Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold258
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: 5730937
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 25
Found at i:3460587 original size:2 final size:2
Alignment explanation
Indices: 3460580--3460611 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3460570 TTTGGAGGGC
3460580 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3460612 AGAGGATTAG
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:3460930 original size:2 final size:2
Alignment explanation
Indices: 3460923--3460956 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3460913 TAATACATAC
3460923 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
3460957 CATTACTGAT
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:3462703 original size:23 final size:23
Alignment explanation
Indices: 3462677--3462725 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
3462667 ATCTATTTAA
* * *
3462677 TAAAAAAATTCATATTATATATT
1 TAAAAAAATTAATAATATAAATT
3462700 TAAAAAAATTAATAATATAAATT
1 TAAAAAAATTAATAATATAAATT
3462723 TAA
1 TAA
3462726 TGTGTCATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
TAAAAAAATTAATAATATAAATT
Found at i:3464195 original size:47 final size:46
Alignment explanation
Indices: 3464096--3464214 Score: 114
Period size: 51 Copynumber: 2.5 Consensus size: 46
3464086 TTTTTACATG
* *
3464096 AATAAAATTATAAATTTTTTATATAAATATTTTGTAACTATTTTAC
1 AATAAAATTATAAATTTTTTAGATAAATATTTAGTAACTATTTTAC
* *
3464142 GAATAAAATTATAAATTTTTTTTACGATAAATATATTAGTAA-TTTTTATATA
1 -AATAAAATTATAAA--TTTTTTA-GATAAATAT-TTAGTAACTATTT-TA-C
* *
3464194 AATAAAGTTATAAATTATTTA
1 AATAAAATTATAAATTTTTTA
3464215 ACAAACAACT
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
47 14 0.23
49 13 0.22
50 12 0.20
51 21 0.35
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (46 bp):
AATAAAATTATAAATTTTTTAGATAAATATTTAGTAACTATTTTAC
Found at i:3464832 original size:6 final size:6
Alignment explanation
Indices: 3464818--3464875 Score: 50
Period size: 6 Copynumber: 10.0 Consensus size: 6
3464808 AATTAATAAG
* * *
3464818 TTATTT TTATAT TTATAT TTATA- -T-TAT TTACAT ATTATTT TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT -TTATAT TTATAT
*
3464864 TAATAT TTATAT
1 TTATAT TTATAT
3464876 ATTTTGATAA
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
3 2 0.05
4 1 0.02
5 1 0.02
6 33 0.80
7 4 0.10
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (6 bp):
TTATAT
Found at i:3464878 original size:22 final size:22
Alignment explanation
Indices: 3464853--3464894 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3464843 ATTTACATAT
*
3464853 TATTTTTAT-ATTAATATTTATA
1 TATTTTGATAATTAA-ATTTATA
3464875 TATTTTGATAATTAAATTTA
1 TATTTTGATAATTAAATTTA
3464895 AATAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TATTTTGATAATTAAATTTATA
Found at i:3466041 original size:24 final size:25
Alignment explanation
Indices: 3466009--3466069 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 25
3465999 ACCTTCCTCA
3466009 TTTACTATTATATAATG--ATATTAAT
1 TTTA-TATTATATAATGTAATA-TAAT
3466034 TTTATATT-TAT-ATGTAATATAAT
1 TTTATATTATATAATGTAATATAAT
*
3466057 TTT-TATCATATAA
1 TTTATATTATATAA
3466070 AAAAATATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
22 6 0.19
23 13 0.42
24 8 0.26
25 4 0.13
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.54
Consensus pattern (25 bp):
TTTATATTATATAATGTAATATAAT
Found at i:3466306 original size:20 final size:20
Alignment explanation
Indices: 3466262--3466304 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
3466252 TACATATAAA
*
3466262 TAAATTTAAAATTTATATTT
1 TAAATTTAAAATTTAAATTT
*
3466282 TAAATTTTAAA-TTAAATTT
1 TAAATTTAAAATTTAAATTT
3466301 TAAA
1 TAAA
3466305 ATATATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TAAATTTAAAATTTAAATTT
Found at i:3466778 original size:3 final size:3
Alignment explanation
Indices: 3466770--3466801 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
3466760 CGCAAAATCA
*
3466770 AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3466802 CGTATTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:3466937 original size:20 final size:21
Alignment explanation
Indices: 3466912--3466952 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
3466902 CAATTTTTTG
*
3466912 ATTTATTTATTTAT-TGTTAA
1 ATTTATTTAATTATATGTTAA
3466932 ATTTATTTAATTATATGTTAA
1 ATTTATTTAATTATATGTTAA
3466953 TTAGTGTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (21 bp):
ATTTATTTAATTATATGTTAA
Found at i:3467055 original size:20 final size:20
Alignment explanation
Indices: 3467019--3467056 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3467009 CAATGTGTTG
*
3467019 ATTAATATAATTTATATTGT
1 ATTAATATAATTCATATTGT
3467039 ATTAATATCAA-TCATATT
1 ATTAATAT-AATTCATATT
3467057 AATTCAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (20 bp):
ATTAATATAATTCATATTGT
Found at i:3467193 original size:17 final size:16
Alignment explanation
Indices: 3467151--3467193 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
3467141 AACATGTTTA
*
3467151 TTTTTTTTTCAATTCT
1 TTTTTTTTTCAATTAT
*
3467167 TTTTAATTTTCAATTAT
1 TTTT-TTTTTCAATTAT
3467184 TTTATTTTTT
1 TTT-TTTTTT
3467194 AAAAAATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 4 0.18
17 17 0.77
18 1 0.05
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTTTTTCAATTAT
Found at i:3467505 original size:19 final size:20
Alignment explanation
Indices: 3467481--3467519 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
3467471 AAGAAGTAAC
3467481 TCATTTCTTGGTATA-AAAA
1 TCATTTCTTGGTATATAAAA
*
3467500 TCATTTCTTGTTATATAAAA
1 TCATTTCTTGGTATATAAAA
3467520 AGCCACTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.46
Consensus pattern (20 bp):
TCATTTCTTGGTATATAAAA
Found at i:3467749 original size:10 final size:10
Alignment explanation
Indices: 3467736--3467768 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
3467726 CAAAATTTTC
3467736 TAAAAAAAAT
1 TAAAAAAAAT
3467746 TAAAAAAAAT
1 TAAAAAAAAT
3467756 TAAAAAAAAT
1 TAAAAAAAAT
3467766 TAA
1 TAA
3467769 TACTTTTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
TAAAAAAAAT
Found at i:3472734 original size:22 final size:23
Alignment explanation
Indices: 3472695--3472740 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
3472685 TTATTTATTT
*
3472695 ATTTAAGTATAAATTAAAAATTA
1 ATTTAAATATAAATTAAAAATTA
3472718 ATTTAAATAT-AATTAAAAATTA
1 ATTTAAATATAAATTAAAAATTA
3472740 A
1 A
3472741 AAAATTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (23 bp):
ATTTAAATATAAATTAAAAATTA
Found at i:3472775 original size:59 final size:59
Alignment explanation
Indices: 3472680--3472809 Score: 165
Period size: 59 Copynumber: 2.2 Consensus size: 59
3472670 TTATATTTTT
* * *
3472680 AATATTTATTTATTTATTTAAGTATAAATTAAAAATTAATTTAAATATAATTAAAAATTAA
1 AATAATTATTTATTTATTAAAGTAAAAATTAAAAATTAATTTAAATATAA-TAAAAA-TAA
* * *
3472741 AA-AATTATTTATTTA-TAAATTAAAAATTAAAAATTTATTTTAATATAATAAAAATAA
1 AATAATTATTTATTTATTAAAGTAAAAATTAAAAATTAATTTAAATATAATAAAAATAA
*
3472798 AATATTTATTTA
1 AATAATTATTTA
3472810 AATAAAATAA
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
57 5 0.08
58 14 0.23
59 28 0.46
60 12 0.20
61 2 0.03
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (59 bp):
AATAATTATTTATTTATTAAAGTAAAAATTAAAAATTAATTTAAATATAATAAAAATAA
Found at i:3472793 original size:28 final size:29
Alignment explanation
Indices: 3472705--3472813 Score: 141
Period size: 30 Copynumber: 3.8 Consensus size: 29
3472695 ATTTAAGTAT
*
3472705 AAATTAAAAATTAATTTAAATATAATTAA
1 AAATTAAAAATTTATTTAAATATAATTAA
* **
3472734 AAATTAAAAAATTATTTATTTATAAATTAA
1 AAATTAAAAATTTATTTAAATAT-AATTAA
*
3472764 AAATTAAAAATTTATTTTAATATAA-TAA
1 AAATTAAAAATTTATTTAAATATAATTAA
3472792 AAA-TAAAATATTTATTTAAATA
1 AAATTAAAA-ATTTATTTAAATA
3472814 AAATAATATA
Statistics
Matches: 69, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
27 5 0.07
28 18 0.26
29 21 0.30
30 25 0.36
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (29 bp):
AAATTAAAAATTTATTTAAATATAATTAA
Found at i:3472818 original size:28 final size:28
Alignment explanation
Indices: 3472686--3472819 Score: 105
Period size: 28 Copynumber: 4.7 Consensus size: 28
3472676 TTTTAATATT
* * * *
3472686 TATTTATTTATTTAAGTATAAATTAAAA
1 TATTTATTTAATAAAATAAAAATTAAAA
* *
3472714 -ATTAATTTAAATATAATTAAAAATTAAAAAA
1 TATTTATTT-AATA-AAATAAAAATT--AAAA
*
3472745 TTATTTATTT-ATAAATTAAAAATTAAAA
1 -TATTTATTTAATAAAATAAAAATTAAAA
*
3472773 -ATTTATTTTAATATAATAAAAA-TAAAA
1 TATTTA-TTTAATAAAATAAAAATTAAAA
3472800 TATTTATTTAAATAAAATAA
1 TATTTATTT-AATAAAATAA
3472820 TATATATATT
Statistics
Matches: 87, Mismatches: 9, Indels: 20
0.75 0.08 0.17
Matches are distributed among these distances:
26 5 0.06
27 18 0.21
28 30 0.34
29 9 0.10
30 11 0.13
31 7 0.08
33 7 0.08
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (28 bp):
TATTTATTTAATAAAATAAAAATTAAAA
Found at i:3476692 original size:6 final size:6
Alignment explanation
Indices: 3476683--3476716 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
3476673 GAAAGGAAGT
* *
3476683 TAGGGT TAGGGT TAGGGC TAGGGC TAGGGC TAGG
1 TAGGGC TAGGGC TAGGGC TAGGGC TAGGGC TAGG
3476717 ATAAGCTGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.09, G:0.50, T:0.24
Consensus pattern (6 bp):
TAGGGC
Found at i:3477329 original size:20 final size:20
Alignment explanation
Indices: 3477306--3477352 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
3477296 TTTTATTAGT
*
3477306 TATTTT-GATATATTATTTAA
1 TATTTTAGATATATTA-TAAA
*
3477326 TATTTATAGATATTTTATAAA
1 TATTT-TAGATATATTATAAA
3477347 TATTTT
1 TATTTT
3477353 TAATATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (20 bp):
TATTTTAGATATATTATAAA
Found at i:3477337 original size:22 final size:21
Alignment explanation
Indices: 3477312--3477360 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
3477302 TAGTTATTTT
*
3477312 GATATATTATTTAATATTTATA
1 GATATATTA-TAAATATTTATA
* *
3477334 GATATTTTATAAATATTTTTA
1 GATATATTATAAATATTTATA
3477355 -ATATAT
1 GATATAT
3477361 AAATTATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 5 0.22
21 10 0.43
22 8 0.35
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (21 bp):
GATATATTATAAATATTTATA
Found at i:3477340 original size:30 final size:30
Alignment explanation
Indices: 3477297--3477358 Score: 74
Period size: 30 Copynumber: 2.0 Consensus size: 30
3477287 TAATATATTT
*
3477297 TTTATTAGTTATTTTGAT-ATATTATTTAATA
1 TTTATTAGATATTTT-ATAATATT-TTTAATA
3477328 TTTA-TAGATATTTTATAAATATTTTTAATA
1 TTTATTAGATATTTTAT-AATATTTTTAATA
3477358 T
1 T
3477359 ATAAATTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
29 2 0.07
30 17 0.61
31 9 0.32
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (30 bp):
TTTATTAGATATTTTATAATATTTTTAATA
Found at i:3477361 original size:28 final size:30
Alignment explanation
Indices: 3477315--3477383 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 30
3477305 TTATTTTGAT
*
3477315 ATATTATTTAATATTTATAGA-TATTTTATAA
1 ATATT-TTTAATA-TTATAAATTATTTTATAA
* *
3477346 ATATTTTTAATA-TATAAATTATTTTTTAT
1 ATATTTTTAATATTATAAATTATTTTATAA
3477375 AT-TTTTTAA
1 ATATTTTTAA
3477384 CAAAATATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 12 0.35
29 10 0.29
30 7 0.21
31 5 0.15
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (30 bp):
ATATTTTTAATATTATAAATTATTTTATAA
Found at i:3477363 original size:17 final size:18
Alignment explanation
Indices: 3477341--3477376 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3477331 ATAGATATTT
3477341 TATAAA-TATTTTTAATA
1 TATAAATTATTTTTAATA
*
3477358 TATAAATTATTTTTTATA
1 TATAAATTATTTTTAATA
3477376 T
1 T
3477377 TTTTTAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TATAAATTATTTTTAATA
Found at i:3477815 original size:16 final size:15
Alignment explanation
Indices: 3477794--3477834 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
3477784 AACAATAGCC
3477794 TAAATACAAAAAATT
1 TAAATACAAAAAATT
3477809 ATAAATAC-AAAAATT
1 -TAAATACAAAAAATT
*
3477824 TAAATTCAAAA
1 TAAATACAAAA
3477835 TTTGCAAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 6 0.26
15 10 0.43
16 7 0.30
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (15 bp):
TAAATACAAAAAATT
Found at i:3477837 original size:13 final size:14
Alignment explanation
Indices: 3477794--3477834 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
3477784 AACAATAGCC
3477794 TAAATACAAAAAATT
1 TAAATAC-AAAAATT
3477809 ATAAATACAAAAATT
1 -TAAATACAAAAATT
*
3477824 TAAATTCAAAA
1 TAAATACAAAA
3477835 TTTGCAAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 10 0.42
15 7 0.29
16 7 0.29
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (14 bp):
TAAATACAAAAATT
Found at i:3478808 original size:2 final size:2
Alignment explanation
Indices: 3478801--3478837 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3478791 CCATTTTTGT
3478801 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
3478838 TGTATTCGAA
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:3484357 original size:2 final size:2
Alignment explanation
Indices: 3484352--3484384 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3484342 CTCTAATACC
3484352 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 A
3484385 CACCACAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3484870 original size:6 final size:6
Alignment explanation
Indices: 3484849--3484880 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
3484839 GTGTCCAGAA
3484849 TTTTA- TTTTA- TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT
3484881 TTGACGAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 10 0.38
6 16 0.62
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:3485293 original size:2 final size:2
Alignment explanation
Indices: 3485286--3485317 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3485276 ATCGTAACCA
3485286 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
3485318 GGCAACATGT
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):
AT
Found at i:3486133 original size:2 final size:2
Alignment explanation
Indices: 3486126--3486154 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3486116 CAAGTTAATT
3486126 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3486155 AAAAATTGTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3486604 original size:3 final size:3
Alignment explanation
Indices: 3486598--3486625 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3486588 TCTCCACCAC
3486598 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3486626 TTGTTCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3488391 original size:2 final size:2
Alignment explanation
Indices: 3488384--3488412 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3488374 AATGCACTAT
3488384 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
3488413 TATCAAATAG
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:3488787 original size:22 final size:24
Alignment explanation
Indices: 3488739--3488788 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 24
3488729 TTATTATTCA
*
3488739 ATTATAATTATATTATCATTTACT
1 ATTATAATTATATTATCATATACT
*
3488763 ATTAT-ATTATA-TATCATATATT
1 ATTATAATTATATTATCATATACT
3488785 ATTA
1 ATTA
3488789 CCTTATAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 13 0.54
23 6 0.25
24 5 0.21
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (24 bp):
ATTATAATTATATTATCATATACT
Found at i:3488794 original size:22 final size:23
Alignment explanation
Indices: 3488745--3488795 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
3488735 TTCAATTATA
* *
3488745 ATTATATTATCATTTACTATTAT
1 ATTATATTATCATATACTATTAC
*
3488768 ATTATA-TATCATATATTATTAC
1 ATTATATTATCATATACTATTAC
*
3488790 CTTATA
1 ATTATA
3488796 AGTATTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (23 bp):
ATTATATTATCATATACTATTAC
Found at i:3492602 original size:23 final size:23
Alignment explanation
Indices: 3492576--3492642 Score: 73
Period size: 23 Copynumber: 2.8 Consensus size: 23
3492566 AAAAATAAAT
3492576 ATATAAAAATTTTATTTTTAATA
1 ATATAAAAATTTTATTTTTAATA
*
3492599 ATATAATAATATTTAATTTATTAATA
1 ATATAA-AA-ATTTTATTT-TTAATA
* *
3492625 ATATATAAA-TATATTTTT
1 ATATAAAAATTTTATTTTT
3492643 TTCGTATATC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
22 2 0.05
23 11 0.30
24 3 0.08
25 10 0.27
26 11 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
ATATAAAAATTTTATTTTTAATA
Found at i:3492613 original size:18 final size:18
Alignment explanation
Indices: 3492592--3492639 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
3492582 AAATTTTATT
3492592 TTTAATA-ATATAATAATA
1 TTTAATATAT-TAATAATA
*
3492610 TTTAATTTATTAATAATA
1 TTTAATATATTAATAATA
*
3492628 TATAAATATATT
1 T-TTAATATATT
3492640 TTTTTCGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAATATATTAATAATA
Found at i:3492635 original size:26 final size:25
Alignment explanation
Indices: 3492573--3492636 Score: 85
Period size: 25 Copynumber: 2.5 Consensus size: 25
3492563 TTTAAAAATA
* *
3492573 AATATATAAAAATTTTATTTTTAAT
1 AATATATAAATATTTAATTTTTAAT
3492598 AATATA-ATAATATTTAATTTATTAAT
1 AATATATA-AATATTTAATTT-TTAAT
3492624 AATATATAAATAT
1 AATATATAAATAT
3492637 ATTTTTTTCG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
24 1 0.03
25 16 0.47
26 16 0.47
27 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
AATATATAAATATTTAATTTTTAAT
Found at i:3495001 original size:19 final size:17
Alignment explanation
Indices: 3494969--3495007 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 17
3494959 TATTAAAATT
3494969 TTAAATAAAATATAATA
1 TTAAATAAAATATAATA
3494986 TTAAATATATAATATAATA
1 TTAAATA-A-AATATAATA
3495005 TTA
1 TTA
3495008 TTTAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 7 0.35
18 1 0.05
19 12 0.60
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAAATAAAATATAATA
Found at i:3495050 original size:16 final size:17
Alignment explanation
Indices: 3494973--3495053 Score: 51
Period size: 16 Copynumber: 4.7 Consensus size: 17
3494963 AAAATTTTAA
3494973 ATAAAATATAATATTAAAT
1 ATAAAATATAATA-T-AAT
* *
3494992 ATATAATATAATATTAT
1 ATAAAATATAATATAAT
* *
3495009 -TTAAATATACCATATCAT
1 ATAAAATATA--ATATAAT
**
3495027 AT-CTATATAATAT-AT
1 ATAAAATATAATATAAT
3495042 ATAAAATATAAT
1 ATAAAATATAAT
3495054 TTTTTTGCCA
Statistics
Matches: 49, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
15 4 0.08
16 18 0.37
17 2 0.04
18 12 0.24
19 13 0.27
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAAAATATAATATAAT
Found at i:3495278 original size:32 final size:33
Alignment explanation
Indices: 3495228--3495352 Score: 85
Period size: 32 Copynumber: 3.6 Consensus size: 33
3495218 ATTCATTGAA
3495228 TTTAATATAATATATTAATTTCATTAATTACTT
1 TTTAATATAATATATTAATTTCATTAATTACTT
* * * *
3495261 TTTAA-ATTATATTTTAA-TTCTTTTAATAAAATAATT
1 TTTAATATAATATATTAATTTC-ATTAAT----TACTT
*
3495297 GAATTTAATATAATATATTAATTTTATTAATTAC-T
1 ---TTTAATATAATATATTAATTTCATTAATTACTT
* * *
3495332 TTTAAAATTATATTTTAATTT
1 TTTAATATAATATATTAATTT
3495353 TTTTAGTAAA
Statistics
Matches: 70, Mismatches: 12, Indels: 21
0.68 0.12 0.20
Matches are distributed among these distances:
31 3 0.04
32 33 0.47
33 5 0.07
35 1 0.01
36 6 0.09
39 5 0.07
40 15 0.21
41 2 0.03
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (33 bp):
TTTAATATAATATATTAATTTCATTAATTACTT
Found at i:3495299 original size:72 final size:72
Alignment explanation
Indices: 3495222--3495364 Score: 250
Period size: 72 Copynumber: 2.0 Consensus size: 72
3495212 AGTCTCATTC
*
3495222 ATTGAATTTAATATAATATATTAATTTCATTAATTACTTTTTAAATTATATTTTAATTCTTTTAA
1 ATTGAATTTAATATAATATATTAATTTCATTAATTACTTTTAAAATTATATTTTAATTCTTTTAA
3495287 TAAAATA
66 TAAAATA
* * *
3495294 ATTGAATTTAATATAATATATTAATTTTATTAATTACTTTTAAAATTATATTTTAATTTTTTTAG
1 ATTGAATTTAATATAATATATTAATTTCATTAATTACTTTTAAAATTATATTTTAATTCTTTTAA
3495359 TAAAAT
66 TAAAAT
3495365 TTGAACAGTT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 67 1.00
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (72 bp):
ATTGAATTTAATATAATATATTAATTTCATTAATTACTTTTAAAATTATATTTTAATTCTTTTAA
TAAAATA
Found at i:3495305 original size:18 final size:18
Alignment explanation
Indices: 3495282--3495320 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3495272 TTTTAATTCT
3495282 TTTAATAAAATA-ATTGAA
1 TTTAATAAAATATATT-AA
*
3495300 TTTAATATAATATATTAA
1 TTTAATAAAATATATTAA
3495318 TTT
1 TTT
3495321 TATTAATTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
TTTAATAAAATATATTAA
Found at i:3496176 original size:18 final size:18
Alignment explanation
Indices: 3496155--3496203 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 18
3496145 CAACAGTCAT
3496155 ATATAATAATTA-TAAATC
1 ATATAA-AATTATTAAATC
*
3496173 ATATAAAAAATTATTAAATT
1 ATAT--AAAATTATTAAATC
3496193 ATATAAAATTA
1 ATATAAAATTA
3496204 ATTTATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 11 0.41
19 5 0.19
20 11 0.41
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATAAAATTATTAAATC
Found at i:3496176 original size:20 final size:20
Alignment explanation
Indices: 3496151--3496200 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
3496141 AATACAACAG
*
3496151 TCATATATAATAATTA-TAAA
1 TCATATA-AAAAATTATTAAA
3496171 TCATATAAAAAATTATTAAA
1 TCATATAAAAAATTATTAAA
*
3496191 TTATATAAAA
1 TCATATAAAA
3496201 TTAATTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 7 0.26
20 20 0.74
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (20 bp):
TCATATAAAAAATTATTAAA
Found at i:3496252 original size:17 final size:17
Alignment explanation
Indices: 3496230--3496262 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3496220 ATCCCTCTTC
3496230 ATATAGTACTTGTTTTG
1 ATATAGTACTTGTTTTG
*
3496247 ATATAGTGCTTGTTTT
1 ATATAGTACTTGTTTT
3496263 AATTTCAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.06, G:0.18, T:0.55
Consensus pattern (17 bp):
ATATAGTACTTGTTTTG
Found at i:3496491 original size:24 final size:24
Alignment explanation
Indices: 3496431--3496492 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
3496421 ATATGATAAT
*
3496431 AATATATCAAA-TATAAATTTTAAA
1 AATATAT-AAATTAAAAATTTTAAA
* *
3496455 ATATATTTTAATTAAAAATTTTAAA
1 A-ATATATAAATTAAAAATTTTAAA
3496480 AATATATAAATTA
1 AATATATAAATTA
3496493 TTCATTCTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
24 13 0.42
25 18 0.58
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
AATATATAAATTAAAAATTTTAAA
Found at i:3498685 original size:13 final size:11
Alignment explanation
Indices: 3498667--3498716 Score: 50
Period size: 13 Copynumber: 4.4 Consensus size: 11
3498657 TGTATTTCTT
3498667 TTAATATGTATA
1 TTAATAT-TATA
3498679 TTAAATATATATA
1 TT-AATAT-TATA
3498692 TTAATATTATA
1 TTAATATTATA
3498703 -T-ATATATATA
1 TTAATAT-TATA
3498713 TTAA
1 TTAA
3498717 AGAATTATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
9 4 0.12
10 5 0.15
11 5 0.15
12 8 0.24
13 11 0.33
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (11 bp):
TTAATATTATA
Found at i:3498698 original size:19 final size:19
Alignment explanation
Indices: 3498676--3498738 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 19
3498666 TTTAATATGT
3498676 ATATTAAATATATATATTA
1 ATATTAAATATATATATTA
3498695 ATATTATATATATATATATTA
1 ATATTA-A-ATATATATATTA
* *
3498716 A-A-GAATTATATATATTA
1 ATATTAAATATATATATTA
*
3498733 AAATTA
1 ATATTA
3498739 TATTTATTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
17 12 0.32
18 2 0.05
19 8 0.22
20 2 0.05
21 13 0.35
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
ATATTAAATATATATATTA
Found at i:3498702 original size:15 final size:16
Alignment explanation
Indices: 3498670--3498750 Score: 60
Period size: 17 Copynumber: 4.9 Consensus size: 16
3498660 ATTTCTTTTA
*
3498670 ATATGTATATTAAATAT
1 ATATATATATT-AATAT
3498687 ATATATTAATATT-ATAT
1 ATATA-T-ATATTAATAT
*
3498704 ATATATATATTAA-AGA
1 ATATATATATTAATA-T
*
3498720 ATTATATATATTAAAAT
1 A-TATATATATTAATAT
*
3498737 -TATATTTATTAATA
1 ATATATATATTAATA
3498751 AATAATAATA
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
15 18 0.34
16 3 0.06
17 25 0.47
18 2 0.04
19 5 0.09
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
ATATATATATTAATAT
Found at i:3498725 original size:17 final size:16
Alignment explanation
Indices: 3498705--3498753 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 16
3498695 ATATTATATA
3498705 TATATATATTAAAGAAT
1 TATATATATTAAA-AAT
3498722 TATATATATT-AAAAT
1 TATATATATTAAAAAT
*
3498737 TATATTTATTAATAAAT
1 TATATATATTAA-AAAT
3498754 AATAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 12 0.41
16 3 0.10
17 14 0.48
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
TATATATATTAAAAAT
Found at i:3499145 original size:17 final size:16
Alignment explanation
Indices: 3499107--3499146 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
3499097 GATTATATAT
*
3499107 ATATATATATATTAAC
1 ATATATATATATTAAA
3499123 AT-TATATATATTGAAA
1 ATATATATATATT-AAA
3499139 ATATATAT
1 ATATATAT
3499147 TAATATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 10 0.48
16 6 0.29
17 5 0.24
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (16 bp):
ATATATATATATTAAA
Found at i:3499415 original size:21 final size:19
Alignment explanation
Indices: 3499391--3499430 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
3499381 AGATATTTCG
*
3499391 TATTTAACTTTTCTTCTTTTT
1 TATTTAA-TTTTATT-TTTTT
3499412 TATTTAATTTTATTTTTTT
1 TATTTAATTTTATTTTTTT
3499431 CCAATTACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 6 0.33
21 7 0.39
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.75
Consensus pattern (19 bp):
TATTTAATTTTATTTTTTT
Found at i:3505892 original size:31 final size:31
Alignment explanation
Indices: 3505857--3505941 Score: 75
Period size: 31 Copynumber: 2.8 Consensus size: 31
3505847 TTACTTTTAT
*
3505857 TTATATTATATAAAAAAATAAATATATAATA
1 TTATATTATATAAAAAAATAAATATATAAAA
* ** *
3505888 TTATACTATA-AATATTAACAAATATATAAAA
1 TTATATTATATAA-AAAAATAAATATATAAAA
* * *
3505919 TTAT-TTATTTATAAATATAAATA
1 TTATATTATATAAAAAAATAAATA
3505942 AATTTTAATA
Statistics
Matches: 40, Mismatches: 12, Indels: 5
0.70 0.21 0.09
Matches are distributed among these distances:
30 12 0.30
31 28 0.70
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (31 bp):
TTATATTATATAAAAAAATAAATATATAAAA
Found at i:3505980 original size:40 final size:41
Alignment explanation
Indices: 3505930--3506010 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 41
3505920 TATTTATTTA
*
3505930 TAAATATAAATAAATTTTAATAAA-ATTTAAAATTAATATCT
1 TAAATATAAATAAATTTAAATAAATATTTAAAATTAA-ATCT
* *
3505971 TAAAT-TAAATTAATTTAAATAAATATTTAAATTTAAATCT
1 TAAATATAAATAAATTTAAATAAATATTTAAAATTAAATCT
3506011 AATCTTATGC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
40 20 0.56
41 16 0.44
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (41 bp):
TAAATATAAATAAATTTAAATAAATATTTAAAATTAAATCT
Found at i:3506006 original size:28 final size:30
Alignment explanation
Indices: 3505953--3506013 Score: 83
Period size: 28 Copynumber: 2.1 Consensus size: 30
3505943 ATTTTAATAA
*
3505953 AATTTAAAATTAATATCTTAAATTAAAT-T
1 AATTTAAAATAAATATCTTAAATTAAATCT
3505982 AATTT-AAATAAATAT-TTAAATTTAAATCT
1 AATTTAAAATAAATATCTTAAA-TTAAATCT
3506011 AAT
1 AAT
3506014 CTTATGCAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 5 0.17
28 15 0.52
29 9 0.31
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (30 bp):
AATTTAAAATAAATATCTTAAATTAAATCT
Found at i:3506007 original size:14 final size:13
Alignment explanation
Indices: 3505950--3506008 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 13
3505940 TAAATTTTAA
3505950 TAAA-ATTTAAAAT
1 TAAATATTT-AAAT
3505963 T-AATATCTTAAAT
1 TAAATAT-TTAAAT
3505976 TAAATTAATTTAAA-
1 TAAA-T-ATTTAAAT
3505990 TAAATATTTAAATT
1 TAAATATTTAAA-T
3506004 TAAAT
1 TAAAT
3506009 CTAATCTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
12 9 0.23
13 9 0.23
14 13 0.33
15 6 0.15
16 2 0.05
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (13 bp):
TAAATATTTAAAT
Found at i:3514103 original size:17 final size:18
Alignment explanation
Indices: 3514069--3514106 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
3514059 GTATGATATT
*
3514069 ATTAATAAATAATTAAAA
1 ATTAATAAATAATAAAAA
*
3514087 ATTAA-AAATTATAAAAA
1 ATTAATAAATAATAAAAA
3514104 ATT
1 ATT
3514107 TAAGTGTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
ATTAATAAATAATAAAAA
Found at i:3514226 original size:17 final size:18
Alignment explanation
Indices: 3514194--3514227 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3514184 TTTAAAAATA
*
3514194 TTTATATATGTATAATTT
1 TTTATATATATATAATTT
3514212 TTTATAT-TATATAATT
1 TTTATATATATATAATT
3514228 ATAGCGTGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTATATATATATAATTT
Found at i:3514586 original size:16 final size:16
Alignment explanation
Indices: 3514567--3514597 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3514557 TATTTTAATA
3514567 AATTTAAATTTAAAAT
1 AATTTAAATTTAAAAT
3514583 AATTTAAATTTAAAA
1 AATTTAAATTTAAAA
3514598 AATAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AATTTAAATTTAAAAT
Found at i:3514743 original size:18 final size:18
Alignment explanation
Indices: 3514720--3514757 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3514710 ATATATAAAT
* *
3514720 AAAATATATTTTTAATAA
1 AAAATAAATATTTAATAA
3514738 AAAATAAATATTTAATAA
1 AAAATAAATATTTAATAA
3514756 AA
1 AA
3514758 TTTAATATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAATAAATATTTAATAA
Found at i:3514762 original size:10 final size:10
Alignment explanation
Indices: 3514740--3514774 Score: 52
Period size: 11 Copynumber: 3.3 Consensus size: 10
3514730 TTTAATAAAA
3514740 AATAAATATTT
1 AATAAA-ATTT
3514751 AATAAAATTT
1 AATAAAATTT
3514761 AATATAAATTT
1 AATA-AAATTT
3514772 AAT
1 AAT
3514775 TTTATTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
AATAAAATTT
Found at i:3514915 original size:18 final size:18
Alignment explanation
Indices: 3514892--3514942 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
3514882 TGAATAAATT
3514892 TAATATTATTA-AATTAAA
1 TAATATTATTATAATT-AA
*
3514910 TAATATTAATATAATTAA
1 TAATATTATTATAATTAA
*
3514928 TAAAATTATATATAA
1 TAATATTAT-TATAA
3514943 ATTTAAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 19 0.68
19 9 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATATTATTATAATTAA
Found at i:3522312 original size:85 final size:85
Alignment explanation
Indices: 3522168--3522335 Score: 223
Period size: 85 Copynumber: 2.0 Consensus size: 85
3522158 TAGATTTTAC
* * * * *
3522168 TATTTGATCATTGGCTTATATTAATATATCTACCATAACATTTTAAAAGGATTAATTAATTTAAA
1 TATTTGATCATTCGCTTATATTAATACATCTACCACAACAGTATAAAAGGATTAATTAATTTAAA
* *
3522233 CTTTTAAGTTGTCAGCTTATT
66 -TTTTAAATGGTCAGCTTATT
* *
3522254 TATTTGATCA-TCGCTTATATTTATACATCTACTC-CAACAGTATAAGAGGATTAATTAATTTAA
1 TATTTGATCATTCGCTTATATTAATACATCTAC-CACAACAGTATAAAAGGATTAATTAATTTAA
3522317 ATTTTAAATGGTCAGCTTA
65 ATTTTAAATGGTCAGCTTA
3522336 AAATAGTTAC
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
84 16 0.22
85 45 0.62
86 11 0.15
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (85 bp):
TATTTGATCATTCGCTTATATTAATACATCTACCACAACAGTATAAAAGGATTAATTAATTTAAA
TTTTAAATGGTCAGCTTATT
Found at i:3525488 original size:13 final size:13
Alignment explanation
Indices: 3525470--3525494 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3525460 CGTGTTGGGA
3525470 GGGGGGGGGGGGT
1 GGGGGGGGGGGGT
3525483 GGGGGGGGGGGG
1 GGGGGGGGGGGG
3525495 GAGAGTGTTC
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:0.00, C:0.00, G:0.96, T:0.04
Consensus pattern (13 bp):
GGGGGGGGGGGGT
Found at i:3533685 original size:19 final size:17
Alignment explanation
Indices: 3533663--3533705 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
3533653 TATTATATAA
*
3533663 TAATTTATTATATATTTTT
1 TAATTT-TTATAT-TTATT
3533682 TAATATTTTATATTTATT
1 TAAT-TTTTATATTTATT
3533700 TAATTT
1 TAATTT
3533706 GATAAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 2 0.09
18 8 0.36
19 10 0.45
20 2 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TAATTTTTATATTTATT
Found at i:3533688 original size:17 final size:18
Alignment explanation
Indices: 3533668--3533703 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
3533658 TATAATAATT
3533668 TATTATATATTT-TTTAA
1 TATTATATATTTATTTAA
*
3533685 TATTTTATATTTATTTAA
1 TATTATATATTTATTTAA
3533703 T
1 T
3533704 TTGATAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TATTATATATTTATTTAA
Found at i:3535228 original size:15 final size:15
Alignment explanation
Indices: 3535208--3535241 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3535198 GGGCTAACGT
3535208 TTTAAAAT-ATATCAA
1 TTTAAAATAATAT-AA
3535223 TTTAAAATAATATAA
1 TTTAAAATAATATAA
3535238 TTTA
1 TTTA
3535242 TAATTGCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (15 bp):
TTTAAAATAATATAA
Found at i:3536853 original size:17 final size:17
Alignment explanation
Indices: 3536814--3536873 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 17
3536804 AAGCACTCAT
3536814 TTTTAAAAACTATCAAA
1 TTTTAAAAACTATCAAA
*
3536831 TTTTTAAAAACTATTTAAA
1 -TTTTAAAAACTA-TCAAA
* *
3536850 TTTAAAAAATTATCCAACA
1 TTTTAAAAACTAT-CAA-A
3536869 TTTTA
1 TTTTA
3536874 TTTTTAAACT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
17 1 0.03
18 24 0.71
19 9 0.26
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTTAAAAACTATCAAA
Found at i:3536913 original size:2 final size:2
Alignment explanation
Indices: 3536908--3536946 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
3536898 TAAAAAGTAC
* *
3536908 AT AT AT AT A- AT AT AT AT AT AT AT AT AG AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3536947 TTTACATGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:3538089 original size:16 final size:16
Alignment explanation
Indices: 3538047--3538090 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
3538037 TATATAACAT
3538047 AAATAAGATAT-A-AAA
1 AAAT-AGATATAATAAA
3538062 AAATA-ATATAATAAA
1 AAATAGATATAATAAA
3538077 AAATAGATATAATA
1 AAATAGATATAATA
3538091 TGAATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 4 0.15
14 2 0.08
15 12 0.46
16 8 0.31
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (16 bp):
AAATAGATATAATAAA
Found at i:3540796 original size:15 final size:15
Alignment explanation
Indices: 3540776--3540811 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
3540766 CTACATCCAT
*
3540776 TTATTATTTTTTTTC
1 TTATTATTATTTTTC
3540791 TTATTATTATTTTTC
1 TTATTATTATTTTTC
3540806 TT-TTAT
1 TTATTAT
3540812 CCTTGTCCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.78
Consensus pattern (15 bp):
TTATTATTATTTTTC
Found at i:3540859 original size:2 final size:2
Alignment explanation
Indices: 3540852--3540885 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3540842 TTTATATTTA
3540852 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
3540886 CTGTGCGTGT
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:3551767 original size:29 final size:30
Alignment explanation
Indices: 3551712--3551778 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
3551702 ATTTTTTAAA
3551712 AAATTTAATAGAAACAATATATTAAATAAT
1 AAATTTAATAGAAACAATATATTAAATAAT
*
3551742 AAATTTATATA-AAATAATA-ATTAAATAAT
1 AAATTTA-ATAGAAACAATATATTAAATAAT
3551771 --ATTTAATA
1 AAATTTAATA
3551779 AATAGTATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
26 3 0.09
27 5 0.14
29 10 0.29
30 14 0.40
31 3 0.09
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (30 bp):
AAATTTAATAGAAACAATATATTAAATAAT
Found at i:3551848 original size:11 final size:10
Alignment explanation
Indices: 3551832--3551991 Score: 95
Period size: 9 Copynumber: 15.9 Consensus size: 10
3551822 TATCAAATTT
3551832 TAAAATTATGA
1 TAAAATTAT-A
3551843 TAAAATTATA
1 TAAAATTATA
* *
3551853 -AAAAATATT
1 TAAAATTATA
3551862 TAAAAATTAT-
1 T-AAAATTATA
3551872 TAAAATTATA
1 TAAAATTATA
* *
3551882 TCATATTATTA
1 TAAAATTA-TA
3551893 TAAAAATTATA
1 T-AAAATTATA
3551904 TTAAATATTAT-
1 -TAAA-ATTATA
3551915 TAAAATTATA
1 TAAAATTATA
3551925 TAAAA-TATTA
1 TAAAATTA-TA
3551935 TTAAAATTATA
1 -TAAAATTATA
*
3551946 TCTAAAATTAAA
1 --TAAAATTATA
* *
3551958 AAAAACTAT-
1 TAAAATTATA
3551967 T--AA-TATA
1 TAAAATTATA
*
3551974 AAAAATTAT-
1 TAAAATTATA
3551983 TAAAATTAT
1 TAAAATTAT
3551992 GTTAAATGTT
Statistics
Matches: 118, Mismatches: 15, Indels: 34
0.71 0.09 0.20
Matches are distributed among these distances:
6 3 0.03
7 2 0.02
9 32 0.27
10 28 0.24
11 31 0.26
12 22 0.19
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (10 bp):
TAAAATTATA
Found at i:3551858 original size:29 final size:29
Alignment explanation
Indices: 3551828--3551945 Score: 101
Period size: 31 Copynumber: 3.8 Consensus size: 29
3551818 AATTTATCAA
*
3551828 ATTTTAAAATTATGATAAAATTATAAAAAAT
1 ATTTAAAAATTAT--TAAAATTATAAAAAAT
* * *
3551859 ATTTAAAAATTATTAAAATTATATCATATT
1 ATTTAAAAATTATTAAAATTATA-AAAAAT
* *
3551889 ATTATAAAAATTATATTAAATATTATTAAAATT
1 ATT-TAAAAA-T-TATTAAA-ATTATAAAAAAT
*
3551922 ATATAAAATATTATTAAAATTATA
1 ATTTAAAA-ATTATTAAAATTATA
3551946 TCTAAAATTA
Statistics
Matches: 72, Mismatches: 9, Indels: 13
0.77 0.10 0.14
Matches are distributed among these distances:
29 10 0.14
30 11 0.15
31 25 0.35
32 7 0.10
33 14 0.19
34 5 0.07
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (29 bp):
ATTTAAAAATTATTAAAATTATAAAAAAT
Found at i:3551919 original size:43 final size:41
Alignment explanation
Indices: 3551826--3552129 Score: 156
Period size: 42 Copynumber: 7.2 Consensus size: 41
3551816 TGAATTTATC
* * *
3551826 AAATT-TTAAAATTATGAT-AAA-ATTATAAAAAATATTTAA
1 AAATTATTAAAATTAT-ATAAAATATTATAAAAATTATATTA
* *
3551865 AAATTATTAAAATTATATCATATTATTATAAAAATTATATTA
1 AAATTATTAAAATTATAT-AAAATATTATAAAAATTATATTA
*
3551907 AATATTATTAAAATTATATAAAATATTATTAAAATTATATCTA
1 AA-ATTATTAAAATTATATAAAATATTATAAAAATTATAT-TA
** * * *
3551950 AAATTAAAAAAAACTATTAATATAAAAAATTATTAAAATTATGTTA
1 AAATT--ATTAAA--ATT-ATATAAAATATTATAAAAATTATATTA
* * * * * *
3551996 AATGTTACTGAAGTTATATATTAAAAATTAT-AAAATTATATCA
1 AA-ATTATTAAAATTATATA--AAATATTATAAAAATTATATTA
* * * * * *
3552039 AAGTTCTCAAGAACTATATTAAAATTTTATAAAAAAT-TATTA
1 AAATTATTAA-AATTATA-TAAAATATTATAAAAATTATATTA
* * *
3552081 AAATAATATAAAA-AAT-TAAAAATATTATACCAAAAAT-TATTA
1 AAATTAT-TAAAATTATAT-AAAATATTATA--AAAATTATATTA
3552123 AAATTAT
1 AAATTAT
3552130 AATAAAAAAT
Statistics
Matches: 208, Mismatches: 36, Indels: 39
0.73 0.13 0.14
Matches are distributed among these distances:
39 8 0.04
40 20 0.10
41 3 0.01
42 81 0.39
43 46 0.22
44 15 0.07
45 3 0.01
46 7 0.03
47 25 0.12
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (41 bp):
AAATTATTAAAATTATATAAAATATTATAAAAATTATATTA
Found at i:3551941 original size:21 final size:21
Alignment explanation
Indices: 3551831--3551946 Score: 130
Period size: 21 Copynumber: 5.6 Consensus size: 21
3551821 TTATCAAATT
3551831 TTAAAATTATGAT-AAA-ATTA
1 TTAAAATTAT-ATAAAATATTA
* * *
3551851 TAAAAAATATTTAAAA-ATTA
1 TTAAAATTATATAAAATATTA
* *
3551871 TTAAAATTATATCATATTATTA
1 TTAAAATTATAT-AAAATATTA
* *
3551893 TAAAAATTATATTAAATATTA
1 TTAAAATTATATAAAATATTA
3551914 TTAAAATTATATAAAATATTA
1 TTAAAATTATATAAAATATTA
3551935 TTAAAATTATAT
1 TTAAAATTATAT
3551947 CTAAAATTAA
Statistics
Matches: 79, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
19 1 0.01
20 24 0.30
21 39 0.49
22 15 0.19
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (21 bp):
TTAAAATTATATAAAATATTA
Found at i:3551953 original size:12 final size:11
Alignment explanation
Indices: 3551831--3551955 Score: 90
Period size: 10 Copynumber: 11.8 Consensus size: 11
3551821 TTATCAAATT
3551831 TTAAAATTATGA
1 TTAAAATTAT-A
3551843 -TAAAATTATA
1 TTAAAATTATA
*
3551853 --AAAAATAT-
1 TTAAAATTATA
*
3551861 TTAAAAAT-TA
1 TTAAAATTATA
3551871 TTAAAATTATA
1 TTAAAATTATA
* *
3551882 -TCATATTATTA
1 TTAAAATTA-TA
*
3551893 TAAAAATTATA
1 TTAAAATTATA
3551904 TT-AAA-TATTA
1 TTAAAATTA-TA
3551914 TTAAAATTATA
1 TTAAAATTATA
3551925 -TAAAA-TATTA
1 TTAAAATTA-TA
3551935 TTAAAATTATA
1 TTAAAATTATA
3551946 TCTAAAATTA
1 T-TAAAATTA
3551956 AAAAAAACTA
Statistics
Matches: 92, Mismatches: 8, Indels: 26
0.73 0.06 0.21
Matches are distributed among these distances:
9 12 0.13
10 34 0.37
11 29 0.32
12 17 0.18
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (11 bp):
TTAAAATTATA
Found at i:3551955 original size:21 final size:20
Alignment explanation
Indices: 3551826--3551955 Score: 122
Period size: 21 Copynumber: 6.3 Consensus size: 20
3551816 TGAATTTATC
3551826 AAATT-TTAAAATTATGA-TA
1 AAATTATTAAAATTAT-ATTA
* *
3551845 AAATTATAAAAAATAT-TTAA
1 AAATTATTAAAATTATATT-A
3551865 AAATTATTAAAATTATATCATA
1 AAATTATTAAAATTATAT--TA
** *
3551887 TTATTATAAAAATTATATTA
1 AAATTATTAAAATTATATTA
*
3551907 AATATTATTAAAATTATATAA
1 AA-ATTATTAAAATTATATTA
3551928 AATATTATTAAAATTATATCTA
1 AA-ATTATTAAAATTATAT-TA
3551950 AAATTA
1 AAATTA
3551956 AAAAAAACTA
Statistics
Matches: 91, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
19 6 0.07
20 25 0.27
21 40 0.44
22 19 0.21
23 1 0.01
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (20 bp):
AAATTATTAAAATTATATTA
Found at i:3551961 original size:21 final size:20
Alignment explanation
Indices: 3551833--3552131 Score: 110
Period size: 21 Copynumber: 14.1 Consensus size: 20
3551823 ATCAAATTTT
3551833 AAAATTATGA-TAAAATTATA
1 AAAATTAT-ATTAAAATTATA
* *
3551853 AAAAATAT-TTAAAAATTATT
1 AAAATTATATT-AAAATTATA
**
3551873 AAAATTATATCATATTATTATA
1 AAAATTATAT--TAAAATTATA
*
3551895 AAAATTATATTAAATATTATT
1 AAAATTATATTAAA-ATTATA
* *
3551916 AAAATTATATAAAATATTATT
1 AAAATTATATTAAA-ATTATA
*
3551937 AAAATTATATCTAAAATTAAAAA
1 AAAATTATAT-TAAAATT--ATA
* *
3551960 AAACTATTAATATAAAAAATTATT
1 AAA--ATT-ATAT-TAAAATTATA
* * *
3551984 AAAATTATGTTAAATGTTACTG
1 AAAATTATATTAAA-ATTA-TA
**
3552006 AAGTTATATATTAAAAATTAT-
1 AAAAT-TATATT-AAAATTATA
* * *
3552027 AAAATTATATCAAAGTTCTCA
1 AAAATTATATTAAAATTAT-A
* *
3552048 AGAACTATATTAAAATTTTATA
1 AAAATTATATTAAAA--TTATA
*
3552070 AAAAAT-TATTAAAATAATATAA
1 AAAATTATATTAAAAT--TAT-A
3552092 AAAATTA-A--AAATATTATA
1 AAAATTATATTAAA-ATTATA
*
3552110 CCAAAAAT-TATTAAAATTATA
1 --AAAATTATATTAAAATTATA
3552131 A
1 A
3552132 TAAAAAATTA
Statistics
Matches: 210, Mismatches: 39, Indels: 61
0.68 0.13 0.20
Matches are distributed among these distances:
18 1 0.00
19 12 0.06
20 41 0.20
21 78 0.37
22 42 0.20
23 16 0.08
24 7 0.03
25 3 0.01
26 10 0.05
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.38
Consensus pattern (20 bp):
AAAATTATATTAAAATTATA
Found at i:3552121 original size:42 final size:42
Alignment explanation
Indices: 3552056--3552149 Score: 140
Period size: 42 Copynumber: 2.3 Consensus size: 42
3552046 CAAGAACTAT
*
3552056 ATTAAAATTTTATA--AAAAATTATTAAAATAAT-ATAAAAA
1 ATTAAAATATTATACCAAAAATTATTAAAATAATAATAAAAA
*
3552095 ATTAAAAATATTATACCAAAAATTATTAAAATTATAATAAAAA
1 ATT-AAAATATTATACCAAAAATTATTAAAATAATAATAAAAA
3552138 ATTAAAATATTA
1 ATTAAAATATTA
3552150 CAAATGGTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
39 3 0.06
40 10 0.20
42 26 0.53
43 10 0.20
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (42 bp):
ATTAAAATATTATACCAAAAATTATTAAAATAATAATAAAAA
Found at i:3552136 original size:21 final size:22
Alignment explanation
Indices: 3552055--3552141 Score: 94
Period size: 21 Copynumber: 4.1 Consensus size: 22
3552045 TCAAGAACTA
*
3552055 TATTAAAATT-TTATAAAAAAT
1 TATTAAAATTATAATAAAAAAT
*
3552076 TATTAAAATAAT-ATAAAAAAT
1 TATTAAAATTATAATAAAAAAT
*
3552097 TA--AAAA-TATTATACCAAAAAT
1 TATTAAAATTATAATA--AAAAAT
3552118 TATTAAAATTATAATAAAAAAT
1 TATTAAAATTATAATAAAAAAT
3552140 TA
1 TA
3552142 AAATATTACA
Statistics
Matches: 56, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
18 2 0.04
19 7 0.12
21 28 0.50
22 9 0.16
23 4 0.07
24 6 0.11
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
TATTAAAATTATAATAAAAAAT
Found at i:3554538 original size:13 final size:13
Alignment explanation
Indices: 3554520--3554573 Score: 58
Period size: 13 Copynumber: 4.1 Consensus size: 13
3554510 ATAAATAATC
3554520 AATAAAAAATATG
1 AATAAAAAATATG
*
3554533 AATAAAAAATA-A
1 AATAAAAAATATG
3554545 AATAAAAAA-ATGG
1 AATAAAAAATAT-G
3554558 CATATAAAAAATATG
1 -A-ATAAAAAATATG
3554573 A
1 A
3554574 GTAAGGAAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
11 1 0.03
12 9 0.26
13 11 0.32
14 2 0.06
15 9 0.26
16 2 0.06
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.20
Consensus pattern (13 bp):
AATAAAAAATATG
Found at i:3558359 original size:25 final size:24
Alignment explanation
Indices: 3558327--3558375 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
3558317 TTAAAACTCA
*
3558327 AATTTCATATTTA-TTTATATAAAT
1 AATTTCAT-TTAATTTTATATAAAT
3558351 AATTATCATTTAATTTTATATAAAT
1 AATT-TCATTTAATTTTATATAAAT
3558376 TTTTAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (24 bp):
AATTTCATTTAATTTTATATAAAT
Found at i:3565448 original size:15 final size:15
Alignment explanation
Indices: 3565428--3565457 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3565418 CAAAGAGTTA
3565428 ATAGTAAAAAGTATC
1 ATAGTAAAAAGTATC
3565443 ATAGTAAAAAGTATC
1 ATAGTAAAAAGTATC
3565458 GAGTTAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.13, T:0.27
Consensus pattern (15 bp):
ATAGTAAAAAGTATC
Found at i:3565923 original size:10 final size:10
Alignment explanation
Indices: 3565899--3565931 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
3565889 CGATTCACAA
3565899 TTTTTTAATT
1 TTTTTTAATT
3565909 ATTTTTT-ATT
1 -TTTTTTAATT
3565919 TTTTTTAATT
1 TTTTTTAATT
3565929 TTT
1 TTT
3565932 AAAAAATAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 6 0.29
10 9 0.43
11 6 0.29
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTTAATT
Found at i:3567081 original size:31 final size:29
Alignment explanation
Indices: 3567026--3567086 Score: 70
Period size: 31 Copynumber: 2.0 Consensus size: 29
3567016 TTACATTACT
* *
3567026 ATTTAATAAAAATAATATTTTTAATTTAA
1 ATTTAATAAAAATAATATTATTAATATAA
3567055 ATTTAATTATAAAAT-ATATATATTAATATAA
1 ATTTAA-TA-AAAATAATAT-TATTAATATAA
3567086 A
1 A
3567087 AATATTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 6 0.22
30 6 0.22
31 15 0.56
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
ATTTAATAAAAATAATATTATTAATATAA
Found at i:3573882 original size:17 final size:18
Alignment explanation
Indices: 3573856--3573890 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3573846 CATTTTTAAT
*
3573856 AATTTTATTAATA-AAAA
1 AATTTAATTAATATAAAA
3573873 AATTTAATTAATATAAAA
1 AATTTAATTAATATAAAA
3573891 TATAATCTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AATTTAATTAATATAAAA
Found at i:3579514 original size:2 final size:2
Alignment explanation
Indices: 3579507--3579538 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3579497 AAGAATATCA
3579507 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3579539 ATGTTAGAAC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3581934 original size:30 final size:30
Alignment explanation
Indices: 3581898--3581956 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
3581888 TTTATTTACG
*
3581898 TTTTTATATTTTTATTTATATTTAAATAAT
1 TTTTTATATTTTTATTCATATTTAAATAAT
3581928 TTTTTATATTTTTATTCATATTTAAATAA
1 TTTTTATATTTTTATTCATATTTAAATAA
3581957 AAAATTAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (30 bp):
TTTTTATATTTTTATTCATATTTAAATAAT
Found at i:3582005 original size:30 final size:30
Alignment explanation
Indices: 3581946--3582101 Score: 145
Period size: 30 Copynumber: 5.1 Consensus size: 30
3581936 TTTTTATTCA
* *
3581946 TATTTAAATAAAAAATTAAATTAAGTTAAATATT
1 TATTTAAAT-ATAAATTAAATT---TTAAAAATT
3581980 TATTTAAATATAAATTAAATTTTAAAAATT
1 TATTTAAATATAAATTAAATTTTAAAAATT
** * *
3582010 TA-TTAAGATACGAATTAAATATTAAAAATA
1 TATTTAA-ATATAAATTAAATTTTAAAAATT
* *
3582040 TATTTAAATATAAATTAAATATTAAAATTT
1 TATTTAAATATAAATTAAATTTTAAAAATT
* * *
3582070 TATTTATATA-AAATAAAATTATAAAAACTT
1 TATTTAAATATAAATTAAATTTTAAAAA-TT
3582100 TA
1 TA
3582102 AGTAGGTAAA
Statistics
Matches: 104, Mismatches: 15, Indels: 10
0.81 0.12 0.08
Matches are distributed among these distances:
29 17 0.16
30 63 0.61
31 4 0.04
33 11 0.11
34 9 0.09
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (30 bp):
TATTTAAATATAAATTAAATTTTAAAAATT
Found at i:3582061 original size:19 final size:20
Alignment explanation
Indices: 3581980--3582067 Score: 51
Period size: 19 Copynumber: 4.5 Consensus size: 20
3581970 GTTAAATATT
3581980 TATTTAAATATAAATTAA-A
1 TATTTAAATATAAATTAAGA
* **
3581999 T-TTTAAAAATTTATTAAGA
1 TATTTAAATATAAATTAAGA
* *
3582018 TACGAATTAAATATTAAA--AATA
1 T---ATTTAAATA-TAAATTAAGA
3582040 TATTTAAATATAAATTAA-A
1 TATTTAAATATAAATTAAGA
*
3582059 TATTAAAAT
1 TATTTAAAT
3582068 TTTATTTATA
Statistics
Matches: 51, Mismatches: 10, Indels: 16
0.66 0.13 0.21
Matches are distributed among these distances:
18 17 0.33
19 20 0.39
20 2 0.04
22 4 0.08
23 6 0.12
24 2 0.04
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (20 bp):
TATTTAAATATAAATTAAGA
Found at i:3582966 original size:13 final size:13
Alignment explanation
Indices: 3582948--3582972 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3582938 CTAGCAAGTC
3582948 GTTTTTTTTTTTG
1 GTTTTTTTTTTTG
3582961 GTTTTTTTTTTT
1 GTTTTTTTTTTT
3582973 CTCATTCAAC
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:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (13 bp):
GTTTTTTTTTTTG
Found at i:3589064 original size:70 final size:72
Alignment explanation
Indices: 3588951--3589090 Score: 239
Period size: 70 Copynumber: 2.0 Consensus size: 72
3588941 CACTTCTTTG
*
3588951 TTATTACATAAAAAAGATATAAAAAGGTAAGTAAAGTA-TTTTTT-AAATAAATTATTAATATAA
1 TTATTACATAAAAAAGATACAAAAAGGTAAGTAAAGTAGTTTTTTAAAATAAATTATTAATATAA
3589014 TTTTTAA
66 TTTTTAA
*
3589021 TTATTACATAAAAAAGATACAAAAAGGTAGGTAAAGTAGTTTTTTTAAAATAAATTATTAATATA
1 TTATTACATAAAAAAGATACAAAAAGGTAAGTAAAGTAG-TTTTTTAAAATAAATTATTAATATA
3589086 ATTTT
65 ATTTT
3589091 ATTAAATGAA
Statistics
Matches: 65, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
70 36 0.55
72 6 0.09
73 23 0.35
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.39
Consensus pattern (72 bp):
TTATTACATAAAAAAGATACAAAAAGGTAAGTAAAGTAGTTTTTTAAAATAAATTATTAATATAA
TTTTTAA
Found at i:3594906 original size:15 final size:15
Alignment explanation
Indices: 3594886--3594917 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
3594876 TCCTTTTAGG
3594886 AAAAAAAAATA-CAA
1 AAAAAAAAATACCAA
3594900 AAAAAAAAATACCAA
1 AAAAAAAAATACCAA
3594915 AAA
1 AAA
3594918 GGCACAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.84, C:0.09, G:0.00, T:0.06
Consensus pattern (15 bp):
AAAAAAAAATACCAA
Found at i:3606020 original size:2 final size:2
Alignment explanation
Indices: 3606013--3606046 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3606003 GTGAAGTTGC
3606013 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3606047 CCAACTTGAC
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3612478 original size:34 final size:34
Alignment explanation
Indices: 3612432--3612650 Score: 266
Period size: 34 Copynumber: 6.5 Consensus size: 34
3612422 GTAAAAACCA
* *
3612432 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCAC
* *
3612466 TCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCAC
* **
3612500 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCAC
* *
3612534 CCATTTAATCAACAATGGTAAGCTACCAAATC-T
1 CCATTTAATCAACAATGGTAACCTACCAAATCAC
* *
3612567 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCAC
* *
3612601 CCATTTAATCAACAAATGGTAAACTACTAAATCA-
1 CCATTTAATCAAC-AATGGTAACCTACCAAATCAC
3612635 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
3612651 TCTCCCACTT
Statistics
Matches: 160, Mismatches: 19, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
33 29 0.18
34 116 0.73
35 15 0.09
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCAC
Found at i:3612546 original size:68 final size:67
Alignment explanation
Indices: 3612430--3612650 Score: 307
Period size: 68 Copynumber: 3.3 Consensus size: 67
3612420 TGGTAAAAAC
* * * *
3612430 CACCATTTAATCAACAATGGCAACCTACCAAATCTCTCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
3612495 AT
66 AT
* * *
3612497 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
3612562 AAT
65 AAT
* * * * * *
3612565 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAAATGGTAAACTACTA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAAC-AATGGTAAGCTACCA
3612630 AAT
65 AAT
3612633 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
3612651 TCTCCCACTT
Statistics
Matches: 135, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
67 43 0.32
68 92 0.68
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.25
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:3612608 original size:101 final size:102
Alignment explanation
Indices: 3612430--3612650 Score: 349
Period size: 101 Copynumber: 2.2 Consensus size: 102
3612420 TGGTAAAAAC
* *
3612430 CACCATTTAATCAACAATGGCAACCTACCAAATCTCTCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTCTCATTTAGTCAACAATGGCAAACCACCAA
*
3612495 ATCACCCATTTAATCAAC-AATGGTAAGCTACCAAATTT
66 ATCACCCATTTAATCAACAAATGGTAAACTACCAAA--T
* *
3612533 C-CCATTTAATCAACAATGGTAAGCTACCAAATCTC-CATTTAGTCAACAATGGCAAACCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTCTCATTTAGTCAACAATGGCAAACCACCAA
*
3612596 ATCACCCATTTAATCAACAAATGGTAAACTACTAAAT
66 ATCACCCATTTAATCAACAAATGGTAAACTACCAAAT
3612633 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
3612651 TCTCCCACTT
Statistics
Matches: 110, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
100 2 0.02
101 60 0.55
102 47 0.43
103 1 0.01
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.25
Consensus pattern (102 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTCTCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAAATGGTAAACTACCAAAT
Found at i:3616743 original size:19 final size:19
Alignment explanation
Indices: 3616716--3616778 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
3616706 TCACGTGTAC
* *
3616716 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
3616735 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
3616754 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
3616773 AGTACC
1 AGTACC
3616779 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:3617130 original size:34 final size:34
Alignment explanation
Indices: 3617084--3617300 Score: 262
Period size: 34 Copynumber: 6.4 Consensus size: 34
3617074 GTAAAAACCA
* *
3617084 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCAC
* *
3617118 TCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCAC
* **
3617152 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCAC
* *
3617186 CCATTTAATCAACAATGGTAAGCTACCAAATC-T
1 CCATTTAATCAACAATGGTAACCTACCAAATCAC
* *
3617219 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCAC
* *
3617253 CCATTTAATCAACAAATGGTAAACTACTAAATCA-
1 CCATTTAATCAAC-AATGGTAACCTACCAAATCAC
3617287 CCATTTAATCAACA
1 CCATTTAATCAACA
3617301 TAAATTTTAT
Statistics
Matches: 158, Mismatches: 19, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
33 27 0.17
34 116 0.73
35 15 0.09
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCAC
Found at i:3617198 original size:68 final size:67
Alignment explanation
Indices: 3617082--3617300 Score: 303
Period size: 68 Copynumber: 3.2 Consensus size: 67
3617072 TGGTAAAAAC
* * * *
3617082 CACCATTTAATCAACAATGGCAACCTACCAAATCTCTCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
3617147 AT
66 AT
* * *
3617149 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
3617214 AAT
65 AAT
* * * * * *
3617217 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAAATGGTAAACTACTA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAAC-AATGGTAAGCTACCA
3617282 AAT
65 AAT
3617285 CACCATTTAATCAACA
1 CACCATTTAATCAACA
3617301 TAAATTTTAT
Statistics
Matches: 133, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
67 43 0.32
68 90 0.68
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.25
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:3617260 original size:101 final size:102
Alignment explanation
Indices: 3617082--3617300 Score: 345
Period size: 101 Copynumber: 2.2 Consensus size: 102
3617072 TGGTAAAAAC
* *
3617082 CACCATTTAATCAACAATGGCAACCTACCAAATCTCTCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTCTCATTTAGTCAACAATGGCAAACCACCAA
*
3617147 ATCACCCATTTAATCAAC-AATGGTAAGCTACCAAATTT
66 ATCACCCATTTAATCAACAAATGGTAAACTACCAAA--T
* *
3617185 C-CCATTTAATCAACAATGGTAAGCTACCAAATCTC-CATTTAGTCAACAATGGCAAACCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTCTCATTTAGTCAACAATGGCAAACCACCAA
*
3617248 ATCACCCATTTAATCAACAAATGGTAAACTACTAAAT
66 ATCACCCATTTAATCAACAAATGGTAAACTACCAAAT
3617285 CACCATTTAATCAACA
1 CACCATTTAATCAACA
3617301 TAAATTTTAT
Statistics
Matches: 108, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
100 2 0.02
101 58 0.54
102 47 0.44
103 1 0.01
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.25
Consensus pattern (102 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTCTCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAAATGGTAAACTACCAAAT
Found at i:3617475 original size:3 final size:3
Alignment explanation
Indices: 3617467--3617492 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3617457 GAAAATTACA
3617467 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
3617493 GAGATTAATA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3618280 original size:31 final size:31
Alignment explanation
Indices: 3618245--3618334 Score: 75
Period size: 32 Copynumber: 3.0 Consensus size: 31
3618235 TTTAATTTTT
3618245 TTTAATTTATTAAAATAATATTTTTTTATAA
1 TTTAATTTATTAAAATAATATTTTTTTATAA
* *
3618276 TTTAAATTTA--AATAAAAATATTTTTATTTATAT
1 TTT-AATTTATTAA-AATAATA-TTTT-TTTATAA
*
3618309 TTTAA---ATTAAAATAA-ATTATTTTATA
1 TTTAATTTATTAAAATAATATTTTTTTATA
3618335 TTATAAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
27 6 0.12
28 3 0.06
29 2 0.04
30 6 0.12
31 11 0.22
32 12 0.24
33 9 0.18
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (31 bp):
TTTAATTTATTAAAATAATATTTTTTTATAA
Found at i:3618306 original size:33 final size:31
Alignment explanation
Indices: 3618239--3618340 Score: 101
Period size: 33 Copynumber: 3.4 Consensus size: 31
3618229 TTGTGATTTA
3618239 ATTTT-TTT-TAATTT--ATTAAAAT--AAT
1 ATTTTATTTATAATTTAAATTAAAATAAAAT
*
3618264 ATTTT-TTTATAATTTAAATTTAAATAAAAAT
1 ATTTTATTTATAATTTAAATTAAAAT-AAAAT
* *
3618295 ATTTTTATTTATATTTTAAATTAAAATAAATT
1 A-TTTTATTTATAATTTAAATTAAAATAAAAT
3618327 ATTTTATATTATAA
1 ATTTTAT-TTATAA
3618341 AAAATTTTCA
Statistics
Matches: 63, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
25 8 0.13
26 6 0.10
28 7 0.11
31 10 0.16
32 14 0.22
33 18 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (31 bp):
ATTTTATTTATAATTTAAATTAAAATAAAAT
Found at i:3618331 original size:20 final size:20
Alignment explanation
Indices: 3618306--3618346 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
3618296 TTTTTATTTA
3618306 TATTTTAAATTA-AAATAAAT
1 TATTTTAAATTATAAA-AAAT
*
3618326 TATTTTATATTATAAAAAAT
1 TATTTTAAATTATAAAAAAT
3618346 T
1 T
3618347 TTCATTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTTTAAATTATAAAAAAT
Found at i:3621640 original size:14 final size:16
Alignment explanation
Indices: 3621621--3621655 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
3621611 TTAACTATAA
3621621 AATATAAAA-AA-TTT
1 AATATAAAATAATTTT
3621635 AATATAAAATAATTTT
1 AATATAAAATAATTTT
3621651 AATAT
1 AATAT
3621656 TTTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 2 0.11
16 8 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATATAAAATAATTTT
Found at i:3622183 original size:30 final size:30
Alignment explanation
Indices: 3622107--3622183 Score: 109
Period size: 30 Copynumber: 2.6 Consensus size: 30
3622097 GTTAGCAATG
** *
3622107 GGACCTGGTGGACCGGGAGGAGGGCCAGGA
1 GGACCTGGTGGATGGGGAGGAGGACCAGGA
3622137 GGACCTGGTGGATGGGGAGGAGGACCAGGA
1 GGACCTGGTGGATGGGGAGGAGGACCAGGA
* *
3622167 GGGCCTGGTGGTTGGGG
1 GGACCTGGTGGATGGGG
3622184 TTCGGGTCCT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.17, C:0.16, G:0.56, T:0.12
Consensus pattern (30 bp):
GGACCTGGTGGATGGGGAGGAGGACCAGGA
Found at i:3622257 original size:24 final size:24
Alignment explanation
Indices: 3622229--3622285 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
3622219 GGGGTCCCGG
*
3622229 CTGGGGTCCGGGACCTGGAGGCCC
1 CTGGGGCCCGGGACCTGGAGGCCC
* **
3622253 CTGGGGCCCTGGATTTGGAGGCCC
1 CTGGGGCCCGGGACCTGGAGGCCC
3622277 CTGGGGCCC
1 CTGGGGCCC
3622286 TGGTTTTGGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.07, C:0.33, G:0.44, T:0.16
Consensus pattern (24 bp):
CTGGGGCCCGGGACCTGGAGGCCC
Found at i:3622286 original size:24 final size:24
Alignment explanation
Indices: 3622244--3622294 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
3622234 GTCCGGGACC
3622244 TGGAGGCCCCTGGGGCCCTGGATT
1 TGGAGGCCCCTGGGGCCCTGGATT
*
3622268 TGGAGGCCCCTGGGGCCCTGGTTT
1 TGGAGGCCCCTGGGGCCCTGGATT
3622292 TGG
1 TGG
3622295 CCCTGGTGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.06, C:0.27, G:0.43, T:0.24
Consensus pattern (24 bp):
TGGAGGCCCCTGGGGCCCTGGATT
Found at i:3627349 original size:26 final size:25
Alignment explanation
Indices: 3627318--3627372 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
3627308 CCCACTCTAT
*
3627318 ATTTAAAATATT-TTATATTTATATAA
1 ATTTAAAATATTAAT-TA-TTATATAA
*
3627344 ATTTAATATATTAATTATTATATAA
1 ATTTAAAATATTAATTATTATATAA
3627369 ATTT
1 ATTT
3627373 TTATATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 12 0.46
26 13 0.50
27 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
ATTTAAAATATTAATTATTATATAA
Found at i:3627370 original size:25 final size:25
Alignment explanation
Indices: 3627335--3627391 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
3627325 ATATTTTATA
3627335 TTTATATAAA-TTTAATATATTAAT
1 TTTATATAAATTTTAATATATTAAT
* *
3627359 TATTATATAAATTTTTATATATTTAT
1 T-TTATATAAATTTTAATATATTAAT
3627385 TTTATAT
1 TTTATAT
3627392 TATATTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 1 0.03
25 15 0.52
26 13 0.45
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
TTTATATAAATTTTAATATATTAAT
Found at i:3627371 original size:12 final size:12
Alignment explanation
Indices: 3627336--3627379 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
3627326 TATTTTATAT
3627336 TTATATAAATTTA
1 TTATATAAA-TTA
* *
3627349 ATATATTAATTA
1 TTATATAAATTA
*
3627361 TTATATAAATTT
1 TTATATAAATTA
3627373 TTATATA
1 TTATATA
3627380 TTTATTTTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 19 0.73
13 7 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TTATATAAATTA
Found at i:3627426 original size:16 final size:16
Alignment explanation
Indices: 3627359--3627426 Score: 53
Period size: 14 Copynumber: 4.8 Consensus size: 16
3627349 ATATATTAAT
*
3627359 TATTATATAAATTTT-
1 TATTATATTAATTTTA
*
3627374 TA-TATATTTATTTTA
1 TATTATATTAATTTTA
3627389 TATTATATT-A---TA
1 TATTATATTAATTTTA
*
3627401 TCTTA-A-TAATTTTA
1 TATTATATTAATTTTA
3627415 TATTATATTAAT
1 TATTATATTAAT
3627427 ATAATTATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 15
0.68 0.07 0.25
Matches are distributed among these distances:
10 1 0.02
11 2 0.05
12 6 0.15
14 16 0.39
15 6 0.15
16 10 0.24
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (16 bp):
TATTATATTAATTTTA
Found at i:3627434 original size:19 final size:20
Alignment explanation
Indices: 3627388--3627437 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
3627378 TATTTATTTT
3627388 ATATTATATTATATCTTAATA
1 ATATTATATTATA-CTTAATA
*
3627409 ATTTTATATTATA-TTAAT-
1 ATATTATATTATACTTAATA
3627427 ATAATTATATT
1 AT-ATTATATT
3627438 TAATATTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 2 0.08
19 12 0.46
21 12 0.46
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
ATATTATATTATACTTAATA
Found at i:3627438 original size:26 final size:25
Alignment explanation
Indices: 3627373--3627446 Score: 82
Period size: 26 Copynumber: 3.0 Consensus size: 25
3627363 ATATAAATTT
3627373 TTATAT-ATT-TATTTTATATTATA
1 TTATATAATTATATTTTATATTATA
*
3627396 TTATAT-CTTAATAATTTTATATTATA
1 TTATATAATT-AT-ATTTTATATTATA
*
3627422 TTAATATAATTATATTTAATATTAT
1 TT-ATATAATTATATTTTATATTAT
3627447 CAAATTTTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
23 8 0.19
25 1 0.02
26 26 0.60
27 6 0.14
28 2 0.05
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (25 bp):
TTATATAATTATATTTTATATTATA
Found at i:3630337 original size:29 final size:29
Alignment explanation
Indices: 3630295--3630352 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
3630285 CACTCTACAA
*
3630295 GGAAGCATAAGATTTCTTCCCATGTAAAT
1 GGAAGCATAAGATTTCTTCCCATATAAAT
*
3630324 GGAAGCATAAGATTTCTTTCCATATAAAT
1 GGAAGCATAAGATTTCTTCCCATATAAAT
3630353 CTTTTCATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (29 bp):
GGAAGCATAAGATTTCTTCCCATATAAAT
Found at i:3634470 original size:2 final size:2
Alignment explanation
Indices: 3634463--3634487 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3634453 TATGTTTGTG
3634463 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
3634488 GTTAAGACTT
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
Done.