Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003208.1 Hibiscus syriacus cultivar Beakdansim tig00006753_pilon, 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: 1278004
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 7
Found at i:925749 original size:29 final size:29
Alignment explanation
Indices: 925707--925778 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
925697 TTTTCTGCAT
**
925707 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
925736 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
925765 ATTCATGTCATGTA
1 ATTCATGTCATGTA
925779 TCATAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:926197 original size:68 final size:67
Alignment explanation
Indices: 926081--926233 Score: 218
Period size: 68 Copynumber: 2.3 Consensus size: 67
926071 TTTTTCTCAT
* * *
926081 GGGGGAATCGGTTCCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACG
1 GGGGGTATCGGTT-CCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCAT-TACG
926146 ATGA
64 ATGA
* *
926150 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAA-CAATCTGGAAATTCATTTCGT
1 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTC-AAGCAATCTGGAAATTCATTACGA
926214 TGA
65 TGA
*
926217 AGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
926234 TTGAATGGGT
Statistics
Matches: 77, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
67 22 0.29
68 41 0.53
69 14 0.18
ACGTcount: A:0.19, C:0.28, G:0.27, T:0.26
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATTACGAT
GA
Found at i:926243 original size:21 final size:21
Alignment explanation
Indices: 926213--926255 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
926203 ATTCATTTCG
* *
926213 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
926234 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
926255 T
1 T
926256 AATCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:926254 original size:67 final size:67
Alignment explanation
Indices: 926082--926255 Score: 201
Period size: 68 Copynumber: 2.6 Consensus size: 67
926072 TTTTCTCATG
* * *
926082 GGGGAATCGGTTCCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGA
1 GGGGTATCGGTT--CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
*
926147 TGAG
64 TGAA
* *
926151 GGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAA-CAATCTGGAAATTCAT-TTCGT
1 GGGGTATCGGTT-CCCCCCTGGGGGTACCGATTCCCCTC-AAGCAATCTGGAAATTCATATACGA
926214 TGAA
64 TGAA
* *
926218 GGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGTATCGGTTCCCCCCTG--GGGGTACCGATTCCCCT
926256 AATCCAGAAA
Statistics
Matches: 94, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
65 6 0.06
67 34 0.36
68 41 0.44
69 13 0.14
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.27
Consensus pattern (67 bp):
GGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATG
AA
Found at i:932321 original size:22 final size:22
Alignment explanation
Indices: 932296--932363 Score: 136
Period size: 22 Copynumber: 3.1 Consensus size: 22
932286 GCTCGTATAA
932296 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
932318 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
932340 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
932362 TG
1 TG
932364 TCCATAAGGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:932621 original size:30 final size:31
Alignment explanation
Indices: 932580--932639 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
932570 TAGCCATAGT
*
932580 ATTTTCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
932610 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
932640 AACTTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:932696 original size:29 final size:29
Alignment explanation
Indices: 932654--932725 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
932644 TTTTCTGCAT
**
932654 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
932683 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
932712 ATTCATGTCATGTA
1 ATTCATGTCATGTA
932726 TCATAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:933140 original size:67 final size:66
Alignment explanation
Indices: 933028--933200 Score: 213
Period size: 67 Copynumber: 2.6 Consensus size: 66
933018 TTTTTCTCAT
* * *
933028 GGGGGAATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGA
1 GGGGGTATCGGTT-CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCAT-TACGA
933093 TGA
64 TGA
* * *
933096 GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCTAGCAATCTGGAAATTCATTTCGTTG
1 GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATTACGATG
933161 A
66 A
* * * *
933162 AGGGGTATCGATT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGGTATCGGTTCCCCCCTG--GGGGTACCGATTCCCCT
933201 AATCCAGAAA
Statistics
Matches: 93, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
65 6 0.06
66 17 0.18
67 58 0.62
68 12 0.13
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (66 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATTACGATG
A
Found at i:933182 original size:21 final size:21
Alignment explanation
Indices: 933158--933200 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
933148 ATTCATTTCG
*
933158 TTGAAGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
933179 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
933200 T
1 T
933201 AATCCAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:937996 original size:20 final size:20
Alignment explanation
Indices: 937940--938000 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
937930 TTTGTTTAAG
* * *
937940 TTGTTTAGTTT-GTTTTGTT
1 TTGTTTTGTTTAGCTTTGAT
*
937959 TTGTTTTGTTTTGCTTTGAT
1 TTGTTTTGTTTAGCTTTGAT
937979 TTGTTTTGATTTAG-TTTGAT
1 TTGTTTTG-TTTAGCTTTGAT
937999 TT
1 TT
938001 TATTTGATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
19 10 0.28
20 22 0.61
21 4 0.11
ACGTcount: A:0.08, C:0.02, G:0.20, T:0.70
Consensus pattern (20 bp):
TTGTTTTGTTTAGCTTTGAT
Found at i:938037 original size:5 final size:5
Alignment explanation
Indices: 937948--938035 Score: 61
Period size: 5 Copynumber: 17.6 Consensus size: 5
937938 AGTTGTTTAG
* * * * * *
937948 TTTGT TTTGT TTTGT TTTGT TTTGC TTTGA TTTGT TTTGA TTT-A GTTTGA
1 TTTGA TTTGA TTTGA TTTGA TTTGA TTTGA TTTGA TTTGA TTTGA -TTTGA
* * * * *
937998 TTTTA TTTGA TGTGA TTTCA TTTCA TTTGA TTTTA TTT
1 TTTGA TTTGA TTTGA TTTGA TTTGA TTTGA TTTGA TTT
938036 TAATAAAATC
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
4 1 0.01
5 68 0.97
6 1 0.01
ACGTcount: A:0.12, C:0.03, G:0.16, T:0.68
Consensus pattern (5 bp):
TTTGA
Found at i:938876 original size:18 final size:18
Alignment explanation
Indices: 938843--938893 Score: 77
Period size: 18 Copynumber: 2.8 Consensus size: 18
938833 ACTGAATATT
*
938843 TGTACCGAATGACCACTA
1 TGTACCGAAGGACCACTA
938861 TGT-CCTGAAGGACCACTA
1 TGTACC-GAAGGACCACTA
938879 TGTACCGAAGGACCA
1 TGTACCGAAGGACCA
938894 ATGATAATAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 2 0.07
18 26 0.87
19 2 0.07
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.20
Consensus pattern (18 bp):
TGTACCGAAGGACCACTA
Found at i:939603 original size:64 final size:63
Alignment explanation
Indices: 939491--939610 Score: 150
Period size: 64 Copynumber: 1.9 Consensus size: 63
939481 CCCTTAACAT
* *
939491 GTGTATCGATGCACTACCTATGCATCGGTACACAAATTACATTCGATGTTTTCATTTTAAGGGG
1 GTGTATCGATACACTACCTATGCATCGATACACAAATTACATTCGATGTTTT-ATTTTAAGGGG
* * * ** * *
939555 GTGTATCGATACACTCCCTATGTATCGATGCACTTATTGCATTTGATGTTTTATTT
1 GTGTATCGATACACTACCTATGCATCGATACACAAATTACATTCGATGTTTTATTT
939611 CATTTGAGAG
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
63 4 0.09
64 43 0.91
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (63 bp):
GTGTATCGATACACTACCTATGCATCGATACACAAATTACATTCGATGTTTTATTTTAAGGGG
Found at i:943816 original size:31 final size:32
Alignment explanation
Indices: 943775--943839 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 32
943765 AAAACATAAC
*
943775 ATATGGTCACTTTCG-GTTTTATTTAATTAAG
1 ATATGATCACTTTCGTGTTTTATTTAATTAAG
* * *
943806 ATATGATCACTTTTGTTTTTTCTTTAATTAAG
1 ATATGATCACTTTCGTGTTTTATTTAATTAAG
943838 AT
1 AT
943840 GTAGTCACCA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 13 0.45
32 16 0.55
ACGTcount: A:0.26, C:0.09, G:0.12, T:0.52
Consensus pattern (32 bp):
ATATGATCACTTTCGTGTTTTATTTAATTAAG
Found at i:944102 original size:29 final size:28
Alignment explanation
Indices: 944012--944104 Score: 98
Period size: 29 Copynumber: 3.2 Consensus size: 28
944002 TGGCAAAATC
944012 TATATATATTAACTTTAAAAAATATTTT
1 TATATATATTAACTTTAAAAAATATTTT
** * *
944040 TATATAAATACTTAAC-TTAAATTTATAATAT
1 TATAT--ATA-TTAACTTTAAA-AAATATTTT
944071 TATATATTATTAACTTTAAAAAATATTTT
1 TATATA-TATTAACTTTAAAAAATATTTT
944100 TATAT
1 TATAT
944105 TAACTTATTA
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
28 5 0.10
29 16 0.31
30 15 0.29
31 15 0.29
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.49
Consensus pattern (28 bp):
TATATATATTAACTTTAAAAAATATTTT
Found at i:944121 original size:27 final size:25
Alignment explanation
Indices: 944081--944206 Score: 82
Period size: 26 Copynumber: 4.8 Consensus size: 25
944071 TATATATTAT
944081 TAAC-TTTAAAAAATATTTTTATAT
1 TAACTTTTAAAAAATATTTTTATAT
*
944105 TAACTTATTAAATAA-A-TTTTATTAT
1 TAACTT-TTAAAAAATATTTTTA-TAT
* *
944130 TAACTTAATTTAAAAA-ATTTTTATTT
1 TAACTT--TTAAAAAATATTTTTATAT
*
944156 TTA-TTTTAAAAAAATATTTTATTATTAT
1 TAACTTTT-AAAAAATA-TTT-TTA-TAT
944184 CTAAACTTTTAAAAACATATTTT
1 -T-AACTTTTAAAAA-ATATTTT
944207 ATTATTATGA
Statistics
Matches: 80, Mismatches: 8, Indels: 23
0.72 0.07 0.21
Matches are distributed among these distances:
23 2 0.03
24 14 0.17
25 14 0.17
26 22 0.28
27 8 0.10
28 2 0.03
29 2 0.03
30 9 0.11
31 7 0.09
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.52
Consensus pattern (25 bp):
TAACTTTTAAAAAATATTTTTATAT
Found at i:944121 original size:60 final size:58
Alignment explanation
Indices: 944012--944131 Score: 163
Period size: 60 Copynumber: 2.0 Consensus size: 58
944002 TGGCAAAATC
*
944012 TATATATATTAACTTTAAAAAATATTTTTATATAAATACTTAACTTAAATTTATAATAT
1 TATATATATTAACTTTAAAAAATATTTTTATATAAATACTTAACATAAATTT-TAATAT
* *
944071 TATATATTATTAACTTTAAAAAATATTTTTATATTAACTTA-TTAA-ATAAATTTTATTAT
1 TATATA-TATTAACTTTAAAAAATATTTTTATA-TAA-ATACTTAACATAAATTTTAATAT
944130 TA
1 TA
944132 ACTTAATTTA
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
59 13 0.24
60 33 0.60
61 7 0.13
62 2 0.04
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (58 bp):
TATATATATTAACTTTAAAAAATATTTTTATATAAATACTTAACATAAATTTTAATAT
Found at i:944130 original size:25 final size:24
Alignment explanation
Indices: 944075--944182 Score: 87
Period size: 24 Copynumber: 4.3 Consensus size: 24
944065 TAATATTATA
944075 TATTATTAAC-T-TTAAAAAATATT
1 TATTATTAACTTATTAAAAAAT-TT
*
944098 TTTATATTAACTTATTAAATAAATTT
1 TAT-TATTAACTTATTAAA-AAATTT
944124 TATTATTAACTTAATTTAAAAAATTTT
1 TATTATTAACTT-A-TTAAAAAA-TTT
* ** *
944151 TATTTTTATTTTA-AAAAAATATTT
1 TATTATTAACTTATTAAAAA-ATTT
944175 TATTATTA
1 TATTATTA
944183 TCTAAACTTT
Statistics
Matches: 70, Mismatches: 7, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
23 2 0.03
24 22 0.31
25 11 0.16
26 14 0.20
27 21 0.30
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (24 bp):
TATTATTAACTTATTAAAAAATTT
Found at i:944180 original size:21 final size:22
Alignment explanation
Indices: 944124--944181 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
944114 AAATAAATTT
* *
944124 TATTATTAACTTAATTTAAAAAAT
1 TATTATT-A-TTATTTTAAAAAAA
* *
944148 TTTTATTTTTATTTTAAAAAAA
1 TATTATTATTATTTTAAAAAAA
944170 TATT-TTATTATT
1 TATTATTATTATT
944182 ATCTAAACTT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 7 0.25
22 15 0.54
24 6 0.21
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TATTATTATTATTTTAAAAAAA
Found at i:944188 original size:23 final size:23
Alignment explanation
Indices: 944141--944188 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
944131 AACTTAATTT
* *
944141 AAAAAATTTTTATTTTTATTTTA
1 AAAAAATTTTTATTATTATTCTA
944164 AAAAAATATTTTATTATTA-TCTA
1 AAAAAAT-TTTTATTATTATTCTA
944187 AA
1 AA
944189 CTTTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
AAAAAATTTTTATTATTATTCTA
Found at i:968104 original size:21 final size:21
Alignment explanation
Indices: 968080--968125 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
968070 CAGCCGACCC
968080 AGGTGGCAGATGTTCCCTCTT
1 AGGTGGCAGATGTTCCCTCTT
*
968101 AGGTGTCAGATGTTCCCTCTT
1 AGGTGGCAGATGTTCCCTCTT
968122 AGGT
1 AGGT
968126 ATCTTGCAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.15, C:0.22, G:0.28, T:0.35
Consensus pattern (21 bp):
AGGTGGCAGATGTTCCCTCTT
Found at i:969678 original size:10 final size:10
Alignment explanation
Indices: 969663--969694 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
969653 GAATCAAAAT
969663 AAAATTATTA
1 AAAATTATTA
969673 AAAATTATTA
1 AAAATTATTA
969683 AAAATTATTA
1 AAAATTATTA
969693 AA
1 AA
969695 TAGTAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
AAAATTATTA
Found at i:969712 original size:11 final size:11
Alignment explanation
Indices: 969663--969714 Score: 54
Period size: 10 Copynumber: 4.9 Consensus size: 11
969653 GAATCAAAAT
969663 AAAATTATT-A
1 AAAATTATTAA
969673 AAAATTATT-A
1 AAAATTATTAA
969683 AAAATTATTAA
1 AAAATTATTAA
* * *
969694 ATAGTAATTAA
1 AAAATTATTAA
*
969705 AAAATAATTA
1 AAAATTATTA
969715 TTAGATAGCT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
10 19 0.53
11 17 0.47
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (11 bp):
AAAATTATTAA
Found at i:969740 original size:27 final size:25
Alignment explanation
Indices: 969685--969746 Score: 70
Period size: 27 Copynumber: 2.4 Consensus size: 25
969675 AATTATTAAA
*
969685 AATTATTAAATAGTAATTAAAAAAT
1 AATTATTAAATAGTAATTAAAAAAC
* **
969710 AATTATTAGATAGCTAAATTAAACTAC
1 AATTATTAAATAG-T-AATTAAAAAAC
969737 AATTATTAAA
1 AATTATTAAA
969747 AAAGTTATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 12 0.40
26 1 0.03
27 17 0.57
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (25 bp):
AATTATTAAATAGTAATTAAAAAAC
Found at i:982349 original size:226 final size:224
Alignment explanation
Indices: 982001--982606 Score: 853
Period size: 226 Copynumber: 2.7 Consensus size: 224
981991 ACCTAATCAA
* * *
982001 TTAATTACTGGAAACATTAT-AATCATAATAACATAACAAGT-ACACTTATATAACGTAATATGT
1 TTAATTACTGGAAACATTATCAACCATAATAACATAACAAGTAACACTTATTTAATGTAATA-GT
* * * * * *
982064 AGTGTCTTTTTAAAG-ATGATGAGACCTTA-AAATTCGACGATAACAAAATAAGTTAATTACTTG
65 AGCGT-TGTTTAAAGCA-GATGGGGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTG
*
982127 ATTTGTTATCAATATTATCAACATATTAGGTAGCGCCTAAAATATTACTAAAGTTTAAGCTGACA
128 ATTTGTTATCAATATTATCAACATATTAGGTAGCGCCTAAAATATTACCAAAGTTTAAGCTGACA
* *
982192 GAGCCTTAGAAATCCGACTATAACAAAATAGG
193 GAGCCTTAGAAATCCGACGATAACAAAATAAG
* * *
982224 TTAATTACTGAAAATATTATCAACCATAGTAACATAACAAGTAACACTTATTTAATGTAATAGAT
1 TTAATTACTGGAAACATTATCAACCATAATAACATAACAAGTAACACTTATTTAATGTAATAG-T
* ** *
982289 AGCGTATGTTTGAAGCAGATGGGGTTTTAGAAATCCGATGATAACAAAATAGGTTAATTACTTGA
65 AGCGT-TGTTTAAAGCAGATGGGGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTGA
* * * **
982354 TTTGTTATCAATATTATCAACGTATTAGGTAGTGCCTAAAATGTTACCAAAGTTTAAGCTGATGG
129 TTTGTTATCAATATTATCAACATATTAGGTAGCGCCTAAAATATTACCAAAGTTTAAGCTGACAG
982419 AGCCTTAGAAATCCGACGATAACAAAATAAG
194 AGCCTTAGAAATCCGACGATAACAAAATAAG
*
982450 TTAATTACTGGAAACATTATCAACCATAATAACATAACAAGTAGA-GCTTATTTAATGTAATAGG
1 TTAATTACTGGAAACATTATCAACCATAATAACATAACAAGTA-ACACTTATTTAATGTAATA-G
* * *
982514 TAGCACTTGTTTAAAGCCGATGGGGCCTTAGAAATCCGACGATAACAAAATAGATTAATTACTTG
64 TAGC-GTTGTTTAAAGCAGATGGGGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTG
982579 ATTTGTTATCAATATTATCAACATATTA
128 ATTTGTTATCAATATTATCAACATATTA
982607 TCGTGTACAT
Statistics
Matches: 338, Mismatches: 37, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
223 18 0.05
224 20 0.06
225 37 0.11
226 260 0.77
227 3 0.01
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (224 bp):
TTAATTACTGGAAACATTATCAACCATAATAACATAACAAGTAACACTTATTTAATGTAATAGTA
GCGTTGTTTAAAGCAGATGGGGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTGATT
TGTTATCAATATTATCAACATATTAGGTAGCGCCTAAAATATTACCAAAGTTTAAGCTGACAGAG
CCTTAGAAATCCGACGATAACAAAATAAG
Found at i:982934 original size:136 final size:130
Alignment explanation
Indices: 982604--982959 Score: 418
Period size: 130 Copynumber: 2.7 Consensus size: 130
982594 TATCAACATA
*
982604 TTATCGTGTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGAATCG
1 TTATCGTGTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCG
* *
982669 ATACTTATATGACA---GTATCGATACTTGTACATTTACGCCTATTTTCATTATACCGGTAGAAA
66 ATACTT-TAT-ACATGTGTATCGATACTTGTACATTTACGCCTATTATCATTATACCAGTAG-AA
982731 CGT
128 CGT
* ** *
982734 TTATCGTGTACATTGTTAATTTACCTATTACTTTAAAGCAATAGGTTTCGAAATTGCACGTATCG
1 TTATCGTGTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCG
** *
982799 ATACTTTATACATGTGTATCGATACTTG-ATGTTTACGCCTATTATCATTATACCAGTAG-ACTT
66 ATACTTTATACATGTGTATCGATACTTGTACATTTACGCCTATTATCATTATACCAGTAGAACGT
* * * *
982862 TTA-CTGTTTTCATTGTAAATTAACCTATTACTCTATTACTTTATAGTAATAGGTTTTGAAATTA
1 TTATC-GTGTACATTG----TTAA--T-TTAC-CTATTACTTTAAAGTAATAGGTTTCGAAATTA
* *
982926 TAAGTATCGATATTTTATATATGTGTATCGATAC
57 TAAGTATCGATACTTTATACATGTGTATCGATAC
982960 ATTTTGCGCA
Statistics
Matches: 194, Mismatches: 20, Indels: 18
0.84 0.09 0.08
Matches are distributed among these distances:
127 1 0.01
128 17 0.09
129 3 0.02
130 93 0.48
131 13 0.07
132 4 0.02
134 1 0.01
135 4 0.02
136 58 0.30
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (130 bp):
TTATCGTGTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCG
ATACTTTATACATGTGTATCGATACTTGTACATTTACGCCTATTATCATTATACCAGTAGAACGT
Found at i:983281 original size:178 final size:176
Alignment explanation
Indices: 982947--983317 Score: 487
Period size: 178 Copynumber: 2.1 Consensus size: 176
982937 ATTTTATATA
*
982947 TGTGTATCGATACATTTTGCGCAAATTGTTTGAGAAGCATATTAGAATAAAAATATCGATACATA
1 TGTGTATCGATAC-TTTTGCGCAAATTGTTTGAGAAGCATACTAGAATAAAAATATCGATACATA
* * * * *
983012 TATAGACATTATCGATACTTGATATTTACGCCTATTATCAATATACCAGTAGACTTTTACCATTT
65 TACAAAAAGTATCGATACTTGATATTTACGCCTATTATCAATAAACCAGTAGACTTTTACCATTT
*
983077 ACATTGTAAATTTACCTATAACTTTAAAGTAATCGGTTTCGAAATTC
130 ACATTGTAAATTTACCTATAACTTTAAAGTAATCGGTTTCGAAAGTC
* * * * *
983124 TGTGTATCGATACTTTGTGCGTGCAAGTTG-TTGAGAAGCATACTAGACTAAAAGTATCTATACC
1 TGTGTATCGATACTTT-TGC--GCAAATTGTTTGAGAAGCATACTAGAATAAAAATATCGATACA
* * *
983188 TATACAAAAAGTATCGATA-TATGATGTTTACGCCTATTATCATTAAACC-GATAGATTTTTACC
63 TATACAAAAAGTATCGATACT-TGATATTTACGCCTATTATCAATAAACCAG-TAGACTTTTACC
* * *
983251 TTTTACATTGTAAATTTACCTATTACTTTAAAGTAATCGGTTTTGAAAGTC
126 ATTTACATTGTAAATTTACCTATAACTTTAAAGTAATCGGTTTCGAAAGTC
**
983302 TAAGTATCGATACTTT
1 TGTGTATCGATACTTT
983318 ATACAGTAAT
Statistics
Matches: 169, Mismatches: 20, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
176 3 0.02
177 18 0.11
178 141 0.83
179 7 0.04
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.38
Consensus pattern (176 bp):
TGTGTATCGATACTTTTGCGCAAATTGTTTGAGAAGCATACTAGAATAAAAATATCGATACATAT
ACAAAAAGTATCGATACTTGATATTTACGCCTATTATCAATAAACCAGTAGACTTTTACCATTTA
CATTGTAAATTTACCTATAACTTTAAAGTAATCGGTTTCGAAAGTC
Found at i:983608 original size:198 final size:199
Alignment explanation
Indices: 983343--983700 Score: 485
Period size: 198 Copynumber: 1.8 Consensus size: 199
983333 TCATTCTCAG
* * * *
983343 CTTTATATATGTGTATCTATACATTTTGCGTGCAAATTTTTTGAGAAGCATACTGGAATAAAAGT
1 CTTTATACATGTGTAACGATACATTTTGCGTGCAAATTTGTTGAGAAGCATACTGGAATAAAAGT
* * * *
983408 ATCGATACCTATATAGACAA-TATCGATACTTGGTATTTACACCTATGATCAATATACC-AGTAG
66 ATCGATACCTATACA-AAAAGTATCGATACTTGATATTTACACCTATGATCAATAGACCGA-TAG
*
983471 ACTTTTA-TCGTTTACATTATAAAGTTACCTATAACTTTAAAGTAATCGTTTCAAAATTCCGCGT
129 ACTTTTACT-ATTTACATTATAAAGTTACCTATAACTTTAAAGTAATCGTTTCAAAATTCCGCGT
983535 ATCGATA
193 ATCGATA
983542 CTTTATACATGTGTAACGATAC-TTTGTGCGTGCAAA-TTGTTGAGAAGCATACTGGACA-AAAA
1 CTTTATACATGTGTAACGATACATTT-TGCGTGCAAATTTGTTGAGAAGCATACTGGA-ATAAAA
* * * *
983604 GTATCGATACCTATACAAAAAGTATCGATACTTGATGTTTACGCCTATTATCATTAGACCGATAG
64 GTATCGATACCTATACAAAAAGTATCGATACTTGATATTTACACCTATGATCAATAGACCGATAG
* * *
983669 ATTTTTACTATTTACATTGTAAATTTACCTAT
129 ACTTTTACTATTTACATTATAAAGTTACCTAT
983701 TATCAGAATG
Statistics
Matches: 138, Mismatches: 16, Indels: 11
0.84 0.10 0.07
Matches are distributed among these distances:
197 3 0.02
198 103 0.75
199 32 0.23
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.37
Consensus pattern (199 bp):
CTTTATACATGTGTAACGATACATTTTGCGTGCAAATTTGTTGAGAAGCATACTGGAATAAAAGT
ATCGATACCTATACAAAAAGTATCGATACTTGATATTTACACCTATGATCAATAGACCGATAGAC
TTTTACTATTTACATTATAAAGTTACCTATAACTTTAAAGTAATCGTTTCAAAATTCCGCGTATC
GATA
Found at i:985571 original size:18 final size:18
Alignment explanation
Indices: 985550--985589 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
985540 TGATTTGATT
985550 AGAAGCCCTTACTTGAGA
1 AGAAGCCCTTACTTGAGA
* **
985568 AGAAGTCCTTGGTTGAGA
1 AGAAGCCCTTACTTGAGA
985586 AGAA
1 AGAA
985590 CCGTGTCTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.23
Consensus pattern (18 bp):
AGAAGCCCTTACTTGAGA
Found at i:986465 original size:201 final size:200
Alignment explanation
Indices: 986112--987506 Score: 1688
Period size: 201 Copynumber: 6.9 Consensus size: 200
986102 GTATCGATAC
* * *
986112 TACGCCTATTATCATTAAATCTG-TAGATTTTTACCGTTTACATTGTAAATTTACCTATTGCTCT
1 TACGCCTATTATCATTAAA-CCGATAGATTTTTACCGTTTACATTGTAAATTTACCTATTACTTT
* *
986176 AAAGAAATAGGTTTCAAAATTATAAGTATCGATACTTGTTACACATGTATCGATATTTTTTTGCG
65 AAAGAAATAGGTTTCAAAATTATAAGTATCGATACTTGTTATACATGTATCGATACTTTTTTGCG
* * * * * *
986241 TGTAAATTGTTTGAGAAGCATATTAGAATAAACGTAACGATACTTATATAATAAGTATCACTACT
130 TGCAAATTGTTTGAGATGCATACTGGAATAAAAGTATCGATACTTATATAATAAGTATCA-TACT
986306 TTATGTT
194 TTATGTT
*
986313 TACACCTATTATCATTAAACCGATAGATTTTTACCGTTTACATTGTAAATTTACCTATTACTTTA
1 TACGCCTATTATCATTAAACCGATAGATTTTTACCGTTTACATTGTAAATTTACCTATTACTTTA
* * *
986378 AAGAAATAGGTTTCAAAATTATAAGTATCGATACTTGTTAAACGTGTGTCGATACTTTTTTGCGT
66 AAGAAATAGGTTTCAAAATTATAAGTATCGATACTTGTTATACATGTATCGATACTTTTTTGCGT
* ** *
986443 GCAAATTGTTTGAGATGCATATTGGAATAAAAGTATCGATACTTATATAATAAACATCGAAACTT
131 GCAAATTGTTTGAGATGCATACTGGAATAAAAGTATCGATACTTATATAATAAGTATC-ATACTT
986508 TATGTT
195 TATGTT
* * * * *
986514 TATGCCTATTATCATTAAACTGGTAGAGTTTTACTGTTTACATTGTAAATTTACCTATTACTTTA
1 TACGCCTATTATCATTAAACCGATAGATTTTTACCGTTTACATTGTAAATTTACCTATTACTTTA
* * *
986579 AAGAAATAGGTTTCAAAATTATAAGTATTGATACTTGTTATAAATGTATCGATACATTTTTGCGT
66 AAGAAATAGGTTTCAAAATTATAAGTATCGATACTTGTTATACATGTATCGATACTTTTTTGCGT
*
986644 GCAAATTGTTTGAGATGCATACTTGAATAAAAGTATCGATACTTATATAATAAGTATCTATACTT
131 GCAAATTGTTTGAGATGCATACTGGAATAAAAGTATCGATACTTATATAATAAGTATC-ATACTT
986709 TATGTT
195 TATGTT
* * * * * * *
986715 TATGCCTATTATTATTAAACATG-TAGATTTTTACCATTTTCATTGTAAATTTTCCTATTTCTTT
1 TACGCCTATTATCATTAAAC-CGATAGATTTTTACCGTTTACATTGTAAATTTACCTATTACTTT
* ** * * * *
986779 AAATAAATAGGTTTTGAAATTATAAGTATTGATACTTTTTGTACACT-TATCGATATTTTTTTGC
65 AAAGAAATAGGTTTCAAAATTATAAGTATCGATACTTGTTATACA-TGTATCGATACTTTTTTGC
* * * * *
986843 GAGCAAATTGTTTGAGATGCATAATGGAATAAAAGTATCGATACGTATGTAATAAGTATTGATAC
129 GTGCAAATTGTTTGAGATGCATACTGGAATAAAAGTATCGATACTTATATAATAAGTA-TCATAC
986908 TTTATGTT
193 TTTATGTT
* * * * * *
986916 TACTCCTATTATCATTCAACCAATAGATTTTTACCATTTTCATTATAAATTTACCTATTACTTTA
1 TACGCCTATTATCATTAAACCGATAGATTTTTACCGTTTACATTGTAAATTTACCTATTACTTTA
* * * * ** *
986981 AA-ATAAAAGGTTTCAAATTTCTAAGTATCGATACTTGTTATATATGTATAAATACTTTTTTGCA
66 AAGA-AATAGGTTTCAAAATTATAAGTATCGATACTTGTTATACATGTATCGATACTTTTTTGCG
* * *
987045 TGCAAATTGTTTAAGATGCATACTGGAATAAAAGTATCGATACCTATATAAAAAGTATCAATACT
130 TGCAAATTGTTTGAGATGCATACTGGAATAAAAGTATCGATACTTATATAATAAGTATC-ATACT
987110 TTATGTT
194 TTATGTT
* * * * * * * * *
987117 TAAGCCCATTGTCATAAAATCGGTAAACTTTTAGCGTTTACATTGTAAATTTACCTATTACTTTA
1 TACGCCTATTATCATTAAACCGATAGATTTTTACCGTTTACATTGTAAATTTACCTATTACTTTA
* * * * * * * *
987182 AAGGAGTAGGTTTCAGAATTATAAGTATTGATACTTTTTATATATGTATGGCTACTTTTTTTGCG
66 AAGAAATAGGTTTCAAAATTATAAGTATCGATACTTGTTATACATGTATCGATAC-TTTTTTGCG
* * * *
987247 TGCAAATTGTTTGAGATGTATACTGGAATAAAAGCATAGATACTTATATAATACGTATCAATACT
130 TGCAAATTGTTTGAGATGCATACTGGAATAAAAGTATCGATACTTATATAATAAGTATC-ATACT
987312 TTATGTT
194 TTATGTT
* * * * * * *
987319 TGCGCCCATTATCATTAAA-CTAGTAAATTTTTACCGTTTCCATTGTATATTTACCTATTACTGT
1 TACGCCTATTATCATTAAACCGA-TAGATTTTTACCGTTTACATTGTAAATTTACCTATTACTTT
* * * * *
987383 AAAGTAATAGGTTTCAAAATTACAAGTATCGATAC-T-TTATATATGGTTATTGATACTTTGTTG
65 AAAGAAATAGGTTTCAAAATTATAAGTATCGATACTTGTTATACAT-G-TATCGATACTTTTTTG
* * * * * * *
987446 CGGGAAAATTGTTTGATATCCATACTAGAATAAAAGTATCGATACATATATAAAAAGTATC
128 CGTGCAAATTGTTTGAGATGCATACTGGAATAAAAGTATCGATACTTATATAATAAGTATC
987507 CAAATTGGAC
Statistics
Matches: 1032, Mismatches: 148, Indels: 28
0.85 0.12 0.02
Matches are distributed among these distances:
200 13 0.01
201 853 0.83
202 166 0.16
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (200 bp):
TACGCCTATTATCATTAAACCGATAGATTTTTACCGTTTACATTGTAAATTTACCTATTACTTTA
AAGAAATAGGTTTCAAAATTATAAGTATCGATACTTGTTATACATGTATCGATACTTTTTTGCGT
GCAAATTGTTTGAGATGCATACTGGAATAAAAGTATCGATACTTATATAATAAGTATCATACTTT
ATGTT
Found at i:986687 original size:20 final size:21
Alignment explanation
Indices: 986662--986708 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
986652 TTTGAGATGC
986662 ATACTTGA-ATAA-AAGTATCG
1 ATACTT-ATATAATAAGTATCG
*
986682 ATACTTATATAATAAGTATCT
1 ATACTTATATAATAAGTATCG
986703 ATACTT
1 ATACTT
986709 TATGTTTATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 10 0.42
21 13 0.54
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.38
Consensus pattern (21 bp):
ATACTTATATAATAAGTATCG
Found at i:987230 original size:21 final size:21
Alignment explanation
Indices: 987201--987241 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
987191 GTTTCAGAAT
*
987201 TATAAGTATTGATACTTTTTA
1 TATAAGTATGGATACTTTTTA
* *
987222 TATATGTATGGCTACTTTTT
1 TATAAGTATGGATACTTTTT
987242 TTGCGTGCAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.07, G:0.12, T:0.54
Consensus pattern (21 bp):
TATAAGTATGGATACTTTTTA
Found at i:990616 original size:27 final size:27
Alignment explanation
Indices: 990565--990616 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
990555 GTCATTGCAT
*
990565 TTTTATTTTTATTTTTCATTTTCTTAG
1 TTTTATTTTTATTTTTCATTGTCTTAG
*
990592 TTTTACTTTTTA-TTTTCCTTGTCTT
1 TTTTA-TTTTTATTTTTCATTGTCTT
990617 TTTTAGGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 16 0.73
28 6 0.27
ACGTcount: A:0.12, C:0.12, G:0.04, T:0.73
Consensus pattern (27 bp):
TTTTATTTTTATTTTTCATTGTCTTAG
Found at i:1000823 original size:54 final size:55
Alignment explanation
Indices: 1000765--1001161 Score: 540
Period size: 54 Copynumber: 7.4 Consensus size: 55
1000755 TTTGTCGGGG
* * *
1000765 TGCACACGTAGTGCTC-ATACGATCGTTCATAAATATATTATGAATTCCGTGGGT
1 TGCACACTTAGTGCTCGATACGGTCGTTCATAAACATATTATGAATTCCGTGGGT
* * * *
1000819 TGCACACTTAGTGCT-GATACGATCATTCATAAACTTATTATGAATTTCGTGGGT
1 TGCACACTTAGTGCTCGATACGGTCGTTCATAAACATATTATGAATTCCGTGGGT
* *
1000873 TGTACACTTAGT-TTCGATACGGTCGTTCATAAACATATTATGAATTCCGTGGGT
1 TGCACACTTAGTGCTCGATACGGTCGTTCATAAACATATTATGAATTCCGTGGGT
** * *
1000927 TGCACACTTAGTGC-CGATACGGTAATTCATAAACATATTATGAATTCTGTTGGT
1 TGCACACTTAGTGCTCGATACGGTCGTTCATAAACATATTATGAATTCCGTGGGT
** * *
1000981 TGCACACTTAGTTAT-GATACGGTCGTTCATAAACATATTATGTATTCTGTGGGT
1 TGCACACTTAGTGCTCGATACGGTCGTTCATAAACATATTATGAATTCCGTGGGT
1001035 TGCACACTTAGTGC-CGATACGGTCGTTCATAAACATATTATGAATTCCGTGGGT
1 TGCACACTTAGTGCTCGATACGGTCGTTCATAAACATATTATGAATTCCGTGGGT
* *
1001089 TGCACACTTAGTG-TCGATACGGTCGTTCATAAACAGATTATGAATTTCGTGGGT
1 TGCACACTTAGTGCTCGATACGGTCGTTCATAAACATATTATGAATTCCGTGGGT
** *
1001143 TATACACTTACTGC-CGATA
1 TGCACACTTAGTGCTCGATA
1001162 GTACACATAG
Statistics
Matches: 304, Mismatches: 32, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
53 1 0.00
54 303 1.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (55 bp):
TGCACACTTAGTGCTCGATACGGTCGTTCATAAACATATTATGAATTCCGTGGGT
Found at i:1005391 original size:2 final size:2
Alignment explanation
Indices: 1005384--1005411 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1005374 ATATTATTCA
1005384 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
1005412 GTATTAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1006086 original size:54 final size:54
Alignment explanation
Indices: 1006028--1006586 Score: 755
Period size: 54 Copynumber: 10.4 Consensus size: 54
1006018 TTCGTTGGAG
*
1006028 TGCACA-TGTAGTGACGATACGGTCGTTCATAAACATATTATGAATTCCATGGGT
1 TGCACACT-TAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCCATGGGT
* * ** * **
1006082 TGCACACTTAGTGTCAATACTGTTATTCATAAACTTATTATGAATTCTGTGGGT
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCCATGGGT
* * * * * * * *
1006136 TGCACACTTAGTGCCAATATGGTCATTCATAAACTTATTATAAATTTCGTGGGT
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCCATGGGT
* * * *
1006190 TACACACTTAATGTCGATACGGTCGTTCATAAACTTATTATGAATTCCTTGGGT
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCCATGGGT
* *
1006244 TGCACACTTAGTGTCGATTCGGTCGTTCATAAACATATTATAAATTCCATGGGT
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCCATGGGT
* *
1006298 TGCACACTTAGTGTCAATATGGTCGTTCATAAACATATTATGAATT-CAGTGGGT
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCCA-TGGGT
* * * *
1006352 TGTACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGATTTCCATGAGT
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCCATGGGT
1006406 TGCACACTTAGT-TCCGATACGGTCGTTCATAAACATATTATGAATTCCATGGGT
1 TGCACACTTAGTGT-CGATACGGTCGTTCATAAACATATTATGAATTCCATGGGT
* * *
1006460 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATCATGAATTCCGTGGAT
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCCATGGGT
* * *
1006514 TGCACACTTAGTGTCGATACGGTTGTTCATAAACATATTATGAATTTCGTGGGT
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCCATGGGT
*
1006568 TGCACACTTAGTGCCGATA
1 TGCACACTTAGTGTCGATA
1006587 GTACACATAG
Statistics
Matches: 448, Mismatches: 52, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
53 2 0.00
54 442 0.99
55 4 0.01
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (54 bp):
TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCCATGGGT
Found at i:1009418 original size:64 final size:64
Alignment explanation
Indices: 1009306--1009472 Score: 166
Period size: 64 Copynumber: 2.6 Consensus size: 64
1009296 GCATCCCTTG
*
1009306 ACAGGTGCATCGATGCACTACCCATGCATCTG-TGCA-TAAATCCTATTCGATGTT-TGTATTTT
1 ACAGGTGCATCGATGCACT-CCTATGCATC-GATGCACTAAATCCTATTCGATGTTATGTATTTT
1009368 A
64 A
* *
1009369 AGCAGGTGCATCGATGCACTCCTTATGCATCGATGCACT-AATGGC-ATTCGATGTTCATTTATT
1 A-CAGGTGCATCGATGCACTCC-TATGCATCGATGCACTAAAT-CCTATTCGATGTT-ATGTATT
1009432 TTA
62 TTA
* *
1009435 A-ATGAGTGCATCGATACACTCCATGTGCATCGATGCAC
1 ACA-G-GTGCATCGATGCACTCC-TATGCATCGATGCAC
1009473 CTTCAACAAA
Statistics
Matches: 89, Mismatches: 6, Indels: 15
0.81 0.05 0.14
Matches are distributed among these distances:
63 4 0.04
64 43 0.48
65 3 0.03
66 39 0.44
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (64 bp):
ACAGGTGCATCGATGCACTCCTATGCATCGATGCACTAAATCCTATTCGATGTTATGTATTTTA
Found at i:1021183 original size:29 final size:29
Alignment explanation
Indices: 1021147--1021213 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
1021137 CATTTTACAC
*
1021147 AAATAGCACCCTTTTCAAAATAATTACCA
1 AAATAGCACCCATTTCAAAATAATTACCA
* * *
1021176 AAATAGCACCCATTTCGAATTATTTACCA
1 AAATAGCACCCATTTCAAAATAATTACCA
*
1021205 GAATAGCAC
1 AAATAGCAC
1021214 AAAATTGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.42, C:0.24, G:0.07, T:0.27
Consensus pattern (29 bp):
AAATAGCACCCATTTCAAAATAATTACCA
Found at i:1021240 original size:57 final size:59
Alignment explanation
Indices: 1021170--1021300 Score: 187
Period size: 57 Copynumber: 2.3 Consensus size: 59
1021160 TTCAAAATAA
*** * *
1021170 TTACCAAAATAGCACCCATTTC-GAATTATTTACCAGAATAGCA-CAAAATTGAATTAT
1 TTACCAAAATAGCACCCAAAACTGAATTATTTACCAGAATAACACCAAAACTGAATTAT
*
1021227 TTACCAGAATAGCA-CCAAAACTGAATTATTTACCAGAATAACACCAAAACTGAATTAT
1 TTACCAAAATAGCACCCAAAACTGAATTATTTACCAGAATAACACCAAAACTGAATTAT
1021285 TTACCAAAATAGCACC
1 TTACCAAAATAGCACC
1021301 GGTAAACGGT
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
56 4 0.06
57 33 0.52
58 26 0.41
59 1 0.02
ACGTcount: A:0.44, C:0.21, G:0.08, T:0.26
Consensus pattern (59 bp):
TTACCAAAATAGCACCCAAAACTGAATTATTTACCAGAATAACACCAAAACTGAATTAT
Found at i:1021255 original size:29 final size:29
Alignment explanation
Indices: 1021192--1021300 Score: 184
Period size: 29 Copynumber: 3.8 Consensus size: 29
1021182 CACCCATTTC
*
1021192 GAATTATTTACCAGAATAGCA-CAAAATT
1 GAATTATTTACCAGAATAGCACCAAAACT
1021220 GAATTATTTACCAGAATAGCACCAAAACT
1 GAATTATTTACCAGAATAGCACCAAAACT
*
1021249 GAATTATTTACCAGAATAACACCAAAACT
1 GAATTATTTACCAGAATAGCACCAAAACT
*
1021278 GAATTATTTACCAAAATAGCACC
1 GAATTATTTACCAGAATAGCACC
1021301 GGTAAACGGT
Statistics
Matches: 76, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
28 21 0.28
29 55 0.72
ACGTcount: A:0.46, C:0.19, G:0.09, T:0.26
Consensus pattern (29 bp):
GAATTATTTACCAGAATAGCACCAAAACT
Found at i:1021338 original size:12 final size:12
Alignment explanation
Indices: 1021305--1021339 Score: 61
Period size: 13 Copynumber: 2.8 Consensus size: 12
1021295 AGCACCGGTA
1021305 AACGGTCGGGTC
1 AACGGTCGGGTC
1021317 AACGGATCGGGTC
1 AACGG-TCGGGTC
1021330 AACGGTCGGG
1 AACGGTCGGG
1021340 CCGGGTCAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.20, C:0.23, G:0.43, T:0.14
Consensus pattern (12 bp):
AACGGTCGGGTC
Found at i:1024890 original size:29 final size:29
Alignment explanation
Indices: 1024849--1024954 Score: 176
Period size: 29 Copynumber: 3.7 Consensus size: 29
1024839 AGCACCATTT
*
1024849 CGAATTATTTACCAGACTAGCACCAAAAC
1 CGAATTATTTACCAGAATAGCACCAAAAC
1024878 CGAATTATTTACCAGAATAGCACCAAAAC
1 CGAATTATTTACCAGAATAGCACCAAAAC
*
1024907 CGAATTATTTACCAGAATAACACCAAAAC
1 CGAATTATTTACCAGAATAGCACCAAAAC
* *
1024936 TGAATTATTTACCAAAATA
1 CGAATTATTTACCAGAATA
1024955 ACATCGATCA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 73 1.00
ACGTcount: A:0.45, C:0.23, G:0.08, T:0.24
Consensus pattern (29 bp):
CGAATTATTTACCAGAATAGCACCAAAAC
Found at i:1024890 original size:57 final size:58
Alignment explanation
Indices: 1024829--1024954 Score: 182
Period size: 58 Copynumber: 2.2 Consensus size: 58
1024819 TTTAAAATAA
*** * *
1024829 TTACCAAAATAGCACC-ATTTCGAATTATTTACCAGACTAGCACCAAAACCGAATTAT
1 TTACCAAAATAGCACCAAAACCGAATTATTTACCAGAATAACACCAAAACCGAATTAT
* *
1024886 TTACCAGAATAGCACCAAAACCGAATTATTTACCAGAATAACACCAAAACTGAATTAT
1 TTACCAAAATAGCACCAAAACCGAATTATTTACCAGAATAACACCAAAACCGAATTAT
1024944 TTACCAAAATA
1 TTACCAAAATA
1024955 ACATCGATCA
Statistics
Matches: 60, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
57 15 0.25
58 45 0.75
ACGTcount: A:0.44, C:0.23, G:0.08, T:0.25
Consensus pattern (58 bp):
TTACCAAAATAGCACCAAAACCGAATTATTTACCAGAATAACACCAAAACCGAATTAT
Found at i:1024990 original size:18 final size:18
Alignment explanation
Indices: 1024967--1025007 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
1024957 ATCGATCAAC
1024967 GGTCGGGTCAACGGGTCG
1 GGTCGGGTCAACGGGTCG
*
1024985 GGTCGGGTCAATGGGTCG
1 GGTCGGGTCAACGGGTCG
1025003 GGTCG
1 GGTCG
1025008 TGACCGGTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.10, C:0.20, G:0.51, T:0.20
Consensus pattern (18 bp):
GGTCGGGTCAACGGGTCG
Found at i:1026266 original size:45 final size:45
Alignment explanation
Indices: 1026216--1026319 Score: 190
Period size: 45 Copynumber: 2.3 Consensus size: 45
1026206 TGTATCTCAA
*
1026216 TTATGGAATCCTTTCGTGTCGATAATGTACCCCTATGCATTTCAT
1 TTATGGCATCCTTTCGTGTCGATAATGTACCCCTATGCATTTCAT
*
1026261 TTATGGCATCCTTTCGTGTCGATAATGTATCCCTATGCATTTCAT
1 TTATGGCATCCTTTCGTGTCGATAATGTACCCCTATGCATTTCAT
1026306 TTATGGCATCCTTT
1 TTATGGCATCCTTT
1026320 AATGCCTTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 57 1.00
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.42
Consensus pattern (45 bp):
TTATGGCATCCTTTCGTGTCGATAATGTACCCCTATGCATTTCAT
Found at i:1026343 original size:45 final size:47
Alignment explanation
Indices: 1026294--1026423 Score: 183
Period size: 47 Copynumber: 2.8 Consensus size: 47
1026284 AATGTATCCC
*
1026294 TATGCATTTCATTTATGGCATCCTTTAATG-CCTTTTAAATG-CGAT
1 TATGCATTTCATTTATGGCATCCTTTCATGCCCTTTTAAATGTCGAT
** **
1026339 TATGCATTTCATTTATGGCATCCTTTCATGCCCTTTTTTATGTTTAT
1 TATGCATTTCATTTATGGCATCCTTTCATGCCCTTTTAAATGTCGAT
* *
1026386 TATACATATCATTTATGGCATCCTTTCATGCCCTTTTA
1 TATGCATTTCATTTATGGCATCCTTTCATGCCCTTTTA
1026424 TACGACATTA
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
45 29 0.39
46 9 0.12
47 37 0.49
ACGTcount: A:0.22, C:0.20, G:0.11, T:0.48
Consensus pattern (47 bp):
TATGCATTTCATTTATGGCATCCTTTCATGCCCTTTTAAATGTCGAT
Found at i:1026674 original size:68 final size:68
Alignment explanation
Indices: 1026460--1027208 Score: 1081
Period size: 68 Copynumber: 11.0 Consensus size: 68
1026450 TAGTCTTTTA
* * * * *
1026460 CTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGACACATTTCTATCAAATGCACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTA
1026525 GGC
66 GGC
* *
1026528 CT-AAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACAC-CTTATGTCAAATGCACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTA
1026591 GGC
66 GGC
* * * * *
1026594 CTCAAAGGCACTTATCCTTTCATCTAGCTGGCATAATTAACACATTTCTATCAAATGCATAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTA
1026659 GGC
66 GGC
* *
1026662 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCTTAATTGACACCTTTCTGTCAAATGCACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTA
1026727 GGC
66 GGC
* * *
1026730 CTCAAAGGCACATAGCCTTTCATCTAATTAGCATAATTGACACATTTCTGT-AAATGCACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTA
1026794 GGC
66 GGC
* * *
1026797 ATCAAAGGCACTTACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTTTGTCAAATGCACA
1 CTCAAAGG--C--ACTTAGCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACA
*
1026862 ATTAGGC
62 GTTAGGC
* * *
1026869 CTCAAACGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTTTGTCAAATGCACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTA
1026934 GGC
66 GGC
* * * *
1026937 CTCAAAGGCACTTAGCCTTTCATCTAACTGACATAATTGGCTCATTTTTGTCAAATGCACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTA
1027002 GGC
66 GGC
* * * *
1027005 CTCAAAGACACTTAGCCATTCATCTAACTGGAATAATTGACACATTTTTGTCAAATGCACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTA
1027070 GGC
66 GGC
* * * * * *
1027073 ATCAAAGGCACTTAGACTTTCATCTAACTGGCATAATGGACACCTTTTTGTCAAATACACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTA
1027138 GGC
66 GGC
* *
1027141 CTCAAAGGCACTTAGCTTTTCTTCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTA
1027206 GGC
66 GGC
1027209 TATTAATATT
Statistics
Matches: 611, Mismatches: 63, Indels: 14
0.89 0.09 0.02
Matches are distributed among these distances:
66 23 0.04
67 96 0.16
68 432 0.71
69 1 0.00
70 1 0.00
71 37 0.06
72 21 0.03
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (68 bp):
CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTA
GGC
Found at i:1027478 original size:54 final size:55
Alignment explanation
Indices: 1027406--1027621 Score: 303
Period size: 55 Copynumber: 3.9 Consensus size: 55
1027396 CTTCTGATAA
* * * ** * *
1027406 TTGCACATATATTTCCCATACGGAAATTTATACACTTAGTATGGATTTCTTAG-T
1 TTGCACACATAGTGCCCATACAAAAATTCATACACTTAGTATGAATTTCTTAGTT
1027460 TTGCACACATAGTGCCCATACAGAAAA-TCATACACTTAGTATGAATTTCTTAGTT
1 TTGCACACATAGTGCCCATACA-AAAATTCATACACTTAGTATGAATTTCTTAGTT
1027515 TTGCACACA-ATGTGCCCATACAAAAATTCATACACTTAGTATGAATTTCTTAGTT
1 TTGCACACATA-GTGCCCATACAAAAATTCATACACTTAGTATGAATTTCTTAGTT
* * *
1027570 TTGCACACAAAGTGCCCATACGAAAATTCATACACTTAGTATAAATTTCTTA
1 TTGCACACATAGTGCCCATACAAAAATTCATACACTTAGTATGAATTTCTTA
1027622 ACTTTTTGCA
Statistics
Matches: 148, Mismatches: 9, Indels: 9
0.89 0.05 0.05
Matches are distributed among these distances:
54 47 0.32
55 100 0.68
56 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Consensus pattern (55 bp):
TTGCACACATAGTGCCCATACAAAAATTCATACACTTAGTATGAATTTCTTAGTT
Found at i:1028083 original size:20 final size:18
Alignment explanation
Indices: 1028058--1028105 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
1028048 GTTTTTAATG
*
1028058 GTATCGATACCTTCCTCATA
1 GTATCGATACC-CCCT-ATA
*
1028078 GTATCGATACCCCCTTTA
1 GTATCGATACCCCCTATA
1028096 GTATCGATAC
1 GTATCGATAC
1028106 TGTGCATCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 12 0.46
19 3 0.12
20 11 0.42
ACGTcount: A:0.25, C:0.29, G:0.12, T:0.33
Consensus pattern (18 bp):
GTATCGATACCCCCTATA
Found at i:1030206 original size:2 final size:2
Alignment explanation
Indices: 1030199--1030238 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1030189 ATTAACCATA
1030199 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1030239 CTTTCTGACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1032128 original size:46 final size:46
Alignment explanation
Indices: 1032019--1032163 Score: 240
Period size: 46 Copynumber: 3.2 Consensus size: 46
1032009 AATGCACCCC
*
1032019 TATGCATTTCATTTATGGCATCCTTTCATG-CCTTTTATACGCTAT
1 TATGCATTTCATTTATGGCATCCTTTCATGCCCTTTTATACGATAT
* *
1032064 TATGTATTTCATTTATGGCATCCTTTCATGCCCCTTTT-TACGTTAT
1 TATGCATTTCATTTATGGCATCCTTTCATG-CCCTTTTATACGATAT
1032110 TATGCATTTCATTTATGGCATCCTTTCATGCCCTTTTATACGATAT
1 TATGCATTTCATTTATGGCATCCTTTCATGCCCTTTTATACGATAT
1032156 TATGCATT
1 TATGCATT
1032164 GATATACATC
Statistics
Matches: 93, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
45 36 0.39
46 51 0.55
47 6 0.06
ACGTcount: A:0.20, C:0.21, G:0.11, T:0.48
Consensus pattern (46 bp):
TATGCATTTCATTTATGGCATCCTTTCATGCCCTTTTATACGATAT
Found at i:1032323 original size:68 final size:68
Alignment explanation
Indices: 1032198--1032996 Score: 1219
Period size: 68 Copynumber: 11.8 Consensus size: 68
1032188 AAGTATTTAA
* *
1032198 CCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCATAGTTAGGCCTCAAAGGCACT
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
1032263 TAG
66 TAG
* * * * * * * *
1032266 CTTTTCCTCTAACTGGCATAATTGACACATTTCTATCAAATGCACAATTATGACTCAAAGGTACT
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
*
1032331 TAA
66 TAG
1032334 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
1032399 TAG
66 TAG
** * *
1032402 CCTTTCATCTAACTTACATAATTGACACCTTTATGTCAAATGCACAGTTTGGCCTCAAAGGCACT
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
1032467 TAG
66 TAG
* * *
1032470 CCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCATAGTTAGGCCTCAAAGACACT
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
1032535 TAG
66 TAG
*
1032538 CCTTTC-TACTAACTGGCATAATTGACACCTTTCTATCAAATGCACAGTTAGGCCTCAAAGGCAC
1 CCTTTCAT-CTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCAC
1032602 TTAG
65 TTAG
* * * *
1032606 CCTTTCATATAACTGCCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCCTCAAAGACACT
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
1032671 TAG
66 TAG
** * *
1032674 CCTTTCATCTAACTGAAATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTAAAAGACACT
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
*
1032739 AAG
66 TAG
* * *
1032742 CCTTTCATCTAACTGGCATAATTGACACCTTTTTGTCAAATACACAATTAGGCCTCAAAGGCACT
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
1032807 TAG
66 TAG
* *
1032810 CCTTTCATCTAACTAGCATAATTGACACCTTTCTGTCAAATGCATAGTTAGGCCTCAAAGGCACT
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
1032875 TAG
66 TAG
*
1032878 TCC-TTCATCTAACAGGCATAATTG-CACCTTTCT-TCAAATGCACAGTTAGGCCTCAAAGGCAC
1 -CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCAC
1032940 TTAG
65 TTAG
* * *
1032944 CCTTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGGACAATTAGGC
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGC
1032997 TATTAATATT
Statistics
Matches: 663, Mismatches: 62, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
65 2 0.00
66 51 0.08
67 19 0.03
68 588 0.89
69 3 0.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (68 bp):
CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACT
TAG
Found at i:1033324 original size:55 final size:55
Alignment explanation
Indices: 1033218--1033465 Score: 349
Period size: 55 Copynumber: 4.5 Consensus size: 55
1033208 TCCCATACGA
* * * *
1033218 AAATTCATACACTTAGTACGGATTTCTTAG-TTTGCACACATAGTG-TCCATACAT
1 AAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGCT-CATACAG
*
1033272 AAAATCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGCTCATACAG
1 AAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGCTCATACAG
* * *
1033327 AAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAATGTGCCCATACGG
1 AAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGCTCATACAG
**
1033382 AAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGC-CTATATGG
1 AAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGCTC-ATACAG
* *
1033437 AAATTCATACACTTGGTATGAACTTCTTA
1 AAATTCATACACTTAGTATGAATTTCTTA
1033466 AATTTTTGCA
Statistics
Matches: 178, Mismatches: 13, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
54 28 0.16
55 149 0.84
56 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (55 bp):
AAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGCTCATACAG
Found at i:1040795 original size:44 final size:43
Alignment explanation
Indices: 1040729--1041067 Score: 459
Period size: 44 Copynumber: 7.8 Consensus size: 43
1040719 CCGTTAGAGT
* * *
1040729 AGGTCCCTTTGCTGTGTCCAAGGGTAAGCCTTACAGTTTACCCC
1 AGGTCCCTTTGTTGTGTGCAAGGATAAGCCTTACAGTTT-CCCC
* *
1040773 AGGTCCATTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
1 AGGTCCCTTTGTTGTGTGCAAGGATAAGCCTTACAGTTTCCCC
*
1040816 AGGTCCCTTTGCTGTGTGCAAGGATAAGCCTTACAGTTTCCCTC
1 AGGTCCCTTTGTTGTGTGCAAGGATAAGCCTTACAGTTTCCC-C
* *
1040860 AGTTCCCTTTGCAT-TGTGCAAGGATAAGCCTTACAGTTTTCCCC
1 AGGTCCCTTTG-TTGTGTGCAAGGATAAGCCTTACAG-TTTCCCC
1040904 AGGTCCCTTTGTTGTGTGCAAGGATAAGCCTTACAGTTTCCCCC
1 AGGTCCCTTTGTTGTGTGCAAGGATAAGCCTTACAGTTT-CCCC
*
1040948 AAGTCCCTTTGTTGTGTGCAAGGATAAGCCTTACAGTTTCCCCC
1 AGGTCCCTTTGTTGTGTGCAAGGATAAGCCTTACAGTTT-CCCC
* *
1040992 AAGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
1 AGGTCCCTTTGTTGTGTGCAAGGATAAGCCTTACAGTTTCCCC
* * *
1041035 AGG-CTCTTTTGCTATGTGCAAGGA-AAGACCTTA
1 AGGTC-CCTTTGTTGTGTGCAAGGATAAG-CCTTA
1041068 TCGTTTTTGC
Statistics
Matches: 271, Mismatches: 17, Indels: 15
0.89 0.06 0.05
Matches are distributed among these distances:
42 4 0.01
43 73 0.27
44 187 0.69
45 7 0.03
ACGTcount: A:0.20, C:0.26, G:0.22, T:0.32
Consensus pattern (43 bp):
AGGTCCCTTTGTTGTGTGCAAGGATAAGCCTTACAGTTTCCCC
Found at i:1041036 original size:131 final size:129
Alignment explanation
Indices: 1040731--1041067 Score: 473
Period size: 131 Copynumber: 2.6 Consensus size: 129
1040721 GTTAGAGTAG
* *
1040731 GTCCCTTTGCTGTGTCCAAGGGTAAGCCTTACAGTTTACCCCAGGTCCATTTGTTGTGTGCAAGG
1 GTCCCTTTGATGTGTGCAAGGGTAAGCCTTACAGTTT-CCCCAGGTCCATTTGTTGTGTGCAAGG
* * *
1040796 GTAAGCCTTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAAGGATAAGCCTTACAGTTTCCCTCA
65 ATAAGCCTTACAGTTTCCCCAAGTCCCTTTGCTGTGTGCAAGGATAAGCCTTACAGTTTCCCCCA
* *
1040861 GTTCCCTTTGCAT-TGTGCAAGGATAAGCCTTACAGTTTTCCCCAGGTCCCTTTGTTGTGTGCAA
1 G-TCCCTTTG-ATGTGTGCAAGGGTAAGCCTTACAG-TTTCCCCAGGTCCATTTGTTGTGTGCAA
*
1040925 GGATAAGCCTTACAGTTTCCCCCAAGTCCCTTTGTTGTGTGCAAGGATAAGCCTTACAGTTTCCC
63 GGATAAGCCTTACAGTTT-CCCCAAGTCCCTTTGCTGTGTGCAAGGATAAGCCTTACAGTTTCCC
1040990 CCAA
127 CC-A
* * * *
1040994 GTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGG-CTCTTTTGCTATGTGCAAGG
1 GTCCCTTTGATGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTC-CATTTGTTGTGTGCAAGG
1041058 A-AAGACCTTA
65 ATAAG-CCTTA
1041068 TCGTTTTTGC
Statistics
Matches: 186, Mismatches: 13, Indels: 15
0.87 0.06 0.07
Matches are distributed among these distances:
130 5 0.03
131 101 0.54
132 78 0.42
133 2 0.01
ACGTcount: A:0.20, C:0.26, G:0.22, T:0.32
Consensus pattern (129 bp):
GTCCCTTTGATGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTCCATTTGTTGTGTGCAAGGA
TAAGCCTTACAGTTTCCCCAAGTCCCTTTGCTGTGTGCAAGGATAAGCCTTACAGTTTCCCCCA
Found at i:1042975 original size:21 final size:21
Alignment explanation
Indices: 1042949--1043000 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
1042939 TACCCAAGTC
1042949 TCGATACTTTTGTGTAAGGTA
1 TCGATACTTTTGTGTAAGGTA
1042970 TCGATACTTTTGTGTAAGGTA
1 TCGATACTTTTGTGTAAGGTA
1042991 TCGATACTTT
1 TCGATACTTT
1043001 CGAGACATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.23, C:0.12, G:0.21, T:0.44
Consensus pattern (21 bp):
TCGATACTTTTGTGTAAGGTA
Found at i:1043342 original size:196 final size:198
Alignment explanation
Indices: 1043112--1043516 Score: 498
Period size: 200 Copynumber: 2.0 Consensus size: 198
1043102 TCTTTACCGG
* * *
1043112 TTTTGTCAAATTTAAACATGTTATATTATCATGTATTGATACATTTGTTTAAGGTATCGATACTT
1 TTTTGTCAAATTTAAACATGTTATATTATCATGTATCGATACATGTGTGTAAGGTATCGATACTT
* * * *
1043177 TATAGCTGA-T-ATTATTGCAATTCTTTTAAATTCCTAAAGTA-CGATACTTTGGTGCATATACT
66 TAGAGAT-ATTCATTATTGCAATTCTTTTAAATTCCTAAAGTATCGATACTTTGGTACATATACC
* * *
1043239 TATAAA-AGTATCGATACAAATGTCAACTATTCC-GATATCTCTTTACCGATTTTGTCAAATTGA
130 TATAAACA-TATCGATACAAATGTCAACAATTCCAG-TATCTCTTTAACGATTTTCTCAAATTGA
1043302 AA-TCGA
193 AACT-GA
* * *
1043308 TTTTGTCAAATTTCAACATGTTATTTTGTCATGTATCGATACATGTGTGTAAGGTATCGATACTT
1 TTTTGTCAAATTTAAACATGTTATATTATCATGTATCGATACATGTGTGTAAGGTATCGATACTT
* * * * * * * * *
1043373 TCGAGATATTTTCCTTTTTTCATTTCTTTTAAATTTCTACAGTATTGATAGTTTGGTACATATAC
66 TAGAGATA--TTCATTATTGCAATTCTTTTAAATTCCTAAAGTATCGATACTTTGGTACATATAC
*
1043438 CTATAAACATATCGATACAAATTTCAACAATTCCAGTATCTCTTTAACGATTTTCTCAAATTGAA
129 CTATAAACATATCGATACAAATGTCAACAATTCCAGTATCTCTTTAACGATTTTCTCAAATTGAA
*
1043503 ACTGG
194 ACTGA
1043508 TTTTGTCAA
1 TTTTGTCAA
1043517 TTTTTAATCG
Statistics
Matches: 177, Mismatches: 24, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
195 1 0.01
196 63 0.36
198 1 0.01
199 25 0.14
200 84 0.47
201 3 0.02
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (198 bp):
TTTTGTCAAATTTAAACATGTTATATTATCATGTATCGATACATGTGTGTAAGGTATCGATACTT
TAGAGATATTCATTATTGCAATTCTTTTAAATTCCTAAAGTATCGATACTTTGGTACATATACCT
ATAAACATATCGATACAAATGTCAACAATTCCAGTATCTCTTTAACGATTTTCTCAAATTGAAAC
TGA
Found at i:1043516 original size:20 final size:20
Alignment explanation
Indices: 1043488--1043580 Score: 64
Period size: 20 Copynumber: 4.6 Consensus size: 20
1043478 TCTTTAACGA
* *
1043488 TTTTCTCAAATTGAAACTGG
1 TTTTGTCAAATTGTAACTGG
* *
1043508 TTTTGTCAATTTTTAA-TCGG
1 TTTTGTCAAATTGTAACT-GG
* * *
1043528 TTTAGTCAAATTCGTTACTTG
1 TTTTGTCAAATT-GTAACTGG
* *
1043549 TTTTGTCAAATTGTTA-TAG
1 TTTTGTCAAATTGTAACTGG
1043568 TATTTGTCAAATT
1 T-TTTGTCAAATT
1043581 TCAACCTGTT
Statistics
Matches: 58, Mismatches: 11, Indels: 8
0.75 0.14 0.10
Matches are distributed among these distances:
19 4 0.07
20 39 0.67
21 14 0.24
22 1 0.02
ACGTcount: A:0.26, C:0.11, G:0.14, T:0.49
Consensus pattern (20 bp):
TTTTGTCAAATTGTAACTGG
Found at i:1044313 original size:2 final size:2
Alignment explanation
Indices: 1044308--1044346 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1044298 GATTACACAC
1044308 AT 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 AT A
1044347 GAAGAAATAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1044616 original size:2 final size:2
Alignment explanation
Indices: 1044604--1044648 Score: 58
Period size: 2 Copynumber: 23.0 Consensus size: 2
1044594 GACTAGAAGC
*
1044604 AT AT A- AT AT AT AT CT AT A- AGT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
1044645 AT AT
1 AT AT
1044649 GATACAATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
1 2 0.05
2 35 0.92
3 1 0.03
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1049027 original size:33 final size:33
Alignment explanation
Indices: 1048990--1049052 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
1048980 CTAGGTTGGA
1048990 CATATAGATTAGCACTTGGCTCTGCAGATTGAC
1 CATATAGATTAGCACTTGGCTCTGCAGATTGAC
*
1049023 CATATGGATTAGCACTTGGCTCTGCAGATT
1 CATATAGATTAGCACTTGGCTCTGCAGATT
1049053 AGCACCCGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (33 bp):
CATATAGATTAGCACTTGGCTCTGCAGATTGAC
Found at i:1051774 original size:26 final size:26
Alignment explanation
Indices: 1051745--1051808 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
1051735 TTTTAAAAAT
*
1051745 TAATATAAATAAA-ACATAATAAATAA
1 TAATATTAATAAATA-ATAATAAATAA
*
1051771 TAATATTATTAAATAATAATAAATAA
1 TAATATTAATAAATAATAATAAATAA
*
1051797 TATTATTAATAA
1 TAATATTAATAA
1051809 TATTAAGCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 32 0.97
27 1 0.03
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (26 bp):
TAATATTAATAAATAATAATAAATAA
Found at i:1051790 original size:19 final size:18
Alignment explanation
Indices: 1051761--1051810 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
1051751 AAATAAAACA
*
1051761 TAATAAATAATAATATTAT
1 TAAT-AATAATAATAATAT
1051780 TAAATAATAATAAATAATAT
1 T-AATAATAAT-AATAATAT
*
1051800 TATTAATAATA
1 TAATAATAATA
1051811 TTAAGCCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 1 0.04
19 15 0.56
20 11 0.41
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAATAATAATAATAATAT
Found at i:1051800 original size:23 final size:22
Alignment explanation
Indices: 1051760--1051810 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
1051750 TAAATAAAAC
1051760 ATAATAAATAATAATATTATTAA
1 ATAATAAATAATAATATTATT-A
1051783 ATAAT-AATAAATAATATTATTA
1 ATAATAAAT-AATAATATTATTA
1051805 ATAATA
1 ATAATA
1051811 TTAAGCCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 9 0.35
23 17 0.65
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
ATAATAAATAATAATATTATTA
Found at i:1054410 original size:45 final size:45
Alignment explanation
Indices: 1054346--1054825 Score: 340
Period size: 45 Copynumber: 10.8 Consensus size: 45
1054336 ATGATATCAG
* * ** * * *
1054346 AAAGGTTGACACTTTTTCGTGAGAGAGTCAAGAATAACACCACTA
1 AAAGGTTGACTCTTCTTCACGAGAAAGTCAAGAATGACAACACTA
** *
1054391 AAAGGTTGACTCTTCTTCGTGAGAAAGTCAAGAAGGACAACACTA
1 AAAGGTTGACTCTTCTTCACGAGAAAGTCAAGAATGACAACACTA
* * *
1054436 AAAGATCGACT-TCTCTTTACGAGAAAGTCAAGAATGACAACACTGA
1 AAAGGTTGACTCT-TCTTCACGAGAAAGTCAAGAATGACAACACT-A
* * * *
1054482 AAA--TTGACT-TCTCTTCACAAGAAAATCAAGAATGACAATACTG
1 AAAGGTTGACTCT-TCTTCACGAGAAAGTCAAGAATGACAACACTA
* * * * * *
1054525 AAAGATTGATTTTTCTTCACGAGAAAGTCAAGAATAATATCACTA
1 AAAGGTTGACTCTTCTTCACGAGAAAGTCAAGAATGACAACACTA
* *
1054570 AAAGGCTGA-TTTCTCTTCACGAGAAAGTCAAGGAA-GACAACACTA
1 AAAGGTTGACTCT-TCTTCACGAGAAAGTCAA-GAATGACAACACTA
* * * * * *
1054615 AAAGATAGACTCCTCTTCAAGAGAAAGTCAAGAAT-ATCATCACGA
1 AAAGGTTGACTCTTCTTCACGAGAAAGTCAAGAATGA-CAACACTA
* * * * * *
1054660 AAAGGTTG-TTTTTTTTCACGAGAAAATCAAGAATGACAATACTG
1 AAAGGTTGACTCTTCTTCACGAGAAAGTCAAGAATGACAACACTA
* * * * * *
1054704 AAAGATTGACT-TCTCTTCACGATAAAGTCAA-AA--ATAATATTG
1 AAAGGTTGACTCT-TCTTCACGAGAAAGTCAAGAATGACAACACTA
* * * *
1054746 AAAGATTGACTCCTCTTCACGAGGAAA-TCAAAAATGACAACACTG
1 AAAGGTTGACTCTTCTTCACGA-GAAAGTCAAGAATGACAACACTA
* *
1054791 AAAGATTGACT-TCTCTTCACGAGAAAGACAAGAAT
1 AAAGGTTGACTCT-TCTTCACGAGAAAGTCAAGAAT
1054826 AATATTGAAA
Statistics
Matches: 349, Mismatches: 66, Indels: 40
0.77 0.15 0.09
Matches are distributed among these distances:
42 31 0.09
43 8 0.02
44 80 0.23
45 221 0.63
46 9 0.03
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.25
Consensus pattern (45 bp):
AAAGGTTGACTCTTCTTCACGAGAAAGTCAAGAATGACAACACTA
Found at i:1054592 original size:134 final size:134
Alignment explanation
Indices: 1054411--1054830 Score: 432
Period size: 134 Copynumber: 3.1 Consensus size: 134
1054401 TCTTCTTCGT
** * * *
1054411 GAGAAAGTCAAGAAGGACAACACTAAAA-GATCGACTTCTCTTTACGAGAAAGTCAAGAATGACA
1 GAGAAAGTCAAGAATAATATCACTAAAAGGAT-GACTTCTCTTCACGAGAAAGTCAAGAA-GACA
*
1054475 ACACTGAAA-ATTGACTTCTCTTCACAAGAAAATCAAGAATGACAATACTGAAAGATTGATTTTT
64 ACACTGAAAGATTGACTCCTCTTCACAAGAAAATCAAGAATGACAATACTGAAAGATTGATTTTT
1054539 CTTCAC
129 CTTCAC
* *
1054545 GAGAAAGTCAAGAATAATATCACTAAAAGGCTGATTTCTCTTCACGAGAAAGTCAAGGAAGACAA
1 GAGAAAGTCAAGAATAATATCACTAAAAGGATGACTTCTCTTCACGAGAAAGTCAA-GAAGACAA
* * * *
1054610 CACTAAAAGATAGACTCCTCTTCA-AGAGAAAGTCAAGAAT-ATC-ATCAC-GAAAAGGTTG-TT
65 CACTGAAAGATTGACTCCTCTTCACA-AGAAAATCAAGAATGA-CAAT-ACTG-AAAGATTGATT
*
1054670 TTTTTTCAC
126 TTTCTTCAC
* * * *
1054679 GAGAAAATCAAGAATGACA-AT-ACTGAAA-GATTGACTTCTCTTCACGATAAAGTCAA-AA-AT
1 GAGAAAGTCAAGAAT-A-ATATCACTAAAAGGA-TGACTTCTCTTCACGAGAAAGTCAAGAAGAC
* * * * * * * *
1054739 AATATTGAAAGATTGACTCCTCTTCACGAGGAAATCAAAAATGACAACACTGAAAGATTGACTTC
63 AACACTGAAAGATTGACTCCTCTTCACAAGAAAATCAAGAATGACAATACTGAAAGATTGATTTT
1054804 TCTTCAC
128 TCTTCAC
*
1054811 GAGAAAGACAAGAATAATAT
1 GAGAAAGTCAAGAATAATAT
1054831 TGAAAGATTG
Statistics
Matches: 236, Mismatches: 34, Indels: 35
0.77 0.11 0.11
Matches are distributed among these distances:
130 1 0.00
131 47 0.20
132 26 0.11
133 1 0.00
134 116 0.49
135 44 0.19
136 1 0.00
ACGTcount: A:0.43, C:0.17, G:0.16, T:0.24
Consensus pattern (134 bp):
GAGAAAGTCAAGAATAATATCACTAAAAGGATGACTTCTCTTCACGAGAAAGTCAAGAAGACAAC
ACTGAAAGATTGACTCCTCTTCACAAGAAAATCAAGAATGACAATACTGAAAGATTGATTTTTCT
TCAC
Found at i:1054686 original size:179 final size:177
Alignment explanation
Indices: 1054366--1054852 Score: 542
Period size: 179 Copynumber: 2.7 Consensus size: 177
1054356 ACTTTTTCGT
* * * * **
1054366 GAGAGAGTCAAGAATAACACCACTAAAAGGTTGACTCTTCTTCGTGAGAAAGTCAAGAAGGACAA
1 GAGAAAGTCAAGAATAATATCACTAAAAGGTTGATTC-TCTTCACGAGAAAGTCAAGAAGGACAA
* *
1054431 CACTAAAAGATCGACTTCTCTTTACGAGAAAGTCAAGAATGACAACACTGAAAATTGACTTCTCT
65 CACTAAAAGATAGACTTCTCTTCACGAGAAAGTCAAGAAT-ACAACACTGAAAATTGACTTCTCT
* *
1054496 TCACAAGAAAATCAAGAATGACAATACTGAAAGATTGATTTTTCTTCAC
129 TCACAAGAAAATCAAGAATGACAATACTGAAAGATTGACTTCTCTTCAC
*
1054545 GAGAAAGTCAAGAATAATATCACTAAAAGGCTGATTTCTCTTCACGAGAAAGTCAAGGAA-GACA
1 GAGAAAGTCAAGAATAATATCACTAAAAGGTTGA-TTCTCTTCACGAGAAAGTCAA-GAAGGACA
* * * * *
1054609 ACACTAAAAGATAGACTCCTCTTCAAGAGAAAGTCAAGAATATCATCAC-GAAAAGGTTG-TTTT
64 ACACTAAAAGATAGACTTCTCTTCACGAGAAAGTCAAGAATA-CAACACTGAAAA--TTGACTTC
* *
1054672 TTTTCACGAGAAAATCAAGAATGACAATACTGAAAGATTGACTTCTCTTCAC
126 TCTTCACAAGAAAATCAAGAATGACAATACTGAAAGATTGACTTCTCTTCAC
* * * * * * *
1054724 GATAAAGTCAAAAATAATAT---TGAAAGATTGACTCCTCTTCACGAGGAAA-TCAAAAATGACA
1 GAGAAAGTCAAGAATAATATCACTAAAAGGTTGA-TTCTCTTCACGA-GAAAGTCAAGAAGGACA
* * * * * *
1054785 ACACTGAAAGATTGACTTCTCTTCACGAGAAAGACAAGAAT--AATATTGAAAGATTGACTCCTC
64 ACACTAAAAGATAGACTTCTCTTCACGAGAAAGTCAAGAATACAACACTGAAA-ATTGACTTCTC
1054848 TTCAC
128 TTCAC
1054853 GAGGGAGTCA
Statistics
Matches: 260, Mismatches: 38, Indels: 25
0.80 0.12 0.08
Matches are distributed among these distances:
173 5 0.02
174 11 0.04
175 3 0.01
176 63 0.24
177 4 0.02
178 6 0.02
179 160 0.62
180 8 0.03
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.24
Consensus pattern (177 bp):
GAGAAAGTCAAGAATAATATCACTAAAAGGTTGATTCTCTTCACGAGAAAGTCAAGAAGGACAAC
ACTAAAAGATAGACTTCTCTTCACGAGAAAGTCAAGAATACAACACTGAAAATTGACTTCTCTTC
ACAAGAAAATCAAGAATGACAATACTGAAAGATTGACTTCTCTTCAC
Found at i:1057665 original size:3 final size:3
Alignment explanation
Indices: 1057657--1057685 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1057647 TGTATAATCT
1057657 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1057686 TTATTAACCT
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1060658 original size:19 final size:19
Alignment explanation
Indices: 1060634--1060675 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1060624 TTAATAAGCT
1060634 AATGCAAAACAAGAATGCA-
1 AATGCAAAACAA-AATGCAC
*
1060653 AATGCAAAAGAAAATGCAC
1 AATGCAAAACAAAATGCAC
1060672 AATG
1 AATG
1060676 TGTTAATTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.57, C:0.14, G:0.17, T:0.12
Consensus pattern (19 bp):
AATGCAAAACAAAATGCAC
Found at i:1065660 original size:13 final size:13
Alignment explanation
Indices: 1065627--1065666 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
1065617 TTATTTTTTT
*
1065627 ATAA-AAAATGAA
1 ATAATAAAATAAA
1065639 ATAAATAAAATAAA
1 AT-AATAAAATAAA
1065653 ATAATAAAATAAA
1 ATAATAAAATAAA
1065666 A
1 A
1065667 CAAAAGATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 2 0.08
13 14 0.56
14 9 0.36
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.20
Consensus pattern (13 bp):
ATAATAAAATAAA
Found at i:1067123 original size:13 final size:14
Alignment explanation
Indices: 1067105--1067134 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1067095 GAAGACCCAA
1067105 TTTCC-TTTTTTTC
1 TTTCCTTTTTTTTC
1067118 TTTCCTTTTTTTTC
1 TTTCCTTTTTTTTC
1067132 TTT
1 TTT
1067135 GGTGTTGCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTCCTTTTTTTTC
Found at i:1069385 original size:10 final size:10
Alignment explanation
Indices: 1069355--1069393 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
1069345 ATTTTACCCT
1069355 TAAT-ATAAA
1 TAATAATAAA
*
1069364 TAAAACATAAA
1 TAATA-ATAAA
1069375 TAATAATAAA
1 TAATAATAAA
1069385 TAATAATAA
1 TAATAATAA
1069394 TATTAACTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
9 3 0.12
10 14 0.54
11 9 0.35
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (10 bp):
TAATAATAAA
Found at i:1074602 original size:19 final size:19
Alignment explanation
Indices: 1074578--1074621 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
1074568 TACATAGAAA
*
1074578 ACAGATCCTAGAATATCTC
1 ACAGATCATAGAATATCTC
*
1074597 ACAGATTATAGAATATCTC
1 ACAGATCATAGAATATCTC
1074616 ACAGAT
1 ACAGAT
1074622 TATGACTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.27
Consensus pattern (19 bp):
ACAGATCATAGAATATCTC
Found at i:1074622 original size:19 final size:19
Alignment explanation
Indices: 1074586--1074624 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1074576 AAACAGATCC
1074586 TAGAATATCTCACAGATTA
1 TAGAATATCTCACAGATTA
1074605 TAGAATATCTCACAGATTA
1 TAGAATATCTCACAGATTA
1074624 T
1 T
1074625 GACTAAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.33
Consensus pattern (19 bp):
TAGAATATCTCACAGATTA
Found at i:1083930 original size:68 final size:69
Alignment explanation
Indices: 1083836--1084046 Score: 246
Period size: 68 Copynumber: 3.0 Consensus size: 69
1083826 TTAACATTTC
* * * *
1083836 ATCTAACTGACATAATTGGCAGCTTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAA
1 ATCTAACTGACATAATTGGCACCTTTCTACCAATTACACAGTTAGACCATTATTATTTTACTCAA
1083901 CACT
66 CACT
1083905 ATCTAACTGA-ATAATTGGCACCTTTCTACCAATTACACAGTTAGACCATTATTATTTTACTCAA
1 ATCTAACTGACATAATTGGCACCTTTCTACCAATTACACAGTTAGACCATTATTATTTTACTCAA
*
1083969 CGGTATTT
66 C---A-CT
* * * *
1083977 AATCGTTCATCTAACATAATTGGCACATTTCTACCAATT-CTATAGTTAGACCATTATTATTTTA
1 -ATC--T-AACTGACATAATTGGCACCTTTCTACCAATTAC-ACAGTTAGACCATTATTATTTTA
1084041 CTCAAC
61 CTCAAC
1084047 GGTAATTAAC
Statistics
Matches: 123, Mismatches: 9, Indels: 12
0.85 0.06 0.08
Matches are distributed among these distances:
68 51 0.41
69 10 0.08
71 1 0.01
72 1 0.01
73 3 0.02
75 1 0.01
76 5 0.04
77 51 0.41
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.37
Consensus pattern (69 bp):
ATCTAACTGACATAATTGGCACCTTTCTACCAATTACACAGTTAGACCATTATTATTTTACTCAA
CACT
Found at i:1084124 original size:81 final size:80
Alignment explanation
Indices: 1083905--1084349 Score: 616
Period size: 81 Copynumber: 5.6 Consensus size: 80
1083895 ACTCAACACT
* * * * *
1083905 ATCTAACTGAATAATTGGCACCTTTCTACCAATTACACAGTTAGACCATTATTATTTTACTCAAC
1 ATCTAACTGCATAATTGGCACATTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAAC
*
1083970 GGTATTTAATCGTTC
66 GGTATTTAACCGTTC
* * *
1083985 ATCTAA---CATAATTGGCACATTTCTACCAATT-CTATAGTTAGACCATTATTATTTTACTCAA
1 ATCTAACTGCATAATTGGCACATTTCTACCAATTGC-ACAGTTAGGCCATTATTCTTTTACTCAA
*
1084046 CGGTAATTAACCGTTC
65 CGGTATTTAACCGTTC
* * * *
1084062 ATCTAACTAGAATAATTGGCACCTTTATACCAATTGCATAGTTAGGCCATTATTCTTTTACTCAA
1 ATCTAACT-GCATAATTGGCACATTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAA
*
1084127 CGTTATTTAACCGTTC
65 CGGTATTTAACCGTTC
1084143 ATCTAACTGGCATAATTGGCACATTTCTACCAATTGCACAGTTAGGCCATTATTC-TTT-CTCAA
1 ATCTAACT-GCATAATTGGCACATTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAA
*
1084206 CGGTATTTAACCATTC
65 CGGTATTTAACCGTTC
* *
1084222 ATCTAATTTACATAATTGGCACATTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAA
1 ATCTAA-CTGCATAATTGGCACATTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAA
*
1084287 CGTTATTTAA-CGTTC
65 CGGTATTTAACCGTTC
*
1084302 ATCTAACTGCCATAATTGGTACATTTCTACCAATTGCACAGTTAGGCC
1 ATCTAACTG-CATAATTGGCACATTTCTACCAATTGCACAGTTAGGCC
1084350 TCAAAGGCAC
Statistics
Matches: 329, Mismatches: 26, Indels: 20
0.88 0.07 0.05
Matches are distributed among these distances:
76 1 0.00
77 70 0.21
79 71 0.22
80 60 0.18
81 126 0.38
82 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (80 bp):
ATCTAACTGCATAATTGGCACATTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAAC
GGTATTTAACCGTTC
Found at i:1084267 original size:160 final size:160
Alignment explanation
Indices: 1083905--1084349 Score: 645
Period size: 160 Copynumber: 2.8 Consensus size: 160
1083895 ACTCAACACT
* * *
1083905 ATCTAACT-GAATAATTGGCACCTTTCTACCAATTACACAGTTAGACCATTATTATTTTACTCAA
1 ATCTAACTAGAATAATTGGCACCTTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAA
* * *
1083969 CGGTATTTAATCGTTCATCTAA---CATAATTGGCACATTTCTACCAATT-CTATAGTTAGACCA
66 CGTTATTTAA-CGTTCATCTAACTGCATAATTGGCACATTTCTACCAATTGC-ACAGTTAGGCCA
* *
1084030 TTATTATTTTACTCAACGGTAATTAACCGTTC
129 TTATTACTTTACTCAACGGTAATTAACCATTC
* *
1084062 ATCTAACTAGAATAATTGGCACCTTTATACCAATTGCATAGTTAGGCCATTATTCTTTTACTCAA
1 ATCTAACTAGAATAATTGGCACCTTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAA
1084127 CGTTATTTAACCGTTCATCTAACTGGCATAATTGGCACATTTCTACCAATTGCACAGTTAGGCCA
66 CGTTATTTAA-CGTTCATCTAACT-GCATAATTGGCACATTTCTACCAATTGCACAGTTAGGCCA
*
1084192 TTATT-CTTT-CTCAACGGTATTTAACCATTC
129 TTATTACTTTACTCAACGGTAATTAACCATTC
* * *
1084222 ATCTAATTTA-CATAATTGGCACATTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCA
1 ATCTAA-CTAGAATAATTGGCACCTTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCA
*
1084286 ACGTTATTTAACGTTCATCTAACTGCCATAATTGGTACATTTCTACCAATTGCACAGTTAGGCC
65 ACGTTATTTAACGTTCATCTAACTG-CATAATTGGCACATTTCTACCAATTGCACAGTTAGGCC
1084350 TCAAAGGCAC
Statistics
Matches: 262, Mismatches: 18, Indels: 14
0.89 0.06 0.05
Matches are distributed among these distances:
157 8 0.03
158 72 0.27
159 50 0.19
160 86 0.33
161 5 0.02
162 40 0.15
163 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (160 bp):
ATCTAACTAGAATAATTGGCACCTTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAA
CGTTATTTAACGTTCATCTAACTGCATAATTGGCACATTTCTACCAATTGCACAGTTAGGCCATT
ATTACTTTACTCAACGGTAATTAACCATTC
Found at i:1084411 original size:68 final size:69
Alignment explanation
Indices: 1084337--1084487 Score: 250
Period size: 68 Copynumber: 2.2 Consensus size: 69
1084327 TCTACCAATT
* * *
1084337 GCACAGTTAGGCCTCAAAGGCACTTAGCCTTTTATCTAACTGGCAT-AATTGACACCTTTCTGTC
1 GCACAGTTAGGCCTCAAAGGCACTTAGCCGTTCATCTAACTGGCATAAAATGACACCTTTCTGTC
1084401 ATAA
66 ATAA
*
1084405 GCACAGTTAGGCCTCAAAGGCACTTAGGCGTTCATCTAACTGGCATAAAATGACACCTTTCTGTC
1 GCACAGTTAGGCCTCAAAGGCACTTAGCCGTTCATCTAACTGGCATAAAATGACACCTTTCTGTC
1084470 ATAA
66 ATAA
*
1084474 GCACATTTAGGCCT
1 GCACAGTTAGGCCT
1084488 ATTAATCTTT
Statistics
Matches: 77, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
68 43 0.56
69 34 0.44
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.28
Consensus pattern (69 bp):
GCACAGTTAGGCCTCAAAGGCACTTAGCCGTTCATCTAACTGGCATAAAATGACACCTTTCTGTC
ATAA
Found at i:1085295 original size:95 final size:95
Alignment explanation
Indices: 1085168--1085357 Score: 233
Period size: 95 Copynumber: 2.0 Consensus size: 95
1085158 CTATACTTCT
* * *
1085168 ATACTATGGTATCGATACCCCCTTCTGGTATCGATAC-TGATTTTAGGTTCGATGTTGCCTAGTA
1 ATACTATGGTATCAATACCCCCTTCTGGTATCGATACAGGATTTTA-ATTCGATGTTGCCTAGTA
* * *
1085232 TCGATTCTCTTACCATGGTATCGATACTACC
65 TCGATACCCTTACCATGGTATCAATACTACC
* * *
1085263 ATACTATGGTA-CTAATACCCCTTTAC-GGTATCGATACAGGTTTTTAATTCGATGTTGCTTAGT
1 ATACTATGGTATC-AATACCCCCTT-CTGGTATCGATACAGGATTTTAATTCGATGTTGCCTAGT
* *
1085326 ATCGATACCCTTATCATGGTATCAATATTACC
64 ATCGATACCCTTACCATGGTATCAATACTACC
1085358 TCTTCGGTAT
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
94 1 0.01
95 73 0.90
96 7 0.09
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (95 bp):
ATACTATGGTATCAATACCCCCTTCTGGTATCGATACAGGATTTTAATTCGATGTTGCCTAGTAT
CGATACCCTTACCATGGTATCAATACTACC
Found at i:1086421 original size:65 final size:65
Alignment explanation
Indices: 1086239--1086423 Score: 202
Period size: 65 Copynumber: 2.9 Consensus size: 65
1086229 TTGGACCCTT
* * * *
1086239 AATGCATTCAATATTTCA-AAATAGCATGAGTGCATCGATGCATGG-CTGGTGCATCGATGCATC
1 AATGCATTCGATGTTTCATAAA-ACCATGAGTGCATCGATGCATGGATTGGTGCATCGATGCATC
1086302 A
65 A
*
1086303 AATGCATTCGATGTTTTCATAAAACCCTGAGTGCATCGATGCAT-GATAT-GTGCATCGATGCAT
1 AATGCATTCGATG-TTTCATAAAACCATGAGTGCATCGATGCATGGAT-TGGTGCATCGATGCAT
*
1086366 GA
64 CA
* **
1086368 AATGCATTCGATG-TTCAATTTATTCCATG-GTGCATCGATGCATGGATTGGTGCATC
1 AATGCATTCGATGTTTC-A-TAAAACCATGAGTGCATCGATGCATGGATTGGTGCATC
1086424 ACGTTGAAAA
Statistics
Matches: 103, Mismatches: 10, Indels: 15
0.80 0.08 0.12
Matches are distributed among these distances:
63 3 0.03
64 28 0.27
65 68 0.66
66 4 0.04
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.31
Consensus pattern (65 bp):
AATGCATTCGATGTTTCATAAAACCATGAGTGCATCGATGCATGGATTGGTGCATCGATGCATCA
Found at i:1087466 original size:36 final size:36
Alignment explanation
Indices: 1087426--1087498 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
1087416 CTTCACTTTC
1087426 TACTTATAACATTCTTATCCAAATTTTTTTCGTCTT
1 TACTTATAACATTCTTATCCAAATTTTTTTCGTCTT
1087462 TACTTATAACATTCTTATCCAAATTTTTTTCGTCTT
1 TACTTATAACATTCTTATCCAAATTTTTTTCGTCTT
1087498 T
1 T
1087499 CGTTTGTAAT
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:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (36 bp):
TACTTATAACATTCTTATCCAAATTTTTTTCGTCTT
Found at i:1091039 original size:81 final size:81
Alignment explanation
Indices: 1090451--1091042 Score: 797
Period size: 81 Copynumber: 7.3 Consensus size: 81
1090441 ATTTGACAAT
* * * ** * * * * **
1090451 TTTCTATCAAATGCACAGCTAATCCATTATTCTTTTATTCAACAGTGTTTAACCTTTTGTCTAAC
1 TTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAAC
1090516 TGGCATAATTGGCACC
66 TGGCATAATTGGCACC
* * ** *
1090532 TTTCTACCAATTGCACAGTTATGCCATTATTCTTTTACTCAACGGTATTTAGCAATTCCTCTAAC
1 TTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAAC
* *
1090597 TGGCATAATTGACACA
66 TGGCATAATTGGCACC
*
1090613 TTTCTACTAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAAC
1 TTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAAC
*
1090678 TGGCATAATTGACACC
66 TGGCATAATTGGCACC
* *
1090694 TTTATACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTAATTAACCGTTCATCTAAC
1 TTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAAC
*
1090759 TGACATAATTGGCACC
66 TGGCATAATTGGCACC
* * ** *
1090775 TTTCTACCAATTGAACAGTTAGGCCATTATTCTTTTACTTAAATGTATTTAACCATTCATCTAAC
1 TTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAAC
*
1090840 TGGCATAATTGGCACT
66 TGGCATAATTGGCACC
* * * * *
1090856 TTTCTTCCAATTTCATAGTTAGGCCATTATTCTTTTACTCAATGGTATTTAATCGTTCATCTAAC
1 TTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAAC
***
1090921 TATTATAATTGGCACC
66 TGGCATAATTGGCACC
* * *
1090937 TTTCTACTAATTGCACAGTTAGGCCATTATTCTTTTACTCATCAGTATTTAACCGTTCATCTAAC
1 TTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAAC
* *
1091002 TTGCATAATTGCCACC
66 TGGCATAATTGGCACC
*
1091018 TTTCTACCAATTTCACAGTTAGGCC
1 TTTCTACCAATTGCACAGTTAGGCC
1091043 TCAAAGGCAC
Statistics
Matches: 448, Mismatches: 63, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 448 1.00
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.39
Consensus pattern (81 bp):
TTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAAC
TGGCATAATTGGCACC
Found at i:1091103 original size:68 final size:68
Alignment explanation
Indices: 1090992--1091177 Score: 284
Period size: 68 Copynumber: 2.7 Consensus size: 68
1090982 TATTTAACCG
* * * * ** *
1090992 TTCATCTAACTTGCATAATTGCCACCTTTCTACCA-ATTTCACAGTTAGGCCTCAAAGGCACTTA
1 TTCATCTAACTGGCATAAATGACACCTTTCTATCATA-AGCACAGTTAGGCCTCAAAGACACTTA
1091056 GCCT
65 GCCT
1091060 TTCATCTAACTGGCATAAATGACACCTTTCTATCATAAGCACAGTTAGGCCTCAAAGACACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTATCATAAGCACAGTTAGGCCTCAAAGACACTTAG
1091125 CCT
66 CCT
*
1091128 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATAAGCACAGTTAGGC
1 TTCATCTAACTGGCATAAATGACACCTTTCTATCATAAGCACAGTTAGGC
1091178 ATATTAATCT
Statistics
Matches: 109, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
68 108 0.99
69 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACCTTTCTATCATAAGCACAGTTAGGCCTCAAAGACACTTAG
CCT
Found at i:1091516 original size:56 final size:53
Alignment explanation
Indices: 1091394--1091538 Score: 166
Period size: 56 Copynumber: 2.6 Consensus size: 53
1091384 ATATTTTTCA
* * * *
1091394 ATACGAACATTCATACACTTGGTAAGAATTTCTTAGTTCGCACATATAGTGCCC
1 ATACGAA-ATTCATACACTTAGTATGAATTTCTTAGTTCGCACACAAAGTGCCC
*
1091448 ATACGGAAATTCATACACTTAGTATGAATTTCCTTATTTTTC-CACACAAAGTGCCC
1 ATAC-GAAATTCATACACTTAGTATGAATTT-CTTA--GTTCGCACACAAAGTGCCC
* *
1091504 ATACAGAAATTCATACACTTAGCATGAATATCTTA
1 ATAC-GAAATTCATACACTTAGTATGAATTTCTTA
1091539 CAATTTTTGC
Statistics
Matches: 79, Mismatches: 8, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
54 25 0.32
55 11 0.14
56 40 0.51
57 3 0.04
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.32
Consensus pattern (53 bp):
ATACGAAATTCATACACTTAGTATGAATTTCTTAGTTCGCACACAAAGTGCCC
Found at i:1092065 original size:95 final size:95
Alignment explanation
Indices: 1091923--1092105 Score: 224
Period size: 95 Copynumber: 1.9 Consensus size: 95
1091913 ACTTCTATAT
* ** *
1091923 TATGGTATCAATACCCTTTTCTGGTATCGATATTGATTTTAGGTTCGATGTTGCCTAGTATCGAT
1 TATGGTATCAATACCCTTTACTGGTATCGATACAGATTTTAGATTCGATGTTGCCTAGTATCGAT
* *
1091988 TCTCTTACCATGGTATCGATACTACCATAC
66 ACCCTTACCATGGTATCGATACTACCATAC
* * * * * *
1092018 TATGGTATCGATACCCCTTTAC-GGTATCGATACAGGTTTTTGATTCGATGTTGCTTATTATTGA
1 TATGGTATCAATA-CCCTTTACTGGTATCGATACAGATTTTAGATTCGATGTTGCCTAGTATCGA
* *
1092082 TACCCTTATCATGGTATTGATACT
65 TACCCTTACCATGGTATCGATACT
1092106 GATTGAATCA
Statistics
Matches: 73, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
95 66 0.90
96 7 0.10
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.41
Consensus pattern (95 bp):
TATGGTATCAATACCCTTTACTGGTATCGATACAGATTTTAGATTCGATGTTGCCTAGTATCGAT
ACCCTTACCATGGTATCGATACTACCATAC
Found at i:1095401 original size:36 final size:37
Alignment explanation
Indices: 1095348--1095418 Score: 92
Period size: 36 Copynumber: 1.9 Consensus size: 37
1095338 AATATATATA
*
1095348 TTCTGATCTGAATGCACTTTGTGTGCATAT-TGTTAT
1 TTCTGATCTGAATGCACTGTGTGTGCATATCTGTTAT
* *
1095384 TTCTGATGTG-ATAGCACTGTGTGTGCTTATCTGTT
1 TTCTGATCTGAAT-GCACTGTGTGTGCATATCTGTT
1095419 CCAACTCTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
35 2 0.07
36 24 0.80
37 4 0.13
ACGTcount: A:0.17, C:0.14, G:0.23, T:0.46
Consensus pattern (37 bp):
TTCTGATCTGAATGCACTGTGTGTGCATATCTGTTAT
Found at i:1095716 original size:17 final size:18
Alignment explanation
Indices: 1095684--1095724 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
1095674 TAGTCTATTT
*
1095684 TATTTTAATGATTTTATA
1 TATTTCAATGATTTTATA
*
1095702 TATTTCAAT-ATTTTATT
1 TATTTCAATGATTTTATA
1095719 TATTTC
1 TATTTC
1095725 TTTTCACCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TATTTCAATGATTTTATA
Found at i:1098086 original size:3 final size:3
Alignment explanation
Indices: 1098078--1098112 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1098068 TTAGCCGAGC
1098078 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1098113 AAACCCAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1112994 original size:23 final size:24
Alignment explanation
Indices: 1112959--1113025 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 24
1112949 TGTGTTTATA
* *
1112959 TTAAAATAGAATACAATTCCTAAT
1 TTAATATATAATACAATTCCTAAT
1112983 TTAATA-ATAATACAA-T-C--AT
1 TTAATATATAATACAATTCCTAAT
*
1113002 TTAATATATAATACAATTCATAAT
1 TTAATATATAATACAATTCCTAAT
1113026 AATTAAAAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
19 8 0.23
20 9 0.26
21 2 0.06
22 1 0.03
23 8 0.23
24 7 0.20
ACGTcount: A:0.51, C:0.10, G:0.01, T:0.37
Consensus pattern (24 bp):
TTAATATATAATACAATTCCTAAT
Found at i:1113025 original size:19 final size:18
Alignment explanation
Indices: 1112983--1113028 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 18
1112973 AATTCCTAAT
1112983 TTAATAATAATACAATCA
1 TTAATAATAATACAATCA
1113001 TTTAATATATAATACAATTCA
1 -TTAATA-ATAATACAA-TCA
1113022 -TAATAAT
1 TTAATAAT
1113029 TAAAAGATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 2 0.08
19 11 0.44
20 9 0.36
21 3 0.12
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (18 bp):
TTAATAATAATACAATCA
Found at i:1126644 original size:2 final size:2
Alignment explanation
Indices: 1126637--1126665 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1126627 TGCCTAAATA
1126637 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 A
1126666 ATAATAATCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1128291 original size:3 final size:3
Alignment explanation
Indices: 1128283--1128316 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
1128273 ACAAAATGTA
1128283 AAT AAT AAT AAT AAT AAT AAT AATT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT
1128317 TTAAAATAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:1128312 original size:10 final size:10
Alignment explanation
Indices: 1128283--1128330 Score: 57
Period size: 10 Copynumber: 4.9 Consensus size: 10
1128273 ACAAAATGTA
1128283 AATAA-TAAT
1 AATAATTAAT
1128292 AATAA-TAAT
1 AATAATTAAT
1128301 AATAATTAAT
1 AATAATTAAT
1128311 AATAATTTAA-
1 AATAA-TTAAT
1128321 AATAACTTAA
1 AATAA-TTAA
1128331 AAACTCGGAC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
9 14 0.39
10 18 0.50
11 4 0.11
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (10 bp):
AATAATTAAT
Found at i:1128719 original size:138 final size:137
Alignment explanation
Indices: 1128515--1128925 Score: 490
Period size: 137 Copynumber: 3.0 Consensus size: 137
1128505 GGTAAATTTG
* * * * * * *
1128515 GAGACAACAAGGTTCCTACACGATGAGAAAATCTGGTTATCTAAGGGTGACGCTGCTCCTAAGTG
1 GAGATAACACGGTTCCTACGCGATGAGGAAATCTGGCTATCTAAGGATGACGCTGCTCCTACGTG
* * *
1128580 ATGAAGAGATCTAGTCGGTGGATAACATTGTTCTTACGTGATGAGGATGTCTGGCCATCTTTAGG
66 ATGAGGAGATCTAGTCGGTGGATGACATTGTTCCTACGTGATGAGGATGTCTGGCCATCTTTAGG
*
1128645 GGTAA-A
131 GATAATA
* * *
1128651 TGAAGATAACACGGTTCCTACGCGATGAGGAACTTTGGCTATCTAAGGATGACG-TGACTACTAC
1 -G-AGATAACACGGTTCCTACGCGATGAGGAAATCTGGCTATCTAAGGATGACGCTG-CTCCTAC
* * *
1128715 GTGATGAGGAGATC-AGGTCGGTGGATGACA-CGATTCCTA-GTTGATGAGGATGTATGGCCATA
63 GTGATGAGGAGATCTA-GTCGGTGGATGACATTG-TTCCTACG-TGATGAGGATGTCTGGCCATC
1128777 TTTAGGGATAATA
125 TTTAGGGATAATA
* ** * * *
1128790 GAGATAACACAGTTCCTACGTAATGACGAAGTCTGGCTATCTAAGGATGACGTTGCTCCTACGTG
1 GAGATAACACGGTTCCTACGCGATGAGGAAATCTGGCTATCTAAGGATGACGCTGCTCCTACGTG
* * * *
1128855 ATGAGGAGATCTGGTCAGTGGATGACATTGTTCCTACGTGATGATGATGTCTGACCATCTTTAGG
66 ATGAGGAGATCTAGTCGGTGGATGACATTGTTCCTACGTGATGAGGATGTCTGGCCATCTTTAGG
1128920 GATAAT
131 GATAAT
1128926 TTTGTTTCAA
Statistics
Matches: 233, Mismatches: 31, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
137 119 0.51
138 113 0.48
139 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (137 bp):
GAGATAACACGGTTCCTACGCGATGAGGAAATCTGGCTATCTAAGGATGACGCTGCTCCTACGTG
ATGAGGAGATCTAGTCGGTGGATGACATTGTTCCTACGTGATGAGGATGTCTGGCCATCTTTAGG
GATAATA
Found at i:1129107 original size:64 final size:65
Alignment explanation
Indices: 1128928--1129195 Score: 328
Period size: 64 Copynumber: 4.0 Consensus size: 65
1128918 GGGATAATTT
* * * * *
1128928 TGTTTCAA-AGGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACAATCTCAATTGTC
1 TGTTTCAAGA-GAAACTGTCTCAAGCGAGAC-AAATTTGTTTCAAAGGAAACAATCTCAA-AG-G
1128992 TTTA
62 TTTA
*
1128996 TGTTTCAAGAGAAA-TGTCTCAAGCGAGACAAAATTTGTTTC-AGGGAAACAATCTCAAAGGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGAC-AAATTTGTTTCAAAGGAAACAATCTCAAAGGTTT
1129059 A
65 A
*
1129060 TGTTTCAAGAGAAATTGTCTCAAGCGAGAC-AATTTGTTTCAAAGGAAACAATCTCAAAGGTTTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAATTTGTTTCAAAGGAAACAATCTCAAAGG----
*
1129124 TTTTT
62 -TTTA
*
1129129 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAGATTTGTTTCAAAAGAAACAATCTCAAAGGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAA-ATTTGTTTCAAAGGAAACAATCTCAAAGGTTT
1129194 A
65 A
1129195 T
1 T
1129196 TAATTTTGTT
Statistics
Matches: 181, Mismatches: 9, Indels: 22
0.85 0.04 0.10
Matches are distributed among these distances:
63 10 0.06
64 36 0.20
65 16 0.09
66 20 0.11
67 25 0.14
68 12 0.07
69 33 0.18
70 1 0.01
71 28 0.15
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.31
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAATTTGTTTCAAAGGAAACAATCTCAAAGGTTTA
Found at i:1132004 original size:12 final size:12
Alignment explanation
Indices: 1131987--1132098 Score: 70
Period size: 13 Copynumber: 9.0 Consensus size: 12
1131977 AAGTGATCCA
1131987 TTTTTTTTC-TT
1 TTTTTTTTCTTT
1131998 TTTTTTTTC---
1 TTTTTTTTCTTT
1132007 TTTTTTTTCTTT
1 TTTTTTTTCTTT
*
1132019 GTTTTTTTCTTT
1 TTTTTTTTCTTT
*
1132031 GTTTATTTTCTCTT
1 -TTTTTTTTCT-TT
* *
1132045 TGTTTTTTGTTT
1 TTTTTTTTCTTT
*
1132057 TTTTCTTTGCTTCT
1 TTTT-TTTTCTT-T
*
1132071 TTTCTCTTTATTTTT
1 TTT-T-TTT-TCTTT
1132086 TGTTTTTTTCTTT
1 T-TTTTTTTCTTT
1132099 GATTTGATCT
Statistics
Matches: 79, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
9 9 0.11
11 9 0.11
12 16 0.20
13 24 0.30
14 9 0.11
15 8 0.10
16 4 0.05
ACGTcount: A:0.02, C:0.11, G:0.05, T:0.82
Consensus pattern (12 bp):
TTTTTTTTCTTT
Found at i:1132040 original size:34 final size:33
Alignment explanation
Indices: 1131988--1132099 Score: 156
Period size: 34 Copynumber: 3.4 Consensus size: 33
1131978 AGTGATCCAT
*
1131988 TTTTTTTCTTT-TTTTTTTCT-TTTTTTTCTTTG
1 TTTTTTTCTTTGTTTTTTTCTCTTTATTT-TTTG
*
1132020 TTTTTTTCTTTGTTTATTTTCTCTTTGTTTTTTG
1 TTTTTTTCTTTGTTT-TTTTCTCTTTATTTTTTG
*
1132054 TTTTTTTCTTTGCTTCTTTTCTCTTTATTTTTTG
1 TTTTTTTCTTTG-TTTTTTTCTCTTTATTTTTTG
1132088 TTTTTTTCTTTG
1 TTTTTTTCTTTG
1132100 ATTTGATCTT
Statistics
Matches: 73, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
32 11 0.15
33 3 0.04
34 51 0.70
35 8 0.11
ACGTcount: A:0.02, C:0.11, G:0.06, T:0.81
Consensus pattern (33 bp):
TTTTTTTCTTTGTTTTTTTCTCTTTATTTTTTG
Found at i:1132099 original size:12 final size:12
Alignment explanation
Indices: 1131988--1132099 Score: 91
Period size: 11 Copynumber: 10.0 Consensus size: 12
1131978 AGTGATCCAT
1131988 TTTTTTTCTTT-
1 TTTTTTTCTTTG
1131999 TTTTTTTC--T-
1 TTTTTTTCTTTG
1132008 TTTTTTTCTTTG
1 TTTTTTTCTTTG
1132020 TTTTTTTCTTTG
1 TTTTTTTCTTTG
*
1132032 TTTATTTTC--TC
1 TTT-TTTTCTTTG
*
1132043 TTTGTTT-TTTG
1 TTTTTTTCTTTG
1132054 TTTTTTTCTTTG
1 TTTTTTTCTTTG
* *
1132066 CTTCTTTTC--TC
1 -TTTTTTTCTTTG
*
1132077 TTTATTT-TTTG
1 TTTTTTTCTTTG
1132088 TTTTTTTCTTTG
1 TTTTTTTCTTTG
1132100 ATTTGATCTT
Statistics
Matches: 80, Mismatches: 10, Indels: 21
0.72 0.09 0.19
Matches are distributed among these distances:
9 9 0.11
10 8 0.10
11 28 0.35
12 23 0.29
13 12 0.15
ACGTcount: A:0.02, C:0.11, G:0.06, T:0.81
Consensus pattern (12 bp):
TTTTTTTCTTTG
Found at i:1135772 original size:2 final size:2
Alignment explanation
Indices: 1135765--1135806 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
1135755 TGCCTAAATA
* *
1135765 AT AT AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1135807 GAATATAGTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1139102 original size:32 final size:32
Alignment explanation
Indices: 1139066--1139134 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
1139056 AACTCCTTAC
1139066 TCTTAACATTTATAACTTCTTCATCCTTTGGT
1 TCTTAACATTTATAACTTCTTCATCCTTTGGT
1139098 TCTTAACATTTATAACTTCTTCATCCTTTGGT
1 TCTTAACATTTATAACTTCTTCATCCTTTGGT
1139130 T-TTAA
1 TCTTAA
1139135 GAAATCTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 4 0.11
32 33 0.89
ACGTcount: A:0.23, C:0.20, G:0.06, T:0.51
Consensus pattern (32 bp):
TCTTAACATTTATAACTTCTTCATCCTTTGGT
Found at i:1141962 original size:19 final size:20
Alignment explanation
Indices: 1141917--1141963 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
1141907 TACAAAATCG
*
1141917 TAAAAAAAATCAACTTATAT
1 TAAATAAAATCAACTTATAT
1141937 TAAATAAAA-CAACATTAT-T
1 TAAATAAAATCAAC-TTATAT
*
1141956 TACATAAA
1 TAAATAAA
1141964 CTTAAACAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (20 bp):
TAAATAAAATCAACTTATAT
Found at i:1145924 original size:3 final size:3
Alignment explanation
Indices: 1145916--1145976 Score: 104
Period size: 3 Copynumber: 20.0 Consensus size: 3
1145906 ACAAAATGTA
*
1145916 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1145964 AATT AAT AAT AAT
1 AA-T AAT AAT AAT
1145977 TTAAAATAAC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
3 52 0.95
4 3 0.05
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:1147277 original size:19 final size:19
Alignment explanation
Indices: 1147253--1147289 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1147243 ATGACCAACA
*
1147253 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
1147272 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
1147290 CATTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:1147338 original size:20 final size:20
Alignment explanation
Indices: 1147315--1147404 Score: 83
Period size: 20 Copynumber: 4.5 Consensus size: 20
1147305 GTTTCCAGAT
* *
1147315 TCGCAATGCGATTTTGACTA
1 TCGCAACGCGATTCTGACTA
**
1147335 TCGCAACGCGATAAT-ACATAA
1 TCGCAACGCGATTCTGAC-T-A
*
1147356 TCGCAACGAGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
* * *
1147376 TCGTAATGCGATTCTGACTG
1 TCGCAACGCGATTCTGACTA
1147396 TCGCAACGC
1 TCGCAACGC
1147405 TGAATTTCAA
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
19 2 0.04
20 37 0.67
21 14 0.25
22 2 0.04
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTA
Found at i:1148248 original size:24 final size:24
Alignment explanation
Indices: 1148221--1148274 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1148211 GTATTCGAAA
1148221 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1148245 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1148269 TTTGAT
1 TTTGAT
1148275 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1150856 original size:140 final size:140
Alignment explanation
Indices: 1150604--1150883 Score: 542
Period size: 140 Copynumber: 2.0 Consensus size: 140
1150594 GCAAACGTTG
1150604 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
*
1150669 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCACAACG
1150734 CGAATTTGAC
131 CGAATTTGAC
1150744 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
*
1150809 TTGAATATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCACAACG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCACAACG
1150874 CGAATTTGAC
131 CGAATTTGAC
1150884 CATCGCAACG
Statistics
Matches: 138, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 138 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.43
Consensus pattern (140 bp):
TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCACAACG
CGAATTTGAC
Found at i:1150882 original size:20 final size:20
Alignment explanation
Indices: 1150857--1151047 Score: 223
Period size: 20 Copynumber: 9.8 Consensus size: 20
1150847 TTACACATTC
* *
1150857 ATTTGAATATCACAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
1150877 ATTTGACCATCGCAACGCAA
1 ATTTGACTATCGCAACGCGA
1150897 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
1150917 ATATGACTATCGCAACAC-A
1 ATTTGACTATCGCAACGCGA
* * *
1150936 A----A-AAGCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
1150951 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1150971 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* *
1150991 ATTTGATTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
*
1151011 ATTTGACTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
1151031 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
1151048 AGAAAATCAC
Statistics
Matches: 146, Mismatches: 19, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
14 7 0.05
15 3 0.02
19 3 0.02
20 133 0.91
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:1150945 original size:54 final size:54
Alignment explanation
Indices: 1150885--1151096 Score: 212
Period size: 54 Copynumber: 3.8 Consensus size: 54
1150875 GAATTTGACC
*
1150885 ATCGCAACGCAAATTTGACTATCGCAACGCGAATATGACTATCGCAAC-ACAAAA
1 ATCGCAACGCAAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGA-AAAA
* * * **
1150939 AGCGCAATGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGTGAATTTGATT
1 ATCGCAACGCAAATTTGACTATCGCAACGCGAATTTGACTATCGCAAC--GAA----AAA
** * *
1150999 ATCGCAACGGGAATTTGACTATCGCAACGGGAATTTGACTATCGCAACGAGAAA
1 ATCGCAACGCAAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAAAAA
* * * * *
1151053 ATCACAAAGCATATTAGACTATCGCAACGCGAA-TTGACTTTCGC
1 ATCGCAACGCAAATTTGACTATCGCAACGCGAATTTGACTATCGC
1151097 GTTGCGATTT
Statistics
Matches: 130, Mismatches: 21, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
53 10 0.08
54 71 0.55
56 1 0.01
57 1 0.01
58 2 0.02
60 45 0.35
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (54 bp):
ATCGCAACGCAAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAAAAA
Found at i:1151111 original size:20 final size:20
Alignment explanation
Indices: 1151086--1151143 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
1151076 GCAACGCGAA
1151086 TTGACTTTCGCGTTGCGATT
1 TTGACTTTCGCGTTGCGATT
**
1151106 TTGACTTTCGTATTGCGATT
1 TTGACTTTCGCGTTGCGATT
* *
1151126 TTGAGTTTAGCGTTGCGA
1 TTGACTTTCGCGTTGCGA
1151144 AAGTGTACCT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.14, C:0.16, G:0.26, T:0.45
Consensus pattern (20 bp):
TTGACTTTCGCGTTGCGATT
Found at i:1151259 original size:36 final size:36
Alignment explanation
Indices: 1151218--1151326 Score: 119
Period size: 36 Copynumber: 3.3 Consensus size: 36
1151208 TTACATTTCA
1151218 ATCAATTAAATAAGCACAAATAAGAATTATTTACAC
1 ATCAATTAAATAAGCACAAATAAGAATTATTTACAC
* * *
1151254 ATCAA-T---TAA--ACAAAT--CAACT-TTTACAA
1 ATCAATTAAATAAGCACAAATAAGAATTATTTACAC
*
1151281 ATCAATTAAACAAGCACAAATAAGAATTATTTACAC
1 ATCAATTAAATAAGCACAAATAAGAATTATTTACAC
1151317 ATCAATTAAA
1 ATCAATTAAA
1151327 CAAATCAACT
Statistics
Matches: 57, Mismatches: 7, Indels: 18
0.70 0.09 0.22
Matches are distributed among these distances:
27 11 0.19
28 4 0.07
30 6 0.11
31 2 0.04
32 3 0.05
33 6 0.11
35 4 0.07
36 21 0.37
ACGTcount: A:0.53, C:0.16, G:0.04, T:0.28
Consensus pattern (36 bp):
ATCAATTAAATAAGCACAAATAAGAATTATTTACAC
Found at i:1151279 original size:27 final size:27
Alignment explanation
Indices: 1151247--1151356 Score: 103
Period size: 27 Copynumber: 3.7 Consensus size: 27
1151237 ATAAGAATTA
*
1151247 TTTACACATCAATTAAACAAATCAACT
1 TTTACAAATCAATTAAACAAATCAACT
* *
1151274 TTTACAAATCAATTAAACAAGCACAAATAAGAATT
1 TTTACAAATCAATT----AA--ACAAAT--CAACT
*
1151309 ATTTACACATCAATTAAACAAATCAACT
1 -TTTACAAATCAATTAAACAAATCAACT
1151337 TTTACAAATCAATTAAACAA
1 TTTACAAATCAATTAAACAA
1151357 GCAAAAATGC
Statistics
Matches: 67, Mismatches: 7, Indels: 18
0.73 0.08 0.20
Matches are distributed among these distances:
27 32 0.48
28 3 0.04
30 6 0.09
31 2 0.03
32 2 0.03
33 6 0.09
35 3 0.04
36 13 0.19
ACGTcount: A:0.52, C:0.18, G:0.02, T:0.28
Consensus pattern (27 bp):
TTTACAAATCAATTAAACAAATCAACT
Found at i:1151303 original size:63 final size:64
Alignment explanation
Indices: 1151195--1151427 Score: 292
Period size: 63 Copynumber: 3.5 Consensus size: 64
1151185 GATTGAAATC
*
1151195 AACAAATCAACTTTTACATTTCAATCAATTAAATAAGCACAAATAAGAATTATTTACACATCAAT
1 AACAAATCAACTTTTACA--T-AATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAAT
1151260 TA
63 TA
1151262 AACAAATCAACTTTTACA-AATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATTA
1 AACAAATCAACTTTTACATAATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATTA
* * * *
1151325 AACAAATCAACTTTTACA-AATCAATTAAACAAGCAAAAATGCTAATAATTCTTATTTTCCTCAT
1 AACAAATCAACTTTTACATAATCAATTAAACAAGCACAAA---TAAGAA---TTA-TTTACACAT
1151389 CAATTA
59 CAATTA
*
1151395 AACAAATCAGACTTTTA-AGAATCAATTAAACAA
1 AACAAATCA-ACTTTTACATAATCAATTAAACAA
1151428 TAAAAAAAAG
Statistics
Matches: 152, Mismatches: 5, Indels: 14
0.89 0.03 0.08
Matches are distributed among these distances:
63 82 0.54
66 5 0.03
67 18 0.12
69 3 0.02
70 23 0.15
71 21 0.14
ACGTcount: A:0.50, C:0.17, G:0.03, T:0.30
Consensus pattern (64 bp):
AACAAATCAACTTTTACATAATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATTA
Found at i:1152791 original size:42 final size:42
Alignment explanation
Indices: 1152732--1152825 Score: 127
Period size: 42 Copynumber: 2.2 Consensus size: 42
1152722 GTGAATCGGG
*
1152732 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGA-CTCTTCAACGATGACAGGGGC
* ** *
1152774 CTCTTGAACGGTGGGAGGGGACTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTTCAACGATGACAGGGGC
1152816 CTCTTGAACG
1 CTCTTGAACG
1152826 ATAGGAGAGG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 42 0.91
43 4 0.09
ACGTcount: A:0.20, C:0.19, G:0.38, T:0.22
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGGACTCTTCAACGATGACAGGGGC
Found at i:1152792 original size:21 final size:21
Alignment explanation
Indices: 1152732--1152846 Score: 88
Period size: 21 Copynumber: 5.5 Consensus size: 21
1152722 GTGAATCGGG
* *
1152732 CTCTTGAATGGTGGGAGGGAC
1 CTCTTGAACGGTGGGAGGGGC
* * **
1152753 CTCTTCAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
*
1152774 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGC
* **
1152795 CTCTTG-AGGGATGATAGGGGC
1 CTCTTGAACGG-TGGGAGGGGC
* * *
1152816 CTCTTGAACGATAGGAGAGGC
1 CTCTTGAACGGTGGGAGGGGC
*
1152837 CTTTTGAACG
1 CTCTTGAACG
1152847 ATGAAAGGTG
Statistics
Matches: 70, Mismatches: 22, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
20 3 0.04
21 65 0.93
22 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.37, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGC
Found at i:1152850 original size:42 final size:42
Alignment explanation
Indices: 1152745--1152850 Score: 115
Period size: 42 Copynumber: 2.5 Consensus size: 42
1152735 TTGAATGGTG
* * *
1152745 GGAG-GGACCTCTTCAACGATGACAGGGGCCTCTTGAACGGTG
1 GGAGAGGA-CTCTTGAACGATGACAGGGGCCTCTTGAACGATA
* ** *
1152787 GGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGATA
1 GGAGAGGACTCTTGAACGATGACAGGGGCCTCTTGAACGATA
* *
1152829 GGAGAGGCCTTTTGAACGATGA
1 GGAGAGGACTCTTGAACGATGA
1152851 AAGGTGAGTT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
42 49 0.94
43 3 0.06
ACGTcount: A:0.24, C:0.18, G:0.38, T:0.21
Consensus pattern (42 bp):
GGAGAGGACTCTTGAACGATGACAGGGGCCTCTTGAACGATA
Found at i:1153355 original size:20 final size:20
Alignment explanation
Indices: 1153330--1153372 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1153320 AATAGTTTCT
1153330 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCGCAACAC
* *
1153350 GAAACTTCAAATCGCAACGC
1 GAAACTTAAAATCGCAACAC
1153370 GAA
1 GAA
1153373 TTTGACTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.47, C:0.26, G:0.14, T:0.14
Consensus pattern (20 bp):
GAAACTTAAAATCGCAACAC
Found at i:1153417 original size:19 final size:19
Alignment explanation
Indices: 1153393--1153444 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
1153383 GCAACGGGAT
* *
1153393 AATCGCAATGCGAAATAAA
1 AATCGCAACGCGAAACAAA
* *
1153412 AATCGCAACGAGAAACCAA
1 AATCGCAACGCGAAACAAA
1153431 AATCGCAACGCGAA
1 AATCGCAACGCGAA
1153445 GCTAAATTCG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.50, C:0.23, G:0.17, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:1153480 original size:20 final size:20
Alignment explanation
Indices: 1153451--1153488 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1153441 CGAAGCTAAA
*
1153451 TTCGCGTTGCGATTTTCATT
1 TTCGCATTGCGATTTTCATT
1153471 TTCGCATTGCGATTTTCA
1 TTCGCATTGCGATTTTCA
1153489 CGTTGCGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.47
Consensus pattern (20 bp):
TTCGCATTGCGATTTTCATT
Found at i:1153512 original size:33 final size:34
Alignment explanation
Indices: 1153455--1153530 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 34
1153445 GCTAAATTCG
*
1153455 CGTTGCGATTTTCATTTTCGCATTGCGATTTTCA
1 CGTTGCGATTTTCATTTTCGCATTGCGATTATCA
* *
1153489 CGTTGCGATTTTTA-TTTCGCATTGCGATTATCC
1 CGTTGCGATTTTCATTTTCGCATTGCGATTATCA
1153522 CGTTGCGAT
1 CGTTGCGAT
1153531 AGTCAAATTC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 26 0.67
34 13 0.33
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.45
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTATCA
Found at i:1153584 original size:20 final size:19
Alignment explanation
Indices: 1153522--1153590 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 19
1153512 GCGATTATCC
* *
1153522 CGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTC-ATTTCG
1153542 CGTTGCGATAGTCATTTCTG
1 CGTTGCGATAGTCATTTC-G
1153562 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
*
1153582 CGTTACGAT
1 CGTTGCGAT
1153591 TTTTAAGTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
19 4 0.09
20 36 0.82
21 4 0.09
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.36
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Done.