Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold220
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: 3999181
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 12171 characters in sequence are not A, C, G, or T
File 4 of 19
Found at i:742053 original size:19 final size:18
Alignment explanation
Indices: 742016--742062 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
742006 ATCTATAAAT
**
742016 TTCTTAAAAATTTTGTGA
1 TTCTTAAAAATTTAATGA
742034 TTCTTAGAAAATTTAATGA
1 TTCTTA-AAAATTTAATGA
*
742053 TTTTTAAAAA
1 TTCTTAAAAA
742063 AATCTATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (18 bp):
TTCTTAAAAATTTAATGA
Found at i:744800 original size:19 final size:18
Alignment explanation
Indices: 744776--744854 Score: 77
Period size: 19 Copynumber: 4.2 Consensus size: 18
744766 CTAAGATTAC
744776 AAAAATTTATGATTTTTTA
1 AAAAATTTATGA-TTTTTA
* *
744795 AAAAATTTTGTGATTCTTA
1 AAAAA-TTTATGATTTTTA
*
744814 AAAAATTTAATGATTCTTAA
1 AAAAATTT-ATGATT-TTTA
* *
744834 AAAAATCTATTATTTTTA
1 AAAAATTTATGATTTTTA
744852 AAA
1 AAA
744855 TTTGTGATTG
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
18 9 0.18
19 25 0.51
20 15 0.31
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.46
Consensus pattern (18 bp):
AAAAATTTATGATTTTTA
Found at i:744816 original size:18 final size:19
Alignment explanation
Indices: 744776--744837 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
744766 CTAAGATTAC
*
744776 AAAAATTT-ATGATTTTTTA
1 AAAAATTTAATGA-TTCTTA
**
744795 AAAAATTTTGTGATTCTTA
1 AAAAATTTAATGATTCTTA
744814 AAAAATTTAATGATTCTTA
1 AAAAATTTAATGATTCTTA
744833 AAAAA
1 AAAAA
744838 ATCTATTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 35 0.92
20 3 0.08
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (19 bp):
AAAAATTTAATGATTCTTA
Found at i:747890 original size:2 final size:2
Alignment explanation
Indices: 747885--747926 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
747875 ATATATATAT
747885 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
747927 GAGTATTTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:748123 original size:2 final size:2
Alignment explanation
Indices: 748116--748145 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
748106 GGTTTTCTTT
*
748116 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
748146 CACTTTTTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:755119 original size:14 final size:14
Alignment explanation
Indices: 755096--755129 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
755086 TATATTTAAT
* *
755096 ATATATATATATAA
1 ATATAAATATAAAA
755110 ATATAAATATAAAA
1 ATATAAATATAAAA
755124 ATATAA
1 ATATAA
755130 TCTTTTCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
ATATAAATATAAAA
Found at i:755428 original size:6 final size:6
Alignment explanation
Indices: 755417--755441 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
755407 AAACAAAGGA
755417 AAAAGC AAAAGC AAAAGC AAAAGC A
1 AAAAGC AAAAGC AAAAGC AAAAGC A
755442 GAAAAGTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.16, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAGC
Found at i:761688 original size:2 final size:2
Alignment explanation
Indices: 761683--761725 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
761673 TATGGGAGTG
*
761683 TA TA TA TA AA 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
761725 T
1 T
761726 GGGACTGGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:771190 original size:28 final size:29
Alignment explanation
Indices: 771153--771216 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
771143 AAATACAGGT
*
771153 ACTGTAAAAAAAATTGAAGAGTCGGAGCA
1 ACTGTAAAAAAAACTGAAGAGTCGGAGCA
771182 ACTGTAAAAAAAACTGAAGAGTCGGAGCA
1 ACTGTAAAAAAAACTGAAGAGTCGGAGCA
771211 AC-GTAA
1 ACTGTAA
771217 GATATAGATA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 4 0.12
29 30 0.88
ACGTcount: A:0.48, C:0.12, G:0.23, T:0.16
Consensus pattern (29 bp):
ACTGTAAAAAAAACTGAAGAGTCGGAGCA
Found at i:775920 original size:22 final size:21
Alignment explanation
Indices: 775874--775921 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
775864 AATTGAGATG
* *
775874 AATTTAATTATAAATATTTAT
1 AATTTAATTATAAATATATAA
775895 AATTTAAATTATTAAATA-ATAA
1 AATTT-AATTA-TAAATATATAA
775917 AATTT
1 AATTT
775922 TTATTTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 5 0.22
22 12 0.52
23 6 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
AATTTAATTATAAATATATAA
Found at i:780872 original size:3 final size:3
Alignment explanation
Indices: 780864--780889 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
780854 AGATTGATTA
780864 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
780890 GATATTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:795649 original size:15 final size:16
Alignment explanation
Indices: 795631--795674 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
795621 AAAATTTATT
795631 TAATTATTAT-TTTAA
1 TAATTATTATATTTAA
*
795646 TAATTTTTATATTTAA
1 TAATTATTATATTTAA
* *
795662 TATTTAATATATT
1 TAATTATTATATT
795675 ATTTTTAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 9 0.38
16 15 0.62
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TAATTATTATATTTAA
Found at i:796224 original size:35 final size:36
Alignment explanation
Indices: 796162--796234 Score: 103
Period size: 36 Copynumber: 2.1 Consensus size: 36
796152 TGATTTTTTT
* *
796162 AAAAATTATCATTTTAAATTATAAATTTTTTAAATA
1 AAAAATTATCATCTTAAATAATAAATTTTTTAAATA
* *
796198 AAAAATTATTATCTTAAATAAT-AATTTTTTTAATA
1 AAAAATTATCATCTTAAATAATAAATTTTTTAAATA
796233 AA
1 AA
796235 TTTTAGATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
35 14 0.42
36 19 0.58
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (36 bp):
AAAAATTATCATCTTAAATAATAAATTTTTTAAATA
Found at i:796230 original size:16 final size:16
Alignment explanation
Indices: 796154--796230 Score: 57
Period size: 16 Copynumber: 4.6 Consensus size: 16
796144 TATTTTTTTG
*
796154 ATTTTTTTAAA-AATT
1 ATTTTTTTAAATAATA
** *
796169 ATCATTTTAAATTATA
1 ATTTTTTTAAATAATA
* *
796185 AATTTTTTAAATAAAAA
1 ATTTTTTTAAAT-AATA
796202 ATTATTATCTTAAATAATA
1 ATT-TT-T-TTAAATAATA
796221 ATTTTTTTAA
1 ATTTTTTTAA
796231 TAAATTTTAG
Statistics
Matches: 46, Mismatches: 11, Indels: 9
0.70 0.17 0.14
Matches are distributed among these distances:
15 9 0.20
16 15 0.33
17 5 0.11
18 4 0.09
19 7 0.15
20 6 0.13
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTTTTTTAAATAATA
Found at i:797106 original size:2 final size:2
Alignment explanation
Indices: 797099--797126 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
797089 GCTTGAGTTC
797099 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
797127 TTATTTATTT
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:798368 original size:47 final size:47
Alignment explanation
Indices: 798312--798418 Score: 117
Period size: 47 Copynumber: 2.3 Consensus size: 47
798302 AATCAATAAA
* **
798312 GATATAATTAAATAAAT-TCAACATAAAATTTGATCAATTTCAAACAT
1 GATAAAATTAAATAAATCT-AACATAAAATTAAATCAATTTCAAACAT
* * * *
798359 GATAAAATTAGATAAATCTAATATAAAATTAAATTAATTTCAAACTT
1 GATAAAATTAAATAAATCTAACATAAAATTAAATCAATTTCAAACAT
*
798406 GACAAAACTTAAA
1 GATAAAA-TTAAA
798419 ACTAATCTTT
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
47 44 0.90
48 5 0.10
ACGTcount: A:0.53, C:0.09, G:0.05, T:0.33
Consensus pattern (47 bp):
GATAAAATTAAATAAATCTAACATAAAATTAAATCAATTTCAAACAT
Found at i:813118 original size:19 final size:18
Alignment explanation
Indices: 813096--813139 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
813086 TAAATATCTT
*
813096 TAATTTATTTTGATTATTA
1 TAATTTAATTT-ATTATTA
*
813115 TAATTTTAATTTATTTTTA
1 TAA-TTTAATTTATTATTA
813134 TAATTT
1 TAATTT
813140 TATATAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 3 0.14
19 12 0.55
20 7 0.32
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (18 bp):
TAATTTAATTTATTATTA
Found at i:815060 original size:2 final size:2
Alignment explanation
Indices: 815053--815089 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
815043 CCAGCACTCT
815053 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
815090 TAAAATGGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:815955 original size:2 final size:2
Alignment explanation
Indices: 815948--815976 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
815938 GTTTATAGCG
815948 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 T
815977 TGATTGTGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:816964 original size:2 final size:2
Alignment explanation
Indices: 816957--816983 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
816947 TAGATGCATT
816957 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 T
816984 GTAAACTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:817053 original size:15 final size:15
Alignment explanation
Indices: 817029--817101 Score: 51
Period size: 15 Copynumber: 4.9 Consensus size: 15
817019 TTTTAACGTA
817029 AAATAA-TTATAATT
1 AAATAATTTATAATT
*
817043 AAATAATTTATATTT
1 AAATAATTTATAATT
* *
817058 AAA-ATTTTGATATATC
1 AAATAATTT-ATA-ATT
* *
817074 AAATTATTTATATTT
1 AAATAATTTATAATT
* *
817089 ATATAATTAATAA
1 AAATAATTTATAA
817102 AAATATAAAT
Statistics
Matches: 43, Mismatches: 12, Indels: 7
0.69 0.19 0.11
Matches are distributed among these distances:
14 10 0.23
15 23 0.53
16 7 0.16
17 3 0.07
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (15 bp):
AAATAATTTATAATT
Found at i:820982 original size:50 final size:50
Alignment explanation
Indices: 820907--821165 Score: 346
Period size: 50 Copynumber: 5.2 Consensus size: 50
820897 AGTTGTTATC
* * * *
820907 ATTGTTGACCA-TCATTCACCAACCTTTAACAATAGAGAAAGGT-AGTCATA
1 ATTGTTGACGATTC-TTCACCAACCTTTGACAATAGAGAGAGGTGA-CCATA
* *
820957 ATTGTTGACGATTCTTCACCAACCTTTGACAATAAAGGGAGGTGACCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGACCATA
*
821007 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGGGAGGTGACCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGACCATA
* * *
821057 ATTGTTGACGATTCTTTACCAACCTTTGACAATAGA-AGGAGGTGATCGTA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGA-GAGGTGACCATA
* *
821107 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGA-AGGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGA-GAGGTGACCATA
821157 ATTGTTGAC
1 ATTGTTGAC
821166 TTTAAGTATA
Statistics
Matches: 190, Mismatches: 16, Indels: 6
0.90 0.08 0.03
Matches are distributed among these distances:
50 187 0.98
51 3 0.02
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (50 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGACCATA
Found at i:825617 original size:50 final size:50
Alignment explanation
Indices: 825556--825800 Score: 350
Period size: 50 Copynumber: 4.9 Consensus size: 50
825546 TTGATTATCA
* *
825556 TTCACCAACCTTTGACAATAGAGAGAGGTGACCATAATTGTTGACGATTC
1 TTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACAATTC
* *
825606 TTCACCAACCTTTGATAATAGA-AGGAGGTGGTCATAATTGTTGACAATTC
1 TTCACCAACCTTTGACAATAGAGA-GAGGTGGCCATAATTGTTGACAATTC
* * * *
825656 TTCACCAATCTTTGACAATAGAGGGAGGTGACCATAATTGTTGACGATTC
1 TTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACAATTC
* *
825706 TTCACCAATCTTTGACAATAGA-AGGAGGTGGTCATAATTGTTGACAATTC
1 TTCACCAACCTTTGACAATAGAGA-GAGGTGGCCATAATTGTTGACAATTC
* *
825756 TTCACCAACCTTTGACAATAGAGGGATGTGGCCATAATTGTTGAC
1 TTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGAC
825801 TTTAAATATA
Statistics
Matches: 173, Mismatches: 18, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
49 1 0.01
50 172 0.99
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (50 bp):
TTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACAATTC
Found at i:825719 original size:100 final size:100
Alignment explanation
Indices: 825556--825800 Score: 436
Period size: 100 Copynumber: 2.5 Consensus size: 100
825546 TTGATTATCA
*
825556 TTCACCAACCTTTGACAATAGAGAGAGGTGACCATAATTGTTGACGATTCTTCACCAACCTTTGA
1 TTCACCAACCTTTGACAATAGAGGGAGGTGACCATAATTGTTGACGATTCTTCACCAACCTTTGA
*
825621 TAATAGAAGGAGGTGGTCATAATTGTTGACAATTC
66 CAATAGAAGGAGGTGGTCATAATTGTTGACAATTC
* *
825656 TTCACCAATCTTTGACAATAGAGGGAGGTGACCATAATTGTTGACGATTCTTCACCAATCTTTGA
1 TTCACCAACCTTTGACAATAGAGGGAGGTGACCATAATTGTTGACGATTCTTCACCAACCTTTGA
825721 CAATAGAAGGAGGTGGTCATAATTGTTGACAATTC
66 CAATAGAAGGAGGTGGTCATAATTGTTGACAATTC
* *
825756 TTCACCAACCTTTGACAATAGAGGGATGTGGCCATAATTGTTGAC
1 TTCACCAACCTTTGACAATAGAGGGAGGTGACCATAATTGTTGAC
825801 TTTAAATATA
Statistics
Matches: 138, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
100 138 1.00
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (100 bp):
TTCACCAACCTTTGACAATAGAGGGAGGTGACCATAATTGTTGACGATTCTTCACCAACCTTTGA
CAATAGAAGGAGGTGGTCATAATTGTTGACAATTC
Found at i:828188 original size:19 final size:19
Alignment explanation
Indices: 828150--828197 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
828140 TTATAAAAAT
*
828150 ATATAATATAATATTTTAA
1 ATATAATATAATATTATAA
828169 ATATAATTATAATA-TATAA
1 ATATAA-TATAATATTATAA
*
828188 AAATAA-ATAA
1 ATATAATATAA
828198 ATATGATATG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 4 0.15
19 15 0.58
20 7 0.27
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATATAATATAATATTATAA
Found at i:833446 original size:51 final size:49
Alignment explanation
Indices: 833385--833480 Score: 113
Period size: 49 Copynumber: 1.9 Consensus size: 49
833375 AATTATTTTA
*
833385 AAGTCCACCCATGCATCGTTTCCAGTGTT-TAAAAGTCTAGAATAGATAAGG
1 AAGTCCACCCA--CAT-GTTTCAAGTGTTATAAAAGTCTAGAATAGATAAGG
* * * *
833436 AAGTCTACCCACCTTTTTTAAGTGTTATAAAAGTCTAGAATAGAT
1 AAGTCCACCCACATGTTTCAAGTGTTATAAAAGTCTAGAATAGAT
833481 TAATATCTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
48 9 0.23
49 20 0.51
51 10 0.26
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (49 bp):
AAGTCCACCCACATGTTTCAAGTGTTATAAAAGTCTAGAATAGATAAGG
Found at i:836742 original size:20 final size:19
Alignment explanation
Indices: 836716--836794 Score: 94
Period size: 17 Copynumber: 4.3 Consensus size: 19
836706 AGCTCGTTAA
836716 AATTAT-TTTTATTATAAT
1 AATTATATTTTATTATAAT
*
836734 ATTTATATTTTA-TA-AAT
1 AATTATATTTTATTATAAT
*
836751 AATTATATTTT-TTATAAA
1 AATTATATTTTATTATAAT
*
836769 AATTATAATTTTATTTTAAT
1 AATTAT-ATTTTATTATAAT
836789 AATTAT
1 AATTAT
836795 TGATTTATTA
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
17 15 0.29
18 15 0.29
19 10 0.20
20 11 0.22
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
AATTATATTTTATTATAAT
Found at i:837503 original size:19 final size:19
Alignment explanation
Indices: 837466--837504 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
837456 ATTTTATCAA
* * *
837466 TTATTTTTAATATTTTATT
1 TTATTTTAAATAATATATT
837485 TTATTTTAAATAATATATT
1 TTATTTTAAATAATATATT
837504 T
1 T
837505 AAAATAATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATTTTAAATAATATATT
Found at i:842505 original size:27 final size:26
Alignment explanation
Indices: 842475--842556 Score: 78
Period size: 27 Copynumber: 3.1 Consensus size: 26
842465 TCATGTAAAT
*
842475 ATATATTTTAAAAATAATTAATTATTA
1 ATATATTTTAAAAATAATTAAATA-TA
*
842502 ATATA--TTAAAATTAATATAAATATA
1 ATATATTTTAAAAATAAT-TAAATATA
* * *
842527 AAATTTTTTAAATATAATTATAATATA
1 ATATATTTTAAAAATAATTA-AATATA
842554 ATA
1 ATA
842557 AAATATATAA
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
25 15 0.34
26 7 0.16
27 22 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
ATATATTTTAAAAATAATTAAATATA
Found at i:842744 original size:3 final size:3
Alignment explanation
Indices: 842736--842771 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
842726 CTTATTCACA
*
842736 ATT ATT ATT CTT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
842772 GTAAAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:842938 original size:16 final size:15
Alignment explanation
Indices: 842911--842948 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 15
842901 TATAAAAAGG
842911 TTTTTAAAAATATATA
1 TTTTT-AAAATATATA
842927 TATTTTAAAATATATA
1 T-TTTTAAAATATATA
842943 TTTTTA
1 TTTTTA
842949 TTATAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.24
16 12 0.57
17 4 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTTTAAAATATATA
Found at i:848584 original size:37 final size:36
Alignment explanation
Indices: 848515--848585 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 36
848505 ATTGATTAAG
* * *
848515 AAAATACTAATTATTTTTTATTTTTAATTTTTAATT
1 AAAATACTAAATATTTTTTATTTATAAGTTTTAATT
848551 AAAATACATAAATATTTTTATATTTAT-AGTTTTAA
1 AAAATAC-TAAATATTTTT-TATTTATAAGTTTTAA
848586 ATAATTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
36 7 0.23
37 17 0.57
38 6 0.20
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (36 bp):
AAAATACTAAATATTTTTTATTTATAAGTTTTAATT
Found at i:855990 original size:124 final size:125
Alignment explanation
Indices: 855795--856021 Score: 393
Period size: 124 Copynumber: 1.8 Consensus size: 125
855785 ATCTCAGAAT
* * *
855795 GTGTTTCCAGATAAAGATGACCTTTCTTTCATCTCATTGCGTTTTATGTGGTATCCTGCTTCTGT
1 GTGTTTCCAGATAAAGATGACCTTGCTTTCATCTCATTGAGTTTTATCTGGTATCCTGCTTCTGT
*
855860 AATAATGCATGTAGTT-AGACATACAAAGCATGAAGAATCCTGACGTGGCATCTTGGAAC
66 AATAATGCATGTAGTTAAGACATACAAAGCATAAAGAATCCTGACGTGGCATCTTGGAAC
**
855919 GTGTTTCTGGATAAAGATGACCTTGCTTTCATCTCATTGAGTTTTATCTGGTATCCTGCTTCTGT
1 GTGTTTCCAGATAAAGATGACCTTGCTTTCATCTCATTGAGTTTTATCTGGTATCCTGCTTCTGT
855984 AATAATGCATGTAGTTAAGACATACAAAGCATAAAGAA
66 AATAATGCATGTAGTTAAGACATACAAAGCATAAAGAA
856022 GCAACAGGAA
Statistics
Matches: 96, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
124 76 0.79
125 20 0.21
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.35
Consensus pattern (125 bp):
GTGTTTCCAGATAAAGATGACCTTGCTTTCATCTCATTGAGTTTTATCTGGTATCCTGCTTCTGT
AATAATGCATGTAGTTAAGACATACAAAGCATAAAGAATCCTGACGTGGCATCTTGGAAC
Found at i:861720 original size:30 final size:31
Alignment explanation
Indices: 861681--861749 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
861671 ATATAAGTAA
*
861681 ATATAAAATTTTA-AAAATAAATATTAATATT
1 ATAT-AAATTTTATAAAACAAATATTAATATT
** *
861712 ATATAAA-TTTATTTACCAAATATTAATATT
1 ATATAAATTTTATAAAACAAATATTAATATT
861742 ATATAAAT
1 ATATAAAT
861750 CTATTAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 4 0.12
30 24 0.75
31 4 0.12
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (31 bp):
ATATAAATTTTATAAAACAAATATTAATATT
Found at i:861775 original size:21 final size:19
Alignment explanation
Indices: 861732--861768 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
861722 ATTTACCAAA
*
861732 TATTAATATTATATAAATC
1 TATTAATAATATATAAATC
861751 TATTAATAATATATAAAT
1 TATTAATAATATATAAAT
861769 TTCTATTCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (19 bp):
TATTAATAATATATAAATC
Found at i:864124 original size:16 final size:17
Alignment explanation
Indices: 864103--864157 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 17
864093 CATATTATAA
864103 TTATATTTAA-AATATT
1 TTATATTTAATAATATT
864119 TTATATTTATATAA-ATT
1 TTATATTTA-ATAATATT
864136 TTAATATATTAATAAT-TT
1 TT-ATAT-TTAATAATATT
864154 TTAT
1 TTAT
864158 TATATAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
16 9 0.26
17 8 0.24
18 14 0.41
19 3 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTATATTTAATAATATT
Found at i:864143 original size:20 final size:19
Alignment explanation
Indices: 864120--864162 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
864110 TAAAATATTT
864120 TATATTTATATAAATTTTAA
1 TATATTTA-ATAAATTTTAA
* *
864140 TATA-TTAATAATTTTTAT
1 TATATTTAATAAATTTTAA
864158 TATAT
1 TATAT
864163 AAATTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 13 0.65
19 3 0.15
20 4 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTTAATAAATTTTAA
Found at i:864150 original size:18 final size:18
Alignment explanation
Indices: 864116--864177 Score: 55
Period size: 17 Copynumber: 3.7 Consensus size: 18
864106 TATTTAAAAT
864116 ATTTT-ATAT-TTATATAA
1 ATTTTAATATATTA-ATAA
864133 ATTTTAATATATTAAT-A
1 ATTTTAATATATTAATAA
*
864150 ATTTTTAT-TA-T-ATAA
1 ATTTTAATATATTAATAA
864165 ATTTTAAATATAT
1 ATTTT-AATATAT
864178 ACTTATATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
14 2 0.05
15 7 0.19
16 4 0.11
17 15 0.41
18 6 0.16
19 3 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTTAATATATTAATAA
Found at i:864176 original size:15 final size:14
Alignment explanation
Indices: 864126--864178 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 14
864116 ATTTTATATT
864126 TATATAAATTTTAA
1 TATATAAATTTTAA
*
864140 TATATTAATAATTTTTAT
1 TATA-T-A-AA-TTTTAA
864158 TATATAAATTTTAAA
1 TATATAAATTTT-AA
864173 TATATA
1 TATATA
864179 CTTATATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
14 8 0.25
15 10 0.31
16 2 0.06
17 3 0.09
18 9 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TATATAAATTTTAA
Found at i:866014 original size:3 final size:3
Alignment explanation
Indices: 866000--866029 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
865990 AATTTAAGAT
*
866000 ATA ATA AGA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
866030 TGAATATCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:866727 original size:2 final size:2
Alignment explanation
Indices: 866720--866761 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
866710 GCCCGTACTG
866720 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
866761 A
1 A
866762 GATGCAGTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:871278 original size:20 final size:20
Alignment explanation
Indices: 871253--871295 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
871243 AAATAAATTT
871253 AATTAAAATAC-ATAAAAATA
1 AATTAAAA-ACTATAAAAATA
*
871273 AATTAAAAACTATAATAATA
1 AATTAAAAACTATAAAAATA
871293 AAT
1 AAT
871296 CAAATTAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (20 bp):
AATTAAAAACTATAAAAATA
Found at i:872419 original size:3 final size:3
Alignment explanation
Indices: 872413--872451 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
872403 CTACTACTAC
872413 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
872452 ATTGTTAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:873382 original size:2 final size:2
Alignment explanation
Indices: 873375--873414 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
873365 GGAATTATCA
*
873375 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
873415 TAAATCTTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:882122 original size:36 final size:36
Alignment explanation
Indices: 882072--882201 Score: 104
Period size: 36 Copynumber: 3.6 Consensus size: 36
882062 TATTGGAAGT
* * * *
882072 TTATTTTATTATTTAAAATAATATAAAAATAAAAAA
1 TTATATTAATATTTAAAATAATATAAAATTAAAATA
*
882108 TTATATTAATATTTATAATTAA-ATTAAAATTAAAATA
1 TTATATTAATATTTA-AAATAATA-TAAAATTAAAATA
* * * *
882145 TT-T-TTATTATTTAAATAATAATTTTAAATTAAAATT
1 TTATATTAATATTT-AA-AATAATATAAAATTAAAATA
* *
882181 TTATATTTATATTTAATATAA
1 TTATATTAATATTTAAAATAA
882202 ATTATACAAA
Statistics
Matches: 74, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
35 9 0.12
36 37 0.50
37 21 0.28
38 7 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (36 bp):
TTATATTAATATTTAAAATAATATAAAATTAAAATA
Found at i:886219 original size:26 final size:26
Alignment explanation
Indices: 886157--886219 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
886147 ATTTTTTTCG
*
886157 AAATATATTAAAAATATTTTTATAATT
1 AAATATA-TAAAAATATTTTTATAAAT
**
886184 ATTTATATAAAAATATTTTTATTAAAT
1 AAATATATAAAAATATTTTTA-TAAAT
886211 AAATA-ATAA
1 AAATATATAA
886220 TTTAAATTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
26 18 0.60
27 12 0.40
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
AAATATATAAAAATATTTTTATAAAT
Found at i:887688 original size:22 final size:21
Alignment explanation
Indices: 887632--887690 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 21
887622 TTATTTATTT
887632 TATAATTAAATTTAAATAAAA
1 TATAATTAAATTTAAATAAAA
* *
887653 TATATTTATTATTTAAA-AATAA
1 TATAATTA-AATTTAAATAA-AA
887675 TATTAATTAAATTTAA
1 TA-TAATTAAATTTAA
887691 TTGATTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
21 9 0.29
22 17 0.55
23 5 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TATAATTAAATTTAAATAAAA
Found at i:887887 original size:40 final size:39
Alignment explanation
Indices: 887839--887927 Score: 90
Period size: 40 Copynumber: 2.2 Consensus size: 39
887829 TTGTTACAAA
* * *
887839 AATATTTTTAAAAAATTAATTGG-TATTTTTTAAAATTCT
1 AATATTTTTAAAAAA-GAAATGGATAATTTTTAAAATTCT
* * *
887878 AATAGTTTTTTAAGAAGAAATGGATAATTTTTAAAATTTT
1 AATA-TTTTTAAAAAAGAAATGGATAATTTTTAAAATTCT
887918 AATAATTTTT
1 AAT-ATTTTT
887928 TAAATATAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
39 9 0.22
40 31 0.76
41 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.08, T:0.49
Consensus pattern (39 bp):
AATATTTTTAAAAAAGAAATGGATAATTTTTAAAATTCT
Found at i:888379 original size:3 final size:3
Alignment explanation
Indices: 888373--888406 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
888363 TTTTTTTTAA
888373 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
888407 GCCATTTTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:890227 original size:115 final size:115
Alignment explanation
Indices: 890025--890248 Score: 376
Period size: 115 Copynumber: 1.9 Consensus size: 115
890015 AAAAGTTTTC
* ** * *
890025 TTCAATGGCATTAAAGACACTTTTGGTTAGTAAGAATACTTGCAGTACTAGAGTGACTAGAAGCA
1 TTCAATGGCATTAAAGACACTTCTAATCAATAAGAATACTTGCAGTACTAGAGTGACTAGAAGCA
* * *
890090 GAACTCTTGGGTCAACCAATTTGTTCATACAATCAATTCATCCCCTCACT
66 GAACCCGTGGGCCAACCAATTTGTTCATACAATCAATTCATCCCCTCACT
890140 TTCAATGGCATTAAAGACACTTCTAATCAATAAGAATACTTGCAGTACTAGAGTGACTAGAAGCA
1 TTCAATGGCATTAAAGACACTTCTAATCAATAAGAATACTTGCAGTACTAGAGTGACTAGAAGCA
890205 GAACCCGTGGGCCAACCAATTTGTTCATACAATCAATTCATCCC
66 GAACCCGTGGGCCAACCAATTTGTTCATACAATCAATTCATCCC
890249 TAAAAAATAT
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
115 101 1.00
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (115 bp):
TTCAATGGCATTAAAGACACTTCTAATCAATAAGAATACTTGCAGTACTAGAGTGACTAGAAGCA
GAACCCGTGGGCCAACCAATTTGTTCATACAATCAATTCATCCCCTCACT
Found at i:896085 original size:17 final size:17
Alignment explanation
Indices: 896046--896086 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
896036 TTACATTTAA
896046 CATATTTAAATTATAAT
1 CATATTTAAATTATAAT
896063 -ATTATTTAAATTATAAT
1 CA-TATTTAAATTATAAT
896080 CATATTT
1 CATATTT
896087 TATTTTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 1 0.05
17 20 0.91
18 1 0.05
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (17 bp):
CATATTTAAATTATAAT
Found at i:896108 original size:24 final size:26
Alignment explanation
Indices: 896055--896124 Score: 81
Period size: 24 Copynumber: 2.7 Consensus size: 26
896045 ACATATTTAA
896055 ATTATAATATTATTTAAATTATAATCAT
1 ATTA-AATATTATTTAAA-TATAATCAT
** *
896083 ATTTTATTTTATTTAAATA-AAT-AT
1 ATTAAATATTATTTAAATATAATCAT
896107 ATTAAATATTATTTAAAT
1 ATTAAATATTATTTAAAT
896125 TGTTAAATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
24 17 0.47
25 3 0.08
26 2 0.06
27 11 0.31
28 3 0.08
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (26 bp):
ATTAAATATTATTTAAATATAATCAT
Found at i:902691 original size:2 final size:2
Alignment explanation
Indices: 902686--902713 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
902676 GTGTGTGTAC
902686 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
902714 TATCCAATAT
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:910209 original size:2 final size:2
Alignment explanation
Indices: 910202--910266 Score: 58
Period size: 2 Copynumber: 32.5 Consensus size: 2
910192 TTTATTTTCT
* * * * * *
910202 TA TA TA TA TA TA TA TA TA TA TA TA TG TG TG TG TG TG 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
* *
910244 TA TA TA TA TA TA TG TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
910267 GTTTAATAAG
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.38, C:0.02, G:0.11, T:0.49
Consensus pattern (2 bp):
TA
Found at i:913692 original size:56 final size:56
Alignment explanation
Indices: 913605--913714 Score: 152
Period size: 56 Copynumber: 2.0 Consensus size: 56
913595 TGACTCTGAC
913605 TCAAGAAAACAATAACCAAGCATAGACCAATACTACAGAAA-ATTTTTAGGTTTGAT
1 TCAAGAAAACAATAACCAAGCATAGACCAATACTACAGAAATA-TTTTAGGTTTGAT
* * * *
913661 TCAAGAAAACAATAACCACA-CATGGATCAATATTCCAGAAATATTTTAGGTTTG
1 TCAAGAAAACAATAACCA-AGCATAGACCAATACTACAGAAATATTTTAGGTTTG
913715 GCGAATTGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
56 46 0.96
57 2 0.04
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.26
Consensus pattern (56 bp):
TCAAGAAAACAATAACCAAGCATAGACCAATACTACAGAAATATTTTAGGTTTGAT
Found at i:919380 original size:3 final size:3
Alignment explanation
Indices: 919372--919397 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
919362 AGAAATGCAT
919372 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
919398 CGCCGTGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:919418 original size:75 final size:75
Alignment explanation
Indices: 919263--919458 Score: 317
Period size: 75 Copynumber: 2.7 Consensus size: 75
919253 CCATGGCTAT
* * * *
919263 AACTAGAAGCAGCAAGAAGATCAAGAAAGAAATGCAT---GAAGAAGAAGAAGAAGAAGAAGACG
1 AACTAGAAGCATCAAGAATACCAAGATAGAAATGCATGAAGAAGAAGAAGAAGAAGAAGAAGACG
919325 CCGTGAATAG
66 CCGTGAATAG
919335 AACTAGAAGCATCAAGAATACCAAGATAGAAATGCATGAAGAAGAAGAAGAAGAAGAAGAAGACG
1 AACTAGAAGCATCAAGAATACCAAGATAGAAATGCATGAAGAAGAAGAAGAAGAAGAAGAAGACG
919400 CCGTGAATAG
66 CCGTGAATAG
* *
919410 AACTAGAAGCATCAAGAATACCAAGATGGAAATGCATGAAAAAGAAGAA
1 AACTAGAAGCATCAAGAATACCAAGATAGAAATGCATGAAGAAGAAGAA
919459 ATAAAGGACC
Statistics
Matches: 115, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
72 33 0.29
75 82 0.71
ACGTcount: A:0.53, C:0.12, G:0.25, T:0.10
Consensus pattern (75 bp):
AACTAGAAGCATCAAGAATACCAAGATAGAAATGCATGAAGAAGAAGAAGAAGAAGAAGAAGACG
CCGTGAATAG
Found at i:920620 original size:21 final size:21
Alignment explanation
Indices: 920595--920638 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
920585 TCTATTTTTT
*
920595 AAAATTATATGTAA-ATAATAA
1 AAAATTATA-ATAATATAATAA
920616 AAAATTATAATAATATAATAA
1 AAAATTATAATAATATAATAA
920637 AA
1 AA
920639 CTCTGCTTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
AAAATTATAATAATATAATAA
Found at i:920701 original size:17 final size:15
Alignment explanation
Indices: 920661--920694 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
920651 ATAAATAGAA
920661 TTATATAAAATTTTT
1 TTATATAAAATTTTT
*
920676 TTAAATAAAATTTTT
1 TTATATAAAATTTTT
920691 TTAT
1 TTAT
920695 CTATAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATATAAAATTTTT
Found at i:921582 original size:19 final size:19
Alignment explanation
Indices: 921554--921603 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 19
921544 TAAATTGAGA
921554 TTAT-AAAATTTTATT-AT
1 TTATCAAAATTTTATTAAT
921571 TTAATCAAAA--TTATTAAT
1 TT-ATCAAAATTTTATTAAT
*
921589 TTATCAGAATTTTAT
1 TTATCAAAATTTTAT
921604 CGTAAAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
17 13 0.48
18 6 0.22
19 8 0.30
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (19 bp):
TTATCAAAATTTTATTAAT
Found at i:921793 original size:2 final size:2
Alignment explanation
Indices: 921786--921817 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
921776 ACGCAAGTGT
921786 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
921818 ACATACCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:931623 original size:174 final size:175
Alignment explanation
Indices: 931329--931676 Score: 565
Period size: 174 Copynumber: 2.0 Consensus size: 175
931319 CGAGATAGTG
931329 TAAGAAAATAATTTTAGTTATCTTAGAGATCAAATGATGGCTTTTTTTTTATGCCAATATAGTAT
1 TAAGAAAATAATTTTAGTTATCTTAGAGATCAAATGATGGC-TTTTTTTTATGCCAATATAGTAT
* * *
931394 TATGATTCTCTAGGTAAATTACATGCAAGTGGGAACATTTTTCAGTTGCATTGATCATTGCTGAA
65 TATGATTCTCTAGGTAAATTACATGCAAGTAGGAACATTTTTCAGCTGCATTGATCATTCCTGAA
* * *
931459 CTCAAAATTTATAATCCCCCCGCCCCCCAAAAAAGGATTATTGCCA
130 CGCAAAATTTAAAATCCCCCCACCCCCCAAAAAAGGATTATTGCCA
* *
931505 TAAGAAAATAATTTTAGTTA-CTTTAGAGATCAAATGATGGC-TTTTTTTATGCTAATGTAGTAT
1 TAAGAAAATAATTTTAGTTATC-TTAGAGATCAAATGATGGCTTTTTTTTATGCCAATATAGTAT
* *
931568 TATGATTCTCTAGGTAAATTACATGCAAGTAGGAACATTTTTCGGCTGTATTGATCATTCCTGAA
65 TATGATTCTCTAGGTAAATTACATGCAAGTAGGAACATTTTTCAGCTGCATTGATCATTCCTGAA
*
931633 CGCAAAATTTAAAATCCCCCCACCCTCCAAAAAAGGATTATTGC
130 CGCAAAATTTAAAATCCCCCCACCCCCCAAAAAAGGATTATTGC
931677 TATTCCCAAA
Statistics
Matches: 160, Mismatches: 11, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
174 120 0.75
175 1 0.01
176 39 0.24
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (175 bp):
TAAGAAAATAATTTTAGTTATCTTAGAGATCAAATGATGGCTTTTTTTTATGCCAATATAGTATT
ATGATTCTCTAGGTAAATTACATGCAAGTAGGAACATTTTTCAGCTGCATTGATCATTCCTGAAC
GCAAAATTTAAAATCCCCCCACCCCCCAAAAAAGGATTATTGCCA
Found at i:935277 original size:12 final size:13
Alignment explanation
Indices: 935254--935287 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
935244 TATATGAACA
*
935254 TATTATTATAAAT
1 TATTAATATAAAT
935267 TA-TAATATAAAT
1 TATTAATATAAAT
935279 TATTAATAT
1 TATTAATAT
935288 GTTAAAATTT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TATTAATATAAAT
Found at i:943806 original size:11 final size:11
Alignment explanation
Indices: 943790--943814 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
943780 ATAACACGCG
943790 TAAGATATGAT
1 TAAGATATGAT
943801 TAAGATATGAT
1 TAAGATATGAT
943812 TAA
1 TAA
943815 TTAATCGTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (11 bp):
TAAGATATGAT
Found at i:946400 original size:16 final size:15
Alignment explanation
Indices: 946375--946406 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
946365 ATTTTAATTC
946375 ATGTACTATTTCTTG
1 ATGTACTATTTCTTG
946390 ATGTCACTATTTCTTG
1 ATGT-ACTATTTCTTG
946406 A
1 A
946407 AGAATTAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.22, C:0.16, G:0.12, T:0.50
Consensus pattern (15 bp):
ATGTACTATTTCTTG
Found at i:948795 original size:2 final size:2
Alignment explanation
Indices: 948788--948812 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
948778 ATCAAAATTT
948788 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
948813 GTAGATAGAT
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:949582 original size:13 final size:14
Alignment explanation
Indices: 949566--949600 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
949556 AGGAAAAGGG
949566 TTTTCTTTTTT-TT
1 TTTTCTTTTTTCTT
949579 TTTTCTTTTTTCTT
1 TTTTCTTTTTTCTT
949593 TTTT-TTTT
1 TTTTCTTTT
949601 GTTGTTTGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 15 0.71
14 6 0.29
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (14 bp):
TTTTCTTTTTTCTT
Found at i:951967 original size:3 final size:3
Alignment explanation
Indices: 951961--951996 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
951951 AATAATAATA
951961 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
951997 CCAACAAATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:952236 original size:2 final size:2
Alignment explanation
Indices: 952229--952262 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
952219 TTCATTTCAA
952229 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
952263 TTATGGTGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:954193 original size:20 final size:22
Alignment explanation
Indices: 954146--954200 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
954136 TATATGAAAT
954146 AAATATAATATAAAAATAATTA
1 AAATATAATATAAAAATAATTA
954168 AAATATAAT-TAAAAA-AA-TA
1 AAATATAATATAAAAATAATTA
954187 AATATATAAATATA
1 AA-ATAT-AATATA
954201 TTAAAATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
19 4 0.13
20 6 0.20
21 9 0.30
22 11 0.37
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
AAATATAATATAAAAATAATTA
Found at i:954218 original size:17 final size:17
Alignment explanation
Indices: 954198--954247 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
954188 ATATATAAAT
954198 ATATTAAAATTTATATA
1 ATATTAAAATTTATATA
954215 ATATT--AA-TTAT-TA
1 ATATTAAAATTTATATA
954228 ACTTATTAAAATTTATATA
1 A--TATTAAAATTTATATA
954247 A
1 A
954248 AATAATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
13 3 0.11
14 4 0.15
15 6 0.22
17 7 0.26
18 4 0.15
19 3 0.11
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATTAAAATTTATATA
Found at i:954257 original size:31 final size:31
Alignment explanation
Indices: 954181--954278 Score: 126
Period size: 31 Copynumber: 3.1 Consensus size: 31
954171 TATAATTAAA
* *
954181 AAAATAAATATATAAATATATTAAAATTTATAT
1 AAAATAATTAT-TAACT-TATTAAAATTTATAT
*
954214 AATATTAATTATTAACTTATTAAAATTTATAT
1 AA-AATAATTATTAACTTATTAAAATTTATAT
*
954246 AAAATAATTATTAACTTATTAAAA-ATATAT
1 AAAATAATTATTAACTTATTAAAATTTATAT
954276 AAA
1 AAA
954279 CATGATAGTG
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
30 8 0.14
31 21 0.36
32 17 0.29
33 6 0.10
34 7 0.12
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (31 bp):
AAAATAATTATTAACTTATTAAAATTTATAT
Found at i:955077 original size:2 final size:2
Alignment explanation
Indices: 955070--955106 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
955060 TTAAGAAAGA
955070 AT AT AT AT AT AT 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 A
955107 GTTGAAGCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:955226 original size:2 final size:2
Alignment explanation
Indices: 955219--955260 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
955209 GAAGGTGTGG
955219 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
955261 CTGGTGCTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:956608 original size:24 final size:23
Alignment explanation
Indices: 956563--956624 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
956553 TTATATTTTT
*
956563 ATATTATATTTATAATATATAATA
1 ATATTATATTTAAAATATATAA-A
956587 ATATTATATTTAAAAT-TAATAAA
1 ATATTATATTTAAAATAT-ATAAA
*
956610 TTAATTAT-TTTAAAA
1 AT-ATTATATTTAAAA
956625 AAACAACTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 10 0.29
24 24 0.71
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATATTATATTTAAAATATATAAA
Found at i:960531 original size:23 final size:23
Alignment explanation
Indices: 960505--960551 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
960495 AAAAAAAATT
960505 ATAAAAACAAAAAAAAAATAAAA
1 ATAAAAACAAAAAAAAAATAAAA
* **
960528 ATAAAAAGAAAATTAAAATAAAA
1 ATAAAAACAAAAAAAAAATAAAA
960551 A
1 A
960552 AATTATTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.13
Consensus pattern (23 bp):
ATAAAAACAAAAAAAAAATAAAA
Found at i:960559 original size:17 final size:17
Alignment explanation
Indices: 960496--960554 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
960486 TTCTTTCTTA
* *
960496 AAAAAAATTATAAAAAC
1 AAAAAAATAATAAAAAT
*
960513 AAAAAAAAAATAAAAAT
1 AAAAAAATAATAAAAAT
*
960530 AAAAAGAA-AATTAAAAT
1 AAAAA-AATAATAAAAAT
960547 AAAAAAAT
1 AAAAAAAT
960555 TATTATAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
16 2 0.06
17 32 0.89
18 2 0.06
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.15
Consensus pattern (17 bp):
AAAAAAATAATAAAAAT
Found at i:960948 original size:18 final size:18
Alignment explanation
Indices: 960910--960948 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
960900 TTTAGCATAA
* *
960910 TTATTTCATATATTTTGT
1 TTATTTCATATAATTTAT
*
960928 TTATTTTATATAATTTAT
1 TTATTTCATATAATTTAT
960946 TTA
1 TTA
960949 CAAATGACAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (18 bp):
TTATTTCATATAATTTAT
Found at i:961107 original size:16 final size:17
Alignment explanation
Indices: 961077--961108 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
961067 ATATTTTTTT
961077 ATAATTAACTTTAAAAA
1 ATAATTAACTTTAAAAA
961094 ATAATTAA-TTTAAAA
1 ATAATTAACTTTAAAA
961109 GTTTACGTTA
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:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAATTAACTTTAAAAA
Found at i:967189 original size:15 final size:14
Alignment explanation
Indices: 967157--967186 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
967147 TAAGAGAGGT
967157 AAATAAT-TTTTAA
1 AAATAATATTTTAA
967170 AAATAATATTTTAA
1 AAATAATATTTTAA
967184 AAA
1 AAA
967187 ATATATTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AAATAATATTTTAA
Found at i:967586 original size:20 final size:20
Alignment explanation
Indices: 967544--967587 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
967534 TAAATTTTAT
* *
967544 TAAATATTTTAATAGTAATA
1 TAAATATTTTAATAGAAAAA
967564 TAAATATTTTATATA-AAAAA
1 TAAATATTTTA-ATAGAAAAA
967584 TAAA
1 TAAA
967588 AAATTTAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
TAAATATTTTAATAGAAAAA
Found at i:969259 original size:29 final size:29
Alignment explanation
Indices: 969227--969296 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 29
969217 ATACATGTAT
*
969227 TATATAAAAAT-TAATTAAAATTTAAAAA
1 TATATAAAAATAAAATTAAAATTTAAAAA
** *
969255 -ATATAAAAATATAAAATTTTAATTTATAAA
1 TATAT-AAAA-ATAAAATTAAAATTTAAAAA
969285 TATATAAAAATA
1 TATATAAAAATA
969297 TTTTAAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
27 4 0.12
28 4 0.12
29 5 0.15
30 17 0.50
31 4 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (29 bp):
TATATAAAAATAAAATTAAAATTTAAAAA
Found at i:969346 original size:18 final size:18
Alignment explanation
Indices: 969323--969371 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 18
969313 AAACGTGCAT
*
969323 TTAATAAATTTATAAATC
1 TTAATAAATTTATAAATA
*
969341 TTAATAATAATTATAAATA
1 TTAATAA-ATTTATAAATA
969360 TT-AT-AATTTATA
1 TTAATAAATTTATA
969372 TGTATTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 6 0.22
17 1 0.04
18 9 0.33
19 11 0.41
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATAAATTTATAAATA
Found at i:969390 original size:23 final size:22
Alignment explanation
Indices: 969361--969403 Score: 77
Period size: 23 Copynumber: 1.9 Consensus size: 22
969351 TTATAAATAT
969361 TATAATTTATATGTATTTTATTA
1 TATAATTTATAT-TATTTTATTA
969384 TATAATTTATATTATTTTAT
1 TATAATTTATATTATTTTAT
969404 CATTCAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (22 bp):
TATAATTTATATTATTTTATTA
Found at i:971681 original size:38 final size:37
Alignment explanation
Indices: 971595--971681 Score: 97
Period size: 38 Copynumber: 2.4 Consensus size: 37
971585 TAATTAAACG
* * *
971595 AAAAA-ATAAATTAAAAATTTAAATTTAAATCTTTAT
1 AAAAATATAAAATAAAAATTTAAATTTAAATATTCAT
* *
971631 -AAAATATAAAAATAAAAATTATATATTTATATATTCAT
1 AAAAATAT-AAAATAAAAATT-TAAATTTAAATATTCAT
971669 AAAAATATAAAAT
1 AAAAATATAAAAT
971682 TATAATATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
35 4 0.10
36 2 0.05
37 11 0.26
38 18 0.43
39 7 0.17
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (37 bp):
AAAAATATAAAATAAAAATTTAAATTTAAATATTCAT
Found at i:973307 original size:34 final size:33
Alignment explanation
Indices: 973264--973357 Score: 99
Period size: 29 Copynumber: 3.0 Consensus size: 33
973254 TCAATGTCAT
973264 AATTTAAATATTTATATTATATTTATATATTATA
1 AATTTAAATATTTAT-TTATATTTATATATTATA
* *
973298 AATTTAAATATAT-TTTATATTT-T-TATTCTA
1 AATTTAAATATTTATTTATATTTATATATTATA
* * *
973328 TA-TTAAAT-TTTATTTATTTTTATATCTTAT
1 AATTTAAATATTTATTTATATTTATATATTAT
973358 TTATCAAGCC
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
28 2 0.04
29 14 0.28
30 8 0.16
31 5 0.10
32 8 0.16
33 1 0.02
34 12 0.24
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (33 bp):
AATTTAAATATTTATTTATATTTATATATTATA
Found at i:973308 original size:15 final size:16
Alignment explanation
Indices: 973262--973308 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 16
973252 ATTCAATGTC
973262 ATAATTTAAATATTTAT
1 ATAATTTAAATA-TTAT
*
973279 ATTATATTTATATATTAT
1 A-TA-ATTTAAATATTAT
973297 A-AATTTAAATAT
1 ATAATTTAAATAT
973309 ATTTTATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 9 0.35
16 1 0.04
17 1 0.04
18 7 0.27
19 8 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATAATTTAAATATTAT
Found at i:976770 original size:19 final size:18
Alignment explanation
Indices: 976751--976792 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
976741 TATATTTTAT
976751 TTTTATATTAATTATATA
1 TTTTATATTAATTATATA
* *
976769 -TTCATATTATTTATATA
1 TTTTATATTAATTATATA
976786 TATTTAT
1 T-TTTAT
976793 TTTGTGATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 3
0.76 0.12 0.12
Matches are distributed among these distances:
17 15 0.79
19 4 0.21
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTATATTAATTATATA
Found at i:982027 original size:2 final size:2
Alignment explanation
Indices: 982020--982054 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
982010 TAACCTATCA
982020 AT AT AT AT AT 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 A
982055 AAACTATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:985970 original size:27 final size:28
Alignment explanation
Indices: 985919--985978 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
985909 TTATAAAAAT
985919 TTTAATATTTTTATATATTCGTATCATA
1 TTTAATATTTTTATATATTCGTATCATA
* *
985947 TTTATATATTTTT-TATATT-TTATCTTA
1 TTTA-ATATTTTTATATATTCGTATCATA
985974 TTTAA
1 TTTAA
985979 GTTATTTCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 1 0.03
27 10 0.34
28 10 0.34
29 8 0.28
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (28 bp):
TTTAATATTTTTATATATTCGTATCATA
Found at i:1002322 original size:149 final size:149
Alignment explanation
Indices: 1002115--1002413 Score: 598
Period size: 149 Copynumber: 2.0 Consensus size: 149
1002105 ACTAACTAAT
1002115 TGCTGCATTTGTTAATTTAACAGTACTGCTAGCGCTGTGACAGTGAGGAGTACTATTAGGAGGCT
1 TGCTGCATTTGTTAATTTAACAGTACTGCTAGCGCTGTGACAGTGAGGAGTACTATTAGGAGGCT
1002180 GAGGGAGCAAACTGAGAGCTGAGCCACCATTGGTGTAATTCTACTTTCTAGAATGATGATTTGCA
66 GAGGGAGCAAACTGAGAGCTGAGCCACCATTGGTGTAATTCTACTTTCTAGAATGATGATTTGCA
1002245 TGTTTTAGCTACAGACTTA
131 TGTTTTAGCTACAGACTTA
1002264 TGCTGCATTTGTTAATTTAACAGTACTGCTAGCGCTGTGACAGTGAGGAGTACTATTAGGAGGCT
1 TGCTGCATTTGTTAATTTAACAGTACTGCTAGCGCTGTGACAGTGAGGAGTACTATTAGGAGGCT
1002329 GAGGGAGCAAACTGAGAGCTGAGCCACCATTGGTGTAATTCTACTTTCTAGAATGATGATTTGCA
66 GAGGGAGCAAACTGAGAGCTGAGCCACCATTGGTGTAATTCTACTTTCTAGAATGATGATTTGCA
1002394 TGTTTTAGCTACAGACTTA
131 TGTTTTAGCTACAGACTTA
1002413 T
1 T
1002414 TGGGATCTTT
Statistics
Matches: 150, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
149 150 1.00
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (149 bp):
TGCTGCATTTGTTAATTTAACAGTACTGCTAGCGCTGTGACAGTGAGGAGTACTATTAGGAGGCT
GAGGGAGCAAACTGAGAGCTGAGCCACCATTGGTGTAATTCTACTTTCTAGAATGATGATTTGCA
TGTTTTAGCTACAGACTTA
Found at i:1010980 original size:2 final size:2
Alignment explanation
Indices: 1010975--1011006 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1010965 GGGAGAGAAT
*
1010975 GA GA GA GA GA GA GA GA GA AA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1011007 ATGGTGGAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1012184 original size:34 final size:33
Alignment explanation
Indices: 1012128--1012201 Score: 78
Period size: 34 Copynumber: 2.2 Consensus size: 33
1012118 AGATTTTGTA
* *
1012128 AAATTATATACTTAAATGAATATCATAAAAAATT
1 AAATTATATACTAAAATAAATATCATAAAAAA-T
** *
1012162 AAATTATAATAC-AAAATAAATATTTTAAAATAT
1 AAATTAT-ATACTAAAATAAATATCATAAAAAAT
1012195 AAATTAT
1 AAATTAT
1012202 TAATTTATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
33 8 0.24
34 22 0.65
35 4 0.12
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.36
Consensus pattern (33 bp):
AAATTATATACTAAAATAAATATCATAAAAAAT
Found at i:1014076 original size:17 final size:17
Alignment explanation
Indices: 1014015--1014089 Score: 57
Period size: 17 Copynumber: 4.4 Consensus size: 17
1014005 TTTTGATTTA
*
1014015 ATATTTAATAATTTAAT
1 ATATTTTATAATTTAAT
* *
1014032 TTAATTTTA-AATTTTAAA
1 AT-ATTTTATAA-TTTAAT
**
1014050 ATA-TAAATAATTTAAT
1 ATATTTTATAATTTAAT
1014066 ATATTTTATAATATT-AT
1 ATATTTTATAAT-TTAAT
1014083 ATATTTT
1 ATATTTT
1014090 TATATGATAT
Statistics
Matches: 44, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
16 10 0.23
17 21 0.48
18 13 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATATTTTATAATTTAAT
Found at i:1014094 original size:15 final size:17
Alignment explanation
Indices: 1014064--1014100 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
1014054 AAATAATTTA
*
1014064 ATATATTTTATAATATT
1 ATATATTTTATAATATG
1014081 ATATATTTT-T-ATATG
1 ATATATTTTATAATATG
1014096 ATATA
1 ATATA
1014101 AATGATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 9 0.47
16 1 0.05
17 9 0.47
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
ATATATTTTATAATATG
Found at i:1014764 original size:2 final size:2
Alignment explanation
Indices: 1014757--1014790 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1014747 CCAACCTTTA
1014757 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1014791 GTCAAGACTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1017343 original size:2 final size:2
Alignment explanation
Indices: 1017336--1017364 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1017326 AATGAAATAC
1017336 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1017365 GTGAAAACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1017720 original size:8 final size:8
Alignment explanation
Indices: 1017709--1017851 Score: 67
Period size: 8 Copynumber: 18.5 Consensus size: 8
1017699 TATGTAATAT
1017709 TATATAAA
1 TATATAAA
1017717 TATAT--A
1 TATATAAA
1017723 TGATATAAA
1 T-ATATAAA
1017732 TATATAAA
1 TATATAAA
1017740 TATATTTAAAA
1 TATA--T-AAA
*
1017751 TTTATATAA
1 TATATA-AA
1017760 TATA-AAA
1 TATATAAA
*
1017767 T-TATTAA
1 TATATAAA
1017774 TATATAAA
1 TATATAAA
**
1017782 -AT-TTTA
1 TATATAAA
*
1017788 TGTATAAA
1 TATATAAA
1017796 -ATATAAAA
1 TATAT-AAA
*
1017804 TAATTTAAA
1 T-ATATAAA
1017813 TATAT---
1 TATATAAA
1017818 T-TATAAA
1 TATATAAA
1017825 TATATAAA
1 TATATAAA
*
1017833 AATATAAA
1 TATATAAA
*
1017841 AATAT-AA
1 TATATAAA
1017848 TATA
1 TATA
1017852 AATTTATAAT
Statistics
Matches: 103, Mismatches: 14, Indels: 37
0.67 0.09 0.24
Matches are distributed among these distances:
4 3 0.03
5 1 0.01
6 6 0.06
7 22 0.21
8 49 0.48
9 12 0.12
10 4 0.04
11 6 0.06
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (8 bp):
TATATAAA
Found at i:1017728 original size:15 final size:15
Alignment explanation
Indices: 1017705--1017737 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1017695 TAATTATGTA
*
1017705 ATATTATATAAATAT
1 ATATGATATAAATAT
1017720 ATATGATATAAATAT
1 ATATGATATAAATAT
1017735 ATA
1 ATA
1017738 AATATATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
ATATGATATAAATAT
Found at i:1017840 original size:16 final size:16
Alignment explanation
Indices: 1017704--1017847 Score: 60
Period size: 17 Copynumber: 8.6 Consensus size: 16
1017694 ATAATTATGT
*
1017704 AATATTATATAAATATA
1 AATA-TATAAAAATATA
* *
1017721 TATGATATAAATATATA
1 AAT-ATATAAAAATATA
* *
1017738 AATATATTTAAAATTTA
1 AATATA-TAAAAATATA
* * *
1017755 TATAATATAAAATTATT
1 AAT-ATATAAAAATATA
*
1017772 AATATAT-AAAAT-TT
1 AATATATAAAAATATA
* *
1017786 TATGTAT-AAAATATAA
1 AATATATAAAAATAT-A
*
1017802 AATAATTTAAATATATTTATA
1 AAT-ATATAAA-A-A--TATA
1017823 AATATATAAAAATATA
1 AATATATAAAAATATA
*
1017839 AAAATATAA
1 AATATATAA
1017848 TATAAATTTA
Statistics
Matches: 94, Mismatches: 22, Indels: 23
0.68 0.16 0.17
Matches are distributed among these distances:
14 12 0.13
15 5 0.05
16 21 0.22
17 33 0.35
18 7 0.07
19 2 0.02
20 7 0.07
21 4 0.04
22 3 0.03
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (16 bp):
AATATATAAAAATATA
Found at i:1017840 original size:28 final size:30
Alignment explanation
Indices: 1017685--1017860 Score: 101
Period size: 29 Copynumber: 5.7 Consensus size: 30
1017675 ATATTATTTT
* * * *
1017685 AAATATGATATAATTATGTAATATTATATAA
1 AAATATAATATAAATATATAA-ATAATATAA
* *
1017716 ATATATATGATATAAATATATAAATATATTTAA
1 A-A-ATATAATATAAATATATAAATA-ATATAA
*
1017749 AATTTATATAATATAAA-ATTATTAAT-ATATAA
1 AA---ATATAATATAAATA-TATAAATAATATAA
* * * *
1017781 AATTTTATGTATAAA-ATATAAAATAATTTAA
1 AAATATA-ATATAAATATAT-AAATAATATAA
* *
1017812 ATATAT-TTATAAATATATAAA-AATATAA
1 AAATATAATATAAATATATAAATAATATAA
*
1017840 AAATATAATATAAATTTATAA
1 AAATATAATATAAATATATAA
1017861 TTATTATGTA
Statistics
Matches: 114, Mismatches: 20, Indels: 24
0.72 0.13 0.15
Matches are distributed among these distances:
28 11 0.10
29 27 0.24
30 14 0.12
31 9 0.08
32 11 0.10
33 24 0.21
34 18 0.16
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (30 bp):
AAATATAATATAAATATATAAATAATATAA
Found at i:1019163 original size:22 final size:21
Alignment explanation
Indices: 1019125--1019172 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
1019115 TTTAAAAAAA
1019125 TAAAATTATTAAATATTTAATT
1 TAAAATTATTAAATA-TTAATT
*
1019147 TAAAATTAATT-AGTATTAATT
1 TAAAATT-ATTAAATATTAATT
*
1019168 AAAAA
1 TAAAA
1019173 AACTAGCTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 10 0.43
22 10 0.43
23 3 0.13
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
TAAAATTATTAAATATTAATT
Found at i:1024175 original size:18 final size:18
Alignment explanation
Indices: 1024152--1024188 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1024142 AGATATGATC
1024152 ATCTAAATATATAAATCT
1 ATCTAAATATATAAATCT
1024170 ATCTAAATATATAAATCT
1 ATCTAAATATATAAATCT
1024188 A
1 A
1024189 GACAACGGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (18 bp):
ATCTAAATATATAAATCT
Found at i:1030895 original size:3 final size:3
Alignment explanation
Indices: 1030876--1030936 Score: 106
Period size: 3 Copynumber: 20.3 Consensus size: 3
1030866 GTCTTCAACT
1030876 ATA ATGA ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1030921 ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA A
1030937 AAGGGTATGG
Statistics
Matches: 56, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.04
3 51 0.91
4 3 0.05
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:1031072 original size:14 final size:14
Alignment explanation
Indices: 1031055--1031085 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1031045 AAATTAACCG
1031055 AACCTAATTTTTCA
1 AACCTAATTTTTCA
*
1031069 AACCTAATTTTTTA
1 AACCTAATTTTTCA
1031083 AAC
1 AAC
1031086 TCAAATTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.19, G:0.00, T:0.42
Consensus pattern (14 bp):
AACCTAATTTTTCA
Found at i:1033356 original size:6 final size:6
Alignment explanation
Indices: 1033347--1033382 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
1033337 AACTAAAAAC
1033347 AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG
1 AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG
1033383 GGAAAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (6 bp):
AAAAGG
Found at i:1033392 original size:18 final size:17
Alignment explanation
Indices: 1033342--1033381 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
1033332 ACGTAAACTA
*
1033342 AAAACAAAAGGAAAAGG
1 AAAAGAAAAGGAAAAGG
1033359 AAAAGGAAAAGGAAAAGG
1 AAAA-GAAAAGGAAAAGG
1033377 AAAAG
1 AAAAG
1033382 GGGAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.70, C:0.03, G:0.28, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAGGAAAAGG
Found at i:1037564 original size:22 final size:22
Alignment explanation
Indices: 1037530--1037586 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
1037520 AATATTAAAT
1037530 AAATTT-TAA-TTTTAATTTTA
1 AAATTTATAATTTTTAATTTTA
* *
1037550 ATATTTATAATTTTTTATTTTA
1 AAATTTATAATTTTTAATTTTA
* *
1037572 AAATTAAAAATTTTT
1 AAATTTATAATTTTT
1037587 TCATATAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 5 0.17
21 3 0.10
22 22 0.73
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
AAATTTATAATTTTTAATTTTA
Found at i:1037578 original size:28 final size:29
Alignment explanation
Indices: 1037508--1037578 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 29
1037498 TATGTAATTA
* *
1037508 TATTTAAAAAATAATATTAAATAAATTTT
1 TATTTTAAAATTAATATTAAATAAATTTT
* ** * *
1037537 AATTTTAATTTTAATATT-TATAATTTTT
1 TATTTTAAAATTAATATTAAATAAATTTT
1037565 TATTTTAAAATTAA
1 TATTTTAAAATTAA
1037579 AAATTTTTTC
Statistics
Matches: 32, Mismatches: 10, Indels: 1
0.74 0.23 0.02
Matches are distributed among these distances:
28 19 0.59
29 13 0.41
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (29 bp):
TATTTTAAAATTAATATTAAATAAATTTT
Found at i:1038514 original size:23 final size:25
Alignment explanation
Indices: 1038488--1038542 Score: 71
Period size: 23 Copynumber: 2.3 Consensus size: 25
1038478 ATATTTTAAA
* *
1038488 TTTAAAATATTAAATA-TAAAT-AT
1 TTTAAAATAATAAAAATTAAATGAT
1038511 TTTAAAA-AATAAAAATTAAATGAT
1 TTTAAAATAATAAAAATTAAATGAT
1038535 TTTAAAAT
1 TTTAAAAT
1038543 GCATCTAGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 6 0.22
23 12 0.44
24 9 0.33
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
TTTAAAATAATAAAAATTAAATGAT
Found at i:1038812 original size:13 final size:14
Alignment explanation
Indices: 1038796--1038824 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1038786 GTAACTTAGA
1038796 TTTTTTTTAAA-AT
1 TTTTTTTTAAATAT
1038809 TTTTTTTTAAATAT
1 TTTTTTTTAAATAT
1038823 TT
1 TT
1038825 ATGTTTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTTTTTAAATAT
Found at i:1038852 original size:11 final size:11
Alignment explanation
Indices: 1038836--1038888 Score: 69
Period size: 11 Copynumber: 5.1 Consensus size: 11
1038826 TGTTTGATAT
1038836 TATATTTAATA
1 TATATTTAATA
1038847 TATATTT-A-A
1 TATATTTAATA
1038856 -ATATTTAATA
1 TATATTTAATA
1038866 TATATTTAA-A
1 TATATTTAATA
1038876 TATATATTAATA
1 TATAT-TTAATA
1038888 T
1 T
1038889 TTAATATTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
8 6 0.16
9 2 0.05
10 8 0.22
11 19 0.51
12 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TATATTTAATA
Found at i:1038861 original size:19 final size:19
Alignment explanation
Indices: 1038837--1038898 Score: 92
Period size: 19 Copynumber: 3.4 Consensus size: 19
1038827 GTTTGATATT
1038837 ATATTTAATATATATTTAA
1 ATATTTAATATATATTTAA
1038856 ATATTTAATATATATTTAA
1 ATATTTAATATATATTTAA
* *
1038875 ATATATATTA-ATATTT-A
1 ATATTTAATATATATTTAA
1038892 ATATTTA
1 ATATTTA
1038899 TCTTAAATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
17 7 0.17
18 6 0.15
19 27 0.68
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATATTTAATATATATTTAA
Found at i:1038868 original size:17 final size:18
Alignment explanation
Indices: 1038837--1038913 Score: 77
Period size: 19 Copynumber: 4.2 Consensus size: 18
1038827 GTTTGATATT
1038837 ATATTTAATATATATTTAA
1 ATATTT-ATATATATTTAA
1038856 ATATTTAATATATATTTAA
1 ATATTT-ATATATATTTAA
*
1038875 ATATATAT-TAATATTT-A
1 ATATTTATAT-ATATTTAA
* *
1038892 ATATTTATCTTAAATTTAA
1 ATATTTAT-ATATATTTAA
1038911 ATA
1 ATA
1038914 ACATAGGAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
17 9 0.18
18 13 0.25
19 29 0.57
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (18 bp):
ATATTTATATATATTTAA
Found at i:1038887 original size:29 final size:31
Alignment explanation
Indices: 1038836--1038906 Score: 103
Period size: 29 Copynumber: 2.4 Consensus size: 31
1038826 TGTTTGATAT
1038836 TATATTT-AATATATATTTAAATATTTAATA
1 TATATTTAAATATATATTTAAATATTTAATA
1038866 TATATTTAAATATATA-TT-AATATTTAATA
1 TATATTTAAATATATATTTAAATATTTAATA
*
1038895 TTTATCTTAAAT
1 TATAT-TTAAAT
1038907 TTAAATAACA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
29 15 0.39
30 15 0.39
31 8 0.21
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (31 bp):
TATATTTAAATATATATTTAAATATTTAATA
Found at i:1039849 original size:11 final size:11
Alignment explanation
Indices: 1039833--1039858 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1039823 TAAATATAAT
1039833 GTAATTTAAAA
1 GTAATTTAAAA
1039844 GTAATTTAAAA
1 GTAATTTAAAA
1039855 GTAA
1 GTAA
1039859 GAAATTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.35
Consensus pattern (11 bp):
GTAATTTAAAA
Found at i:1042438 original size:22 final size:21
Alignment explanation
Indices: 1042413--1042463 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
1042403 ATAAGTATGA
*
1042413 AAATATAATTCTTTAAATAAA-T
1 AAATATAAAT-TTTAAA-AAATT
1042435 AAATATAAAATTTTAAAAAATT
1 AAATAT-AAATTTTAAAAAATT
1042457 AAATATA
1 AAATATA
1042464 TTTATATCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 4 0.15
22 19 0.73
23 3 0.12
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
AAATATAAATTTTAAAAAATT
Found at i:1043932 original size:51 final size:51
Alignment explanation
Indices: 1043876--1043978 Score: 179
Period size: 51 Copynumber: 2.0 Consensus size: 51
1043866 TCATGATACA
*
1043876 TAAGGATAAAACGAATGCTATGTTTCATTTAGTGTTTACAGGCCATGAAAT
1 TAAGGATAAAACGAATGCTATGTTTCATTTAGTGTTTACAGACCATGAAAT
* *
1043927 TAAGGATAAAACGAATGCTATGTTTCGTTTAGTGTTTACAGATCATGAAAT
1 TAAGGATAAAACGAATGCTATGTTTCATTTAGTGTTTACAGACCATGAAAT
1043978 T
1 T
1043979 CGTACACAGG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (51 bp):
TAAGGATAAAACGAATGCTATGTTTCATTTAGTGTTTACAGACCATGAAAT
Found at i:1048950 original size:29 final size:29
Alignment explanation
Indices: 1048918--1049005 Score: 108
Period size: 28 Copynumber: 3.1 Consensus size: 29
1048908 TTTTTTTAAT
**
1048918 ATAAAAAAGTATTTAAATATAAATTAAAA
1 ATAAAAATTTATTTAAATATAAATTAAAA
* * *
1048947 ATAACAATTTATTTTAATAT-AATAAAAA
1 ATAAAAATTTATTTAAATATAAATTAAAA
1048975 ATAAAAATTTATTTAAATA-AAATTATAAA
1 ATAAAAATTTATTTAAATATAAATTA-AAA
1049004 AT
1 AT
1049006 TGAGGGACTT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
28 28 0.57
29 21 0.43
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (29 bp):
ATAAAAATTTATTTAAATATAAATTAAAA
Found at i:1055078 original size:2 final size:2
Alignment explanation
Indices: 1055071--1055117 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1055061 ATGCTATATG
1055071 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1055113 CT CT C
1 CT CT C
1055118 ATCTTTTGGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Done.