Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold52
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: 1774672
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 127110 characters in sequence are not A, C, G, or T
File 4 of 9
Found at i:723972 original size:20 final size:20
Alignment explanation
Indices: 723947--723984 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
723937 TTTAATTAAT
723947 ATTAAATT-TAAATATAAATA
1 ATTAAATTCTAAAT-TAAATA
723967 ATTAAATTCTAAATTAAA
1 ATTAAATTCTAAATTAAA
723985 AATAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (20 bp):
ATTAAATTCTAAATTAAATA
Found at i:724050 original size:32 final size:32
Alignment explanation
Indices: 723955--724057 Score: 106
Period size: 32 Copynumber: 3.3 Consensus size: 32
723945 ATATTAAATT
* * *
723955 TAAATATAAATAATTAAATTCTAAATTAAAAA
1 TAAATATAAATAATTTAATTTTTAATTAAAAA
* *
723987 TAAAAAT-AA-AATTT-ATTTTTAATAAATAAA
1 TAAATATAAATAATTTAATTTTTAATTAA-AAA
* *
724017 TAAATTTAAATAATTTAATTTTTATTTAAAAA
1 TAAATATAAATAATTTAATTTTTAATTAAAAA
724049 TAAAT-TAAA
1 TAAATATAAA
724058 ATTTTAAAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
29 9 0.16
30 12 0.21
31 8 0.14
32 19 0.33
33 10 0.17
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (32 bp):
TAAATATAAATAATTTAATTTTTAATTAAAAA
Found at i:724178 original size:27 final size:29
Alignment explanation
Indices: 724106--724181 Score: 77
Period size: 31 Copynumber: 2.5 Consensus size: 29
724096 AATTACCGAT
724106 AAAAATTTTATTTCATCAAAATAAATAATA
1 AAAAATTTTATTT-ATCAAAATAAATAATA
724136 ATAAATATTTTTTATTT-T-AAAATAAAT-ATA
1 A-AAA-A--TTTTATTTATCAAAATAAATAATA
724166 AAAAATTTATATTTAT
1 AAAAATTT-TATTTAT
724182 GTCAAAGTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
26 3 0.08
27 5 0.12
28 2 0.05
29 3 0.08
30 5 0.12
31 12 0.30
32 2 0.05
34 8 0.20
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (29 bp):
AAAAATTTTATTTATCAAAATAAATAATA
Found at i:724424 original size:2 final size:2
Alignment explanation
Indices: 724417--724465 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
724407 TGAAATAGAC
* * *
724417 AT AT AT AT AT AT AT AT AA AT AT AT AA AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
724459 AT AT AT A
1 AT AT AT A
724466 GAAAGAGAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:724764 original size:40 final size:41
Alignment explanation
Indices: 724673--724769 Score: 116
Period size: 40 Copynumber: 2.5 Consensus size: 41
724663 AATTTTAAAA
*
724673 AATTTATAAT-TAAATTTAAATAAAATATATTTTAAATATT
1 AATTTATAATATAAATTTAAATAAAATATATTTAAAATATT
724713 AAGTTT-TAATATAAA-TT-AATAAAAATATATTTAAAAT-TT
1 AA-TTTATAATATAAATTTAAAT-AAAATATATTTAAAATATT
*
724752 AATTTATAA-ATATATTTA
1 AATTTATAATATAAATTTA
724770 TTTTTTTTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
38 7 0.14
39 12 0.24
40 23 0.47
41 7 0.14
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (41 bp):
AATTTATAATATAAATTTAAATAAAATATATTTAAAATATT
Found at i:726207 original size:12 final size:12
Alignment explanation
Indices: 726191--726223 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
726181 TCCTGACCAG
726191 CTTTCTTCTTCT
1 CTTTCTTCTTCT
*
726203 TTTTCTTCTTCT
1 CTTTCTTCTTCT
726215 CTTTCTTCT
1 CTTTCTTCT
726224 CTTCAATAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (12 bp):
CTTTCTTCTTCT
Found at i:729512 original size:15 final size:16
Alignment explanation
Indices: 729486--729515 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
729476 ATATTTATTA
729486 TAATTAATTATAATAT
1 TAATTAATTATAATAT
729502 TAATT-ATTATAATA
1 TAATTAATTATAATA
729516 ATTTAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TAATTAATTATAATAT
Found at i:730310 original size:63 final size:63
Alignment explanation
Indices: 730231--730909 Score: 695
Period size: 63 Copynumber: 10.7 Consensus size: 63
730221 TCACTTTGGG
* * * * *
730231 CCTGTCGATATTTGGCATCTGGAAGAGGAACACCTGAACCAGGGTTTTTGACAGGTTCCATGC
1 CCTGTCCATATCTGGCATGTGGAAGAGGAATACCTGAACCAGGGTCTTTGACAGGTTCCATGC
** * * * *
730294 CCTGTGGATATTTGGCATGTGGAAGAGGAATACCTGAACCATGATCTTTGATAGGTTCCATGC
1 CCTGTCCATATCTGGCATGTGGAAGAGGAATACCTGAACCAGGGTCTTTGACAGGTTCCATGC
* * * * *
730357 CCTGTCCATACCTGGCATATGGAAGAGGAATACTTGAACCAGGGCCTTTGACAGGTTCTATGC
1 CCTGTCCATATCTGGCATGTGGAAGAGGAATACCTGAACCAGGGTCTTTGACAGGTTCCATGC
* * * * *
730420 ACTGTCCACATCAGGCATGTGGAAGAGGAATTCCTG-ACACAGGGTCTTTGACAGGTTCTATGC
1 CCTGTCCATATCTGGCATGTGGAAGAGGAATACCTGAAC-CAGGGTCTTTGACAGGTTCCATGC
* * * *
730483 CCTATCCATATCAGGCATGTGGAAGAGGAATACCTGAACCAGAGTCTTTGACAGGTTCTATGC
1 CCTGTCCATATCTGGCATGTGGAAGAGGAATACCTGAACCAGGGTCTTTGACAGGTTCCATGC
* * * * * * * *
730546 CCTGTCTATACCAGGCATGTGGAAGAGGGACACCTGAACTAGAGTCTTTGACAGGTTCTATGC
1 CCTGTCCATATCTGGCATGTGGAAGAGGAATACCTGAACCAGGGTCTTTGACAGGTTCCATGC
*
730609 CTTGTCCATACATGACAATGGCATGTGGAAGAGGAATACCTGAACCAGGGTCTTTGACAGGTTCC
1 CCTGTCCAT--AT--C--TGGCATGTGGAAGAGGAATACCTGAACCAGGGTCTTTGACAGGTTCC
*
730674 GTGC
60 ATGC
* * * * *
730678 CCTCTCGATATCTGACATGTGGAAGAGCAAAACCTGAACCAGCAGGGTCTTTGACAGGTTCCATG
1 CCTGTCCATATCTGGCATGTGGAAGAGGAATACCTGAA-C--CAGGGTCTTTGACAGGTTCCATG
730743 -
63 C
* * *
730743 CCTGTCAAT-TCTGGCATGTGGAAGAGCAAAACCTGAACCAGCAGGATCTTTGACAGGTTCCATG
1 CCTGTCCATATCTGGCATGTGGAAGAGGAATACCTGAACCAG--GG-TCTTTGACAGGTTCCATG
730807 C
63 C
* * * * ** * *
730808 CCTGTCGATATCTGGCATGCGGAAGAGCAAAACCTGAACCA-TATATATTGACAAGTT-CATGC
1 CCTGTCCATATCTGGCATGTGGAAGAGGAATACCTGAACCAGGGTCT-TTGACAGGTTCCATGC
* * * *
730870 CCTGTCGATATCTGGCATGT-GAAGAGCAAAACCTCAACCA
1 CCTGTCCATATCTGGCATGTGGAAGAGGAATACCTGAACCA
730910 TGTATGTTGA
Statistics
Matches: 534, Mismatches: 65, Indels: 36
0.84 0.10 0.06
Matches are distributed among these distances:
61 22 0.04
62 28 0.05
63 314 0.59
64 48 0.09
65 17 0.03
66 52 0.10
67 3 0.01
69 50 0.09
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (63 bp):
CCTGTCCATATCTGGCATGTGGAAGAGGAATACCTGAACCAGGGTCTTTGACAGGTTCCATGC
Found at i:731858 original size:17 final size:17
Alignment explanation
Indices: 731807--731861 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
731797 TAGTTGGCTC
*
731807 AAAATCTATA-AAATAT
1 AAAATTTATATAAATAT
731823 -AAA-TTAT-TAAAATATT
1 AAAATTTATAT-AAATA-T
731839 AAAATTTATATAAATAT
1 AAAATTTATATAAATAT
731856 AAAATT
1 AAAATT
731862 ATTTTAAACA
Statistics
Matches: 32, Mismatches: 1, Indels: 11
0.73 0.02 0.25
Matches are distributed among these distances:
14 3 0.09
15 8 0.25
16 1 0.03
17 10 0.31
18 9 0.28
19 1 0.03
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
AAAATTTATATAAATAT
Found at i:733349 original size:22 final size:23
Alignment explanation
Indices: 733298--733349 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 23
733288 TTAGAAGTTA
*
733298 AATTTTATTATTTTAAAAATATT
1 AATTATATTATTTTAAAAATATT
* * *
733321 AA-AATATTATTTTTAAGATA-T
1 AATTATATTATTTTAAAAATATT
733342 AATTATAT
1 AATTATAT
733350 AATTAAATGT
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
21 3 0.13
22 18 0.78
23 2 0.09
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
AATTATATTATTTTAAAAATATT
Found at i:735926 original size:14 final size:14
Alignment explanation
Indices: 735907--735934 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
735897 CTAACAACAT
735907 TTGCTACTTTCCAA
1 TTGCTACTTTCCAA
735921 TTGCTACTTTCCAA
1 TTGCTACTTTCCAA
735935 GAACATGTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.29, G:0.07, T:0.43
Consensus pattern (14 bp):
TTGCTACTTTCCAA
Found at i:737348 original size:17 final size:17
Alignment explanation
Indices: 737326--737372 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
737316 TACTCTAGAC
737326 ACAAAAAGAAAAAAAAA
1 ACAAAAAGAAAAAAAAA
* *
737343 ACAAAAA-CAAAAACAA
1 ACAAAAAGAAAAAAAAA
*
737359 A-AGAAAGAAAAAAA
1 ACAAAAAGAAAAAAA
737373 GATAGAAAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
15 4 0.17
16 13 0.54
17 7 0.29
ACGTcount: A:0.85, C:0.09, G:0.06, T:0.00
Consensus pattern (17 bp):
ACAAAAAGAAAAAAAAA
Found at i:741774 original size:66 final size:65
Alignment explanation
Indices: 741592--741775 Score: 300
Period size: 63 Copynumber: 2.8 Consensus size: 65
741582 TGCCCATACC
*
741592 CAAAAGAAACTGATAACAAGGTCAACCACAATCCAAGATAATGACTTGCTTTTTAGAATATCAAG
1 CAAAAGAAACTGATAACAAGGTCAACTACAATCCAAGATAATGACTTGCTTTTTAGAATATCAAG
*
741657 C-AAA-AAACTGATAACAGGGTCAACTACAATCCAAGATAATGACTTGCTTTTTAGAATATCAAG
1 CAAAAGAAACTGATAACAAGGTCAACTACAATCCAAGATAATGACTTGCTTTTTAGAATATCAAG
* * *
741720 CAAAAAGAAACTGATAACAAAGTCAACTACAATCCAAGATAATGACTGGTTTTTTA
1 C-AAAAGAAACTGATAACAAGGTCAACTACAATCCAAGATAATGACTTGCTTTTTA
741776 AACACCAAAC
Statistics
Matches: 110, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
63 58 0.53
64 3 0.03
65 4 0.04
66 45 0.41
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.24
Consensus pattern (65 bp):
CAAAAGAAACTGATAACAAGGTCAACTACAATCCAAGATAATGACTTGCTTTTTAGAATATCAAG
Found at i:745027 original size:19 final size:19
Alignment explanation
Indices: 744991--745028 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
744981 AATCGTAAGA
*
744991 ATTTTTTTATATTGATTTT
1 ATTTTTTTATATTAATTTT
745010 ATTTTTTTAT-TATAATTTT
1 ATTTTTTTATAT-TAATTTT
745029 TTTAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (19 bp):
ATTTTTTTATATTAATTTT
Found at i:745220 original size:2 final size:2
Alignment explanation
Indices: 745213--745250 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
745203 CAAATGCTAC
745213 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
745251 GCATAAATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:746024 original size:3 final size:3
Alignment explanation
Indices: 746016--746049 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
746006 TTAAAACAAA
*
746016 TAT TAT TAT TAT TAT TAT TAT AAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
746050 TTTAAATTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:747463 original size:2 final size:2
Alignment explanation
Indices: 747456--747482 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
747446 CTACTAGAAG
747456 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
747483 GACATAATTA
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:751772 original size:15 final size:14
Alignment explanation
Indices: 751744--751784 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
751734 TTTTATTTAA
*
751744 ATTTAATTATAAAT
1 ATTTAATTAAAAAT
751758 ATTTATATTAAAAAT
1 ATTTA-ATTAAAAAT
751773 ATTT--TTAAAAAT
1 ATTTAATTAAAAAT
751785 TTCTTAACGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 8 0.32
14 5 0.20
15 12 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATTTAATTAAAAAT
Found at i:751909 original size:27 final size:27
Alignment explanation
Indices: 751878--751929 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
751868 AAATCGTTTC
751878 AATTTAATCAATAAACACTTTTAATTT
1 AATTTAATCAATAAACACTTTTAATTT
* *
751905 AATTTAATCAATGAATACTTTTAAT
1 AATTTAATCAATAAACACTTTTAAT
751930 CGAGGGTCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (27 bp):
AATTTAATCAATAAACACTTTTAATTT
Found at i:752734 original size:6 final size:6
Alignment explanation
Indices: 752723--752779 Score: 50
Period size: 6 Copynumber: 10.0 Consensus size: 6
752713 TATATTCGTC
* * *
752723 TTATAT TTATAT ATTTTA- TTATA- TTATAA TTATAT TTA-AA TTAT-T
1 TTATAT TTATAT -TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
752768 TTATAT TTATAT
1 TTATAT TTATAT
752780 AGATTTTAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
5 17 0.40
6 21 0.50
7 4 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
TTATAT
Found at i:752771 original size:22 final size:21
Alignment explanation
Indices: 752732--752779 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
752722 CTTATATTTA
*
752732 TATATTTTATTATATTATAAT
1 TATATTTAATTATATTATAAT
* *
752753 TATATTTAAATTATTTTATATT
1 TATATTT-AATTATATTATAAT
752775 TATAT
1 TATAT
752780 AGATTTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TATATTTAATTATATTATAAT
Found at i:753307 original size:95 final size:98
Alignment explanation
Indices: 753203--753393 Score: 289
Period size: 98 Copynumber: 2.0 Consensus size: 98
753193 TCAACAGATA
753203 TTTCCTAGATAAAGTGA-ATAATTAAACTAAGGTTTCCTTTAATC-TTTTTTTGTT-AATTTTCT
1 TTTCCTAGATAAAGTGATATAATTAAACTAAGGTTTCCTTTAATCTTTTTTTTGTTAAATTTTCT
753265 TTCTATTTTTGTTCATTCAACTCCTTTATTTGC
66 TTCTATTTTTGTTCATTCAACTCCTTTATTTGC
* * * * *
753298 TTTCCTAGATAAAGTGATGTAATTAAATTATGGTTTCTTTTAATCTTTTTTTTTTTAAATTTTCT
1 TTTCCTAGATAAAGTGATATAATTAAACTAAGGTTTCCTTTAATCTTTTTTTTGTTAAATTTTCT
* * *
753363 TTCTATTTTTGTTCCTTTAACTCTTTTATTT
66 TTCTATTTTTGTTCATTCAACTCCTTTATTT
753394 ATTTTTATAC
Statistics
Matches: 85, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
95 17 0.20
96 23 0.27
97 9 0.11
98 36 0.42
ACGTcount: A:0.23, C:0.13, G:0.08, T:0.57
Consensus pattern (98 bp):
TTTCCTAGATAAAGTGATATAATTAAACTAAGGTTTCCTTTAATCTTTTTTTTGTTAAATTTTCT
TTCTATTTTTGTTCATTCAACTCCTTTATTTGC
Found at i:754442 original size:25 final size:25
Alignment explanation
Indices: 754412--754462 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
754402 ATGTCGGACA
754412 CATATGAGTATCTAATACTTAACAC
1 CATATGAGTATCTAATACTTAACAC
754437 CATATGAGTATCTAATACTTAACAC
1 CATATGAGTATCTAATACTTAACAC
754462 C
1 C
754463 CAAGTCGGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.39, C:0.22, G:0.08, T:0.31
Consensus pattern (25 bp):
CATATGAGTATCTAATACTTAACAC
Found at i:761587 original size:20 final size:18
Alignment explanation
Indices: 761539--761599 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 18
761529 TAATTTTTAT
761539 TTAATTTT--AAAATTAA
1 TTAATTTTAAAAAATTAA
761555 TTAATTTTAAAAAATTAA
1 TTAATTTTAAAAAATTAA
761573 TTTATATTTATAAAAAA-TAA
1 -TTA-ATTT-TAAAAAATTAA
761593 TT-ATTTT
1 TTAATTTT
761600 TTTACCTATT
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
16 9 0.22
17 4 0.10
18 8 0.20
19 5 0.12
20 7 0.17
21 7 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTAATTTTAAAAAATTAA
Found at i:761596 original size:19 final size:18
Alignment explanation
Indices: 761542--761600 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 18
761532 TTTTTATTTA
*
761542 ATTTT-AAAATTAATTA-
1 ATTTTAAAAAATAATTAT
761558 ATTTTAAAAAATTAATTTAT
1 ATTTTAAAAAA-TAA-TTAT
761578 ATTTATAAAAAATAATTAT
1 ATTT-TAAAAAATAATTAT
761597 -TTTT
1 ATTTT
761601 TTACCTATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
16 5 0.14
17 5 0.14
18 6 0.16
19 7 0.19
20 7 0.19
21 7 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTTAAAAAATAATTAT
Found at i:761603 original size:21 final size:21
Alignment explanation
Indices: 761547--761594 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
761537 ATTTAATTTT
761547 AAAATTAA-TTA-ATTT-TAA
1 AAAATTAATTTATATTTATAA
761565 AAAATTAATTTATATTTATAA
1 AAAATTAATTTATATTTATAA
761586 AAAA-TAATT
1 AAAATTAATT
761595 ATTTTTTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.30
19 3 0.11
20 9 0.33
21 7 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AAAATTAATTTATATTTATAA
Found at i:761638 original size:16 final size:18
Alignment explanation
Indices: 761608--761641 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
761598 TTTTTACCTA
761608 TTATATAATATATGATAT
1 TTATATAATATATGATAT
761626 TTATAT-ATA-ATGATAT
1 TTATATAATATATGATAT
761642 AAATAATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 3 0.19
18 6 0.38
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (18 bp):
TTATATAATATATGATAT
Found at i:761693 original size:20 final size:19
Alignment explanation
Indices: 761670--761710 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
761660 ATTTAAAATC
761670 AATTAAATTAATTTAAGTTT
1 AATTAAATTAATTTAA-TTT
* *
761690 AATTTAATTATTTTAATTT
1 AATTAAATTAATTTAATTT
761709 AA
1 AA
761711 AATTTTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
AATTAAATTAATTTAATTT
Found at i:762526 original size:2 final size:2
Alignment explanation
Indices: 762519--762558 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
762509 TCTCAAATTA
* * *
762519 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT TT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
762559 TTATTCCTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (2 bp):
AT
Found at i:764108 original size:18 final size:17
Alignment explanation
Indices: 764087--764132 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
764077 TAATTATATC
764087 TATAATATAT-ATT-AT
1 TATAATATATAATTCAT
764102 TATTATATATATAATTCAT
1 TA-TA-ATATATAATTCAT
764121 TA-AATATATAAT
1 TATAATATATAAT
764133 GAAAATGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 2 0.07
16 11 0.41
17 7 0.26
18 3 0.11
19 4 0.15
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (17 bp):
TATAATATATAATTCAT
Found at i:764221 original size:3 final size:3
Alignment explanation
Indices: 764206--764270 Score: 67
Period size: 3 Copynumber: 20.3 Consensus size: 3
764196 TAATTCCTTA
*
764206 ATT ATT ATAT ATT ATT ATT ATT ATT ATT ATAT ATT ATT ATAT ATAT ATA
1 ATT ATT AT-T ATT ATT ATT ATT ATT ATT AT-T ATT ATT AT-T AT-T ATT
* *
764255 ATA ATA ATT ATT ATT A
1 ATT ATT ATT ATT ATT A
764271 AATTTGGTGT
Statistics
Matches: 57, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
3 44 0.77
4 13 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:764225 original size:16 final size:16
Alignment explanation
Indices: 764206--764270 Score: 75
Period size: 16 Copynumber: 4.2 Consensus size: 16
764196 TAATTCCTTA
764206 ATTATTATATATTATT
1 ATTATTATATATTATT
764222 ATTATTAT-TATTATAT
1 ATTATTATATATTAT-T
764238 ATTATTATATA-TA-T
1 ATTATTATATATTATT
* *
764252 ATAATAATA-ATTATT
1 ATTATTATATATTATT
764267 ATTA
1 ATTA
764271 AATTTGGTGT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
13 1 0.02
14 10 0.24
15 10 0.24
16 19 0.45
17 2 0.05
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTATTATATATTATT
Found at i:769400 original size:33 final size:33
Alignment explanation
Indices: 769359--769427 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
769349 CGATTAAATT
769359 AAGGATT-AAGACATAATTTTGATAGA-TTTTAC
1 AAGGATTAAAG-CATAATTTTGATAGACTTTTAC
* *
769391 AAGGAATTAAAGTATAATTTTGATGGACTTTTAC
1 AAGG-ATTAAAGCATAATTTTGATAGACTTTTAC
769425 AAG
1 AAG
769428 ATTTATCACA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 4 0.12
33 16 0.50
34 12 0.38
ACGTcount: A:0.41, C:0.06, G:0.17, T:0.36
Consensus pattern (33 bp):
AAGGATTAAAGCATAATTTTGATAGACTTTTAC
Found at i:771039 original size:20 final size:21
Alignment explanation
Indices: 771000--771047 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
770990 TTTATTGATT
*
771000 ATTTAAATTTTAAATTTTAAA
1 ATTTAAATTATAAATTTTAAA
*
771021 ATTTAAA-TATAATTTTTAAA
1 ATTTAAATTATAAATTTTAAA
*
771041 AATTAAA
1 ATTTAAA
771048 AAATTATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTTAAATTATAAATTTTAAA
Found at i:771056 original size:21 final size:20
Alignment explanation
Indices: 771014--771056 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
771004 AAATTTTAAA
* *
771014 TTTTAAAATTTAAATATAAT
1 TTTTAAAATTAAAAAATAAT
*
771034 TTTTAAAAATTAAAAAATTAT
1 TTTT-AAAATTAAAAAATAAT
771055 TT
1 TT
771057 ACATATTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTTAAAATTAAAAAATAAT
Found at i:773218 original size:16 final size:17
Alignment explanation
Indices: 773199--773243 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
773189 ACTATATATC
773199 TTAAAATTTATATTA-T
1 TTAAAATTTATATTATT
*
773215 TT-AAA-TTATCAATATT
1 TTAAAATTTAT-ATTATT
773231 TTAAAATTTATAT
1 TTAAAATTTATAT
773244 AAATATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 7
0.72 0.06 0.22
Matches are distributed among these distances:
14 4 0.17
15 6 0.26
16 5 0.22
17 4 0.17
18 4 0.17
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAAAATTTATATTATT
Found at i:779813 original size:2 final size:2
Alignment explanation
Indices: 779806--779836 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
779796 CTAGACAGGG
779806 GA GA GA GA GA GA GA GA GA GA GA GA GA G- GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
779837 AGGCGAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:785693 original size:16 final size:16
Alignment explanation
Indices: 785672--785704 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
785662 ATGGCGCGCC
785672 CCTTCTCAATTTGGCT
1 CCTTCTCAATTTGGCT
785688 CCTTCTCAATTTGGCT
1 CCTTCTCAATTTGGCT
785704 C
1 C
785705 AAACTTATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.33, G:0.12, T:0.42
Consensus pattern (16 bp):
CCTTCTCAATTTGGCT
Found at i:786058 original size:146 final size:148
Alignment explanation
Indices: 785855--786194 Score: 403
Period size: 146 Copynumber: 2.3 Consensus size: 148
785845 AATCGTGGAG
* * * *
785855 TGTAACAATATGGATGAACTGGATTAAATTCGCTTCCTGGTACATTCAGTATGTACAT-GTTGAA
1 TGTAACAATATGGATGAACTGGATTAAATTCTCTTCCTGGTACATTCAGGATATACATGGTGGAA
* * *
785919 GATCTTTGTTTTGGCT-ATTGTTAAGTTCTAGCTTGGTTGCCAT-GCTCATTG-AACAAGTT-CA
66 GATCTTTG-TTTGG-TAAGTGTTAAG-T-TAGCCTGGCTGCCATGGC-CATTGCAA-AAGTTGC-
*
785980 TTATGGAGG-CAAGAAGTGA-G-GAT
124 -TATAGAGGTCAAGAAGTGAGGAGAT
* * *
786003 TGTAAC-A-ATGGATGAACTGGATTATATTCTCTTCCTGGTACATTTAGGATATACATGGTGGAG
1 TGTAACAATATGGATGAACTGGATTAAATTCTCTTCCTGGTACATTCAGGATATACATGGTGGAA
*
786066 GATCTTTGTTTGGTAAGTGTTAAGTTAGCCTGGCTGCCATGGCCATTGCAAAGGTTGCTATAGAG
66 GATCTTTGTTTGGTAAGTGTTAAGTTAGCCTGGCTGCCATGGCCATTGCAAAAGTTGCTATAGAG
*
786131 GTTAAGAAGTGAGGAGAT
131 GTCAAGAAGTGAGGAGAT
* *
786149 TGTAACAATATTGATGAACTGGACTAAATTCTCTTCCTGGTACATT
1 TGTAACAATATGGATGAACTGGATTAAATTCTCTTCCTGGTACATT
786195 GAGCATTCAT
Statistics
Matches: 166, Mismatches: 16, Indels: 20
0.82 0.08 0.10
Matches are distributed among these distances:
143 7 0.04
144 31 0.19
145 8 0.05
146 66 0.40
147 14 0.08
148 40 0.24
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (148 bp):
TGTAACAATATGGATGAACTGGATTAAATTCTCTTCCTGGTACATTCAGGATATACATGGTGGAA
GATCTTTGTTTGGTAAGTGTTAAGTTAGCCTGGCTGCCATGGCCATTGCAAAAGTTGCTATAGAG
GTCAAGAAGTGAGGAGAT
Found at i:787058 original size:36 final size:36
Alignment explanation
Indices: 787018--787090 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
787008 GTTACATTAG
787018 CGGGGTACGTAAAGATCAATTGTATGAATTCAAAGT
1 CGGGGTACGTAAAGATCAATTGTATGAATTCAAAGT
787054 CGGGGTACGTAAAGATCAATTGTATGAATTCAAAGT
1 CGGGGTACGTAAAGATCAATTGTATGAATTCAAAGT
787090 C
1 C
787091 TGGTTATTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27
Consensus pattern (36 bp):
CGGGGTACGTAAAGATCAATTGTATGAATTCAAAGT
Found at i:792233 original size:45 final size:44
Alignment explanation
Indices: 792153--792248 Score: 165
Period size: 44 Copynumber: 2.2 Consensus size: 44
792143 AAAACTGGGT
792153 TTTTTTTCCCTTTAATTTTTGTAAATTAGGGTTTTTTTTCTTTG
1 TTTTTTTCCCTTTAATTTTTGTAAATTAGGGTTTTTTTTCTTTG
* *
792197 TTTTTTTCCCTTTAATTTTTGTAAATTTGGGTTTTTTTTCTTTT
1 TTTTTTTCCCTTTAATTTTTGTAAATTAGGGTTTTTTTTCTTTG
792241 TCTTTTTT
1 T-TTTTTT
792249 GGATTTTGTT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 43 0.88
45 6 0.12
ACGTcount: A:0.11, C:0.09, G:0.09, T:0.70
Consensus pattern (44 bp):
TTTTTTTCCCTTTAATTTTTGTAAATTAGGGTTTTTTTTCTTTG
Found at i:792560 original size:17 final size:17
Alignment explanation
Indices: 792538--792626 Score: 55
Period size: 16 Copynumber: 5.3 Consensus size: 17
792528 TTAATTTTAA
792538 AAAAATTTAAATATTTT
1 AAAAATTTAAATATTTT
792555 AAAAA-TTATAAT-TTTAT
1 AAAAATTTA-AATATTT-T
* * *
792572 ATTTATATTTAAATA-TAT
1 A--AAAATTTAAATATTTT
*
792590 -AAAATATAAATATTTT
1 AAAAATTTAAATATTTT
792606 AAAAATATTAAA-A-TTT
1 AAAAAT-TTAAATATTTT
792622 AAAAA
1 AAAAA
792627 ACCTAAATCA
Statistics
Matches: 55, Mismatches: 8, Indels: 19
0.67 0.10 0.23
Matches are distributed among these distances:
15 9 0.16
16 16 0.29
17 16 0.29
18 5 0.09
19 6 0.11
20 3 0.05
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAAAATTTAAATATTTT
Found at i:792627 original size:17 final size:17
Alignment explanation
Indices: 792576--792627 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
792566 TTTTATATTT
* * *
792576 ATATTTAAATATATAAA
1 ATATTAAAATTTAAAAA
*
792593 ATA-TAAATATTTTAAAA
1 ATATTAAA-ATTTAAAAA
792610 ATATTAAAATTTAAAAA
1 ATATTAAAATTTAAAAA
792627 A
1 A
792628 CCTAAATCAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
16 3 0.11
17 21 0.75
18 4 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATATTAAAATTTAAAAA
Found at i:793396 original size:3 final size:3
Alignment explanation
Indices: 793388--793426 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
793378 ATTTTTTCAA
793388 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
793427 TTGTATCATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:795227 original size:3 final size:3
Alignment explanation
Indices: 795219--795248 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
795209 TTTTTATTTA
795219 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
795249 GTGGTATGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:795780 original size:15 final size:14
Alignment explanation
Indices: 795756--795785 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
795746 ATTTTTTTTC
795756 TTTATATAAAAATA
1 TTTATATAAAAATA
795770 TTTATTATAAAAATA
1 TTTA-TATAAAAATA
795785 T
1 T
795786 AATCTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TTTATATAAAAATA
Found at i:796253 original size:22 final size:21
Alignment explanation
Indices: 796227--796267 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
796217 TTATTTTATT
796227 TAAAT-TTAATTATAAAAATATC
1 TAAATATT-ATTA-AAAAATATC
796249 TAAATATTATTAAAAAATA
1 TAAATATTATTAAAAAATA
796268 AATTTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 9 0.50
23 2 0.11
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
TAAATATTATTAAAAAATATC
Found at i:801279 original size:71 final size:71
Alignment explanation
Indices: 801182--801320 Score: 260
Period size: 71 Copynumber: 2.0 Consensus size: 71
801172 ATGTCTCTTG
801182 GAGGCAAGGAGAAATATATTCAAGGCTTAATATTAAATTCGTAAATGCTGAAGTTCAGTGAATTT
1 GAGGCAAGGAGAAATATATTCAAGGCTTAATATTAAATTCGTAAATGCTGAAGTTCAGTGAATTT
801247 GGTCAA
66 GGTCAA
* *
801253 GAGGCAAGGAGAAATATATTCGAGGCTTAATATTACATTCGTAAATGCTGAAGTTCAGTGAATTT
1 GAGGCAAGGAGAAATATATTCAAGGCTTAATATTAAATTCGTAAATGCTGAAGTTCAGTGAATTT
801318 GGT
66 GGT
801321 TTTCTTATGA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 66 1.00
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.30
Consensus pattern (71 bp):
GAGGCAAGGAGAAATATATTCAAGGCTTAATATTAAATTCGTAAATGCTGAAGTTCAGTGAATTT
GGTCAA
Found at i:802790 original size:2 final size:2
Alignment explanation
Indices: 802785--802941 Score: 136
Period size: 2 Copynumber: 79.0 Consensus size: 2
802775 TGTGTGTGGG
* * * * *
802785 TA TA TA TA TA TA TA TA TA TA TA TA TA TG CA TG TA TG TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
802827 TG TA CA CA TA TA TA TA TA TA TA TA TG TG TA TA TA TA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
802869 CA TA TA TG TA TA TA TA TA CA TA CA TA TA TG TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
802911 TG TA TA TG TA TA TA TA TA TA CA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
802942 ATTTGTGGTT
Statistics
Matches: 120, Mismatches: 34, Indels: 2
0.77 0.22 0.01
Matches are distributed among these distances:
1 1 0.01
2 119 0.99
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (2 bp):
TA
Found at i:806891 original size:17 final size:17
Alignment explanation
Indices: 806871--806905 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
806861 TTTATATTAA
806871 AATTTATTAGTATATAT
1 AATTTATTAGTATATAT
* *
806888 AATTTTTTAGTGTATAT
1 AATTTATTAGTATATAT
806905 A
1 A
806906 TAAAGCTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (17 bp):
AATTTATTAGTATATAT
Found at i:808766 original size:15 final size:15
Alignment explanation
Indices: 808748--808802 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
808738 ATTCATATCA
808748 ATACTGAAGTTATAG
1 ATACTGAAGTTATAG
*
808763 ATACTGAA-AT-TA-
1 ATACTGAAGTTATAG
*
808775 ATACTTCCAAGTTATAG
1 ATAC-T-GAAGTTATAG
808792 ATACTGAAGTT
1 ATACTGAAGTT
808803 CTTCGATACA
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
12 4 0.13
13 3 0.10
14 3 0.10
15 14 0.45
16 3 0.10
17 4 0.13
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.35
Consensus pattern (15 bp):
ATACTGAAGTTATAG
Found at i:812434 original size:28 final size:28
Alignment explanation
Indices: 812402--812474 Score: 80
Period size: 27 Copynumber: 2.6 Consensus size: 28
812392 TAGTTCACCC
812402 AATTTTTATTAAATAAAG-TTTAAATATA
1 AATTTTTATTAAATAAAGATTT-AATATA
*
812430 AATTTTTAATT-AA-AAAGATTTAATTTA
1 AATTTTT-ATTAAATAAAGATTTAATATA
*
812457 AATTATTATTTAAATAAA
1 AATTTTTA-TTAAATAAA
812475 AATATTATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
26 1 0.03
27 17 0.45
28 14 0.37
29 6 0.16
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.47
Consensus pattern (28 bp):
AATTTTTATTAAATAAAGATTTAATATA
Found at i:812475 original size:31 final size:29
Alignment explanation
Indices: 812431--812498 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
812421 TTAAATATAA
* *
812431 ATTTTTAATTAAAAAGATTTAATTTAAATT
1 ATTTTTAAATAAAAAGA-TTAATTTAAAAT
* *
812461 ATTATTTAAATAAAAATATTATTTTAAAAT
1 ATT-TTTAAATAAAAAGATTAATTTAAAAT
812491 ATTTTTAA
1 ATTTTTAA
812499 TTATTTAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 5 0.15
30 16 0.48
31 12 0.36
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (29 bp):
ATTTTTAAATAAAAAGATTAATTTAAAAT
Found at i:813085 original size:35 final size:36
Alignment explanation
Indices: 812996--813085 Score: 87
Period size: 35 Copynumber: 2.5 Consensus size: 36
812986 TCAAATTTTA
** *
812996 TTTAAATAATAAAATATAACTTGTTATTTAAATTAAT
1 TTTAAATAATAAAATA-AAAATATTATTTAAATTAAT
* *
813033 TATT-AATATTAATATAAAAATATT-TTTAATATT-AT
1 T-TTAAATAATAAAATAAAAATATTATTTAA-ATTAAT
813068 TTTAAATAATAAAATAAA
1 TTTAAATAATAAAATAAA
813086 TTTTAAATCT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
34 2 0.05
35 20 0.47
36 8 0.19
37 11 0.26
38 2 0.05
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (36 bp):
TTTAAATAATAAAATAAAAATATTATTTAAATTAAT
Found at i:813277 original size:14 final size:15
Alignment explanation
Indices: 813249--813303 Score: 69
Period size: 14 Copynumber: 3.8 Consensus size: 15
813239 AAGTTTTACT
* *
813249 ATATAAATATTTTTC
1 ATATATATATATTTC
813264 ATATA-ATATATTTC
1 ATATATATATATTTC
*
813278 ATATATATATATAT-
1 ATATATATATATTTC
813292 ATATATATATAT
1 ATATATATATAT
813304 GATTACGATT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
14 25 0.68
15 12 0.32
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (15 bp):
ATATATATATATTTC
Found at i:813283 original size:2 final size:2
Alignment explanation
Indices: 813264--813303 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
813254 AATATTTTTC
*
813264 AT AT A- AT AT AT TT CAT 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
813304 GATTACGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.94
3 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:815103 original size:2 final size:2
Alignment explanation
Indices: 815096--815122 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
815086 TCTAAGGTTT
815096 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
815123 GGAGGATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:815877 original size:241 final size:244
Alignment explanation
Indices: 815436--815998 Score: 699
Period size: 241 Copynumber: 2.3 Consensus size: 244
815426 AAAATAATAT
* * * *
815436 TTTTATGACCAAATATCAAAGCATGATGTTTACCCAAAATCATTGTCCTCTAAGAAAACGGAAAA
1 TTTTATGACCAAATATC-AAGCATGATGGTTATCCAAAATCATTGCCCTCT-AGAAAAAGGAAAA
* * * * *
815501 GAAATCTACAGCATTAGCTATGTTACTTGGATTTTTCATGTTTTCTAAAGTATTAATGTATGACA
64 GAAATCTACCGCATTAACTATG-TAC-T-GACTTTTCATGTTTTCTAAAGTATTAATGTATAAAA
* * * ** * *
815566 CTTATTTAGATATGAGCATATCTATATCAGGCAAATGCCCGTATTCAAAATTTACTCTCGAGTCT
126 CATATTTAGATATCAGCATATCCATATCAAACAAATACCCGTATTCAAAATTCACTCTCGAGTCT
* **
815631 ATAGAATCTTTACTACAGCTACAACTGTTTGAACATTACAAAAAAAAAAAAAAAAGG
191 ATAGAATCTTTACTACAGCTACAACTGCTTGAACA--A-AAAAAAAAAAAAAAAACA
*
815688 TTTTATGACCAAATATCAAGCATGATGGTTAATCCAAAATCATTGCCCTCTAGAAAAGGGAAAAG
1 TTTTATGACCAAATATCAAGCATGATGGTT-ATCCAAAATCATTGCCCTCTAGAAAAAGGAAAAG
* *
815753 AAATCTACCGCATTAACTATG-A-T-ACTTTT-ATGTTTTCTAAAGTATTCATGTCTAAAACATA
65 AAATCTACCGCATTAACTATGTACTGACTTTTCATGTTTTCTAAAGTATTAATGTATAAAACATA
* * * *
815814 -TTA-A-ATCAGCATATCCATATCAAACACATACCCGTATTTAACATTCACTCTCGAGTTTATAG
130 TTTAGATATCAGCATATCCATATCAAACAAATACCCGTATTCAAAATTCACTCTCGAGTCTATAG
*** *
815876 AATCTTTACTACAGCTACAACTGCTTGAACAAAACCGAAAAAAAGAAACA
195 AATCTTTACTACAGCTACAACTGCTTGAACAAAAAAAAAAAAAAAAAACA
* * *
815926 TTTTATGACCAAATATCAAGCATGATGATTATCCAAAATCATTGCCCTCCAGAAAAAGAAAAAGA
1 TTTTATGACCAAATATCAAGCATGATGGTTATCCAAAATCATTGCCCTCTAGAAAAAGGAAAAGA
815991 AATCTACC
66 AATCTACC
815999 ACGTCAGTTA
Statistics
Matches: 277, Mismatches: 33, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
237 40 0.14
238 41 0.15
239 1 0.00
241 78 0.28
242 1 0.00
243 3 0.01
244 27 0.10
245 5 0.02
247 1 0.00
249 1 0.00
251 44 0.16
252 35 0.13
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (244 bp):
TTTTATGACCAAATATCAAGCATGATGGTTATCCAAAATCATTGCCCTCTAGAAAAAGGAAAAGA
AATCTACCGCATTAACTATGTACTGACTTTTCATGTTTTCTAAAGTATTAATGTATAAAACATAT
TTAGATATCAGCATATCCATATCAAACAAATACCCGTATTCAAAATTCACTCTCGAGTCTATAGA
ATCTTTACTACAGCTACAACTGCTTGAACAAAAAAAAAAAAAAAAAACA
Found at i:818661 original size:20 final size:20
Alignment explanation
Indices: 818617--818664 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
818607 TATTTACTAC
*
818617 TTATTTACTATTAAAATTAT
1 TTATTTAATATTAAAATTAT
* * *
818637 ATATTTAATATTTAAATTTT
1 TTATTTAATATTAAAATTAT
818657 TTATTTAA
1 TTATTTAA
818665 ATAAAGTTGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
TTATTTAATATTAAAATTAT
Found at i:822002 original size:22 final size:21
Alignment explanation
Indices: 821971--822014 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
821961 TAAATTATTT
* *
821971 AAATTTTAAAATTTTATAAAA
1 AAATTTTAAAAATTAATAAAA
821992 AAATTATTAAAAATTAATAAAA
1 AAATT-TTAAAAATTAATAAAA
822014 A
1 A
822015 TAACATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAATTTTAAAAATTAATAAAA
Found at i:822074 original size:12 final size:13
Alignment explanation
Indices: 822057--822093 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
822047 TGATTTAAAT
822057 AATTTAT-TTATA
1 AATTTATATTATA
822069 AATTTATATT-TA
1 AATTTATATTATA
*
822081 CATTTATATTATA
1 AATTTATATTATA
822094 TATAATGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 18 0.82
13 4 0.18
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (13 bp):
AATTTATATTATA
Found at i:822558 original size:14 final size:15
Alignment explanation
Indices: 822539--822581 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 15
822529 TATTATATTT
822539 TATTAT-TTTATATA
1 TATTATATTTATATA
*
822553 TATTATATTCATATA
1 TATTATATTTATATA
822568 -ATTATATTTA-ATA
1 TATTATATTTATATA
822581 T
1 T
822582 TATCAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 3 0.12
14 15 0.60
15 7 0.28
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (15 bp):
TATTATATTTATATA
Found at i:822876 original size:15 final size:14
Alignment explanation
Indices: 822810--822889 Score: 54
Period size: 15 Copynumber: 5.5 Consensus size: 14
822800 AAGAATTAGG
822810 AAAAATAAAAA-TA
1 AAAAATAAAAATTA
** *
822823 ATTAATCAAAATTTA
1 AAAAAT-AAAAATTA
* *
822838 AATAATCAAAATTA
1 AAAAATAAAAATTA
822852 AAAATTATAAAAATTA
1 AAAA--ATAAAAATTA
*
822868 AAAGAATAAAAAATA
1 AAA-AATAAAAATTA
*
822883 AATAATA
1 AAAAATA
822890 TAAACCACAT
Statistics
Matches: 52, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
13 4 0.08
14 17 0.33
15 18 0.35
16 12 0.23
17 1 0.02
ACGTcount: A:0.70, C:0.03, G:0.01, T:0.26
Consensus pattern (14 bp):
AAAAATAAAAATTA
Found at i:822879 original size:16 final size:16
Alignment explanation
Indices: 822845--822893 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
822835 TTAAATAATC
*
822845 AAAATTAAAAATTATA
1 AAAATTAAAAAATATA
822861 AAAATTAAAAGAATA-A
1 AAAATTAAAA-AATATA
*
822877 AAAA-TAAATAATATA
1 AAAATTAAAAAATATA
822892 AA
1 AA
822894 CCACATATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
14 4 0.14
15 7 0.24
16 15 0.52
17 3 0.10
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (16 bp):
AAAATTAAAAAATATA
Found at i:823071 original size:14 final size:16
Alignment explanation
Indices: 823031--823070 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
823021 TTTTTTAATT
823031 AAAAAATATAAGCTTA
1 AAAAAATATAAGCTTA
*
823047 AAAAAATATAAGCTTT
1 AAAAAATATAAGCTTA
823063 AAAAAATA
1 AAAAAATA
823071 AAAGATCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.25
Consensus pattern (16 bp):
AAAAAATATAAGCTTA
Found at i:832159 original size:17 final size:17
Alignment explanation
Indices: 832126--832167 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
832116 AAATAATTTT
*
832126 AATATTTAAATATAATA
1 AATATTTAAATAAAATA
832143 AATATTT-AATAAAAATA
1 AATATTTAAAT-AAAATA
*
832160 TATATTTA
1 AATATTTA
832168 GCTAAATAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AATATTTAAATAAAATA
Found at i:833942 original size:19 final size:19
Alignment explanation
Indices: 833913--833971 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
833903 ATATAAAAAT
*
833913 AATATAATAAATAT-TATA
1 AATATATTAAATATATATA
833931 AGATATATTAAATATATATA
1 A-ATATATTAAATATATATA
* *
833951 ATTATATTAAAATTTATATA
1 AATATATT-AAATATATATA
833971 A
1 A
833972 TAAATATAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 1 0.03
19 18 0.51
20 16 0.46
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
AATATATTAAATATATATA
Found at i:833980 original size:9 final size:9
Alignment explanation
Indices: 833884--833982 Score: 62
Period size: 9 Copynumber: 11.0 Consensus size: 9
833874 TTATGATATT
833884 AATATAATA
1 AATATAATA
* *
833893 AATTTAACA
1 AATATAATA
*
833902 AATATAAAAA
1 AATAT-AATA
833912 TAATATAATA
1 -AATATAATA
*
833922 AATATTATA
1 AATATAATA
*
833931 AGATATATTA
1 A-ATATAATA
833941 AATATATATA
1 AATATA-ATA
* *
833951 ATTATATTA
1 AATATAATA
833960 AA-AT--T-
1 AATATAATA
*
833965 TATATAATA
1 AATATAATA
833974 AATATAATA
1 AATATAATA
833983 TTTAAAATAT
Statistics
Matches: 68, Mismatches: 14, Indels: 16
0.69 0.14 0.16
Matches are distributed among these distances:
5 1 0.01
6 3 0.04
8 3 0.04
9 36 0.53
10 20 0.29
11 5 0.07
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (9 bp):
AATATAATA
Found at i:842099 original size:16 final size:17
Alignment explanation
Indices: 842073--842104 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
842063 TAAACTTGTA
842073 TCTTATATTTTTTTAAT
1 TCTTATATTTTTTTAAT
842090 TCTT-TATTTTTTTAA
1 TCTTATATTTTTTTAA
842105 AGTATACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (17 bp):
TCTTATATTTTTTTAAT
Found at i:845494 original size:13 final size:13
Alignment explanation
Indices: 845476--845500 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
845466 TTCAAAATTT
845476 ATTTATTTAAAAA
1 ATTTATTTAAAAA
845489 ATTTATTTAAAA
1 ATTTATTTAAAA
845501 CTTAATTTAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTATTTAAAAA
Found at i:846626 original size:20 final size:19
Alignment explanation
Indices: 846594--846633 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
846584 CATTCATTTA
846594 AAATATTAAATATTTATAT
1 AAATATTAAATATTTATAT
*
846613 AAATTTTAATATATTTATAT
1 AAATATTAA-ATATTTATAT
846633 A
1 A
846634 TTTATATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AAATATTAAATATTTATAT
Found at i:847599 original size:22 final size:22
Alignment explanation
Indices: 847574--847615 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
847564 TATTATTAAA
* *
847574 AAATTTAATTATAAAAATATAT
1 AAATATAAATATAAAAATATAT
847596 AAATATAAATATAAAAATAT
1 AAATATAAATATAAAAATAT
847616 TTTTTAATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AAATATAAATATAAAAATATAT
Found at i:848170 original size:2 final size:2
Alignment explanation
Indices: 848165--848196 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
848155 TCTCTCTCTC
848165 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
848197 ACTTTGGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:848555 original size:33 final size:33
Alignment explanation
Indices: 848518--848582 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
848508 TTTGTGTTAT
*
848518 CTAATTAAAGAAGAAAATTATGGGAAATGATAA
1 CTAATTAAAGAAGAAAATTATGAGAAATGATAA
* *
848551 CTAATTAAGGAAGTAAATTATGAGAAATGATA
1 CTAATTAAAGAAGAAAATTATGAGAAATGATA
848583 TAAATATTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.18, T:0.26
Consensus pattern (33 bp):
CTAATTAAAGAAGAAAATTATGAGAAATGATAA
Found at i:903801 original size:2 final size:2
Alignment explanation
Indices: 903794--903827 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
903784 ATTTTTCTAC
*
903794 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
903828 TCTTTTGATT
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:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:905641 original size:13 final size:13
Alignment explanation
Indices: 905623--905650 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
905613 TATTTTTTAA
905623 AATATTTATATTT
1 AATATTTATATTT
905636 AATATTTATATTT
1 AATATTTATATTT
905649 AA
1 AA
905651 AATATATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:905666 original size:9 final size:11
Alignment explanation
Indices: 905642--905667 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
905632 ATTTAATATT
905642 TATATTTAAAA
1 TATATTTAAAA
905653 TATATTTAAAA
1 TATATTTAAAA
905664 TATA
1 TATA
905668 AATATTACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TATATTTAAAA
Found at i:907337 original size:17 final size:17
Alignment explanation
Indices: 907311--907344 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
907301 GAAATACCAA
*
907311 TAATTGTTGTATCAAAG
1 TAATTCTTGTATCAAAG
*
907328 TAATTCTTGTTTCAAAG
1 TAATTCTTGTATCAAAG
907345 GAAAAACAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.44
Consensus pattern (17 bp):
TAATTCTTGTATCAAAG
Found at i:909438 original size:12 final size:12
Alignment explanation
Indices: 909372--909440 Score: 56
Period size: 12 Copynumber: 5.8 Consensus size: 12
909362 TAATAATTAA
*
909372 TATATATAATTT
1 TATATATTATTT
909384 TA-A-ATTATATT
1 TATATATTAT-TT
909395 TATAT-TTATCTT
1 TATATATTAT-TT
*
909407 TATTTTATTA-TT
1 TA-TATATTATTT
909419 TATAATATTATTT
1 TAT-ATATTATTT
909432 TATATATTA
1 TATATATTA
909441 ACTTTGCTTC
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
10 4 0.09
11 6 0.13
12 26 0.57
13 7 0.15
14 3 0.07
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (12 bp):
TATATATTATTT
Found at i:909795 original size:16 final size:17
Alignment explanation
Indices: 909771--909835 Score: 53
Period size: 18 Copynumber: 3.8 Consensus size: 17
909761 GAAAATTTTA
*
909771 TTTA-ATTTTTAATAAT
1 TTTATATTTTTAAAAAT
*
909787 TTTATTTTTTTAAAAATT
1 TTTATATTTTTAAAAA-T
* *
909805 TTTAAATTTTGAATAAA-
1 TTTATATTTTTAA-AAAT
909822 TTTATACTTTTTAA
1 TTTATA-TTTTTAA
909836 TATTTATATT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
16 4 0.11
17 14 0.37
18 17 0.45
19 3 0.08
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (17 bp):
TTTATATTTTTAAAAAT
Found at i:909986 original size:17 final size:16
Alignment explanation
Indices: 909949--909985 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
909939 TGGAGTCAAA
*
909949 TTTTGATTAAATTTAT
1 TTTTTATTAAATTTAT
909965 TTTTTATTAAATTTAT
1 TTTTTATTAAATTTAT
909981 TTTTT
1 TTTTT
909986 TGATTTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (16 bp):
TTTTTATTAAATTTAT
Found at i:919469 original size:2 final size:2
Alignment explanation
Indices: 919432--919456 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
919422 GATTAAAGTG
919432 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
919457 AAGAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:919571 original size:13 final size:13
Alignment explanation
Indices: 919553--919579 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
919543 TCTTAATCAT
919553 TATTTATAAATTA
1 TATTTATAAATTA
919566 TATTTATAAATTA
1 TATTTATAAATTA
919579 T
1 T
919580 GAGAAAAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TATTTATAAATTA
Found at i:920471 original size:4 final size:4
Alignment explanation
Indices: 920462--920493 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
920452 AAACAAATGG
920462 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
920494 TGTTTTCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:921051 original size:47 final size:47
Alignment explanation
Indices: 920963--921064 Score: 107
Period size: 47 Copynumber: 2.2 Consensus size: 47
920953 TATTAGATTG
* * * **
920963 ATTTAAATTAAATTAAATAAGATAAGATTTTTTTTAATTAAAATC-A
1 ATTTAATTTAAATTAAATAAAAAAAGATTTTTACTAATTAAAATCTA
* * * *
921009 ATTTTAATTTAATTTAAATAAAAAAATATTTTTACTATTTAAATTCTA
1 A-TTTAATTTAAATTAAATAAAAAAAGATTTTTACTAATTAAAATCTA
921057 ATTTAATT
1 ATTTAATT
921065 CAACCCGAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
46 1 0.02
47 42 0.93
48 2 0.04
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (47 bp):
ATTTAATTTAAATTAAATAAAAAAAGATTTTTACTAATTAAAATCTA
Found at i:921712 original size:12 final size:12
Alignment explanation
Indices: 921691--921737 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
921681 TATTTAGATT
921691 TTATTATAAATA
1 TTATTATAAATA
*
921703 TTAATATAAA-A
1 TTATTATAAATA
* *
921714 ATATTTTAAATA
1 TTATTATAAATA
921726 TTATTATAAATA
1 TTATTATAAATA
921738 ATAAAACGAG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
11 8 0.29
12 20 0.71
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TTATTATAAATA
Found at i:921723 original size:23 final size:24
Alignment explanation
Indices: 921692--921740 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
921682 ATTTAGATTT
921692 TATTATAAATATTAATATAAA-AA
1 TATTATAAATATTAATATAAATAA
* *
921715 TATTTTAAATATTATTATAAATAA
1 TATTATAAATATTAATATAAATAA
921739 TA
1 TA
921741 AAACGAGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TATTATAAATATTAATATAAATAA
Found at i:922187 original size:2 final size:2
Alignment explanation
Indices: 922180--922214 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
922170 GCAAATCTCC
922180 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 T
922215 TGATAAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:929806 original size:26 final size:26
Alignment explanation
Indices: 929772--929828 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
929762 TGTACGTGTC
*
929772 ATATTCATA-ATATTTTTAAT-TATTA
1 ATATTCATATA-AATTTTAATATATTA
929797 TATATTCATATAAATTTTAATATATTA
1 -ATATTCATATAAATTTTAATATATTA
929824 ATATT
1 ATATT
929829 TTTTATCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 22 0.79
27 6 0.21
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (26 bp):
ATATTCATATAAATTTTAATATATTA
Found at i:929917 original size:16 final size:16
Alignment explanation
Indices: 929849--929923 Score: 50
Period size: 17 Copynumber: 4.7 Consensus size: 16
929839 TAATTTAAAA
*
929849 AATTATATATTTATATT
1 AATTATAT-TTTATTTT
*
929866 ATATTCATA-TTAATTTT
1 A-ATT-ATATTTTATTTT
929883 --TTATATTTTATTTT
1 AATTATATTTTATTTT
*
929897 AATTAT-TTTTCTTTT
1 AATTATATTTTATTTT
*
929912 ACATTATCTTTT
1 A-ATTATATTTT
929924 TAAAGTGTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
13 3 0.06
14 9 0.19
15 9 0.19
16 9 0.19
17 11 0.23
18 3 0.06
19 3 0.06
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.65
Consensus pattern (16 bp):
AATTATATTTTATTTT
Found at i:930366 original size:27 final size:25
Alignment explanation
Indices: 930329--930401 Score: 78
Period size: 25 Copynumber: 2.9 Consensus size: 25
930319 TAATAATTAT
930329 ATTTAAAATATTTTATATTTATATAAA
1 ATTTAAAATA-TTTATA-TTATATAAA
* *
930356 ATTTAATATATTTATATTATATAAT
1 ATTTAAAATATTTATATTATATAAA
* *
930381 TTTTAAAA-ATATAT-TTATATA
1 ATTTAAAATATTTATATTATATA
930402 TATTGTACTC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
23 7 0.17
24 5 0.12
25 14 0.34
26 6 0.15
27 9 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
ATTTAAAATATTTATATTATATAAA
Found at i:930371 original size:18 final size:19
Alignment explanation
Indices: 930326--930371 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
930316 AAATAATAAT
930326 TATATTTA-AAATATTT--
1 TATATTTATAAATATTTAA
*
930342 TATATTTATATAAAATTTAA
1 TATATTTATA-AATATTTAA
930362 TATATTTATA
1 TATATTTATA
930372 TTATATAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 8 0.32
17 1 0.04
18 6 0.24
20 10 0.40
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TATATTTATAAATATTTAA
Found at i:930385 original size:25 final size:26
Alignment explanation
Indices: 930329--930404 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 26
930319 TAATAATTAT
930329 ATTTAAA-ATATTTTATATTTATATAAA
1 ATTTAAATATA-TTTATA-TTATATAAA
*
930356 ATTT-AATATATTTATATTATATAAT
1 ATTTAAATATATTTATATTATATAAA
*
930381 TTTTAAAAATATATTTATA-TATAT
1 ATTT--AAATATATTTATATTATAT
930405 TGTACTCATA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
25 11 0.26
26 8 0.19
27 12 0.28
28 12 0.28
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
ATTTAAATATATTTATATTATATAAA
Found at i:931708 original size:34 final size:34
Alignment explanation
Indices: 931665--931781 Score: 173
Period size: 34 Copynumber: 3.5 Consensus size: 34
931655 GTAAAAACCA
* *
931665 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
* *
931699 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
* *
931733 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
931766 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
931782 TCTCCCACTT
Statistics
Matches: 75, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 15 0.20
34 60 0.80
ACGTcount: A:0.40, C:0.26, G:0.07, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAAACTACCAAATCTC
Found at i:936233 original size:34 final size:34
Alignment explanation
Indices: 936190--936305 Score: 171
Period size: 34 Copynumber: 3.4 Consensus size: 34
936180 GTAAAAACCA
* *
936190 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
* *
936224 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
* *
936258 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
936291 CCATTTAATCAACAA
1 CCATTTAATCAACAA
936306 ATCACTAATT
Statistics
Matches: 74, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 14 0.19
34 60 0.81
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAAACTACCAAATCTC
Found at i:939721 original size:15 final size:15
Alignment explanation
Indices: 939698--939731 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
939688 GTCACAGTAT
*
939698 TTTTTATTTTTTTAA
1 TTTTAATTTTTTTAA
*
939713 TTTTAATTTTTTTTA
1 TTTTAATTTTTTTAA
939728 TTTT
1 TTTT
939732 TTAAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTAATTTTTTTAA
Found at i:939781 original size:45 final size:47
Alignment explanation
Indices: 939727--939814 Score: 126
Period size: 45 Copynumber: 1.9 Consensus size: 47
939717 AATTTTTTTT
*
939727 ATTTTTTAAAAAATATAA-TAATTAAT-ATTTTAATTTATTAATGTA
1 ATTTTTTAAAAAATATAATTAAATAATAATTTTAATTTATTAATGTA
* * *
939772 ATTTTTTAAAAAATTTAATTAAATATTAATTTTATTTTATTAA
1 ATTTTTTAAAAAATATAATTAAATAATAATTTTAATTTATTAA
939815 AAATAATAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 17 0.46
46 6 0.16
47 14 0.38
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (47 bp):
ATTTTTTAAAAAATATAATTAAATAATAATTTTAATTTATTAATGTA
Found at i:939818 original size:33 final size:34
Alignment explanation
Indices: 939762--939827 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 34
939752 TATTTTAATT
*
939762 TATTAATGTAATTTTTTAAAAAAT-TTAATTAAA
1 TATTAATGTAATTTTTTAAAAAATAATAATTAAA
* *
939795 TATTAATTTTATTTTATT-AAAAATAATAATTAA
1 TATTAATGTAATTTT-TTAAAAAATAATAATTAA
939828 TACATAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 19 0.68
34 9 0.32
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (34 bp):
TATTAATGTAATTTTTTAAAAAATAATAATTAAA
Found at i:940043 original size:14 final size:14
Alignment explanation
Indices: 940024--940070 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
940014 GCACTCGTAA
940024 AAAAAACATATTTT
1 AAAAAACATATTTT
* *
940038 AAAAAATATTTTTT
1 AAAAAACATATTTT
* *
940052 TAAAAACTTA-TTT
1 AAAAAACATATTTT
940065 AAAAAA
1 AAAAAA
940071 TTTAAAAATT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
13 8 0.31
14 18 0.69
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (14 bp):
AAAAAACATATTTT
Found at i:940266 original size:18 final size:19
Alignment explanation
Indices: 940239--940297 Score: 61
Period size: 18 Copynumber: 3.2 Consensus size: 19
940229 AAAATAATTT
940239 TATT-TTTAATA-AAATAA
1 TATTATTTAATATAAATAA
*
940256 TATTATTTAATTTATCAATAA
1 TATTATTTAA--TATAAATAA
*
940277 T-TTATTAAATATAAATAA
1 TATTATTTAATATAAATAA
940295 TAT
1 TAT
940298 ATACTTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
17 4 0.12
18 14 0.41
19 1 0.03
20 9 0.26
21 6 0.18
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
TATTATTTAATATAAATAA
Found at i:940604 original size:8 final size:8
Alignment explanation
Indices: 940586--940686 Score: 53
Period size: 8 Copynumber: 11.5 Consensus size: 8
940576 AAAAATGTAA
940586 ATTTA-AT
1 ATTTATAT
940593 ATTTATAT
1 ATTTATAT
940601 ATTTATTTTAT
1 ATTTA---TAT
940612 ATTTATAT
1 ATTTATAT
*
940620 TTTTATA-
1 ATTTATAT
*
940627 ATTTTATTAG
1 A-TTTA-TAT
940637 ATTATTATAT
1 A-T-TTATAT
*
940647 ATTTATGAA
1 ATTTAT-AT
940656 ATTTTAATAT
1 A-TTT-ATAT
*
940666 ATTTTTAT
1 ATTTATAT
940674 ATTTATATT
1 ATTTATA-T
940683 ATTT
1 ATTT
940687 TTATTTTTTA
Statistics
Matches: 75, Mismatches: 7, Indels: 22
0.72 0.07 0.21
Matches are distributed among these distances:
7 5 0.07
8 33 0.44
9 13 0.17
10 11 0.15
11 13 0.17
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (8 bp):
ATTTATAT
Found at i:940613 original size:19 final size:19
Alignment explanation
Indices: 940586--940701 Score: 64
Period size: 19 Copynumber: 6.3 Consensus size: 19
940576 AAAAATGTAA
*
940586 ATTTAATATTTATATATTT
1 ATTTTATATTTATATATTT
940605 ATTTTATATTTATAT-TTT
1 ATTTTATATTTATATATTT
* * *
940623 -TATAAT-TTTAT-TAGATT
1 ATTTTATATTTATATA-TTT
* *
940640 ATTATATATTTATGAAATTT
1 ATTTTATATTTAT-ATATTT
** *
940660 -TAATATATTTTTATATTT
1 ATTTTATATTTATATATTT
* * *
940678 ATATTATTTTTAT-TTTTT
1 ATTTTATATTTATATATTT
940696 ATTTTA
1 ATTTTA
940702 ATTATTTTTT
Statistics
Matches: 73, Mismatches: 17, Indels: 15
0.70 0.16 0.14
Matches are distributed among these distances:
15 1 0.01
16 5 0.07
17 6 0.08
18 20 0.27
19 38 0.52
20 2 0.03
21 1 0.01
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (19 bp):
ATTTTATATTTATATATTT
Found at i:940632 original size:27 final size:27
Alignment explanation
Indices: 940586--940680 Score: 83
Period size: 27 Copynumber: 3.6 Consensus size: 27
940576 AAAAATGTAA
*
940586 ATTTA-ATATTTAT-ATATTTATTTTAT
1 ATTTATATATTTATAAT-TTTATTATAT
* *
940612 ATTTATATTTTTATAATTTTATTAGAT
1 ATTTATATATTTATAATTTTATTATAT
940639 -TATTATATATTTATGAAATTTTA--ATAT
1 AT-TTATATATTTAT--AATTTTATTATAT
*
940666 ATTTTTATATTTATA
1 ATTTATATATTTATA
940681 TTATTTTTAT
Statistics
Matches: 57, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
25 1 0.02
26 6 0.11
27 40 0.70
28 3 0.05
29 7 0.12
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (27 bp):
ATTTATATATTTATAATTTTATTATAT
Found at i:940686 original size:27 final size:26
Alignment explanation
Indices: 940591--940709 Score: 88
Period size: 29 Copynumber: 4.6 Consensus size: 26
940581 TGTAAATTTA
* *
940591 ATATTTATATA-TTTATTTTATATTT
1 ATATTTATATATTTTATTATATTTTT
* *
940616 ATATTTTTATAATTTTATTAGATTATTAT
1 ATATTTATAT-ATTTTATTATATT-TT-T
* *
940645 ATATTTATGAAATTTTAATATATTTTT
1 ATATTTAT-ATATTTTATTATATTTTT
940672 ATATTTATAT-TATTT-TTAT-TTTTT
1 ATATTTATATAT-TTTATTATATTTTT
940696 AT-TTTA-ATTATTTT
1 ATATTTATA-TATTTT
940710 TTTGCTTTAT
Statistics
Matches: 76, Mismatches: 10, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
22 1 0.01
23 8 0.11
24 8 0.11
25 13 0.17
26 5 0.07
27 17 0.22
28 4 0.05
29 19 0.25
30 1 0.01
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (26 bp):
ATATTTATATATTTTATTATATTTTT
Found at i:940698 original size:22 final size:22
Alignment explanation
Indices: 940665--940725 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 22
940655 AATTTTAATA
940665 TATTTTTATATTTATATTATTTT
1 TATTTTT-TATTTATATTATTTT
940688 TATTTTTTATTT-TAATTATTTT
1 TATTTTTTATTTAT-ATTATTTT
*
940710 T-TTGCTTTATTTATAT
1 TATT-TTTTATTTATAT
940726 CAAAACTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
21 3 0.09
22 23 0.68
23 8 0.24
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.74
Consensus pattern (22 bp):
TATTTTTTATTTATATTATTTT
Found at i:940972 original size:29 final size:31
Alignment explanation
Indices: 940927--941005 Score: 71
Period size: 29 Copynumber: 2.7 Consensus size: 31
940917 AGATTTAATT
* *
940927 TAATTT-TATTATTTTTATAATTT-TTTA-TA
1 TAATTTATATT-TATTTATAATTTGATTATTA
940956 TAATTTATATTTA-TT-TAATTTGATTATTA
1 TAATTTATATTTATTTATAATTTGATTATTA
* *
940985 TATTTTATATTCATTTA-AATT
1 TAATTTATATTTATTTATAATT
941006 ATAAATATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
27 6 0.15
28 5 0.12
29 20 0.49
30 10 0.24
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (31 bp):
TAATTTATATTTATTTATAATTTGATTATTA
Found at i:940974 original size:15 final size:15
Alignment explanation
Indices: 940950--941008 Score: 50
Period size: 15 Copynumber: 4.0 Consensus size: 15
940940 TTTATAATTT
*
940950 TTTATATAATTTATA
1 TTTATTTAATTTATA
*
940965 TTTATTTAATTT-GA
1 TTTATTTAATTTATA
*
940979 -TTATTATATTTTATA
1 TTTATT-TAATTTATA
* *
940994 TTCATTTAAATTATA
1 TTTATTTAATTTATA
941009 AATATTAAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
13 5 0.15
14 6 0.18
15 19 0.56
16 4 0.12
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (15 bp):
TTTATTTAATTTATA
Found at i:941233 original size:2 final size:2
Alignment explanation
Indices: 941226--941251 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
941216 ATGCAAGGTG
941226 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
941252 TAAGAACATG
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:944244 original size:30 final size:29
Alignment explanation
Indices: 944210--944298 Score: 101
Period size: 29 Copynumber: 3.0 Consensus size: 29
944200 TGACTAAAAA
*
944210 ATGAATCGTTAATGA-AATTTTTTAAAAGTT
1 ATGAATCGTAAAT-ATAA-TTTTTAAAAGTT
*
944240 ATGAATGGTAAATATAATTTTTAAAAGTT
1 ATGAATCGTAAATATAATTTTTAAAAGTT
944269 ATGAAT-GAATAAAATATAATTTTTAAAAGT
1 ATGAATCG--T-AAATATAATTTTTAAAAGT
944299 ATCGGATAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
28 1 0.02
29 19 0.36
30 14 0.26
31 19 0.36
ACGTcount: A:0.46, C:0.01, G:0.12, T:0.40
Consensus pattern (29 bp):
ATGAATCGTAAATATAATTTTTAAAAGTT
Found at i:944269 original size:29 final size:31
Alignment explanation
Indices: 944228--944298 Score: 119
Period size: 29 Copynumber: 2.4 Consensus size: 31
944218 TTAATGAAAT
*
944228 TTTTTAAAAGTTATGAATG-GT-AAATATAA
1 TTTTTAAAAGTTATGAATGAATAAAATATAA
944257 TTTTTAAAAGTTATGAATGAATAAAATATAA
1 TTTTTAAAAGTTATGAATGAATAAAATATAA
944288 TTTTTAAAAGT
1 TTTTTAAAAGT
944299 ATCGGATAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 19 0.49
30 1 0.03
31 19 0.49
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.42
Consensus pattern (31 bp):
TTTTTAAAAGTTATGAATGAATAAAATATAA
Found at i:944533 original size:50 final size:50
Alignment explanation
Indices: 944474--944779 Score: 312
Period size: 50 Copynumber: 6.1 Consensus size: 50
944464 GTAAAGTGAT
* * *
944474 TTGACTATTCTTCACCAACTTTTAATAATCCAGAGAGATGACCGTAATTG
1 TTGACTATTCTTCACCAACTTTTGATAATCAAGAGAGGTGACCGTAATTG
* * * **
944524 TTGACTATTCTTTACCAA-TCTTTGACAATTAAGAGAGGTGGTCGTAATTG
1 TTGACTATTCTTCACCAACT-TTTGATAATCAAGAGAGGTGACCGTAATTG
* * * * *
944574 TTGACTATTCTTCACTAACCTTTGATAATCGATAGAGGTGATCGTAATTG
1 TTGACTATTCTTCACCAACTTTTGATAATCAAGAGAGGTGACCGTAATTG
* * * *
944624 TTGCCTATTCTTTATCAA-TCTTTGACAATCTAA-AGAGGTGACCGTAATTG
1 TTGACTATTCTTCACCAACT-TTTGATAATC-AAGAGAGGTGACCGTAATTG
* * * * * *
944674 TTAACTATTCTTTATCAACTTTTGATAATTAAGAGAGATGATCGTAATTG
1 TTGACTATTCTTCACCAACTTTTGATAATCAAGAGAGGTGACCGTAATTG
* * * * *
944724 TTGACTATTCTTCATCAACCTTTGATAATAAAGAAATGTGACCGTAATTG
1 TTGACTATTCTTCACCAACTTTTGATAATCAAGAGAGGTGACCGTAATTG
944774 TTGACT
1 TTGACT
944780 CTAAGCATCT
Statistics
Matches: 212, Mismatches: 38, Indels: 12
0.81 0.15 0.05
Matches are distributed among these distances:
49 3 0.01
50 207 0.98
51 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (50 bp):
TTGACTATTCTTCACCAACTTTTGATAATCAAGAGAGGTGACCGTAATTG
Found at i:944647 original size:100 final size:100
Alignment explanation
Indices: 944474--944779 Score: 391
Period size: 100 Copynumber: 3.1 Consensus size: 100
944464 GTAAAGTGAT
* * * * *
944474 TTGACTATTCTTCACCAACTTTTAATAATCCAGAGAGATGACCGTAATTGTTGACTATTCTTTAC
1 TTGACTATTCTTCACTAACTTTTGATAATCAAGAGAGATGATCGTAATTGTTGACTATTCTTTAT
**
944539 CAATCTTTGACAATTAAGAGAGGTGGTCGTAATTG
66 CAATCTTTGACAATTAAGAGAGGTGACCGTAATTG
* * * * *
944574 TTGACTATTCTTCACTAACCTTTGATAATCGATAGAGGTGATCGTAATTGTTGCCTATTCTTTAT
1 TTGACTATTCTTCACTAACTTTTGATAATCAAGAGAGATGATCGTAATTGTTGACTATTCTTTAT
944639 CAATCTTTGACAATCTAA-AGAGGTGACCGTAATTG
66 CAATCTTTGACAAT-TAAGAGAGGTGACCGTAATTG
* * * *
944674 TTAACTATTCTTTA-TCAACTTTTGATAATTAAGAGAGATGATCGTAATTGTTGACTATTCTTCA
1 TTGACTATTCTTCACT-AACTTTTGATAATCAAGAGAGATGATCGTAATTGTTGACTATTCTTTA
* * * * *
944738 TCAACCTTTGATAATAAAGAAATGTGACCGTAATTG
65 TCAATCTTTGACAATTAAGAGAGGTGACCGTAATTG
944774 TTGACT
1 TTGACT
944780 CTAAGCATCT
Statistics
Matches: 177, Mismatches: 26, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
99 3 0.02
100 171 0.97
101 3 0.02
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (100 bp):
TTGACTATTCTTCACTAACTTTTGATAATCAAGAGAGATGATCGTAATTGTTGACTATTCTTTAT
CAATCTTTGACAATTAAGAGAGGTGACCGTAATTG
Found at i:944770 original size:150 final size:150
Alignment explanation
Indices: 944507--944776 Score: 400
Period size: 150 Copynumber: 1.8 Consensus size: 150
944497 AATAATCCAG
* * *
944507 AGAGATGACCGTAATTGTTGACTATTCTTTACCAATCTTTGACAATTAAGAGAGGTGGTCGTAAT
1 AGAGATGACCGTAATTGTTAACTATTCTTTACCAATCTTTGACAATTAAGAGAGATGATCGTAAT
** * * *
944572 TGTTGACTATTCTTCACTAACCTTTGATAATCGATAGAGGTGATCGTAATTGTTGCCTATTCTTT
66 TGTTGACTATTCTTCACTAACCTTTGATAATAAAGAAAGGTGACCGTAATTGTTGCCTATTCTTT
944637 ATCAATCTTTGACAATCTAA
131 ATCAATCTTTGACAATCTAA
* * *
944657 AGAGGTGACCGTAATTGTTAACTATTCTTTATCAA-CTTTTGATAATTAAGAGAGATGATCGTAA
1 AGAGATGACCGTAATTGTTAACTATTCTTTACCAATC-TTTGACAATTAAGAGAGATGATCGTAA
*
944721 TTGTTGACTATTCTTCA-TCAACCTTTGATAATAAAGAAATGTGACCGTAATTGTTG
65 TTGTTGACTATTCTTCACT-AACCTTTGATAATAAAGAAAGGTGACCGTAATTGTTG
944777 ACTCTAAGCA
Statistics
Matches: 106, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
149 2 0.02
150 104 0.98
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.38
Consensus pattern (150 bp):
AGAGATGACCGTAATTGTTAACTATTCTTTACCAATCTTTGACAATTAAGAGAGATGATCGTAAT
TGTTGACTATTCTTCACTAACCTTTGATAATAAAGAAAGGTGACCGTAATTGTTGCCTATTCTTT
ATCAATCTTTGACAATCTAA
Found at i:947451 original size:2 final size:2
Alignment explanation
Indices: 947444--947480 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
947434 GAAGCTGCGA
947444 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
947481 AAATTTTTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:948595 original size:16 final size:17
Alignment explanation
Indices: 948571--948616 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
948561 TAATATATTT
*
948571 TTATATTTATATTAT-A
1 TTATTTTTATATTATAA
948587 TT-TGTTTTATATT-TAA
1 TTAT-TTTTATATTATAA
948603 TTATTTTTATATTA
1 TTATTTTTATATTA
948617 AAACTAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
15 2 0.08
16 22 0.88
17 1 0.04
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (17 bp):
TTATTTTTATATTATAA
Found at i:948611 original size:10 final size:11
Alignment explanation
Indices: 948571--948616 Score: 58
Period size: 11 Copynumber: 4.3 Consensus size: 11
948561 TAATATATTT
948571 TTATATTTATA
1 TTATATTTATA
* *
948582 TTATATTTGTT
1 TTATATTTATA
948593 TTATATTTA-A
1 TTATATTTATA
*
948603 TTATTTTTATA
1 TTATATTTATA
948614 TTA
1 TTA
948617 AAACTAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
10 8 0.28
11 21 0.72
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (11 bp):
TTATATTTATA
Found at i:948897 original size:14 final size:14
Alignment explanation
Indices: 948878--948905 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
948868 TTATATTTAT
948878 TTAAATTTTAAATA
1 TTAAATTTTAAATA
948892 TTAAATTTTAAATA
1 TTAAATTTTAAATA
948906 AATTAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTAAATTTTAAATA
Found at i:950958 original size:34 final size:34
Alignment explanation
Indices: 950903--951119 Score: 258
Period size: 34 Copynumber: 6.4 Consensus size: 34
950893 TGGACCTCGA
*
950903 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* * *
950936 TGTTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* * * *
950970 TGATGACTAAATGGGAGATTTGGTAACTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* **
951004 TGTTGATTAAATGAGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* * *
951038 TATTGATTAAATGGATGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* * *
951072 TGTTGACTAAAT-GGTAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGT-GATTTGGTAGCTTACCAT
951106 TGTTGATTAAATGG
1 TGTTGATTAAATGG
951120 TGGTTTTTAC
Statistics
Matches: 154, Mismatches: 27, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
33 14 0.09
34 139 0.90
35 1 0.01
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
Found at i:951095 original size:102 final size:101
Alignment explanation
Indices: 950903--951119 Score: 317
Period size: 102 Copynumber: 2.1 Consensus size: 101
950893 TGGACCTCGA
** * * * * *
950903 TGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 TGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGATGATTTGGTGGCTTACC
950968 ATTGATGACTAAATGGGAGATTTGGTAACTTACCAT
66 ATTGATGACTAAATGGGAGATTTGGTAACTTACCAT
951004 TGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGATGATTTGGTGGCTTAC
1 TGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGATGATTTGGTGGCTTAC
* * ** *
951069 CATTGTTGACTAAATGGTAGATTTGGTAGGTTGCCAT
65 CATTGATGACTAAATGGGAGATTTGGTAACTTACCAT
951106 TGTTGATTAAATGG
1 TGTTGATTAAATGG
951120 TGGTTTTTAC
Statistics
Matches: 103, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 14 0.14
102 89 0.86
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (101 bp):
TGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGATGATTTGGTGGCTTACC
ATTGATGACTAAATGGGAGATTTGGTAACTTACCAT
Found at i:955587 original size:34 final size:34
Alignment explanation
Indices: 955530--955748 Score: 280
Period size: 34 Copynumber: 6.5 Consensus size: 34
955520 AAGTGGGAGA
*
955530 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
955563 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
955597 ATTGATGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* **
955631 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
955665 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
955699 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
955733 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
955749 TGGTTTTTAC
Statistics
Matches: 160, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
33 17 0.11
34 142 0.89
35 1 0.01
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Done.