2049592 CATTTGATGCTCAAAGGTTTGA
1 CATTGGATGCTCAAAAGATTGA
2049614 CATTGGATGCTCAAAAGATTGA
1 CATTGGATGCTCAAAAGATTGA
2049636 TGGGGTAGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (22 bp):
CATTGGATGCTCAAAAGATTGA
Found at i:2050299 original size:8 final size:7
Alignment explanation
Indices: 2050288--2050354 Score: 55
Period size: 8 Copynumber: 8.9 Consensus size: 7
2050278 TTTTTGCTTT
2050288 TTTTTTCC
1 TTTTTT-C
2050296 TTTTGTTC
1 TTTT-TTC
*
2050304 TTGTTTC
1 TTTTTTC
2050311 TCTTTTTC
1 T-TTTTTC
2050319 TTTGTTT-
1 TTT-TTTC
*
2050326 TTTTTGC
1 TTTTTTC
2050333 TTTTTTGC
1 TTTTTT-C
2050341 TTCTTTTC
1 TT-TTTTC
2050349 TTTTTT
1 TTTTTT
2050355 GTTCTTGATT
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
6 2 0.04
7 18 0.37
8 23 0.47
9 6 0.12
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.78
Consensus pattern (7 bp):
TTTTTTC
Found at i:2050353 original size:16 final size:16
Alignment explanation
Indices: 2050279--2050360 Score: 57
Period size: 17 Copynumber: 5.1 Consensus size: 16
2050269 TCTTTTTGAT
*
2050279 TTTTGCTTTTTTTTTCC
1 TTTTGCTTTTTTGTT-C
2050296 TTTTG-TTCTTGTT-TCTC
1 TTTTGCTT-TT-TTGT-TC
* *
2050313 TTTTTCTTTGTT-TT-
1 TTTTGCTTTTTTGTTC
2050327 TTTTGCTTTTTTGCTTC
1 TTTTGCTTTTTTG-TTC
2050344 TTTT-CTTTTTTGTTC
1 TTTTGCTTTTTTGTTC
2050359 TT
1 TT
2050361 GATTGGATCT
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
14 10 0.19
15 6 0.11
16 15 0.28
17 18 0.33
18 5 0.09
ACGTcount: A:0.00, C:0.15, G:0.09, T:0.77
Consensus pattern (16 bp):
TTTTGCTTTTTTGTTC
Found at i:2051531 original size:8 final size:8
Alignment explanation
Indices: 2051515--2051553 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
2051505 AATGTAGATG
2051515 AAAATGCA
1 AAAATGCA
*
2051523 AAAAGGCA
1 AAAATGCA
2051531 AAAATGC-
1 AAAATGCA
2051538 AAAATGCA
1 AAAATGCA
*
2051546 AGAATGCA
1 AAAATGCA
2051554 CGAAATGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (8 bp):
AAAATGCA
Found at i:2051541 original size:15 final size:15
Alignment explanation
Indices: 2051515--2051553 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2051505 AATGTAGATG
2051515 AAAATGCAAAAAGGCA
1 AAAATGC-AAAAGGCA
*
2051531 AAAATGCAAAATGCA
1 AAAATGCAAAAGGCA
*
2051546 AGAATGCA
1 AAAATGCA
2051554 CGAAATGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAAATGCAAAAGGCA
Found at i:2052097 original size:18 final size:18
Alignment explanation
Indices: 2052074--2052113 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
2052064 ATTAGTCTTT
2052074 CAGAAGTGGATGTGAATC
1 CAGAAGTGGATGTGAATC
2052092 CAGAAGTGGATGTGAATC
1 CAGAAGTGGATGTGAATC
2052110 CAGA
1 CAGA
2052114 CTTGAAGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.33, T:0.20
Consensus pattern (18 bp):
CAGAAGTGGATGTGAATC
Found at i:2054702 original size:15 final size:15
Alignment explanation
Indices: 2054682--2054719 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
2054672 ATATATATAT
*
2054682 ATAATAATAACATGA
1 ATAATAATAAAATGA
*
2054697 ATAATAAAAAAATGA
1 ATAATAATAAAATGA
2054712 ATAA-AATA
1 ATAATAATA
2054720 TCCATATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 3 0.15
15 17 0.85
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (15 bp):
ATAATAATAAAATGA
Found at i:2057739 original size:28 final size:29
Alignment explanation
Indices: 2057699--2057758 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
2057689 TGTATCTTTT
*
2057699 CTTGCTAATATA-TTTGTTTTATTGTTTA
1 CTTGCTAATATATTTTGTTTTATTGATTA
*
2057727 CTTGCTACTATATTTTGTTTTATTGATTA
1 CTTGCTAATATATTTTGTTTTATTGATTA
2057756 CTT
1 CTT
2057759 TTAAATATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 11 0.38
29 18 0.62
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.60
Consensus pattern (29 bp):
CTTGCTAATATATTTTGTTTTATTGATTA
Found at i:2057943 original size:42 final size:42
Alignment explanation
Indices: 2057883--2058049 Score: 280
Period size: 42 Copynumber: 4.0 Consensus size: 42
2057873 CCAGTTAAAC
*
2057883 CTTCTAATAATCCGATTGGAAATTCCAATGATTCACCTAATA
1 CTTCTAATAATCCTATTGGAAATTCCAATGATTCACCTAATA
* * * *
2057925 CTTCTAAAAATCCTATTGGAAATTTCAAAGAATCACCTAATA
1 CTTCTAATAATCCTATTGGAAATTCCAATGATTCACCTAATA
2057967 CTTCTAATAATCCTATTGGAAATTCCAATGATTCACCTAATA
1 CTTCTAATAATCCTATTGGAAATTCCAATGATTCACCTAATA
*
2058009 CTTCTAATAATCCTATTGGAAATTCCAATAATTCACCTAAT
1 CTTCTAATAATCCTATTGGAAATTCCAATGATTCACCTAAT
2058050 GATTCGGTTG
Statistics
Matches: 115, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 115 1.00
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.34
Consensus pattern (42 bp):
CTTCTAATAATCCTATTGGAAATTCCAATGATTCACCTAATA
Found at i:2058047 original size:24 final size:24
Alignment explanation
Indices: 2057978--2058047 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 24
2057968 TTCTAATAAT
*
2057978 CCTATTGGAAATTCCAATGATTCA
1 CCTATTGGAAATTCCAATAATTCA
* * *
2058002 CCTAAT---ACTTCTAATAA-T--
1 CCTATTGGAAATTCCAATAATTCA
2058020 CCTATTGGAAATTCCAATAATTCA
1 CCTATTGGAAATTCCAATAATTCA
2058044 CCTA
1 CCTA
2058048 ATGATTCGGT
Statistics
Matches: 33, Mismatches: 7, Indels: 12
0.63 0.13 0.23
Matches are distributed among these distances:
18 5 0.15
20 1 0.03
21 17 0.52
22 1 0.03
24 9 0.27
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.34
Consensus pattern (24 bp):
CCTATTGGAAATTCCAATAATTCA
Found at i:2059468 original size:3 final size:3
Alignment explanation
Indices: 2059462--2059507 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
2059452 ATTAATTAAT
2059462 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2059508 TATCGAATGG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2059943 original size:43 final size:46
Alignment explanation
Indices: 2059831--2059947 Score: 143
Period size: 47 Copynumber: 2.6 Consensus size: 46
2059821 GGGACAGACT
* *
2059831 TGTTCCGCTGTCACTCAGGGAATATCAAATCTTGGAAGAGAGTGATT
1 TGTTCCGCTTTCACTCAGGGAATATCAAATCTTGG-AGAGAGTGATA
*
2059878 TGTTCCGCTTTCACTCAAGGAATATCAAATCTT-G-GA-AGTGATA
1 TGTTCCGCTTTCACTCAGGGAATATCAAATCTTGGAGAGAGTGATA
* *
2059921 TGTTCCGC-TTCTTCTGAGGGAATATCA
1 TGTTCCGCTTTC-ACTCAGGGAATATCA
2059948 TATTTGAGGG
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
42 3 0.05
43 26 0.41
44 2 0.03
46 1 0.02
47 31 0.49
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.32
Consensus pattern (46 bp):
TGTTCCGCTTTCACTCAGGGAATATCAAATCTTGGAGAGAGTGATA
Found at i:2060189 original size:111 final size:110
Alignment explanation
Indices: 2059877--2060278 Score: 541
Period size: 107 Copynumber: 3.7 Consensus size: 110
2059867 AGAGAGTGAT
* *
2059877 TTGTTCCGCTTTCACTCA-AGGAATATCAAATCTTGG-A-AG-TGATATGTTCCGCTTCTTCTGA
1 TTGTTCCGCTATCACTCAGA-GAATATCAAATCTTGGAAGAGATGATATGTTCCGCTTCTTCTAA
* * *
2059938 GGGAATATCATATTTGAGGGAGTTGATCCATTGAATCGGGGTAGAC
65 GGGAATATCATATATGGGGGAGTTGATCCATTGAATCGGGGCAGAC
* ** *
2059984 TTGTTCCGCTATCACTCAGGGAATATCAAATCTTGG-A-AG-TGATATGTTTTGTTTCTTCTAAG
1 TTGTTCCGCTATCACTCAGAGAATATCAAATCTTGGAAGAGATGATATGTTCCGCTTCTTCTAAG
* *
2060046 GGAATATCATATCTGGGGGAGTTGATCCATTGAATCGAGGCAGAC
66 GGAATATCATATATGGGGGAGTTGATCCATTGAATCGGGGCAGAC
* * * * *
2060091 TTGTTCCACTGTGACTCAGAGAATATCAAATCTTGGAAGAGAATGATTTGTTCCGTTTCTTCTAA
1 TTGTTCCGCTATCACTCAGAGAATATCAAATCTTGGAAGAG-ATGATATGTTCCGCTTCTTCTAA
* *
2060156 GGGAATATCAGATATGGGGGAGATGATCCATTGAATCGGGGCAGAC
65 GGGAATATCATATATGGGGGAGTTGATCCATTGAATCGGGGCAGAC
* *
2060202 TTGTTCCGCTTTCACTCA-AGAATATCAAATCTTGGAAGAGAGTGATATGTTCTGCTTCTTCTAA
1 TTGTTCCGCTATCACTCAGAGAATATCAAATCTTGGAAGAGA-TGATATGTTCCGCTTCTTCTAA
2060266 GGGAATATCATAT
65 GGGAATATCATAT
2060279 CTGTAAATTA
Statistics
Matches: 261, Mismatches: 28, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
107 128 0.49
108 1 0.00
109 3 0.01
110 53 0.20
111 76 0.29
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (110 bp):
TTGTTCCGCTATCACTCAGAGAATATCAAATCTTGGAAGAGATGATATGTTCCGCTTCTTCTAAG
GGAATATCATATATGGGGGAGTTGATCCATTGAATCGGGGCAGAC
Found at i:2062099 original size:99 final size:99
Alignment explanation
Indices: 2061923--2062122 Score: 285
Period size: 99 Copynumber: 2.0 Consensus size: 99
2061913 GTAGTTTGCC
* * *
2061923 TTTATCAGGCTAGCTAAATCTTATTCATAAAGCCGGGGCATTTAACCAATTACTCTAGAGGGACA
1 TTTATCAGGCTAGCTAAATCTTATCCATAAAGCCGGAGCATTTAACCAATTACTCTAGAGAGACA
*
2061988 ACTCAAGCTTTA-TTGTATATATATTATAATCACA
66 ACTCAAGCTTTATTTGTATACATA-TATAATCACA
* * * * *
2062022 TTTATCAGGCTAGCTGAATCTTATCCATAAAGTCGGATCGTTTAACCAATTTCTCTAGAGAGACA
1 TTTATCAGGCTAGCTAAATCTTATCCATAAAGCCGGAGCATTTAACCAATTACTCTAGAGAGACA
* *
2062087 ACTCAAGTTTTATTTGTATACATATATAATTACA
66 ACTCAAGCTTTATTTGTATACATATATAATCACA
2062121 TT
1 TT
2062123 ATGGGTATAC
Statistics
Matches: 89, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
99 79 0.89
100 10 0.11
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (99 bp):
TTTATCAGGCTAGCTAAATCTTATCCATAAAGCCGGAGCATTTAACCAATTACTCTAGAGAGACA
ACTCAAGCTTTATTTGTATACATATATAATCACA
Found at i:2069967 original size:97 final size:97
Alignment explanation
Indices: 2069847--2070244 Score: 422
Period size: 97 Copynumber: 4.3 Consensus size: 97
2069837 CAAGTAAATT
* * * * *
2069847 CTAACATAACAACTATACATCCAATAAACAAACATAATATCCAATAATATTGAATTCATAACAAC
1 CTAAAATAACAACTAAACATCCAATAAATAGACATAATATCCAATAATATTGAATTCACAACAAC
2069912 TAAATAGAAAATAAATAACAAATAAACAACAA
66 TAAATAGAAAATAAATAACAAATAAACAACAA
*
2069944 CTAAAATAGCAACTAAACATCCAATAAATAGACATAATATCCAATAATATTGAATTCACAACAAC
1 CTAAAATAACAACTAAACATCCAATAAATAGACATAATATCCAATAATATTGAATTCACAACAAC
* *
2070009 CAAATAGCAAATAAAT-----AT------CAA
66 TAAATAGAAAATAAATAACAAATAAACAACAA
* * *
2070030 CTAAAATAACAACTAAACATCCAATAAATAGACATAATATACAATAATATTGAATTGA-ATTC-A
1 CTAAAATAACAACTAAACATCCAATAAATAGACATAATATCCAATAATATTGAATTCACA-ACAA
** * * *
2070093 C-----ACCAACTAAATAACAAATAAATAGCAA
65 CTAAATAGAAAATAAATAACAAATAAACAACAA
* * * *
2070121 CTAAAATAGCAATTAAACATCCAA-AAATAGACATAATATCTAATAATATTGAACTCACAACAAC
1 CTAAAATAACAACTAAACATCCAATAAATAGACATAATATCCAATAATATTGAATTCACAACAAC
*
2070185 TAAATA-ACAAATAAACAACAAATAAACAACAA
66 TAAATAGA-AAATAAATAACAAATAAACAACAA
* * *
2070217 CTAAAATAACAAATAAACAACAAATAAA
1 CTAAAATAACAACTAAACATCCAATAAA
2070245 CAGCAAGTAA
Statistics
Matches: 250, Mismatches: 30, Indels: 42
0.78 0.09 0.13
Matches are distributed among these distances:
80 9 0.04
85 5 0.02
86 59 0.24
90 30 0.12
91 28 0.11
92 2 0.01
96 41 0.16
97 76 0.30
ACGTcount: A:0.58, C:0.17, G:0.03, T:0.21
Consensus pattern (97 bp):
CTAAAATAACAACTAAACATCCAATAAATAGACATAATATCCAATAATATTGAATTCACAACAAC
TAAATAGAAAATAAATAACAAATAAACAACAA
Found at i:2070020 original size:86 final size:86
Alignment explanation
Indices: 2069923--2070210 Score: 407
Period size: 86 Copynumber: 3.3 Consensus size: 86
2069913 AAATAGAAAA
2069923 TAAATAACAAATAAACAACAACTAAAATAGCAACTAAACATCCAATAAATAGACATAATATCCAA
1 TAAATAACAAATAAACAACAACTAAAATAGCAACTAAACATCCAATAAATAGACATAATATCCAA
2069988 TAATATTGAATTCACAACAAC
66 TAATATTGAATTCACAACAAC
* * * * * *
2070009 CAAATAGCAAATAAATATCAACTAAAATAACAACTAAACATCCAATAAATAGACATAATATACAA
1 TAAATAACAAATAAACAACAACTAAAATAGCAACTAAACATCCAATAAATAGACATAATATCCAA
*
2070074 TAATATTGAATTGAATTCACACCAAC
66 T-A-A-T--ATTGAATTCACAACAAC
* * * *
2070100 TAAATAACAAATAAATAGCAACTAAAATAGCAATTAAACATCCAA-AAATAGACATAATATCTAA
1 TAAATAACAAATAAACAACAACTAAAATAGCAACTAAACATCCAATAAATAGACATAATATCCAA
*
2070164 TAATATTGAACTCACAACAAC
66 TAATATTGAATTCACAACAAC
*
2070185 TAAATAACAAATAAACAACAAATAAA
1 TAAATAACAAATAAACAACAACTAAA
2070211 CAACAACTAA
Statistics
Matches: 178, Mismatches: 19, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
85 38 0.21
86 60 0.34
87 2 0.01
88 2 0.01
89 2 0.01
90 18 0.10
91 56 0.31
ACGTcount: A:0.58, C:0.17, G:0.04, T:0.22
Consensus pattern (86 bp):
TAAATAACAAATAAACAACAACTAAAATAGCAACTAAACATCCAATAAATAGACATAATATCCAA
TAATATTGAATTCACAACAAC
Found at i:2070199 original size:11 final size:11
Alignment explanation
Indices: 2070177--2070246 Score: 95
Period size: 11 Copynumber: 6.3 Consensus size: 11
2070167 TATTGAACTC
*
2070177 ACAACAACTAA
1 ACAACAAATAA
*
2070188 ATAACAAATAA
1 ACAACAAATAA
2070199 ACAACAAATAA
1 ACAACAAATAA
*
2070210 ACAACAACTAAA
1 ACAACAAAT-AA
*
2070222 ATAACAAATAA
1 ACAACAAATAA
2070233 ACAACAAATAA
1 ACAACAAATAA
2070244 ACA
1 ACA
2070247 GCAAGTAATT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
11 42 0.82
12 9 0.18
ACGTcount: A:0.70, C:0.19, G:0.00, T:0.11
Consensus pattern (11 bp):
ACAACAAATAA
Found at i:2070229 original size:34 final size:33
Alignment explanation
Indices: 2070177--2070246 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 33
2070167 TATTGAACTC
2070177 ACAACAACTAAATAACAAATAAACAACAAATAA
1 ACAACAACTAAATAACAAATAAACAACAAATAA
2070210 ACAACAACTAAAATAACAAATAAACAACAAATAA
1 ACAACAACT-AAATAACAAATAAACAACAAATAA
2070244 ACA
1 ACA
2070247 GCAAGTAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 9 0.25
34 27 0.75
ACGTcount: A:0.70, C:0.19, G:0.00, T:0.11
Consensus pattern (33 bp):
ACAACAACTAAATAACAAATAAACAACAAATAA
Found at i:2070231 original size:23 final size:23
Alignment explanation
Indices: 2070177--2070244 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
2070167 TATTGAACTC
* *
2070177 ACAACAACTAAATAACAAAT-AA
1 ACAACAAATAAACAACAAATAAA
*
2070199 ACAACAAATAAACAACAACTAAA
1 ACAACAAATAAACAACAAATAAA
*
2070222 ATAACAAATAAACAACAAATAAA
1 ACAACAAATAAACAACAAATAAA
2070245 CAGCAAGTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
22 17 0.43
23 23 0.57
ACGTcount: A:0.71, C:0.18, G:0.00, T:0.12
Consensus pattern (23 bp):
ACAACAAATAAACAACAAATAAA
Found at i:2075856 original size:14 final size:14
Alignment explanation
Indices: 2075835--2075867 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
2075825 TGTAGCATAC
2075835 ACATTATAT-TA-T
1 ACATTATATATATT
2075847 ACATTATATATATT
1 ACATTATATATATT
2075861 ACATTAT
1 ACATTAT
2075868 TCACGATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.47
13 2 0.11
14 8 0.42
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (14 bp):
ACATTATATATATT
Found at i:2076877 original size:29 final size:29
Alignment explanation
Indices: 2076814--2076877 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
2076804 ACCCCGATTG
2076814 TCTTTTAATTTTATCCTCTATTTTCTTGT
1 TCTTTTAATTTTATCCTCTATTTTCTTGT
*
2076843 TATTTTAA-TTTAGTCC-CTATTATTACTT-T
1 TCTTTTAATTTTA-TCCTCTATT-TT-CTTGT
2076872 TCTTTT
1 TCTTTT
2076878 GAAATTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
28 9 0.30
29 18 0.60
30 3 0.10
ACGTcount: A:0.17, C:0.16, G:0.03, T:0.64
Consensus pattern (29 bp):
TCTTTTAATTTTATCCTCTATTTTCTTGT
Found at i:2088285 original size:65 final size:63
Alignment explanation
Indices: 2088181--2088350 Score: 229
Period size: 65 Copynumber: 2.7 Consensus size: 63
2088171 CTATTTACAA
* *
2088181 AAGATTGGATTTCAACTTCACAACAAAAGATATCCAACTCAAAGCCAATTTGATGAAACTTATTC
1 AAGATTGGATTTCAACTTCACAACGAAAGATATCCAACTCAAAGCCAATTTGATGAAAC--AATC
* * * *
2088246 AAGATTGTATTTCAACTTCACAATGAAAGATATCCAACTCAAAACCAATTTGGTGAAACAATC
1 AAGATTGGATTTCAACTTCACAACGAAAGATATCCAACTCAAAGCCAATTTGATGAAACAATC
* *
2088309 ---CTTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGC
1 AAGATTGGATTTCAACTTCACAACGAAAGATATCCAACTCAAAGC
2088351 TCAACTTCAC
Statistics
Matches: 94, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
60 37 0.39
63 3 0.03
65 54 0.57
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.26
Consensus pattern (63 bp):
AAGATTGGATTTCAACTTCACAACGAAAGATATCCAACTCAAAGCCAATTTGATGAAACAATC
Found at i:2089057 original size:21 final size:21
Alignment explanation
Indices: 2089033--2089082 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
2089023 TAACATACAC
* *
2089033 ATTATATTATACATTATATAT
1 ATTATACTATACATGATATAT
* *
2089054 ATTACACTATTCATGATATAT
1 ATTATACTATACATGATATAT
2089075 ATATATAC
1 AT-TATAC
2089083 ATATTATTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.42, C:0.10, G:0.02, T:0.46
Consensus pattern (21 bp):
ATTATACTATACATGATATAT
Found at i:2089095 original size:23 final size:24
Alignment explanation
Indices: 2089047--2089104 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
2089037 TATTATACAT
*
2089047 TATATATAT-TACACTATTCATGA
1 TATATATATATACACTATTCATAA
2089070 TATATATATATACA-TATT-ATTAA
1 TATATATATATACACTATTCA-TAA
2089093 TATACTATATAT
1 TATA-TATATAT
2089105 TTTTATTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
22 1 0.03
23 19 0.61
24 11 0.35
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.47
Consensus pattern (24 bp):
TATATATATATACACTATTCATAA
Found at i:2090298 original size:2 final size:2
Alignment explanation
Indices: 2090291--2090324 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2090281 CCTAACATTT
2090291 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
2090325 ATTTTTTGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2091043 original size:5 final size:5
Alignment explanation
Indices: 2091024--2091077 Score: 72
Period size: 5 Copynumber: 10.8 Consensus size: 5
2091014 GTCCGTCCGT
* * * *
2091024 CTCGT CTCGG CTCGG CTCGG CACGG CACGG CACGG CTCGG CTCGG CTCGG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG
2091074 CTCG
1 CTCG
2091078 TGGTCGTGGT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.06, C:0.41, G:0.37, T:0.17
Consensus pattern (5 bp):
CTCGG
Found at i:2091086 original size:6 final size:6
Alignment explanation
Indices: 2091075--2091123 Score: 80
Period size: 6 Copynumber: 8.2 Consensus size: 6
2091065 TCGGCTCGGC
* *
2091075 TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
2091123 T
1 T
2091124 AATACGTGTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.04, C:0.16, G:0.49, T:0.31
Consensus pattern (6 bp):
TCGTGG
Found at i:2097006 original size:5 final size:5
Alignment explanation
Indices: 2096987--2097040 Score: 72
Period size: 5 Copynumber: 10.8 Consensus size: 5
2096977 GTCCGTCCGT
* * * *
2096987 CTCGT CTCGG CTCGG CTCGG CACGG CACGG CACGG CTCGG CTCGG CTCGG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG
2097037 CTCG
1 CTCG
2097041 TGGTCGTGGT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.06, C:0.41, G:0.37, T:0.17
Consensus pattern (5 bp):
CTCGG
Found at i:2097049 original size:6 final size:6
Alignment explanation
Indices: 2097038--2097086 Score: 80
Period size: 6 Copynumber: 8.2 Consensus size: 6
2097028 TCGGCTCGGC
* *
2097038 TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
2097086 T
1 T
2097087 AATACGTGTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.04, C:0.16, G:0.49, T:0.31
Consensus pattern (6 bp):
TCGTGG
Found at i:2098223 original size:17 final size:17
Alignment explanation
Indices: 2098180--2098215 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
2098170 ATTAATTCAC
2098180 AAACCAAAATTAACTAA
1 AAACCAAAATTAACTAA
2098197 AAACCAAAATTAACTAA
1 AAACCAAAATTAACTAA
2098214 AA
1 AA
2098216 TATAAAATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.67, C:0.17, G:0.00, T:0.17
Consensus pattern (17 bp):
AAACCAAAATTAACTAA
Found at i:2103136 original size:13 final size:13
Alignment explanation
Indices: 2103118--2103142 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2103108 TTAATCAAAT
2103118 ATTATATAAGAGA
1 ATTATATAAGAGA
2103131 ATTATATAAGAG
1 ATTATATAAGAG
2103143 TATATCAAAT
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:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (13 bp):
ATTATATAAGAGA
Found at i:2103170 original size:2 final size:2
Alignment explanation
Indices: 2103163--2103193 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2103153 TTTAGAATCC
2103163 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2103194 GGTCCAAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2105545 original size:42 final size:41
Alignment explanation
Indices: 2105497--2105577 Score: 99
Period size: 41 Copynumber: 2.0 Consensus size: 41
2105487 CACAAAATGA
* *
2105497 TACTTTAGCGACGTTTCTTAAAAAAACGCCGCAATAGAGTAG
1 TACTTTAGAGACGTTT-TTAAAAAAACGCCGCAAAAGAGTAG
** * *
2105539 TACTTTAGAGGTGTTTTTATACAAACGCCGCAAAAGAGT
1 TACTTTAGAGACGTTTTTAAAAAAACGCCGCAAAAGAGT
2105578 TAATCTATAG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
41 20 0.61
42 13 0.39
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (41 bp):
TACTTTAGAGACGTTTTTAAAAAAACGCCGCAAAAGAGTAG
Found at i:2105568 original size:41 final size:41
Alignment explanation
Indices: 2105520--2105873 Score: 133
Period size: 41 Copynumber: 8.7 Consensus size: 41
2105510 TTTCTTAAAA
*
2105520 AAACGCCGCAATAGAGTAGTACTTTAGAGGTGTTTTTATAC
1 AAACGCCGCAATAGAATAGTACTTTAGAGGTGTTTTTATAC
* * * * * * *
2105561 AAACGCCGCAAAAGAGTTAAT-CTATAGTGGCGTTTTT-TCAAT
1 AAACGCCGCAATAGA-ATAGTACTTTAGAGGTGTTTTTAT--AC
* * * * *
2105603 AAACGCCGCAACATAATAGTATTTTAGCGATGTTTTTATAC
1 AAACGCCGCAATAGAATAGTACTTTAGAGGTGTTTTTATAC
* * * * * *
2105644 AAATGACGTAATAGAATA-CATCTATAGTAGCGT-TTTTTA-AT
1 AAACGCCGCAATAGAATAGTA-CTTTAG-AG-GTGTTTTTATAC
* * * *
2105685 AAATGCCGCAAGAGAATAGTACTTTAGCGGCGTTTTTATAC
1 AAACGCCGCAATAGAATAGTACTTTAGAGGTGTTTTTATAC
* * * * * * *
2105726 AAATGCAGTAATAGAGT--TCATCTATAG-TGTCGTTTTTA-AT
1 AAACGCCGCAATAGAATAGT-A-CTTTAGAGGT-GTTTTTATAC
* * * *
2105766 AAACGACGCAACAAAATAGTACTTTAGCA--CGTTTTTATAC
1 AAACGCCGCAATAGAATAGTACTTTAG-AGGTGTTTTTATAC
* * *
2105806 AAACGCCGCAATAGAAT-TTATCTATA-ATGGTGTTTTT-TAAA
1 AAACGCCGCAATAGAATAGTA-CTTTAGA-GGTGTTTTTAT-AC
* * *
2105847 AAACGCCACAATAAAATAATACTTTAG
1 AAACGCCGCAATAGAATAGTACTTTAG
2105874 CAAATAGAGT
Statistics
Matches: 222, Mismatches: 65, Indels: 51
0.66 0.19 0.15
Matches are distributed among these distances:
38 1 0.00
39 11 0.05
40 47 0.21
41 122 0.55
42 39 0.18
43 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.32
Consensus pattern (41 bp):
AAACGCCGCAATAGAATAGTACTTTAGAGGTGTTTTTATAC
Found at i:2105713 original size:82 final size:82
Alignment explanation
Indices: 2105520--2105874 Score: 365
Period size: 82 Copynumber: 4.3 Consensus size: 82
2105510 TTTCTTAAAA
* * * * ** * *
2105520 AAACGCCGCAATAGAGTAGTACTTTAGAGGTGTTTTTATACAAACGCCGCAAAAGAGTTA-ATCT
1 AAACGCCGCAACAAAATAGTACTTTAGCGACGTTTTTATACAAACGCCGCAATAGA-ATACATCT
2105584 ATAGTGGCGTTTTTTCAAT
65 ATAGTGGCGTTTTTT-AAT
* * * * * *
2105603 AAACGCCGCAACATAATAGTATTTTAGCGATGTTTTTATACAAATGACGTAATAGAATACATCTA
1 AAACGCCGCAACAAAATAGTACTTTAGCGACGTTTTTATACAAACGCCGCAATAGAATACATCTA
*
2105668 TAGTAGCGTTTTTTAAT
66 TAGTGGCGTTTTTTAAT
* * * * * * * * *
2105685 AAATGCCGCAAGAGAATAGTACTTTAGCGGCGTTTTTATACAAATGCAGTAATAGAGTTCATCTA
1 AAACGCCGCAACAAAATAGTACTTTAGCGACGTTTTTATACAAACGCCGCAATAGAATACATCTA
*
2105750 TAGTGTCG-TTTTTAAT
66 TAGTGGCGTTTTTTAAT
* **
2105766 AAACGACGCAACAAAATAGTACTTTAGC-ACGTTTTTATACAAACGCCGCAATAGAATTTATCTA
1 AAACGCCGCAACAAAATAGTACTTTAGCGACGTTTTTATACAAACGCCGCAATAGAATACATCTA
* * *
2105830 TAATGGTGTTTTTTAAA
66 TAGTGGCGTTTTTTAAT
* * *
2105847 AAACGCCACAATAAAATAATACTTTAGC
1 AAACGCCGCAACAAAATAGTACTTTAGC
2105875 AAATAGAGTT
Statistics
Matches: 228, Mismatches: 42, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
80 35 0.15
81 63 0.28
82 66 0.29
83 64 0.28
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.32
Consensus pattern (82 bp):
AAACGCCGCAACAAAATAGTACTTTAGCGACGTTTTTATACAAACGCCGCAATAGAATACATCTA
TAGTGGCGTTTTTTAAT
Found at i:2105843 original size:81 final size:82
Alignment explanation
Indices: 2105520--2105874 Score: 381
Period size: 83 Copynumber: 4.3 Consensus size: 82
2105510 TTTCTTAAAA
* * * * ** * * *
2105520 AAACGCCGCAATAGAGTAGTACTTTAGAGGTGTTTTTATACAAACGCCGCAAAAGAGTTAATCTA
1 AAACGCCGCAACAAAATAGTACTTTAGCGACGTTTTTATACAAACGCCGCAATAGAATTCATCTA
2105585 TAGTGGCGTTTTTTCAAT
66 TAGTGGCGTTTTTT-AAT
* * * * * * *
2105603 AAACGCCGCAACATAATAGTATTTTAGCGATGTTTTTATACAAATGACGTAATAGAATACATCTA
1 AAACGCCGCAACAAAATAGTACTTTAGCGACGTTTTTATACAAACGCCGCAATAGAATTCATCTA
*
2105668 TAGTAGCGTTTTTTAAT
66 TAGTGGCGTTTTTTAAT
* * * * * * * *
2105685 AAATGCCGCAAGAGAATAGTACTTTAGCGGCGTTTTTATACAAATGCAGTAATAGAGTTCATCTA
1 AAACGCCGCAACAAAATAGTACTTTAGCGACGTTTTTATACAAACGCCGCAATAGAATTCATCTA
*
2105750 TAGTGTCG-TTTTTAAT
66 TAGTGGCGTTTTTTAAT
* *
2105766 AAACGACGCAACAAAATAGTACTTTAGC-ACGTTTTTATACAAACGCCGCAATAGAATTTATCTA
1 AAACGCCGCAACAAAATAGTACTTTAGCGACGTTTTTATACAAACGCCGCAATAGAATTCATCTA
* * *
2105830 TAATGGTGTTTTTTAAA
66 TAGTGGCGTTTTTTAAT
* * *
2105847 AAACGCCACAATAAAATAATACTTTAGC
1 AAACGCCGCAACAAAATAGTACTTTAGC
2105875 AAATAGAGTT
Statistics
Matches: 227, Mismatches: 44, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
80 35 0.15
81 63 0.28
82 64 0.28
83 65 0.29
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.32
Consensus pattern (82 bp):
AAACGCCGCAACAAAATAGTACTTTAGCGACGTTTTTATACAAACGCCGCAATAGAATTCATCTA
TAGTGGCGTTTTTTAAT
Found at i:2106763 original size:2 final size:2
Alignment explanation
Indices: 2106756--2106785 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2106746 TTTTTATGGA
*
2106756 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2106786 TGTATAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2109231 original size:43 final size:41
Alignment explanation
Indices: 2109178--2109307 Score: 138
Period size: 41 Copynumber: 3.1 Consensus size: 41
2109168 ATCATGAGCT
* * *
2109178 CTTTTGCGGCGTTTGTATCCAAAAACACCGTTATAGAGCTGA
1 CTTTTGCGGCGTTTGTATACAAAAACGCCG-TATAGATCTGA
* * *
2109220 CATTTTGCGGCGTTTGTATAAAAAAACGCCG-CTAGATATGA
1 C-TTTTGCGGCGTTTGTATACAAAAACGCCGTATAGATCTGA
* *
2109261 GCTTTTGCGGCGTTTGT-TTCAAAAATGCCGCTATAGATCTGA
1 -CTTTTGCGGCGTTTGTATACAAAAACGCCG-TATAGATCTGA
2109303 CTTTT
1 CTTTT
2109308 TGCGACATTT
Statistics
Matches: 73, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
40 10 0.14
41 27 0.37
42 10 0.14
43 26 0.36
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (41 bp):
CTTTTGCGGCGTTTGTATACAAAAACGCCGTATAGATCTGA
Found at i:2109267 original size:41 final size:41
Alignment explanation
Indices: 2109178--2109277 Score: 112
Period size: 43 Copynumber: 2.4 Consensus size: 41
2109168 ATCATGAGCT
** *
2109178 CTTTTGCGGCGTTTGTATCCAAAAACACCGTTATAGAGCTGA
1 CTTTTGCGGCGTTTGTATAAAAAAACACCG-TATAGAGATGA
* * *
2109220 CATTTTGCGGCGTTTGTATAAAAAAACGCCG-CTAGATATGA
1 C-TTTTGCGGCGTTTGTATAAAAAAACACCGTATAGAGATGA
2109261 GCTTTTGCGGCGTTTGT
1 -CTTTTGCGGCGTTTGT
2109278 TTCAAAAATG
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
41 22 0.44
42 2 0.04
43 26 0.52
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (41 bp):
CTTTTGCGGCGTTTGTATAAAAAAACACCGTATAGAGATGA
Found at i:2110148 original size:37 final size:36
Alignment explanation
Indices: 2110098--2110258 Score: 145
Period size: 37 Copynumber: 4.4 Consensus size: 36
2110088 ATATATACAC
* *
2110098 ATATATAT-TATATAGTTTGCAAATTGTTTTTGAAAAT
1 ATATATATATATATAGTTT--AAAATATTTTTGAAAAT
* *
2110135 ACATATATAATATATAGTTTAAAACATTTTTGAAAAT
1 ATATATAT-ATATATAGTTTAAAATATTTTTGAAAAT
*
2110172 ATGTATAT-TATATAGTTTTTAAAATATTTTTGAAAAT
1 ATATATATATATATAG--TTTAAAATATTTTTGAAAAT
**
2110209 -TATATA-ATATATAGTTTTTGAAAACGTTTTT-AAAAT
1 ATATATATATATATAG--TTT-AAAATATTTTTGAAAAT
2110245 ATATATA-ATATATA
1 ATATATATATATATA
2110259 CTTTTGAAAA
Statistics
Matches: 107, Mismatches: 10, Indels: 14
0.82 0.08 0.11
Matches are distributed among these distances:
35 7 0.07
36 22 0.21
37 68 0.64
39 10 0.09
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.47
Consensus pattern (36 bp):
ATATATATATATATAGTTTAAAATATTTTTGAAAAT
Found at i:2110227 original size:36 final size:37
Alignment explanation
Indices: 2110124--2110324 Score: 207
Period size: 37 Copynumber: 5.4 Consensus size: 37
2110114 TTGCAAATTG
2110124 TTTTTGAAAATACATATATAATATATAG--TTTAAAACA
1 TTTTTGAAAAT--ATATATAATATATAGTTTTTAAAACA
* * *
2110161 TTTTTGAAAATATGTATATTATATAGTTTTTAAAATA
1 TTTTTGAAAATATATATAATATATAGTTTTTAAAACA
*
2110198 TTTTTGAAAAT-TATATAATATATAGTTTTTGAAAACG
1 TTTTTGAAAATATATATAATATATAGTTTTT-AAAACA
* *
2110235 TTTTT-AAAATATATATAATATATACTTTTGAAAAC-
1 TTTTTGAAAATATATATAATATATAGTTTTTAAAACA
* * * *
2110270 GTTATGAAAACATTTATATAATATATAATTTTTAAAAACCA
1 TTTTTG-AAA-ATATATATAATATATAGTTTTT-AAAA-CA
2110311 -TTTTGAAAATATAT
1 TTTTTGAAAATATAT
2110325 TTTTTGAAAA
Statistics
Matches: 138, Mismatches: 16, Indels: 19
0.80 0.09 0.11
Matches are distributed among these distances:
35 16 0.12
36 27 0.20
37 59 0.43
38 24 0.17
39 7 0.05
40 5 0.04
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (37 bp):
TTTTTGAAAATATATATAATATATAGTTTTTAAAACA
Found at i:2110306 original size:27 final size:27
Alignment explanation
Indices: 2110276--2110375 Score: 82
Period size: 26 Copynumber: 3.7 Consensus size: 27
2110266 AAACGTTATG
2110276 AAAACATTTATATAATATATAATTTTTA
1 AAAACATTT-TATAATATATAATTTTTA
*
2110304 AAAACCATTTTGA-AA-ATAT-ATTTTTT
1 AAAA-CATTTT-ATAATATATAATTTTTA
* * * *
2110330 GAAA-ATTATATAATATATAGTTTTTG
1 AAAACATTTTATAATATATAATTTTTA
* *
2110356 AAAACGTTTTAAAATATATA
1 AAAACATTTTATAATATATA
2110376 TAATATATAC
Statistics
Matches: 57, Mismatches: 9, Indels: 13
0.72 0.11 0.16
Matches are distributed among these distances:
23 1 0.02
24 6 0.11
25 4 0.07
26 17 0.30
27 16 0.28
28 7 0.12
29 6 0.11
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (27 bp):
AAAACATTTTATAATATATAATTTTTA
Found at i:2110330 original size:127 final size:128
Alignment explanation
Indices: 2110198--2110435 Score: 444
Period size: 126 Copynumber: 1.9 Consensus size: 128
2110188 TTTTAAAATA
2110198 TTTTTGAAAATTATATAATATATAGTTTTTGAAAACGTTTTTAAAATATATATAATATATACTTT
1 TTTTTGAAAATTATATAATATATAGTTTTTGAAAACG-TTTTAAAATATATATAATATATACTTT
2110263 TGAAAACGTTATGAAAACATTTATATA-ATATATA-ATTTTTAAAAACCATTTTGAAAATATAT
65 TGAAAACGTTATGAAAACATTTATATATATATATAGATTTTTAAAAACCATTTTGAAAATATAT
2110325 TTTTTGAAAATTATATAATATATAGTTTTTGAAAACGTTTTAAAATATATATAATATATACTTTT
1 TTTTTGAAAATTATATAATATATAGTTTTTGAAAACGTTTTAAAATATATATAATATATACTTTT
*
2110390 GAAAACGTTATGAAAACATTTATATATATATATAGTTTTTTAAAAA
66 GAAAACGTTATGAAAACATTTATATATATATATAGATTTTTAAAAA
2110436 AAACATTTTA
Statistics
Matches: 108, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
126 54 0.50
127 44 0.41
128 10 0.09
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.45
Consensus pattern (128 bp):
TTTTTGAAAATTATATAATATATAGTTTTTGAAAACGTTTTAAAATATATATAATATATACTTTT
GAAAACGTTATGAAAACATTTATATATATATATAGATTTTTAAAAACCATTTTGAAAATATAT
Found at i:2110331 original size:15 final size:16
Alignment explanation
Indices: 2110311--2110340 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2110301 TTAAAAACCA
2110311 TTTTGAAAA-TATATT
1 TTTTGAAAATTATATT
2110326 TTTTGAAAATTATAT
1 TTTTGAAAATTATAT
2110341 AATATATAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (16 bp):
TTTTGAAAATTATATT
Found at i:2110347 original size:25 final size:25
Alignment explanation
Indices: 2110283--2110359 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 25
2110273 ATGAAAACAT
*
2110283 TTATATAATATATAATTTTTAAAAA
1 TTATATAATATATAATTTTTGAAAA
** * * *
2110308 CCATTTTGAAAATATATTTTTTGAAAA
1 TTA-TAT-AATATATAATTTTTGAAAA
*
2110335 TTATATAATATATAGTTTTTGAAAA
1 TTATATAATATATAATTTTTGAAAA
2110360 CGTTTTAAAA
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
25 18 0.46
26 4 0.10
27 17 0.44
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (25 bp):
TTATATAATATATAATTTTTGAAAA
Found at i:2110380 original size:36 final size:37
Alignment explanation
Indices: 2110326--2110479 Score: 154
Period size: 36 Copynumber: 4.1 Consensus size: 37
2110316 AAAATATATT
*
2110326 TTTTGAAAA-TTATATAATATATAGTTTTTGAAAACG
1 TTTTAAAAATTTATATAATATATAGTTTTTGAAAACG
* *
2110362 TTTT-AAAATATATATAATATATA-CTTTTGAAAACG
1 TTTTAAAAATTTATATAATATATAGTTTTTGAAAACG
* * *
2110397 TTATGAAAACATTTATATATATATATAGTTTTTTAAAAAAAACA
1 TT-TTAAAA-ATTTATATA-ATATATAG-TTTTT---GAAAACG
*
2110441 TTTTAAAAATTTATATATTATAT-GTTTTTGAAAACG
1 TTTTAAAAATTTATATAATATATAGTTTTTGAAAACG
2110477 TTT
1 TTT
2110480 ATATATATAT
Statistics
Matches: 97, Mismatches: 11, Indels: 20
0.76 0.09 0.16
Matches are distributed among these distances:
35 17 0.18
36 26 0.27
37 3 0.03
38 8 0.08
39 12 0.12
40 1 0.01
41 9 0.09
42 9 0.09
43 5 0.05
44 7 0.07
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (37 bp):
TTTTAAAAATTTATATAATATATAGTTTTTGAAAACG
Found at i:2111868 original size:14 final size:15
Alignment explanation
Indices: 2111849--2111881 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
2111839 TTTTTTTATC
2111849 TATTTTTATTATT-T
1 TATTTTTATTATTGT
2111863 TA-TTTTATTATTGT
1 TATTTTTATTATTGT
2111877 TATTT
1 TATTT
2111882 CTTTCCCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.59
14 5 0.29
15 2 0.12
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (15 bp):
TATTTTTATTATTGT
Found at i:2113215 original size:3 final size:3
Alignment explanation
Indices: 2113184--2113240 Score: 59
Period size: 3 Copynumber: 20.0 Consensus size: 3
2113174 TATAAAAAAA
*
2113184 ATT A-T ATT A-T ATT ATA ATAT ATT -TT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT
*
2113227 ATT -TT ATT TTT ATT
1 ATT ATT ATT ATT ATT
2113241 TTTGTAAGTC
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
2 8 0.18
3 35 0.78
4 2 0.04
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2113229 original size:23 final size:24
Alignment explanation
Indices: 2113188--2113240 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
2113178 AAAAAAATTA
2113188 TATTA-TATTATAATATATTTTAT
1 TATTATTATTATAATATATTTTAT
*
2113211 TATTATTATTATTAT-TATTTTAT
1 TATTATTATTATAATATATTTTAT
*
2113234 TTTTATT
1 TATTATT
2113241 TTTGTAAGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 19 0.70
24 8 0.30
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (24 bp):
TATTATTATTATAATATATTTTAT
Found at i:2113581 original size:10 final size:10
Alignment explanation
Indices: 2113568--2113598 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
2113558 GGATCGATTG
2113568 AAAACCAGAA
1 AAAACCAGAA
2113578 AAAACCAGAA
1 AAAACCAGAA
2113588 AAAACCAGAA
1 AAAACCAGAA
2113598 A
1 A
2113599 TTTTGTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.71, C:0.19, G:0.10, T:0.00
Consensus pattern (10 bp):
AAAACCAGAA
Found at i:2115770 original size:14 final size:14
Alignment explanation
Indices: 2115751--2115781 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2115741 TTTTCTTTGA
*
2115751 TTTATTTAATATTT
1 TTTATTTAACATTT
2115765 TTTATTTAACATTT
1 TTTATTTAACATTT
2115779 TTT
1 TTT
2115782 TAGAATAATT
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:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTATTTAACATTT
Found at i:2119378 original size:103 final size:103
Alignment explanation
Indices: 2119199--2119526 Score: 611
Period size: 103 Copynumber: 3.2 Consensus size: 103
2119189 GAAGAGGGTC
2119199 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
2119264 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
*
2119302 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
*
2119367 TTGATCTTTGGCATATGTATATGATTCTTAAAGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
*
2119405 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
*
2119470 TTGATCTTCGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
*
2119508 TATGTGGTCCTTAGGGACA
1 TATGTGGTCCTTCGGGACA
2119527 ACTTTATATG
Statistics
Matches: 218, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 218 1.00
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:2119562 original size:23 final size:23
Alignment explanation
Indices: 2119536--2119598 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
2119526 AACTTTATAT
* *
2119536 GGCACTTCGGTGCATTTCTATGC
1 GGCACTTCGGTGCAATTCTAAGC
* *
2119559 GGCACTACGGTGCAATTCTAAGT
1 GGCACTTCGGTGCAATTCTAAGC
2119582 GGCACTTCGGTGCAATT
1 GGCACTTCGGTGCAATT
2119599 ATACGAGCTG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.19, C:0.24, G:0.27, T:0.30
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTAAGC
Found at i:2125638 original size:27 final size:27
Alignment explanation
Indices: 2125608--2125696 Score: 79
Period size: 27 Copynumber: 3.2 Consensus size: 27
2125598 ACATGAAGTG
2125608 CATCGATGCATTAATTTAAAAAGAAAA
1 CATCGATGCATTAATTTAAAAAGAAAA
** ** * * ***
2125635 CATCGAATGCCATCGATGCATAAGGAGTG
1 CATCG-ATG-CATTAATTTAAAAAGAAAA
2125664 CATCGATGCATTAATTTAAAAAGAAAA
1 CATCGATGCATTAATTTAAAAAGAAAA
2125691 CATCGA
1 CATCGA
2125697 ATGCCATCGA
Statistics
Matches: 42, Mismatches: 18, Indels: 4
0.66 0.28 0.06
Matches are distributed among these distances:
27 21 0.50
28 6 0.14
29 15 0.36
ACGTcount: A:0.44, C:0.16, G:0.17, T:0.24
Consensus pattern (27 bp):
CATCGATGCATTAATTTAAAAAGAAAA
Found at i:2125664 original size:56 final size:56
Alignment explanation
Indices: 2125589--2125729 Score: 255
Period size: 56 Copynumber: 2.5 Consensus size: 56
2125579 GTTTAAGGTG
* * *
2125589 CATCGATGCACATGAAGTGCATCGATGCATTAATTTAAAAAGAAAACATCGAATGC
1 CATCGATGCATAAGGAGTGCATCGATGCATTAATTTAAAAAGAAAACATCGAATGC
2125645 CATCGATGCATAAGGAGTGCATCGATGCATTAATTTAAAAAGAAAACATCGAATGC
1 CATCGATGCATAAGGAGTGCATCGATGCATTAATTTAAAAAGAAAACATCGAATGC
2125701 CATCGATGCATAAGGAGTGCATCGATGCA
1 CATCGATGCATAAGGAGTGCATCGATGCA
2125730 CCCCATTAAA
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 82 1.00
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.23
Consensus pattern (56 bp):
CATCGATGCATAAGGAGTGCATCGATGCATTAATTTAAAAAGAAAACATCGAATGC
Found at i:2125668 original size:29 final size:29
Alignment explanation
Indices: 2125635--2125725 Score: 87
Period size: 29 Copynumber: 3.2 Consensus size: 29
2125625 AAAAAGAAAA
2125635 CATCGAATGCCATCGATGCATAAGGAGTG
1 CATCGAATGCCATCGATGCATAAGGAGTG
** ** * * ***
2125664 CATCG-ATG-CATTAATTTAAAAAGAAAA
1 CATCGAATGCCATCGATGCATAAGGAGTG
2125691 CATCGAATGCCATCGATGCATAAGGAGTG
1 CATCGAATGCCATCGATGCATAAGGAGTG
2125720 CATCGA
1 CATCGA
2125726 TGCACCCCAT
Statistics
Matches: 42, Mismatches: 18, Indels: 4
0.66 0.28 0.06
Matches are distributed among these distances:
27 15 0.36
28 6 0.14
29 21 0.50
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (29 bp):
CATCGAATGCCATCGATGCATAAGGAGTG
Found at i:2126409 original size:103 final size:103
Alignment explanation
Indices: 2126228--2126452 Score: 414
Period size: 103 Copynumber: 2.2 Consensus size: 103
2126218 GTAGAGGGTC
2126228 TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
*
2126293 TTGATATTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATATTCGGCATATGTATATGATTCTTAAGGAATGA
*
2126331 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
*
2126396 TTGATCTTCGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATATTCGGCATATGTATATGATTCTTAAGGAATGA
*
2126434 TATGTGGTCCTTAGGGACA
1 TATGTGGTCCTTCGGGACA
2126453 ACTTTATATG
Statistics
Matches: 118, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 118 1.00
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
TTGATATTCGGCATATGTATATGATTCTTAAGGAATGA
Found at i:2126488 original size:23 final size:23
Alignment explanation
Indices: 2126462--2126529 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
2126452 AACTTTATAT
*
2126462 GGCACTTCGGTGCATTTCTATGC
1 GGCACTTCGGTGCATTTCTACGC
* * * *
2126485 GGCACTACGGTGTAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
2126508 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
2126530 AGCTGTGGTG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.18, C:0.24, G:0.26, T:0.32
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:2127827 original size:95 final size:95
Alignment explanation
Indices: 2127662--2127915 Score: 375
Period size: 95 Copynumber: 2.6 Consensus size: 95
2127652 TATTATGTAT
** **
2127662 ATATACAATAAATCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTATTAATAA
1 ATATACAATAAAGATTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTATGGATAA
* *
2127727 GATTCAGGTAGCCTGATAAAGGTGATTATA
66 GATTCAGCTAGCCTGATAAAGGCGATTATA
*
2127757 ATATACAATAAAGATTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGATAA
1 ATATACAATAAAGATTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTATGGATAA
*
2127822 TATTCAGCTAGCCTGATAAAGGCGATTATA
66 GATTCAGCTAGCCTGATAAAGGCGATTATA
* *
2127852 ATAT-CTATACAATGATATTAAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTATGG
1 ATATACAATA-AA-G--ATTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTATGG
2127916 GTCCAACTAG
Statistics
Matches: 144, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
94 4 0.03
95 93 0.65
96 1 0.01
98 46 0.32
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (95 bp):
ATATACAATAAAGATTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTATGGATAA
GATTCAGCTAGCCTGATAAAGGCGATTATA
Found at i:2129341 original size:240 final size:241
Alignment explanation
Indices: 2129009--2129604 Score: 804
Period size: 240 Copynumber: 2.4 Consensus size: 241
2128999 ATGCCCACAA
* *
2129009 ATCCACGATTTCAACTTCAC-AGCGAATGATATCGTGCCCATCAACTCTAGATTGGATTTCAACT
1 ATCCACGATTTCAACTTCACGA-AGAAGGATATCGTG--CA-CAACTCTAGATTGGATTTCAACT
*
2129073 TCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACGGCGAATGGGCTTCCCAATTTCATTCA
62 TCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACGGCGAAGGGGCTTCCCAATTTCATTCA
* *
2129138 GAGACAATTTCAACTTCACGGCGAAGGATATTGGACTCGAAACAATACAAGCTTGGATTTCAACA
127 GAGACAATTTCAACTTAACGGCGAAGAATATTGGACTCGAAACAATACAAGCTTGGATTTCAA-A
* * *
2129203 -TCACGATGAAGGATATTCAAGTCAAGGCTCAACTTCACAACAAATGGGTC
191 TTCACGATGAAGAATAATCAAGTCAAGGCTCAACTTCACAACAAATGGGCC
* *
2129253 ATCCACGATTTCAACTTCACGAAGAAGGATATCGTGC-CAATTCTAGATTGTATTTCAACTTCAC
1 ATCCACGATTTCAACTTCACGAAGAAGGATATCGTGCACAACTCTAGATTGGATTTCAACTTCAC
* * *
2129317 GACGAAGGATATCCAATTCAAAGCTCAACTTCACGGCGAAGGGGCTTCCCAGTTTCATTCAGAGC
66 AACGAAGGATATCCAATTCAAAGCTCAACTTCACGGCGAAGGGGCTTCCCAATTTCATTCAGAGA
* *
2129382 CAATTTCAACTTAACGGCGAATAATATTGTACTCGAAACAATACAAGCTTGGATTTCAAATTCAC
131 CAATTTCAACTTAACGGCGAAGAATATTGGACTCGAAACAATACAAGCTTGGATTTCAAATTCAC
*
2129447 GATGAAGAATAATCAAGTCAAGGCTCAACTTCACAACGAATGGGCC
196 GATGAAGAATAATCAAGTCAAGGCTCAACTTCACAACAAATGGGCC
* *
2129493 ATCCACGGTTTCAACTTCACGATGAAGGGA-ATCGTGCTCACCAGCAACATTCATCTTTAGATTG
1 ATCCACGATTTCAACTTCACGAAGAA-GGATATCGTG-----CA-C-A-A--C-TC--TAGATTG
* * *
2129557 GATTTTAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCAC
52 GATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCAC
2129605 AACGAAAGGG
Statistics
Matches: 313, Mismatches: 22, Indels: 24
0.87 0.06 0.07
Matches are distributed among these distances:
239 1 0.00
240 217 0.69
241 3 0.01
242 1 0.00
244 32 0.10
245 2 0.01
247 1 0.00
248 1 0.00
249 1 0.00
252 2 0.01
254 52 0.17
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (241 bp):
ATCCACGATTTCAACTTCACGAAGAAGGATATCGTGCACAACTCTAGATTGGATTTCAACTTCAC
AACGAAGGATATCCAATTCAAAGCTCAACTTCACGGCGAAGGGGCTTCCCAATTTCATTCAGAGA
CAATTTCAACTTAACGGCGAAGAATATTGGACTCGAAACAATACAAGCTTGGATTTCAAATTCAC
GATGAAGAATAATCAAGTCAAGGCTCAACTTCACAACAAATGGGCC
Found at i:2129600 original size:124 final size:124
Alignment explanation
Indices: 2129430--2129715 Score: 421
Period size: 124 Copynumber: 2.3 Consensus size: 124
2129420 CAATACAAGC
* * * * *
2129430 TTGGATTTCAAATTCACGATGAAGAATAAT-CAAGTCAAGGCTCAACTTCACAACGAATGGGCCA
1 TTGGATTTCAACTTCACGACGAAGGAT-ATCCAACTCAAGGCTCAACTTCACAACGAAAGGGCCA
* * * *
2129494 TCCACGGTTTCAACTTCACGATGAAGGGAATCGTGCTCACCAGCAACATTCATCTTTAGA
65 TCCACGGTTTCAACTTCACGAAGAAGGGAATCGTGCTCACAAGCAACATGCATCTCTAGA
* * *
2129554 TTGGATTTTAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAAGGGTCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAGGCTCAACTTCACAACGAAAGGGCCAT
* *
2129619 CCACGGTTTCAACTTCACGAAGAAGGGAATCGTGCTCTCAAGCATCATGCATCTCTAGA
66 CCACGGTTTCAACTTCACGAAGAAGGGAATCGTGCTCACAAGCAACATGCATCTCTAGA
*
2129678 TTGGATTTCAACTTCACGACGAAAGATATCCAACTCAA
1 TTGGATTTCAACTTCACGACGAAGGATATCCAACTCAA
2129716 AGAAGAAGTT
Statistics
Matches: 145, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
123 2 0.01
124 143 0.99
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (124 bp):
TTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAGGCTCAACTTCACAACGAAAGGGCCAT
CCACGGTTTCAACTTCACGAAGAAGGGAATCGTGCTCACAAGCAACATGCATCTCTAGA
Found at i:2130533 original size:12 final size:11
Alignment explanation
Indices: 2130504--2130533 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
2130494 AAAATAAATA
2130504 TGCTTTTGGGG
1 TGCTTTTGGGG
2130515 TGCTTTTGGGG
1 TGCTTTTGGGG
2130526 TGGCTTTT
1 T-GCTTTT
2130534 AATATTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.00, C:0.10, G:0.40, T:0.50
Consensus pattern (11 bp):
TGCTTTTGGGG
Found at i:2132736 original size:18 final size:18
Alignment explanation
Indices: 2132713--2132767 Score: 83
Period size: 18 Copynumber: 3.1 Consensus size: 18
2132703 AGGGATTATC
2132713 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
2132731 AGTGGTCATTCGAGACAT
1 AGTGGTCCTTCGGGACAT
*
2132749 AGTGATCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
2132767 A
1 A
2132768 TACAGTGGTC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:2132785 original size:22 final size:22
Alignment explanation
Indices: 2132757--2132855 Score: 162
Period size: 22 Copynumber: 4.5 Consensus size: 22
2132747 ATAGTGATCC
2132757 TTCGGGACATATACAGTGGTCA
1 TTCGGGACATATACAGTGGTCA
*
2132779 TTTGGGACATATACAGTGGTCA
1 TTCGGGACATATACAGTGGTCA
* * *
2132801 TTTGGGACATATATAGTGGTCC
1 TTCGGGACATATACAGTGGTCA
2132823 TTCGGGACATATACAGTGGTCA
1 TTCGGGACATATACAGTGGTCA
2132845 TTCGGGACATA
1 TTCGGGACATA
2132856 GTGATCCTAC
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 71 1.00
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.30
Consensus pattern (22 bp):
TTCGGGACATATACAGTGGTCA
Found at i:2134151 original size:2 final size:2
Alignment explanation
Indices: 2134095--2134140 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
2134085 CATTATGTTC
*
2134095 AT AT AT AT AT AC 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
2134137 AT AT
1 AT AT
2134141 TATGCATATA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2137032 original size:2 final size:2
Alignment explanation
Indices: 2137025--2137055 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2137015 GAAGGCAAAT
2137025 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2137056 TGTTATTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2137655 original size:20 final size:21
Alignment explanation
Indices: 2137631--2137824 Score: 110
Period size: 20 Copynumber: 9.7 Consensus size: 21
2137621 AGTTTCCAGT
*
2137631 TTCGCAACGCGAATTTGT-AAA
1 TTCGCAACGCGAA-TAGTCAAA
*
2137652 -TCGCAACAC-AGA-AGTCAAA
1 TTCGCAACGCGA-ATAGTCAAA
2137671 TTCGCAACGC-AATAGTCAAA
1 TTCGCAACGCGAATAGTCAAA
2137691 TTCGCAACGCG-ATAGTCAAA
1 TTCGCAACGCGAATAGTCAAA
** *
2137711 TTCGCAACGTAAATTTGT-AAA
1 TTCGCAACGCGAA-TAGTCAAA
*
2137732 -TCGCAACAC--ATAAGTCAAA
1 TTCGCAACGCGAAT-AGTCAAA
* * * *
2137751 TTGGCAACAC-AAAAGTTAAA
1 TTCGCAACGCGAATAGTCAAA
* *
2137771 TTTGCAACGCGGAAT-TTCAAA
1 TTCGCAACGC-GAATAGTCAAA
* *
2137792 TTCGCAAC-TGAAT-TTCAAA
1 TTCGCAACGCGAATAGTCAAA
*
2137811 TTCGCAACACGAAT
1 TTCGCAACGCGAAT
2137825 TTAATTTCGT
Statistics
Matches: 139, Mismatches: 20, Indels: 29
0.74 0.11 0.15
Matches are distributed among these distances:
17 1 0.01
18 5 0.04
19 26 0.19
20 86 0.62
21 16 0.12
22 5 0.04
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.23
Consensus pattern (21 bp):
TTCGCAACGCGAATAGTCAAA
Found at i:2137675 original size:40 final size:39
Alignment explanation
Indices: 2137631--2137758 Score: 152
Period size: 40 Copynumber: 3.2 Consensus size: 39
2137621 AGTTTCCAGT
2137631 TTCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAA
1 TTCGCAACGC-AATTTGTAAATCGCAACACAGAAGTCAAA
* *
2137671 TTCGCAACGCAA-TAGTCAAATTCGCAACGC-GATAGTCAAA
1 TTCGCAACGCAATTTGT-AAA-TCGCAACACAGA-AGTCAAA
* *
2137711 TTCGCAACGTAAATTTGTAAATCGCAACACATAAGTCAAA
1 TTCGCAACG-CAATTTGTAAATCGCAACACAGAAGTCAAA
*
2137751 TTGGCAAC
1 TTCGCAAC
2137759 ACAAAAGTTA
Statistics
Matches: 75, Mismatches: 7, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
38 3 0.04
39 7 0.09
40 56 0.75
41 6 0.08
42 3 0.04
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.22
Consensus pattern (39 bp):
TTCGCAACGCAATTTGTAAATCGCAACACAGAAGTCAAA
Found at i:2137726 original size:80 final size:81
Alignment explanation
Indices: 2137631--2137820 Score: 244
Period size: 80 Copynumber: 2.4 Consensus size: 81
2137621 AGTTTCCAGT
* * *
2137631 TTCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACGCAATAGTCAAATTCGC
1 TTCGCAACGTGAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACACAAAAGTCAAATTCGC
2137696 AACGC-G-ATAGTCAAA
66 AACGCGGAAT-GTCAAA
* * * * *
2137711 TTCGCAACGTAAATTTGTAAATCGCAACACATAAGTCAAATTGGCAACACAAAAGTTAAATTTGC
1 TTCGCAACGTGAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACACAAAAGTCAAATTCGC
*
2137776 AACGCGGAATTTCAAA
66 AACGCGGAATGTCAAA
*
2137792 TTCGCAAC-TGAATTT-CAAATTCGCAACAC
1 TTCGCAACGTGAATTTGTAAA-TCGCAACAC
2137821 GAATTTAATT
Statistics
Matches: 96, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
79 3 0.03
80 77 0.80
81 14 0.15
82 2 0.02
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.23
Consensus pattern (81 bp):
TTCGCAACGTGAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACACAAAAGTCAAATTCGC
AACGCGGAATGTCAAA
Found at i:2137778 original size:40 final size:40
Alignment explanation
Indices: 2137648--2137778 Score: 133
Period size: 40 Copynumber: 3.3 Consensus size: 40
2137638 CGCGAATTTG
* *
2137648 TAAA-TCGCAACACAGAAGTCAAATTCGCAACGCAATAGT
1 TAAATTCGCAACACATAAGTCAAATTCGCAACGCAAAAGT
* * * **
2137687 CAAATTCGCAACGCGAT-AGTCAAATTCGCAACGTAAATTT
1 TAAATTCGCAACAC-ATAAGTCAAATTCGCAACGCAAAAGT
* *
2137727 GTAAA-TCGCAACACATAAGTCAAATTGGCAACACAAAAGT
1 -TAAATTCGCAACACATAAGTCAAATTCGCAACGCAAAAGT
*
2137767 TAAATTTGCAAC
1 TAAATTCGCAAC
2137779 GCGGAATTTC
Statistics
Matches: 72, Mismatches: 15, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
39 9 0.12
40 59 0.82
41 4 0.06
ACGTcount: A:0.43, C:0.21, G:0.15, T:0.21
Consensus pattern (40 bp):
TAAATTCGCAACACATAAGTCAAATTCGCAACGCAAAAGT
Found at i:2137793 original size:21 final size:19
Alignment explanation
Indices: 2137768--2137826 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 19
2137758 CACAAAAGTT
*
2137768 AAATTTGCAACGCGGAATTTC
1 AAATTCGCAAC-C-GAATTTC
*
2137789 AAATTCGCAACTGAATTTC
1 AAATTCGCAACCGAATTTC
2137808 AAATTCGCAACACGAATTT
1 AAATTCGCAAC-CGAATTT
2137827 AATTTCGTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 18 0.53
20 6 0.18
21 10 0.29
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (19 bp):
AAATTCGCAACCGAATTTC
Found at i:2137806 original size:19 final size:19
Alignment explanation
Indices: 2137782--2137818 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
2137772 TTGCAACGCG
2137782 GAATTTCAAATTCGCAACT
1 GAATTTCAAATTCGCAACT
2137801 GAATTTCAAATTCGCAAC
1 GAATTTCAAATTCGCAAC
2137819 ACGAATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.30
Consensus pattern (19 bp):
GAATTTCAAATTCGCAACT
Found at i:2137826 original size:20 final size:20
Alignment explanation
Indices: 2137587--2137826 Score: 104
Period size: 20 Copynumber: 12.0 Consensus size: 20
2137577 AAATGACCAA
*
2137587 CAAATTCGCAACGCG-ATCTC
1 CAAATTCGCAACGCGAAT-TT
* * *
2137607 CAATTTCGCAAC-CCAGTTT
1 CAAATTCGCAACGCGAATTT
**
2137626 CCAGTTTCGCAACGCGAATTT
1 -CAAATTCGCAACGCGAATTT
* * *
2137647 GTAAA-TCGCAACACAGAA-GT
1 -CAAATTCGCAACGC-GAATTT
*
2137667 CAAATTCGCAACGC-AATAGT
1 CAAATTCGCAACGCGAAT-TT
*
2137687 CAAATTCGCAACGCG-ATAGT
1 CAAATTCGCAACGCGAAT-TT
**
2137707 CAAATTCGCAACGTAAATTT
1 CAAATTCGCAACGCGAATTT
* * **
2137727 GTAAA-TCGCAACAC-ATAAGT
1 -CAAATTCGCAACGCGA-ATTT
* * * *
2137747 CAAATTGGCAACACAAAAGTT
1 CAAATTCGCAACGC-GAATTT
*
2137768 -AAATTTGCAACGCGGAATTT
1 CAAATTCGCAACGC-GAATTT
*
2137788 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAATTT
*
2137807 CAAATTCGCAACACGAATTT
1 CAAATTCGCAACGCGAATTT
2137827 AATTTCGTAA
Statistics
Matches: 169, Mismatches: 35, Indels: 32
0.72 0.15 0.14
Matches are distributed among these distances:
18 2 0.01
19 27 0.16
20 113 0.67
21 26 0.15
22 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATTT
Found at i:2137833 original size:19 final size:20
Alignment explanation
Indices: 2137769--2137838 Score: 65
Period size: 19 Copynumber: 3.6 Consensus size: 20
2137759 ACAAAAGTTA
*
2137769 AATTT-GCAACGCGGAATTTC
1 AATTTCGCAACAC-GAATTTC
* *
2137789 AAATTCGCAAC-TGAATTTC
1 AATTTCGCAACACGAATTTC
*
2137808 AAATTCGCAACACGAATTT-
1 AATTTCGCAACACGAATTTC
*
2137827 AATTTCGTAACA
1 AATTTCGCAACA
2137839 GGTTTTAGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
19 28 0.65
20 10 0.23
21 5 0.12
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (20 bp):
AATTTCGCAACACGAATTTC
Found at i:2138006 original size:14 final size:16
Alignment explanation
Indices: 2137987--2138023 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2137977 TCCCCATCTC
2137987 TAATTTT-TTT-TACA
1 TAATTTTATTTCTACA
*
2138001 TAATTTTATTTCTATA
1 TAATTTTATTTCTACA
2138017 TAATTTT
1 TAATTTT
2138024 CAATGATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 3 0.15
16 10 0.50
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (16 bp):
TAATTTTATTTCTACA
Found at i:2138792 original size:24 final size:24
Alignment explanation
Indices: 2138765--2138818 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2138755 GTATTTGAAA
2138765 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
2138789 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
2138813 TTTGAT
1 TTTGAT
2138819 GATGTGATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:2139001 original size:3 final size:3
Alignment explanation
Indices: 2138993--2139020 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2138983 ATATAACCCT
2138993 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
2139021 TCCCCGAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2141379 original size:20 final size:20
Alignment explanation
Indices: 2141350--2141399 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
2141340 ATGTTGCGAT
*
2141350 CAACGCGAAAGTCAAATTCG
1 CAACGCGAAAGTAAAATTCG
*
2141370 CAACGTGAAAGTAAAATTCG
1 CAACGCGAAAGTAAAATTCG
*
2141390 CAATGCGAAA
1 CAACGCGAAA
2141400 TAAGCGTTGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.44, C:0.20, G:0.20, T:0.16
Consensus pattern (20 bp):
CAACGCGAAAGTAAAATTCG
Found at i:2143176 original size:23 final size:23
Alignment explanation
Indices: 2143150--2143194 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2143140 CACCACAGCT
*
2143150 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
2143173 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
2143195 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:2143915 original size:64 final size:63
Alignment explanation
Indices: 2143782--2143938 Score: 158
Period size: 64 Copynumber: 2.4 Consensus size: 63
2143772 TAATGAGGGT
* * * ** *
2143782 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTACTGGG
1 ATGCATCGATGCA-TACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
* *
2143846 ATGCATCGATGCATGACTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATT-TTAAA-A
1 ATGCATCGATGCAT-ACTAATGCATCGATGCA-TAAAATGCATTCGATG-TTCTATTATTAAAGA
2143908 G
63 G
*
2143909 AGTGCATCGATGCATTACCAATGCATCGAT
1 A-TGCATCGATGCA-TACTAATGCATCGAT
2143939 ACATCTTCAA
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
63 3 0.04
64 68 0.86
65 8 0.10
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCATACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
Found at i:2150322 original size:149 final size:149
Alignment explanation
Indices: 2150052--2150366 Score: 585
Period size: 149 Copynumber: 2.1 Consensus size: 149
2150042 TATAAATGCA
* *
2150052 CCGAAGTACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATATAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
*
2150117 TCCTTAAGGATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
*
2150182 CAAAGAATATATATATATC
131 CAAAGAATATACATATATC
2150201 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
2150266 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
*
2150331 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
2150350 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
2150367 CCATCTACCC
Statistics
Matches: 161, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 161 1.00
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CAAAGAATATACATATATC
Found at i:2150954 original size:64 final size:63
Alignment explanation
Indices: 2150821--2150977 Score: 158
Period size: 64 Copynumber: 2.4 Consensus size: 63
2150811 TAATGAGGGT
* * * ***
2150821 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTACTGGG
1 ATGCATCGATGCA-TACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTACAAAG
* *
2150885 ATGCATCGATGCATGACTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATT-TTA-AAA
1 ATGCATCGATGCAT-ACTAATGCATCGATGCA-TAAAATGCATTCGATG-TTCTATTATTACAAA
2150947 G
63 G
*
2150948 ATTGCATCGATGCATTACCAATGCATCGAT
1 A-TGCATCGATGCA-TACTAATGCATCGAT
2150978 ACATCTTCAA
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
63 3 0.04
64 68 0.86
65 8 0.10
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCATACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTACAAAG
Found at i:2152135 original size:14 final size:14
Alignment explanation
Indices: 2152100--2152136 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
2152090 GTCAAATTCA
2152100 CAACGCG-AAATCG
1 CAACGCGAAAATCG
2152113 CAAAC-CGAAAATCG
1 C-AACGCGAAAATCG
2152127 CAACGCGAAA
1 CAACGCGAAA
2152137 GTCAAATTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 6 0.29
14 15 0.71
ACGTcount: A:0.46, C:0.30, G:0.19, T:0.05
Consensus pattern (14 bp):
CAACGCGAAAATCG
Found at i:2152282 original size:66 final size:64
Alignment explanation
Indices: 2152211--2152345 Score: 234
Period size: 66 Copynumber: 2.1 Consensus size: 64
2152201 AGTTTAAAAC
2152211 AACAAATCAACTTTTACAAATCAATTAAACAAGCTAAAAAATAATTCTTATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATCAATTAAACAAGC-AAAAAATAATTCTTATTTACACATC-AATT
2152276 A
64 A
* *
2152277 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTA
2152341 AACAA
1 AACAA
2152346 GCAAAAAATA
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
64 10 0.15
65 23 0.34
66 34 0.51
ACGTcount: A:0.51, C:0.18, G:0.01, T:0.30
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTA
Found at i:2152346 original size:37 final size:37
Alignment explanation
Indices: 2152296--2152382 Score: 174
Period size: 37 Copynumber: 2.4 Consensus size: 37
2152286 ACTTTTACAA
2152296 ATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTC
1 ATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTC
2152333 ATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTC
1 ATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTC
2152370 ATCAATTAAACAA
1 ATCAATTAAACAA
2152383 ATCAACTTTC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.48, C:0.18, G:0.02, T:0.31
Consensus pattern (37 bp):
ATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTC
Found at i:2152542 original size:24 final size:24
Alignment explanation
Indices: 2152515--2152567 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
2152505 TTTGCTCAAA
2152515 CAACACTTTCTACACATCTAAAAC
1 CAACACTTTCTACACATCTAAAAC
*
2152539 CAACACTTTCTATACATCTAAAAC
1 CAACACTTTCTACACATCTAAAAC
2152563 CAACA
1 CAACA
2152568 AACAACAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.43, C:0.32, G:0.00, T:0.25
Consensus pattern (24 bp):
CAACACTTTCTACACATCTAAAAC
Found at i:2153819 original size:21 final size:21
Alignment explanation
Indices: 2153793--2153889 Score: 99
Period size: 21 Copynumber: 4.6 Consensus size: 21
2153783 GGGCGGGACT
*
2153793 TCTTGAACGATGACAGGGGCC
1 TCTTGAACGATGAGAGGGGCC
* * *
2153814 TCTTGAACGGTGGGAGGGGCT
1 TCTTGAACGATGAGAGGGGCC
*
2153835 TCTTCG-ATGATGAGAGGGGCC
1 TCTT-GAACGATGAGAGGGGCC
*
2153856 TCTTGAACGAT-AGGAGGCGCC
1 TCTTGAACGATGA-GAGGGGCC
*
2153877 TCTTGAATGATGA
1 TCTTGAACGATGA
2153890 TAGGTGCATC
Statistics
Matches: 61, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
20 2 0.03
21 57 0.93
22 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.24
Consensus pattern (21 bp):
TCTTGAACGATGAGAGGGGCC
Found at i:2153872 original size:42 final size:42
Alignment explanation
Indices: 2153793--2153889 Score: 124
Period size: 42 Copynumber: 2.3 Consensus size: 42
2153783 GGGCGGGACT
* * * * *
2153793 TCTTGAACGATGACAGGGGCCTCTTGAACGGTGGGAGGGGCT
1 TCTTGAATGATGACAGGGGCCTCTTGAACGATAGGAGGCGCC
*
2153835 TCTTCG-ATGATGAGAGGGGCCTCTTGAACGATAGGAGGCGCC
1 TCTT-GAATGATGACAGGGGCCTCTTGAACGATAGGAGGCGCC
2153877 TCTTGAATGATGA
1 TCTTGAATGATGA
2153890 TAGGTGCATC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
41 1 0.02
42 45 0.96
43 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.24
Consensus pattern (42 bp):
TCTTGAATGATGACAGGGGCCTCTTGAACGATAGGAGGCGCC
Found at i:2156514 original size:22 final size:22
Alignment explanation
Indices: 2156487--2156529 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2156477 GGAGATAGAC
2156487 GGATTTCGTCGGAGATGGGGAT
1 GGATTTCGTCGGAGATGGGGAT
2156509 GGATTTCGTCGGAGATGGGGA
1 GGATTTCGTCGGAGATGGGGA
2156530 CAGATGTCGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.09, G:0.47, T:0.26
Consensus pattern (22 bp):
GGATTTCGTCGGAGATGGGGAT
Found at i:2156539 original size:22 final size:22
Alignment explanation
Indices: 2156492--2156539 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
2156482 TAGACGGATT
** *
2156492 TCGTCGGAGATGGGGATGGATT
1 TCGTCGGAGATGGGGACAGATG
2156514 TCGTCGGAGATGGGGACAGATG
1 TCGTCGGAGATGGGGACAGATG
2156536 TCGT
1 TCGT
2156540 TGTAGAGAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.19, C:0.12, G:0.44, T:0.25
Consensus pattern (22 bp):
TCGTCGGAGATGGGGACAGATG
Found at i:2156675 original size:20 final size:20
Alignment explanation
Indices: 2156650--2156784 Score: 175
Period size: 20 Copynumber: 6.8 Consensus size: 20
2156640 TGTGTTTCGT
2156650 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGC
*
2156670 GTTGCGAATTTGACT-TCTGT
1 GTTGCGAATTTGACTATC-GC
* *
2156690 GTTGTGAATTTGACTTAT-GT
1 GTTGCGAATTTGAC-TATCGC
2156710 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGC
* * *
2156730 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTATCGC
2156750 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGC
*
2156770 GTTACGAATTTGACT
1 GTTGCGAATTTGACT
2156785 TCTATGTTGC
Statistics
Matches: 100, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
19 5 0.05
20 93 0.93
21 1 0.01
22 1 0.01
ACGTcount: A:0.19, C:0.15, G:0.24, T:0.41
Consensus pattern (20 bp):
GTTGCGAATTTGACTATCGC
Found at i:2156716 original size:60 final size:60
Alignment explanation
Indices: 2156646--2156784 Score: 226
Period size: 60 Copynumber: 2.3 Consensus size: 60
2156636 ATATTGTGTT
*
2156646 TCGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTGTGAATTTGACTTA
1 TCGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGAC-TA
*
2156707 T-GTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTA
1 TCGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGACTA
* *
2156766 TCGCGTTACGAATTTGACT
1 TCGTGTTGCGAATTTGACT
2156785 TCTATGTTGC
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
59 3 0.04
60 69 0.95
61 1 0.01
ACGTcount: A:0.19, C:0.15, G:0.24, T:0.42
Consensus pattern (60 bp):
TCGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGACTA
Found at i:2156785 original size:40 final size:40
Alignment explanation
Indices: 2156650--2156821 Score: 197
Period size: 40 Copynumber: 4.3 Consensus size: 40
2156640 TGTGTTTCGT
* * * *
2156650 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACT-TCTGT
1 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATC-GC
* *
2156690 GTTGTGAATTTGACTTATGTGTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGC
2156730 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGC
* * * *
2156770 GTTACGAATTTGACTTCTATGTTGCG-ATTT-ACAAATTCGC
1 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGAC-TA-TCGC
*
2156810 GTTGCAAATTTG
1 GTTGCGAATTTG
2156822 TTGGTCATTT
Statistics
Matches: 115, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
38 2 0.02
39 5 0.04
40 106 0.92
41 2 0.02
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.41
Consensus pattern (40 bp):
GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGC
Found at i:2157318 original size:22 final size:23
Alignment explanation
Indices: 2157293--2157337 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2157283 AAAATATTTT
2157293 AAAGTTAAAAT-AAATAATTTAA
1 AAAGTTAAAATGAAATAATTTAA
* *
2157315 AAAGTTAGAGTGAAATAATTTAA
1 AAAGTTAAAATGAAATAATTTAA
2157338 GAGATTAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.58, C:0.00, G:0.11, T:0.31
Consensus pattern (23 bp):
AAAGTTAAAATGAAATAATTTAA
Found at i:2158393 original size:83 final size:83
Alignment explanation
Indices: 2158233--2158415 Score: 210
Period size: 83 Copynumber: 2.2 Consensus size: 83
2158223 CAAAAAGCGC
* * * *
2158233 TTTATAGTGGCATTTTTCAAACAAATGCCGTAATAGAGTGGTAATTTAGCGGCATTTATAGCATA
1 TTTATAGTGGCATTTTTCAAACAAACGCCGTAATAGAGTGCTAATTTAGCAGCATTTATAGCAGA
2158298 AACACTGGAATAGGGTTG
66 AACACTGGAATAGGGTTG
* * * * * *
2158316 TTTATAGTGGTATTTTTCCAATAAACGCCGTAATAGAGTTCTAATTTAGCAGCATTTTTAG-GGA
1 TTTATAGTGGCATTTTTCAAACAAACGCCGTAATAGAGTGCTAATTTAGCAGCATTTATAGCAGA
2158380 AA-A-TGTCGTAATAGGGTTG
66 AACACTG--G-AATAGGGTTG
* *
2158399 TTTGTAGTGGCGTTTTT
1 TTTATAGTGGCATTTTT
2158416 AGACAAATGC
Statistics
Matches: 84, Mismatches: 13, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
80 2 0.02
81 1 0.01
82 4 0.05
83 77 0.92
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.37
Consensus pattern (83 bp):
TTTATAGTGGCATTTTTCAAACAAACGCCGTAATAGAGTGCTAATTTAGCAGCATTTATAGCAGA
AACACTGGAATAGGGTTG
Found at i:2158899 original size:22 final size:22
Alignment explanation
Indices: 2158870--2158918 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
2158860 GTGTTTTTCT
2158870 GCTTTCGAATAGAAAAATAATA
1 GCTTTCGAATAGAAAAATAATA
* * *
2158892 TCTTTCGAATGGGAAAATAATA
1 GCTTTCGAATAGAAAAATAATA
2158914 GCTTT
1 GCTTT
2158919 TGAAAACGTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (22 bp):
GCTTTCGAATAGAAAAATAATA
Found at i:2160148 original size:42 final size:42
Alignment explanation
Indices: 2160094--2160174 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 42
2160084 GTATTTTTAT
* * *
2160094 ACAAACGTCGCAATAGATGTAATA-TATAGCGGCATTTTTTCA
1 ACAAACGCCGCAAAAGA-GTAATACGATAGCGGCATTTTTTCA
* *
2160136 ACAAACGCCGCAAAAGAGTTATACGATAGTGGCATTTTT
1 ACAAACGCCGCAAAAGAGTAATACGATAGCGGCATTTTT
2160175 AAACACAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
41 5 0.15
42 28 0.85
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (42 bp):
ACAAACGCCGCAAAAGAGTAATACGATAGCGGCATTTTTTCA
Found at i:2162226 original size:16 final size:16
Alignment explanation
Indices: 2162195--2162228 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
2162185 CTTGCTCCCA
2162195 TAAAATTTTATCAATT
1 TAAAATTTTATCAATT
2162211 TAAAAGTTTTAT-AATT
1 TAAAA-TTTTATCAATT
2162227 TA
1 TA
2162229 GGAGTGATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (16 bp):
TAAAATTTTATCAATT
Found at i:2167655 original size:21 final size:21
Alignment explanation
Indices: 2167631--2167676 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
2167621 CCGAAAATGA
*
2167631 AGCAAGGGAAACAGAGAGACC
1 AGCAACGGAAACAGAGAGACC
* * *
2167652 AGCAACGGAAGCATAGAGAGC
1 AGCAACGGAAACAGAGAGACC
2167673 AGCA
1 AGCA
2167677 GCAGAAGCAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.46, C:0.20, G:0.33, T:0.02
Consensus pattern (21 bp):
AGCAACGGAAACAGAGAGACC
Found at i:2167683 original size:21 final size:21
Alignment explanation
Indices: 2167645--2167718 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
2167635 AGGGAAACAG
* * *
2167645 AGAGACCAGCAACGGAAGCAT
1 AGAGAGCAGCAACAGAAGCAC
*
2167666 AGAGAGCAGCAGCAGAAGCAC
1 AGAGAGCAGCAACAGAAGCAC
* *
2167687 AGAGAGAAGCATC-GACAGCAC
1 AGAGAGCAGCAACAGA-AGCAC
*
2167708 AGAGAGAAGCA
1 AGAGAGCAGCA
2167719 TCATATCAGC
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
20 2 0.04
21 44 0.96
ACGTcount: A:0.45, C:0.22, G:0.31, T:0.03
Consensus pattern (21 bp):
AGAGAGCAGCAACAGAAGCAC
Found at i:2168106 original size:43 final size:43
Alignment explanation
Indices: 2168039--2168128 Score: 126
Period size: 43 Copynumber: 2.1 Consensus size: 43
2168029 ATTCTGTGTT
*
2168039 CTTTAGCAGCGTTTGTAACAAAAAACGCCACTATATACCAGAC
1 CTTTAGCAGCGTTTGTAACAAAAAAAGCCACTATATACCAGAC
* * * * *
2168082 CTTTAGCGGCGTTTGTATCCAAAAAAGCCGCTATATACCAGAT
1 CTTTAGCAGCGTTTGTAACAAAAAAAGCCACTATATACCAGAC
2168125 CTTT
1 CTTT
2168129 TACGGATGCG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (43 bp):
CTTTAGCAGCGTTTGTAACAAAAAAAGCCACTATATACCAGAC
Found at i:2170601 original size:21 final size:21
Alignment explanation
Indices: 2170577--2170630 Score: 92
Period size: 20 Copynumber: 2.6 Consensus size: 21
2170567 TTTTCCAAAT
2170577 TCGCAACACAGAATTTGTAAA
1 TCGCAACACAGAATTTGTAAA
*
2170598 TCGCAACGC-GAATTTGTAAA
1 TCGCAACACAGAATTTGTAAA
2170618 TCGCAACACAGAA
1 TCGCAACACAGAA
2170631 AACAAATTCG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (21 bp):
TCGCAACACAGAATTTGTAAA
Found at i:2170612 original size:20 final size:20
Alignment explanation
Indices: 2170557--2170624 Score: 82
Period size: 20 Copynumber: 3.3 Consensus size: 20
2170547 ATTTCTTTTC
* **
2170557 CGCAACGCGATTTTCCAAATT
1 CGCAACGCGAATTTGTAAA-T
*
2170578 CGCAACACAGAATTTGTAAAT
1 CGCAACGC-GAATTTGTAAAT
2170599 CGCAACGCGAATTTGTAAAT
1 CGCAACGCGAATTTGTAAAT
2170619 CGCAAC
1 CGCAAC
2170625 ACAGAAAACA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
20 18 0.44
21 15 0.37
22 8 0.20
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (20 bp):
CGCAACGCGAATTTGTAAAT
Found at i:2170641 original size:20 final size:20
Alignment explanation
Indices: 2170618--2170663 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
2170608 AATTTGTAAA
2170618 TCGCAACACAGAAAACAAAT
1 TCGCAACACAGAAAACAAAT
* **
2170638 TCGCAACACATAAGTCAAAT
1 TCGCAACACAGAAAACAAAT
2170658 TCGCAA
1 TCGCAA
2170664 AACGCGTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.48, C:0.26, G:0.11, T:0.15
Consensus pattern (20 bp):
TCGCAACACAGAAAACAAAT
Found at i:2171284 original size:20 final size:19
Alignment explanation
Indices: 2171254--2171298 Score: 72
Period size: 20 Copynumber: 2.3 Consensus size: 19
2171244 TCGCAACGCT
2171254 ATTTTATTTTCGCGTTGCG
1 ATTTTATTTTCGCGTTGCG
2171273 ATTTTCATTTTCGCGTTGCG
1 ATTTT-ATTTTCGCGTTGCG
*
2171293 AATTTA
1 ATTTTA
2171299 AGTTTCAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.16, C:0.16, G:0.18, T:0.51
Consensus pattern (19 bp):
ATTTTATTTTCGCGTTGCG
Found at i:2171304 original size:20 final size:20
Alignment explanation
Indices: 2171261--2171304 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2171251 GCTATTTTAT
* * *
2171261 TTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGAATTTAAG
2171281 TTTCGCGTTGCGAATTTAAG
1 TTTCGCGTTGCGAATTTAAG
2171301 TTTC
1 TTTC
2171305 AGAAACTACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.18, G:0.20, T:0.48
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTAAG
Found at i:2173045 original size:21 final size:21
Alignment explanation
Indices: 2173021--2173117 Score: 63
Period size: 21 Copynumber: 4.6 Consensus size: 21
2173011 TGGTGCATGG
2173021 CGTGATGAGGTACGAT-CTTTA
1 CGTGATGAGGTA-GATGCTTTA
* *
2173042 CGTGGTGAGGTAGATGTTTTA
1 CGTGATGAGGTAGATGCTTTA
* ** *
2173063 CGCGATGA-AAATGGTGCTTTA
1 CGTGATGAGGTA-GATGCTTTA
* ** *
2173084 CGTGGTGAGGTATCTACTTTA
1 CGTGATGAGGTAGATGCTTTA
*
2173105 CATGATGAGGTAG
1 CGTGATGAGGTAG
2173118 CCGCTCTACG
Statistics
Matches: 55, Mismatches: 18, Indels: 6
0.70 0.23 0.08
Matches are distributed among these distances:
20 4 0.07
21 50 0.91
22 1 0.02
ACGTcount: A:0.24, C:0.11, G:0.32, T:0.33
Consensus pattern (21 bp):
CGTGATGAGGTAGATGCTTTA
Done.