Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_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: 21326069
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 89
Found at i:863515 original size:4 final size:4
Alignment explanation
Indices: 863506--863601 Score: 59
Period size: 4 Copynumber: 22.8 Consensus size: 4
863496 GGTAGTAATT
* * * * **
863506 TTTA TTTA TTT- CTAA TTTA TTTG TTTA TTTA TTTA TTCAA CTCGAA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT-TA -T-TTA TTTA
* *
863556 TTTA TTTAA TTTGAA TTTA TTTA TTTA GTTA TTTA TTTA TATA TTT
1 TTTA TTT-A TTT--A TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
863602 GAAGGGATAT
Statistics
Matches: 72, Mismatches: 14, Indels: 12
0.73 0.14 0.12
Matches are distributed among these distances:
3 1 0.01
4 57 0.79
5 6 0.08
6 8 0.11
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (4 bp):
TTTA
Found at i:863581 original size:19 final size:19
Alignment explanation
Indices: 863532--863582 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
863522 TTATTTGTTT
*
863532 ATTTATTTATTCAACTCGA
1 ATTTATTTATTTAACTCGA
* *
863551 ATTTATTTATTTAATTTGA
1 ATTTATTTATTTAACTCGA
863570 ATTTATTTATTTA
1 ATTTATTTATTTA
863583 GTTATTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.59
Consensus pattern (19 bp):
ATTTATTTATTTAACTCGA
Found at i:865841 original size:30 final size:30
Alignment explanation
Indices: 865723--865824 Score: 152
Period size: 30 Copynumber: 3.4 Consensus size: 30
865713 CCCGAAGGAC
* * *
865723 CTATCCAGAGGTCACAAAGA-CCCCGATAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
865752 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
865782 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
865812 CTATCCATAGGTC
1 CTATCCAGAGGTC
865825 TCGAAGAACC
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
29 19 0.29
30 47 0.71
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:865841 original size:60 final size:60
Alignment explanation
Indices: 865726--865849 Score: 153
Period size: 60 Copynumber: 2.1 Consensus size: 60
865716 GAAGGACCTA
* *
865726 TCCAGAGGTCACAAAGACCCCGATAACTATCCAGAGGTCATAAAGATCCTCGGT-AACTG
1 TCCAGAGGTCACAAAGACCCCGATAACTATCCAGAGGTCATAAAGAACCTAGGTAAACTG
* * * * *
865785 TCCAGAGGTCATAAAGATCCTCGGTAACTATCCATAGGTC-TCGAAGAACCTAGGTAAACTG
1 TCCAGAGGTCACAAAGA-CCCCGATAACTATCCAGAGGTCAT-AAAGAACCTAGGTAAACTG
865846 TCCA
1 TCCA
865850 TATGTCTCGA
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
59 17 0.31
60 29 0.53
61 9 0.16
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (60 bp):
TCCAGAGGTCACAAAGACCCCGATAACTATCCAGAGGTCATAAAGAACCTAGGTAAACTG
Found at i:865857 original size:31 final size:31
Alignment explanation
Indices: 865810--865874 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
865800 GATCCTCGGT
*
865810 AACTATCCATAGGTCTCG-AAGAACCTAGGTA
1 AACTATCCATAGGTCTCGAAAG-ACATAGGTA
* *
865841 AACTGTCCATATGTCTCGAAAGACATAGGTA
1 AACTATCCATAGGTCTCGAAAGACATAGGTA
865872 AAC
1 AAC
865875 CCTCAACTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 27 0.90
32 3 0.10
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (31 bp):
AACTATCCATAGGTCTCGAAAGACATAGGTA
Found at i:866740 original size:63 final size:64
Alignment explanation
Indices: 866602--866775 Score: 228
Period size: 63 Copynumber: 2.7 Consensus size: 64
866592 TAATGAAGGT
* * * * ** *
866602 ATGCATCGATGCACTACTGATGCATCGGTGCA-TAAAATACATTCGATGTTTGTTTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACT-AATTGCATTCGATGTTTCCTTATTAATGGG
*
866666 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCG-TGTTTCCTTATTAATGGG
1 ATGCATCGATGCACT-ACTTATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGG
*
866729 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGAT
1 ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGAT
866776 TTATTTTAAA
Statistics
Matches: 96, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
63 57 0.59
64 38 0.40
65 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGG
Found at i:868194 original size:3 final size:3
Alignment explanation
Indices: 868186--868212 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
868176 TTAGGGTGAT
868186 GTG GTG GTG GTG GTG GTG GTG GTG GTG
1 GTG GTG GTG GTG GTG GTG GTG GTG GTG
868213 ATCAAAGTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.67, T:0.33
Consensus pattern (3 bp):
GTG
Found at i:868352 original size:25 final size:25
Alignment explanation
Indices: 868313--868369 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
868303 ATTGGCATCA
*
868313 TTAGTTGTTTAAATTTGTAATT-TTT
1 TTAGTTATTTAAA-TTGTAATTCTTT
* *
868338 TTAGTTATTTGAATTGTATTTCTTT
1 TTAGTTATTTAAATTGTAATTCTTT
868363 TTAGTTA
1 TTAGTTA
868370 ATCAAACTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 7 0.25
25 21 0.75
ACGTcount: A:0.23, C:0.02, G:0.12, T:0.63
Consensus pattern (25 bp):
TTAGTTATTTAAATTGTAATTCTTT
Found at i:869145 original size:18 final size:18
Alignment explanation
Indices: 869124--869158 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
869114 AATGTTTCTT
*
869124 CCACATCAGGAATCTCTA
1 CCACATCAAGAATCTCTA
*
869142 CCACGTCAAGAATCTCT
1 CCACATCAAGAATCTCT
869159 GCAAAACTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.34, G:0.11, T:0.23
Consensus pattern (18 bp):
CCACATCAAGAATCTCTA
Found at i:873576 original size:20 final size:20
Alignment explanation
Indices: 873547--873585 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
873537 AGAGCTCATA
*
873547 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
873567 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
873586 GTGGTGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:876103 original size:13 final size:13
Alignment explanation
Indices: 876085--876133 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
876075 ATAAAAAATA
876085 ATTAAATACAAAC
1 ATTAAATACAAAC
876098 ATTAAATACAAAC
1 ATTAAATACAAAC
* * *
876111 GTTACAATTCAAATA
1 ATTA-AATACAAA-C
876126 ATTAAATA
1 ATTAAATA
876134 ATAAAAACAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
13 16 0.55
14 10 0.34
15 3 0.10
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (13 bp):
ATTAAATACAAAC
Found at i:876205 original size:25 final size:25
Alignment explanation
Indices: 876129--876209 Score: 79
Period size: 25 Copynumber: 3.5 Consensus size: 25
876119 TCAAATAATT
876129 AAAT-AATAAAAACATTAAGAAACA
1 AAATAAATAAAAACATTAAGAAACA
*
876153 AAATAAATAAAAA-GTT------CA
1 AAATAAATAAAAACATTAAGAAACA
*
876171 TAATTAAATAAAAACATTAAGAAACA
1 -AAATAAATAAAAACATTAAGAAACA
876197 AAATAAATAAAAA
1 AAATAAATAAAAA
876210 ATCCATAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 17
0.68 0.06 0.26
Matches are distributed among these distances:
18 2 0.05
19 12 0.27
20 2 0.05
24 6 0.14
25 20 0.45
26 2 0.05
ACGTcount: A:0.70, C:0.06, G:0.04, T:0.20
Consensus pattern (25 bp):
AAATAAATAAAAACATTAAGAAACA
Found at i:876242 original size:43 final size:44
Alignment explanation
Indices: 876133--876252 Score: 206
Period size: 44 Copynumber: 2.8 Consensus size: 44
876123 ATAATTAAAT
* *
876133 AATAAAAACATTAAGAAACAAAATAAATAAAAAGTTCATAATTA
1 AATAAAAACATTAAGAAACAAAATAAATAAAAAATCCATAATTA
876177 AATAAAAACATTAAGAAACAAAATAAATAAAAAATCCATAATTA
1 AATAAAAACATTAAGAAACAAAATAAATAAAAAATCCATAATTA
*
876221 AAT-AAAACATTAAGAAACAAAATAAATTAAAA
1 AATAAAAACATTAAGAAACAAAATAAATAAAAA
876253 CAAGTCTATC
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
43 28 0.38
44 45 0.62
ACGTcount: A:0.68, C:0.07, G:0.03, T:0.21
Consensus pattern (44 bp):
AATAAAAACATTAAGAAACAAAATAAATAAAAAATCCATAATTA
Found at i:881081 original size:21 final size:21
Alignment explanation
Indices: 881055--881097 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
881045 AAGGATTTCC
881055 TCTTTGATAAAAATAATTATA
1 TCTTTGATAAAAATAATTATA
881076 TCTTTGATAAAAATAATTATA
1 TCTTTGATAAAAATAATTATA
881097 T
1 T
881098 TCATACATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.44
Consensus pattern (21 bp):
TCTTTGATAAAAATAATTATA
Found at i:881199 original size:16 final size:17
Alignment explanation
Indices: 881167--881200 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
881157 GTAATGTGAC
881167 TATATTTAAATAATTAA
1 TATATTTAAATAATTAA
881184 TATATTTAAA-AATTAA
1 TATATTTAAATAATTAA
881200 T
1 T
881201 TAAGTTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TATATTTAAATAATTAA
Found at i:885046 original size:41 final size:41
Alignment explanation
Indices: 884968--885068 Score: 123
Period size: 41 Copynumber: 2.5 Consensus size: 41
884958 GGCGTTTATT
* * *
884968 ACAAAAACACCGCTAAAGTACAAGACTAATGCGGCGTTTGA
1 ACAAAAACGCCACTAAAGTACAAGACTAATGCAGCGTTTGA
* *
885009 ACAAAAACGCCACTAAAGTACAAGTCT-ATAGCAGCGTTTGT
1 ACAAAAACGCCACTAAAGTACAAGACTAAT-GCAGCGTTTGA
* *
885050 TCACAAACGCCACTAAAGT
1 ACAAAAACGCCACTAAAGT
885069 TTGAGTCTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
40 2 0.04
41 50 0.96
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.19
Consensus pattern (41 bp):
ACAAAAACGCCACTAAAGTACAAGACTAATGCAGCGTTTGA
Found at i:885076 original size:41 final size:41
Alignment explanation
Indices: 884971--885110 Score: 117
Period size: 41 Copynumber: 3.4 Consensus size: 41
884961 GTTTATTACA
* * * * *
884971 AAAACACCGCTAAAGTACAAGACTA-ATGCGGCGTTTG-AAC
1 AAAACGCCACTAAAGTACAAGTCTATA-GCGTCGTTTGTATC
885011 AAAAACGCCACTAAAGTACAAGTCTATAGCAG-CGTTTGT-TC
1 -AAAACGCCACTAAAGTACAAGTCTATAGC-GTCGTTTGTATC
*** * * *
885052 ACAAACGCCACTAAAGTTTGAGTCTTTCGCGTCGTTTGTATT
1 A-AAACGCCACTAAAGTACAAGTCTATAGCGTCGTTTGTATC
885094 AAAACGCCACTAAAGTA
1 AAAACGCCACTAAAGTA
885111 AGAGTATTTT
Statistics
Matches: 82, Mismatches: 11, Indels: 12
0.78 0.10 0.11
Matches are distributed among these distances:
40 2 0.02
41 76 0.93
42 4 0.05
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (41 bp):
AAAACGCCACTAAAGTACAAGTCTATAGCGTCGTTTGTATC
Found at i:885128 original size:41 final size:40
Alignment explanation
Indices: 885012--885130 Score: 123
Period size: 41 Copynumber: 2.9 Consensus size: 40
885002 CGTTTGAACA
* *
885012 AAAACGCCACTAAAGTACA-AGTCTATAGCAGCGTTTGTTC
1 AAAACGCCACTAAAGTA-AGAGTCTTTAGCATCGTTTGTTC
** * * *
885052 ACAAACGCCACTAAAGTTTGAGTCTTTCGCGTCGTTTGTATT
1 A-AAACGCCACTAAAGTAAGAGTCTTTAGCATCGTTTGT-TC
* *
885094 AAAACGCCACTAAAGTAAGAGTATTTTGCATCGTTTG
1 AAAACGCCACTAAAGTAAGAGTCTTTAGCATCGTTTG
885131 ATAAAAAAAA
Statistics
Matches: 64, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
40 1 0.02
41 61 0.95
42 2 0.03
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Consensus pattern (40 bp):
AAAACGCCACTAAAGTAAGAGTCTTTAGCATCGTTTGTTC
Found at i:886794 original size:19 final size:19
Alignment explanation
Indices: 886770--886809 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
886760 GATTAGTTAG
886770 TAAAAATATAA-ATAATTAT
1 TAAAAA-ATAATATAATTAT
*
886789 TAAAAAATAATATTATTAT
1 TAAAAAATAATATAATTAT
886808 TA
1 TA
886810 TTTTAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAAAAATAATATAATTAT
Found at i:887525 original size:3 final size:3
Alignment explanation
Indices: 887517--887546 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
887507 GACTCAGTCG
887517 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
887547 TGTACATAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:894468 original size:15 final size:16
Alignment explanation
Indices: 894442--894474 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
894432 TAAATATATT
*
894442 TATTTAAAAATATTAA
1 TATTTAAAAATATAAA
894458 TATTT-AAAATATAAA
1 TATTTAAAAATATAAA
894473 TA
1 TA
894475 ATATATTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TATTTAAAAATATAAA
Found at i:900628 original size:45 final size:45
Alignment explanation
Indices: 900560--900648 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 45
900550 CAGTGATATT
*
900560 TGCAGCTGGCTGAGGAACATTATTACTCACACTTGTACCATGCAA
1 TGCAGCTGGCTGAGGAACATTATTACTCACACTTGGACCATGCAA
* * **
900605 TGCAGCTGGCTGAGGGGA-TTTATTACTCGTACTTGGACCATGCA
1 TGCAGCTGGCTGA-GGAACATTATTACTCACACTTGGACCATGCA
900649 GAAAAGCACA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
45 35 0.92
46 3 0.08
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (45 bp):
TGCAGCTGGCTGAGGAACATTATTACTCACACTTGGACCATGCAA
Found at i:903585 original size:38 final size:38
Alignment explanation
Indices: 903510--903588 Score: 122
Period size: 38 Copynumber: 2.1 Consensus size: 38
903500 CTTAGATGAG
*
903510 ATGCATTTAACTCATGCCATTAATATACCACTAGATTC
1 ATGCATTTAACTCATGCCATTAATATACAACTAGATTC
* * *
903548 ATGCATTTAACTCCTGCCATTAATATACAATTGGATTC
1 ATGCATTTAACTCATGCCATTAATATACAACTAGATTC
903586 ATG
1 ATG
903589 TATTATACAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.33, C:0.22, G:0.10, T:0.35
Consensus pattern (38 bp):
ATGCATTTAACTCATGCCATTAATATACAACTAGATTC
Found at i:904078 original size:15 final size:15
Alignment explanation
Indices: 904053--904090 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
904043 ATAATAAACA
904053 ATTAT-AAATATATT
1 ATTATAAAATATATT
904067 ATTATAAAATATATT
1 ATTATAAAATATATT
*
904082 ATTTTAAAA
1 ATTATAAAA
904091 AATTAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 5 0.23
15 17 0.77
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTATAAAATATATT
Found at i:910343 original size:21 final size:23
Alignment explanation
Indices: 910317--910361 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
910307 AGGCGTGTTC
*
910317 ACTAAT-TGATTTATA-ATATAA
1 ACTAATCTGATATATATATATAA
910338 ACTAATCCTGATATATATATATAA
1 ACTAAT-CTGATATATATATATAA
910362 TTCAACAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 6 0.30
23 8 0.40
24 6 0.30
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (23 bp):
ACTAATCTGATATATATATATAA
Found at i:923185 original size:31 final size:31
Alignment explanation
Indices: 922937--923183 Score: 368
Period size: 31 Copynumber: 8.0 Consensus size: 31
922927 GAGTCGAGGG
*
922937 TTACTTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
922968 TTACCTATGTTCTTTGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* * *
922999 TTACCTATTTTCTTTGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
923030 TTACCTATGTTCTTTGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
923061 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* ** *
923092 TTACCTTTGTTCTTCAAGATATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* * *
923123 TTACCTATGTTCTTTGAGACATATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
923154 TTACCTATGTTCTTCGGAACATATGGACTG
1 TTACCTATGTTCTTCGGGACATATGGACTG
923184 ATCCTTTGGG
Statistics
Matches: 197, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 197 1.00
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:924491 original size:17 final size:18
Alignment explanation
Indices: 924471--924518 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
924461 ATTAATGTCT
*
924471 AAAAATTATTAAAATAA-
1 AAAAATTATTAAAAAAAG
* *
924488 AAAAATAAGTAAAAAAAG
1 AAAAATTATTAAAAAAAG
924506 AAAAATTATTAAA
1 AAAAATTATTAAA
924519 TGAAATAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (18 bp):
AAAAATTATTAAAAAAAG
Found at i:924578 original size:14 final size:15
Alignment explanation
Indices: 924538--924579 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
924528 AAAATAATAC
924538 TGAAAATGAAATAACA
1 TGAAAATGAAA-AACA
* *
924554 TAAAAAGGAAAAA-A
1 TGAAAATGAAAAACA
924568 TGAAAATGAAAA
1 TGAAAATGAAAA
924580 TTTGAATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 11 0.50
15 2 0.09
16 9 0.41
ACGTcount: A:0.69, C:0.02, G:0.14, T:0.14
Consensus pattern (15 bp):
TGAAAATGAAAAACA
Found at i:925222 original size:602 final size:610
Alignment explanation
Indices: 924232--925361 Score: 1886
Period size: 602 Copynumber: 1.8 Consensus size: 610
924222 GTATTGCCCC
*
924232 TTCGGTACCAATTAATTTGTCGGTTGTCTTAATTGCGAAAATTAAAATTTAAATCAAAATTTAAA
1 TTCGGTACCAATTAATTTATCGGTTGTCTTAATTGCGAAAATTAAAATTTAAATCAAAATTTAAA
* *
924297 AAATTCAATTCAAATTGCTTACCTTTGATTGGTTGAGATTACTACTGAAAAAGTCAAAAAAGAAT
66 AAATTCAATTCAAATTGCTTACCTTTGATCGGTTGAAATTACTACTGAAAAAGTCAAAAAAGAAT
924362 GTTAAATTGAAAAATAAAAATGAATAAAGAAATATCCAATAAAAGGAGAAAAGCAAAGGTTAAAA
131 GTTAAATTGAAAAATAAAAATGAATAAAGAAATATCCAATAAAAGGAG--AAG--AA-G--AAAA
* *
924427 AAGGTTTTAAAAAATAATAAATAAATAAAATCATATTAATGTCTAAAAATTATTAAAATAAAAAA
189 AAGGTTTTAAAAAATAATAAATAAATAAAATCATATTAA--TCTAAAAATGAATAAAATAAAAAA
* *
924492 ATAAGTAAAAAAAGAAAAATTATTAAATGAAATAATAAAATAATACTGAAAATGAAATAACATAA
252 ATAAGTAAAAAAAGAAAAATTATTAAAAGAAATAATAAAATAATAATGAAAATGAAATAACATAA
924557 AAAGGAAAAAATGAAAATGAAAATTTGAATTAAAGGATTAAATAATAAAAACTAGAAAATTAATG
317 AAAGGAAAAAATGAAAATGAAAATTTGAATTAAAGGATTAAATAATAAAAACTAGAAAATTAATG
* *
924622 TCTAAAAAAATAAAATAAATAATAGAACCCATAATGT-AAAAAAACAACACTTTTCAAACACTAA
382 TCTAAAAAAATAAAATAAATAATACAACCCATAATGTAAAAAAAACAACACTTTCCAAACACTAA
924686 AATATAATAAACCCATACAATTAGAGCTAAAGTATAAATTATCCAAAATTACAGATTAGAAATCG
447 AATATAATAAACCCATACAATTAGAGCTAAAGTATAAATTATCCAAAATTACAGATTAGAAATCG
924751 AAATAAACAATAATATTTAGCGAGGTCCGGGCATGTAAATAAACCAAAGCAAATTATATTAATAC
512 AAATAAACAATAATATTTAGCGAGGTCCGGGCATGTAAATAAACCAAAGCAAATTATATTAATAC
924816 AATCAAGGAATGATTAACACTCTTGTGCTGTTTT
577 AATCAAGGAATGATTAACACTCTTGTGCTGTTTT
*
924850 TTCGGTACCAATTAATTTATCGGTTGTTTTAATTGCGAAAATTAAAATTTAAATCAAAATTTAAA
1 TTCGGTACCAATTAATTTATCGGTTGTCTTAATTGCGAAAATTAAAATTTAAATCAAAATTTAAA
*
924915 AAATTCAATTCAAATTGCTTACCTTTGATCGGTTGAAATTACTACTG-AAAAGTCAGAAAAGAAT
66 AAATTCAATTCAAATTGCTTACCTTTGATCGGTTGAAATTACTACTGAAAAAGTCAAAAAAGAAT
* *
924979 GTTAAATTGAAAAATAAAAATGAATAAAGAAATTTTCAATAAAA-G-G-AG-A-AAAAAAGGTTT
131 GTTAAATTGAAAAATAAAAATGAATAAAGAAATATCCAATAAAAGGAGAAGAAGAAAAAAGGTTT
*
925039 TAAAAAATAATAAATAAATAAAATCATATTAA-C-AAAAA-GAATAATAATAAACAAATAAGTAA
196 TAAAAAATAATAAATAAATAAAATCATATTAATCTAAAAATGAATAA-AATAAAAAAATAAGTAA
925101 AAACAAGAAAAATTATTAAAAGAAATAATAAAATAATAATGAAAATGAAATAACATAAAAAGGAA
260 AAA-AAGAAAAATTATTAAAAGAAATAATAAAATAATAATGAAAATGAAATAACATAAAAAGGAA
*
925166 AAAAT-ATAAATGAAATTTTGAATTAAAGGATTAAATAATAAAAACTAGAAAATTAATGTCTAAA
324 AAAATGA-AAATGAAAATTTGAATTAAAGGATTAAATAATAAAAACTAGAAAATTAATGTCTAAA
*
925230 AAAATAAAATAAATAATACAACCCATGATGTAAAAAAAAAACAACACTTTCCAAACACTAAAATA
388 AAAATAAAATAAATAATACAACCCATAATGT--AAAAAAAACAACACTTTCCAAACACTAAAATA
* * *
925295 TAATGAACCCATACAATTAGAGCTAATGTATAAATTATCCAAAATTATAGATTAGAAATCGAAAT
451 TAATAAACCCATACAATTAGAGCTAAAGTATAAATTATCCAAAATTACAGATTAGAAATCGAAAT
925360 AA
516 AA
925362 TTAAAAATAT
Statistics
Matches: 487, Mismatches: 19, Indels: 25
0.92 0.04 0.05
Matches are distributed among these distances:
600 4 0.01
601 25 0.05
602 150 0.31
605 137 0.28
609 1 0.00
612 2 0.00
615 1 0.00
616 1 0.00
617 58 0.12
618 108 0.22
ACGTcount: A:0.54, C:0.09, G:0.10, T:0.27
Consensus pattern (610 bp):
TTCGGTACCAATTAATTTATCGGTTGTCTTAATTGCGAAAATTAAAATTTAAATCAAAATTTAAA
AAATTCAATTCAAATTGCTTACCTTTGATCGGTTGAAATTACTACTGAAAAAGTCAAAAAAGAAT
GTTAAATTGAAAAATAAAAATGAATAAAGAAATATCCAATAAAAGGAGAAGAAGAAAAAAGGTTT
TAAAAAATAATAAATAAATAAAATCATATTAATCTAAAAATGAATAAAATAAAAAAATAAGTAAA
AAAAGAAAAATTATTAAAAGAAATAATAAAATAATAATGAAAATGAAATAACATAAAAAGGAAAA
AATGAAAATGAAAATTTGAATTAAAGGATTAAATAATAAAAACTAGAAAATTAATGTCTAAAAAA
ATAAAATAAATAATACAACCCATAATGTAAAAAAAACAACACTTTCCAAACACTAAAATATAATA
AACCCATACAATTAGAGCTAAAGTATAAATTATCCAAAATTACAGATTAGAAATCGAAATAAACA
ATAATATTTAGCGAGGTCCGGGCATGTAAATAAACCAAAGCAAATTATATTAATACAATCAAGGA
ATGATTAACACTCTTGTGCTGTTTT
Found at i:925379 original size:38 final size:40
Alignment explanation
Indices: 925336--925422 Score: 160
Period size: 38 Copynumber: 2.2 Consensus size: 40
925326 AAATTATCCA
925336 AAATTATAGATTAGAAATCGAAATAATT-AAAA-ATATAT
1 AAATTATAGATTAGAAATCGAAATAATTAAAAATATATAT
925374 AAATTATAGATTAGAAATCGAAATAATTAAAAATATATAT
1 AAATTATAGATTAGAAATCGAAATAATTAAAAATATATAT
925414 AAATTATAG
1 AAATTATAG
925423 TGACCAAAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
38 28 0.60
39 4 0.09
40 15 0.32
ACGTcount: A:0.57, C:0.02, G:0.08, T:0.32
Consensus pattern (40 bp):
AAATTATAGATTAGAAATCGAAATAATTAAAAATATATAT
Found at i:926700 original size:16 final size:15
Alignment explanation
Indices: 926679--926729 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 15
926669 CCTGAACCAC
926679 AATAAAAAATAAAAT
1 AATAAAAAATAAAAT
926694 --TAATAAAATAAAAT
1 AATAA-AAAATAAAAT
926708 AATAATAATAATAATAAT
1 AATAA-AA-AATAA-AAT
926726 AATA
1 AATA
926730 TATTTTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
13 3 0.10
14 10 0.32
16 6 0.19
17 5 0.16
18 7 0.23
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AATAAAAAATAAAAT
Found at i:926713 original size:3 final size:3
Alignment explanation
Indices: 926694--926729 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
926684 AAAATAAAAT
926694 TAA TAA -AA TAA -AA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
926730 TATTTTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:926834 original size:38 final size:37
Alignment explanation
Indices: 926787--927189 Score: 489
Period size: 38 Copynumber: 10.8 Consensus size: 37
926777 TTAAAAATTC
*
926787 AAAACTATATATTATATA-ATTTTCAAAATGTTTTTA
1 AAAACCATATATTATATATATTTTCAAAATGTTTTTA
*
926823 AAAACCATATA-T-TATATATTTTCAAAATATTTTTTA
1 AAAACCATATATTATATATATTTTCAAAAT-GTTTTTA
926859 AAAACCATATATTATATATATTTTCAAAATGTTTTTTA
1 AAAACCATATATTATATATATTTTCAAAATG-TTTTTA
* *
926897 AAAATCATATATTATATATGTTTTCAAAATGTTTTTA
1 AAAACCATATATTATATATATTTTCAAAATGTTTTTA
926934 AAAACCATATATTATATA-AGTTTTCAAAAATGTTTTTA
1 AAAACCATATATTATATATA-TTTTC-AAAATGTTTTTA
926972 AAAACCATATATTATATA-AGTTTTCAAAATGTTTTTTTA
1 AAAACCATATATTATATATA-TTTTCAAAATG--TTTTTA
*
927011 AAAACCATATATTATATATGTTTTCAAAATGTTTTTA
1 AAAACCATATATTATATATATTTTCAAAATGTTTTTA
* * *
927048 AAAAACATATATTATATATGTTTTCAAAATGTTTTCGA
1 AAAACCATATATTATATATATTTTCAAAATGTTTT-TA
** * * *
927086 AAAACTGTATAATATACATACATTTTCAAAAATCG-TTTTC
1 AAAACCATAT-AT-TATATATATTTTC-AAAAT-GTTTTTA
* *
927126 AAAACTATATATTATATATATTTTCAAAATG-TTTTC
1 AAAACCATATATTATATATATTTTCAAAATGTTTTTA
* *
927162 AAAACTATATAATATATATA-TTTCAAAA
1 AAAACCATATATTATATATATTTTCAAAA
927190 ACGATTTTTT
Statistics
Matches: 330, Mismatches: 22, Indels: 31
0.86 0.06 0.08
Matches are distributed among these distances:
34 4 0.01
35 20 0.06
36 52 0.16
37 80 0.24
38 107 0.32
39 39 0.12
40 19 0.06
41 8 0.02
42 1 0.00
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.44
Consensus pattern (37 bp):
AAAACCATATATTATATATATTTTCAAAATGTTTTTA
Found at i:926966 original size:76 final size:73
Alignment explanation
Indices: 926787--927189 Score: 492
Period size: 75 Copynumber: 5.4 Consensus size: 73
926777 TTAAAAATTC
*
926787 AAAACTATATATTATATAATTTTCAAAATGTTTTTAAAAACCATATATTATATA--TTTTCAAAA
1 AAAACCATATATTATATAATTTTCAAAATGTTTTTAAAAACCATATATTATATATGTTTTCAAAA
*
926850 TATTTTTTA
66 T-GTTTTTA
*
926859 AAAACCATATATTATATATATTTTCAAAATGTTTTTTAAAAATCATATATTATATATGTTTTCAA
1 AAAACCATATATTATATA-ATTTTCAAAATG-TTTTTAAAAACCATATATTATATATGTTTTCAA
926924 AATGTTTTTA
64 AATGTTTTTA
*
926934 AAAACCATATATTATATAAGTTTTCAAAAATGTTTTTAAAAACCATATATTATATAAGTTTTCAA
1 AAAACCATATATTATATAA-TTTTC-AAAATGTTTTTAAAAACCATATATTATATATGTTTTCAA
926999 AATGTTTTTTTA
64 AATG--TTTTTA
* *
927011 AAAACCATATATTATATATGTTTTCAAAATGTTTTTAAAAAACATATATTATATATGTTTTCAAA
1 AAAACCATATATTATATA-ATTTTCAAAATGTTTTTAAAAACCATATATTATATATGTTTTCAAA
*
927076 ATGTTTTCGA
65 ATGTTTT-TA
** * * * *
927086 AAAACTGTATAATATACATACATTTTCAAAAATCG-TTTTCAAAACTATATATTATATATATTTT
1 AAAACCATAT-AT-TATATA-ATTTTC-AAAAT-GTTTTTAAAAACCATATATTATATATGTTTT
*
927150 CAAAATG-TTTTC
61 CAAAATGTTTTTA
* *
927162 AAAACTATATAATATAT-ATATTTCAAAA
1 AAAACCATATATTATATAAT-TTTCAAAA
927190 ACGATTTTTT
Statistics
Matches: 293, Mismatches: 23, Indels: 30
0.85 0.07 0.09
Matches are distributed among these distances:
72 23 0.08
73 16 0.05
74 32 0.11
75 74 0.25
76 68 0.23
77 42 0.14
78 37 0.13
79 1 0.00
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.44
Consensus pattern (73 bp):
AAAACCATATATTATATAATTTTCAAAATGTTTTTAAAAACCATATATTATATATGTTTTCAAAA
TGTTTTTA
Found at i:928303 original size:86 final size:85
Alignment explanation
Indices: 927958--928588 Score: 815
Period size: 86 Copynumber: 7.4 Consensus size: 85
927948 ATGTGTCATC
* * *
927958 GAGCTGAATGAAATC-AGACTCGACA-GTTTTTTGTTGACAGATAACCCTTCTCGCCTTGTGTTG
1 GAGCTGAATGTAATCGA-ACTCGA-AGGTTTTTT-TTGACAGATAACCCTTCTCGCCTTGAGTTA
* *
928021 TGCTGTAAATTTGACATGCACTT
63 TGCTGTAAATTTGATATGCCCTT
* * * *
928044 GAGCTGAATAG-AATCGAAATCGAAGGTATTTATTGACAGATAACCCTTCTCACCTTGAGTTATG
1 GAGCTGAAT-GTAATCGAACTCGAAGGTTTTTTTTGACAGATAACCCTTCTCGCCTTGAGTTATG
*
928108 CTGTAAATTTGATATGTCCTT
65 CTGTAAATTTGATATGCCCTT
*
928129 GAGCTGAATGTAATCGAACTCGAAGGTTTTTTTGCTGACAGATAACCCCTTCTCGCCTTGAGCTA
1 GAGCTGAATGTAATCGAACTCGAAGGTTTTTTT--TGACAGATAA-CCCTTCTCGCCTTGAGTTA
* *
928194 TGCTGTAGATTTGATATGTCCTT
63 TGCTGTAAATTTGATATGCCCTT
* * * *
928217 GAGCTGAATGTAATCAAACTTGAAGGTTTTTTTCTAACAGATAGCCCTTCTCGCCTTGAGTTATG
1 GAGCTGAATGTAATCGAACTCGAAGGTTTTTTT-TGACAGATAACCCTTCTCGCCTTGAGTTATG
928282 CTGTAAATTTGATATGCCCTT
65 CTGTAAATTTGATATGCCCTT
* ** **
928303 GAGCTGAATGTAATTGAACTCGAAGG-TTTGGTTGACAGATAGTCCTTCTCGCCTTGAGTTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTTTTTTTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
*
928367 TGTAAATTTGATATGGCCTT
66 TGTAAATTTGATATGCCCTT
* *
928387 GAGCTGAATGTAATCGAACTCGAAGGTTTTTTGCTGGA-AGATAACCCTTCTCGCCTTGAGCTAT
1 GAGCTGAATGTAATCGAACTCGAAGGTTTTTT--TTGACAGATAACCCTTCTCGCCTTGAGTTAT
928451 GCTGTAAATTTGATATGCCCTT
64 GCTGTAAATTTGATATGCCCTT
** * * * *
928473 GAGCTGAATGTAATCGAACTCGAAGG-TTTGGTTGACAGATAGCCCTTTTCGCCTTGAGCTATGT
1 GAGCTGAATGTAATCGAACTCGAAGGTTTTTTTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
* *
928537 TGTAAATTTGATAAGGCCTT
66 TGTAAATTTGATATGCCCTT
* *
928557 GAGCTGAATGTAATCGAACTTGAAGATTTTTT
1 GAGCTGAATGTAATCGAACTCGAAGGTTTTTT
928589 GCCGGCAGAT
Statistics
Matches: 483, Mismatches: 50, Indels: 25
0.87 0.09 0.04
Matches are distributed among these distances:
83 3 0.01
84 142 0.29
85 89 0.18
86 155 0.32
87 24 0.05
88 70 0.14
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.35
Consensus pattern (85 bp):
GAGCTGAATGTAATCGAACTCGAAGGTTTTTTTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
TGTAAATTTGATATGCCCTT
Found at i:928437 original size:170 final size:170
Alignment explanation
Indices: 927958--928605 Score: 858
Period size: 170 Copynumber: 3.8 Consensus size: 170
927948 ATGTGTCATC
* * * * * * *
927958 GAGCTGAATGAAATC-AGACTCGACAGTTTTTTGTTGACAGATAACCCTTCTCGCCTTGTGTTGT
1 GAGCTGAATGTAATCGA-ACTCGA-AG-GTTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCTAT
* * *
928022 GCTGTAAATTTGACAT-GCACTTGAGCTGAATAG-AATCGAAATCGAAGGTATTTAT--TGACAG
63 GCTGTAAATTTGATATGGC-CTTGAGCTGAAT-GTAATCGAACTCGAAGGT-TTTTTGCTGACAG
* *
928083 ATAACCCTTCTCACCTTGAGTTATGCTGTAAATTTGATATGTCCTT
125 ATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCCTT
* * *
928129 GAGCTGAATGTAATCGAACTCGAAGGTTTTTTTGCTGACAGATAACCCCTTCTCGCCTTGAGCTA
1 GAGCTGAATGTAATCGAACTCGAAGG---TTTGGTTGACAGAT-AGCCCTTCTCGCCTTGAGCTA
* * * * * *
928194 TGCTGTAGATTTGATATGTCCTTGAGCTGAATGTAATCAAACTTGAAGGTTTTTTTCTAACAGAT
62 TGCTGTAAATTTGATATGGCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTTGCTGACAGAT
*
928259 AGCCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCCTT
127 AACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCCTT
* * *
928303 GAGCTGAATGTAATTGAACTCGAAGGTTTGGTTGACAGATAGTCCTTCTCGCCTTGAGTTATGCT
1 GAGCTGAATGTAATCGAACTCGAAGGTTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCT
928368 GTAAATTTGATATGGCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTTGCTGGA-AGATAAC
66 GTAAATTTGATATGGCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTTGCT-GACAGATAAC
*
928432 CCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTT
130 CCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCCTT
* *
928473 GAGCTGAATGTAATCGAACTCGAAGGTTTGGTTGACAGATAGCCCTTTTCGCCTTGAGCTATGTT
1 GAGCTGAATGTAATCGAACTCGAAGGTTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCT
* * * * *
928538 GTAAATTTGATAAGGCCTTGAGCTGAATGTAATCGAACTTGAAGATTTTTTGCCGGCAGATAACC
66 GTAAATTTGATATGGCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTTGCTGACAGATAACC
928603 CTT
131 CTT
928606 ATCGTATTGA
Statistics
Matches: 424, Mismatches: 42, Indels: 23
0.87 0.09 0.05
Matches are distributed among these distances:
169 1 0.00
170 240 0.57
171 33 0.08
172 19 0.04
173 57 0.13
174 74 0.17
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (170 bp):
GAGCTGAATGTAATCGAACTCGAAGGTTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCT
GTAAATTTGATATGGCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTTGCTGACAGATAACC
CTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCCTT
Found at i:930425 original size:12 final size:13
Alignment explanation
Indices: 930404--930428 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
930394 TATGAAAATA
930404 AAGTTAAAAAAAC
1 AAGTTAAAAAAAC
930417 AAGTTAAAAAAA
1 AAGTTAAAAAAA
930429 TTTGAGAAAG
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:0.72, C:0.04, G:0.08, T:0.16
Consensus pattern (13 bp):
AAGTTAAAAAAAC
Found at i:931100 original size:150 final size:150
Alignment explanation
Indices: 930817--931102 Score: 369
Period size: 150 Copynumber: 1.9 Consensus size: 150
930807 TGATATAGGT
* * * *
930817 GTTTGAGGTGTCTTCAAAGTTGCATCTGACCCACTGATTCTTAAATCTACGGGCCAGTCTCGGAC
1 GTTTGAGGTGTCTTCAAAGTTGCATCTGACCCACTCATTCTTAAACCCACGGGCCAGTCTCGAAC
* * * ** * *
930882 TACATTCATGGAAGCCCTTTTGCTTGGATTTCCTTTTCTATCCTCTTGCGCCTTATGTTTTTCGC
66 TACATTCATGGAAACCCTTCTGCTTGGATTTCCTTTTCTACCCTCTTGCGCCTTACATTCTTCAC
930947 AGGAATCCTCCGTTGAAGAA
131 AGGAATCCTCCGTTGAAGAA
* *** *
930967 GTTTGAGGTGTTTTCCTGGTTGCATCTGCCCCA-TCCATTCTTAAACCCACGGGCCAGTCTCGAA
1 GTTTGAGGTGTCTTCAAAGTTGCATCTGACCCACT-CATTCTTAAACCCACGGGCCAGTCTCGAA
* * *
931031 TTACATTCATGGAAACCCTTCTGCTTGGATTTCATTTT-TCACCCTTTTGCGCCTTACATTCTTC
65 CTACATTCATGGAAACCCTTCTGCTTGGATTTCCTTTTCT-ACCCTCTTGCGCCTTACATTCTTC
931095 ACAGGAAT
129 ACAGGAAT
931103 TCTCTGTTAA
Statistics
Matches: 115, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
149 2 0.02
150 113 0.98
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (150 bp):
GTTTGAGGTGTCTTCAAAGTTGCATCTGACCCACTCATTCTTAAACCCACGGGCCAGTCTCGAAC
TACATTCATGGAAACCCTTCTGCTTGGATTTCCTTTTCTACCCTCTTGCGCCTTACATTCTTCAC
AGGAATCCTCCGTTGAAGAA
Found at i:935350 original size:2 final size:2
Alignment explanation
Indices: 935293--935331 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
935283 AATAATAATA
* * *
935293 AT AT AT AT CT TT AA AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
935332 AAGTTTTCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:935363 original size:24 final size:26
Alignment explanation
Indices: 935318--935367 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 26
935308 TATATATATA
935318 TATATATATATATAAAGTTTTCAAAAC
1 TATATATATATATAAAG-TTTCAAAAC
935345 TATATAT-TATATAAA-TTTCAAAA
1 TATATATATATATAAAGTTTCAAAA
935368 TGGTTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.35
26 8 0.35
27 7 0.30
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (26 bp):
TATATATATATATAAAGTTTCAAAAC
Found at i:935374 original size:36 final size:36
Alignment explanation
Indices: 935334--935450 Score: 141
Period size: 36 Copynumber: 3.3 Consensus size: 36
935324 TATATATAAA
*
935334 GTTTTCAAAACTATATATTATATAAATTTCAAAATG
1 GTTTTCAAAACTATATATTATATAATTTTCAAAATG
* *
935370 GTTTTAAAAACCATATATTATAT-ATTTTCAAAATG
1 GTTTTCAAAACTATATATTATATAATTTTCAAAATG
* * *
935405 ATTTTTAAAAATCATATATTATATATATTTTCAAAAT-
1 GTTTTCAAAACT-ATATATTATATA-ATTTTCAAAATG
935442 G-TTTCAAAA
1 GTTTTCAAAA
935451 TGTTTTTTAA
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
35 19 0.28
36 39 0.57
38 11 0.16
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (36 bp):
GTTTTCAAAACTATATATTATATAATTTTCAAAATG
Found at i:935387 original size:38 final size:37
Alignment explanation
Indices: 935335--935729 Score: 311
Period size: 38 Copynumber: 10.2 Consensus size: 37
935325 ATATATAAAG
* * *
935335 TTTTCAAAACTATATATTATATA-AATTTCAAAATGG
1 TTTTAAAAACTATATATTATATATATTTTCAAAATGT
*
935371 TTTTAAAAACCATATA-T-TATATATTTTCAAAATGAT
1 TTTTAAAAACTATATATTATATATATTTTCAAAATG-T
*
935407 TTTTAAAAATCATATATTATATATATTTTCAAAATGTTTCAAAATGTT
1 TTTTAAAAA-C-TATA-TAT-TATA---T--ATAT-TTTCAAAATG-T
935455 TTTTAAAAACTATATATTATATA-AGTTTTCAAAATGTT
1 TTTTAAAAACTATATATTATATATA-TTTTCAAAATG-T
* * * * *
935493 TTTTTAAAACTATATATTGTATATGTTTTCAGAATAT
1 TTTTAAAAACTATATATTATATATATTTTCAAAATGT
* * *
935530 TTTTAAAAAATCATATATTATATATGTTTTCAAAATAT
1 TTTTAAAAACT-ATATATTATATATATTTTCAAAATGT
* *
935568 TTTTAAAAAACCATATATTATATATATTTTTAAAATGT
1 TTTT-AAAAACTATATATTATATATATTTTCAAAATGT
* * *
935606 TTTCAAAAAACTATATAATATATATACATTTTCAAAAAAACCG-
1 TTT-TAAAAACTATAT-AT-TATATATATTTTC---AAAA-TGT
*
935649 TTTTCAAAACTATATATTATATATATTTTCAAAA--T
1 TTTTAAAAACTATATATTATATATATTTTCAAAATGT
* * * *
935684 TTTTCAAAACTATATAATATATACA-TTTCAAAAATGA
1 TTTTAAAAACTATATATTATATATATTTTC-AAAATGT
935721 TTTTAAAAA
1 TTTTAAAAA
935730 AAACAAAAAC
Statistics
Matches: 297, Mismatches: 33, Indels: 57
0.77 0.09 0.15
Matches are distributed among these distances:
34 8 0.03
35 39 0.13
36 23 0.08
37 23 0.08
38 110 0.37
39 11 0.04
40 23 0.08
41 4 0.01
42 12 0.04
43 7 0.02
44 5 0.02
45 4 0.01
46 4 0.01
47 4 0.01
48 20 0.07
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.45
Consensus pattern (37 bp):
TTTTAAAAACTATATATTATATATATTTTCAAAATGT
Found at i:935447 original size:48 final size:48
Alignment explanation
Indices: 935395--935493 Score: 157
Period size: 48 Copynumber: 2.1 Consensus size: 48
935385 TATTATATAT
935395 TTTCAAAATGATTTTTAAAAA-TCATATATTATATATA-TTTTCAAAATG
1 TTTCAAAATGATTTTTAAAAACT-ATATATTATATA-AGTTTTCAAAATG
*
935443 TTTCAAAATGTTTTTTAAAAACTATATATTATATAAGTTTTCAAAATG
1 TTTCAAAATGATTTTTAAAAACTATATATTATATAAGTTTTCAAAATG
935491 TTT
1 TTT
935494 TTTTAAAACT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
47 1 0.02
48 46 0.96
49 1 0.02
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.47
Consensus pattern (48 bp):
TTTCAAAATGATTTTTAAAAACTATATATTATATAAGTTTTCAAAATG
Found at i:935664 original size:42 final size:39
Alignment explanation
Indices: 935574--935717 Score: 126
Period size: 35 Copynumber: 3.8 Consensus size: 39
935564 ATATTTTTAA
* * * *
935574 AAAACCATATAT-TATATATATTTT--TAAAATGTTTTC
1 AAAACTATATATATATATACATTTTCAAAAAAAGTTTTC
935610 AAAAAACTATATAATATATATACATTTTCAAAAAAACCGTTTTC
1 --AAAACTATAT-ATATATATACATTTTCAAAAAAA--GTTTTC
* *
935654 AAAACTATATAT-TATATATATTTTC---AAAATTTTTC
1 AAAACTATATATATATATACATTTTCAAAAAAAGTTTTC
935689 AAAACTATATA-ATATATACA-TTTCAAAAA
1 AAAACTATATATATATATACATTTTCAAAAA
935718 TGATTTTAAA
Statistics
Matches: 89, Mismatches: 7, Indels: 21
0.76 0.06 0.18
Matches are distributed among these distances:
34 4 0.04
35 23 0.26
37 6 0.07
38 9 0.10
39 2 0.02
40 23 0.26
41 2 0.02
42 14 0.16
44 6 0.07
ACGTcount: A:0.48, C:0.10, G:0.01, T:0.40
Consensus pattern (39 bp):
AAAACTATATATATATATACATTTTCAAAAAAAGTTTTC
Found at i:936219 original size:15 final size:16
Alignment explanation
Indices: 936199--936228 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
936189 AATTCTCTAG
936199 TTCTCCT-CTTTCTTC
1 TTCTCCTCCTTTCTTC
936214 TTCTCCTCCTTTCTT
1 TTCTCCTCCTTTCTT
936229 TCTATTTTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (16 bp):
TTCTCCTCCTTTCTTC
Found at i:939408 original size:25 final size:26
Alignment explanation
Indices: 939380--939434 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
939370 AGTAATAATC
*
939380 ATAATATTACTT-TTAAATAAAAACA
1 ATAATATCACTTCTTAAATAAAAACA
*
939405 AT-A-ATCCCTTGCTTAAATAAAAACA
1 ATAATATCACTT-CTTAAATAAAAACA
939430 ATAAT
1 ATAAT
939435 TTATCGTGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
23 5 0.21
24 1 0.04
25 17 0.71
26 1 0.04
ACGTcount: A:0.53, C:0.13, G:0.02, T:0.33
Consensus pattern (26 bp):
ATAATATCACTTCTTAAATAAAAACA
Found at i:942578 original size:31 final size:31
Alignment explanation
Indices: 942543--942606 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
942533 CAATACAGTA
*
942543 CCCCAACATTTAGTGC-GTTTGCAAAATGGTC
1 CCCCAACATTTAGT-CTATTTGCAAAATGGTC
*
942574 CCCCAACATTTAGTCTATTTGCAATATGGTC
1 CCCCAACATTTAGTCTATTTGCAAAATGGTC
942605 CC
1 CC
942607 GACCGTTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 1 0.03
31 29 0.97
ACGTcount: A:0.25, C:0.28, G:0.16, T:0.31
Consensus pattern (31 bp):
CCCCAACATTTAGTCTATTTGCAAAATGGTC
Found at i:944593 original size:31 final size:31
Alignment explanation
Indices: 944551--944610 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
944541 AACGGTCGAG
944551 GACCATATTGCAAACAAACTAAATGTTGGGA
1 GACCATATTGCAAACAAACTAAATGTTGGGA
* **
944582 GACCATTTTGCAAACGGACTAAATGTTGG
1 GACCATATTGCAAACAAACTAAATGTTGG
944611 AGGACTATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.25
Consensus pattern (31 bp):
GACCATATTGCAAACAAACTAAATGTTGGGA
Found at i:946200 original size:35 final size:36
Alignment explanation
Indices: 946154--946233 Score: 119
Period size: 36 Copynumber: 2.2 Consensus size: 36
946144 TCCATTCTAG
946154 TTGAATCGAAAGTG-CGATGCCTCCTTCT-GTTCGAC
1 TTGAATCGAAAGTGCCGATG-CTCCTTCTCGTTCGAC
* *
946189 TTGAATCGAAAGTGCCGATGCTTCTTTTCGTTCGAC
1 TTGAATCGAAAGTGCCGATGCTCCTTCTCGTTCGAC
946225 TTGAATCGA
1 TTGAATCGA
946234 TGCAAACTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
35 20 0.49
36 21 0.51
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.34
Consensus pattern (36 bp):
TTGAATCGAAAGTGCCGATGCTCCTTCTCGTTCGAC
Found at i:946637 original size:13 final size:13
Alignment explanation
Indices: 946603--946648 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
946593 TAAATCTATA
946603 ACGCGCATTTATG
1 ACGCGCATTTATG
*
946616 A--CACATTTATG
1 ACGCGCATTTATG
*
946627 ACGCTCATTTATG
1 ACGCGCATTTATG
946640 ACGCGCATT
1 ACGCGCATT
946649 GCGCGTCATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
11 10 0.36
13 18 0.64
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (13 bp):
ACGCGCATTTATG
Found at i:946763 original size:85 final size:85
Alignment explanation
Indices: 946620--946783 Score: 247
Period size: 85 Copynumber: 1.9 Consensus size: 85
946610 TTTATGACAC
* * * *
946620 ATTTATGACGCTCATTTATGACGCGCATTGCGCGTCATTGAAGCCCCCGTCACAAATGAAGATGA
1 ATTTATGACACGCATTTATGACGCACATTGCGCGTCATTGAAGCCCCCGTCACAAATGAAGACGA
*
946685 CACACATTTGTGTGCCATAA
66 CACACATTCGTGTGCCATAA
** * *
946705 ATTTATGACACGCATTTATGACTTACATTGCGTGTCATTGAAGCCCCCGTCATAAATGAAGACGA
1 ATTTATGACACGCATTTATGACGCACATTGCGCGTCATTGAAGCCCCCGTCACAAATGAAGACGA
946770 CACACATTCGTGTG
66 CACACATTCGTGTG
946784 TCGTGATTGT
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
85 70 1.00
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.28
Consensus pattern (85 bp):
ATTTATGACACGCATTTATGACGCACATTGCGCGTCATTGAAGCCCCCGTCACAAATGAAGACGA
CACACATTCGTGTGCCATAA
Found at i:948656 original size:36 final size:36
Alignment explanation
Indices: 948611--948702 Score: 148
Period size: 36 Copynumber: 2.6 Consensus size: 36
948601 GAAGAAAAGA
* *
948611 GTAATTTAGTGCAAAGATTACTGAAAGAAATTAAGT
1 GTAACTTAGTGCAAAGATTACAGAAAGAAATTAAGT
*
948647 GTAACTTAGTGCAAAGGTTACAGAAAGAAATTAAGT
1 GTAACTTAGTGCAAAGATTACAGAAAGAAATTAAGT
*
948683 GGAACTTAGTGCAAAGATTA
1 GTAACTTAGTGCAAAGATTA
948703 GTGCAATATA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.43, C:0.08, G:0.22, T:0.27
Consensus pattern (36 bp):
GTAACTTAGTGCAAAGATTACAGAAAGAAATTAAGT
Found at i:953336 original size:19 final size:20
Alignment explanation
Indices: 953306--953344 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
953296 TTCCCCTTTA
*
953306 AAGGGGGAATCGGTTCCCTC
1 AAGGGGGAATCGATTCCCTC
953326 AAGGGGG-ATCGATTCCCTC
1 AAGGGGGAATCGATTCCCTC
953345 TGCACCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.21, C:0.26, G:0.33, T:0.21
Consensus pattern (20 bp):
AAGGGGGAATCGATTCCCTC
Found at i:953601 original size:4 final size:4
Alignment explanation
Indices: 953592--953617 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
953582 AATGTTAAAA
953592 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
953618 TAAACACCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:958846 original size:20 final size:20
Alignment explanation
Indices: 958798--958849 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
958788 AGCGTGGGGA
*
958798 GAATCGGTACCCCCTATGAG
1 GAATCGGTTCCCCCTATGAG
*
958818 GAATCGGTTCCCCCTATGGG
1 GAATCGGTTCCCCCTATGAG
958838 GAATCGGTTCCC
1 GAATCGGTTCCC
958850 TAAGTGTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.19, C:0.31, G:0.27, T:0.23
Consensus pattern (20 bp):
GAATCGGTTCCCCCTATGAG
Found at i:961533 original size:20 final size:20
Alignment explanation
Indices: 961508--961552 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
961498 ACTCAACCTC
*
961508 ACAACTAACGGTAACCTCTA
1 ACAACTAAAGGTAACCTCTA
*
961528 ACAACTAAATGTAACCTCTA
1 ACAACTAAAGGTAACCTCTA
961548 ACAAC
1 ACAAC
961553 AATCATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.44, C:0.29, G:0.07, T:0.20
Consensus pattern (20 bp):
ACAACTAAAGGTAACCTCTA
Found at i:962911 original size:3 final size:3
Alignment explanation
Indices: 962903--962935 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
962893 ATTATTTATA
962903 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
962936 GAAAAACTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:963787 original size:3 final size:3
Alignment explanation
Indices: 963779--963877 Score: 144
Period size: 3 Copynumber: 33.0 Consensus size: 3
963769 ATTAATTTAT
* * *
963779 TTA TTA TTA TTA TAA TTA TAA TTA TTA TTA TTA TTA TTA TTA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
963827 TTA CTA TTA TTA TTA TTA TTA TTA TTA TAA ATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
963875 TTA
1 TTA
963878 AATAAATATA
Statistics
Matches: 84, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 84 1.00
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:963890 original size:2 final size:2
Alignment explanation
Indices: 963883--963907 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
963873 TATTAAATAA
963883 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
963908 AAATAATAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:964023 original size:16 final size:16
Alignment explanation
Indices: 964000--964040 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
963990 TTCTAACCCT
964000 AGCCGCCTCTGCCTCCC
1 AGCCGCCTCTGCCT-CC
964017 A-CCGCCTCTGCCTCC
1 AGCCGCCTCTGCCTCC
964032 AGCCGCCTC
1 AGCCGCCTC
964041 AATGGTTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.13
16 19 0.83
17 1 0.04
ACGTcount: A:0.07, C:0.59, G:0.17, T:0.17
Consensus pattern (16 bp):
AGCCGCCTCTGCCTCC
Found at i:964278 original size:13 final size:13
Alignment explanation
Indices: 964260--964284 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
964250 AAACGGGGAC
964260 AGAGACAGAAAAG
1 AGAGACAGAAAAG
964273 AGAGACAGAAAA
1 AGAGACAGAAAA
964285 TACACAGAGA
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:0.64, C:0.08, G:0.28, T:0.00
Consensus pattern (13 bp):
AGAGACAGAAAAG
Found at i:964293 original size:19 final size:19
Alignment explanation
Indices: 964271--964307 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
964261 GAGACAGAAA
964271 AGAGAGACAGA-AAATACAC
1 AGAGAGA-AGAGAAATACAC
964290 AGAGAGAAGAGAAATACA
1 AGAGAGAAGAGAAATACA
964308 GAGAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.59, C:0.11, G:0.24, T:0.05
Consensus pattern (19 bp):
AGAGAGAAGAGAAATACAC
Found at i:965272 original size:21 final size:22
Alignment explanation
Indices: 965246--965295 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
965236 ATAGTTATAA
965246 ATATATATAAT-AATTATTTAT
1 ATATATATAATAAATTATTTAT
* *
965267 ATATATTTAATAAATTATTTTT
1 ATATATATAATAAATTATTTAT
965289 ATA-ATAT
1 ATATATAT
965296 TGAAGAAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
ATATATATAATAAATTATTTAT
Found at i:965474 original size:15 final size:16
Alignment explanation
Indices: 965451--965497 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
965441 TATTTTAAAT
965451 AAATAAATATATTTTA
1 AAATAAATATATTTTA
*
965467 AAAT-AATATGATTATA
1 AAATAAATAT-ATTTTA
*
965483 AATTAAATATATTTT
1 AAATAAATATATTTT
965498 TGAATTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 5 0.19
16 16 0.62
17 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (16 bp):
AAATAAATATATTTTA
Found at i:967221 original size:31 final size:30
Alignment explanation
Indices: 967175--967247 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 30
967165 TTTAAGCACT
*
967175 TAAAGTA-ATTTTTGGTCAAAATAAGTACC
1 TAAAGTATCTTTTTGGTCAAAATAAGTACC
* *
967204 TAAAATTATCTTTTTGGTCAAAATAGGTACC
1 T-AAAGTATCTTTTTGGTCAAAATAAGTACC
967235 TAAAGTATCTTTT
1 TAAAGTATCTTTT
967248 GGTAATACTA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 1 0.03
30 16 0.42
31 21 0.55
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.40
Consensus pattern (30 bp):
TAAAGTATCTTTTTGGTCAAAATAAGTACC
Found at i:967259 original size:29 final size:30
Alignment explanation
Indices: 967175--967271 Score: 110
Period size: 29 Copynumber: 3.3 Consensus size: 30
967165 TTTAAGCACT
* *
967175 TAAAGTA-ATTTTTGGTCAAAATAAGTACC
1 TAAAGTATCTTTTTGGTCAAAATAGGTACC
*
967204 TAAAATTATCTTTTTGGTCAAAATAGGTACC
1 T-AAAGTATCTTTTTGGTCAAAATAGGTACC
* *
967235 TAAAGTATC-TTTTGGT-AATACTAGGCACC
1 TAAAGTATCTTTTTGGTCAA-AATAGGTACC
967264 TAAAGTAT
1 TAAAGTAT
967272 TCAATTTATT
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
28 2 0.03
29 24 0.41
30 12 0.20
31 21 0.36
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36
Consensus pattern (30 bp):
TAAAGTATCTTTTTGGTCAAAATAGGTACC
Found at i:970262 original size:25 final size:25
Alignment explanation
Indices: 970233--970322 Score: 117
Period size: 25 Copynumber: 3.6 Consensus size: 25
970223 CCTTGTAGAT
* * * *
970233 CTCGTAGTAGTGCACTCGAAAGTGC
1 CTCGTAGGATTGCACTCAAAAATGC
*
970258 CTCGTAGGATTGCACTAAAAAATGC
1 CTCGTAGGATTGCACTCAAAAATGC
*
970283 TTCGTAGGATTGCACTCAAAAATGC
1 CTCGTAGGATTGCACTCAAAAATGC
*
970308 CTCGTAGGGTTGCAC
1 CTCGTAGGATTGCAC
970323 CATAGGTGCC
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 56 1.00
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (25 bp):
CTCGTAGGATTGCACTCAAAAATGC
Found at i:971325 original size:31 final size:31
Alignment explanation
Indices: 971287--971366 Score: 94
Period size: 30 Copynumber: 2.6 Consensus size: 31
971277 TCCAAAATTT
971287 AACTTTTAAAATTTTATATTTTTAGTC-CTTA
1 AACTTTTAAAATTTTATATTTTTAGTCTC-TA
* * *
971318 AACTTTTACAATTTTACA-CTTTAGTCTCTA
1 AACTTTTAAAATTTTATATTTTTAGTCTCTA
*
971348 AACTTTCAAAA-TTTATATT
1 AACTTTTAAAATTTTATATT
971367 CCAGTCACCA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
29 5 0.12
30 18 0.45
31 17 0.43
ACGTcount: A:0.34, C:0.14, G:0.03, T:0.50
Consensus pattern (31 bp):
AACTTTTAAAATTTTATATTTTTAGTCTCTA
Found at i:976857 original size:25 final size:25
Alignment explanation
Indices: 976828--976885 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
976818 CCTCGTAGAT
* *
976828 CTCGTAGTAGTGCAATCGAATGTGC
1 CTCGTAGGAGTGCAATCGAAAGTGC
* *
976853 CTCGTAGGATTGCACTCGAAAGTGC
1 CTCGTAGGAGTGCAATCGAAAGTGC
*
976878 CTCATAGG
1 CTCGTAGG
976886 GTTGCACCAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (25 bp):
CTCGTAGGAGTGCAATCGAAAGTGC
Found at i:976890 original size:25 final size:25
Alignment explanation
Indices: 976838--976892 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
976828 CTCGTAGTAG
* * *
976838 TGCAATCGAATGTGCCTCGTAGGAT
1 TGCACTCGAAAGTGCCTCATAGGAT
*
976863 TGCACTCGAAAGTGCCTCATAGGGT
1 TGCACTCGAAAGTGCCTCATAGGAT
976888 TGCAC
1 TGCAC
976893 CATAGGTGCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (25 bp):
TGCACTCGAAAGTGCCTCATAGGAT
Found at i:977895 original size:31 final size:31
Alignment explanation
Indices: 977857--977936 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
977847 TCTAAAATTT
*
977857 AACTTTTAAAATTTTACATTTTTAGTC-CTTA
1 AACTTTTAAAATTTTACATTTTTAGTCTC-CA
* *
977888 AACTTTTACAATTTTACA-CTTTAGTCTCCA
1 AACTTTTAAAATTTTACATTTTTAGTCTCCA
*
977918 AACTTTCAAAA-TTTACATT
1 AACTTTTAAAATTTTACATT
977937 CCAATCACCA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
29 6 0.15
30 17 0.41
31 18 0.44
ACGTcount: A:0.34, C:0.17, G:0.03, T:0.46
Consensus pattern (31 bp):
AACTTTTAAAATTTTACATTTTTAGTCTCCA
Found at i:985646 original size:63 final size:63
Alignment explanation
Indices: 985572--985693 Score: 151
Period size: 63 Copynumber: 1.9 Consensus size: 63
985562 CACTACTTTA
985572 AAATAAAAACATCAAAT-GCCA-TCAGTGTATCGATGCACAAG-TAGTGCATCGATGCACCCCCT
1 AAATAAAAACATCAAATAG-CATTCA-TGTATCGATGCA-AAGATAGTGCATCGATGCACCCCCT
985634 T
63 T
* * * * *
985635 AAATACAAACATCGAATAGGATTTATGTATCGATGCATAGATAGTGCATCGATGCACCC
1 AAATAAAAACATCAAATAGCATTCATGTATCGATGCAAAGATAGTGCATCGATGCACCC
985694 GTCAAAGGAT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
62 2 0.04
63 46 0.90
64 3 0.06
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (63 bp):
AAATAAAAACATCAAATAGCATTCATGTATCGATGCAAAGATAGTGCATCGATGCACCCCCTT
Found at i:986403 original size:23 final size:23
Alignment explanation
Indices: 986337--986395 Score: 109
Period size: 23 Copynumber: 2.6 Consensus size: 23
986327 ATCTTATATA
*
986337 GCACTACGGTGCAATTCTACGTG
1 GCACTTCGGTGCAATTCTACGTG
986360 GCACTTCGGTGCAATTCTACGTG
1 GCACTTCGGTGCAATTCTACGTG
986383 GCACTTCGGTGCA
1 GCACTTCGGTGCA
986396 TTTATACGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GCACTTCGGTGCAATTCTACGTG
Found at i:993308 original size:23 final size:23
Alignment explanation
Indices: 993272--993331 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
993262 AATCTTATAT
* * *
993272 GGCACTACGATGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACAC
*
993295 GGCACTTCGGTGCAATTCTACAT
1 GGCACTTCGGTGCAATTCTACAC
993318 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
993332 TTTATACAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.25
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACAC
Found at i:993339 original size:23 final size:23
Alignment explanation
Indices: 993270--993339 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
993260 ATAATCTTAT
* * *
993270 ATGGCACTACGATGCAATTCTAC
1 ATGGCACTTCGGTGCAATTATAC
** *
993293 GCGGCACTTCGGTGCAATTCTAC
1 ATGGCACTTCGGTGCAATTATAC
*
993316 ATGGCACTTCGGTGCATTTATAC
1 ATGGCACTTCGGTGCAATTATAC
993339 A
1 A
993340 AGCTGTTGTG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (23 bp):
ATGGCACTTCGGTGCAATTATAC
Found at i:997268 original size:17 final size:17
Alignment explanation
Indices: 997236--997290 Score: 80
Period size: 17 Copynumber: 3.4 Consensus size: 17
997226 AAAGAAAGAA
997236 AATA-AATAAA-ATAAT
1 AATATAATAAATATAAT
997251 AA-ATAATAAATCATAAT
1 AATATAATAAAT-ATAAT
997268 AATATAATAAATATAAT
1 AATATAATAAATATAAT
997285 AATATA
1 AATATA
997291 CTATACTATA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
14 1 0.03
15 8 0.22
17 18 0.50
18 9 0.25
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (17 bp):
AATATAATAAATATAAT
Found at i:997318 original size:17 final size:19
Alignment explanation
Indices: 997236--997290 Score: 69
Period size: 18 Copynumber: 2.9 Consensus size: 19
997226 AAAGAAAGAA
* *
997236 AATAAATAAAATAATAAAT
1 AATAAATATAATAATATAT
997255 AATAAATCATAAT-A-ATAT
1 AATAAAT-ATAATAATATAT
997273 AATAAATATAATAATATA
1 AATAAATATAATAATATA
997291 CTATACTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
17 5 0.16
18 11 0.35
19 11 0.35
20 4 0.13
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
AATAAATATAATAATATAT
Found at i:997361 original size:39 final size:39
Alignment explanation
Indices: 997313--997592 Score: 322
Period size: 39 Copynumber: 7.1 Consensus size: 39
997303 ATATACATAT
* *
997313 AAATATTTTCAAAAACTATATATTATATATATGTTTTGA
1 AAATGTTTTCAAAAACTATATATTATATATATGTTTTCA
* *
997352 AAATGTTTTCAAAAACTATATACTATATGTA--TTTTCA
1 AAATGTTTTCAAAAACTATATATTATATATATGTTTTCA
*
997389 AAATGTTTTTAAAAACTAATATATTATATATATGTTTTCA
1 AAATGTTTTCAAAAACT-ATATATTATATATATGTTTTCA
* * *
997429 AAATGTTTTCAAAAACTATATTTTATAAATATGTTTACA
1 AAATGTTTTCAAAAACTATATATTATATATATGTTTTCA
* *
997468 AAATGTTTACAAAAACTATATTATATATATATATATATATAT-A
1 AAATGTTTTCAAAAACTATA-TAT-TATATATATGT-T-T-TCA
997511 TATATATGTGTTTTCAAAAACTATATA-T-TATATATGTTTTCA
1 -A-A-A--TGTTTTCAAAAACTATATATTATATATATGTTTTCA
997553 AAATGTTTTCAAAAACTATATATTATATATA--TTTTCA
1 AAATGTTTTCAAAAACTATATATTATATATATGTTTTCA
997590 AAA
1 AAA
997593 ATATTTATAT
Statistics
Matches: 207, Mismatches: 18, Indels: 34
0.80 0.07 0.13
Matches are distributed among these distances:
37 49 0.24
38 13 0.06
39 73 0.35
40 25 0.12
41 11 0.05
42 3 0.01
43 3 0.01
44 9 0.04
45 2 0.01
46 1 0.00
47 2 0.01
48 16 0.08
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.45
Consensus pattern (39 bp):
AAATGTTTTCAAAAACTATATATTATATATATGTTTTCA
Found at i:997496 original size:2 final size:2
Alignment explanation
Indices: 997484--997517 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
997474 TTACAAAAAC
997484 TA TA T- 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 TA TA T
997518 GTGTTTTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:997548 original size:26 final size:27
Alignment explanation
Indices: 997505--997555 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
997495 TATATATATA
*
997505 TATATATATATATGTGTTTTCAAAAAC
1 TATATATATATATATGTTTTCAAAAAC
997532 TATATAT-TATATATGTTTTCAAAA
1 TATATATATATATATGTTTTCAAAA
997556 TGTTTTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (27 bp):
TATATATATATATATGTTTTCAAAAAC
Found at i:997602 original size:87 final size:86
Alignment explanation
Indices: 997432--997604 Score: 233
Period size: 85 Copynumber: 2.0 Consensus size: 86
997422 GTTTTCAAAA
*
997432 TGTTTTCAAAAACTATATTTTATAAATATGTTTACAAAATGTTTACAAAAACTATATTATATATA
1 TGTTTTCAAAAACTATATATTAT-AATATGTTTACAAAATGTTTACAAAAACTATATTATATATA
* *
997497 TATATATATATATATATATATG
65 TATATAAAAATATATATATATG
* *
997519 TGTTTTCAAAAACTATATATTAT-ATATGTTTTCAAAATGTTTTCAAAAACTATA-TATTATATA
1 TGTTTTCAAAAACTATATATTATAATATGTTTACAAAATGTTTACAAAAACTATATTA-TATATA
* *
997582 TATTTTCAAAAATATTTATATAT
65 TA-TAT-AAAAATATATATATAT
997605 ATATATATAT
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
84 2 0.03
85 37 0.49
86 2 0.03
87 35 0.46
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.46
Consensus pattern (86 bp):
TGTTTTCAAAAACTATATATTATAATATGTTTACAAAATGTTTACAAAAACTATATTATATATAT
ATATAAAAATATATATATATG
Found at i:997608 original size:24 final size:26
Alignment explanation
Indices: 997558--997610 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
997548 TTTCAAAATG
997558 TTTTCAAAAACTATATATTATATATA
1 TTTTCAAAAACTATATATTATATATA
*
997584 TTTTCAAAAA-TATTTATATATATATA
1 TTTTCAAAAACTATATAT-TATATATA
997610 T
1 T
997611 ATATTAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (26 bp):
TTTTCAAAAACTATATATTATATATA
Found at i:997616 original size:39 final size:37
Alignment explanation
Indices: 997521--997598 Score: 129
Period size: 37 Copynumber: 2.1 Consensus size: 37
997511 TATATATGTG
* *
997521 TTTTCAAAAACTATATATTATATATGTTTTCAAAATG
1 TTTTCAAAAACTATATATTATATATATTTTCAAAATA
997558 TTTTCAAAAACTATATATTATATATATTTTCAAAAATA
1 TTTTCAAAAACTATATATTATATATATTTTC-AAAATA
997596 TTT
1 TTT
997599 ATATATATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
37 30 0.79
38 8 0.21
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (37 bp):
TTTTCAAAAACTATATATTATATATATTTTCAAAATA
Found at i:998638 original size:12 final size:13
Alignment explanation
Indices: 998613--998642 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
998603 TCTCTTCCCC
998613 TTCTCCATCCTTT
1 TTCTCCATCCTTT
998626 TTCTCCA-CCTTT
1 TTCTCCATCCTTT
998638 TTCTC
1 TTCTC
998643 GGTCGTTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.07, C:0.40, G:0.00, T:0.53
Consensus pattern (13 bp):
TTCTCCATCCTTT
Found at i:999721 original size:182 final size:183
Alignment explanation
Indices: 999431--999798 Score: 602
Period size: 182 Copynumber: 2.0 Consensus size: 183
999421 AAATTAAATG
* *
999431 TTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAATTATAAAATAAATATTTCAG
1 TTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAG
999496 ATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAATT
66 ATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAATT
* *
999561 -GAGTTTTAAATTGTTTGGGCTTAGCCCAAATGTTATATATAATATATATAATA
131 GGA-TTTTAAATGGTTTGGGCTGAGCCCAAATGTTATATATAATATATATAATA
999614 TTTTTAATT-AAAAAACAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAAATTT-
1 TTTTTAATTCAAAAAA-AGTTTACAATTAATTTAAATAATATATAATTATAAAAT-AAAAATTTC
*
999677 ATAT-AATTTTTTAATTAATTAATATTGATTTATG-TTTAAAAGTTATTGGATCTTAAATTATTA
64 AGATAAATTTTTTAATTAATTAATATTGATTTA-GATTTAAAAGTTATTGGATCTTAAATTATTA
* *
999740 ATTGGATTTTAAATGGTTTGGGCTGAGCCCATATGTTATATATAATATATTTAATA
128 ATTGGATTTTAAATGGTTTGGGCTGAGCCCAAATGTTATATATAATATATATAATA
999796 TTT
1 TTT
999799 AAAATTTAAT
Statistics
Matches: 174, Mismatches: 7, Indels: 9
0.92 0.04 0.05
Matches are distributed among these distances:
182 115 0.66
183 52 0.30
184 7 0.04
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (183 bp):
TTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAG
ATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAATT
GGATTTTAAATGGTTTGGGCTGAGCCCAAATGTTATATATAATATATATAATA
Found at i:1002145 original size:20 final size:21
Alignment explanation
Indices: 1002120--1002166 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
1002110 GGTTGTGACA
1002120 ATTTCTAGCCA-TTGGGGATG
1 ATTTCTAGCCATTTGGGGATG
*
1002140 ATTTCTAGCTATTTGGGGATG
1 ATTTCTAGCCATTTGGGGATG
*
1002161 TTTTCT
1 ATTTCT
1002167 CTACAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.17, C:0.13, G:0.26, T:0.45
Consensus pattern (21 bp):
ATTTCTAGCCATTTGGGGATG
Found at i:1003865 original size:18 final size:18
Alignment explanation
Indices: 1003842--1003895 Score: 99
Period size: 18 Copynumber: 3.0 Consensus size: 18
1003832 ACTGAATATT
1003842 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
1003860 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
1003878 TGTCCCGAAGAACCACTA
1 TGTCCCGAAGGACCACTA
1003896 ATAATCCCTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.30, C:0.33, G:0.20, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1010242 original size:24 final size:24
Alignment explanation
Indices: 1010215--1010330 Score: 155
Period size: 24 Copynumber: 4.8 Consensus size: 24
1010205 TTCGATTTGA
1010215 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
1010239 ATTCTGATCTGATA-TCTGACATAG
1 ATTCTGATCTGATACT-TGACATGG
* *
1010263 ATTCTGATCTGATATTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
1010287 ATTCTGATCTGATACTTGATC-TGG
1 ATTCTGATCTGATACTTGA-CATGG
* *
1010311 ATTTTGATATGATACTTGAC
1 ATTCTGATCTGATACTTGAC
1010331 CTGATTTATG
Statistics
Matches: 83, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
23 2 0.02
24 79 0.95
25 2 0.02
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:1010251 original size:48 final size:48
Alignment explanation
Indices: 1010197--1010330 Score: 130
Period size: 48 Copynumber: 2.8 Consensus size: 48
1010187 TGAATATTTT
*
1010197 ATCTGATTTTCGATTTGAATTCTGATCTGATACTTGACATGGATTCTG
1 ATCTGATTTTCGATATGAATTCTGATCTGATACTTGACATGGATTCTG
* * * *
1010245 ATCTGA-TATCTGACAT-AGATTCTGATCTGATATTTGACTTGGATTCTG
1 ATCTGATTTTC-GATATGA-ATTCTGATCTGATACTTGACATGGATTCTG
* * * * *
1010293 ATCTGATACTT-GATCTGGATTTTGATATGATACTTGAC
1 ATCTGAT-TTTCGATATGAATTCTGATCTGATACTTGAC
1010331 CTGATTTATG
Statistics
Matches: 68, Mismatches: 13, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
47 4 0.06
48 63 0.93
50 1 0.01
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.43
Consensus pattern (48 bp):
ATCTGATTTTCGATATGAATTCTGATCTGATACTTGACATGGATTCTG
Found at i:1012440 original size:13 final size:13
Alignment explanation
Indices: 1012411--1012453 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
1012401 GGTCACAACC
1012411 TGACCCGACCC--
1 TGACCCGACCCGT
1012422 -GACCCGACCCGT
1 TGACCCGACCCGT
1012434 TGACCCGACCCGT
1 TGACCCGACCCGT
1012447 TGACCCG
1 TGACCCG
1012454 TTGACCGGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.34
13 19 0.66
ACGTcount: A:0.16, C:0.49, G:0.23, T:0.12
Consensus pattern (13 bp):
TGACCCGACCCGT
Found at i:1014909 original size:24 final size:24
Alignment explanation
Indices: 1014882--1014997 Score: 155
Period size: 24 Copynumber: 4.8 Consensus size: 24
1014872 TTCGATTTGA
1014882 ATTCTGATATGATACTTGACATGG
1 ATTCTGATATGATACTTGACATGG
*
1014906 ATTCTGATATGATA-TCTGACATAG
1 ATTCTGATATGATACT-TGACATGG
* *
1014930 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATATGATACTTGACATGG
*
1014954 ATTCTGATCTGATACTTGATC-TGG
1 ATTCTGATATGATACTTGA-CATGG
*
1014978 ATTTTGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
1014998 CTGATTTATG
Statistics
Matches: 83, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
23 2 0.02
24 79 0.95
25 2 0.02
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.41
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:1014975 original size:12 final size:12
Alignment explanation
Indices: 1014934--1015002 Score: 54
Period size: 12 Copynumber: 5.8 Consensus size: 12
1014924 ACATAGATTC
1014934 TGATCTGATACT
1 TGATCTGATACT
*
1014946 TGA-CTTGGATTC-
1 TGATC-T-GATACT
1014958 TGATCTGATACT
1 TGATCTGATACT
*
1014970 TGATCTGGAT-TT
1 TGATCT-GATACT
*
1014982 TGATATGATACT
1 TGATCTGATACT
*
1014994 TGACCTGAT
1 TGATCTGAT
1015003 TTATGTTTTG
Statistics
Matches: 44, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
11 8 0.18
12 28 0.64
13 8 0.18
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.42
Consensus pattern (12 bp):
TGATCTGATACT
Found at i:1015062 original size:30 final size:30
Alignment explanation
Indices: 1015028--1015085 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
1015018 TGATATCTCC
*
1015028 GTTTGACTGGTTTTGGTGCATAGTTGACTG
1 GTTTGACCGGTTTTGGTGCATAGTTGACTG
1015058 GTTTGACCGGTTTTGGTGCATAGTTGAC
1 GTTTGACCGGTTTTGGTGCATAGTTGAC
1015086 CGGTCACAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.14, C:0.12, G:0.33, T:0.41
Consensus pattern (30 bp):
GTTTGACCGGTTTTGGTGCATAGTTGACTG
Found at i:1015116 original size:13 final size:13
Alignment explanation
Indices: 1015116--1015159 Score: 70
Period size: 13 Copynumber: 3.4 Consensus size: 13
1015106 CCGTTGACCC
*
1015116 GACCCAACCCGTT
1 GACCCGACCCGTT
*
1015129 TACCCGACCCGTT
1 GACCCGACCCGTT
1015142 GACCCGACCCGTT
1 GACCCGACCCGTT
1015155 GACCC
1 GACCC
1015160 ATTGACCGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.18, C:0.48, G:0.18, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1015152 original size:18 final size:18
Alignment explanation
Indices: 1015094--1015139 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
1015084 ACCGGTCACA
1015094 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
* *
1015112 ACCCGACCCAACCCGTTT
1 ACCCGACCCGACCCGTTG
1015130 ACCCGACCCG
1 ACCCGACCCG
1015140 TTGACCCGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.20, C:0.52, G:0.17, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:1015158 original size:21 final size:19
Alignment explanation
Indices: 1015134--1015186 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 19
1015124 CCGTTTACCC
1015134 GACCCGTTGACCCGACCCGTT
1 GACCCGTTGACCCGA--CGTT
*
1015155 GACCCATTGA-CCGACGTT
1 GACCCGTTGACCCGACGTT
1015173 GACCACTGTTGACC
1 GACC-C-GTTGACC
1015187 AAAACTTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
18 8 0.30
19 1 0.04
20 8 0.30
21 10 0.37
ACGTcount: A:0.19, C:0.38, G:0.23, T:0.21
Consensus pattern (19 bp):
GACCCGTTGACCCGACGTT
Found at i:1017397 original size:24 final size:24
Alignment explanation
Indices: 1017370--1017485 Score: 164
Period size: 24 Copynumber: 4.8 Consensus size: 24
1017360 TTCGATTTGA
1017370 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
1017394 ATTCTGATCTGATA-TCTGACATAG
1 ATTCTGATCTGATACT-TGACATGG
*
1017418 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
1017442 ATTCTGATCTGATACTTGATC-TGG
1 ATTCTGATCTGATACTTGA-CATGG
* *
1017466 ATTTTGATATGATACTTGAC
1 ATTCTGATCTGATACTTGAC
1017486 CTGATTTATG
Statistics
Matches: 84, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
23 2 0.02
24 80 0.95
25 2 0.02
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.41
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:1017406 original size:48 final size:48
Alignment explanation
Indices: 1017352--1017485 Score: 139
Period size: 48 Copynumber: 2.8 Consensus size: 48
1017342 TGAATATTTT
*
1017352 ATCTGATTTTCGATTTGAATTCTGATCTGATACTTGACATGGATTCTG
1 ATCTGATTTTCGATATGAATTCTGATCTGATACTTGACATGGATTCTG
* * *
1017400 ATCTGA-TATCTGACAT-AGATTCTGATCTGATACTTGACTTGGATTCTG
1 ATCTGATTTTC-GATATGA-ATTCTGATCTGATACTTGACATGGATTCTG
* * * * *
1017448 ATCTGATACTT-GATCTGGATTTTGATATGATACTTGAC
1 ATCTGAT-TTTCGATATGAATTCTGATCTGATACTTGAC
1017486 CTGATTTATG
Statistics
Matches: 70, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
47 4 0.06
48 65 0.93
50 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.42
Consensus pattern (48 bp):
ATCTGATTTTCGATATGAATTCTGATCTGATACTTGACATGGATTCTG
Found at i:1017463 original size:12 final size:12
Alignment explanation
Indices: 1017422--1017490 Score: 54
Period size: 12 Copynumber: 5.8 Consensus size: 12
1017412 ACATAGATTC
1017422 TGATCTGATACT
1 TGATCTGATACT
*
1017434 TGA-CTTGGATTC-
1 TGATC-T-GATACT
1017446 TGATCTGATACT
1 TGATCTGATACT
*
1017458 TGATCTGGAT-TT
1 TGATCT-GATACT
*
1017470 TGATATGATACT
1 TGATCTGATACT
*
1017482 TGACCTGAT
1 TGATCTGAT
1017491 TTATGTTTTG
Statistics
Matches: 44, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
11 8 0.18
12 28 0.64
13 8 0.18
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.42
Consensus pattern (12 bp):
TGATCTGATACT
Found at i:1019571 original size:18 final size:18
Alignment explanation
Indices: 1019548--1019582 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1019538 ACCGGTCACA
1019548 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1019566 ACCCGACCCGACCCGTT
1 ACCCGACCCGACCCGTT
1019583 TACGACCCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.51, G:0.20, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:1021879 original size:24 final size:24
Alignment explanation
Indices: 1021852--1021967 Score: 164
Period size: 24 Copynumber: 4.8 Consensus size: 24
1021842 TTCGATTTGA
1021852 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
1021876 ATTCTGATCTGATA-TCTGACATAG
1 ATTCTGATCTGATACT-TGACATGG
*
1021900 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
1021924 ATTCTGATCTGATACTTGATC-TGG
1 ATTCTGATCTGATACTTGA-CATGG
* *
1021948 ATTTTGATATGATACTTGAC
1 ATTCTGATCTGATACTTGAC
1021968 CTGATTTATG
Statistics
Matches: 84, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
23 2 0.02
24 80 0.95
25 2 0.02
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.41
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:1021888 original size:48 final size:48
Alignment explanation
Indices: 1021834--1021967 Score: 139
Period size: 48 Copynumber: 2.8 Consensus size: 48
1021824 TGAATATTTT
*
1021834 ATCTGATTTTCGATTTGAATTCTGATCTGATACTTGACATGGATTCTG
1 ATCTGATTTTCGATATGAATTCTGATCTGATACTTGACATGGATTCTG
* * *
1021882 ATCTGA-TATCTGACAT-AGATTCTGATCTGATACTTGACTTGGATTCTG
1 ATCTGATTTTC-GATATGA-ATTCTGATCTGATACTTGACATGGATTCTG
* * * * *
1021930 ATCTGATACTT-GATCTGGATTTTGATATGATACTTGAC
1 ATCTGAT-TTTCGATATGAATTCTGATCTGATACTTGAC
1021968 CTGATTTATG
Statistics
Matches: 70, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
47 4 0.06
48 65 0.93
50 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.42
Consensus pattern (48 bp):
ATCTGATTTTCGATATGAATTCTGATCTGATACTTGACATGGATTCTG
Found at i:1021945 original size:12 final size:12
Alignment explanation
Indices: 1021904--1021972 Score: 54
Period size: 12 Copynumber: 5.8 Consensus size: 12
1021894 ACATAGATTC
1021904 TGATCTGATACT
1 TGATCTGATACT
*
1021916 TGA-CTTGGATTC-
1 TGATC-T-GATACT
1021928 TGATCTGATACT
1 TGATCTGATACT
*
1021940 TGATCTGGAT-TT
1 TGATCT-GATACT
*
1021952 TGATATGATACT
1 TGATCTGATACT
*
1021964 TGACCTGAT
1 TGATCTGAT
1021973 TTATGTTTTG
Statistics
Matches: 44, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
11 8 0.18
12 28 0.64
13 8 0.18
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.42
Consensus pattern (12 bp):
TGATCTGATACT
Found at i:1024958 original size:18 final size:18
Alignment explanation
Indices: 1024935--1025042 Score: 198
Period size: 18 Copynumber: 6.0 Consensus size: 18
1024925 ACTGAATATT
1024935 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
1024953 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
1024971 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
1024989 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
1025007 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
1025025 TATCCCGAAGAACCACTA
1 TGTCCCGAAGGACCACTA
1025043 ATAATCCCTC
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 88 1.00
ACGTcount: A:0.30, C:0.33, G:0.20, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1032316 original size:21 final size:21
Alignment explanation
Indices: 1032283--1032322 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1032273 TCAGGACATG
*
1032283 GAGTATCAATACTCCTTTAAT
1 GAGTATCAATACTACTTTAAT
**
1032304 GAGTATCGGTACTACTTTA
1 GAGTATCAATACTACTTTA
1032323 TGATTTTTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (21 bp):
GAGTATCAATACTACTTTAAT
Found at i:1033473 original size:38 final size:37
Alignment explanation
Indices: 1033431--1033517 Score: 104
Period size: 38 Copynumber: 2.3 Consensus size: 37
1033421 TATTAAAAAT
1033431 AATTATTATATATATATAATATTAATAAATTTAAATTA
1 AATTA-TATATATATATAATATTAATAAATTTAAATTA
* * * * *
1033469 AATTAAAAAATATATATAATATTTATATATTTAATTTA
1 AATT-ATATATATATATAATATTAATAAATTTAAATTA
1033507 AA-TATATATAT
1 AATTATATATAT
1033518 CCGGCCCGAT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
36 6 0.15
37 1 0.02
38 33 0.80
39 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (37 bp):
AATTATATATATATATAATATTAATAAATTTAAATTA
Found at i:1034052 original size:4 final size:4
Alignment explanation
Indices: 1034043--1034336 Score: 498
Period size: 4 Copynumber: 73.0 Consensus size: 4
1034033 CAGGTACTTC
1034043 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1034091 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1034139 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1034187 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
1034235 CATA CATA CATA CATA CATA CATA CATA CATA CATA TATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * *
1034283 CATA TGCATA CATG CATG CATG CATG CATG CATA CATG CATG CATA CATA
1 CATA --CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1034333 CATA
1 CATA
1034337 TACTTGTTTG
Statistics
Matches: 282, Mismatches: 6, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
4 278 0.99
6 4 0.01
ACGTcount: A:0.47, C:0.24, G:0.03, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:1039404 original size:17 final size:17
Alignment explanation
Indices: 1039361--1039406 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
1039351 GCCCCAAGCC
*
1039361 CCAGACCCAAAACCCGA
1 CCAGACCCAAAACCCAA
1039378 CCAGGACCCAAAA-CCAA
1 CCA-GACCCAAAACCCAA
1039395 CCGAGACCCAAA
1 CC-AGACCCAAA
1039407 TTTAATACCC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 16 0.62
18 10 0.38
ACGTcount: A:0.43, C:0.43, G:0.13, T:0.00
Consensus pattern (17 bp):
CCAGACCCAAAACCCAA
Found at i:1041623 original size:20 final size:20
Alignment explanation
Indices: 1041589--1041629 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1041579 AGTCATTGTG
* *
1041589 TTTATGTTTTTTTTTTATTT
1 TTTATGTTGTGTTTTTATTT
*
1041609 TTTATGTTGTGTTTTTCTTT
1 TTTATGTTGTGTTTTTATTT
1041629 T
1 T
1041630 CTTTTTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.07, C:0.02, G:0.10, T:0.80
Consensus pattern (20 bp):
TTTATGTTGTGTTTTTATTT
Found at i:1053849 original size:18 final size:18
Alignment explanation
Indices: 1053826--1053873 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
1053816 TTCTGGTCGT
1053826 GCTTGTTCCTCGGGTAGA
1 GCTTGTTCCTCGGGTAGA
*
1053844 GCTTGTTCCTCGGGTGGA
1 GCTTGTTCCTCGGGTAGA
1053862 GCTTGTTCCTCG
1 GCTTGTTCCTCG
1053874 TACTATTCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.06, C:0.25, G:0.33, T:0.35
Consensus pattern (18 bp):
GCTTGTTCCTCGGGTAGA
Found at i:1055492 original size:21 final size:23
Alignment explanation
Indices: 1055439--1055498 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
1055429 AGAACCCCAG
*
1055439 GGGGGTATTGATTCCCCTTCAAA
1 GGGGGTATCGATTCCCCTTCAAA
* *
1055462 GGGGGAATCGGTTCCCCTTC-AA
1 GGGGGTATCGATTCCCCTTCAAA
1055484 -GGGGTATCGATTCCC
1 GGGGGTATCGATTCCC
1055499 TCTGCACCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 13 0.41
22 2 0.06
23 17 0.53
ACGTcount: A:0.18, C:0.25, G:0.30, T:0.27
Consensus pattern (23 bp):
GGGGGTATCGATTCCCCTTCAAA
Found at i:1059356 original size:22 final size:21
Alignment explanation
Indices: 1059314--1059353 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1059304 GAGCTTATTT
*
1059314 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1059335 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1059354 ACAATTTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1061070 original size:17 final size:17
Alignment explanation
Indices: 1061037--1061080 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1061027 TGATTTCTCT
1061037 TTGATTCTCTCTTGATTC
1 TTGATTCT-TCTTGATTC
* *
1061055 TTGATTCTTGTTGATTG
1 TTGATTCTTCTTGATTC
*
1061072 TTGTTTCTT
1 TTGATTCTT
1061081 ATTATTGATC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.09, C:0.14, G:0.16, T:0.61
Consensus pattern (17 bp):
TTGATTCTTCTTGATTC
Found at i:1070555 original size:7 final size:7
Alignment explanation
Indices: 1070543--1070588 Score: 58
Period size: 7 Copynumber: 6.3 Consensus size: 7
1070533 CCTACGAAAG
1070543 AAAAGAA
1 AAAAGAA
1070550 AAAAGAAA
1 AAAAG-AA
1070558 AAAAGAA
1 AAAAGAA
1070565 GAAAA-AGA
1 -AAAAGA-A
1070573 AAAAGAA
1 AAAAGAA
1070580 AAAAGAA
1 AAAAGAA
1070587 AA
1 AA
1070589 GAAAATGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
7 22 0.63
8 13 0.37
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:1070556 original size:12 final size:11
Alignment explanation
Indices: 1070539--1070593 Score: 74
Period size: 12 Copynumber: 4.7 Consensus size: 11
1070529 TACACCTACG
1070539 AAAGAAAAGAAA
1 AAAGAAAA-AAA
1070551 AAAGAAAAAAA
1 AAAGAAAAAAA
*
1070562 GAAGAAAAAGAA
1 AAAGAAAAA-AA
1070574 AAAGAAAAAAGA
1 AAAGAAAAAA-A
1070586 AAAGAAAA
1 AAAGAAAA
1070594 TGAGATGAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
11 12 0.31
12 27 0.69
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAA
Found at i:1070568 original size:18 final size:18
Alignment explanation
Indices: 1070539--1070593 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
1070529 TACACCTACG
1070539 AAAGAAAAGAAAAAAGAA
1 AAAGAAAAGAAAAAAGAA
1070557 AAA-AAGAAG-AAAAAGAA
1 AAAGAA-AAGAAAAAAGAA
1070574 AAAGAAAA-AAGAAAAGAA
1 AAAGAAAAGAA-AAAAGAA
1070592 AA
1 AA
1070594 TGAGATGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
17 16 0.48
18 17 0.52
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (18 bp):
AAAGAAAAGAAAAAAGAA
Found at i:1070573 original size:24 final size:24
Alignment explanation
Indices: 1070539--1070593 Score: 78
Period size: 23 Copynumber: 2.3 Consensus size: 24
1070529 TACACCTACG
1070539 AAAG-AAAAGAAAAAAGAAAAAA-A
1 AAAGAAAAAG-AAAAAGAAAAAAGA
*
1070562 GAAGAAAAAGAAAAAGAAAAAAGA
1 AAAGAAAAAGAAAAAGAAAAAAGA
1070586 AAAGAAAA
1 AAAGAAAA
1070594 TGAGATGAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 15 0.54
24 13 0.46
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (24 bp):
AAAGAAAAAGAAAAAGAAAAAAGA
Found at i:1070601 original size:5 final size:5
Alignment explanation
Indices: 1070593--1070618 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1070583 AGAAAAGAAA
1070593 ATGAG ATGAG ATGAG ATGAG ATGAG A
1 ATGAG ATGAG ATGAG ATGAG ATGAG A
1070619 GGTTCAAGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.19
Consensus pattern (5 bp):
ATGAG
Found at i:1071840 original size:136 final size:136
Alignment explanation
Indices: 1071627--1072162 Score: 714
Period size: 136 Copynumber: 3.9 Consensus size: 136
1071617 ATCGATCAAC
* * * *
1071627 ATTTCCAATGGAGAGTTCATAATGAAAAGAACTCATCCGAAAAAGGGAGAATAAGTTCATAATGA
1 ATTTCCAATGGAGAGTTCATAATGATAAGAACTCATCCGACAGAGGGAGAAAAAGTTCATAATGA
* * *
1071692 GAAGAACTTGTTCGACCTATTACTTGATTCACGACATTTCAAATCAGCAACGCCTCGCTTGAGGG
66 GAAGAACTTGTTCGACCTATTACTCGATTCACAACATTTCGAATCAGCAACGCCTCGCTTGAGGG
1071757 ATTAAT
131 ATTAAT
* *
1071763 ATTTCCAATGGAGAGTTCATAATGATAAGAACTAACCCGACAGAGGGAGAAAAAGTTCATAATGA
1 ATTTCCAATGGAGAGTTCATAATGATAAGAACTCATCCGACAGAGGGAGAAAAAGTTCATAATGA
* * * * *
1071828 GAAGAACTTGTTCGACTTATTGCTCGATTCACGACATTTCGAATCAGCAATGCCTCGCTTGTGGG
66 GAAGAACTTGTTCGACCTATTACTCGATTCACAACATTTCGAATCAGCAACGCCTCGCTTGAGGG
*
1071893 ATTAAC
131 ATTAAT
* * * * *
1071899 ATTTCCAATTGAGAGTTCATATTGATAAGAACTCATCGGACAGAGGGATAAGAAGTTCATAATGA
1 ATTTCCAATGGAGAGTTCATAATGATAAGAACTCATCCGACAGAGGGAGAAAAAGTTCATAATGA
* * *
1071964 GAAGAACATGTTTGACCTATTAC-CTGATTCACAACATTTCGAATCAGCAAGTGCCTCGCTTGAG
66 GAAGAACTTGTTCGACCTATTACTC-GATTCACAACATTTCGAATCAGCAA-CGCCTCGCTTGAG
*
1072028 GGATTGAT
129 GGATTAAT
** * * * * *
1072036 ATTTCCAATAAAGAGTTCATAATGAGAAGAAATCATCCGACAGAGGAAGAACAAGTTCATAATAA
1 ATTTCCAATGGAGAGTTCATAATGATAAGAACTCATCCGACAGAGGGAGAAAAAGTTCATAATGA
* * * * * *
1072101 TAAGAACTTGTTTGACCTATTTCTCGATTCACAACATTTTGAATCAACAACGCCTCTCTTGA
66 GAAGAACTTGTTCGACCTATTACTCGATTCACAACATTTCGAATCAGCAACGCCTCGCTTGA
1072163 AATATCAGTA
Statistics
Matches: 352, Mismatches: 45, Indels: 6
0.87 0.11 0.01
Matches are distributed among these distances:
135 1 0.00
136 234 0.66
137 116 0.33
138 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (136 bp):
ATTTCCAATGGAGAGTTCATAATGATAAGAACTCATCCGACAGAGGGAGAAAAAGTTCATAATGA
GAAGAACTTGTTCGACCTATTACTCGATTCACAACATTTCGAATCAGCAACGCCTCGCTTGAGGG
ATTAAT
Found at i:1072204 original size:273 final size:271
Alignment explanation
Indices: 1071620--1072205 Score: 695
Period size: 273 Copynumber: 2.1 Consensus size: 271
1071610 AAGATAAATC
* * * * *
1071620 GATCAACATTTCCAATGGAGAGTTCATAATGAAAAGAACTCATCCGAAAAAGGGAGAATAAGTTC
1 GATCAACATGTCCAATAGAAAGATCAT-ATGAAAAGAACTCATCCGAAAAAGGGAGAAGAAGTTC
* * *
1071685 ATAATGAGAAGAACTTGTTCGACCTATTACTTGATTCACGACATTTCAAATCAGCAACGCCTCGC
65 ATAATGAGAAGAACATGTTCGACCTATTACCTGATTCACAACATTTCAAATCAGCAACGCCTCGC
** * * *
1071750 TTGAGGGATTAATATTTCCAATGGAGAGTTCATAATGATAAGAACTAACCCGACAGAGGGAGAAA
130 TTGAGGGATTAATATTTCCAATAAAGAGTTCATAATGAGAAGAAATAACCCGACAGAGGAAGAAA
* * * * *
1071815 AAGTTCATAATGAGAAGAACTTGTTCGACTTATTGCTCGATTCACGACATTTCGAATCAGCAATG
195 AAGTTCATAATAAGAAGAACTTGTTCGACCTATTGCTCGATTCACAACATTTCGAATCAACAACG
***
1071880 CCTCGCTTGTGG
260 CCTCGCTTGAAA
* * * * * * * * * *
1071892 GATTAACATTTCCAATTGAGAGTTCATATTGATAAGAACTCATCGGACAGAGGGATAAGAAGTTC
1 GATCAACATGTCCAATAGAAAGATCATA-TGAAAAGAACTCATCCGAAAAAGGGAGAAGAAGTTC
* * *
1071957 ATAATGAGAAGAACATGTTTGACCTATTACCTGATTCACAACATTTCGAATCAGCAAGTGCCTCG
65 ATAATGAGAAGAACATGTTCGACCTATTACCTGATTCACAACATTTCAAATCAGCAA-CGCCTCG
* * *
1072022 CTTGAGGGATTGATATTTCCAATAAAGAGTTCATAATGAGAAGAAATCATCCGACAGAGGAAGAA
129 CTTGAGGGATTAATATTTCCAATAAAGAGTTCATAATGAGAAGAAATAACCCGACAGAGGAAGAA
* * * * *
1072087 CAAGTTCATAATAATAAGAACTTGTTTGACCTATTTCTCGATTCACAACATTTTGAATCAACAAC
194 AAAGTTCATAATAAGAAGAACTTGTTCGACCTATTGCTCGATTCACAACATTTCGAATCAACAAC
*
1072152 GCCTCTCTTGAAA
259 GCCTCGCTTGAAA
* ** * * *
1072165 TATCAGTATGTCTAGTAGAAAGATCATGATGAGAAGAACTC
1 GATCAACATGTCCAATAGAAAGATCAT-ATGAAAAGAACTC
1072206 GTAGCTTGAA
Statistics
Matches: 264, Mismatches: 47, Indels: 5
0.84 0.15 0.02
Matches are distributed among these distances:
271 1 0.00
272 107 0.41
273 155 0.59
274 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (271 bp):
GATCAACATGTCCAATAGAAAGATCATATGAAAAGAACTCATCCGAAAAAGGGAGAAGAAGTTCA
TAATGAGAAGAACATGTTCGACCTATTACCTGATTCACAACATTTCAAATCAGCAACGCCTCGCT
TGAGGGATTAATATTTCCAATAAAGAGTTCATAATGAGAAGAAATAACCCGACAGAGGAAGAAAA
AGTTCATAATAAGAAGAACTTGTTCGACCTATTGCTCGATTCACAACATTTCGAATCAACAACGC
CTCGCTTGAAA
Done.