Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold167
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: 4199719
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.33
Warning! 197959 characters in sequence are not A, C, G, or T
File 16 of 22
Found at i:2594756 original size:25 final size:26
Alignment explanation
Indices: 2594706--2594757 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
2594696 TCGAATCAAT
* *
2594706 TTAAAAATTAATTTTATTATTTTTTA
1 TTAAAAATTAATTTTATTAATATTTA
2594732 TTAAAAA-TAATTTTATTAATATTTA
1 TTAAAAATTAATTTTATTAATATTTA
2594757 T
1 T
2594758 ATATTTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 17 0.71
26 7 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
TTAAAAATTAATTTTATTAATATTTA
Found at i:2595911 original size:232 final size:225
Alignment explanation
Indices: 2595482--2595923 Score: 505
Period size: 232 Copynumber: 1.9 Consensus size: 225
2595472 CCAATTTCAA
****
2595482 ATTTTAAATTATTATCTAATATTTAAATTTTAAAAAATAATATTATCTTGATTTTGGGGAACGGT
1 ATTTTAAATTATTATCTAATATTTAAATTTTAAAAAATAATATTATCTTGATTTAAAAGAACGGT
** * * * * *
2595547 TACAATTATTTAGAATCAATTTTTTTTGTTCTTAAAAAAATAAAAATTGGAACGATTTTAGGAGA
66 TACAACGATTGAAAATCAATTTTTTTTGTTCTTAAAAAAATAAAAACTGGAACGACTTTAGAAGA
* * *
2595612 AAAAAACTTGAATTTTTTTTCATCCACTCTTTGTCTATATTACTTTTATTGTCTTCTTTGAGAGA
131 AAAAAACTTGAATTTTTTTTCATCCACTCTTTGTCGATATTACTTTTATTGTCTTATTTAAGAGA
2595677 GATTAACGACGCACTAATATTTGTAGTGTT
196 GATTAACGACGCACTAATATTTGTAGTGTT
* * **
2595707 ATTTTAAATTATTATTTAATTTTTAAATTTT-AAAAATAATATTATCTTGATTTAAAAGATTGG-
1 ATTTTAAATTATTATCTAATATTTAAATTTTAAAAAATAATATTATCTTGATTTAAAAGAACGGT
* * *
2595770 TACAACGGTTGAAAATCAAGATTTTTTTTTTGTTCTTCATGAAAAAAATAGAAACTGGAACGGCT
66 TACAACGATTGAAAATC-A-A--TTTTTTTTGTTC-T--T-AAAAAAATAAAAACTGGAACGACT
** * * * *
2595835 TTAGAAGAAAAAAAACTTGAATATTTTTTT-ATTTACTTTTTGTCGGTGTTACTTTTATCT-TTT
123 TTAGAAG-AAAAAAACTTGAAT-TTTTTTTCATCCACTCTTTGTCGATATTACTTTTAT-TGTCT
*
2595898 TATTTAAGAGAGATTAATGACGCACT
185 TATTTAAGAGAGATTAACGACGCACT
2595924 CGAGAGACAG
Statistics
Matches: 178, Mismatches: 28, Indels: 15
0.81 0.13 0.07
Matches are distributed among these distances:
223 12 0.07
224 27 0.15
225 30 0.17
227 12 0.07
228 1 0.01
230 1 0.01
231 26 0.15
232 61 0.34
233 8 0.04
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (225 bp):
ATTTTAAATTATTATCTAATATTTAAATTTTAAAAAATAATATTATCTTGATTTAAAAGAACGGT
TACAACGATTGAAAATCAATTTTTTTTGTTCTTAAAAAAATAAAAACTGGAACGACTTTAGAAGA
AAAAAACTTGAATTTTTTTTCATCCACTCTTTGTCGATATTACTTTTATTGTCTTATTTAAGAGA
GATTAACGACGCACTAATATTTGTAGTGTT
Found at i:2597191 original size:15 final size:13
Alignment explanation
Indices: 2597156--2597207 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 13
2597146 TAACGGTTCG
2597156 AATTATTATTTAA
1 AATTATTATTTAA
2597169 AATATATTATATTAAA
1 AAT-TATTAT-TT-AA
2597185 AATTATT-TTT-A
1 AATTATTATTTAA
*
2597196 AATTAATATTTA
1 AATTATTATTTA
2597208 TTTATTTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
11 7 0.21
12 3 0.09
13 5 0.15
14 7 0.21
15 6 0.18
16 5 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATTATTATTTAA
Found at i:2597213 original size:22 final size:22
Alignment explanation
Indices: 2597187--2597229 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2597177 ATATTAAAAA
2597187 TTATTTTTA-AATTAATATTTAT
1 TTATTTTTATAATTAA-ATTTAT
2597209 TTATTTTTATAATTAAATTTA
1 TTATTTTTATAATTAAATTTA
2597230 AGTAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TTATTTTTATAATTAAATTTAT
Found at i:2602634 original size:17 final size:16
Alignment explanation
Indices: 2602581--2602635 Score: 56
Period size: 17 Copynumber: 3.3 Consensus size: 16
2602571 ACTATTAAAT
2602581 TAAATTTATATTTAAGA
1 TAAATTTAT-TTTAAGA
** * *
2602598 TTTATTTATTTTCAGT
1 TAAATTTATTTTAAGA
2602614 TAAATTTTATTTTAAGA
1 TAAA-TTTATTTTAAGA
2602631 TAAAT
1 TAAAT
2602636 ATATCTTTTG
Statistics
Matches: 29, Mismatches: 8, Indels: 3
0.73 0.20 0.08
Matches are distributed among these distances:
16 8 0.28
17 21 0.72
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (16 bp):
TAAATTTATTTTAAGA
Found at i:2603650 original size:2 final size:2
Alignment explanation
Indices: 2603643--2603679 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2603633 TAATAACATG
2603643 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
2603680 GTGGTGGTCG
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:2604171 original size:24 final size:26
Alignment explanation
Indices: 2604125--2604174 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
2604115 AATATAAATT
* *
2604125 TATAAAATATATATATTTTTATTTGA
1 TATAAAATATATAAATTTATATTTGA
2604151 TATAAAAT-TA-AAATTTATATTTGA
1 TATAAAATATATAAATTTATATTTGA
2604175 AGTACGAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 12 0.55
25 2 0.09
26 8 0.36
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (26 bp):
TATAAAATATATAAATTTATATTTGA
Found at i:2605845 original size:12 final size:13
Alignment explanation
Indices: 2605828--2605858 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
2605818 AATAAATTCA
2605828 AAATTTTCAAA-C
1 AAATTTTCAAATC
2605840 AAATTTTCAAATC
1 AAATTTTCAAATC
2605853 AAATTT
1 AAATTT
2605859 CCTTTTGCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (13 bp):
AAATTTTCAAATC
Found at i:2612295 original size:2 final size:2
Alignment explanation
Indices: 2612288--2612313 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2612278 ACCTGATAAC
2612288 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
2612314 GCAGTGGTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2612901 original size:25 final size:25
Alignment explanation
Indices: 2612848--2612901 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
2612838 CTCATCAAAT
*
2612848 ATTTTTATAAAAAATAAATAATTTT
1 ATTTTTATAAAAAATAAATAATTTA
* *
2612873 ATTTTTAT-TAAAATAATATTATTTA
1 ATTTTTATAAAAAATAA-ATAATTTA
2612898 ATTT
1 ATTT
2612902 ATTAATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 7 0.28
25 18 0.72
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
ATTTTTATAAAAAATAAATAATTTA
Found at i:2613588 original size:16 final size:16
Alignment explanation
Indices: 2613564--2613617 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
2613554 TATTTATCTC
2613564 AAATTTAAATTTTTTT
1 AAATTTAAATTTTTTT
*
2613580 AAATATAAATTATTTTT
1 AAATTTAAATT-TTTTT
*
2613597 -AATTTAAATTATTTT
1 AAATTTAAATTTTTTT
2613612 AAATTT
1 AAATTT
2613618 TAATATTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 4 0.12
16 24 0.73
17 5 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AAATTTAAATTTTTTT
Found at i:2614234 original size:24 final size:24
Alignment explanation
Indices: 2614189--2614235 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2614179 TTATTTTATA
2614189 TTTTATGATTAAATTAAAAATATT
1 TTTTATGATTAAATTAAAAATATT
*
2614213 TTTTATTGATTAAA-TAATAATAT
1 TTTTA-TGATTAAATTAAAAATAT
2614236 GAATCGAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (24 bp):
TTTTATGATTAAATTAAAAATATT
Found at i:2616242 original size:16 final size:16
Alignment explanation
Indices: 2616223--2616279 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
2616213 TTTTATATAA
2616223 AAATAATTATTTAAAT
1 AAATAATTATTTAAAT
* **
2616239 AAATATTTATTTTGAT
1 AAATAATTATTTAAAT
2616255 AATTATAA-TA-TTAAAT
1 AA--ATAATTATTTAAAT
2616271 AAATAATTA
1 AAATAATTA
2616280 AAAAATATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
14 4 0.12
15 2 0.06
16 21 0.66
17 2 0.06
18 3 0.09
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (16 bp):
AAATAATTATTTAAAT
Found at i:2618843 original size:2 final size:2
Alignment explanation
Indices: 2618838--2618870 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2618828 GTCAATATAT
2618838 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
2618871 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2618875 original size:2 final size:2
Alignment explanation
Indices: 2618870--2618912 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2618860 ACACACACAC
2618870 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
2618912 A
1 A
2618913 GAAGATAACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2619240 original size:18 final size:20
Alignment explanation
Indices: 2619205--2619241 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
2619195 ATTTAAAATA
2619205 TTATAAATTTATATAATTTT
1 TTATAAATTTATATAATTTT
2619225 TTAT-AATTTA-ATAATTT
1 TTATAAATTTATATAATTT
2619242 ATATTATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 6 0.35
20 4 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTATAAATTTATATAATTTT
Found at i:2619267 original size:33 final size:33
Alignment explanation
Indices: 2619179--2619267 Score: 77
Period size: 32 Copynumber: 2.9 Consensus size: 33
2619169 ATTATATATT
2619179 TTTATATTATA-ATAATATTTAAAATA-TT-ATAA
1 TTTATATTATATA-AAT-TTTAAAATATTTAATAA
* * *
2619211 ---AT-TTATATAATTTTTTATA-ATTTAATAA
1 TTTATATTATATAAATTTTAAAATATTTAATAA
2619239 TTTATATTATATAAATTTTAAAATATTTA
1 TTTATATTATATAAATTTTAAAATATTTA
2619268 TATTACTATC
Statistics
Matches: 43, Mismatches: 6, Indels: 15
0.67 0.09 0.23
Matches are distributed among these distances:
26 1 0.02
27 7 0.16
28 11 0.26
29 3 0.07
31 2 0.05
32 14 0.33
33 5 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (33 bp):
TTTATATTATATAAATTTTAAAATATTTAATAA
Found at i:2619528 original size:2 final size:2
Alignment explanation
Indices: 2619515--2619548 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2619505 GGTTTTTCAA
*
2619515 AT AT AT AA 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
2619549 CTTATGAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2620801 original size:33 final size:32
Alignment explanation
Indices: 2620749--2620810 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
2620739 TATTTTTTAA
* *
2620749 ATTTTATAATATTTTATATTTTTTATTTAAACTC
1 ATTTAATAATA-TTTA-ATATTTTATTTAAACTC
2620783 ATTTAATAA-ATTTAATATTTTATTTAAA
1 ATTTAATAATATTTAATATTTTATTTAAA
2620811 TTCTCTCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 13 0.50
32 4 0.15
33 1 0.04
34 8 0.31
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (32 bp):
ATTTAATAATATTTAATATTTTATTTAAACTC
Found at i:2620984 original size:3 final size:3
Alignment explanation
Indices: 2620976--2621013 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
2620966 CAAAGAAAAT
*
2620976 TAA TAA TAA TAA TAA TAA TAA TAA TAA GTAG TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA T
2621014 TGATTCTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 30 0.94
4 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2621095 original size:31 final size:31
Alignment explanation
Indices: 2621060--2621121 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
2621050 TTTCCTCAAC
2621060 CTTATCAACTTGTTCATGGATCTCGTTTATT
1 CTTATCAACTTGTTCATGGATCTCGTTTATT
*
2621091 CTTATCAACTTGTTCATGGATCTTGTTTATT
1 CTTATCAACTTGTTCATGGATCTCGTTTATT
2621122 TGTCTCCCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.19, C:0.18, G:0.13, T:0.50
Consensus pattern (31 bp):
CTTATCAACTTGTTCATGGATCTCGTTTATT
Found at i:2623892 original size:24 final size:22
Alignment explanation
Indices: 2623873--2623938 Score: 71
Period size: 24 Copynumber: 2.9 Consensus size: 22
2623863 CATAAATATG
2623873 ATATAAATAAAATTATTAAAAAT
1 ATATAAATAAAATTATT-AAAAT
*
2623896 AATATAAATAATATT-TTAAAAT
1 -ATATAAATAAAATTATTAAAAT
*
2623918 TTATATAATATAAATTATTAA
1 ATATA-AATA-AAATTATTAA
2623939 CGTATCAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
21 4 0.11
22 9 0.25
23 6 0.17
24 17 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
ATATAAATAAAATTATTAAAAT
Found at i:2624338 original size:2 final size:2
Alignment explanation
Indices: 2624331--2624359 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2624321 GTTTCTCTTT
2624331 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
2624360 GTGTGTGTGT
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:2624560 original size:3 final size:3
Alignment explanation
Indices: 2624552--2624587 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
2624542 ATTAATTAAT
2624552 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
2624588 TGCTCTTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2625148 original size:14 final size:14
Alignment explanation
Indices: 2625115--2625141 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2625105 GTATTTCACG
2625115 ATTAAAATTAAAAA
1 ATTAAAATTAAAAA
2625129 ATTAAAATTAAAA
1 ATTAAAATTAAAA
2625142 TCTTAAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
ATTAAAATTAAAAA
Found at i:2625798 original size:21 final size:21
Alignment explanation
Indices: 2625772--2625812 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2625762 TGGCAAGTGG
2625772 AATTTGCACTTTTGACTTCAA
1 AATTTGCACTTTTGACTTCAA
*
2625793 AATTTGCTCTTTTGACTTCA
1 AATTTGCACTTTTGACTTCA
2625813 CCAATGCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (21 bp):
AATTTGCACTTTTGACTTCAA
Found at i:2626259 original size:2 final size:2
Alignment explanation
Indices: 2626252--2626276 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2626242 ATCTTAACAT
2626252 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
2626277 TTGAACAAAA
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:2626777 original size:22 final size:21
Alignment explanation
Indices: 2626728--2626782 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
2626718 AATTATTATC
*
2626728 ATTAAATAAATAAAATTTATAT
1 ATTAAA-AAATAAAATATATAT
*
2626750 ATTTAAAAAATAATAATATATGT
1 A-TTAAAAAATAA-AATATATAT
2626773 ATTAAAAAAT
1 ATTAAAAAAT
2626783 TATTAAACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 16 0.55
23 13 0.45
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
ATTAAAAAATAAAATATATAT
Found at i:2629077 original size:25 final size:25
Alignment explanation
Indices: 2629049--2629101 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
2629039 TAGATTATTC
2629049 ATCTAAAATATTATTAATAATTGGA
1 ATCTAAAATATTATTAATAATTGGA
*
2629074 ATCTTAAATATTATTAATAATTGGA
1 ATCTAAAATATTATTAATAATTGGA
2629099 ATC
1 ATC
2629102 GAATTTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.42
Consensus pattern (25 bp):
ATCTAAAATATTATTAATAATTGGA
Found at i:2634271 original size:3 final size:3
Alignment explanation
Indices: 2634263--2634297 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2634253 CTTCCCACTC
2634263 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2634298 AGCAAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2634829 original size:13 final size:13
Alignment explanation
Indices: 2634802--2634836 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
2634792 CAAGTGACAT
*
2634802 AAATTTAAT-TAA
1 AAATTAAATATAA
2634814 AAATTAAATATAA
1 AAATTAAATATAA
2634827 AAATTAAATA
1 AAATTAAATA
2634837 AAATAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 8 0.38
13 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
AAATTAAATATAA
Found at i:2634904 original size:18 final size:17
Alignment explanation
Indices: 2634873--2634908 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
2634863 ATATATATAA
*
2634873 ATTTTTTAATTTTTTTT
1 ATTTTTTAAATTTTTTT
2634890 ATTTTTATAAATTTTTTT
1 ATTTTT-TAAATTTTTTT
2634908 A
1 A
2634909 AAATTATTTA
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:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (17 bp):
ATTTTTTAAATTTTTTT
Found at i:2635192 original size:35 final size:38
Alignment explanation
Indices: 2635153--2635242 Score: 100
Period size: 35 Copynumber: 2.4 Consensus size: 38
2635143 AATTGGTTTA
2635153 ATAATTTATATATT-TATGTTAAA-ATTATATATT-T-T
1 ATAATTTATATATTATAT-TTAAATATTATATATTATAT
*
2635188 ATAATATTATA-ATTATATTTAAATTATTTTATATTATAT
1 ATAAT-TTATATATTATATTTAAA-TATTATATATTATAT
2635227 ATAATTTAATATATTA
1 ATAATTT-ATATATTA
2635243 ATACTTTATA
Statistics
Matches: 46, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
35 13 0.28
36 8 0.17
37 9 0.20
38 3 0.07
39 9 0.20
40 4 0.09
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (38 bp):
ATAATTTATATATTATATTTAAATATTATATATTATAT
Found at i:2635273 original size:32 final size:32
Alignment explanation
Indices: 2635215--2635277 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
2635205 TTTAAATTAT
* *
2635215 TTTATATTATATATAATTTAATATATTAATAC
1 TTTATATTAAATATAATTTAAGATATTAATAC
*
2635247 TTTATATTAAAT-TAATTTTGAGATATTAATA
1 TTTATATTAAATATAA-TTTAAGATATTAATA
2635278 TATTATTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 3 0.11
32 24 0.89
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (32 bp):
TTTATATTAAATATAATTTAAGATATTAATAC
Found at i:2645811 original size:21 final size:21
Alignment explanation
Indices: 2645787--2645828 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2645777 TGAAACAAAT
*
2645787 ATTAGATTTAAATA-AAATTAA
1 ATTA-ATTTAAAAATAAATTAA
*
2645808 ATTATTTTAAAAATAAATTAA
1 ATTAATTTAAAAATAAATTAA
2645829 GTTTTCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
ATTAATTTAAAAATAAATTAA
Found at i:2647073 original size:21 final size:21
Alignment explanation
Indices: 2647049--2647118 Score: 58
Period size: 21 Copynumber: 3.3 Consensus size: 21
2647039 TTTTAAAATT
2647049 TAACTCAATTAATTTATATAA
1 TAACTCAATTAATTTATATAA
2647070 TAACTC--TTAAAATCTTA-A-AA
1 TAACTCAATT--AAT-TTATATAA
*
2647090 TTTAACTTAATTAATTTATATAA
1 --TAACTCAATTAATTTATATAA
2647113 TAACTC
1 TAACTC
2647119 TTAAAATATG
Statistics
Matches: 38, Mismatches: 2, Indels: 18
0.66 0.03 0.31
Matches are distributed among these distances:
19 2 0.05
20 2 0.05
21 18 0.47
22 12 0.32
23 2 0.05
24 2 0.05
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (21 bp):
TAACTCAATTAATTTATATAA
Found at i:2647088 original size:43 final size:43
Alignment explanation
Indices: 2647032--2647125 Score: 170
Period size: 43 Copynumber: 2.2 Consensus size: 43
2647022 CAAAAACTCA
*
2647032 CTTAAAATTTTAAAATTTAACTCAATTAATTTATATAATAACT
1 CTTAAAATCTTAAAATTTAACTCAATTAATTTATATAATAACT
*
2647075 CTTAAAATCTTAAAATTTAACTTAATTAATTTATATAATAACT
1 CTTAAAATCTTAAAATTTAACTCAATTAATTTATATAATAACT
2647118 CTTAAAAT
1 CTTAAAAT
2647126 ATGATATTTA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.44
Consensus pattern (43 bp):
CTTAAAATCTTAAAATTTAACTCAATTAATTTATATAATAACT
Found at i:2647150 original size:43 final size:43
Alignment explanation
Indices: 2647032--2647144 Score: 149
Period size: 43 Copynumber: 2.7 Consensus size: 43
2647022 CAAAAACTCA
** *
2647032 CTTAAAATTTTAAAATTTAACTCAATTAATTTATATAATAACT
1 CTTAAAATCATAAAATTTAACTAAATTAATTTATATAATAACT
* *
2647075 CTTAAAATCTTAAAATTTAACTTAATTAATTTATATAATAACT
1 CTTAAAATCATAAAATTTAACTAAATTAATTTATATAATAACT
* *
2647118 CTTAAAAT-ATGATATTTAA-TAAATTAA
1 CTTAAAATCATAAAATTTAACTAAATTAA
2647145 AATTTAAACC
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
41 7 0.11
42 8 0.12
43 49 0.77
ACGTcount: A:0.48, C:0.08, G:0.01, T:0.43
Consensus pattern (43 bp):
CTTAAAATCATAAAATTTAACTAAATTAATTTATATAATAACT
Found at i:2647273 original size:2 final size:2
Alignment explanation
Indices: 2647200--2647254 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
2647190 CTTTGTTAAA
* *
2647200 AT AT AC AT AT AT AT AT AT AT AT AT AT AC 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
2647242 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
2647255 AAAGGAAGTT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2648410 original size:21 final size:21
Alignment explanation
Indices: 2648384--2648425 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2648374 AAGAAAAGAA
2648384 ATAAACAGTAATCCAGTTCAC
1 ATAAACAGTAATCCAGTTCAC
* *
2648405 ATAAACTGTAATGCAGTTCAC
1 ATAAACAGTAATCCAGTTCAC
2648426 GTTCTTTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.26
Consensus pattern (21 bp):
ATAAACAGTAATCCAGTTCAC
Found at i:2651978 original size:3 final size:3
Alignment explanation
Indices: 2651970--2652011 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
2651960 GAAGCATTAA
* *
2651970 TGT TGT TGT TAT TGT TGT TAT TGT TGT TGT TGT TGT TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
2652012 CAAGTATAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.05, C:0.00, G:0.29, T:0.67
Consensus pattern (3 bp):
TGT
Found at i:2653144 original size:20 final size:21
Alignment explanation
Indices: 2653119--2653171 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
2653109 TTTTAATTAT
*
2653119 TATTAAAATTTTTAT-TTTTA
1 TATTAAAATTTATATATTTTA
*
2653139 TATTAATATTTATATATTTTA
1 TATTAAAATTTATATATTTTA
2653160 TAATT-AAATTTA
1 T-ATTAAAATTTA
2653172 AATAAAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 13 0.46
21 12 0.43
22 3 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTAAAATTTATATATTTTA
Found at i:2653150 original size:18 final size:16
Alignment explanation
Indices: 2653094--2653151 Score: 53
Period size: 18 Copynumber: 3.3 Consensus size: 16
2653084 TTAAATAAAG
2653094 TTTATTTTTATTTAAT
1 TTTATTTTTATTTAAT
* *
2653110 TTTAATTATTATTAAAATT
1 TTT-ATTTTTATT-TAA-T
2653129 TTTATTTTTATATTAAT
1 TTTATTTTTAT-TTAAT
2653146 ATTTAT
1 -TTTAT
2653152 ATATTTTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
16 3 0.09
17 9 0.27
18 16 0.48
19 5 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTATTTTTATTTAAT
Found at i:2653323 original size:2 final size:2
Alignment explanation
Indices: 2653276--2653310 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
2653266 TTTTTTATGT
2653276 TA TA TA -A TCA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA T
2653311 TTTTAAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 28 0.90
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2654531 original size:29 final size:30
Alignment explanation
Indices: 2654462--2654568 Score: 82
Period size: 30 Copynumber: 3.7 Consensus size: 30
2654452 TAGAGACTTG
* **
2654462 TTTAGATATACAT-TAAAAATTAAGGATTTA
1 TTTAGATA-AAATATAAAAATTAAAAATTTA
2654492 TTTAGATAAAATATAAAAATTAAAAATTTA
1 TTTAGATAAAATATAAAAATTAAAAATTTA
* * *
2654522 -TTATG-T-AAA-ATAAAAGTTAACACTTTA
1 TTTA-GATAAAATATAAAAATTAAAAATTTA
* *
2654549 TTTAAATATAATA-AAAAATT
1 TTTAGATAAAATATAAAAATT
2654569 TTATTTAAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
27 15 0.24
28 7 0.11
29 15 0.24
30 25 0.40
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (30 bp):
TTTAGATAAAATATAAAAATTAAAAATTTA
Found at i:2655286 original size:41 final size:43
Alignment explanation
Indices: 2655216--2655305 Score: 109
Period size: 42 Copynumber: 2.1 Consensus size: 43
2655206 TTTAAATCAA
*
2655216 TTAAATTTAAATTATTATTTAAATAATAAAA-AATATTTTTA-T
1 TTAAATTTAAATTATAATTTAAATAATAAAATAAT-TTTTTATT
2655258 TTAAATTT-AATTATAAATATT-AAT-ATAAAATAATTTTTTATT
1 TTAAATTTAAATTAT-AAT-TTAAATAATAAAATAATTTTTTATT
2655300 TTAAAT
1 TTAAAT
2655306 AATAAAATAA
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
41 18 0.42
42 23 0.53
43 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (43 bp):
TTAAATTTAAATTATAATTTAAATAATAAAATAATTTTTTATT
Found at i:2657598 original size:2 final size:2
Alignment explanation
Indices: 2657591--2657617 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2657581 AAGTTTTTCC
2657591 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 A
2657618 GAGAGAGAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2657622 original size:2 final size:2
Alignment explanation
Indices: 2657617--2657650 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2657607 ATATATATAT
2657617 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
2657651 TGTCCATAGA
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):
AG
Found at i:2663810 original size:6 final size:6
Alignment explanation
Indices: 2663799--2663826 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2663789 AATATATGTA
2663799 AAATAT AAATAT AAATAT AAATAT AAAT
1 AAATAT AAATAT AAATAT AAATAT AAAT
2663827 TTTTAATACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATAT
Found at i:2664211 original size:22 final size:22
Alignment explanation
Indices: 2664185--2664227 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2664175 AAAGTTTCAG
2664185 ATTTTAGAACAATATGTAGATC
1 ATTTTAGAACAATATGTAGATC
2664207 ATTTTAGAACAATATGTAGAT
1 ATTTTAGAACAATATGTAGAT
2664228 TTTTTGAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.37
Consensus pattern (22 bp):
ATTTTAGAACAATATGTAGATC
Found at i:2664686 original size:3 final size:3
Alignment explanation
Indices: 2664678--2664723 Score: 76
Period size: 3 Copynumber: 15.3 Consensus size: 3
2664668 CTTCAGCTCC
2664678 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCAT T-T TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC-T TCT TCT TCT
2664723 T
1 T
2664724 TGTTATCTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 37 0.90
4 2 0.05
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:2665354 original size:11 final size:11
Alignment explanation
Indices: 2665340--2665381 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
2665330 TATAAAAAAT
2665340 TTATATTTATA
1 TTATATTTATA
2665351 TTATATTT-TAA
1 TTATATTTAT-A
*
2665362 TTATTTTTATA
1 TTATATTTATA
2665373 TTATATTTA
1 TTATATTTA
2665382 AAATTATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 1 0.04
11 25 0.93
12 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTATATTTATA
Found at i:2665391 original size:15 final size:16
Alignment explanation
Indices: 2665371--2665401 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2665361 ATTATTTTTA
2665371 TATTATAT-TTAAAAT
1 TATTATATCTTAAAAT
2665386 TATTATATCTTAAAAT
1 TATTATATCTTAAAAT
2665402 ATAATATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
TATTATATCTTAAAAT
Found at i:2665408 original size:15 final size:14
Alignment explanation
Indices: 2665370--2665408 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
2665360 AATTATTTTT
2665370 ATATTATATTTAAA
1 ATATTATATTTAAA
2665384 ATTATTATATCTTAAA
1 A-TATTATAT-TTAAA
*
2665400 ATATAATAT
1 ATATTATAT
2665409 AATAATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 15 0.68
16 6 0.27
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (14 bp):
ATATTATATTTAAA
Found at i:2667436 original size:21 final size:21
Alignment explanation
Indices: 2667395--2667440 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2667385 GAAAATGTAA
* * *
2667395 TGTAAATCTTTAATTAGATCC
1 TGTAAATCCTTAATGAAATCC
2667416 TGTAAATCCTTAATGAAATCC
1 TGTAAATCCTTAATGAAATCC
2667437 -GTAA
1 TGTAA
2667441 CAGGTCCTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (21 bp):
TGTAAATCCTTAATGAAATCC
Found at i:2667846 original size:26 final size:27
Alignment explanation
Indices: 2667816--2667872 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
2667806 TAACTATTTA
*
2667816 AAAAATTAATTAT-TTATATTATTATAT
1 AAAAATTAATTATATTACA-TATTATAT
*
2667843 AAAAACTAA-TATATTACATATTATAT
1 AAAAATTAATTATATTACATATTATAT
2667869 AAAA
1 AAAA
2667873 TATAATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (27 bp):
AAAAATTAATTATATTACATATTATAT
Found at i:2668061 original size:16 final size:16
Alignment explanation
Indices: 2668036--2668069 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2668026 CTAATGAATA
* *
2668036 AATTATTTTCATAACT
1 AATTAATTTCAAAACT
2668052 AATTAATTTCAAAACT
1 AATTAATTTCAAAACT
2668068 AA
1 AA
2668070 ATGAACTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTAATTTCAAAACT
Found at i:2669777 original size:7 final size:7
Alignment explanation
Indices: 2669744--2669776 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
2669734 CTTGTGAGTT
2669744 ATGATTA
1 ATGATTA
2669751 ATGATTA
1 ATGATTA
2669758 ATGATTA
1 ATGATTA
*
2669765 ATGATCA
1 ATGATTA
2669772 ATGAT
1 ATGAT
2669777 CTAACTGCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.42, C:0.03, G:0.15, T:0.39
Consensus pattern (7 bp):
ATGATTA
Found at i:2673050 original size:20 final size:19
Alignment explanation
Indices: 2673011--2673052 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
2673001 TTTCGAACAC
2673011 AATTTTAGTAAAATTTAAA
1 AATTTTAGTAAAATTTAAA
2673030 AATTTTA-TATAAATTTAAA
1 AATTTTAGTA-AAATTTAAA
2673049 AATT
1 AATT
2673053 AATATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 2 0.09
19 20 0.91
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
AATTTTAGTAAAATTTAAA
Found at i:2673058 original size:20 final size:19
Alignment explanation
Indices: 2673021--2673060 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2673011 AATTTTAGTA
*
2673021 AAATTTAAAAATTTTATAT
1 AAATTTAAAAATTATATAT
2673040 AAATTTAAAAATTAATATAT
1 AAATTTAAAAATT-ATATAT
2673060 A
1 A
2673061 TATATATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATTTAAAAATTATATAT
Found at i:2674007 original size:10 final size:10
Alignment explanation
Indices: 2673992--2674019 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
2673982 TGATTGTAAT
2673992 AAAAAATATA
1 AAAAAATATA
2674002 AAAAAATATA
1 AAAAAATATA
2674012 AAAAAATA
1 AAAAAATA
2674020 GTGGCTTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (10 bp):
AAAAAATATA
Found at i:2676220 original size:16 final size:16
Alignment explanation
Indices: 2676199--2676231 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2676189 ATGAGAAAGG
2676199 AATTGAATGTGACATA
1 AATTGAATGTGACATA
*
2676215 AATTGAATTTGACATA
1 AATTGAATGTGACATA
2676231 A
1 A
2676232 TTAATCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.33
Consensus pattern (16 bp):
AATTGAATGTGACATA
Found at i:2678005 original size:32 final size:31
Alignment explanation
Indices: 2677953--2678060 Score: 137
Period size: 32 Copynumber: 3.5 Consensus size: 31
2677943 AAGTTTTTTT
* *
2677953 TATTATTAAATTTACGAATAATTATGTTTAA
1 TATTATCAAATTTATGAATAATTATGTTTAA
* * *
2677984 TATTCATCAAATTTATAAATAATTTTATTTAA
1 TATT-ATCAAATTTATGAATAATTATGTTTAA
*
2678016 TATTTATCAAATTTATGAATAATTATGTCTAA
1 TA-TTATCAAATTTATGAATAATTATGTTTAA
2678048 T-TTATCAAATTTA
1 TATTATCAAATTTA
2678061 AATTTAATAT
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
30 12 0.18
31 4 0.06
32 48 0.73
33 2 0.03
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.49
Consensus pattern (31 bp):
TATTATCAAATTTATGAATAATTATGTTTAA
Found at i:2678974 original size:26 final size:26
Alignment explanation
Indices: 2678945--2679002 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
2678935 ATAAATATTT
* *
2678945 ATATTATAA-TATTATTAAATACATAA
1 ATATTATAATTAATA-TAAATAAATAA
*
2678971 ATATTATAATTAATATAATTAAATAA
1 ATATTATAATTAATATAAATAAATAA
2678997 ATATTA
1 ATATTA
2679003 ATATGATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 24 0.86
27 4 0.14
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
ATATTATAATTAATATAAATAAATAA
Found at i:2679006 original size:32 final size:31
Alignment explanation
Indices: 2678926--2679016 Score: 93
Period size: 30 Copynumber: 3.0 Consensus size: 31
2678916 GAAGTGAATT
*
2678926 TTAATTAAAATAAATATTTATATTATAA-T-A
1 TTAATT-AAATAAATATTAATATTATAATTAA
*
2678956 TT-ATTAAATACATA--AATATTATAATTAA
1 TTAATTAAATAAATATTAATATTATAATTAA
* *
2678984 TATAATTAAATAAATATTAATATGATATTTAA
1 T-TAATTAAATAAATATTAATATTATAATTAA
2679016 T
1 T
2679017 GTTAAATAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
26 9 0.18
27 1 0.02
28 10 0.20
29 4 0.08
30 13 0.26
32 13 0.26
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (31 bp):
TTAATTAAATAAATATTAATATTATAATTAA
Found at i:2684071 original size:24 final size:24
Alignment explanation
Indices: 2684044--2684092 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
2684034 CACATCTTAT
*
2684044 AATTAATATAGA-TTATTAAATAAA
1 AATTAATAT-GACTGATTAAATAAA
2684068 AATTAATATGACTGATTAAATAAA
1 AATTAATATGACTGATTAAATAAA
2684092 A
1 A
2684093 TTTTGATGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 2 0.09
24 21 0.91
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.35
Consensus pattern (24 bp):
AATTAATATGACTGATTAAATAAA
Found at i:2687369 original size:26 final size:27
Alignment explanation
Indices: 2687340--2687411 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
2687330 TAGTTACTAA
* *
2687340 TTTTGACAAA-CAAAAAGAACTATCAT
1 TTTTGACAAATAAAAAAAAACTATCAT
*
2687366 TTTTTACAAATAAAAAAAAACTATCAT
1 TTTTGACAAATAAAAAAAAACTATCAT
* * *
2687393 TTTTAAAAAATATAAAAAA
1 TTTTGACAAATAAAAAAAA
2687412 TAATTTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
26 9 0.23
27 30 0.77
ACGTcount: A:0.57, C:0.10, G:0.03, T:0.31
Consensus pattern (27 bp):
TTTTGACAAATAAAAAAAAACTATCAT
Found at i:2687370 original size:27 final size:27
Alignment explanation
Indices: 2687351--2687411 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
2687341 TTTGACAAAC
*
2687351 AAAAAGAACTATCATTTTTTACAAATA
1 AAAAAAAACTATCATTTTTTACAAATA
* *
2687378 AAAAAAAACTATCATTTTTAAAAAATA
1 AAAAAAAACTATCATTTTTTACAAATA
*
2687405 TAAAAAA
1 AAAAAAA
2687412 TAATTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.61, C:0.08, G:0.02, T:0.30
Consensus pattern (27 bp):
AAAAAAAACTATCATTTTTTACAAATA
Found at i:2687704 original size:2 final size:2
Alignment explanation
Indices: 2687697--2687723 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2687687 CAGAATTGTA
2687697 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 A
2687724 ACGTAAAAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2688839 original size:27 final size:28
Alignment explanation
Indices: 2688804--2688876 Score: 91
Period size: 26 Copynumber: 2.7 Consensus size: 28
2688794 ATATTATATC
2688804 AAATAATATTATATAATATATAAAATT-T
1 AAAT-ATATTATATAATATATAAAATTAT
* *
2688832 AAATATATTAT-TTATGTATAAAATTAT
1 AAATATATTATATAATATATAAAATTAT
2688859 AAATAT-TTATATAA-ATAT
1 AAATATATTATATAATATAT
2688877 TATATATTCT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
26 19 0.49
27 16 0.41
28 4 0.10
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (28 bp):
AAATATATTATATAATATATAAAATTAT
Found at i:2688883 original size:19 final size:20
Alignment explanation
Indices: 2688831--2688884 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 20
2688821 ATATAAAATT
2688831 TAAATA-TAT-TATTTATGTA
1 TAAATATTATATATTTA-GTA
2688850 TAAA-ATTATAAATATTTA-TA
1 TAAATATTAT--ATATTTAGTA
2688870 TAAATATTATATATT
1 TAAATATTATATATT
2688885 CTAATTCTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
18 1 0.03
19 12 0.40
20 6 0.20
21 5 0.17
22 6 0.20
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
TAAATATTATATATTTAGTA
Found at i:2689064 original size:11 final size:11
Alignment explanation
Indices: 2688960--2689066 Score: 55
Period size: 11 Copynumber: 9.4 Consensus size: 11
2688950 TAAGTATTTA
2688960 ATAATTATATAT
1 ATAATTATAT-T
2688972 ATAATCTATATT
1 ATAAT-TATATT
2688984 ATTACAGTTATATT
1 A-TA-A-TTATATT
2688998 -TAATATATAATT
1 ATAAT-TAT-ATT
2689010 AATACA-TATATT
1 -ATA-ATTATATT
2689022 AT-ATTATA-T
1 ATAATTATATT
2689031 ATAA-TAT-TT
1 ATAATTATATT
* *
2689040 CTTTATTATATT
1 -ATAATTATATT
*
2689052 ATAATTATGTT
1 ATAATTATATT
2689063 ATAA
1 ATAA
2689067 AATAAGTATA
Statistics
Matches: 75, Mismatches: 5, Indels: 31
0.68 0.05 0.28
Matches are distributed among these distances:
9 8 0.11
10 8 0.11
11 21 0.28
12 17 0.23
13 10 0.13
14 9 0.12
15 2 0.03
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (11 bp):
ATAATTATATT
Found at i:2689532 original size:14 final size:13
Alignment explanation
Indices: 2689499--2689534 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 13
2689489 GATCATGATA
2689499 AATAAAAAAAATG
1 AATAAAAAAAATG
2689512 AATTAAAAAAAATG
1 AA-TAAAAAAAATG
2689526 ATATAAAAA
1 A-ATAAAAA
2689535 CATTAAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.10
14 18 0.86
15 1 0.05
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (13 bp):
AATAAAAAAAATG
Found at i:2689691 original size:52 final size:52
Alignment explanation
Indices: 2689635--2689739 Score: 156
Period size: 52 Copynumber: 2.0 Consensus size: 52
2689625 AATATGTGGT
* * * *
2689635 TGACAATGAACCAAGTGTGTGGTTATTATATAATATTTAGAAAGATCTCTTA
1 TGACAATAAACCAAATGTGTGGTTATTATATAATATCTAGAAAAATCTCTTA
* *
2689687 TGACAGTAAACCAAATGTGTGGTTATTATATAATATCTAGAAAAATCTTTTA
1 TGACAATAAACCAAATGTGTGGTTATTATATAATATCTAGAAAAATCTCTTA
2689739 T
1 T
2689740 CATGTGAGAC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (52 bp):
TGACAATAAACCAAATGTGTGGTTATTATATAATATCTAGAAAAATCTCTTA
Found at i:2694937 original size:2 final size:2
Alignment explanation
Indices: 2694930--2694956 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2694920 ACTGAAGATG
2694930 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 A
2694957 CACCCACACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2695269 original size:11 final size:11
Alignment explanation
Indices: 2695266--2695358 Score: 81
Period size: 11 Copynumber: 8.5 Consensus size: 11
2695256 ATAATATTTA
2695266 TATATTTATAT
1 TATATTTATAT
2695277 TATATTTATA-
1 TATATTTATAT
2695287 T-TATTT-T-T
1 TATATTTATAT
*
2695295 TATATAT-TAT
1 TATATTTATAT
2695305 TATATTTTATTAT
1 TATA-TTTA-TAT
2695318 TATATTTATAT
1 TATATTTATAT
2695329 TAT-TTTATAAT
1 TATATTTAT-AT
2695340 TAAATTATTTATAT
1 T--A-TATTTATAT
2695354 TATAT
1 TATAT
2695359 AATTATAACA
Statistics
Matches: 69, Mismatches: 2, Indels: 22
0.74 0.02 0.24
Matches are distributed among these distances:
8 2 0.03
9 10 0.14
10 11 0.16
11 24 0.35
12 5 0.07
13 8 0.12
14 4 0.06
15 5 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TATATTTATAT
Found at i:2695279 original size:22 final size:22
Alignment explanation
Indices: 2695254--2695365 Score: 72
Period size: 22 Copynumber: 5.0 Consensus size: 22
2695244 TATATAAATC
*
2695254 TTATAATATTTATATATTTATA
1 TTATATTATTTATATATTTATA
*
2695276 TTATATTTATATTAT-TTTTTATA
1 TTATA-TTAT-TTATATATTTATA
*
2695299 -TATTATTATATTTTAT-TATTATA
1 TTA-TATTAT-TTATATAT-TTATA
* *
2695322 TTTATATTATTT-TATAATTAAA
1 -TTATATTATTTATATATTTATA
*
2695344 TTAT-TTATATTATATAATTATA
1 TTATATTAT-TTATATATTTATA
2695366 ACATATTTAA
Statistics
Matches: 74, Mismatches: 6, Indels: 20
0.74 0.06 0.20
Matches are distributed among these distances:
20 4 0.05
21 6 0.08
22 32 0.43
23 20 0.27
24 10 0.14
25 2 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TTATATTATTTATATATTTATA
Found at i:2695346 original size:16 final size:16
Alignment explanation
Indices: 2695311--2695349 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2695301 TTATTATATT
* *
2695311 TTATTATTATATTTATA
1 TTATT-TTATAATTAAA
2695328 TTATTTTATAATTAAA
1 TTATTTTATAATTAAA
2695344 TTATTT
1 TTATTT
2695350 ATATTATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATTTTATAATTAAA
Found at i:2695365 original size:8 final size:7
Alignment explanation
Indices: 2695259--2695365 Score: 69
Period size: 6 Copynumber: 16.4 Consensus size: 7
2695249 AAATCTTATA
2695259 ATAT-TT
1 ATATATT
2695265 ATATATT
1 ATATATT
2695272 -TATATT
1 ATATATT
2695278 ATAT-TT
1 ATATATT
2695284 ATATTATT
1 ATA-TATT
2695292 -T-T-TT
1 ATATATT
2695296 ATATATT
1 ATATATT
2695303 ATTATATT
1 A-TATATT
2695311 -T-TATT
1 ATATATT
2695316 ATTATATT
1 A-TATATT
2695324 -TATATT
1 ATATATT
2695330 AT-T-TT
1 ATATATT
2695335 ATA-ATT
1 ATATATT
*
2695341 AAATTATT
1 ATA-TATT
2695349 -TATATT
1 ATATATT
2695355 ATATAATT
1 ATAT-ATT
2695363 ATA
1 ATA
2695366 ACATATTTAA
Statistics
Matches: 81, Mismatches: 2, Indels: 34
0.69 0.02 0.29
Matches are distributed among these distances:
4 2 0.02
5 10 0.12
6 32 0.40
7 16 0.20
8 21 0.26
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (7 bp):
ATATATT
Found at i:2695379 original size:17 final size:17
Alignment explanation
Indices: 2695334--2695403 Score: 52
Period size: 17 Copynumber: 4.0 Consensus size: 17
2695324 TATATTATTT
* **
2695334 TATAATTAAATTATTTA
1 TATAATAAAATTATAAA
* *
2695351 TATTATATAATTATAACA
1 TATAATAAAATTATAA-A
*
2695369 TAT-TTAAAATTAATAAA
1 TATAATAAAATT-ATAAA
2695386 TATAATAAAATGTATAAA
1 TATAATAAAAT-TATAAA
2695404 GAAAAGAATC
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
17 21 0.51
18 19 0.46
19 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (17 bp):
TATAATAAAATTATAAA
Found at i:2697699 original size:2 final size:2
Alignment explanation
Indices: 2697694--2697729 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
2697684 TCTCAAAAAC
* *
2697694 TA TA TA TA TA TA TA TA TA TA TA TT TA TT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2697730 GCTGCTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:2701961 original size:2 final size:2
Alignment explanation
Indices: 2701954--2701983 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2701944 CTAGAAAAAG
2701954 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2701984 AAATGAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2702749 original size:19 final size:20
Alignment explanation
Indices: 2702699--2702787 Score: 66
Period size: 21 Copynumber: 4.7 Consensus size: 20
2702689 AACACATGAT
2702699 TATTTAAATATAATATAAAAA
1 TATTTAAATATAATAT-AAAA
* * *
2702720 AATTAAAATATAATAT-ACA
1 TATTTAAATATAATATAAAA
2702739 TATTTAAATAT--T-T-AAA
1 TATTTAAATATAATATAAAA
*
2702755 -ATTTATATA-AATATAAAA
1 TATTTAAATATAATATAAAA
*
2702773 TAATTTTAATATAAT
1 T-ATTTAAATATAAT
2702788 TTTAATATAA
Statistics
Matches: 52, Mismatches: 9, Indels: 14
0.69 0.12 0.19
Matches are distributed among these distances:
15 8 0.15
16 4 0.08
17 2 0.04
18 3 0.06
19 11 0.21
20 7 0.13
21 17 0.33
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (20 bp):
TATTTAAATATAATATAAAA
Found at i:2702778 original size:27 final size:27
Alignment explanation
Indices: 2702700--2702778 Score: 72
Period size: 27 Copynumber: 2.9 Consensus size: 27
2702690 ACACATGATT
* *
2702700 ATTTAAATATAATATAAAA-AAATTAAA
1 ATTTATATA-AATATAAAATAATTTAAA
* * *
2702727 ATATAATATACATATTTAAAT-ATTTAAA
1 AT-TTATATAAATA-TAAAATAATTTAAA
2702755 ATTTATATAAATATAAAATAATTT
1 ATTTATATAAATATAAAATAATTT
2702779 TAATATAATT
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
26 5 0.12
27 18 0.45
28 17 0.43
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (27 bp):
ATTTATATAAATATAAAATAATTTAAA
Found at i:2702786 original size:11 final size:11
Alignment explanation
Indices: 2702772--2702798 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2702762 TAAATATAAA
2702772 ATAATTTTAAT
1 ATAATTTTAAT
2702783 ATAATTTTAAT
1 ATAATTTTAAT
2702794 ATAAT
1 ATAAT
2702799 AAAATATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
ATAATTTTAAT
Found at i:2702824 original size:29 final size:30
Alignment explanation
Indices: 2702760--2702827 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
2702750 TTAAAATTTA
*
2702760 TATAA-AT-ATAAAATAATTTTAATATAAT
1 TATAATATAATAAAATAATATTAATATAAT
*
2702788 TTTAATATAATAAAAT-ATATTAATATAAT
1 TATAATATAATAAAATAATATTAATATAAT
2702817 TCATATATATA
1 T-ATA-ATATA
2702828 TATATATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
28 4 0.12
29 15 0.45
30 9 0.27
31 5 0.15
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (30 bp):
TATAATATAATAAAATAATATTAATATAAT
Found at i:2703398 original size:30 final size:30
Alignment explanation
Indices: 2703362--2703421 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
2703352 AATAAATTTA
2703362 ATAATT-ATAATAATTATATT-ATATTTAAAT
1 ATAATTAAT-ATAA-TATATTAATATTTAAAT
2703392 ATAATTAATATAATATATTAATATTTAAAT
1 ATAATTAATATAATATATTAATATTTAAAT
2703422 TTTGAATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 6 0.21
30 20 0.71
31 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
ATAATTAATATAATATATTAATATTTAAAT
Found at i:2703400 original size:37 final size:36
Alignment explanation
Indices: 2703320--2703441 Score: 90
Period size: 37 Copynumber: 3.3 Consensus size: 36
2703310 TTACATGAAA
* * *
2703320 AATTAATAATTATTAAAAAGTGATA-TAATTTTAATA-
1 AATTAATAATTA-TAATAA-TTATATTAATTTAAATAT
2703356 AATTTAATAATTATAATAATTATATTATATTTAAATAT
1 AA-TTAATAATTATAATAATTATATTA-ATTTAAATAT
* * *
2703394 AATTAATATAATATATTAA-TAT-TTAAATTTTGAATAT
1 AATTAATA-ATTATAATAATTATATT-AA-TTTAAATAT
*
2703431 ATTTAATAATT
1 AATTAATAATT
2703442 TATAGGATGT
Statistics
Matches: 71, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
35 4 0.06
36 14 0.20
37 43 0.61
38 10 0.14
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (36 bp):
AATTAATAATTATAATAATTATATTAATTTAAATAT
Found at i:2703909 original size:21 final size:20
Alignment explanation
Indices: 2703848--2703911 Score: 53
Period size: 21 Copynumber: 3.1 Consensus size: 20
2703838 CGTGCTTTGG
*
2703848 ATTAGTATTTTATAAATAA-AA
1 ATTA-TATTTAAT-AATAATAA
*
2703869 ATTAT-TTTAATTAAT-TTAA
1 ATTATATTTAA-TAATAATAA
2703888 ATTATTATTTAATAATAATAA
1 ATTA-TATTTAATAATAATAA
2703909 ATT
1 ATT
2703912 TTAAATTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
19 13 0.37
20 7 0.20
21 15 0.43
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
ATTATATTTAATAATAATAA
Found at i:2703932 original size:28 final size:29
Alignment explanation
Indices: 2703883--2703944 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
2703873 TTTTAATTAA
* *
2703883 TTTAAATTATTATTTAATAATA-ATAAAT
1 TTTAAATTATAATTTAAAAATATATAAAT
2703911 TTTAAATTA-AATTATAAAAATATATAAAT
1 TTTAAATTATAATT-TAAAAATATATAAAT
*
2703940 ATTAA
1 TTTAA
2703945 TATAAATCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 3 0.10
28 16 0.55
29 10 0.34
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
TTTAAATTATAATTTAAAAATATATAAAT
Found at i:2704366 original size:13 final size:13
Alignment explanation
Indices: 2704348--2704425 Score: 75
Period size: 13 Copynumber: 5.6 Consensus size: 13
2704338 ATTTTTACAT
2704348 TAAAATTATTTAA
1 TAAAATTATTTAA
2704361 TAAAATTAATTTATA
1 TAAAATT-ATTTA-A
*
2704376 TAATATATTTTATTAA
1 TAA-A-ATTAT-TTAA
*
2704392 TAAAATTTTTTAA
1 TAAAATTATTTAA
* *
2704405 TAATATAATTTAA
1 TAAAATTATTTAA
2704418 TAAAATTA
1 TAAAATTA
2704426 AAAATTTATG
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
13 27 0.50
14 10 0.19
15 5 0.09
16 6 0.11
17 6 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TAAAATTATTTAA
Found at i:2704392 original size:31 final size:29
Alignment explanation
Indices: 2704357--2704416 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
2704347 TTAAAATTAT
*
2704357 TTAATAAAATTAATTTATATAATATATTTTA
1 TTAATAAAATT-ATTTA-ATAATATAATTTA
*
2704388 TTAATAAAATTTTTTAATAATATAATTTA
1 TTAATAAAATTATTTAATAATATAATTTA
2704417 ATAAAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 12 0.44
30 4 0.15
31 11 0.41
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (29 bp):
TTAATAAAATTATTTAATAATATAATTTA
Found at i:2704402 original size:16 final size:16
Alignment explanation
Indices: 2704357--2704415 Score: 50
Period size: 16 Copynumber: 3.8 Consensus size: 16
2704347 TTAAAATTAT
*
2704357 TTAATAAAATTAATTTA
1 TTAATAAAATT-TTTTA
* *
2704374 -T-ATAATATATTTTA
1 TTAATAAAATTTTTTA
2704388 TTAATAAAATTTTTTA
1 TTAATAAAATTTTTTA
* *
2704404 ATAATATAATTT
1 TTAATAAAATTT
2704416 AATAAAATTA
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
14 4 0.12
15 7 0.21
16 22 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAATAAAATTTTTTA
Found at i:2704691 original size:12 final size:12
Alignment explanation
Indices: 2704671--2704725 Score: 71
Period size: 12 Copynumber: 4.8 Consensus size: 12
2704661 TTATTATTAA
2704671 TTTATATTATAT
1 TTTATATTATAT
*
2704683 TTTAAATTATAT
1 TTTATATTATAT
2704695 TTTAT-TT-TAT
1 TTTATATTATAT
2704705 TCTTATATTATA-
1 T-TTATATTATAT
2704717 TTTATATTA
1 TTTATATTA
2704726 CGTCATTATA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
10 4 0.11
11 14 0.37
12 18 0.47
13 2 0.05
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (12 bp):
TTTATATTATAT
Found at i:2711885 original size:12 final size:12
Alignment explanation
Indices: 2711839--2711883 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
2711829 TATAGTTTGG
2711839 TATTTTT-TAAA
1 TATTTTTATAAA
*
2711850 TTTTTTTGATAAA
1 TATTTTT-ATAAA
*
2711863 TATTTTTATTAA
1 TATTTTTATAAA
2711875 TATTTTTAT
1 TATTTTTAT
2711884 TATTACTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
11 6 0.21
12 13 0.45
13 10 0.34
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (12 bp):
TATTTTTATAAA
Found at i:2714645 original size:10 final size:10
Alignment explanation
Indices: 2714632--2714669 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
2714622 ATTTATTTTA
2714632 ATAAAAAAAT
1 ATAAAAAAAT
2714642 ATAAAAAAAT
1 ATAAAAAAAT
2714652 AATAAAAATAAT
1 -ATAAAAA-AAT
2714664 A-AAAAA
1 ATAAAAA
2714670 GAAGAGACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 15 0.58
11 8 0.31
12 3 0.12
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (10 bp):
ATAAAAAAAT
Found at i:2714647 original size:8 final size:9
Alignment explanation
Indices: 2714631--2714668 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
2714621 AATTTATTTT
2714631 AATAA-AAA
1 AATAATAAA
*
2714639 AATATAAAAA
1 AATA-ATAAA
2714649 AATAATAAA
1 AATAATAAA
2714658 AATAATAAA
1 AATAATAAA
2714667 AA
1 AA
2714669 AGAAGAGACA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
8 4 0.15
9 16 0.59
10 7 0.26
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (9 bp):
AATAATAAA
Found at i:2716850 original size:2 final size:2
Alignment explanation
Indices: 2716843--2716870 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2716833 TCTTTGCATG
2716843 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
2716871 GGTCCTTGTT
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):
TA
Found at i:2717681 original size:14 final size:13
Alignment explanation
Indices: 2717662--2717691 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
2717652 AGAATAAATA
2717662 TATATATATTATAT
1 TATATATATTAT-T
2717676 TATATATATTATT
1 TATATATATTATT
2717689 TAT
1 TAT
2717692 TATTTAGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATATATATTATT
Found at i:2717681 original size:16 final size:16
Alignment explanation
Indices: 2717659--2717694 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
2717649 AAAAGAATAA
2717659 ATATATATATATTATATT
1 ATATATAT-TATT-TATT
2717677 ATATATATTATTTATT
1 ATATATATTATTTATT
2717693 AT
1 AT
2717695 TTAGATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 4 0.22
18 8 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATATATATTATTTATT
Found at i:2718291 original size:32 final size:31
Alignment explanation
Indices: 2718244--2718303 Score: 93
Period size: 32 Copynumber: 1.9 Consensus size: 31
2718234 GAATATTTGA
* *
2718244 ATATTTTAAATTTTATATAATATAAAATATTC
1 ATATATTAAAATTTATA-AATATAAAATATTC
2718276 ATATATTAAAATTTATAAATATAAAATA
1 ATATATTAAAATTTATAAATATAAAATA
2718304 ATTTAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 11 0.42
32 15 0.58
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (31 bp):
ATATATTAAAATTTATAAATATAAAATATTC
Found at i:2718297 original size:16 final size:15
Alignment explanation
Indices: 2718250--2718302 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 15
2718240 TTGAATATTT
*
2718250 TAAATTTTATATAATA
1 TAAAATTTATA-AATA
*
2718266 TAAAATATTCATATAT-
1 TAAAAT-TT-ATAAATA
2718282 TAAAATTTATAAATA
1 TAAAATTTATAAATA
2718297 TAAAAT
1 TAAAAT
2718303 AATTTAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 5 0.16
15 8 0.26
16 11 0.35
17 4 0.13
18 3 0.10
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
TAAAATTTATAAATA
Found at i:2718310 original size:16 final size:15
Alignment explanation
Indices: 2718262--2718312 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
2718252 AATTTTATAT
*
2718262 AATATAAAATATTCA
1 AATATAAAATATTTA
*
2718277 TATATTAAAAT-TTATA
1 AATA-TAAAATATT-TA
2718293 AATATAAAATAATTTA
1 AATATAAAAT-ATTTA
2718309 AATA
1 AATA
2718313 AATTATAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
15 11 0.38
16 16 0.55
17 2 0.07
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (15 bp):
AATATAAAATATTTA
Found at i:2718341 original size:18 final size:18
Alignment explanation
Indices: 2718258--2718344 Score: 61
Period size: 18 Copynumber: 5.4 Consensus size: 18
2718248 TTTAAATTTT
*
2718258 ATATAATATAAA-ATATTC
1 ATATAATA-AAATATATTA
* *
2718276 ATATATTAAAATTTA-TA
1 ATATAATAAAATATATTA
2718293 A-AT-ATAAAATA-ATT-
1 ATATAATAAAATATATTA
2718307 -TA-AAT-AAAT-TA-TA
1 ATATAATAAAATATATTA
2718320 ATATAATAAAATATATTA
1 ATATAATAAAATATATTA
2718338 ATATAAT
1 ATATAAT
2718345 TGATATGTTC
Statistics
Matches: 53, Mismatches: 5, Indels: 22
0.66 0.06 0.28
Matches are distributed among these distances:
12 1 0.02
13 5 0.09
14 6 0.11
15 10 0.19
16 6 0.11
17 7 0.13
18 18 0.34
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (18 bp):
ATATAATAAAATATATTA
Found at i:2718936 original size:24 final size:24
Alignment explanation
Indices: 2718909--2718954 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
2718899 ATATAAAAAT
2718909 AATATAA-TAATTATGATATATTTA
1 AATATAATTAA-TATGATATATTTA
*
2718933 AATATAATTAATATTATATATT
1 AATATAATTAATATGATATATT
2718955 AACATTCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (24 bp):
AATATAATTAATATGATATATTTA
Found at i:2719886 original size:14 final size:13
Alignment explanation
Indices: 2719867--2719900 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
2719857 ATTCAATTCA
2719867 TTAATAATAAAATT
1 TTAATAATAAAA-T
*
2719881 TTAATAATATAAT
1 TTAATAATAAAAT
2719894 TTAATAA
1 TTAATAA
2719901 AATCAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAATAATAAAAT
Found at i:2720202 original size:17 final size:19
Alignment explanation
Indices: 2720167--2720249 Score: 93
Period size: 17 Copynumber: 4.5 Consensus size: 19
2720157 CATTAGTAAT
2720167 TTATA-TTATATAATTATTA
1 TTATATTTATATAATTA-TA
*
2720186 ATATATTTATATAATTATA
1 TTATATTTATATAATTATA
2720205 TTATATTT-TA-AATTATA
1 TTATATTTATATAATTATA
**
2720222 TTATATTT-TATTTTTATA
1 TTATATTTATATAATTATA
*
2720240 GTATATTTAT
1 TTATATTTAT
2720250 GACACGTAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
17 17 0.30
18 14 0.25
19 14 0.25
20 11 0.20
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (19 bp):
TTATATTTATATAATTATA
Found at i:2720232 original size:12 final size:12
Alignment explanation
Indices: 2720200--2720247 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
2720190 ATTTATATAA
2720200 TTATATTATATT
1 TTATATTATATT
*
2720212 TTAAATTATATT
1 TTATATTATATT
* *
2720224 ATATTTTAT-TT
1 TTATATTATATT
*
2720235 TTATAGTATATT
1 TTATATTATATT
2720247 T
1 T
2720248 ATGACACGTA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
11 8 0.29
12 20 0.71
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (12 bp):
TTATATTATATT
Found at i:2720523 original size:18 final size:19
Alignment explanation
Indices: 2720502--2720581 Score: 64
Period size: 18 Copynumber: 4.4 Consensus size: 19
2720492 TACATATGAG
2720502 ATAATTAAATAATATA-AA
1 ATAATTAAATAATATATAA
2720520 ATAA-TAATATAATA-ATAA
1 ATAATTAA-ATAATATATAA
*
2720538 ATAATATAAA-AATATATTA
1 ATAAT-TAAATAATATATAA
* *
2720557 ATATTTAATTAAT-T-TAA
1 ATAATTAAATAATATATAA
*
2720574 ATTATTAA
1 ATAATTAA
2720582 TATATAATAA
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
17 12 0.24
18 24 0.48
19 11 0.22
20 3 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATAATTAAATAATATATAA
Found at i:2720535 original size:8 final size:8
Alignment explanation
Indices: 2720515--2720610 Score: 65
Period size: 8 Copynumber: 11.9 Consensus size: 8
2720505 ATTAAATAAT
*
2720515 ATAAAATA
1 ATAATATA
2720523 ATAATATA
1 ATAATATA
2720531 ATAATA-A
1 ATAATATA
2720538 ATAATATA
1 ATAATATA
*
2720546 AAAATATA
1 ATAATATA
*
2720554 TTAATATTTA
1 ATAATA--TA
*
2720564 ATTAATTTA
1 A-TAATATA
*
2720573 A-ATTATTA
1 ATAATA-TA
2720581 AT-ATATA
1 ATAATATA
*
2720588 ATAATTTA
1 ATAATATA
2720596 TATAATAT-
1 -ATAATATA
2720604 ATAATAT
1 ATAATAT
2720611 TTTATATACG
Statistics
Matches: 69, Mismatches: 11, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
7 20 0.29
8 34 0.49
9 9 0.13
10 2 0.03
11 4 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
ATAATATA
Found at i:2720546 original size:23 final size:23
Alignment explanation
Indices: 2720509--2720610 Score: 68
Period size: 23 Copynumber: 4.5 Consensus size: 23
2720499 GAGATAATTA
*
2720509 AATAATATAAAATAATAATATAAT
1 AATAA-ATAATATAATAATATAAT
* *
2720533 AATAAATAATATAAAAATATATT
1 AATAAATAATATAATAATATAAT
** *
2720556 AATATTTAAT-TAAT-TTA-AAT
1 AATAAATAATATAATAATATAAT
* * *
2720576 TATTAAT-ATATAATAATTTATAT
1 AATAAATAATATAATAATATA-AT
*
2720599 AATATATAATAT
1 AATAAATAATAT
2720611 TTTATATACG
Statistics
Matches: 56, Mismatches: 17, Indels: 10
0.67 0.20 0.12
Matches are distributed among these distances:
19 2 0.04
20 9 0.16
21 3 0.05
22 4 0.07
23 29 0.52
24 9 0.16
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
AATAAATAATATAATAATATAAT
Found at i:2720583 original size:24 final size:24
Alignment explanation
Indices: 2720525--2720610 Score: 77
Period size: 23 Copynumber: 3.5 Consensus size: 24
2720515 ATAAAATAAT
* * **
2720525 AATATAATAATAAATAAT-ATAAA
1 AATATATTAATATATAATAATTTA
*
2720548 AATATATTAATATTTAATTAATTTA
1 AATATATTAATATATAA-TAATTTA
2720573 AAT-TATTAATATATAATAATTTA
1 AATATATTAATATATAATAATTTA
*
2720596 TATAATATATAATAT
1 AAT-ATAT-TAATAT
2720611 TTTATATACG
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
23 23 0.45
24 13 0.25
25 9 0.18
26 6 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
AATATATTAATATATAATAATTTA
Found at i:2720592 original size:10 final size:10
Alignment explanation
Indices: 2720510--2720609 Score: 54
Period size: 10 Copynumber: 10.3 Consensus size: 10
2720500 AGATAATTAA
*
2720510 ATAATATAAA
1 ATAATATATA
2720520 ATAATA-AT-
1 ATAATATATA
2720528 ATAATA-ATAA
1 ATAATATAT-A
2720538 ATAATATA-A
1 ATAATATATA
2720547 A-AATATAT-
1 ATAATATATA
*
2720555 -TAATATTTA
1 ATAATATATA
*
2720564 ATTAATTTAAATTA
1 A-TAA--TATA-TA
*
2720578 TTAATATATA
1 ATAATATATA
*
2720588 ATAATTTAT-
1 ATAATATATA
2720597 ATAATATATA
1 ATAATATATA
2720607 ATA
1 ATA
2720610 TTTTATATAC
Statistics
Matches: 69, Mismatches: 9, Indels: 24
0.68 0.09 0.24
Matches are distributed among these distances:
8 20 0.29
9 11 0.16
10 24 0.35
11 7 0.10
13 5 0.07
14 2 0.03
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
ATAATATATA
Found at i:2729120 original size:12 final size:12
Alignment explanation
Indices: 2729103--2729127 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2729093 TGGGTTAAGT
2729103 TTAATTAGTTTA
1 TTAATTAGTTTA
2729115 TTAATTAGTTTA
1 TTAATTAGTTTA
2729127 T
1 T
2729128 GCAGCATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (12 bp):
TTAATTAGTTTA
Found at i:2732048 original size:2 final size:2
Alignment explanation
Indices: 2732041--2732076 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2732031 ACATTCCATC
*
2732041 TA TA TA TA TA CA 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
2732077 AGACAGAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2732844 original size:2 final size:2
Alignment explanation
Indices: 2732837--2732869 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2732827 TCCTTATGTA
2732837 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
2732870 ATGTAAGCTG
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:2733698 original size:12 final size:12
Alignment explanation
Indices: 2733646--2733699 Score: 56
Period size: 12 Copynumber: 4.5 Consensus size: 12
2733636 TTTATTTTGT
*
2733646 TATTTAAAATAA
1 TATTTAAATTAA
* *
2733658 TATTAAAATTTA
1 TATTTAAATTAA
*
2733670 TTTTTAAATTAA
1 TATTTAAATTAA
2733682 TATTTACAATTAA
1 TATTTA-AATTAA
2733695 -ATTTA
1 TATTTA
2733700 TATAAAAATA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
12 28 0.82
13 6 0.18
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (12 bp):
TATTTAAATTAA
Found at i:2734783 original size:14 final size:14
Alignment explanation
Indices: 2734750--2734785 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 14
2734740 TTAATAAAAA
2734750 ATTTATA-ATTAAT
1 ATTTATATATTAAT
2734763 -TTT-TATATTAAT
1 ATTTATATATTAAT
2734775 ATTTATATATT
1 ATTTATATATT
2734786 TTATAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
11 2 0.10
12 9 0.45
13 3 0.15
14 6 0.30
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
ATTTATATATTAAT
Found at i:2734851 original size:20 final size:20
Alignment explanation
Indices: 2734809--2734849 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2734799 TAAATAAAAT
*
2734809 AATTATTAAATATTAATTTA
1 AATTAATAAATATTAATTTA
*
2734829 AATTAATAAAT-TTTATTTA
1 AATTAATAAATATTAATTTA
2734848 AA
1 AA
2734850 ATGTAACTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATTAATAAATATTAATTTA
Found at i:2735486 original size:40 final size:40
Alignment explanation
Indices: 2735431--2735509 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
2735421 AACTTGAGTC
*
2735431 TAGCAATGCATTGACTCGATTCAATTCAATTACATCCTAA
1 TAGCAATGCATTGACTCGACTCAATTCAATTACATCCTAA
* **
2735471 TAGCAATGTATTGACTCGACTCAATTCGTTTACATCCTA
1 TAGCAATGCATTGACTCGACTCAATTCAATTACATCCTA
2735510 TCGGTGCATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.34
Consensus pattern (40 bp):
TAGCAATGCATTGACTCGACTCAATTCAATTACATCCTAA
Done.