Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015270.1 Kokia drynarioides strain JFW-HI SEQ_130315, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1190338
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 752 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:881414 original size:30 final size:30
Alignment explanation
Indices: 881364--881420 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
881354 ATTTAAATAC
**
881364 CAAATTAAAAAAAGTATTAAAT-TCAAGTA
1 CAAATTAAAAAAAAAATTAAATATCAAGTA
881393 CAAATTAAAAAAAAAATTTAAATATCAA
1 CAAATTAAAAAAAAAA-TTAAATATCAA
881421 ATTTAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 14 0.58
30 6 0.25
31 4 0.17
ACGTcount: A:0.63, C:0.07, G:0.04, T:0.26
Consensus pattern (30 bp):
CAAATTAAAAAAAAAATTAAATATCAAGTA
Found at i:882719 original size:19 final size:19
Alignment explanation
Indices: 882691--882734 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
882681 GGCTAGCACT
882691 AAAA-GAAACCAAAATTCA
1 AAAAGGAAACCAAAATTCA
882709 AAAAGGAAACCAAAATTCA
1 AAAAGGAAACCAAAATTCA
*
882728 AGAAGGA
1 AAAAGGA
882735 GACTGGTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 4 0.17
19 20 0.83
ACGTcount: A:0.64, C:0.14, G:0.14, T:0.09
Consensus pattern (19 bp):
AAAAGGAAACCAAAATTCA
Found at i:889692 original size:6 final size:6
Alignment explanation
Indices: 889678--889716 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
889668 CTCCTACATT
*
889678 AATAAC AATACC AATACC AATACC AATACC AATACC AAT
1 AATACC AATACC AATACC AATACC AATACC AATACC AAT
889717 CGATTTAAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.54, C:0.28, G:0.00, T:0.18
Consensus pattern (6 bp):
AATACC
Found at i:899844 original size:29 final size:29
Alignment explanation
Indices: 899793--899848 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
899783 AAATTAGATC
* * **
899793 AAATCAAAATTTATGTATGAAATTACACA
1 AAATCAAAATTCATATAAAAAATTACACA
899822 AAATCAAAATTCATATAAAAAATTACA
1 AAATCAAAATTCATATAAAAAATTACA
899849 AATTAAACCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.57, C:0.11, G:0.04, T:0.29
Consensus pattern (29 bp):
AAATCAAAATTCATATAAAAAATTACACA
Found at i:906576 original size:20 final size:21
Alignment explanation
Indices: 906532--906576 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
906522 TAAACAATAA
*
906532 AAAATTTTAATATGATTATAT
1 AAAATTTTAATATGATTAAAT
906553 AAAATTATTAA-ATG-TTAAAT
1 AAAATT-TTAATATGATTAAAT
906573 AAAA
1 AAAA
906577 ATAATAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 9 0.41
21 9 0.41
22 4 0.18
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (21 bp):
AAAATTTTAATATGATTAAAT
Found at i:906577 original size:21 final size:22
Alignment explanation
Indices: 906531--906578 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
906521 CTAAACAATA
*
906531 AAAAATTTTAATATGATTATAT
1 AAAAATTTTAATATGATTAAAT
906553 -AAAATTATTAA-ATG-TTAAAT
1 AAAAATT-TTAATATGATTAAAT
906573 AAAAAT
1 AAAAAT
906579 AATAAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 5 0.22
21 14 0.61
22 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (22 bp):
AAAAATTTTAATATGATTAAAT
Found at i:921256 original size:2 final size:2
Alignment explanation
Indices: 921245--921273 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
921235 AACATTAAAA
921245 AT AT -T 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
921274 CTTAAATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:924938 original size:16 final size:18
Alignment explanation
Indices: 924907--924941 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
924897 CCAGTCCGAT
924907 TAAATAAATCATTAAAAA
1 TAAATAAATCATTAAAAA
924925 TAAA-AAAT-ATTAAAAA
1 TAAATAAATCATTAAAAA
924941 T
1 T
924942 CTAGTTCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 4 0.24
18 4 0.24
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAATAAATCATTAAAAA
Found at i:927951 original size:23 final size:22
Alignment explanation
Indices: 927925--927982 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 22
927915 TTTTTTTTTT
*
927925 TTTAAATTTTATAAAATAGGATA
1 TTTAAATTTTATAAAATAAG-TA
* *
927948 TTTAAATATTTTTACAATAAGTA
1 TTTAAAT-TTTATAAAATAAGTA
927971 TTTAAATTTTAT
1 TTTAAATTTTAT
927983 TTATACTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 4 0.13
23 16 0.53
24 10 0.33
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (22 bp):
TTTAAATTTTATAAAATAAGTA
Found at i:928215 original size:15 final size:15
Alignment explanation
Indices: 928195--928224 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
928185 ATCGATTGAG
928195 TTGAATTTAAGTATT
1 TTGAATTTAAGTATT
928210 TTGAATTTAAGTATT
1 TTGAATTTAAGTATT
928225 ATAATACGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (15 bp):
TTGAATTTAAGTATT
Found at i:934346 original size:22 final size:22
Alignment explanation
Indices: 934302--934364 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
934292 GACGGCGGAT
*
934302 TGAACGAG-GAGA-AAAGA-AG
1 TGAAAGAGCGAGAGAAAGAGAG
934321 TGAAATG-GCGAG-GAAAGGAGAG
1 TGAAA-GAGCGAGAGAAA-GAGAG
934343 TGAAAGAGCGAGAGAAAGAGAG
1 TGAAAGAGCGAGAGAAAGAGAG
934365 GAGAGCCATG
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
19 5 0.14
20 7 0.19
21 3 0.08
22 17 0.47
23 4 0.11
ACGTcount: A:0.48, C:0.05, G:0.41, T:0.06
Consensus pattern (22 bp):
TGAAAGAGCGAGAGAAAGAGAG
Found at i:938697 original size:47 final size:46
Alignment explanation
Indices: 938620--938715 Score: 113
Period size: 47 Copynumber: 2.0 Consensus size: 46
938610 TGAATATTAA
* *
938620 TTATGTATTAATCATTTCAAAATTCGTGATTA-CTTTTCTCAATAATG
1 TTATGTACTAATCATTTCAAAATTCATGATTATCTTTT-T-AATAATG
* **
938667 TTATGTACTACTCATTTCAATGTTCATGATTATTCTTTTTAATAATG
1 TTATGTACTAATCATTTCAAAATTCATGATTA-TCTTTTTAATAATG
938714 TT
1 TT
938716 TTAATCATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
47 36 0.86
48 1 0.02
49 5 0.12
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.50
Consensus pattern (46 bp):
TTATGTACTAATCATTTCAAAATTCATGATTATCTTTTTAATAATG
Found at i:939002 original size:3 final size:3
Alignment explanation
Indices: 938996--939024 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
938986 AAATTATTAA
938996 CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
939025 ACACATTGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.66, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:955836 original size:17 final size:18
Alignment explanation
Indices: 955814--955847 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
955804 TATATAATGT
955814 AATTTGATTTTT-TTTGC
1 AATTTGATTTTTCTTTGC
955831 AATTTGATTTTTCTTTG
1 AATTTGATTTTTCTTTG
955848 TTATCTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.18, C:0.06, G:0.12, T:0.65
Consensus pattern (18 bp):
AATTTGATTTTTCTTTGC
Found at i:956680 original size:29 final size:28
Alignment explanation
Indices: 956638--956772 Score: 119
Period size: 30 Copynumber: 4.6 Consensus size: 28
956628 GGAGGTCCCT
* *
956638 AAACTATCAAAAAATTATATTTTGACCCC-
1 AAACT-TCCAAAAATTA-ATTTTAACCCCA
*
956667 AAACTTCTCTAAAATTCAACTTTTAACCCCA
1 AAACTTC-CAAAAATT-AA-TTTTAACCCCA
* **
956698 AAACTTCCAAAAATTACATTTTTACCCTT
1 AAACTTCCAAAAATTA-ATTTTAACCCCA
*
956727 GAACTTCCAAAAATCCTAATTTTAACCCCA
1 AAACTTCCAAAAAT--TAATTTTAACCCCA
*
956757 AAACTTTCAAAAATTA
1 AAACTTCCAAAAATTA
956773 TCATTTTACC
Statistics
Matches: 86, Mismatches: 13, Indels: 15
0.75 0.11 0.13
Matches are distributed among these distances:
28 4 0.05
29 34 0.40
30 39 0.45
31 9 0.10
ACGTcount: A:0.42, C:0.24, G:0.01, T:0.32
Consensus pattern (28 bp):
AAACTTCCAAAAATTAATTTTAACCCCA
Found at i:956721 original size:30 final size:29
Alignment explanation
Indices: 956638--956912 Score: 129
Period size: 29 Copynumber: 9.3 Consensus size: 29
956628 GGAGGTCCCT
* * *
956638 AAACTATCAAAAAATTATATTTTGACCCC-
1 AAACT-TCCAAAAATTACATTTTAACCCCA
*
956667 AAACTTCTCTAAAATT-CAACTTTTAACCCCA
1 AAACTTC-CAAAAATTAC-A-TTTTAACCCCA
* **
956698 AAACTTCCAAAAATTACATTTTTACCCTT
1 AAACTTCCAAAAATTACATTTTAACCCCA
*
956727 GAACTTCCAAAAATCCTA-ATTTTAACCCCA
1 AAACTTCCAAAAAT--TACATTTTAACCCCA
* ***
956757 AAACTTTCAAAAATTATCATTTT-ACCTTG
1 AAACTTCCAAAAATTA-CATTTTAACCCCA
* * * *
956786 AAACCTCTAAAAAATCT-CGATTTTGACCTCA
1 AAACTTC-CAAAAAT-TAC-ATTTTAACCCCA
**
956817 AAACTT-TTAAAATTACCATTTT-ACCCTC-
1 AAACTTCCAAAAATTA-CATTTTAACCC-CA
* * * * *
956845 GAACCTCAAAAAATTCCATTTTTGACCCCA
1 AAACTTCCAAAAATTACA-TTTTAACCCCA
*
956875 AAAC-TCTCAAAAATTACTATTTT-ACCCCC
1 AAACTTC-CAAAAATTAC-ATTTTAACCCCA
956904 AAACTTCCA
1 AAACTTCCA
956913 CATTTCCATT
Statistics
Matches: 188, Mismatches: 35, Indels: 46
0.70 0.13 0.17
Matches are distributed among these distances:
28 14 0.07
29 77 0.41
30 76 0.40
31 21 0.11
ACGTcount: A:0.39, C:0.26, G:0.03, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATTACATTTTAACCCCA
Found at i:956740 original size:59 final size:59
Alignment explanation
Indices: 956677--956901 Score: 219
Period size: 59 Copynumber: 3.8 Consensus size: 59
956667 AAACTTCTCT
* *
956677 AAAATTCAACTTTTAACCCCAAAACTTCCAAAAATTA-CATTTTTACCCTTGAACTTC-CA
1 AAAATTCAA-TTTTAACCCCAAAACTTCCAAAAATTACCA-TTTTACCCTTGAACCTCTAA
* * *
956736 AAAATCCTAATTTTAACCCCAAAACTTTCAAAAATTATCATTTTA-CCTTGAAACCTCTAA
1 AAAATTC-AATTTTAACCCCAAAACTTCCAAAAATTACCATTTTACCCTTG-AACCTCTAA
* * * ** *
956796 AAAATCTCGATTTTGACCTCAAAACTT-TTAAAATTACCATTTTACCCTCGAACCTC-AA
1 AAAAT-TCAATTTTAACCCCAAAACTTCCAAAAATTACCATTTTACCCTTGAACCTCTAA
* * *
956854 AAAATTCCATTTTTGACCCCAAAAC-TCTCAAAAATTACTATTTTACCC
1 AAAATT-CAATTTTAACCCCAAAACTTC-CAAAAATTACCATTTTACCC
956902 CCAAACTTCC
Statistics
Matches: 139, Mismatches: 18, Indels: 18
0.79 0.10 0.10
Matches are distributed among these distances:
57 2 0.01
58 27 0.19
59 79 0.57
60 30 0.22
61 1 0.01
ACGTcount: A:0.39, C:0.26, G:0.03, T:0.33
Consensus pattern (59 bp):
AAAATTCAATTTTAACCCCAAAACTTCCAAAAATTACCATTTTACCCTTGAACCTCTAA
Found at i:956907 original size:29 final size:29
Alignment explanation
Indices: 956638--956908 Score: 109
Period size: 30 Copynumber: 9.2 Consensus size: 29
956628 GGAGGTCCCT
*
956638 AAACTATCAAAAAATTA-TATTTTGACCCC-
1 AAACTCTC-AAAAATTACTATTTT-ACCCCA
* *
956667 AAACTTCTCTAAAATTCAACT-TTTAACCCCA
1 AAAC-TCTCAAAAATT--ACTATTTTACCCCA
**
956698 AAACT-TCCAAAAATTAC-ATTTTTACCCTT
1 AAACTCT-CAAAAATTACTA-TTTTACCCCA
* *
956727 GAACT-TCCAAAAA-TCCTAATTTTAACCCCA
1 AAACTCT-CAAAAATTACT-ATTTT-ACCCCA
* **
956757 AAACTTTCAAAAATTA-TCATTTTACCTTGA
1 AAACTCTCAAAAATTACT-ATTTTACC-CCA
* * * *
956787 AACCTCTAAAAAATCT-CGATTTTGACCTCA
1 AAACTCTCAAAAAT-TACTATTTT-ACCCCA
** *
956817 AAACT-TTTAAAATTACCATTTTACCCTC-
1 AAACTCTCAAAAATTACTATTTTACCC-CA
* *
956845 GAAC-CTCAAAAAATT-CCATTTTTGACCCCA
1 AAACTCTC-AAAAATTACTA-TTTT-ACCCCA
*
956875 AAACTCTCAAAAATTACTATTTTACCCCC
1 AAACTCTCAAAAATTACTATTTTACCCCA
956904 AAACT
1 AAACT
956909 TCCACATTTC
Statistics
Matches: 184, Mismatches: 32, Indels: 52
0.69 0.12 0.19
Matches are distributed among these distances:
28 15 0.08
29 71 0.39
30 78 0.42
31 19 0.10
32 1 0.01
ACGTcount: A:0.39, C:0.26, G:0.03, T:0.32
Consensus pattern (29 bp):
AAACTCTCAAAAATTACTATTTTACCCCA
Found at i:960500 original size:31 final size:31
Alignment explanation
Indices: 960445--960531 Score: 117
Period size: 31 Copynumber: 2.9 Consensus size: 31
960435 AAAATAATAA
* *
960445 TTTTGG-ACGCTCGGGAGC-AAAATGGTAAT
1 TTTTGGAAGGCTCGGGATCAAAAATGGTAAT
*
960474 TTTTGGAAGGCTTGAGG-TCAAAAATGGTAAT
1 TTTTGGAAGGCTCG-GGATCAAAAATGGTAAT
960505 TTTTGGAAGGCTCGGGATCAAAAATGG
1 TTTTGGAAGGCTCGGGATCAAAAATGG
960532 AGTTTTTAGA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
29 6 0.12
30 8 0.16
31 36 0.72
ACGTcount: A:0.30, C:0.10, G:0.31, T:0.29
Consensus pattern (31 bp):
TTTTGGAAGGCTCGGGATCAAAAATGGTAAT
Found at i:960563 original size:59 final size:59
Alignment explanation
Indices: 960494--960888 Score: 439
Period size: 59 Copynumber: 6.7 Consensus size: 59
960484 CTTGAGGTCA
*
960494 AAAATGGTAATTTTTGGAAGGCTCGGGATCAAAAATGGAGTTTTTAGACATTCGAGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGGGATCAAAAATGGAGTTTTTAGACATTCGAGGGT
* *
960553 AAAATGGTAATTTTTGGAAGGTTTC-GGAT-AAAAATGGAGTTTTTAAACATCCG-GGGAT
1 AAAATGGTAATTTTTGGAAGG-TTCGGGATCAAAAATGGAGTTTTTAGACATTCGAGGG-T
* * * * *
960611 AAAATGGAAATTTTTGGAAGGTTCGAGATAAAAAACGGAGTTTTTAGACATTCGGGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGGGATCAAAAATGGAGTTTTTAGACATTCGAGGGT
* * * * * *
960670 AAAATGATAATTTTTGAAAGTTTCGGGGTCAAAAATGGAATTTTTGGA-AGTTCGAGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGGGATCAAAAATGGAGTTTTTAGACA-TTCGAGGGT
* * *
960729 AAAATGGTAA-TTTTGGAAGGTTTGGGATAAAAAATGGAGTTTTTAGACA-TCTAAGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGGGATCAAAAATGGAGTTTTTAGACATTC-GAGGGT
* * * * * *
960787 AAAATGGTAAATTTTGGAAGGTCCGAGATCCAAAACGGAGTTTTTAGACATCCG-GAGGT
1 AAAATGGTAATTTTTGGAAGGTTCGGGATCAAAAATGGAGTTTTTAGACATTCGAG-GGT
* * *
960846 AAAATGGTAATTTTTAGAAGTTTCAGGG-TC-AAAATGGAATTTT
1 AAAATGGTAATTTTTGGAAGGTTC-GGGATCAAAAATGGAGTTTT
960889 GGAAAGTTTA
Statistics
Matches: 281, Mismatches: 43, Indels: 25
0.81 0.12 0.07
Matches are distributed among these distances:
57 8 0.03
58 104 0.37
59 161 0.57
60 8 0.03
ACGTcount: A:0.35, C:0.07, G:0.27, T:0.31
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGAAGGTTCGGGATCAAAAATGGAGTTTTTAGACATTCGAGGGT
Found at i:960567 original size:29 final size:27
Alignment explanation
Indices: 960525--960888 Score: 105
Period size: 29 Copynumber: 12.5 Consensus size: 27
960515 CTCGGGATCA
*
960525 AAAATGGAGTTTTTAGACA-TTCGAGGGT
1 AAAATGGAATTTTTAGA-AGTTCG-GGGT
* *
960553 AAAATGGTAATTTTTGGAAGGTTTC-GGAT
1 AAAATGG-AATTTTTAGAA-G-TTCGGGGT
* * *
960582 AAAAATGGAGTTTTTA-AACATCCGGGGAT
1 -AAAATGGAATTTTTAGAA-GTTCGGGG-T
* * *
960611 AAAATGGAAATTTTTGGAAGGTTCGAGAT
1 AAAATGG-AATTTTTAGAA-GTTCGGGGT
* *
960640 AAAAAACGGAGTTTTTAGACA-TTCGGGGGT
1 --AAAATGGAATTTTTAGA-AGTTC-GGGGT
*
960670 AAAATGATAATTTTT-GAAAGTTTCGGGGT
1 AAAATG-GAATTTTTAG-AAG-TTCGGGGT
*
960699 CAAAAATGGAATTTTTGGAAGTTCGAGGGT
1 --AAAATGGAATTTTTAGAAGTTCG-GGGT
* * *
960729 AAAATGGTAA-TTTTGGAAGGTTTGGGAT
1 AAAATGG-AATTTTTAGAA-GTTCGGGGT
* **
960757 AAAAAATGGAGTTTTTAGACA-TCTAAGGGT
1 --AAAATGGAATTTTTAGA-AGT-TCGGGGT
* * * * *
960787 AAAATGGTAAATTTTGGAAGGTCCGAGAT
1 AAAATGG-AATTTTTAGAA-GTTCGGGGT
* * *
960816 CCAAAACGGAGTTTTTAGACA-TCCGGAGGT
1 --AAAATGGAATTTTTAGA-AGTTCGG-GGT
*
960846 AAAATGGTAATTTTTAGAAGTTTCAGGGT
1 AAAATGG-AATTTTTAGAAG-TTCGGGGT
960875 CAAAATGGAATTTT
1 -AAAATGGAATTTT
960889 GGAAAGTTTA
Statistics
Matches: 247, Mismatches: 50, Indels: 77
0.66 0.13 0.21
Matches are distributed among these distances:
27 2 0.01
28 59 0.24
29 83 0.34
30 78 0.32
31 25 0.10
ACGTcount: A:0.35, C:0.07, G:0.27, T:0.32
Consensus pattern (27 bp):
AAAATGGAATTTTTAGAAGTTCGGGGT
Found at i:960695 original size:30 final size:29
Alignment explanation
Indices: 960661--960751 Score: 87
Period size: 30 Copynumber: 3.1 Consensus size: 29
960651 TTTTTAGACA
960661 TTCGGGGGTAAAATGATAATTTTTGAAAGT
1 TTCGGGGGTAAAATG-TAATTTTTGAAAGT
* *
960691 TTC-GGGGTCAAAAATGGAATTTTTGGAAG-
1 TTCGGGGGT--AAAATGTAATTTTTGAAAGT
* * *
960720 TTCGAGGGTAAAATGGTAATTTTGGAAGGT
1 TTCGGGGGTAAAAT-GTAATTTTTGAAAGT
960750 TT
1 TT
960752 GGGATAAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
28 5 0.10
29 18 0.37
30 20 0.41
31 6 0.12
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.35
Consensus pattern (29 bp):
TTCGGGGGTAAAATGTAATTTTTGAAAGT
Found at i:960759 original size:28 final size:27
Alignment explanation
Indices: 960665--960760 Score: 86
Period size: 28 Copynumber: 3.3 Consensus size: 27
960655 TAGACATTCG
* *
960665 GGGGTAAAATGATAATTTTTGAAAGTTT
1 GGGGTAAAATGGTAA-TTTTGGAAGTTT
*
960693 CGGGGTCAAAAATGG-AATTTTTGGAAGTTC
1 -GGGGT--AAAATGGTAA-TTTTGGAAGTTT
960723 GAGGGTAAAATGGTAATTTTGGAAGGTTT
1 G-GGGTAAAATGGTAATTTTGGAA-GTTT
*
960752 GGGATAAAA
1 GGGGTAAAA
960761 AATGGAGTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
28 22 0.39
29 12 0.21
30 17 0.30
31 6 0.11
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.32
Consensus pattern (27 bp):
GGGGTAAAATGGTAATTTTGGAAGTTT
Found at i:960804 original size:176 final size:175
Alignment explanation
Indices: 960494--960892 Score: 549
Period size: 176 Copynumber: 2.3 Consensus size: 175
960484 CTTGAGGTCA
* ** * * *
960494 AAAATGGTAATTTTTGGAAGGCTCGGGATCAAAAATGGAGTTTTTAGACATTCGAGGGTAAAATG
1 AAAATGGTAATTTTTGAAAGTTTCGGGGTCAAAAATGGAATTTTTGGA-ATTCGAGGGTAAAATG
**
960559 GTAATTTTTGGAAGGTTTCGGATAAAAATGGAGTTTTTAAACATCCGGGGATAAAATGGAAATTT
65 GTAATTTTTGGAAGGTTTCGGATAAAAATGGAGTTTTTAAACATCAAGGGATAAAATGGAAATTT
* * *
960624 TTGGAAGGTTCGAGATAAAAAACGGAGTTTTTAGACATTCGGGGGT
130 TTGGAAGGTCCGAGATAAAAAACGGAGTTTTTAGACATCCGGAGGT
*
960670 AAAATGATAATTTTTGAAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAATG
1 AAAATGGTAATTTTTGAAAGTTTCGGGGTCAAAAATGGAATTTTTGGAA-TTCGAGGGTAAAATG
* *
960735 GTAA-TTTTGGAAGGTTTGGGATAAAAAATGGAGTTTTTAGACATCTAAGGG-TAAAATGGTAAA
65 GTAATTTTTGGAAGGTTTCGGAT-AAAAATGGAGTTTTTAAACATC-AAGGGATAAAATGG-AAA
**
960798 -TTTTGGAAGGTCCGAGATCCAAAACGGAGTTTTTAGACATCCGGAGGT
127 TTTTTGGAAGGTCCGAGATAAAAAACGGAGTTTTTAGACATCCGGAGGT
*
960846 AAAATGGTAATTTTT-AGAAGTTTCAGGGTC-AAAATGGAA-TTTTGGAA
1 AAAATGGTAATTTTTGA-AAGTTTCGGGGTCAAAAATGGAATTTTTGGAA
960893 AGTTTAGGGG
Statistics
Matches: 200, Mismatches: 18, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
174 8 0.04
175 28 0.14
176 158 0.79
177 6 0.03
ACGTcount: A:0.35, C:0.07, G:0.27, T:0.31
Consensus pattern (175 bp):
AAAATGGTAATTTTTGAAAGTTTCGGGGTCAAAAATGGAATTTTTGGAATTCGAGGGTAAAATGG
TAATTTTTGGAAGGTTTCGGATAAAAATGGAGTTTTTAAACATCAAGGGATAAAATGGAAATTTT
TGGAAGGTCCGAGATAAAAAACGGAGTTTTTAGACATCCGGAGGT
Found at i:960883 original size:117 final size:117
Alignment explanation
Indices: 960494--960865 Score: 450
Period size: 117 Copynumber: 3.2 Consensus size: 117
960484 CTTGAGGTCA
* *
960494 AAAATGGTAATTTTTGGAAGGCTCGGGATCAAAAATGGAGTTTTTAGACATTCGAGGGTAAAATG
1 AAAATGGTAATTTTTGGAAGGTTCGGGATAAAAAATGGAGTTTTTAGACATTCGAGGGTAAAATG
*
960559 GTAATTTTTGGAAGGTTTCGGAT-AAAAATGGAGTTTTTAAACATCCGG-GGAT
66 GTAATTTTTGGAAGG-TTCGGATCAAAAATGGAGTTTTTAGACATCCGGAGG-T
* * * *
960611 AAAATGGAAATTTTTGGAAGGTTCGAGATAAAAAACGGAGTTTTTAGACATTCGGGGGTAAAATG
1 AAAATGGTAATTTTTGGAAGGTTCGGGATAAAAAATGGAGTTTTTAGACATTCGAGGGTAAAATG
* * * * * * *
960676 ATAATTTTTGAAAGTTTCGGGGTCAAAAATGGAATTTTTGGA-AGTTC-GAGGGT
66 GTAATTTTTGGAAGGTTC-GGATCAAAAATGGAGTTTTTAGACA-TCCGGA-GGT
* *
960729 AAAATGGTAA-TTTTGGAAGGTTTGGGATAAAAAATGGAGTTTTTAGACA-TCTAAGGGTAAAAT
1 AAAATGGTAATTTTTGGAAGGTTCGGGATAAAAAATGGAGTTTTTAGACATTC-GAGGGTAAAAT
* * * *
960792 GGTAAATTTTGGAAGGTCCGAGATCCAAAACGGAGTTTTTAGACATCCGGAGGT
65 GGTAATTTTTGGAAGGTTCG-GATCAAAAATGGAGTTTTTAGACATCCGGAGGT
*
960846 AAAATGGTAATTTTTAGAAG
1 AAAATGGTAATTTTTGGAAG
960866 TTTCAGGGTC
Statistics
Matches: 213, Mismatches: 32, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
116 6 0.03
117 167 0.78
118 38 0.18
119 2 0.01
ACGTcount: A:0.35, C:0.07, G:0.27, T:0.31
Consensus pattern (117 bp):
AAAATGGTAATTTTTGGAAGGTTCGGGATAAAAAATGGAGTTTTTAGACATTCGAGGGTAAAATG
GTAATTTTTGGAAGGTTCGGATCAAAAATGGAGTTTTTAGACATCCGGAGGT
Found at i:960895 original size:29 final size:28
Alignment explanation
Indices: 960846--960990 Score: 87
Period size: 30 Copynumber: 4.9 Consensus size: 28
960836 ATCCGGAGGT
*
960846 AAAATGGTAATTTT-TAGAAGTTTCAGGGTC
1 AAAATGG-AATTTTGGA-AAGTTT-AGGGTC
**
960876 AAAATGGAATTTTGGAAAGTTTAGGGGA
1 AAAATGGAATTTTGGAAAGTTTAGGGTC
* * **
960904 AAAATGTAATTTAT-GAAAATATCGGGGTC
1 AAAATGGAATTT-TGGAAAGT-TTAGGGTC
**
960933 AAAAATAAAATTTTGGAGAAGTTTAAGGGTC
1 -AAAATGGAATTTTGGA-AAGTTT-AGGGTC
** *
960964 AAAATATAATTTTTGGACAGTTTAGGG
1 AAAATGGAA-TTTTGGAAAGTTTAGGG
960991 ACCTCTAGGG
Statistics
Matches: 91, Mismatches: 16, Indels: 17
0.73 0.13 0.14
Matches are distributed among these distances:
28 20 0.22
29 22 0.24
30 34 0.37
31 15 0.16
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.32
Consensus pattern (28 bp):
AAAATGGAATTTTGGAAAGTTTAGGGTC
Found at i:960962 original size:176 final size:176
Alignment explanation
Indices: 960610--960980 Score: 411
Period size: 176 Copynumber: 2.1 Consensus size: 176
960600 CATCCGGGGA
* * *
960610 TAAAATGGAAATTTTTGGAAGGTTCGAGATAAAAAACGGAGTTTTTAGACATTCGGGGGTAAAAT
1 TAAAATGGAAATTTTTGGAAGGTCCGAGATAAAAAACGGAGTTTTTAGACATCCGGAGGTAAAAT
* * *
960675 GATAATTTTTGAAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAATGGTAAT
66 GATAATTTTTGAAAGTTTCAGGGTCAAAAATGGAATTTTTGGAAGTTAGAGGGAAAAATGGTAAT
** * ** * *
960740 TTTGGAAGGTTTGGGATAAAAAATGGAGTTTTTAGACATCTAAGGG
131 TTTGGAAAATTCGGGATAAAAAATAAAATTTTGAGACATCTAAGGG
**
960786 TAAAATGGTAAA-TTTTGGAAGGTCCGAGATCCAAAACGGAGTTTTTAGACATCCGGAGGTAAAA
1 TAAAATGG-AAATTTTTGGAAGGTCCGAGATAAAAAACGGAGTTTTTAGACATCCGGAGGTAAAA
*
960850 TGGTAATTTTT-AGAAGTTTCAGGGTC-AAAATGGAA-TTTTGGAAAGTTTAG-GGGAAAAAT-G
65 TGATAATTTTTGA-AAGTTTCAGGGTCAAAAATGGAATTTTTGG-AAG-TTAGAGGGAAAAATGG
* * *
960910 TAATTTAT-GAAAATATCGGGGTCAAAAATAAAATTTTGGAGA-AGTTTAAGGG
127 TAATTT-TGGAAAAT-TCGGGATAAAAAATAAAATTTT-GAGACA-TCTAAGGG
960962 TCAAAAT--ATAATTTTTGGA
1 T-AAAATGGA-AATTTTTGGA
960981 CAGTTTAGGG
Statistics
Matches: 165, Mismatches: 19, Indels: 22
0.80 0.09 0.11
Matches are distributed among these distances:
174 18 0.11
175 41 0.25
176 98 0.59
177 8 0.05
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.31
Consensus pattern (176 bp):
TAAAATGGAAATTTTTGGAAGGTCCGAGATAAAAAACGGAGTTTTTAGACATCCGGAGGTAAAAT
GATAATTTTTGAAAGTTTCAGGGTCAAAAATGGAATTTTTGGAAGTTAGAGGGAAAAATGGTAAT
TTTGGAAAATTCGGGATAAAAAATAAAATTTTGAGACATCTAAGGG
Found at i:962002 original size:22 final size:22
Alignment explanation
Indices: 961966--962028 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 22
961956 CCCTTGTTAT
* **
961966 TATTTGTTTAATATTACCAAAAA
1 TATTT-TTTATTATTAAAAAAAA
961989 TATTTTTTATTATTAAAAAAAAA
1 TATTTTTTATTATT-AAAAAAAA
962012 TATTATTATTATTATTA
1 TATT-TT-TTATTATTA
962029 TTATTATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 8 0.24
23 15 0.44
24 3 0.09
25 8 0.24
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (22 bp):
TATTTTTTATTATTAAAAAAAA
Found at i:962018 original size:3 final size:3
Alignment explanation
Indices: 962012--962040 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
962002 TAAAAAAAAA
962012 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
962041 ATGCTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:962900 original size:6 final size:6
Alignment explanation
Indices: 962827--962927 Score: 57
Period size: 6 Copynumber: 17.0 Consensus size: 6
962817 ATGGACTTTG
* * * *
962827 AATTTA ATTTTA AAGTTTA AGTTTTA AAATT- -ATTTCA AATTTA AA-CTA
1 AATTTA AATTTA AA-TTTA A-ATTTA AATTTA AATTT-A AATTTA AATTTA
* ** ** *
962875 AATTGA AATTTA AA-ACA AATTTA AATTTA AAAATG AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
962922 AATTTA
1 AATTTA
962928 GAAATAAATC
Statistics
Matches: 68, Mismatches: 20, Indels: 14
0.67 0.20 0.14
Matches are distributed among these distances:
4 3 0.04
5 7 0.10
6 44 0.65
7 14 0.21
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.44
Consensus pattern (6 bp):
AATTTA
Found at i:962907 original size:18 final size:18
Alignment explanation
Indices: 962869--962923 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
962859 TTTCAAATTT
*
962869 AAACTAAATTGAAATTT-A
1 AAAC-AAATTTAAATTTAA
962887 AAACAAATTTAAATTTAA
1 AAACAAATTTAAATTTAA
**
962905 AAATGAATTTAAATTTAA
1 AAACAAATTTAAATTTAA
962923 A
1 A
962924 TTTAGAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
17 11 0.33
18 22 0.67
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.35
Consensus pattern (18 bp):
AAACAAATTTAAATTTAA
Found at i:962920 original size:24 final size:24
Alignment explanation
Indices: 962891--962941 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
962881 AATTTAAAAC
* *
962891 AAATTTAAATTTAAAAATGAATTT
1 AAATTTAAATTTAAAAATAAATCT
*
962915 AAATTTAAATTTAGAAATAAATCT
1 AAATTTAAATTTAAAAATAAATCT
962939 AAA
1 AAA
962942 ATAATTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATTTAAATTTAAAAATAAATCT
Found at i:962935 original size:12 final size:11
Alignment explanation
Indices: 962896--962951 Score: 51
Period size: 12 Copynumber: 4.9 Consensus size: 11
962886 AAAACAAATT
962896 TAAATTTAAAAA
1 TAAATTT-AAAA
* *
962908 TGAATTTAAATT
1 TAAATTTAAA-A
962920 TAAATTTAGAAA
1 TAAATTTA-AAA
*
962932 TAAATCTAAAA
1 TAAATTTAAAA
962943 T-AATTTAAA
1 TAAATTTAAA
962952 CTTTACCAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
10 7 0.19
11 7 0.19
12 20 0.56
13 2 0.06
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.38
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:962936 original size:18 final size:17
Alignment explanation
Indices: 962849--962923 Score: 80
Period size: 17 Copynumber: 4.4 Consensus size: 17
962839 AAGTTTAAGT
*
962849 TTTAAAAT-TATTTCAAA
1 TTTAAAATAAATTT-AAA
* *
962866 TTTAAACTAAATTGAAA
1 TTTAAAATAAATTTAAA
*
962883 TTTAAAACAAATTTAAA
1 TTTAAAATAAATTTAAA
*
962900 TTTAAAAATGAATTTAAA
1 TTT-AAAATAAATTTAAA
962918 TTTAAA
1 TTTAAA
962924 TTTAGAAATA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
17 30 0.62
18 18 0.38
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (17 bp):
TTTAAAATAAATTTAAA
Found at i:963848 original size:23 final size:24
Alignment explanation
Indices: 963809--963859 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
963799 TAATAGGGAT
963809 TTTCAATATACAATTCA-TATCAC
1 TTTCAATATACAATTCACTATCAC
* *
963832 TTTCAAT-TCCAATTTCACTTTCAC
1 TTTCAATATACAA-TTCACTATCAC
963856 TTTC
1 TTTC
963860 GCTTTCAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 4 0.17
23 11 0.46
24 9 0.38
ACGTcount: A:0.29, C:0.25, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTCAATATACAATTCACTATCAC
Found at i:973458 original size:20 final size:20
Alignment explanation
Indices: 973409--973458 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
973399 ATTTTTTTTT
*
973409 AAATCGAGTCAAGTAAAATG
1 AAATCGAGTCAAGTAAAATC
** *
973429 AAATTCGAGTTGAGTCAAATC
1 AAA-TCGAGTCAAGTAAAATC
973450 AAATCGAGT
1 AAATCGAGT
973459 GAAATTGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.24
Consensus pattern (20 bp):
AAATCGAGTCAAGTAAAATC
Found at i:973778 original size:19 final size:19
Alignment explanation
Indices: 973751--973791 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
973741 TTTTGGAATT
* *
973751 TTTATAAAAATATTTTAAA
1 TTTAAAAAAATATTTGAAA
973770 TTTAAAAAAATATTTGAAA
1 TTTAAAAAAATATTTGAAA
973789 TTT
1 TTT
973792 TTTTGTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
TTTAAAAAAATATTTGAAA
Found at i:974502 original size:342 final size:343
Alignment explanation
Indices: 973877--975335 Score: 2562
Period size: 342 Copynumber: 4.3 Consensus size: 343
973867 CAAGTTTAAA
* * *
973877 TTTTCAATTTAGTTCTTTGTAAATTTACATTATTACCCTCCCAAAAATATAAGTAACCCCTTCTC
1 TTTTCAATTTAGTTCTTTGTAAATTTACACTATAACCCTCCCAAAAATATAAGTAACCCCCTCTC
* *
973942 AAGGTTTAAGATTTTTGCAATTTAAAAAACGGTTCAACTATTCCGCATCAATTAATCAATTAATG
66 AAGGTTTAAGATTTTTGCAATTTAAAAAACGATTCAACTATTCCGCATCAATTCATCAATTAATG
* * *
974007 ATTTAATCATTTAAAAGTCTTTCTCTAAATCAGTATCTGATCAATTCTTAATATGATTGAAACAA
131 ATTTAATCGTTTAAAAGTTTTTCTCTAAATCAGTACCTGATCAATTCTTAATATGATTGAAACAA
* * * * *
974072 TTTAATTCACACATCCTCTCATTTCCTCTACCTTTTATCTATCCAAATAAAAGTACGCACTCATG
196 TTCAATTCACACATCCTCCCATTTCCTCTACCTTTTATCTATCCAAACAAAAATACCCACTCATG
* *
974137 CTGAACTTCTACAACAAGGTTGTGGTCAGTGGCGGAGCCACGTTAAGGCCCAGAAGAGTCATGGG
261 TTGAACTTCTACAACAAGGTTGTGGTCAGTGGCGGAGCCACGTTAAGGCCCAGAAGAGCCATGGG
974202 CCCTCCAAGTTTAA-TTT
326 CCCTCCAAGTTTAATTTT
* *
974219 TTTTCAATTTAGTTCTTTGTAAATTTACACTATAACCCTCCAAAAAATATAAGTAACCTCCTCTC
1 TTTTCAATTTAGTTCTTTGTAAATTTACACTATAACCCTCCCAAAAATATAAGTAACCCCCTCTC
974284 AAGGTTTAAGATTTTTGCAATTTAAAAAACGATTCAACTATTCCGCATCAATTCATCAATTAATG
66 AAGGTTTAAGATTTTTGCAATTTAAAAAACGATTCAACTATTCCGCATCAATTCATCAATTAATG
* * *
974349 ATTTAATCGTTTAAAAGTTTTTCTCTAAATCAGTACCTGATTAATTCTTGACATGATTGAAACAA
131 ATTTAATCGTTTAAAAGTTTTTCTCTAAATCAGTACCTGATCAATTCTTAATATGATTGAAACAA
974414 TTCAATTCACACATCCTCCCATTTCCTCTACCTTTTATCTATCCAAACAAAAATACCCACTCATG
196 TTCAATTCACACATCCTCCCATTTCCTCTACCTTTTATCTATCCAAACAAAAATACCCACTCATG
*
974479 TTGAACTTCTACAACAAGGTTGTGGTCAGTGGCGGACCCACGTTAAGGCCCAGAAGAGCCATGGG
261 TTGAACTTCTACAACAAGGTTGTGGTCAGTGGCGGAGCCACGTTAAGGCCCAGAAGAGCCATGGG
974544 CCCTCCAAGTTTAA-TTT
326 CCCTCCAAGTTTAATTTT
974561 TTTTCAATTTAGTTCTTTGTAAATTTACACTATAACCCTCCCAAAAATATAAGTAACCCCCTCTC
1 TTTTCAATTTAGTTCTTTGTAAATTTACACTATAACCCTCCCAAAAATATAAGTAACCCCCTCTC
974626 AAGGTTTAAGATTTTTGCAATTTAAAAAACGATTCAACTATTCCGCATCAATTCATCAATTAATG
66 AAGGTTTAAGATTTTTGCAATTTAAAAAACGATTCAACTATTCCGCATCAATTCATCAATTAATG
* *
974691 ATTTAATCGTTTAAAAGTTTTTCTCTAAATCAATACCTGATCAATTCTTGATATGATTGAAACAA
131 ATTTAATCGTTTAAAAGTTTTTCTCTAAATCAGTACCTGATCAATTCTTAATATGATTGAAACAA
974756 TTCAATTCACACATCCTCCCATTTCCTCTACCTTTTATCTATCCAAACAAAAATACCCACTCATG
196 TTCAATTCACACATCCTCCCATTTCCTCTACCTTTTATCTATCCAAACAAAAATACCCACTCATG
* *
974821 TTGAACTTCTAAAACAAGGTTGTGGTCAGTGGCGGAGCCACGTTAAGGCCCAGAAGAGCCATGGA
261 TTGAACTTCTACAACAAGGTTGTGGTCAGTGGCGGAGCCACGTTAAGGCCCAGAAGAGCCATGGG
974886 CCCTCCAAGTTTAATTTT
326 CCCTCCAAGTTTAATTTT
974904 TTTTCAATTTAGTTCTTTGTAAATTTACACTATAACCCTCCCAAAAATATAAGTAACCCCCTCTC
1 TTTTCAATTTAGTTCTTTGTAAATTTACACTATAACCCTCCCAAAAATATAAGTAACCCCCTCTC
974969 AAGGTTTAAGATTTTTGCAATTTAAAAAACGATTCAACTATTCCGCATCAATTCATCAATTAATG
66 AAGGTTTAAGATTTTTGCAATTTAAAAAACGATTCAACTATTCCGCATCAATTCATCAATTAATG
975034 ATTTAATCGTTTAAAAGTTTTTCTCTAAATCAGTACCTGATCAATTCTTAATATGATTGAAACAA
131 ATTTAATCGTTTAAAAGTTTTTCTCTAAATCAGTACCTGATCAATTCTTAATATGATTGAAACAA
* **
975099 TTCAATTCACACATCCTCACATTTCCTCTACCTTTTATCTATTGAAACAAAAATACCCACTCATG
196 TTCAATTCACACATCCTCCCATTTCCTCTACCTTTTATCTATCCAAACAAAAATACCCACTCATG
* *
975164 TTGAACTTCTACAACAAGATTGTGGTCAGTGGCGGAGCCACGTTAAGGCCCAGAAGAGCCATGAG
261 TTGAACTTCTACAACAAGGTTGTGGTCAGTGGCGGAGCCACGTTAAGGCCCAGAAGAGCCATGGG
975229 CCCTCCAAGTTTAATTATTTT
326 CCCTCCAAGTTT-A--ATTTT
* * * * *
975250 TTTTCAATTTAATTCTTTGTAAATTTAAACTATGACCCTCCCAAAAATATAAGTAGCTCCCTCTC
1 TTTTCAATTTAGTTCTTTGTAAATTTACACTATAACCCTCCCAAAAATATAAGTAACCCCCTCTC
975315 AAGGTTTAAGATTTTTGCAAT
66 AAGGTTTAAGATTTTTGCAAT
975336 ATATTTATTA
Statistics
Matches: 1070, Mismatches: 43, Indels: 4
0.96 0.04 0.00
Matches are distributed among these distances:
342 652 0.61
343 331 0.31
344 1 0.00
346 86 0.08
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.34
Consensus pattern (343 bp):
TTTTCAATTTAGTTCTTTGTAAATTTACACTATAACCCTCCCAAAAATATAAGTAACCCCCTCTC
AAGGTTTAAGATTTTTGCAATTTAAAAAACGATTCAACTATTCCGCATCAATTCATCAATTAATG
ATTTAATCGTTTAAAAGTTTTTCTCTAAATCAGTACCTGATCAATTCTTAATATGATTGAAACAA
TTCAATTCACACATCCTCCCATTTCCTCTACCTTTTATCTATCCAAACAAAAATACCCACTCATG
TTGAACTTCTACAACAAGGTTGTGGTCAGTGGCGGAGCCACGTTAAGGCCCAGAAGAGCCATGGG
CCCTCCAAGTTTAATTTT
Found at i:975221 original size:685 final size:687
Alignment explanation
Indices: 973877--975335 Score: 2564
Period size: 685 Copynumber: 2.1 Consensus size: 687
973867 CAAGTTTAAA
* * *
973877 TTTTCAATTTAGTTCTTTGTAAATTTACATTATTACCCTCCCAAAAATATAAGTAACCCCTTCTC
1 TTTTCAATTTAGTTCTTTGTAAATTTACACTATAACCCTCCCAAAAATATAAGTAACCCCCTCTC
*
973942 AAGGTTTAAGATTTTTGCAATTTAAAAAACGGTTCAACTATTCCGCATCAATTAATCAATTAATG
66 AAGGTTTAAGATTTTTGCAATTTAAAAAACGATTCAACTATTCCGCATCAATTAATCAATTAATG
* *
974007 ATTTAATCATTTAAAAGTCTTTCTCTAAATCAGTATCTGATCAATTCTTAATATGATTGAAACAA
131 ATTTAATCATTTAAAAGTCTTTCTCTAAATCAATACCTGATCAATTCTTAATATGATTGAAACAA
* * * * *
974072 TTTAATTCACACATCCTCTCATTTCCTCTACCTTTTATCTATCCAAATAAAAGTACGCACTCATG
196 TTCAATTCACACATCCTCCCATTTCCTCTACCTTTTATCTATCCAAACAAAAATACCCACTCATG
* * *
974137 CTGAACTTCTACAACAAGGTTGTGGTCAGTGGCGGAGCCACGTTAAGGCCCAGAAGAGTCATGGG
261 CTGAACTTCTAAAACAAGGTTGTGGTCAGTGGCGGAGCCACGTTAAGGCCCAGAAGAGCCATGGA
974202 CCCTCCAAGTTTAATTTTTTTCAATTTAGTTCTTTGTAAATTTACACTATAACCCTCCAAAAAAT
326 CCCTCCAAGTTTAATTTTTTTCAATTTAGTTCTTTGTAAATTTACACTATAACCCTCCAAAAAAT
*
974267 ATAAGTAACCTCCTCTCAAGGTTTAAGATTTTTGCAATTTAAAAAACGATTCAACTATTCCGCAT
391 ATAAGTAACCCCCTCTCAAGGTTTAAGATTTTTGCAATTTAAAAAACGATTCAACTATTCCGCAT
*
974332 CAATTCATCAATTAATGATTTAATCGTTTAAAAGTTTTTCTCTAAATCAGTACCTGATTAATTCT
456 CAATTCATCAATTAATGATTTAATCGTTTAAAAGTTTTTCTCTAAATCAGTACCTGATCAATTCT
* *
974397 TGACATGATTGAAACAATTCAATTCACACATCCTCCCATTTCCTCTACCTTTTATCTATCCAAAC
521 TAACATGATTGAAACAATTCAATTCACACATCCTCACATTTCCTCTACCTTTTATCTATCCAAAC
*
974462 AAAAATACCCACTCATGTTGAACTTCTACAACAAGGTTGTGGTCAGTGGCGGACCCACGTTAAGG
586 AAAAATACCCACTCATGTTGAACTTCTACAACAAGATTGTGGTCAGTGGCGGACCCACGTTAAGG
*
974527 CCCAGAAGAGCCATGGGCCCTCCAAGTTT-A-A-TTT
651 CCCAGAAGAGCCATGAGCCCTCCAAGTTTAATATTTT
974561 TTTTCAATTTAGTTCTTTGTAAATTTACACTATAACCCTCCCAAAAATATAAGTAACCCCCTCTC
1 TTTTCAATTTAGTTCTTTGTAAATTTACACTATAACCCTCCCAAAAATATAAGTAACCCCCTCTC
*
974626 AAGGTTTAAGATTTTTGCAATTTAAAAAACGATTCAACTATTCCGCATCAATTCATCAATTAATG
66 AAGGTTTAAGATTTTTGCAATTTAAAAAACGATTCAACTATTCCGCATCAATTAATCAATTAATG
* * *
974691 ATTTAATCGTTTAAAAGTTTTTCTCTAAATCAATACCTGATCAATTCTTGATATGATTGAAACAA
131 ATTTAATCATTTAAAAGTCTTTCTCTAAATCAATACCTGATCAATTCTTAATATGATTGAAACAA
974756 TTCAATTCACACATCCTCCCATTTCCTCTACCTTTTATCTATCCAAACAAAAATACCCACTCATG
196 TTCAATTCACACATCCTCCCATTTCCTCTACCTTTTATCTATCCAAACAAAAATACCCACTCATG
*
974821 TTGAACTTCTAAAACAAGGTTGTGGTCAGTGGCGGAGCCACGTTAAGGCCCAGAAGAGCCATGGA
261 CTGAACTTCTAAAACAAGGTTGTGGTCAGTGGCGGAGCCACGTTAAGGCCCAGAAGAGCCATGGA
*
974886 CCCTCCAAGTTTAATTTTTTTTCAATTTAGTTCTTTGTAAATTTACACTATAACCCTCCCAAAAA
326 CCCTCCAAGTTTAA-TTTTTTTCAATTTAGTTCTTTGTAAATTTACACTATAACCCTCCAAAAAA
974951 TATAAGTAACCCCCTCTCAAGGTTTAAGATTTTTGCAATTTAAAAAACGATTCAACTATTCCGCA
390 TATAAGTAACCCCCTCTCAAGGTTTAAGATTTTTGCAATTTAAAAAACGATTCAACTATTCCGCA
975016 TCAATTCATCAATTAATGATTTAATCGTTTAAAAGTTTTTCTCTAAATCAGTACCTGATCAATTC
455 TCAATTCATCAATTAATGATTTAATCGTTTAAAAGTTTTTCTCTAAATCAGTACCTGATCAATTC
* **
975081 TTAATATGATTGAAACAATTCAATTCACACATCCTCACATTTCCTCTACCTTTTATCTATTGAAA
520 TTAACATGATTGAAACAATTCAATTCACACATCCTCACATTTCCTCTACCTTTTATCTATCCAAA
*
975146 CAAAAATACCCACTCATGTTGAACTTCTACAACAAGATTGTGGTCAGTGGCGGAGCCACGTTAAG
585 CAAAAATACCCACTCATGTTGAACTTCTACAACAAGATTGTGGTCAGTGGCGGACCCACGTTAAG
975211 GCCCAGAAGAGCCATGAGCCCTCCAAGTTTAATTATTTT
650 GCCCAGAAGAGCCATGAGCCCTCCAAGTTTAA-TATTTT
* * * * *
975250 TTTTCAATTTAATTCTTTGTAAATTTAAACTATGACCCTCCCAAAAATATAAGTAGCTCCCTCTC
1 TTTTCAATTTAGTTCTTTGTAAATTTACACTATAACCCTCCCAAAAATATAAGTAACCCCCTCTC
975315 AAGGTTTAAGATTTTTGCAAT
66 AAGGTTTAAGATTTTTGCAAT
975336 ATATTTATTA
Statistics
Matches: 735, Mismatches: 35, Indels: 5
0.95 0.05 0.01
Matches are distributed among these distances:
684 320 0.44
685 329 0.45
686 1 0.00
688 1 0.00
689 84 0.11
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.34
Consensus pattern (687 bp):
TTTTCAATTTAGTTCTTTGTAAATTTACACTATAACCCTCCCAAAAATATAAGTAACCCCCTCTC
AAGGTTTAAGATTTTTGCAATTTAAAAAACGATTCAACTATTCCGCATCAATTAATCAATTAATG
ATTTAATCATTTAAAAGTCTTTCTCTAAATCAATACCTGATCAATTCTTAATATGATTGAAACAA
TTCAATTCACACATCCTCCCATTTCCTCTACCTTTTATCTATCCAAACAAAAATACCCACTCATG
CTGAACTTCTAAAACAAGGTTGTGGTCAGTGGCGGAGCCACGTTAAGGCCCAGAAGAGCCATGGA
CCCTCCAAGTTTAATTTTTTTCAATTTAGTTCTTTGTAAATTTACACTATAACCCTCCAAAAAAT
ATAAGTAACCCCCTCTCAAGGTTTAAGATTTTTGCAATTTAAAAAACGATTCAACTATTCCGCAT
CAATTCATCAATTAATGATTTAATCGTTTAAAAGTTTTTCTCTAAATCAGTACCTGATCAATTCT
TAACATGATTGAAACAATTCAATTCACACATCCTCACATTTCCTCTACCTTTTATCTATCCAAAC
AAAAATACCCACTCATGTTGAACTTCTACAACAAGATTGTGGTCAGTGGCGGACCCACGTTAAGG
CCCAGAAGAGCCATGAGCCCTCCAAGTTTAATATTTT
Found at i:976349 original size:15 final size:15
Alignment explanation
Indices: 976321--976356 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
976311 TTAAATTGAT
*
976321 TAATTTTAATTTTTG
1 TAATTTTAAATTTTG
976336 TAATTTTAAATTTTG
1 TAATTTTAAATTTTG
*
976351 AAATTT
1 TAATTT
976357 CTTAATGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (15 bp):
TAATTTTAAATTTTG
Found at i:978218 original size:9 final size:9
Alignment explanation
Indices: 978206--978242 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
978196 TGCGACCCAT
978206 GGTGGCGGC
1 GGTGGCGGC
978215 GGTGGCGGC
1 GGTGGCGGC
978224 GGTGGCGGC
1 GGTGGCGGC
*
978233 GGTGGTGGC
1 GGTGGCGGC
978242 G
1 G
978243 AGATTTCTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.00, C:0.19, G:0.68, T:0.14
Consensus pattern (9 bp):
GGTGGCGGC
Found at i:989987 original size:28 final size:29
Alignment explanation
Indices: 989943--989997 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
989933 CGAGTATTCG
*
989943 AAAGTTTAGGATGTAA-TTAGAATAATTT
1 AAAGTTTAGGATGTAATTTAAAATAATTT
989971 AAAGTTTAGGTAT-TAATTTAAAATAAT
1 AAAGTTTAGG-ATGTAATTTAAAATAAT
989998 GGGTATAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.40
Consensus pattern (29 bp):
AAAGTTTAGGATGTAATTTAAAATAATTT
Found at i:993817 original size:15 final size:16
Alignment explanation
Indices: 993800--993849 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
993790 TGTTTCTTAT
993800 AATATTTATATATTTA
1 AATATTTATATATTTA
*
993816 ATTATTT-TA-ATTATA
1 AATATTTATATATT-TA
*
993831 AATATTTAT-TATTTG
1 AATATTTATATATTTA
993846 AATA
1 AATA
993850 ATAATTCAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
14 3 0.11
15 15 0.54
16 10 0.36
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (16 bp):
AATATTTATATATTTA
Found at i:993844 original size:22 final size:23
Alignment explanation
Indices: 993809--993853 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
993799 TAATATTTAT
* *
993809 ATATTTAATTATTTTAATTATAA
1 ATATTTAATTATTTGAATAATAA
993832 ATATTT-ATTATTTGAATAATAA
1 ATATTTAATTATTTGAATAATAA
993854 TTCAAGTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
ATATTTAATTATTTGAATAATAA
Found at i:995963 original size:3 final size:3
Alignment explanation
Indices: 995955--995988 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
995945 TCTTTTATCA
*
995955 AAT AAT AAT AAT AAT AAT ACT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
995989 TATTCCTAAA
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:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:997043 original size:16 final size:16
Alignment explanation
Indices: 997022--997055 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
997012 TATACAAGGA
*
997022 TTAATTTGTCTATTTT
1 TTAATTTGTCCATTTT
997038 TTAATTTGTCCATTTT
1 TTAATTTGTCCATTTT
997054 TT
1 TT
997056 TGAATAGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.09, G:0.06, T:0.68
Consensus pattern (16 bp):
TTAATTTGTCCATTTT
Found at i:1005903 original size:2 final size:2
Alignment explanation
Indices: 1005896--1005923 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1005886 AGTTTTTAGG
1005896 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
1005924 AAACAACACA
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:1006396 original size:28 final size:27
Alignment explanation
Indices: 1006365--1006425 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
1006355 TATACCAACT
*
1006365 TATACAAATTATAAATA-TTATAAAAAAA
1 TATAAAAATTAT-AATAGTT-TAAAAAAA
* *
1006393 TATAAAAATTCTAATAGTTTATAAAAA
1 TATAAAAATTATAATAGTTTAAAAAAA
1006420 TATAAA
1 TATAAA
1006426 TTAATAAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 17 0.59
28 12 0.41
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (27 bp):
TATAAAAATTATAATAGTTTAAAAAAA
Found at i:1006454 original size:21 final size:20
Alignment explanation
Indices: 1006429--1006506 Score: 63
Period size: 21 Copynumber: 3.9 Consensus size: 20
1006419 ATATAAATTA
*
1006429 ATAAAACATATTTAAAATTTT
1 ATAAAACATA-TTAAAATTCT
*
1006450 ATAAAAACGTATTAAAATTCT
1 AT-AAAACATATTAAAATTCT
* * *
1006471 ATAAAA-ATCATAAAAAATAT
1 ATAAAACAT-ATTAAAATTCT
1006491 -TAAAA-ATATTAAAATT
1 ATAAAACATATTAAAATT
1006507 GATATAAAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
18 7 0.15
19 8 0.17
20 12 0.26
21 13 0.28
22 7 0.15
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.35
Consensus pattern (20 bp):
ATAAAACATATTAAAATTCT
Found at i:1006543 original size:19 final size:18
Alignment explanation
Indices: 1006365--1006548 Score: 63
Period size: 19 Copynumber: 9.8 Consensus size: 18
1006355 TATACCAACT
* * *
1006365 TATACAAATTATAAATAT
1 TATAAAAATTATAAAAAA
* *
1006383 TATAAAAAAATATAAAAAT
1 TAT-AAAAATTATAAAAAA
* * *
1006402 TCTAATAGTT-TATAAAAA
1 TATAAAAATTATA-AAAAA
1006420 TAT--AAATTAATAAAACATA
1 TATAAAAATT-ATAAAA-A-A
* * *
1006439 TTTAAAATTTTATAAAAACG
1 TATAAAA-ATTATAAAAA-A
* *
1006459 TATTAAAATTCTATAAAAA
1 TATAAAAATTATA-AAAAA
* *
1006478 TCATAAAAAATATTAAAAA
1 T-ATAAAAATTATAAAAAA
* *
1006497 TATTAAAATTGATATAAAA
1 TATAAAAATT-ATAAAAAA
*
1006516 T-TACTAAATTATAAAAAA
1 TATA-AAAATTATAAAAAA
1006534 TCATAAAAATT-TAAA
1 T-ATAAAAATTATAAA
1006549 TTGGATTAGA
Statistics
Matches: 119, Mismatches: 32, Indels: 30
0.66 0.18 0.17
Matches are distributed among these distances:
16 3 0.03
17 5 0.04
18 36 0.30
19 45 0.38
20 20 0.17
21 8 0.07
22 2 0.02
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (18 bp):
TATAAAAATTATAAAAAA
Found at i:1021938 original size:2 final size:2
Alignment explanation
Indices: 1021931--1021956 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1021921 TTTAATTTCA
1021931 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
1021957 TAACAATGTT
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:1030715 original size:9 final size:9
Alignment explanation
Indices: 1030701--1030726 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1030691 GCGCATCGCG
1030701 GCGGCGGCA
1 GCGGCGGCA
1030710 GCGGCGGCA
1 GCGGCGGCA
1030719 GCGGCGGC
1 GCGGCGGC
1030727 TCTGACTGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.08, C:0.35, G:0.58, T:0.00
Consensus pattern (9 bp):
GCGGCGGCA
Found at i:1039931 original size:20 final size:20
Alignment explanation
Indices: 1039898--1039936 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1039888 AAATGTTTTT
1039898 TAAAAACATAATATTATAAAA
1 TAAAAACATAATATT-TAAAA
*
1039919 TAAAAATAT-ATATTTAAA
1 TAAAAACATAATATTTAAA
1039937 TAATATTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 5 0.29
21 8 0.47
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (20 bp):
TAAAAACATAATATTTAAAA
Found at i:1041942 original size:29 final size:30
Alignment explanation
Indices: 1041894--1041953 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
1041884 TTAAATTAAT
1041894 AATAATAAAATTATATTTTAA-CTTTAAAA
1 AATAATAAAATTATATTTTAACCTTTAAAA
*
1041923 AATAATAAAATTTTGA-TTTAACCCTTTAAAA
1 AATAATAAAATTAT-ATTTTAA-CCTTTAAAA
1041954 TTTATAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
29 18 0.67
30 1 0.04
31 8 0.30
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.40
Consensus pattern (30 bp):
AATAATAAAATTATATTTTAACCTTTAAAA
Found at i:1042556 original size:14 final size:15
Alignment explanation
Indices: 1042537--1042567 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1042527 TAATTCTAAT
1042537 TTGTAATAT-TTTTA
1 TTGTAATATATTTTA
1042551 TTGTAATATATTTTA
1 TTGTAATATATTTTA
1042566 TT
1 TT
1042568 ATTGTTAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (15 bp):
TTGTAATATATTTTA
Found at i:1054725 original size:76 final size:76
Alignment explanation
Indices: 1054599--1054750 Score: 295
Period size: 76 Copynumber: 2.0 Consensus size: 76
1054589 CAATTTAATC
*
1054599 CCTATCAATTTCGAAAGTGAGCAACTAAGGACAATTAAGCATGGAGTTAATGTCTTCCATCAATT
1 CCTATCAATTTCGAAAGTGAGCAACTAAAGACAATTAAGCATGGAGTTAATGTCTTCCATCAATT
1054664 GTACATATTTT
66 GTACATATTTT
1054675 CCTATCAATTTCGAAAGTGAGCAACTAAAGACAATTAAGCATGGAGTTAATGTCTTCCATCAATT
1 CCTATCAATTTCGAAAGTGAGCAACTAAAGACAATTAAGCATGGAGTTAATGTCTTCCATCAATT
1054740 GTACATATTTT
66 GTACATATTTT
1054751 TTATTGGTAT
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (76 bp):
CCTATCAATTTCGAAAGTGAGCAACTAAAGACAATTAAGCATGGAGTTAATGTCTTCCATCAATT
GTACATATTTT
Found at i:1057134 original size:3 final size:3
Alignment explanation
Indices: 1057126--1057157 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1057116 AGGGAGATTC
1057126 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GG
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GG
1057158 AAGAGGTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.69, T:0.31
Consensus pattern (3 bp):
GGT
Found at i:1057878 original size:17 final size:16
Alignment explanation
Indices: 1057847--1057890 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
1057837 AATTTTCATA
1057847 ATAATAAATTTCTGAC
1 ATAATAAATTTCTGAC
*
1057863 ATAATCAATCTTCTGAC
1 ATAATAAAT-TTCTGAC
* *
1057880 AAAATATATTT
1 ATAATAAATTT
1057891 ATTAGAGTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.39
Consensus pattern (16 bp):
ATAATAAATTTCTGAC
Found at i:1064049 original size:31 final size:32
Alignment explanation
Indices: 1063983--1064050 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 32
1063973 ATTTGAAAAA
* * *
1063983 AAAAAAAAAGAAAACATATTGAGTGAATGAGG
1 AAAAAAAAAGAAAACATATTGAATGAAGGAAG
*
1064015 AAAAAAAATGAAAA-ATATT-AATGAGAGGAAG
1 AAAAAAAAAGAAAACATATTGAATGA-AGGAAG
1064046 AAAAA
1 AAAAA
1064051 GATGAGCAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 4 0.13
31 14 0.45
32 13 0.42
ACGTcount: A:0.65, C:0.01, G:0.19, T:0.15
Consensus pattern (32 bp):
AAAAAAAAAGAAAACATATTGAATGAAGGAAG
Found at i:1081519 original size:18 final size:18
Alignment explanation
Indices: 1081496--1081536 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1081486 ATAGGTTTTA
1081496 AATTAAATAAATTT-AATT
1 AATTAAA-AAATTTAAATT
1081514 AATTAAAAAATTTAAATT
1 AATTAAAAAATTTAAATT
1081532 AATTA
1 AATTA
1081537 CACCTTGAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AATTAAAAAATTTAAATT
Found at i:1086910 original size:23 final size:23
Alignment explanation
Indices: 1086862--1086910 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1086852 ATGGAATTTC
* *
1086862 AAAATTCAAAAAATACAAATATT
1 AAAATTCAAAAAATACAAAGACT
* *
1086885 AAAATTCACAAAGTACAAAGACT
1 AAAATTCAAAAAATACAAAGACT
1086908 AAA
1 AAA
1086911 TATGCAACTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.63, C:0.12, G:0.04, T:0.20
Consensus pattern (23 bp):
AAAATTCAAAAAATACAAAGACT
Found at i:1089193 original size:4 final size:4
Alignment explanation
Indices: 1089184--1089213 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
1089174 TTTCAGCACT
1089184 TGGA TGGA TGGA TGGA TGGA TGGA TGGA TG
1 TGGA TGGA TGGA TGGA TGGA TGGA TGGA TG
1089214 TCCATACGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.50, T:0.27
Consensus pattern (4 bp):
TGGA
Found at i:1093223 original size:3 final size:3
Alignment explanation
Indices: 1093215--1093247 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1093205 ATGAACCATA
1093215 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1093248 ATGTGAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1111602 original size:97 final size:97
Alignment explanation
Indices: 1111427--1111620 Score: 257
Period size: 97 Copynumber: 2.0 Consensus size: 97
1111417 AACCTTGAAA
*
1111427 AAGGATATTCGATTATCTTGATTTGAAGAAAAATCGCACCAAGTAAGTTAAGGCACAAATTTTAA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATCGCACCAAGTAAGTTAAGGCACAAATTTTAA
*
1111492 GAACCAGAGATAAATAAACATTGCATCGATTT
66 GAACCAGAAATAAATAAACATTGCATCGATTT
* * * * *
1111524 AAGGGTATTCGATTAT-TCCGATTTGAAGAAAAATTGCGCCTAGTAAGTTAAGGCACAAATTTTT
1 AAGGATATTCGATTATCT-CGATTTGAAGAAAAATCGCACCAAGTAAGTTAAGGCACAAATTTTA
* * * *
1111588 ATAACTC-GAAATAAATCAATATTGCCTCGATTT
65 AGAAC-CAGAAATAAATAAACATTGCATCGATTT
1111621 TAAAGGTGTT
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
96 1 0.01
97 82 0.98
98 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (97 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATCGCACCAAGTAAGTTAAGGCACAAATTTTAA
GAACCAGAAATAAATAAACATTGCATCGATTT
Found at i:1111892 original size:29 final size:29
Alignment explanation
Indices: 1111858--1111934 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
1111848 GGATGCCTAG
*
1111858 GGGTAAATTAGTAATTTTGAACACTTTGA
1 GGGTAAATTAGTAATTTTGAACACTTGGA
* *
1111887 GGGTAAAATAGTAATTTTTGGACACTTGGA
1 GGGTAAATTAGTAA-TTTTGAACACTTGGA
*
1111917 -GGAAAATTAGTAATTTTG
1 GGGTAAATTAGTAATTTTG
1111935 GGAAAGTTCG
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
28 5 0.12
29 24 0.57
30 13 0.31
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.36
Consensus pattern (29 bp):
GGGTAAATTAGTAATTTTGAACACTTGGA
Found at i:1111912 original size:30 final size:30
Alignment explanation
Indices: 1111858--1111991 Score: 95
Period size: 29 Copynumber: 4.6 Consensus size: 30
1111848 GGATGCCTAG
* *
1111858 GGGTAAATTAGTAA-TTTTGAACACTTTGA
1 GGGTAAAATAGTAATTTTTGAACACTTGGA
*
1111887 GGGTAAAATAGTAATTTTTGGACACTTGGA
1 GGGTAAAATAGTAATTTTTGAACACTTGGA
* * *
1111917 -GG-AAAATTAGTAATTTTGGGAA-AGTTCG-
1 GGGTAAAA-TAGTAATTTT-TGAACACTTGGA
*
1111945 GGGTCAAAA-ATGTAATTTTTGAATA-TTCGG-
1 GGGT-AAAATA-GTAATTTTTGAACACTT-GGA
*
1111975 GGGTAAAATGGTAATTT
1 GGGTAAAATAGTAATTT
1111992 AGAAAAAGTT
Statistics
Matches: 85, Mismatches: 10, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
28 4 0.05
29 48 0.56
30 29 0.34
31 4 0.05
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.35
Consensus pattern (30 bp):
GGGTAAAATAGTAATTTTTGAACACTTGGA
Found at i:1112079 original size:29 final size:29
Alignment explanation
Indices: 1111975--1112115 Score: 74
Period size: 29 Copynumber: 4.8 Consensus size: 29
1111965 GAATATTCGG
* * * *
1111975 GGGTAAAATGGTAATTTAGAAAAAGTTTG
1 GGGTAAAATAGAAATTTTGAAAAAGTTTA
* * *
1112004 GGGTTAAAAAAAGGAATTTTTG--GAAGTTTA
1 GGG-T-AAAATA-GAAATTTTGAAAAAGTTTA
* * *
1112034 GGGGTACAATGGTAATTTTGAAAAAGTTTA
1 -GGGTAAAATAGAAATTTTGAAAAAGTTTA
* * *
1112064 GGGTAAAAATAG-AATTTT-TAGAAGTTCGA
1 GGGT-AAAATAGAAATTTTGAAAAAGTT-TA
*
1112093 GGGTAAAATGGAAATTTTGAAAA
1 GGGTAAAATAGAAATTTTGAAAA
1112116 GTTAAGAAGT
Statistics
Matches: 81, Mismatches: 21, Indels: 19
0.67 0.17 0.16
Matches are distributed among these distances:
28 19 0.23
29 27 0.33
30 22 0.27
31 7 0.09
32 6 0.07
ACGTcount: A:0.41, C:0.01, G:0.26, T:0.31
Consensus pattern (29 bp):
GGGTAAAATAGAAATTTTGAAAAAGTTTA
Found at i:1112103 original size:58 final size:57
Alignment explanation
Indices: 1111858--1112312 Score: 283
Period size: 58 Copynumber: 7.8 Consensus size: 57
1111848 GGATGCCTAG
* * * * * *
1111858 GGGTAAATTAGTAATTTTGAACACTTTGAGGGT-AAAATAGTAATTTTTGGACACTTGGA
1 GGGTAAAATGGTAATTTTGAAAAGTTT-AGGGTAAAAATAG-AATTTTTGGA-AGTTCGA
* * ** * *
1111917 -GG-AAAATTAGTAATTTTGGGAAAGTTCGGGGTCAAAAAT-GTAATTTTT-GAATATTCGG
1 GGGTAAAA-TGGTAATTTT-GAAAAGTTTAGGGT-AAAAATAG-AATTTTTGGAA-GTTCGA
* * * *
1111975 GGGTAAAATGGTAATTTAGAAAAAGTTTGGGGTTAAAAAAAGGAATTTTTGGAAGTT-TA
1 GGGTAAAATGGTAATTTTG-AAAAGTTTAGGG-TAAAAATA-GAATTTTTGGAAGTTCGA
* *
1112034 GGGGTACAATGGTAATTTTGAAAAAGTTTAGGGTAAAAATAGAATTTTTAGAAGTTCGA
1 -GGGTAAAATGGTAATTTTG-AAAAGTTTAGGGTAAAAATAGAATTTTTGGAAGTTCGA
* * * * *
1112093 GGGTAAAATGGAAATTTTGAAAAGTTAAGAAGTCAAAAATGGAATTTTTGGACA--TCTA
1 GGGTAAAATGGTAATTTTGAAAAGTTTAG-GGT-AAAAATAGAATTTTTGGA-AGTTCGA
* * * *
1112151 GGGGTAAATTGGTAATTTTTG-GAAGTTTAGGGTTAAAAATGGAATTTTTGGAAGTTTG-
1 -GGGTAAAATGGTAA-TTTTGAAAAGTTTAGGG-TAAAAATAGAATTTTTGGAAGTTCGA
* * * *
1112209 GTGGTAAAATGGTAATTATTGGAAA-TTTTGAGG-CAAAAT-GTAATTTTTGGAAGTT-TA
1 G-GGTAAAATGGTAATT-TTGAAAAGTTTAG-GGTAAAAATAG-AATTTTTGGAAGTTCGA
* * *
1112266 GGGTAAAAT-GTAATTTTTGAAAGGTTTAGGGTTAAAATATAATTTTT
1 GGGTAAAATGGTAA-TTTTGAAAAGTTTAGGGTAAAAATAGAATTTTT
1112313 AAAAATTCAG
Statistics
Matches: 317, Mismatches: 47, Indels: 67
0.74 0.11 0.16
Matches are distributed among these distances:
55 11 0.03
56 27 0.09
57 37 0.12
58 96 0.30
59 88 0.28
60 54 0.17
61 4 0.01
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.35
Consensus pattern (57 bp):
GGGTAAAATGGTAATTTTGAAAAGTTTAGGGTAAAAATAGAATTTTTGGAAGTTCGA
Found at i:1112181 original size:29 final size:29
Alignment explanation
Indices: 1112018--1112312 Score: 211
Period size: 29 Copynumber: 10.2 Consensus size: 29
1112008 TAAAAAAAGG
*
1112018 AATTTTTGGAAGTTTAGGGGTACAATGGT
1 AATTTTTGGAAGTTTAGGGGTAAAATGGT
* *
1112047 AA-TTTTGAAAAAGTTTA-GGGTAAAAATAG-
1 AATTTTTG--GAAGTTTAGGGGT-AAAATGGT
* *
1112076 AATTTTTAGAAG-TTCGAGGGTAAAATGG-
1 AATTTTTGGAAGTTTAG-GGGTAAAATGGT
* * * **
1112104 AAATTTTGAAAAGTTAAGAAGTCAAAAATGG-
1 AATTTTTG-GAAGTTTAGGGGT--AAAATGGT
* *
1112135 AATTTTTGGACA-TCTAGGGGTAAATTGGT
1 AATTTTTGGA-AGTTTAGGGGTAAAATGGT
*
1112164 AATTTTTGGAAGTTTAGGGTTAAAAATGG-
1 AATTTTTGGAAGTTTAGGGGT-AAAATGGT
1112193 AATTTTTGGAAGTTT-GGTGGTAAAATGGT
1 AATTTTTGGAAGTTTAGG-GGTAAAATGGT
* * * * *
1112222 AATTATTGGAAATTTTGAGGCAAAAT-GT
1 AATTTTTGGAAGTTTAGGGGTAAAATGGT
1112250 AATTTTTGGAAGTTTA-GGGTAAAAT-GT
1 AATTTTTGGAAGTTTAGGGGTAAAATGGT
* * *
1112277 AATTTTTGAAAGGTTTAGGGTTAAAAT-AT
1 AATTTTTGGAA-GTTTAGGGGTAAAATGGT
1112306 AATTTTT
1 AATTTTT
1112313 AAAAATTCAG
Statistics
Matches: 210, Mismatches: 37, Indels: 38
0.74 0.13 0.13
Matches are distributed among these distances:
27 21 0.10
28 56 0.27
29 87 0.41
30 31 0.15
31 15 0.07
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.37
Consensus pattern (29 bp):
AATTTTTGGAAGTTTAGGGGTAAAATGGT
Found at i:1112389 original size:30 final size:29
Alignment explanation
Indices: 1112299--1112394 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 29
1112289 GTTTAGGGTT
* *
1112299 AAAATAT-AATTTTTAAAAATTCAGAAGTA
1 AAAATATAAATTTTGAAAAATTCAG-AGTC
* ** * *
1112328 AAAATATAATTTTTGTGAAGTTCGGAGGTC
1 AAAATATAAATTTTGAAAAATTCAGA-GTC
*
1112358 AAAATATAAATTTTGAAAACTTCAAGAGTC
1 AAAATATAAATTTTGAAAAATTC-AGAGTC
1112388 AAAATAT
1 AAAATAT
1112395 GATTTTTAGA
Statistics
Matches: 52, Mismatches: 12, Indels: 5
0.75 0.17 0.07
Matches are distributed among these distances:
29 8 0.15
30 42 0.81
31 2 0.04
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.33
Consensus pattern (29 bp):
AAAATATAAATTTTGAAAAATTCAGAGTC
Found at i:1113388 original size:17 final size:16
Alignment explanation
Indices: 1113342--1113388 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
1113332 GTTTCCTTTT
1113342 TTTATT-TATTAT-TA
1 TTTATTATATTATATA
1113356 TTTATTAT-TTATTATA
1 TTTATTATATTA-TATA
1113372 TTTATTATATTGATATA
1 TTTATTATATT-ATATA
1113389 AATATATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
14 9 0.32
15 2 0.07
16 10 0.36
17 6 0.21
18 1 0.04
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (16 bp):
TTTATTATATTATATA
Found at i:1114107 original size:18 final size:17
Alignment explanation
Indices: 1114076--1114150 Score: 80
Period size: 18 Copynumber: 4.3 Consensus size: 17
1114066 AACCTTTGAT
*
1114076 TAAATTAAATTTTAAAA
1 TAAATTAAAATTTAAAA
1114093 TAAATTTAAAATTTAAAA
1 TAAA-TTAAAATTTAAAA
* *
1114111 TAAAATT-AAACTCAAAA
1 T-AAATTAAAATTTAAAA
1114128 TAAATTAAAATTTTAAAA
1 TAAATTAAAA-TTTAAAA
*
1114146 AAAAT
1 TAAAT
1114151 CCAAAATTGG
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
16 5 0.10
17 16 0.33
18 24 0.50
19 3 0.06
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAATTAAAATTTAAAA
Found at i:1114281 original size:20 final size:20
Alignment explanation
Indices: 1114244--1114281 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1114234 TCTAGCAATG
*
1114244 AAATTAGTTATAACTTTATT
1 AAATTAGTTATAAATTTATT
1114264 AAATTA-TTAGTAAATTTA
1 AAATTAGTTA-TAAATTTA
1114282 CGTTTTGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (20 bp):
AAATTAGTTATAAATTTATT
Found at i:1114751 original size:22 final size:22
Alignment explanation
Indices: 1114726--1114849 Score: 144
Period size: 22 Copynumber: 5.7 Consensus size: 22
1114716 TATATTATTA
* *
1114726 TTTTGGTGCTGTTTTTTTGCTG
1 TTTTGGTGCTATTTTTTTACTG
1114748 TTTTGGTTGCTA-TTTTTTACTG
1 TTTTGG-TGCTATTTTTTTACTG
* * *
1114770 TTTTGGTGTTGTGTTTTTACTG
1 TTTTGGTGCTATTTTTTTACTG
* *
1114792 TTTTGATG-TTTTTTTTTACTG
1 TTTTGGTGCTATTTTTTTACTG
* *
1114813 TTTTGGTGCTATTTTTTTATTA
1 TTTTGGTGCTATTTTTTTACTG
1114835 TTTTGGTGCTATTTT
1 TTTTGGTGCTATTTT
1114850 ATTGTTATTT
Statistics
Matches: 87, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
21 21 0.24
22 62 0.71
23 4 0.05
ACGTcount: A:0.07, C:0.06, G:0.20, T:0.66
Consensus pattern (22 bp):
TTTTGGTGCTATTTTTTTACTG
Found at i:1114830 original size:43 final size:44
Alignment explanation
Indices: 1114726--1114849 Score: 153
Period size: 43 Copynumber: 2.9 Consensus size: 44
1114716 TATATTATTA
* *
1114726 TTTTGGTGCTGTTTTTTTGCTGTTTTGGTTGCTATTTTTTACTG
1 TTTTGGTGCTGTTTTTTTACTGTTTTGGATGCTATTTTTTACTG
* * * *
1114770 TTTTGGTGTTGTGTTTTTACTGTTTT-GATGTTTTTTTTTACTG
1 TTTTGGTGCTGTTTTTTTACTGTTTTGGATGCTATTTTTTACTG
* * *
1114813 TTTTGGTGCTATTTTTTTATTATTTTGG-TGCTATTTT
1 TTTTGGTGCTGTTTTTTTACTGTTTTGGATGCTATTTT
1114850 ATTGTTATTT
Statistics
Matches: 66, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
43 42 0.64
44 24 0.36
ACGTcount: A:0.07, C:0.06, G:0.20, T:0.66
Consensus pattern (44 bp):
TTTTGGTGCTGTTTTTTTACTGTTTTGGATGCTATTTTTTACTG
Found at i:1114857 original size:22 final size:22
Alignment explanation
Indices: 1114813--1114887 Score: 78
Period size: 22 Copynumber: 3.3 Consensus size: 22
1114803 TTTTTTACTG
* *
1114813 TTTTGGTGCTATTTTTTTATTA
1 TTTTGGTGCTATTTTATTGTTA
1114835 TTTTGGTGCTATTTTATTGTTA
1 TTTTGGTGCTATTTTATTGTTA
* * * *
1114857 TTTTTGTTGTTGTTTTGGTTGTTA
1 -TTTTGGTGCTATTTT-ATTGTTA
1114881 TTTTGGT
1 TTTTGGT
1114888 TGTTTGGATG
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
22 20 0.45
23 18 0.41
24 6 0.14
ACGTcount: A:0.09, C:0.03, G:0.20, T:0.68
Consensus pattern (22 bp):
TTTTGGTGCTATTTTATTGTTA
Found at i:1114866 original size:12 final size:12
Alignment explanation
Indices: 1114832--1114891 Score: 70
Period size: 12 Copynumber: 5.2 Consensus size: 12
1114822 TATTTTTTTA
1114832 TTATTTTGG-TG
1 TTATTTTGGTTG
* *
1114843 CTATTTT-ATTG
1 TTATTTTGGTTG
*
1114854 TTATTTTTGTTG
1 TTATTTTGGTTG
*
1114866 TTGTTTTGGTTG
1 TTATTTTGGTTG
1114878 TTATTTTGGTTG
1 TTATTTTGGTTG
1114890 TT
1 TT
1114892 TGGATGTTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
11 14 0.35
12 26 0.65
ACGTcount: A:0.08, C:0.02, G:0.22, T:0.68
Consensus pattern (12 bp):
TTATTTTGGTTG
Found at i:1114883 original size:24 final size:21
Alignment explanation
Indices: 1114851--1114905 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 21
1114841 TGCTATTTTA
1114851 TTGTTATTTTTGTTGTTGTTTTGG
1 TTGTTATTTTTG--GTTG-TTTGG
1114875 TTGTTA-TTTTGGTTGTTTGG
1 TTGTTATTTTTGGTTGTTTGG
*
1114895 ATGTTATTTTT
1 TTGTTATTTTT
1114906 ATTCGTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 10 0.34
21 8 0.28
23 5 0.17
24 6 0.21
ACGTcount: A:0.07, C:0.00, G:0.24, T:0.69
Consensus pattern (21 bp):
TTGTTATTTTTGGTTGTTTGG
Found at i:1116285 original size:29 final size:30
Alignment explanation
Indices: 1116225--1116302 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 30
1116215 GTATATTTGG
* *
1116225 AATTCAATCATTATATTTTT-ATTTTAAGA
1 AATTCAATCTTTATATTTTTAAATTTAAGA
* *
1116254 AATTTAATCTTTATATTTTTAAATTTCA-A
1 AATTCAATCTTTATATTTTTAAATTTAAGA
*
1116283 AATTCAA-GTTTA-ATTTTTAA
1 AATTCAATCTTTATATTTTTAA
1116303 TACTGTTTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
27 8 0.19
28 4 0.10
29 25 0.60
30 5 0.12
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (30 bp):
AATTCAATCTTTATATTTTTAAATTTAAGA
Found at i:1126744 original size:155 final size:155
Alignment explanation
Indices: 1126462--1126751 Score: 426
Period size: 155 Copynumber: 1.9 Consensus size: 155
1126452 TTTTAGCCAT
* * * **
1126462 CTTTAGACAACATAATTCAAGTGATCGTTACATACGAATGTGTCAACAACTTAGTATTACGGAAC
1 CTTTAGACAACACAATTCAAGTGATCATTACATACGAATCTGTCAACAACTTAGTATTACAAAAC
* *
1126527 TGACATGGTTGCTTTCTTTTAATAAGGATGTTTATTTTGGGTGGTATACATATTATACCTTGTTT
66 TGACATGGTTGCTTTCTTTTAATAAGGATGTTTATTTTAGGTGGTATACATATTATAACTTGTTT
1126592 AAAGGTGAATTTGATTGATGTTCAC
131 AAAGGTGAATTTGATTGATGTTCAC
*
1126617 CTTTAGACAACACAATTCAAGTGATCATTACATACGAATCTGCTC-ACAACTTTGTATTACAAAA
1 CTTTAGACAACACAATTCAAGTGATCATTACATACGAATCTG-TCAACAACTTAGTATTACAAAA
* *
1126681 CTGACATTGTTGCTTT-TTCTTAATAATGATGATGTTATTTTAGGT-GT-TACATATTATAACTT
65 CTGACATGGTTGCTTTCTT-TTAATAAGGATG-T-TTATTTTAGGTGGTATACATATTATAACTT
1126743 GTTTAAAGG
127 GTTTAAAGG
1126752 AAGGTGGTAA
Statistics
Matches: 121, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
154 2 0.02
155 104 0.86
156 5 0.04
157 10 0.08
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (155 bp):
CTTTAGACAACACAATTCAAGTGATCATTACATACGAATCTGTCAACAACTTAGTATTACAAAAC
TGACATGGTTGCTTTCTTTTAATAAGGATGTTTATTTTAGGTGGTATACATATTATAACTTGTTT
AAAGGTGAATTTGATTGATGTTCAC
Found at i:1128843 original size:23 final size:23
Alignment explanation
Indices: 1128817--1128860 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1128807 TAAAATTAAA
1128817 TTTTAATT-TTTATAATTTTAATT
1 TTTTAATTATTTA-AATTTTAATT
*
1128840 TTTTATTTATTTAAATTTTAA
1 TTTTAATTATTTAAATTTTAA
1128861 AATTTAGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (23 bp):
TTTTAATTATTTAAATTTTAATT
Found at i:1129657 original size:2 final size:2
Alignment explanation
Indices: 1129650--1129690 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1129640 TACACTCTTT
1129650 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1129691 TTTCTGCAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1129794 original size:12 final size:12
Alignment explanation
Indices: 1129777--1129816 Score: 71
Period size: 12 Copynumber: 3.3 Consensus size: 12
1129767 GAAAGTTCTA
1129777 CTTCAGTTTCAG
1 CTTCAGTTTCAG
1129789 CTTCAGTTTCAG
1 CTTCAGTTTCAG
*
1129801 CTTCAGTTTCAA
1 CTTCAGTTTCAG
1129813 CTTC
1 CTTC
1129817 TTTAACAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.17, C:0.28, G:0.12, T:0.42
Consensus pattern (12 bp):
CTTCAGTTTCAG
Found at i:1134378 original size:18 final size:19
Alignment explanation
Indices: 1134330--1134378 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
1134320 AAAATAATTT
*
1134330 AATAAATACAATAAATATG
1 AATAAATACAATAAAGATG
1134349 AA-AAATACAATACAAGA-G
1 AATAAATACAATA-AAGATG
1134367 AATAAATA-AATA
1 AATAAATACAATA
1134379 TGCCAAGACA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 17 0.63
19 10 0.37
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.20
Consensus pattern (19 bp):
AATAAATACAATAAAGATG
Found at i:1134603 original size:16 final size:16
Alignment explanation
Indices: 1134582--1134613 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1134572 CACAAAAAAA
1134582 CAATTAAAATATGATC
1 CAATTAAAATATGATC
1134598 CAATTAAAATATGATC
1 CAATTAAAATATGATC
1134614 TAAGAAGGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.31
Consensus pattern (16 bp):
CAATTAAAATATGATC
Found at i:1139376 original size:6 final size:6
Alignment explanation
Indices: 1139365--1139403 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
1139355 CTAAAAGTAC
1139365 ACCAAT ACCAAT ACCAAT ACCAAT ACCAAT ACCAAT ACC
1 ACCAAT ACCAAT ACCAAT ACCAAT ACCAAT ACCAAT ACC
1139404 GCATCCATTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.49, C:0.36, G:0.00, T:0.15
Consensus pattern (6 bp):
ACCAAT
Found at i:1145403 original size:14 final size:14
Alignment explanation
Indices: 1145380--1145411 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1145370 AAGATATTTA
1145380 ATATAATTTTAAAT
1 ATATAATTTTAAAT
*
1145394 ATATATTTTTAAAT
1 ATATAATTTTAAAT
1145408 ATAT
1 ATAT
1145412 GCCTAAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATATAATTTTAAAT
Found at i:1145503 original size:54 final size:54
Alignment explanation
Indices: 1145439--1145547 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
1145429 TATATTTAGA
1145439 TATTCTTACAAGATAATATTCCATAATAATATTTTAATAGAAACTCGTGATTGT
1 TATTCTTACAAGATAATATTCCATAATAATATTTTAATAGAAACTCGTGATTGT
1145493 TATTCTTACAAGATAATATTCCATAATAATATTTTAATAGAAACTCGTGATTGT
1 TATTCTTACAAGATAATATTCCATAATAATATTTTAATAGAAACTCGTGATTGT
1145547 T
1 T
1145548 GACTCCATTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (54 bp):
TATTCTTACAAGATAATATTCCATAATAATATTTTAATAGAAACTCGTGATTGT
Found at i:1163666 original size:31 final size:32
Alignment explanation
Indices: 1163629--1163688 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
1163619 GATCAAGGAT
1163629 AAAATATGAGA-AAATTATTATTTTTAAAGAG
1 AAAATATGAGATAAATTATTATTTTTAAAGAG
* *
1163660 AAAATATGAGATAATTTATTGTTTTTAAA
1 AAAATATGAGATAAATTATTATTTTTAAA
1163689 AAACAAAATA
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:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (32 bp):
AAAATATGAGATAAATTATTATTTTTAAAGAG
Found at i:1172494 original size:34 final size:38
Alignment explanation
Indices: 1172456--1172530 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 38
1172446 TAATTTTGAA
*
1172456 TTTAAAATTTTTTGGA-TTTTTT-AAAT-AT-AAAAAT
1 TTTAAAAGTTTTTGGATTTTTTTGAAATAATAAAAAAT
1172490 TTTAAAAGTTTTTGGATTTTTTTGAAATAATAAAAAAT
1 TTTAAAAGTTTTTGGATTTTTTTGAAATAATAAAAAAT
1172528 TTT
1 TTT
1172531 GGGATTTGGA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
34 15 0.42
35 6 0.17
36 4 0.11
37 2 0.06
38 9 0.25
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (38 bp):
TTTAAAAGTTTTTGGATTTTTTTGAAATAATAAAAAAT
Found at i:1189348 original size:8 final size:8
Alignment explanation
Indices: 1189335--1189368 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
1189325 TAATTAAATT
1189335 TTAAAAAA
1 TTAAAAAA
1189343 TTAAAAAA
1 TTAAAAAA
*
1189351 TGAACAAAA
1 TTAA-AAAA
1189360 TTAAAAAA
1 TTAAAAAA
1189368 T
1 T
1189369 CGACTAATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (8 bp):
TTAAAAAA
Done.