Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007952.1 Hibiscus syriacus cultivar Beakdansim tig00110377_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: 3169409
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 16
Found at i:938305 original size:42 final size:42
Alignment explanation
Indices: 938207--938307 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 42
938197 CGGCGGGCGG
* * * *
938207 GACCTCTTGAACGATGACGGGGGCCTCTTGAATGGTGGGAGT
1 GACCTCTTGAATGATGACGGGGGCCTCTTGAACGATAGGAGT
* *
938249 GGCTTCTTCG-ATGATGA-GAGGGGCCTCTTGAACGATAGGAG-
1 GACCTCTT-GAATGATGACG-GGGGCCTCTTGAACGATAGGAGT
938290 GCACCTCTTGAATGATGA
1 G-ACCTCTTGAATGATGA
938308 TAGGTGCATT
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
41 3 0.06
42 43 0.91
43 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.35, T:0.25
Consensus pattern (42 bp):
GACCTCTTGAATGATGACGGGGGCCTCTTGAACGATAGGAGT
Found at i:940372 original size:20 final size:20
Alignment explanation
Indices: 940349--940387 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
940339 CTTAAATTCA
*
940349 CAACTCGAAAATGAAAATCG
1 CAACGCGAAAATGAAAATCG
940369 CAACGCGAAAATGAAAATC
1 CAACGCGAAAATGAAAATC
940388 ACTTTGTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.21, G:0.15, T:0.13
Consensus pattern (20 bp):
CAACGCGAAAATGAAAATCG
Found at i:940860 original size:20 final size:20
Alignment explanation
Indices: 940835--940955 Score: 104
Period size: 20 Copynumber: 6.0 Consensus size: 20
940825 GCGTAAAAAC
940835 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
940855 ATTTGAC-TTCTGTGTTGCG-
1 ATTTGACTTTC-GCGTTGCGA
* * ***
940874 ATTT-ACAAATTCACAACGCGA
1 ATTTGAC--TTTCGCGTTGCGA
940895 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
** *
940915 ATTTGACTTTCGTATTGCAA
1 ATTTGACTTTCGCGTTGCGA
*
940935 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
940955 A
1 A
940956 ATTGGAAACT
Statistics
Matches: 77, Mismatches: 18, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
18 2 0.03
19 7 0.09
20 59 0.77
21 7 0.09
22 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:940991 original size:20 final size:19
Alignment explanation
Indices: 940943--940995 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
940933 AAATTTGACT
940943 ATCGCGTTGCGAAATTGGA
1 ATCGCGTTGCGAAATTGGA
* *
940962 AACTGAGTTGCGAAATTGGA
1 ATC-GCGTTGCGAAATTGGA
940982 ATTCGCGTTGCGAA
1 A-TCGCGTTGCGAA
940996 TTTGTAGGTC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 2 0.07
20 25 0.89
21 1 0.04
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.26
Consensus pattern (19 bp):
ATCGCGTTGCGAAATTGGA
Found at i:942291 original size:26 final size:26
Alignment explanation
Indices: 942255--942307 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
942245 GGGAAAAAAA
942255 TAAAATCAGAATATAGTTATTAAGGG
1 TAAAATCAGAATATAGTTATTAAGGG
942281 TAAAATCAGAATATAGTTATTAAGGG
1 TAAAATCAGAATATAGTTATTAAGGG
942307 T
1 T
942308 CAAACTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.45, C:0.04, G:0.19, T:0.32
Consensus pattern (26 bp):
TAAAATCAGAATATAGTTATTAAGGG
Found at i:944581 original size:2 final size:2
Alignment explanation
Indices: 944574--944601 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
944564 AACCAAACCA
944574 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
944602 TAAGTTCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:947516 original size:183 final size:183
Alignment explanation
Indices: 947208--947570 Score: 726
Period size: 183 Copynumber: 2.0 Consensus size: 183
947198 AATTGTTGTT
947208 TCATCCATAAAACTTGTGCTCAACAACTACCGGCTGAAATGTATTCCACTTCAGTGGTAGATAAT
1 TCATCCATAAAACTTGTGCTCAACAACTACCGGCTGAAATGTATTCCACTTCAGTGGTAGATAAT
947273 GCAACTCAATTTTGTTTCTTTGAAAACCATAAAATCAACATATTTCCTAGGAATTGGCAAGTACC
66 GCAACTCAATTTTGTTTCTTTGAAAACCATAAAATCAACATATTTCCTAGGAATTGGCAAGTACC
947338 AGAGAAGGCATCCTCCATAATCTGCATCAGAGAAGGCATGCAAGATAAAGTAG
131 AGAGAAGGCATCCTCCATAATCTGCATCAGAGAAGGCATGCAAGATAAAGTAG
947391 TCATCCATAAAACTTGTGCTCAACAACTACCGGCTGAAATGTATTCCACTTCAGTGGTAGATAAT
1 TCATCCATAAAACTTGTGCTCAACAACTACCGGCTGAAATGTATTCCACTTCAGTGGTAGATAAT
947456 GCAACTCAATTTTGTTTCTTTGAAAACCATAAAATCAACATATTTCCTAGGAATTGGCAAGTACC
66 GCAACTCAATTTTGTTTCTTTGAAAACCATAAAATCAACATATTTCCTAGGAATTGGCAAGTACC
947521 AGAGAAGGCATCCTCCATAATCTGCATCAGAGAAGGCATGCAAGATAAAG
131 AGAGAAGGCATCCTCCATAATCTGCATCAGAGAAGGCATGCAAGATAAAG
947571 CTAGAGTCTC
Statistics
Matches: 180, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
183 180 1.00
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.27
Consensus pattern (183 bp):
TCATCCATAAAACTTGTGCTCAACAACTACCGGCTGAAATGTATTCCACTTCAGTGGTAGATAAT
GCAACTCAATTTTGTTTCTTTGAAAACCATAAAATCAACATATTTCCTAGGAATTGGCAAGTACC
AGAGAAGGCATCCTCCATAATCTGCATCAGAGAAGGCATGCAAGATAAAGTAG
Found at i:952010 original size:65 final size:64
Alignment explanation
Indices: 951940--952088 Score: 167
Period size: 65 Copynumber: 2.3 Consensus size: 64
951930 TACACTAGGG
* * * ** *
951940 GTGCATCGGTACACTAATTACATTCGATATTTCA-AATGAGCCTGGAGTGCATCGATTCATGG-T
1 GTGCATCGGTACACAAAATACATTCGAT-GTTCAGAAT-AGCCAAGAGTGCATCGATGCATGGCT
952003 CT
64 -T
* **
952005 GTGCATCGGTACACAAAATGCATTCGATGTTCAGAATATTCAAGAGTGCATCGATGCATGGCTT
1 GTGCATCGGTACACAAAATACATTCGATGTTCAGAATAGCCAAGAGTGCATCGATGCATGGCTT
952069 GTGCATCGGGTACACAAAAT
1 GTGCATC-GGTACACAAAAT
952089 GCATCCGAAA
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
64 31 0.43
65 41 0.57
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (64 bp):
GTGCATCGGTACACAAAATACATTCGATGTTCAGAATAGCCAAGAGTGCATCGATGCATGGCTT
Found at i:954747 original size:54 final size:53
Alignment explanation
Indices: 954653--954760 Score: 180
Period size: 54 Copynumber: 2.0 Consensus size: 53
954643 TGCTTTGGGA
* *
954653 CAAGTACGATGCATTGGTTCCTTCCTTGTGAATGTCCTAATTATCACGTTAAT
1 CAAGTACGATACATTAGTTCCTTCCTTGTGAATGTCCTAATTATCACGTTAAT
*
954706 CAAGTACGATACATTAGTTCCTTGTCTTGTGAATGTCCTAATTATCACGTTAAT
1 CAAGTACGATACATTAGTTCCTT-CCTTGTGAATGTCCTAATTATCACGTTAAT
954760 C
1 C
954761 TGGATCACCT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
53 21 0.41
54 30 0.59
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (53 bp):
CAAGTACGATACATTAGTTCCTTCCTTGTGAATGTCCTAATTATCACGTTAAT
Found at i:960252 original size:41 final size:42
Alignment explanation
Indices: 960169--960253 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
960159 AAAATTAGTC
960169 AAGAAAACAATTTATATTGAAAGAGTTTGAATGATCTAAAGG
1 AAGAAAACAATTTATATTGAAAGAGTTTGAATGATCTAAAGG
960211 AAGAAAACAATTTATATTGAAAGAG-TTGAATGATCTAAAGG
1 AAGAAAACAATTTATATTGAAAGAGTTTGAATGATCTAAAGG
960252 AA
1 AA
960254 CACTTAGAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 18 0.42
42 25 0.58
ACGTcount: A:0.49, C:0.05, G:0.19, T:0.27
Consensus pattern (42 bp):
AAGAAAACAATTTATATTGAAAGAGTTTGAATGATCTAAAGG
Found at i:962220 original size:16 final size:18
Alignment explanation
Indices: 962188--962222 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
962178 ATATAAAAAC
962188 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
962206 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
962222 A
1 A
962223 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:962258 original size:20 final size:20
Alignment explanation
Indices: 962233--962270 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
962223 AATGAGTAAA
962233 ATATATAAAAAAGTAAAAGC
1 ATATATAAAAAAGTAAAAGC
* *
962253 ATATATATATAAGTAAAA
1 ATATATAAAAAAGTAAAA
962271 TAATAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (20 bp):
ATATATAAAAAAGTAAAAGC
Found at i:962842 original size:37 final size:36
Alignment explanation
Indices: 962794--962895 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
962784 ATAGTAGAAC
*
962794 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCATATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
962831 TTTATCATATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCATATTTTTAGGAGTTTGAATCCTAGAAAAT
962865 TCTATCATATTTTTAGGAGTTTGAATCCTAG
1 TCTATCATATTTTTAGGAGTTTGAATCCTAG
962896 TATGACGAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
34 33 0.55
37 27 0.45
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.44
Consensus pattern (36 bp):
TCTATCATATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:963742 original size:105 final size:104
Alignment explanation
Indices: 963443--964379 Score: 1398
Period size: 105 Copynumber: 9.0 Consensus size: 104
963433 CATTGTTCCA
* * ***
963443 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAA-TTGTCTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAA-ATTGAAAGTTGT-TGTTGACAA
* * * * *
963507 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
63 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* ** *
963549 AGTCCAATATCCTTCGTTATGAAGTTGAAATTGAATTTG-AA-TGAAA-TT-TTGTTGACAAGCA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAAAGTTGTTGTTGACAAGCA
963610 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
963649 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAGATTGGAAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GAAAGTTGTTGTTGACAAGC
* *
963714 AGCGATCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
963754 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTATTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GAAAGTTGTTGTTGACAAGC
* *
963819 AGCGGTCCCTTCGTCGCGAAGTTGAACTTGCGTTGTCTGA
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
963859 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA-AAGTTGTTGTTGACAAGC
963924 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
963964 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA-AAGTTGTTGTTGACAAGC
*
964029 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
964069 AGTCCAATATCCTTCATTGTAAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA-AAGTTGTTGTTGACAAGC
*
964134 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
964174 AGTCCAATATCCTTCATTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA-AAGTTGTTGTTGACAAGC
*
964239 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTGG
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
964279 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA-AAGTTG-TTGTTGACAAG
* * *
964344 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
64 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
964380 CCTCGAGTGC
Statistics
Matches: 774, Mismatches: 50, Indels: 14
0.92 0.06 0.02
Matches are distributed among these distances:
100 81 0.10
101 2 0.00
102 7 0.01
103 4 0.01
104 4 0.01
105 602 0.78
106 74 0.10
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (104 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAAAGTTGTTGTTGACAAGCA
GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:965157 original size:67 final size:66
Alignment explanation
Indices: 965022--965179 Score: 201
Period size: 68 Copynumber: 2.4 Consensus size: 66
965012 AAGATATCTG
* * **
965022 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGA-
965087 TT
65 TT
* * * * *
965089 TGTGTTTCAAGAGTAACTGTCTCAAGGGAGATAAAATT-TGTTTTAGGGGAAATAAATTCAAAGG
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGA
965153 TT
65 TT
*
965155 TTGTTTCAAGGGAAACTGTCTCAAG
1 TTGTTTCAAGAGAAACTGTCTCAAG
965180 ATAGACGAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
65 22 0.28
66 3 0.04
67 23 0.29
68 31 0.39
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.33
Consensus pattern (66 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGAT
T
Found at i:965195 original size:65 final size:67
Alignment explanation
Indices: 965023--965196 Score: 183
Period size: 65 Copynumber: 2.6 Consensus size: 67
965013 AGATATCTGT
* * * * * ** *
965023 TGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAGAAAATT-TGTTTTAAGGGAAATAAATTCAAAGAGT
965088 TTG
65 TTG
* * * *
965091 TGTTTCAAGAGTAACTGTCTCAAGGGAGATAAAATTTGTTTTAGGGGAAATAAATTCAAAG-GTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAGAAAATTTGTTTTAAGGGAAATAAATTCAAAGAGTT
965155 T-
66 TG
* *
965156 TGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA-TTGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGA-GAAAATTTGTTT
965197 CAAGAGAGAC
Statistics
Matches: 91, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
65 31 0.34
66 7 0.08
67 22 0.24
68 31 0.34
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.33
Consensus pattern (67 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGAGAAAATTTGTTTTAAGGGAAATAAATTCAAAGAGTT
TG
Found at i:966280 original size:22 final size:22
Alignment explanation
Indices: 966255--966305 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
966245 TTGTGTTTGG
966255 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
966277 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
966299 TCAAAGG
1 TCAAAGG
966306 ATTGATGGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:966934 original size:20 final size:21
Alignment explanation
Indices: 966911--966970 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
966901 TTGTCCCCTT
*
966911 TTTTTTATTTTTGTTCTTT-C
1 TTTTTTATTCTTGTTCTTTCC
* *
966931 TTTTTTGTTCTTGTTTTTTCC
1 TTTTTTATTCTTGTTCTTTCC
*
966952 TTTTTTGCTTCTT-TTCTTT
1 TTTTTT-ATTCTTGTTCTTT
966971 TTTCTTTTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
20 16 0.48
21 12 0.36
22 5 0.15
ACGTcount: A:0.02, C:0.13, G:0.07, T:0.78
Consensus pattern (21 bp):
TTTTTTATTCTTGTTCTTTCC
Found at i:966981 original size:22 final size:22
Alignment explanation
Indices: 966927--966979 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
966917 ATTTTTGTTC
966927 TTTCTTTTTTG-TTCTTGTTTT
1 TTTCTTTTTTGCTTCTTGTTTT
* *
966948 TTCCTTTTTTGCTTCTTTTCTTT
1 TTTCTTTTTTGCTTCTTGT-TTT
966971 TTTCTTTTT
1 TTTCTTTTT
966980 GCCCTTTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 10 0.37
22 6 0.22
23 11 0.41
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (22 bp):
TTTCTTTTTTGCTTCTTGTTTT
Found at i:970188 original size:16 final size:18
Alignment explanation
Indices: 970156--970190 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
970146 ATATAAAAAC
970156 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
970174 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
970190 A
1 A
970191 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:970231 original size:24 final size:23
Alignment explanation
Indices: 970200--970258 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 23
970190 AAATGAGTAA
*
970200 AATATATAAAAAAGTAAAAGCAT
1 AATATATAAAAAAGTAAAAGAAT
* * *
970223 ATATATATATATAAGTAAAATAAT
1 A-ATATATAAAAAAGTAAAAGAAT
970247 AATA-ATAAAAAA
1 AATATATAAAAAA
970259 AGAAAATCAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
22 6 0.21
23 4 0.14
24 19 0.66
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (23 bp):
AATATATAAAAAAGTAAAAGAAT
Found at i:970814 original size:37 final size:36
Alignment explanation
Indices: 970766--970867 Score: 154
Period size: 34 Copynumber: 2.9 Consensus size: 36
970756 ATAGTAGAAC
*
970766 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCATATTTTTAGGAGTTTGAATCCTAG-AAAAT
* *
970803 TTTATTATATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCATATTTTTAGGAGTTTGAATCCTAGAAAAT
970837 TCTATCATATTTTTAGGAGTTTGAATCCTAG
1 TCTATCATATTTTTAGGAGTTTGAATCCTAG
970868 TAGGACGAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
34 32 0.55
37 26 0.45
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (36 bp):
TCTATCATATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:972445 original size:14 final size:15
Alignment explanation
Indices: 972414--972447 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
972404 TGCTCAGTAT
972414 GGGATGAGTCATATA
1 GGGATGAGTCATATA
*
972429 GGGATGTGTCA-ATA
1 GGGATGAGTCATATA
972443 GGGAT
1 GGGAT
972448 TGAGGGGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.29, C:0.06, G:0.38, T:0.26
Consensus pattern (15 bp):
GGGATGAGTCATATA
Found at i:972788 original size:21 final size:21
Alignment explanation
Indices: 972762--972806 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
972752 TCCCAATTTG
972762 TACTACTCTTATATATGCTCT
1 TACTACTCTTATATATGCTCT
972783 TACTACTCTTATATATGCTCT
1 TACTACTCTTATATATGCTCT
972804 TAC
1 TAC
972807 CTAGTTCAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.24, C:0.24, G:0.04, T:0.47
Consensus pattern (21 bp):
TACTACTCTTATATATGCTCT
Found at i:986018 original size:19 final size:19
Alignment explanation
Indices: 985994--986033 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
985984 CGAATAATTT
*
985994 AATCGAATATATAATATTA
1 AATCGAATATAAAATATTA
*
986013 AATCGAATATAAAATCTTA
1 AATCGAATATAAAATATTA
986032 AA
1 AA
986034 ATTCAATAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (19 bp):
AATCGAATATAAAATATTA
Found at i:986152 original size:13 final size:13
Alignment explanation
Indices: 986134--986167 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
986124 TAAGATTTTC
*
986134 TTTGAAAATCATT
1 TTTGAAAATCAAT
986147 TTTG-AAATCAAT
1 TTTGAAAATCAAT
986159 TTTGAAAAT
1 TTTGAAAAT
986168 TACTCCCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (13 bp):
TTTGAAAATCAAT
Found at i:986809 original size:15 final size:15
Alignment explanation
Indices: 986789--986817 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
986779 TTTCTCTCTC
986789 GTTATCTAAACCAAT
1 GTTATCTAAACCAAT
986804 GTTATCTAAACCAA
1 GTTATCTAAACCAA
986818 AGGTGTTAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.31
Consensus pattern (15 bp):
GTTATCTAAACCAAT
Found at i:987402 original size:12 final size:13
Alignment explanation
Indices: 987385--987417 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
987375 ATGGGCAAAA
*
987385 TTTGAAAACTAT-
1 TTTGAAAACAATG
987397 TTTGAAAACAATG
1 TTTGAAAACAATG
987410 TTTGAAAA
1 TTTGAAAA
987418 ATCATAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.36
Consensus pattern (13 bp):
TTTGAAAACAATG
Found at i:1003429 original size:16 final size:17
Alignment explanation
Indices: 1003401--1003432 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1003391 GTTATCGTAA
1003401 AAAAATTATTTAATTTT
1 AAAAATTATTTAATTTT
1003418 AAAAATTA-TTAATTT
1 AAAAATTATTTAATTT
1003433 ACTAATAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AAAAATTATTTAATTTT
Found at i:1014632 original size:65 final size:64
Alignment explanation
Indices: 1014538--1014678 Score: 162
Period size: 65 Copynumber: 2.2 Consensus size: 64
1014528 TTTCGATGCA
* *
1014538 GCATTCGATGTTTCAAAATAGCCAGAGTGCATC-GATGCATTGCT-GGTGTATCGATGCATCAAA
1 GCATTCGATGTTTCAAAATAGCCACAGTGCATCAG-TGCA-TGCTAGGTGCATCGATGCATCAAA
1014601 T
64 T
* * * * *
1014602 GCATTCGATGATTTCATAAA-ATCCTCAGTGCATCAGTGCATGGTATGTGCATCGATGCATGAAA
1 GCATTCGATG-TTTCA-AAATAGCCACAGTGCATCAGTGCATGCTAGGTGCATCGATGCATCAAA
1014666 T
64 T
1014667 GCATTCGATGTT
1 GCATTCGATGTT
1014679 CAATTTAACT
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
64 15 0.23
65 47 0.71
66 4 0.06
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (64 bp):
GCATTCGATGTTTCAAAATAGCCACAGTGCATCAGTGCATGCTAGGTGCATCGATGCATCAAAT
Found at i:1014717 original size:65 final size:63
Alignment explanation
Indices: 1014563--1014728 Score: 167
Period size: 65 Copynumber: 2.6 Consensus size: 63
1014553 AAATAGCCAG
* * * *
1014563 AGTGCATCGATGCATTGCTGGTGTATCGATGCATCAAATGCATTCGATGATTTCATAAAATCCTC
1 AGTGCATCGGTGCATGGTTGGTGCATCGATGCATCAAATGCATTCGATGA-TTCATAAAA-CCTC
* * **
1014628 AGTGCATCAGTGCATGGTAT-GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAA-CTC
1 AGTGCATCGGTGCATGGT-TGGTGCATCGATGCATCAAATGCATTCGATGATTC-ATAAAACCTC
*
1014690 ATGGTGCATCGGTGCATGGATTGGTGCATCGGTGCATCA
1 A--GTGCATCGGTGCATGG-TTGGTGCATCGATGCATCA
1014729 CTCTGAAAAA
Statistics
Matches: 84, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
62 4 0.05
63 3 0.04
64 20 0.24
65 56 0.67
66 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (63 bp):
AGTGCATCGGTGCATGGTTGGTGCATCGATGCATCAAATGCATTCGATGATTCATAAAACCTC
Found at i:1017234 original size:19 final size:20
Alignment explanation
Indices: 1017210--1017248 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
1017200 AAAAATCGTT
1017210 GATTTTGAGCAAGAG-TGGA
1 GATTTTGAGCAAGAGATGGA
* *
1017229 GATTTTTAGGAAGAGATGGA
1 GATTTTGAGCAAGAGATGGA
1017249 CGAACGGCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.33, C:0.03, G:0.36, T:0.28
Consensus pattern (20 bp):
GATTTTGAGCAAGAGATGGA
Found at i:1021282 original size:22 final size:21
Alignment explanation
Indices: 1021240--1021279 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1021230 GAGTTTATTT
*
1021240 TCATTTTTAAATTTTGAAACA
1 TCATTTTTAAATTTTAAAACA
*
1021261 TCATTTTTATATTTTAAAA
1 TCATTTTTAAATTTTAAAA
1021280 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTAAATTTTAAAACA
Found at i:1023273 original size:18 final size:17
Alignment explanation
Indices: 1023221--1023267 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
1023211 GTACACTAAG
1023221 AGTGCATCGAATGCA-CA
1 AGTGCATCG-ATGCATCA
*
1023238 TGTGCATCGATGCATCA
1 AGTGCATCGATGCATCA
1023255 AGTGCATTCGATG
1 AGTGCA-TCGATG
1023268 TTTCAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 5 0.19
17 15 0.58
18 6 0.23
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:1023437 original size:65 final size:64
Alignment explanation
Indices: 1023239--1023448 Score: 205
Period size: 65 Copynumber: 3.2 Consensus size: 64
1023229 GAATGCACAT
* * ** * *
1023239 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAAT-AGCCAGAGTGCATCGATGCATTGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAG-GTGCATCGATGCATGGTTG
* * * *
1023303 GTGTATCGATACATCAAATGCATTCGATGTTTTC-ATAAAATCCTCA-GTGCATCGGTGCATGGT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCAATATAAT--TCAGGTGCATCGATGCATGGT
1023366 AT-
63 -TG
* *
1023368 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCA-GGTGCATCGATGCATGG-TT
1023432 G
64 G
*
1023433 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
1023449 CTCTGAAAAA
Statistics
Matches: 118, Mismatches: 18, Indels: 19
0.76 0.12 0.12
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 49 0.42
65 60 0.51
66 1 0.01
67 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAGGTGCATCGATGCATGGTTG
Found at i:1031416 original size:106 final size:106
Alignment explanation
Indices: 1031226--1031435 Score: 330
Period size: 106 Copynumber: 2.0 Consensus size: 106
1031216 GAGATGTTGG
* * * *
1031226 TGCTGATCTACCTCATTATGTGATAGAATCGAGCTAAAAGTTGATGTTGATCCAACTCCTTCTGC
1 TGCTAATCTACCTCATTATGTGATAGAATCGAGCTAAAAGTTGACGCTGATCCAACTCCTTCTAC
*
1031291 GATGGATTTGAGCGAAATAAATGTCAATCCACCTCCTTTAA
66 GATGGATTTGAGCAAAATAAATGTCAATCCACCTCCTTTAA
* * * *
1031332 TGCTAATCTACCTCCTTCTGTGATAGAATTGAGCTAAAAGTTGACGCTGATCCAACTTCTTCTAC
1 TGCTAATCTACCTCATTATGTGATAGAATCGAGCTAAAAGTTGACGCTGATCCAACTCCTTCTAC
*
1031397 GATGGATTTGAGCAAAATAAATGTCGATCCACCTCCTTT
66 GATGGATTTGAGCAAAATAAATGTCAATCCACCTCCTTT
1031436 TGTGATGGAA
Statistics
Matches: 94, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
106 94 1.00
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (106 bp):
TGCTAATCTACCTCATTATGTGATAGAATCGAGCTAAAAGTTGACGCTGATCCAACTCCTTCTAC
GATGGATTTGAGCAAAATAAATGTCAATCCACCTCCTTTAA
Found at i:1031907 original size:30 final size:30
Alignment explanation
Indices: 1031871--1032020 Score: 147
Period size: 30 Copynumber: 4.8 Consensus size: 30
1031861 AGACGAAATT
*
1031871 TGTTTCAAGGGAAACAATCTCAAAGGTTGG
1 TGTTTCAAGGGAAACTATCTCAAAGGTTGG
* *
1031901 TGTTTCAAGAGAAACTGTCTCAAAGGTTGG
1 TGTTTCAAGGGAAACTATCTCAAAGGTTGG
* ***
1031931 TGTTTCAAGAGAAACTATCTCAAGAGAGATAAAACA
1 TGTTTCAAGGGAAACTATCTCAA-AG-G-T---TGG
* * *
1031967 TGTTTCAAGGGAAACAATCTCAAATGTGGG
1 TGTTTCAAGGGAAACTATCTCAAAGGTTGG
*
1031997 TGTTTCAAGGGAAACTGTCTCAAA
1 TGTTTCAAGGGAAACTATCTCAAA
1032021 ACTCGTTTCA
Statistics
Matches: 99, Mismatches: 15, Indels: 12
0.79 0.12 0.10
Matches are distributed among these distances:
30 71 0.72
31 2 0.02
32 1 0.01
33 2 0.02
34 1 0.01
35 1 0.01
36 21 0.21
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (30 bp):
TGTTTCAAGGGAAACTATCTCAAAGGTTGG
Found at i:1032135 original size:36 final size:36
Alignment explanation
Indices: 1032086--1032169 Score: 132
Period size: 36 Copynumber: 2.3 Consensus size: 36
1032076 AAAGTTTATA
** * *
1032086 TTTCAAGAAAAACTATCTCAAGGGAGACAAAATTTG
1 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCG
1032122 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCG
1 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCG
1032158 TTTCAAGGGAAA
1 TTTCAAGGGAAA
1032170 TGTTTTCAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (36 bp):
TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCG
Found at i:1032232 original size:21 final size:21
Alignment explanation
Indices: 1032206--1032253 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
1032196 AAACTGTCTA
1032206 AAGGGAGACAAATTTTGTTTC
1 AAGGGAGACAAATTTTGTTTC
* *
1032227 AAGGGAGATAAATTTTGTTTT
1 AAGGGAGACAAATTTTGTTTC
1032248 AAGGGA
1 AAGGGA
1032254 AACTGTCTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.33
Consensus pattern (21 bp):
AAGGGAGACAAATTTTGTTTC
Found at i:1032295 original size:39 final size:39
Alignment explanation
Indices: 1032225--1032661 Score: 514
Period size: 39 Copynumber: 11.4 Consensus size: 39
1032215 AAATTTTGTT
* ** *
1032225 TCAAGGGAGAT-AAAT-TT-TGTTTTAAGGGAAACTGTC
1 TCAAGCGAGATAAAATCTTATGTTTCGAGGGAAACTATC
* * *
1032261 TCAAGGGAGACAAAA-CTTTATGTTTCGAGAGAAACTATC
1 TCAAGCGAGATAAAATC-TTATGTTTCGAGGGAAACTATC
* * * *
1032300 TCAAGAGAGATAAAATCTTCTATTTCGAGGGAAATTATC
1 TCAAGCGAGATAAAATCTTATGTTTCGAGGGAAACTATC
* *
1032339 TCAAGCGAGATAAAATCTTCTGTTTCGAGGGTAACTATC
1 TCAAGCGAGATAAAATCTTATGTTTCGAGGGAAACTATC
* *
1032378 TCAAGCGAGATAAAATCTTCTGTTTC-AGGGGAACTATC
1 TCAAGCGAGATAAAATCTTATGTTTCGAGGGAAACTATC
* *
1032416 TCAAGCGAGATAAAATCTTCTGTTTCGAGAGAAACTA--
1 TCAAGCGAGATAAAATCTTATGTTTCGAGGGAAACTATC
* * *
1032453 TCAAGCGAG--AAAATCTTCTATTTCTAGGGAAACTATC
1 TCAAGCGAGATAAAATCTTATGTTTCGAGGGAAACTATC
* *
1032490 TCAAGCGAGACAAAATCTTATGTTTCTAGGGAAACTATC
1 TCAAGCGAGATAAAATCTTATGTTTCGAGGGAAACTATC
* * *
1032529 TCAAGCGAGATAAAATCTTCTATTTCGAGGGAAACTATT
1 TCAAGCGAGATAAAATCTTATGTTTCGAGGGAAACTATC
* * *
1032568 TCAAGCGAGATAAAATCTTTTATTTCAAGGGAAACTATC
1 TCAAGCGAGATAAAATCTTATGTTTCGAGGGAAACTATC
* * *
1032607 TCAAGTGAGATAAAATCTTCTGTTTCGGGGGAAACTATC
1 TCAAGCGAGATAAAATCTTATGTTTCGAGGGAAACTATC
*
1032646 TCAAGTGAGATAAAAT
1 TCAAGCGAGATAAAAT
1032662 ATTCTTTAAA
Statistics
Matches: 355, Mismatches: 36, Indels: 17
0.87 0.09 0.04
Matches are distributed among these distances:
35 23 0.06
36 10 0.03
37 21 0.06
38 39 0.11
39 261 0.74
40 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (39 bp):
TCAAGCGAGATAAAATCTTATGTTTCGAGGGAAACTATC
Found at i:1032342 original size:78 final size:78
Alignment explanation
Indices: 1032249--1032661 Score: 568
Period size: 78 Copynumber: 5.4 Consensus size: 78
1032239 TTTTGTTTTA
* * * * *
1032249 AGGGAAACTGTCTCAAGGGAGACAAAA-CTTTATGTTTCGAGAGAAACTATCTCAAGAGAGATAA
1 AGGGAAACTATCTCAAGCGAGATAAAATC-TTATGTTTCGAGGGAAACTATCTCAAGCGAGATAA
1032313 AATCTTCTATTTCG
65 AATCTTCTATTTCG
* * *
1032327 AGGGAAATTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGTAACTATCTCAAGCGAGATAAA
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTATGTTTCGAGGGAAACTATCTCAAGCGAGATAAA
*
1032392 ATCTTCTGTTTC-
66 ATCTTCTATTTCG
* * *
1032404 AGGGGAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGAGAAACTA--TCAAGCGAG--AAA
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTATGTTTCGAGGGAAACTATCTCAAGCGAGATAAA
*
1032465 ATCTTCTATTTCT
66 ATCTTCTATTTCG
* *
1032478 AGGGAAACTATCTCAAGCGAGACAAAATCTTATGTTTCTAGGGAAACTATCTCAAGCGAGATAAA
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTATGTTTCGAGGGAAACTATCTCAAGCGAGATAAA
1032543 ATCTTCTATTTCG
66 ATCTTCTATTTCG
* * * * *
1032556 AGGGAAACTATTTCAAGCGAGATAAAATCTTTTATTTCAAGGGAAACTATCTCAAGTGAGATAAA
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTATGTTTCGAGGGAAACTATCTCAAGCGAGATAAA
*
1032621 ATCTTCTGTTTCG
66 ATCTTCTATTTCG
* *
1032634 GGGGAAACTATCTCAAGTGAGATAAAAT
1 AGGGAAACTATCTCAAGCGAGATAAAAT
1032662 ATTCTTTAAA
Statistics
Matches: 299, Mismatches: 30, Indels: 12
0.88 0.09 0.04
Matches are distributed among these distances:
73 14 0.05
74 44 0.15
75 9 0.03
76 9 0.03
77 45 0.15
78 177 0.59
79 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (78 bp):
AGGGAAACTATCTCAAGCGAGATAAAATCTTATGTTTCGAGGGAAACTATCTCAAGCGAGATAAA
ATCTTCTATTTCG
Found at i:1032899 original size:75 final size:74
Alignment explanation
Indices: 1032712--1032899 Score: 227
Period size: 76 Copynumber: 2.5 Consensus size: 74
1032702 TCGAGTGAAA
* * * *
1032712 CAAGCGAGACAAATCTTGTTTTAAGAAAAACAATCTTAAGTGAAATAAATCTTCTTGTTTCGAGT
1 CAAGTGAGACAAATC-TGTTTTAAGAAAAACAATCTCAAGTCAAATAAATCGTCTTGTTTCGAGT
1032777 AAAAACTGTCT
65 AAAAAC-GTCT
* * * *
1032788 CAAGTGAGAGAAATATTGTTTTAAGAAAAACAATCTCGAGTCAAATGAAAT-GTCTTTTTTCGAG
1 CAAGTGAGACAAAT-CTGTTTTAAGAAAAACAATCTCAAGTCAAAT-AAATCGTCTTGTTTCGAG
1032852 TAAAATA-GTCT
64 TAAAA-ACGTCT
*
1032863 CAAGTGAGACAAAGTCCGTTTTAAGAAAAACAATCTC
1 CAAGTGAGACAAA-TCTGTTTTAAGAAAAACAATCTC
1032900 CAATGAGATA
Statistics
Matches: 97, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
75 36 0.37
76 56 0.58
77 5 0.05
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (74 bp):
CAAGTGAGACAAATCTGTTTTAAGAAAAACAATCTCAAGTCAAATAAATCGTCTTGTTTCGAGTA
AAAACGTCT
Found at i:1038717 original size:21 final size:22
Alignment explanation
Indices: 1038692--1038737 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
1038682 TGCAAATATT
1038692 AAAA-TAACAGT-AGCTAAATCA
1 AAAATTAACAGTGA-CTAAATCA
*
1038713 AAAATTAACAGTGACTAAATTA
1 AAAATTAACAGTGACTAAATCA
1038735 AAA
1 AAA
1038738 TAAAACAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 4 0.18
22 17 0.77
23 1 0.05
ACGTcount: A:0.59, C:0.11, G:0.09, T:0.22
Consensus pattern (22 bp):
AAAATTAACAGTGACTAAATCA
Found at i:1041360 original size:6 final size:6
Alignment explanation
Indices: 1041351--1042071 Score: 1435
Period size: 6 Copynumber: 120.3 Consensus size: 6
1041341 AATAATTATG
1041351 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
1041399 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
1041447 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
1041495 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
1041543 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
1041591 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
1041639 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
1041687 ATTAAA ATTAAA ATT-AA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
1041734 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
1041782 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
1041830 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
1041878 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
1041926 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
1041974 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
1042022 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
1042070 AT
1 AT
1042072 ATATCATAAT
Statistics
Matches: 714, Mismatches: 0, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
5 5 0.01
6 709 0.99
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
ATTAAA
Found at i:1042145 original size:6 final size:6
Alignment explanation
Indices: 1042134--1042159 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1042124 TGTCTCCATA
1042134 AATTTT AATTTT AATTTT AATTTT AA
1 AATTTT AATTTT AATTTT AATTTT AA
1042160 ATATAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
AATTTT
Found at i:1047473 original size:23 final size:24
Alignment explanation
Indices: 1047427--1047474 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1047417 AATTTTAAGA
**
1047427 AAAAATATTTAATGTAATTATAAT
1 AAAAATATTTAATCAAATTATAAT
*
1047451 AAAAATATTTTATCAAATT-TAAT
1 AAAAATATTTAATCAAATTATAAT
1047474 A
1 A
1047475 TCATTATATG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (24 bp):
AAAAATATTTAATCAAATTATAAT
Found at i:1047926 original size:11 final size:11
Alignment explanation
Indices: 1047872--1047911 Score: 57
Period size: 10 Copynumber: 3.8 Consensus size: 11
1047862 ATATCAATTT
1047872 AAATATAATAA
1 AAATATAATAA
1047883 AAATATAA-AA
1 AAATATAATAA
*
1047893 AAGTA-AATAA
1 AAATATAATAA
1047903 AAATATAAT
1 AAATATAAT
1047912 TATAATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 2 0.08
10 12 0.48
11 11 0.44
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (11 bp):
AAATATAATAA
Found at i:1047936 original size:17 final size:17
Alignment explanation
Indices: 1047875--1047926 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
1047865 TCAATTTAAA
*
1047875 TATAATAAAAATATAAAA
1 TATAATAAAAATAT-AAT
*
1047893 AAGTAAATAAAAATATAAT
1 TA-T-AATAAAAATATAAT
1047912 TATAATAAAAATATA
1 TATAATAAAAATATA
1047927 TTTTATATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 12 0.41
18 2 0.07
19 4 0.14
20 11 0.38
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (17 bp):
TATAATAAAAATATAAT
Found at i:1048752 original size:15 final size:15
Alignment explanation
Indices: 1048710--1048752 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
1048700 GTTTTTCTTC
1048710 CAAATTTATTTA-TT
1 CAAATTTATTTATTT
1048724 CAAAAATTTA-TTATTT
1 C--AAATTTATTTATTT
1048740 CAAATTTATTTAT
1 CAAATTTATTTAT
1048753 ATTAAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
14 8 0.32
15 7 0.28
16 10 0.40
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (15 bp):
CAAATTTATTTATTT
Found at i:1049627 original size:18 final size:17
Alignment explanation
Indices: 1049573--1049621 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
1049563 TTGGACTCCT
* *
1049573 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
1049591 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
1049609 AGTGCATTCGATG
1 AGTGCA-TCGATG
1049622 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:1049662 original size:64 final size:61
Alignment explanation
Indices: 1049593--1049802 Score: 190
Period size: 64 Copynumber: 3.2 Consensus size: 61
1049583 TGCACTAAGA
1049593 GTGCATCGATGCATGAAGTGCATTCGATGTTTGAAAAATAGCCTGGTGCATCGATGCATGGATT
1 GTGCATCGATGCATGAA-TGCATTCGATGTTT-AAAAATAG-CTGGTGCATCGATGCATGGATT
* * *
1049657 GTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATCAG--AGTGCATCGATGCATGGAG
1 GTGCATCGATGCAT-GAATGCATTCGATG-TTTAA--AAAT-AGCTGGTGCATCGATGCATGGAT
*
1049720 A
61 T
* * ** * *
1049721 GTGCATCGGTGCATGGAATGCATTCGATGTTTCAACTTATTCATTGATGCATCGATGCATGGTAT
1 GTGCATCGATGCAT-GAATGCATTCGATGTTTAAAAATA-GC--TGGTGCATCGATGCATGG-AT
1049786 T
61 T
1049787 GATGCATCGATGCATG
1 G-TGCATCGATGCATG
1049803 GTATTGATGC
Statistics
Matches: 118, Mismatches: 16, Indels: 22
0.76 0.10 0.14
Matches are distributed among these distances:
60 1 0.01
61 2 0.02
63 4 0.03
64 70 0.59
65 20 0.17
66 7 0.06
67 14 0.12
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (61 bp):
GTGCATCGATGCATGAATGCATTCGATGTTTAAAAATAGCTGGTGCATCGATGCATGGATT
Found at i:1049723 original size:19 final size:19
Alignment explanation
Indices: 1049699--1049749 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1049689 TAATTAAATC
1049699 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
1049718 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
1049737 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
1049750 TTTCAACTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:1049830 original size:21 final size:21
Alignment explanation
Indices: 1049763--1049823 Score: 113
Period size: 21 Copynumber: 2.9 Consensus size: 21
1049753 CAACTTATTC
1049763 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
1049784 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
1049805 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
1049824 CCTTTGAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:1059677 original size:20 final size:22
Alignment explanation
Indices: 1059647--1059702 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
1059637 ATCCCCGCTA
1059647 TGTATCGATACA-CTATGAATG
1 TGTATCGATACATCTATGAATG
*
1059668 TGTA-CGATACATTCTTTGAATG
1 TGTATCGATACA-TCTATGAATG
1059690 TGTATCGATACAT
1 TGTATCGATACAT
1059703 TGAGGAGTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 7 0.23
21 4 0.13
22 13 0.42
23 7 0.23
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (22 bp):
TGTATCGATACATCTATGAATG
Found at i:1061211 original size:15 final size:15
Alignment explanation
Indices: 1061191--1061220 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1061181 ACTGCTATCG
1061191 TTTTTCTTTCTTTTT
1 TTTTTCTTTCTTTTT
1061206 TTTTTCTTTCTTTTT
1 TTTTTCTTTCTTTTT
1061221 CTTTGTGGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (15 bp):
TTTTTCTTTCTTTTT
Found at i:1063985 original size:33 final size:33
Alignment explanation
Indices: 1063942--1064026 Score: 152
Period size: 33 Copynumber: 2.6 Consensus size: 33
1063932 TTGTTTTTGA
*
1063942 GTTTTACTAACGTGCGCCACCCACCTCCAAGGG
1 GTTTTGCTAACGTGCGCCACCCACCTCCAAGGG
1063975 GTTTTGCTAACGTGCGCCACCCACCTCCAAGGG
1 GTTTTGCTAACGTGCGCCACCCACCTCCAAGGG
*
1064008 GTTTTGTTAACGTGCGCCA
1 GTTTTGCTAACGTGCGCCA
1064027 TTTAATGAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.19, C:0.33, G:0.24, T:0.25
Consensus pattern (33 bp):
GTTTTGCTAACGTGCGCCACCCACCTCCAAGGG
Found at i:1064267 original size:5 final size:6
Alignment explanation
Indices: 1064213--1064266 Score: 67
Period size: 6 Copynumber: 9.2 Consensus size: 6
1064203 TGCTTGATTG
* *
1064213 AATAAA AAT-AA AAT-AA AATAAA AACGAAA AGTAAA AATAAA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AA-TAAA AATAAA AATAAA AATAAA
1064260 AATAAA A
1 AATAAA A
1064267 TTGTAACGGA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
5 10 0.24
6 28 0.67
7 4 0.10
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.15
Consensus pattern (6 bp):
AATAAA
Found at i:1073741 original size:182 final size:182
Alignment explanation
Indices: 1073533--1074273 Score: 1131
Period size: 182 Copynumber: 4.1 Consensus size: 182
1073523 GATACAAATA
* * * *
1073533 AAAAATGTATCGATCCATATCAATATAACAGGTAAAAATATGACAAAACCGGTCTCAAAATGACC
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAAACCGGTCTAAAAATGACA
* * *
1073598 AAACCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATACTTTATTTTAAGTATCGACACTTT
66 AAACCGGTAAAGCGCCACCGGATATGTTAAAAGTGTCGATACTTTATTATAAGTATCGACACTTT
* ** *
1073663 TGGAATTTAAAAGACAAGCAGTAATAACGTTTATAAAGTGTCGATACCTTAT
131 TGGAATTTAAAAGACAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTAT
* * * * * *
1073715 AAAAATTTATCGATCCATAACAATATATCATGTAAAAATATGATAAAATCGGTCTCAAAATGAAA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAAACCGGTCTAAAAATGACA
* * * * * *
1073780 AAACTGGTAAAGAGCTATCGGATATGTTGAAACTGTCGATACTTTATTATAAGTATCGACACTTT
66 AAACCGGTAAAGCGCCACCGGATATGTTAAAAGTGTCGATACTTTATTATAAGTATCGACACTTT
*
1073845 TGGAATTTAAAAGACAAGCAGTAATAGCGCCTATAAAGTATCGATACTTTAT
131 TGGAATTTAAAAGACAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTAT
* * * *
1073897 AAAAATGTATCAACCCATAACAATATAACAGTTAAAAATATGATAAAACTGGTCTAAAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAAACCGGTCTAAAAATGACA
*
1073962 AAACCGGTAAAGCGCCACCGGATATGTTAAAAGTGTCGATACTTTATTATAAGTATCGTCACTTT
66 AAACCGGTAAAGCGCCACCGGATATGTTAAAAGTGTCGATACTTTATTATAAGTATCGACACTTT
* * * * *
1074027 TGGAATTTAAAAGAGAAACAATAATAGCGCCTATAAAGTGTCTATATTTTAT
131 TGGAATTTAAAAGACAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTAT
* * * *
1074079 AAAAATGTACCGATGCATAACAATATAATAGGTAAAAATATGATAAAACCAGTCTAAAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAAACCGGTCTAAAAATGACA
1074144 AAACCGGTAAAGCGCCACCGGATATGTTAAAAGTGTCGATACTTTATTATAAGTATCGACACTTT
66 AAACCGGTAAAGCGCCACCGGATATGTTAAAAGTGTCGATACTTTATTATAAGTATCGACACTTT
*
1074209 TGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTAT
131 TGGAATTTAAAAGACAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTAT
1074261 AAAAATGTATCGA
1 AAAAATGTATCGA
1074274 CACTTGGGTT
Statistics
Matches: 504, Mismatches: 55, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
182 504 1.00
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (182 bp):
AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAAACCGGTCTAAAAATGACA
AAACCGGTAAAGCGCCACCGGATATGTTAAAAGTGTCGATACTTTATTATAAGTATCGACACTTT
TGGAATTTAAAAGACAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTAT
Found at i:1076186 original size:22 final size:23
Alignment explanation
Indices: 1076136--1076190 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
1076126 AACGTTTTTG
*
1076136 TTTT-TTATATAAAATGATAGTA
1 TTTTATTATATAAAATGATAGAA
*
1076158 TAGTTATTATATAAAATGATA-AA
1 T-TTTATTATATAAAATGATAGAA
1076181 TTTTATTATA
1 TTTTATTATA
1076191 AATGCAAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 9 0.32
23 4 0.14
24 15 0.54
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (23 bp):
TTTTATTATATAAAATGATAGAA
Found at i:1076887 original size:18 final size:18
Alignment explanation
Indices: 1076864--1076902 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1076854 GAAAAAATAT
1076864 GAAGAAGAAAAGATAGAG
1 GAAGAAGAAAAGATAGAG
*
1076882 GAAGAAGAAAAGATTGAG
1 GAAGAAGAAAAGATAGAG
1076900 GAA
1 GAA
1076903 ATGAGGAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.33, T:0.08
Consensus pattern (18 bp):
GAAGAAGAAAAGATAGAG
Found at i:1078480 original size:19 final size:19
Alignment explanation
Indices: 1078456--1078504 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1078446 AATGTAGGGT
1078456 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1078475 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
1078494 TAATTTTGTAT
1 TAATTTTGTAT
1078505 GTGAATGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1079937 original size:200 final size:200
Alignment explanation
Indices: 1078841--1079989 Score: 1454
Period size: 201 Copynumber: 5.7 Consensus size: 200
1078831 AAGTTTCCAA
*
1078841 AAAAATGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATATTT-CAAT
1 AAAAA-GTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAA-ATTTACAAT
* *
1078905 GTAACCGGTATAAATAGACCGGTTTTATGAGAGAATAGGTCTACATAATGTATCGACACTTTTGT
64 GTAACCGGTATAAATAGACCGGTTTTATGAGAAAATAAGTCTACATAATGTATCGACACTTTT-T
*
1078970 -AATTTGTGTCGATACTTTTTGTCCAGAATGAATGCTCAAAAGGGGTGCACGCATAAAGTGTCGA
128 AAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAA-GGGTGCACGCATAAAGTGTCGA
1079034 TACATTTAT
192 TACATTTAT
* * * *
1079043 AAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTCATTTTTCAATGT
1 AAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGT
** * * * **
1079108 AAGAGGTATAAATAGACCGGTTTTATGAGAGAATAAGTCTACCTAATGTATCGACACTTGTGGAA
66 AACCGGTATAAATAGACCGGTTTTATGAGAAAATAAGTCTACATAATGTATCGACACTTTTTAAA
* *
1079173 TTTGTGTCGATACATTTTGTCCAGAATGAATGCCCAAAAGGGGTGCACGCATAAAGTGTCGAAAC
131 TTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAA-GGGTGCACGCATAAAGTGTCGATAC
1079238 ATTTAT
195 ATTTAT
* * * * *
1079244 AAAAAGTGTTGATCCCAAAAACATCGAAACCCATAATTCTAATGTAATAGGTAATTTTTCAATGT
1 AAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGT
* * * * **
1079309 AACCGGTAAAAAAAGACCGGTTTTATGAGATAATAAGTCTACATAATGTATCGACACTTGTGGAA
66 AACCGGTATAAATAGACCGGTTTTATGAGAAAATAAGTCTACATAATGTATCGACACTTTTTAAA
** * * *
1079374 TTTGTGTCGATACTTTGTT-TAAATTAAATGAATGCCCAAAATGGTTCACGCATAAAGTGTCGAT
131 TTTGTGTCGATACTTT-TTGTCCA--GAATGAATGCCCAAAAGGGTGCACGCATAAAGTGTCGAT
1079438 ACATTT-T
193 ACATTTAT
** *** * * *
1079445 AAATTGTATCGATCCC-AAAACATCGAAACATTTAATTACAATGTAAAAGGTAAATTAACAATGT
1 AAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGT
* ** ** * *
1079509 AACCGGTACAAATTTACC-AATTTATGAGAAAAT-AGTTATACATAATGTATCGACACTTTTTAT
66 AACCGGTATAAATAGACCGGTTTTATGAGAAAATAAG-TCTACATAATGTATCGACACTTTTTAA
* * * * *
1079572 ATTTATGTCGATACTTTTTGTCTAGAATGAAT-ACCAAACTGGGTGCACGCATAAAGTGTTGATA
130 ATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAA-AGGGTGCACGCATAAAGTGTCGATA
1079636 CATTT-T
194 CATTTAT
* * * * *
1079642 AAATTA-TATCGATCCCAAAAACATCGAAACCGATAATTACAATGTAATAGGTAAATTAATAATG
1 AAA-AAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATG
* ** * * *
1079706 TAACTGGTATAAATTTATCGGTTTTATGAGAAAATAGGTCTACATAATGTATCGACATTTTTTAA
65 TAACCGGTATAAATAGACCGGTTTTATGAGAAAATAAGTCTACATAATGTATCGACACTTTTTAA
* *
1079771 ATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAGGGTACACCCATAAAGTGTCGATAC
130 ATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAGGGTGCACGCATAAAGTGTCGATAC
1079836 ATTTAT
195 ATTTAT
* * * *
1079842 AAAAGGAATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTCCAATGT
1 AAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGT
* * * *
1079907 AACCGGTATAAATATACAGATTTTATGAGAAAATAAGTCTACATAATGTATTGACACTTTTTAAA
66 AACCGGTATAAATAGACCGGTTTTATGAGAAAATAAGTCTACATAATGTATCGACACTTTTTAAA
*
1079972 TTGGTGTCGATACTTTTT
131 TTTGTGTCGATACTTTTT
1079990 TTAAATTACG
Statistics
Matches: 833, Mismatches: 99, Indels: 32
0.86 0.10 0.03
Matches are distributed among these distances:
196 5 0.01
197 47 0.06
198 63 0.08
199 145 0.17
200 194 0.23
201 331 0.40
202 33 0.04
203 15 0.02
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (200 bp):
AAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGT
AACCGGTATAAATAGACCGGTTTTATGAGAAAATAAGTCTACATAATGTATCGACACTTTTTAAA
TTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAGGGTGCACGCATAAAGTGTCGATACA
TTTAT
Found at i:1081025 original size:25 final size:25
Alignment explanation
Indices: 1080991--1081042 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
1080981 TTTAAAATGC
1080991 TTGCACTTGTGTACAAATCCTATCA
1 TTGCACTTGTGTACAAATCCTATCA
1081016 TTGCACTTGTGTACAAATCCTATCA
1 TTGCACTTGTGTACAAATCCTATCA
1081041 TT
1 TT
1081043 CAACAGGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (25 bp):
TTGCACTTGTGTACAAATCCTATCA
Found at i:1084641 original size:92 final size:94
Alignment explanation
Indices: 1084460--1084640 Score: 260
Period size: 92 Copynumber: 2.0 Consensus size: 94
1084450 TTGTGTAATT
* **
1084460 TGTGTCGATACTTTTTGTCCAGAATTAATGCCCAAAAGGGGTGCACGCATAAAGTGTCGATACAT
1 TGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAGAAGTGCACGCATAAAGTGTCGATACAT
1084525 TTATAAAAAGTCTCGATCCCAAAAACATA
66 TTATAAAAAGTCTCGATCCCAAAAACATA
* * *
1084554 TGTGTCGATACTTTTT-TCCAGAATGAATGTCC-AACGAAGTGCACGCATAAAGTGTTGATACAT
1 TGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAGAAGTGCACGCATAAAGTGTCGATACAT
** *
1084617 TTA-AAATTGTGTCGATCCCAAAAA
66 TTATAAAAAGTCTCGATCCCAAAAA
1084641 ATCGAAAACG
Statistics
Matches: 78, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
91 18 0.23
92 30 0.38
93 14 0.18
94 16 0.21
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (94 bp):
TGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAGAAGTGCACGCATAAAGTGTCGATACAT
TTATAAAAAGTCTCGATCCCAAAAACATA
Found at i:1086614 original size:39 final size:39
Alignment explanation
Indices: 1086564--1086674 Score: 104
Period size: 39 Copynumber: 2.8 Consensus size: 39
1086554 TTTTCTTTAT
* *
1086564 AATTCTCAAATTATTTTACTCTAACATTCTAAATTTTTA
1 AATTCTTAAATTATTTTACTCTAACATTCTAAATTCTTA
* *
1086603 ATTTCTT-AA--ATTTTACCATCATAACATTTTAAATTCTTA
1 AATTCTTAAATTATTTTA-C-TC-TAACATTCTAAATTCTTA
* *
1086642 AATTCTTAAATTATTTCA-TGTTAACATTCTAAA
1 AATTCTTAAATTATTTTACT-CTAACATTCTAAA
1086675 ATATTTTTAA
Statistics
Matches: 57, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
36 6 0.11
37 1 0.02
38 4 0.07
39 39 0.68
40 2 0.04
42 5 0.09
ACGTcount: A:0.37, C:0.14, G:0.01, T:0.48
Consensus pattern (39 bp):
AATTCTTAAATTATTTTACTCTAACATTCTAAATTCTTA
Found at i:1086650 original size:16 final size:15
Alignment explanation
Indices: 1086589--1086653 Score: 53
Period size: 16 Copynumber: 4.2 Consensus size: 15
1086579 TTACTCTAAC
1086589 ATTC-TAAATTTTTAA
1 ATTCTTAAA-TTTTAA
* *
1086604 TTTCTTAAATTTTACC
1 ATTCTTAAATTTTA-A
*
1086620 A-TCATAACATTTTAA
1 ATTCTTAA-ATTTTAA
1086635 ATTCTTAAATTCTTAA
1 ATTCTTAAATT-TTAA
1086651 ATT
1 ATT
1086654 ATTTCATGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
15 17 0.44
16 22 0.56
ACGTcount: A:0.37, C:0.12, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTCTTAAATTTTAA
Found at i:1087072 original size:2 final size:2
Alignment explanation
Indices: 1087065--1087089 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1087055 AAAATAAATG
1087065 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 T
1087090 GTAATGTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1087146 original size:20 final size:20
Alignment explanation
Indices: 1087099--1087146 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
1087089 TGTAATGTTC
*
1087099 AATAAAAACATAATATTTAA
1 AATAAAAACATAATATTAAA
*
1087119 CATAAAAACATAATA-TAAA
1 AATAAAAACATAATATTAAA
1087138 AATATAAAA
1 AATA-AAAA
1087147 TTCAATTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (20 bp):
AATAAAAACATAATATTAAA
Found at i:1087179 original size:13 final size:13
Alignment explanation
Indices: 1087120--1087180 Score: 52
Period size: 13 Copynumber: 4.5 Consensus size: 13
1087110 AATATTTAAC
*
1087120 ATAAAAACATAAT
1 ATAAAAATATAAT
*
1087133 ATAAAAATATAAA
1 ATAAAAATATAAT
* *
1087146 ATTCAATTAATA-AAC
1 A-T-AA-AAATATAAT
1087161 ATAAAAATATAAT
1 ATAAAAATATAAT
1087174 ATAAAAA
1 ATAAAAA
1087181 CTAACGATGT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
12 4 0.11
13 23 0.61
14 2 0.05
15 5 0.13
16 4 0.11
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (13 bp):
ATAAAAATATAAT
Found at i:1090398 original size:65 final size:65
Alignment explanation
Indices: 1090249--1090405 Score: 201
Period size: 65 Copynumber: 2.4 Consensus size: 65
1090239 TACACTAAGG
* * * * **
1090249 GTGCATCGATACACTAATTACATTCGATGTTTCAAATGAGCCTGGAGTGCATCGATGCATGGTCT
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAATGAGCCACGAGTGCATCGATGCATGGTCT
**
1090314 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAAT-ATTCACGAGTGCATCGATGCATGG-C
1 GTGCATCGGTACACAAAATGCATTCGATGTTTC-AAATGAGCCACGAGTGCATCGATGCATGGTC
1090377 TT
65 -T
*
1090379 GTGCATCGGTACACAAAATGTATTCGA
1 GTGCATCGGTACACAAAATGCATTCGA
1090406 AATGGGTGTG
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
64 1 0.01
65 76 0.94
66 4 0.05
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (65 bp):
GTGCATCGGTACACAAAATGCATTCGATGTTTCAAATGAGCCACGAGTGCATCGATGCATGGTCT
Found at i:1094715 original size:20 final size:21
Alignment explanation
Indices: 1094676--1094715 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1094666 GAACCTTTAA
* *
1094676 GATCATCAATTTTCTTTTGAT
1 GATCATCAATTTACTCTTGAT
1094697 GATCATC-ATTTACTCTTGA
1 GATCATCAATTTACTCTTGA
1094716 AAGTAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.47
Consensus pattern (21 bp):
GATCATCAATTTACTCTTGAT
Found at i:1095284 original size:22 final size:21
Alignment explanation
Indices: 1095259--1095307 Score: 80
Period size: 22 Copynumber: 2.3 Consensus size: 21
1095249 CTCTTCATCA
1095259 TCATCTACATTCGAATCACTC
1 TCATCTACATTCGAATCACTC
*
1095280 TTCATCTTCATTCGAATCACTC
1 -TCATCTACATTCGAATCACTC
1095302 TCATCT
1 TCATCT
1095308 TTTGTTGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 6 0.23
22 20 0.77
ACGTcount: A:0.24, C:0.33, G:0.04, T:0.39
Consensus pattern (21 bp):
TCATCTACATTCGAATCACTC
Found at i:1096734 original size:26 final size:27
Alignment explanation
Indices: 1096676--1096735 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 27
1096666 GGTTATTATA
* * *
1096676 GTCATTTTAGAGTTTAAGGGTATTTTG
1 GTCATTTAAGAGTTTAAGGGCATCTTG
*
1096703 GCCATTTAAG-GTTTAAGGGCATCTTG
1 GTCATTTAAGAGTTTAAGGGCATCTTG
*
1096729 TTCATTT
1 GTCATTT
1096736 CAATATTTGA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 19 0.70
27 8 0.30
ACGTcount: A:0.22, C:0.10, G:0.23, T:0.45
Consensus pattern (27 bp):
GTCATTTAAGAGTTTAAGGGCATCTTG
Found at i:1099295 original size:14 final size:14
Alignment explanation
Indices: 1099276--1099305 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1099266 TTAAATGATA
1099276 AACGAACACAAATG
1 AACGAACACAAATG
*
1099290 AACGAACATAAATG
1 AACGAACACAAATG
1099304 AA
1 AA
1099306 TGTAAACGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.17, G:0.13, T:0.10
Consensus pattern (14 bp):
AACGAACACAAATG
Found at i:1099344 original size:33 final size:34
Alignment explanation
Indices: 1099274--1099359 Score: 93
Period size: 33 Copynumber: 2.6 Consensus size: 34
1099264 ATTTAAATGA
* * * *
1099274 TAAACGAACACAAATGAACGAACATAAATGAATG
1 TAAACGAACATAAATGAACGAAAATAAACGAACG
* *
1099308 TAAACGAACATAAATGGAC-AAAATAAACGAGCG
1 TAAACGAACATAAATGAACGAAAATAAACGAACG
* *
1099341 TAAATGAACATAAACGAAC
1 TAAACGAACATAAATGAAC
1099360 AAACCTAAAC
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
33 26 0.60
34 17 0.40
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.14
Consensus pattern (34 bp):
TAAACGAACATAAATGAACGAAAATAAACGAACG
Found at i:1099394 original size:33 final size:33
Alignment explanation
Indices: 1099357--1099429 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
1099347 AACATAAACG
*
1099357 AACAAACCTAAACAAACACAATAAATGAACATA
1 AACAAACCTAAACAAACACAACAAATGAACATA
* ** *
1099390 AACAAACTTGCACAAACATAACAAATGAACATA
1 AACAAACCTAAACAAACACAACAAATGAACATA
*
1099423 ATCAAAC
1 AACAAAC
1099430 ACAATAAATG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.60, C:0.22, G:0.04, T:0.14
Consensus pattern (33 bp):
AACAAACCTAAACAAACACAACAAATGAACATA
Found at i:1099430 original size:37 final size:37
Alignment explanation
Indices: 1099342--1099430 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 37
1099332 AAACGAGCGT
* * *
1099342 AAATGAACATAAACGAACAAACCTAAACAAACACAAT
1 AAATGAACATAATCAAACAAACCTAAACAAACACAAC
* ** *
1099379 AAATGAAC---AT-AAACAAACTTGCACAAACATAAC
1 AAATGAACATAATCAAACAAACCTAAACAAACACAAC
1099412 AAATGAACATAATCAAACA
1 AAATGAACATAATCAAACA
1099431 CAATAAATGA
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
33 25 0.61
34 1 0.02
36 2 0.05
37 13 0.32
ACGTcount: A:0.61, C:0.20, G:0.06, T:0.13
Consensus pattern (37 bp):
AAATGAACATAATCAAACAAACCTAAACAAACACAAC
Found at i:1099676 original size:34 final size:34
Alignment explanation
Indices: 1099638--1099703 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
1099628 ATTGGTCTAA
* *
1099638 ATATAAACGAA-ATGACATAAATGAACATACATGG
1 ATATAAACGAACA-AACATAAACGAACATACATGG
*
1099672 ATATAAATGAACAAACATAAACGAACATACAT
1 ATATAAACGAACAAACATAAACGAACATACAT
1099704 ACATGAACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 27 0.96
35 1 0.04
ACGTcount: A:0.56, C:0.14, G:0.11, T:0.20
Consensus pattern (34 bp):
ATATAAACGAACAAACATAAACGAACATACATGG
Found at i:1099711 original size:14 final size:14
Alignment explanation
Indices: 1099674--1099728 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
1099664 ATACATGGAT
*
1099674 ATAAATGAACAAAC
1 ATAAATGAACATAC
*
1099688 ATAAACGAACATAC
1 ATAAATGAACATAC
* *
1099702 ATACATGAACATAT
1 ATAAATGAACATAC
* *
1099716 ATGAACGAACATA
1 ATAAATGAACATA
1099729 AACGAACAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.56, C:0.16, G:0.09, T:0.18
Consensus pattern (14 bp):
ATAAATGAACATAC
Found at i:1099720 original size:38 final size:38
Alignment explanation
Indices: 1099662--1099754 Score: 116
Period size: 38 Copynumber: 2.4 Consensus size: 38
1099652 ACATAAATGA
* *
1099662 ACATACATGGATATAAATGAACAAACATAAACGAACAT
1 ACATACATGAACATAAATGAACAAACATAAACGAACAT
* * *
1099700 ACATACATGAACATATATGAACGAACATAAACGAACAA
1 ACATACATGAACATAAATGAACAAACATAAACGAACAT
*
1099738 AAATGA-ATGAACATAAA
1 ACAT-ACATGAACATAAA
1099755 CGAATGGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
38 46 0.98
39 1 0.02
ACGTcount: A:0.57, C:0.15, G:0.11, T:0.17
Consensus pattern (38 bp):
ACATACATGAACATAAATGAACAAACATAAACGAACAT
Found at i:1101344 original size:32 final size:32
Alignment explanation
Indices: 1101308--1101388 Score: 126
Period size: 32 Copynumber: 2.5 Consensus size: 32
1101298 GAATCTACTG
* * *
1101308 TGCATTGTCTGAATGTAGGACTAACTCTGGTA
1 TGCATTATCTGAATGCAAGACTAACTCTGGTA
*
1101340 TGCATTATCTGAATGCAAGATTAACTCTGGTA
1 TGCATTATCTGAATGCAAGACTAACTCTGGTA
1101372 TGCATTATCTGAATGCA
1 TGCATTATCTGAATGCA
1101389 TCACTAGTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (32 bp):
TGCATTATCTGAATGCAAGACTAACTCTGGTA
Found at i:1101405 original size:32 final size:32
Alignment explanation
Indices: 1101308--1101408 Score: 103
Period size: 32 Copynumber: 3.2 Consensus size: 32
1101298 GAATCTACTG
* * ** *
1101308 TGCATTGTCTGAATGTAGGACTAACTCTGGTA
1 TGCATTATCTGAATGCAACACTAACTCTAGTA
* * *
1101340 TGCATTATCTGAATGCAAGATTAACTCTGGTA
1 TGCATTATCTGAATGCAACACTAACTCTAGTA
* **
1101372 TGCATTATCTGAATGCATCACTAGTTCTAGTA
1 TGCATTATCTGAATGCAACACTAACTCTAGTA
1101404 TGCAT
1 TGCAT
1101409 ATATTAATAT
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 59 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.36
Consensus pattern (32 bp):
TGCATTATCTGAATGCAACACTAACTCTAGTA
Found at i:1102381 original size:19 final size:20
Alignment explanation
Indices: 1102335--1102383 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
1102325 CTAGTTGTAG
* *
1102335 TATCGATACTCTTGGGTAAG
1 TATCGATACTCTTGGGAAAA
*
1102355 TTTCGATACTCTT-GGAAAA
1 TATCGATACTCTTGGGAAAA
1102374 TATCGATACT
1 TATCGATACT
1102384 AAAATGGATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (20 bp):
TATCGATACTCTTGGGAAAA
Found at i:1102426 original size:19 final size:19
Alignment explanation
Indices: 1102402--1102480 Score: 106
Period size: 19 Copynumber: 4.1 Consensus size: 19
1102392 TTCTGTTACT
1102402 GAAAGTATCGATACTCTTG
1 GAAAGTATCGATACTCTTG
*
1102421 GAAAGTATCGATACTCTGAG
1 GAAAGTATCGATACTCT-TG
1102441 GTAAAGTATCGATACTCTT-
1 G-AAAGTATCGATACTCTTG
*
1102460 GAAATGTATTGATACTCTTG
1 GAAA-GTATCGATACTCTTG
1102480 G
1 G
1102481 CCTGAAATCC
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
18 3 0.06
19 31 0.58
20 3 0.06
21 16 0.30
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.33
Consensus pattern (19 bp):
GAAAGTATCGATACTCTTG
Found at i:1105530 original size:21 final size:21
Alignment explanation
Indices: 1105488--1105540 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1105478 ATTCTGACTA
1105488 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * **
1105509 TCGCGTTGCGATTTTCTTAAT
1 TCGCATTGCGATTTCCCAAAT
*
1105530 TCGCAATGCGA
1 TCGCATTGCGA
1105541 ATACATAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:1105555 original size:20 final size:20
Alignment explanation
Indices: 1105530--1105636 Score: 126
Period size: 20 Copynumber: 5.3 Consensus size: 20
1105520 TTTTCTTAAT
*
1105530 TCGCAATGCGAATACATAAA
1 TCGCAATGCGAATACGTAAA
* ** *
1105550 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
* *
1105571 TCGTAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
1105591 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1105611 TCGCAATGCGAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
1105631 TCGCAA
1 TCGCAA
1105637 CGAGATTCTG
Statistics
Matches: 72, Mismatches: 13, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
19 1 0.01
20 58 0.81
21 13 0.18
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1105646 original size:20 final size:20
Alignment explanation
Indices: 1105586--1105646 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
1105576 ATGCGATTAC
* *
1105586 GTAAATCGCAATGCGAATAC-
1 GTAAATCGCAACGAGAAT-CT
* *
1105606 GTAAATCGCAATGCGAATCT
1 GTAAATCGCAACGAGAATCT
*
1105626 GTAAATCGCAACGAGATTCT
1 GTAAATCGCAACGAGAATCT
1105646 G
1 G
1105647 ACTATCGCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
19 1 0.03
20 36 0.97
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (20 bp):
GTAAATCGCAACGAGAATCT
Found at i:1106491 original size:24 final size:24
Alignment explanation
Indices: 1106464--1106517 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1106454 GTATTCGAAA
1106464 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1106488 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1106512 TTTGAT
1 TTTGAT
1106518 GATTTTTCAG
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:1108930 original size:20 final size:21
Alignment explanation
Indices: 1108905--1108978 Score: 109
Period size: 20 Copynumber: 3.7 Consensus size: 21
1108895 GACATTCATT
1108905 TGACTATCGCAACGC-GAATA
1 TGACTATCGCAACGCGGAATA
*
1108925 TGACTATCGCAACACGGAA-A
1 TGACTATCGCAACGCGGAATA
*
1108945 TGACTATCGTAACGCGGAAT-
1 TGACTATCGCAACGCGGAATA
1108965 TGACTATCGCAACG
1 TGACTATCGCAACG
1108979 AGAGAATTGC
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
20 45 0.94
21 3 0.06
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (21 bp):
TGACTATCGCAACGCGGAATA
Found at i:1109012 original size:33 final size:34
Alignment explanation
Indices: 1108970--1109045 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 34
1108960 GGAATTGACT
* *
1108970 ATCGCAACGAGAGAATTGCAATGCG-AAATGAAA
1 ATCGCAACGAGAGAATCGCAATGAGAAAATGAAA
*
1109003 ATCGCAACGAGTGAATCGCAATGAGAAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGAGAAAATGAAA
1109037 ATCGCAACG
1 ATCGCAACG
1109046 CGAAATTAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 22 0.56
34 17 0.44
ACGTcount: A:0.45, C:0.17, G:0.24, T:0.14
Consensus pattern (34 bp):
ATCGCAACGAGAGAATCGCAATGAGAAAATGAAA
Found at i:1109117 original size:33 final size:33
Alignment explanation
Indices: 1109060--1109144 Score: 134
Period size: 33 Copynumber: 2.5 Consensus size: 33
1109050 ATTAGTTTCG
1109060 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
*
1109094 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
**
1109127 CGTTGCGATAGTCATTTC
1 CGTTGCGATTTTCATTTC
1109145 CGTGTTGCGG
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 34 0.71
34 14 0.29
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:1109276 original size:14 final size:14
Alignment explanation
Indices: 1109257--1109293 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1109247 CATCAATTAA
1109257 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1109271 ACAAATCATCTTTT
1 ACAAATCAACATTT
1109285 ACAAATCAA
1 ACAAATCAA
1109294 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1110682 original size:21 final size:21
Alignment explanation
Indices: 1110658--1110716 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
1110648 TTGGGAGAGA
* *
1110658 CCTCTTCAACGATGACAGTGG
1 CCTCTTGAACGATGACAGGGG
* **
1110679 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGACAGGGG
1110700 CCTCTTGAACGATGACA
1 CCTCTTGAACGATGACA
1110717 TATGAGTCGG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.22, C:0.25, G:0.31, T:0.22
Consensus pattern (21 bp):
CCTCTTGAACGATGACAGGGG
Found at i:1111221 original size:20 final size:20
Alignment explanation
Indices: 1111198--1111266 Score: 111
Period size: 20 Copynumber: 3.5 Consensus size: 20
1111188 GAAACTTAAA
1111198 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
1111218 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
1111238 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
1111258 ATCGCAACG
1 ATCGCAACG
1111267 AGAGAATCGC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1111336 original size:20 final size:20
Alignment explanation
Indices: 1111311--1111454 Score: 174
Period size: 20 Copynumber: 7.5 Consensus size: 20
1111301 GATTCTTTCG
**
1111311 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
1111331 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
1111351 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1111371 TTGCAATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1111391 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
* * **
1111405 TCGCGATAGTCATTTTTGTG
1 TTGCGATAGTCATTTTCGCA
1111425 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
1111445 TTGCGATAGT
1 TTGCGATAGT
1111455 AAACTATTCT
Statistics
Matches: 106, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
14 6 0.06
16 6 0.06
18 5 0.05
20 89 0.84
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:1111359 original size:40 final size:40
Alignment explanation
Indices: 1111273--1111454 Score: 174
Period size: 40 Copynumber: 4.9 Consensus size: 40
1111263 AACGAGAGAA
* **
1111273 TCGCAATGCGATTTTCA-TTTCGCATTGCGAT--TC--TT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
**
1111308 TCG--TTGCGATAGTCAAATTCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
*
1111346 TCGCATTGCGATAGTCATTTTCGCATTGCAATAGTCATTT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
* *
1111386 TCGCATTGCGAT--TC--TCTCG--TCGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
* **
1111420 TTGTGTTGCGATAGTCATTTTCGCATTGCGATAGT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGT
1111455 AAACTATTCT
Statistics
Matches: 119, Mismatches: 15, Indels: 21
0.77 0.10 0.14
Matches are distributed among these distances:
33 9 0.08
34 35 0.29
35 3 0.03
36 8 0.07
38 11 0.09
40 53 0.45
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.40
Consensus pattern (40 bp):
TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
Found at i:1113375 original size:20 final size:20
Alignment explanation
Indices: 1113327--1113366 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1113317 CTGAAACTTT
*
1113327 AAATCGCAACACGAAAATGA
1 AAATCGCAACACAAAAATGA
1113347 AAATCGCAACACAAAAATGA
1 AAATCGCAACACAAAAATGA
1113367 CTATCGCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.57, C:0.20, G:0.12, T:0.10
Consensus pattern (20 bp):
AAATCGCAACACAAAAATGA
Found at i:1114045 original size:20 final size:20
Alignment explanation
Indices: 1114022--1114115 Score: 134
Period size: 20 Copynumber: 4.7 Consensus size: 20
1114012 CGATAGTCAG
1114022 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1114042 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * **
1114062 AATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
*
1114083 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1114103 ATTCGCATTGCGA
1 ATTCGCATTGCGA
1114116 ATTAGGAAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
20 48 0.76
21 15 0.24
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.37
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1114097 original size:41 final size:40
Alignment explanation
Indices: 1114024--1114115 Score: 130
Period size: 41 Copynumber: 2.3 Consensus size: 40
1114014 ATAGTCAGAT
**
1114024 TCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTACAAATTCGCATTGCGATTTACGTAA
* * *
1114064 TCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACGTAT
1 TCGCATTGCGA-TTTACAAATTCGCATTGCGATTTACGTAA
1114105 TCGCATTGCGA
1 TCGCATTGCGA
1114116 ATTAGGAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 11 0.24
41 35 0.76
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.37
Consensus pattern (40 bp):
TCGCATTGCGATTTACAAATTCGCATTGCGATTTACGTAA
Found at i:1114097 original size:61 final size:60
Alignment explanation
Indices: 1114002--1114115 Score: 183
Period size: 61 Copynumber: 1.9 Consensus size: 60
1113992 GCGCTATGTA
*
1114002 AATCGCATTGCGATAGTCAGATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGT
1 AATCGCATTGCGATAGTCAAATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGT
** *
1114062 AATCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACGTATTCGCATTGCGA
1 AATCGCATTGCGATAGT-CAAATTCGCATTGCGATTTACGTATTCGCATTGCGA
1114116 ATTAGGAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
60 15 0.31
61 34 0.69
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (60 bp):
AATCGCATTGCGATAGTCAAATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGT
Found at i:1114136 original size:21 final size:21
Alignment explanation
Indices: 1114112--1114172 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
1114102 TATTCGCATT
1114112 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
*
1114133 GCGAATTAGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
* *
1114154 GCG-ATTACGTAAATCGCAA
1 GCGAATTAGGAAAATCGCAA
1114173 TGTGATAGTC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
20 14 0.38
21 23 0.62
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:1114174 original size:20 final size:21
Alignment explanation
Indices: 1113999--1114171 Score: 128
Period size: 20 Copynumber: 8.5 Consensus size: 21
1113989 ATGGCGCTAT
1113999 GTAAATCGCATTGCGA--TA-
1 GTAAATCGCATTGCGATTTAC
*
1114017 GTCAGATTCGCATTGCGATTTAC
1 GT-A-AATCGCATTGCGATTTAC
*
1114040 GT-ATTCGCATTGCGATTTAC
1 GTAAATCGCATTGCGATTTAC
*
1114060 GT-AATCGCATTGCGATTTTC
1 GTAAATCGCATTGCGATTTAC
* *
1114080 -CAAATTCGCGTTGCGATTTAC
1 GTAAA-TCGCATTGCGATTTAC
* * *
1114101 GT-ATTCGCATTGCGAATTAG
1 GTAAATCGCATTGCGATTTAC
* ** * *
1114121 GAAAATCGCAACGCGAATTAG
1 GTAAATCGCATTGCGATTTAC
* *
1114142 GAAAATCGCAATGCGA-TTAC
1 GTAAATCGCATTGCGATTTAC
1114162 GTAAATCGCA
1 GTAAATCGCA
1114172 ATGTGATAGT
Statistics
Matches: 128, Mismatches: 18, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
18 2 0.02
19 1 0.01
20 76 0.59
21 45 0.35
22 2 0.02
23 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (21 bp):
GTAAATCGCATTGCGATTTAC
Found at i:1115169 original size:16 final size:15
Alignment explanation
Indices: 1115118--1115169 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
1115108 ATTATCAATT
* *
1115118 ATAAAATCAACTAAA
1 ATAAAATTAATTAAA
1115133 ATAAAATTAATTATAA
1 ATAAAATTAATTA-AA
*
1115149 CATAAATTATAATTAAA
1 -ATAAAAT-TAATTAAA
1115166 ATAA
1 ATAA
1115170 TTTTATTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 11 0.35
16 6 0.19
17 8 0.26
18 6 0.19
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (15 bp):
ATAAAATTAATTAAA
Found at i:1115294 original size:35 final size:35
Alignment explanation
Indices: 1115236--1115304 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
1115226 TAAATTTTGT
* * *
1115236 TATATAATTAATAAATTTTTAATTTGTGTTATAAA
1 TATATAATTAATAAATTTATAATTTATATTATAAA
*
1115271 TATATTATT-ATAATATTTATAATTTATATTATAA
1 TATATAATTAATAA-ATTTATAATTTATATTATAA
1115305 TCAATATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 4 0.14
35 25 0.86
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (35 bp):
TATATAATTAATAAATTTATAATTTATATTATAAA
Found at i:1115482 original size:14 final size:14
Alignment explanation
Indices: 1115424--1115494 Score: 58
Period size: 14 Copynumber: 5.2 Consensus size: 14
1115414 AATAGTATAA
*
1115424 ATATTATAATAAAT
1 ATATTATAATTAAT
* *
1115438 ATATTCTTATGTAAT
1 ATATTATAAT-TAAT
*
1115453 -TTTTATAATT--T
1 ATATTATAATTAAT
1115464 ATATTATAATTAAT
1 ATATTATAATTAAT
* *
1115478 ATATTATTATTATT
1 ATATTATAATTAAT
1115492 ATA
1 ATA
1115495 CTATTCCATT
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
11 1 0.02
12 9 0.20
13 1 0.02
14 30 0.68
15 3 0.07
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (14 bp):
ATATTATAATTAAT
Found at i:1115574 original size:12 final size:12
Alignment explanation
Indices: 1115554--1115620 Score: 66
Period size: 12 Copynumber: 5.4 Consensus size: 12
1115544 TTTTTAAAAT
*
1115554 TAATATATTTTA
1 TAATTTATTTTA
1115566 TAATTTATTTTA
1 TAATTTATTTTA
1115578 -AATTTATATTT-
1 TAATTTAT-TTTA
1115589 TAATATTATATTTTA
1 T-A-ATT-TATTTTA
1115604 TAATTTATTTTA
1 TAATTTATTTTA
*
1115616 CAATT
1 TAATT
1115621 AATATATTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
11 7 0.15
12 25 0.53
13 4 0.09
14 7 0.15
15 4 0.09
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (12 bp):
TAATTTATTTTA
Found at i:1115589 original size:13 final size:14
Alignment explanation
Indices: 1115532--1115611 Score: 71
Period size: 12 Copynumber: 5.8 Consensus size: 14
1115522 TTGTAATAAA
*
1115532 TTATAATTAATATTT
1 TTATAATTTATA-TT
*
1115547 TTAAAATTAATATATT
1 TTATAATT--TATATT
1115563 TTATAA-TT-TATT
1 TTATAATTTATATT
1115575 TTA-AATTTATA-T
1 TTATAATTTATATT
1115587 TT-TAATATTATATT
1 TTATAAT-TTATATT
1115601 TTATAATTTAT
1 TTATAATTTAT
1115612 TTTACAATTA
Statistics
Matches: 54, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
11 2 0.04
12 15 0.28
13 8 0.15
14 7 0.13
15 12 0.22
16 7 0.13
17 3 0.06
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTATAATTTATATT
Found at i:1115621 original size:25 final size:24
Alignment explanation
Indices: 1115554--1115621 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 24
1115544 TTTTTAAAAT
*
1115554 TAATATATTTTATAATT-TATTTTA
1 TAATTTATTTTA-AATTATATTTTA
1115578 -AATTTATATTTTAATATTATATTTTA
1 TAA-TT-TATTTTAA-ATTATATTTTA
1115604 TAATTTATTTTACAATTA
1 TAATTTATTTTA-AATTA
1115622 ATATATTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
23 2 0.05
24 2 0.05
25 21 0.57
26 10 0.27
27 2 0.05
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (24 bp):
TAATTTATTTTAAATTATATTTTA
Found at i:1121419 original size:18 final size:18
Alignment explanation
Indices: 1121380--1121419 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1121370 CGAATGATTG
**
1121380 AATTGAATATAATCTTTT
1 AATTGAATATAATCTTAA
1121398 AATTGAATATAATCTTAA
1 AATTGAATATAATCTTAA
1121416 AATT
1 AATT
1121420 TGTAAAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (18 bp):
AATTGAATATAATCTTAA
Found at i:1123280 original size:2 final size:2
Alignment explanation
Indices: 1123275--1123320 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1123265 ATGAAAAATG
1123275 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1123317 TA TA
1 TA TA
1123321 CATGTATAAA
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):
TA
Found at i:1123875 original size:22 final size:21
Alignment explanation
Indices: 1123815--1123875 Score: 52
Period size: 22 Copynumber: 2.9 Consensus size: 21
1123805 TCGAGACTGC
* *
1123815 AAGAACAGTATCGGTA-TTAT
1 AAGAACAGTATCGATACTAAT
* * * *
1123835 ATGAACAATATTGAAACTAACT
1 AAGAACAGTATCGATACTAA-T
1123857 AAGAACAGTATCGATACTA
1 AAGAACAGTATCGATACTA
1123876 GATGAACTAT
Statistics
Matches: 29, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
20 11 0.38
21 2 0.07
22 16 0.55
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (21 bp):
AAGAACAGTATCGATACTAAT
Found at i:1127242 original size:22 final size:22
Alignment explanation
Indices: 1127214--1127274 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
1127204 GGGTCTACGC
*
1127214 GGTCCTTCGGGACATATACAGA
1 GGTCCTTCGGGACAAATACAGA
*
1127236 GGTCCTTCGGGACAAATACATA
1 GGTCCTTCGGGACAAATACAGA
*
1127258 GGTCCTTCAGGACAAAT
1 GGTCCTTCGGGACAAAT
1127275 TTCACATGCC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.23
Consensus pattern (22 bp):
GGTCCTTCGGGACAAATACAGA
Found at i:1133655 original size:23 final size:23
Alignment explanation
Indices: 1133613--1133694 Score: 82
Period size: 23 Copynumber: 3.7 Consensus size: 23
1133603 TTAGTGCAGA
*
1133613 GGGAATCGATACCCCC-TTGAAG
1 GGGAATCGATTCCCCCTTTGAAG
* *
1133635 GGGAACCGATTCCCCCTTTGAAT
1 GGGAATCGATTCCCCCTTTGAAG
*
1133658 GGGAATTGATTCCCTCCTTT--A-
1 GGGAATCGATTCCC-CCTTTGAAG
*
1133679 GGGAATCGATACCCCC
1 GGGAATCGATTCCCCC
1133695 ACGAGTTCGG
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
20 2 0.04
21 12 0.24
22 15 0.29
23 17 0.33
24 5 0.10
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.24
Consensus pattern (23 bp):
GGGAATCGATTCCCCCTTTGAAG
Found at i:1135998 original size:22 final size:22
Alignment explanation
Indices: 1135970--1136017 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
1135960 GGAACTGATT
1135970 CCCCCCAAGGGGGTACCGAATC
1 CCCCCCAAGGGGGTACCGAATC
* *
1135992 CCCCCCAAGGGGGTACCTATTC
1 CCCCCCAAGGGGGTACCGAATC
1136014 CCCC
1 CCCC
1136018 TGATCAACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.19, C:0.46, G:0.23, T:0.12
Consensus pattern (22 bp):
CCCCCCAAGGGGGTACCGAATC
Found at i:1141131 original size:22 final size:22
Alignment explanation
Indices: 1141106--1141166 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
1141096 GGGTATATGC
*
1141106 GGTCCTTCGGGACATATACAGA
1 GGTCCTTCGGGACAAATACAGA
* *
1141128 GGTCCTTCGGAACAAATACATA
1 GGTCCTTCGGGACAAATACAGA
* *
1141150 GGTCATTCGGGATAAAT
1 GGTCCTTCGGGACAAAT
1141167 TTCACATGCC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.25
Consensus pattern (22 bp):
GGTCCTTCGGGACAAATACAGA
Found at i:1146422 original size:21 final size:24
Alignment explanation
Indices: 1146395--1146454 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 24
1146385 AACCAAAAGG
1146395 AGTAGTATCGGTACCA-TA-ACTA
1 AGTAGTATCGGTACCACTACACTA
*
1146417 AG-AGTATCGGTACTACTACACTA
1 AGTAGTATCGGTACCACTACACTA
*
1146440 AGTAGTATCGATACC
1 AGTAGTATCGGTACC
1146455 GTATATGGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 12 0.38
22 4 0.12
23 6 0.19
24 10 0.31
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (24 bp):
AGTAGTATCGGTACCACTACACTA
Found at i:1147906 original size:16 final size:16
Alignment explanation
Indices: 1147885--1147917 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1147875 GAATGCACAA
1147885 TATAAAGATGTACCAT
1 TATAAAGATGTACCAT
1147901 TATAAAGATGTACCAT
1 TATAAAGATGTACCAT
1147917 T
1 T
1147918 CTCAGAGGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (16 bp):
TATAAAGATGTACCAT
Found at i:1160265 original size:12 final size:12
Alignment explanation
Indices: 1160250--1160289 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
1160240 TTGCACGGAT
1160250 ACGGATACGGGG
1 ACGGATACGGGG
1160262 ACGGATACGGGG
1 ACGGATACGGGG
**
1160274 ACGGGGACGGGG
1 ACGGATACGGGG
1160286 ACGG
1 ACGG
1160290 GAAACGGCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.23, C:0.17, G:0.55, T:0.05
Consensus pattern (12 bp):
ACGGATACGGGG
Found at i:1160267 original size:18 final size:18
Alignment explanation
Indices: 1160244--1160283 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1160234 GCTATGTTGC
*
1160244 ACGGATACGGATACGGGG
1 ACGGATACGGAGACGGGG
*
1160262 ACGGATACGGGGACGGGG
1 ACGGATACGGAGACGGGG
1160280 ACGG
1 ACGG
1160284 GGACGGGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.50, T:0.07
Consensus pattern (18 bp):
ACGGATACGGAGACGGGG
Found at i:1160277 original size:6 final size:6
Alignment explanation
Indices: 1160256--1160290 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1160246 GGATACGGAT
**
1160256 ACGGGG ACGGAT ACGGGG ACGGGG ACGGGG ACGGG
1 ACGGGG ACGGGG ACGGGG ACGGGG ACGGGG ACGGG
1160291 AAACGGCAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.20, C:0.17, G:0.60, T:0.03
Consensus pattern (6 bp):
ACGGGG
Done.