Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008062.1 Hibiscus syriacus cultivar Beakdansim tig00110557_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: 2089609
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 9
Found at i:959012 original size:2 final size:2
Alignment explanation
Indices: 959005--959054 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
958995 TATAGATGTG
959005 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
959047 AT AT AT AT
1 AT AT AT AT
959055 GGGTTAGAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:960304 original size:35 final size:35
Alignment explanation
Indices: 960258--960326 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
960248 CATCACGTCT
960258 CTATAATCATGGATGGAACTAGCT-AAATAAATAAG
1 CTATAATCATGGATGGAACTAG-TGAAATAAATAAG
960293 CTATAATCATGGATGGAACTAGTGAAATAAATAA
1 CTATAATCATGGATGGAACTAGTGAAATAAATAA
960327 CAACAACGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
34 1 0.03
35 32 0.97
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.26
Consensus pattern (35 bp):
CTATAATCATGGATGGAACTAGTGAAATAAATAAG
Found at i:960438 original size:30 final size:31
Alignment explanation
Indices: 960398--960469 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 31
960388 TATTAATTTT
* ** *
960398 TTTATTTTTATTCAT-TTAAAATTTTATAAA
1 TTTAATTTTATTCATATTAAAAACTCATAAA
*
960428 TTTAATTTTA-TCCTATTAAAAACTCATAAA
1 TTTAATTTTATTCATATTAAAAACTCATAAA
*
960458 TTTAAATTTATT
1 TTTAATTTTATT
960470 TTCTTAATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
29 3 0.09
30 30 0.88
31 1 0.03
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (31 bp):
TTTAATTTTATTCATATTAAAAACTCATAAA
Found at i:961626 original size:2 final size:2
Alignment explanation
Indices: 961619--961652 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
961609 CCAAAGCTTA
*
961619 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
961653 TAGTGACGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:961852 original size:16 final size:19
Alignment explanation
Indices: 961825--961864 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
961815 ATTTTCAAGG
961825 TAAATATATTAAT-AAA-A
1 TAAATATATTAATCAAAGA
961842 TAAAT-TATTAATCAAAGA
1 TAAATATATTAATCAAAGA
961860 TAAAT
1 TAAAT
961865 CAATTTTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.33
17 8 0.38
18 6 0.29
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (19 bp):
TAAATATATTAATCAAAGA
Found at i:964207 original size:20 final size:20
Alignment explanation
Indices: 964178--964225 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
964168 AGAGCTTTCT
*
964178 CTTTCCCCTTCGCCTTTGAG
1 CTTTCACCTTCGCCTTTGAG
*
964198 CTTTCACCTTGGCCTTTGAG
1 CTTTCACCTTCGCCTTTGAG
964218 CTTTCACC
1 CTTTCACC
964226 CACTTCTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.08, C:0.38, G:0.15, T:0.40
Consensus pattern (20 bp):
CTTTCACCTTCGCCTTTGAG
Found at i:969676 original size:114 final size:110
Alignment explanation
Indices: 969422--969710 Score: 320
Period size: 114 Copynumber: 2.6 Consensus size: 110
969412 TGTTGAGGTG
969422 TCTTCTGGGTCTGCCTCATTACTTTTCTGCTTCTACACCTAAGGGGTTTACTTCTTTGC-TGCCC
1 TCTTCTGGGTCTGCCTCATTACTTTTCTGCTTCTACACCTAAGGGGTTTACTTCTTTGCTTGCCC
* * *
969486 GGCTCATCTTCAATGCTTGATATTTGTGGGTCAGGTCCCATTTGGCA
66 GACTCATCATCAATGCTTGATATTTGT-GG-CAGGTCCCATTCGGCA
* * * * *
969533 TCTTCTGCGTATGCCTCATTACTTCTCTGCTTCTACACCCAAGGGATTTACTTCTTTGCTTGCTG
1 TCTTCTGGGTCTGCCTCATTACTTTTCTGCTTCTACACCTAAGGGGTTTACTTCTTTGCTTGC--
* *
969598 CCTGACTATGGGATCATCAAT-CTTTGATCTTTGT-G-A-GTCCCATTCGGCA
64 CC-GAC--T--CATCATCAATGC-TTGATATTTGTGGCAGGTCCCATTCGGCA
* * * *
969647 TGTTCTGGGTCTGCCTCATTATTTTTCTGCTTCTACTCCTAAGGGGTTTACTTTTTTGC-TGCCC
1 TCTTCTGGGTCTGCCTCATTACTTTTCTGCTTCTACACCTAAGGGGTTTACTTCTTTGCTTGCCC
969711 AGCTATGGGA
Statistics
Matches: 150, Mismatches: 19, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
111 56 0.37
112 3 0.02
113 3 0.02
114 64 0.43
115 3 0.02
117 2 0.01
118 1 0.01
119 18 0.12
ACGTcount: A:0.14, C:0.26, G:0.19, T:0.41
Consensus pattern (110 bp):
TCTTCTGGGTCTGCCTCATTACTTTTCTGCTTCTACACCTAAGGGGTTTACTTCTTTGCTTGCCC
GACTCATCATCAATGCTTGATATTTGTGGCAGGTCCCATTCGGCA
Found at i:979227 original size:57 final size:57
Alignment explanation
Indices: 979139--979250 Score: 215
Period size: 57 Copynumber: 2.0 Consensus size: 57
979129 ACCAACAATA
*
979139 TAAACTCCTATGAGAAATAGAAAATGGGCTTTTCCTTCTTCCTCCTATCTCTCAAAC
1 TAAACTCCTATGAGAAATAGAAAATGAGCTTTTCCTTCTTCCTCCTATCTCTCAAAC
979196 TAAACTCCTATGAGAAATAGAAAATGAGCTTTTCCTTCTTCCTCCTATCTCTCAA
1 TAAACTCCTATGAGAAATAGAAAATGAGCTTTTCCTTCTTCCTCCTATCTCTCAA
979251 TCTAGAGATA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.30, C:0.26, G:0.10, T:0.34
Consensus pattern (57 bp):
TAAACTCCTATGAGAAATAGAAAATGAGCTTTTCCTTCTTCCTCCTATCTCTCAAAC
Found at i:983526 original size:3 final size:3
Alignment explanation
Indices: 983518--983574 Score: 69
Period size: 3 Copynumber: 18.7 Consensus size: 3
983508 CTTTTTTGTA
** *
983518 TAT TAT TAT TAT CGT TAT TTT TAT TAT TAT TAT TAT TAT TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
*
983564 TAT TAA TAT TA
1 TAT TAT TAT TA
983575 CATTTTACAT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:983644 original size:11 final size:10
Alignment explanation
Indices: 983608--983645 Score: 58
Period size: 11 Copynumber: 3.6 Consensus size: 10
983598 AAGCCCAATA
983608 CAACAAGGCC
1 CAACAAGGCC
983618 CAACCAAGGCC
1 CAA-CAAGGCC
983629 CAACATAGGCC
1 CAACA-AGGCC
983640 CAACAA
1 CAACAA
983646 CCCATCAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 6 0.23
11 20 0.77
ACGTcount: A:0.42, C:0.39, G:0.16, T:0.03
Consensus pattern (10 bp):
CAACAAGGCC
Found at i:983683 original size:25 final size:25
Alignment explanation
Indices: 983649--983723 Score: 123
Period size: 25 Copynumber: 3.0 Consensus size: 25
983639 CCAACAACCC
*
983649 ATCAGTTTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
983674 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
* *
983699 AACAAATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
983724 TCCCCTATCC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:987752 original size:30 final size:31
Alignment explanation
Indices: 987716--987775 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
987706 TCTTGCTTGC
987716 ACTAACTC-GTTTCTCT-ATTTTGTTTGTGTT
1 ACTAACTCAGTTTCTCTCA-TTTGTTTGTGTT
* *
987746 ACTAACTCATTTTTTCTCATTTGTTTGTGT
1 ACTAACTCAGTTTCTCTCATTTGTTTGTGT
987776 CATTTTTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 8 0.31
31 17 0.65
32 1 0.04
ACGTcount: A:0.15, C:0.17, G:0.12, T:0.57
Consensus pattern (31 bp):
ACTAACTCAGTTTCTCTCATTTGTTTGTGTT
Found at i:990875 original size:18 final size:17
Alignment explanation
Indices: 990831--990877 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
990821 GAGTGCAAAG
*
990831 ATCAAACCAAAGAAAAA
1 ATCAAAGCAAAGAAAAA
990848 A-CAAAGAGCAAAGAGAAAA
1 ATC-AA-AGCAAAGA-AAAA
990867 ATCAAAGCAAA
1 ATCAAAGCAAA
990878 AATCAAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 1 0.04
17 3 0.12
18 13 0.52
19 7 0.28
20 1 0.04
ACGTcount: A:0.68, C:0.15, G:0.13, T:0.04
Consensus pattern (17 bp):
ATCAAAGCAAAGAAAAA
Found at i:990880 original size:12 final size:11
Alignment explanation
Indices: 990861--990898 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
990851 AAGAGCAAAG
990861 AGAAAAATCAA
1 AGAAAAATCAA
990872 AGCAAAAATCAA
1 AG-AAAAATCAA
*
990884 AGAAAAAGCAA
1 AGAAAAATCAA
990895 AGAA
1 AGAA
990899 CAAAGAGGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.71, C:0.11, G:0.13, T:0.05
Consensus pattern (11 bp):
AGAAAAATCAA
Found at i:990891 original size:18 final size:18
Alignment explanation
Indices: 990870--990904 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
990860 GAGAAAAATC
990870 AAAGCAAA-AATCAAAGAA
1 AAAGCAAAGAA-CAAAGAA
990888 AAAGCAAAGAACAAAGA
1 AAAGCAAAGAACAAAGA
990905 GGACAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.71, C:0.11, G:0.14, T:0.03
Consensus pattern (18 bp):
AAAGCAAAGAACAAAGAA
Found at i:990903 original size:12 final size:11
Alignment explanation
Indices: 990861--990903 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
990851 AAGAGCAAAG
*
990861 AGAAAAATCAA
1 AGAAAAAGCAA
*
990872 AGCAAAAATCAA
1 AG-AAAAAGCAA
990884 AGAAAAAGCAA
1 AGAAAAAGCAA
990895 AGAACAAAG
1 AGAA-AAAG
990904 AGGACAAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 14 0.48
12 15 0.52
ACGTcount: A:0.70, C:0.12, G:0.14, T:0.05
Consensus pattern (11 bp):
AGAAAAAGCAA
Found at i:992148 original size:28 final size:28
Alignment explanation
Indices: 992108--992161 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
992098 ATATATATAT
*
992108 ATATATACATACATCAACTCATACATAC
1 ATATATACATACATCAACACATACATAC
992136 ATATATACATACATCAACACATACAT
1 ATATATACATACATCAACACATACAT
992162 GCATGTTACA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (28 bp):
ATATATACATACATCAACACATACATAC
Found at i:992627 original size:36 final size:36
Alignment explanation
Indices: 992532--992630 Score: 171
Period size: 36 Copynumber: 2.8 Consensus size: 36
992522 GATTTTTCTA
*
992532 AAAACAAATTTTGTCTCGCTGGAGACAATTTATTTC
1 AAAACAAATTTTGTCTCGCTTGAGACAATTTATTTC
992568 AAAACAAATTTTGTCTCGCTTGAGACAATTTATTTC
1 AAAACAAATTTTGTCTCGCTTGAGACAATTTATTTC
**
992604 AAAACAAATTTTGTCTCATTTGAGACA
1 AAAACAAATTTTGTCTCGCTTGAGACA
992631 TTTTCCCTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 60 1.00
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.36
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCGCTTGAGACAATTTATTTC
Found at i:992959 original size:101 final size:100
Alignment explanation
Indices: 992753--992981 Score: 248
Period size: 101 Copynumber: 2.3 Consensus size: 100
992743 TGAGAATTTT
** * *
992753 AAAACAAATTGCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCACT
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
* * * *
992818 AAAAACAAAATCTCACCTTAGTTTGTTGTTTCTTTC
66 AAAAACAAAATCTCACCTCACTTAGTCGTTTC-TTC
* * *
992854 AAAACAAATTTTGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTGTTTCAC-
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
* * * *
992918 ATTAAACAAAGT-TGATCTCACTTGAGATCGTTTC-TC
66 A-AAAACAAAATCTCACCTCACTT-AG-TCGTTTCTTC
*
992954 AAAAACAAACTTTGTCTCGCTTGAGACA
1 -AAAACAAATTTTGTCTCGCTTGAGACA
992982 ATTGCTCTAA
Statistics
Matches: 107, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
100 10 0.09
101 91 0.85
102 6 0.06
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.37
Consensus pattern (100 bp):
AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
AAAAACAAAATCTCACCTCACTTAGTCGTTTCTTC
Found at i:992997 original size:36 final size:34
Alignment explanation
Indices: 992954--993051 Score: 101
Period size: 36 Copynumber: 2.8 Consensus size: 34
992944 ATCGTTTCTC
992954 AAAAACAAACTTTGTCTCGCTTGAGACAAT-TGCTCT
1 AAAAACAAA-TTTGTCTCGCTTGAGACAATAT-CT-T
** *
992990 AAAAACAAATTTTGTCTCATTTGAGACTATATCTT
1 AAAAACAAA-TTTGTCTCGCTTGAGACAATATCTT
*
993025 -AAAGCAAATTTCGTCTCGCTTGAGACA
1 AAAAACAAATTT-GTCTCGCTTGAGACA
993052 TCATTTTCTC
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
33 3 0.06
34 19 0.37
35 1 0.02
36 28 0.54
37 1 0.02
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (34 bp):
AAAAACAAATTTGTCTCGCTTGAGACAATATCTT
Found at i:993356 original size:28 final size:28
Alignment explanation
Indices: 993293--993396 Score: 129
Period size: 28 Copynumber: 3.6 Consensus size: 28
993283 TCTGGAGACA
* * *
993293 GTTTCTCTTGAGATAAATCTTTGAGTCT
1 GTTTCTTTTGAAAAAAATCTTTGAGTCT
*
993321 GTTCCTTTTGAATAAAAATCTTTGAGT-T
1 GTTTCTTTTGAA-AAAAATCTTTGAGTCT
993349 GTTTCTTTTGAAACAAATATCTTTGAGTCT
1 GTTTCTTTTGAAA-AAA-ATCTTTGAGTCT
*
993379 ATTTCTTTTGAAAAAAAT
1 GTTTCTTTTGAAAAAAAT
993397 TTATCTCCTA
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
27 1 0.02
28 26 0.39
29 26 0.39
30 13 0.20
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.46
Consensus pattern (28 bp):
GTTTCTTTTGAAAAAAATCTTTGAGTCT
Found at i:993386 original size:30 final size:29
Alignment explanation
Indices: 993309--993394 Score: 122
Period size: 29 Copynumber: 3.0 Consensus size: 29
993299 CTTGAGATAA
*
993309 ATCTTTGAGTCTGTTCCTTTTGAATAAAA-
1 ATCTTTGAGTCTGTTTCTTTTGAA-AAAAT
993338 ATCTTTGAGT-TGTTTCTTTTGAAACAAAT
1 ATCTTTGAGTCTGTTTCTTTTGAAA-AAAT
*
993367 ATCTTTGAGTCTATTTCTTTTGAAAAAA
1 ATCTTTGAGTCTGTTTCTTTTGAAAAAA
993395 ATTTATCTCC
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
27 1 0.02
28 15 0.29
29 23 0.44
30 13 0.25
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.47
Consensus pattern (29 bp):
ATCTTTGAGTCTGTTTCTTTTGAAAAAAT
Found at i:993451 original size:61 final size:63
Alignment explanation
Indices: 993350--993488 Score: 151
Period size: 62 Copynumber: 2.2 Consensus size: 63
993340 CTTTGAGTTG
**
993350 TTTCTTTTGAAACAAATATCTTTGAGTCTATTTCTTTTGAAA-AAAATTTATCTC-CTAAAGACA
1 TTTCTTTTG-AA-AAATATCTTTGAGTCTATTTCCCTTGAAACAAAATTT-TCTCTCTAAAGACA
993413 A
63 A
* * **
993414 TTTCTTTTGAAAAA-ATCTTTGAGT-TGGTTTCCCTTGAAACAAAATTTTGTCTCTCGAGACAA
1 TTTCTTTTGAAAAATATCTTTGAGTCT-ATTTCCCTTGAAACAAAATTTTCTCTCTAAAGACAA
*
993476 CTTCTTTTGAAAA
1 TTTCTTTTGAAAA
993489 TACCCACCTT
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
60 1 0.02
61 23 0.35
62 30 0.46
63 2 0.03
64 9 0.14
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (63 bp):
TTTCTTTTGAAAAATATCTTTGAGTCTATTTCCCTTGAAACAAAATTTTCTCTCTAAAGACAA
Found at i:993628 original size:15 final size:15
Alignment explanation
Indices: 993605--993648 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
993595 TTTTGAGTCG
*
993605 TTTCACTTGAAACAT
1 TTTCTCTTGAAACAT
993620 TTTCTCTTGAAACAT
1 TTTCTCTTGAAACAT
*
993635 TTTCTCTTAAAACA
1 TTTCTCTTGAAACA
993649 AGATCATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (15 bp):
TTTCTCTTGAAACAT
Found at i:994057 original size:40 final size:40
Alignment explanation
Indices: 993999--994352 Score: 223
Period size: 40 Copynumber: 8.4 Consensus size: 40
993989 CCAGTCGTCC
* * * * *
993999 TCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCT
1 TCATCACGTATGAGCCGTGTCATCCCTAGACCAGAACTCT
* * * *
994039 TCATCACGTATGAGCCGTGTCAACCATAGATAACCAG-CCGTCC
1 TCATCACGTATGAGCCGTGTCATCCCTAG---ACCAGAAC-TCT
* * *
994082 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTATGAGCCGTGTCATC-CC--TAGA---CCAGAACTCT
* * *
994128 TCATCACGTATGAGCCGTGTCATTCCTCGACCAGATCTCT
1 TCATCACGTATGAGCCGTGTCATCCCTAGACCAGAACTCT
* *
994168 TCATCACGTATGAGCCGTGTCA-CCCTAGATAACCAG-CCGTCC
1 TCATCACGTATGAGCCGTGTCATCCCTAG---ACCAGAAC-TCT
* * *
994210 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTATGAGCCGTGTCATC-CC--TAGA---CCAGAACTCT
* * *
994256 TCACCACGTATGAGCCGTGTCATTCCC-CGACCAGATCTCT
1 TCATCACGTATGAGCCGTGTCA-TCCCTAGACCAGAACTCT
* * *
994296 TCATCACGTAGGAGCCGTGTCAACCATAGATAACCA-AACTCT
1 TCATCACGTATGAGCCGTGTCATCCCTAG---ACCAGAACTCT
994338 TCATCACGTATGAGC
1 TCATCACGTATGAGC
994353 AGTGGCGTCC
Statistics
Matches: 243, Mismatches: 43, Indels: 54
0.71 0.13 0.16
Matches are distributed among these distances:
39 6 0.02
40 84 0.35
41 1 0.00
42 46 0.19
43 39 0.16
44 3 0.01
45 2 0.01
46 58 0.24
47 4 0.02
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.25
Consensus pattern (40 bp):
TCATCACGTATGAGCCGTGTCATCCCTAGACCAGAACTCT
Found at i:994134 original size:46 final size:45
Alignment explanation
Indices: 994029--994352 Score: 195
Period size: 46 Copynumber: 7.6 Consensus size: 45
994019 CATCCCCAGA
* * * **
994029 CCAGATCTCTTCATCACGTATGAGCCGTGTCA--ACCATAGATAA
1 CCAGAACTCTTCATCACGTATGAGCCGTGTTATCACCTTAGATGG
* * * *
994072 CCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGG
1 CCAGAAC-TCTTCATCACGTATGAGCCGTGTTATCACC-TTAGATGG
* * *
994118 CCAGAACTCTTCATCACGTATGAGCCGTGTCAT-TCC-TCGA---
1 CCAGAACTCTTCATCACGTATGAGCCGTGTTATCACCTTAGATGG
* * **
994158 CCAGATCTCTTCATCACGTATGAGCCGTG---TCACCCTAGATAA
1 CCAGAACTCTTCATCACGTATGAGCCGTGTTATCACCTTAGATGG
* * * *
994200 CCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGG
1 CCAGAAC-TCTTCATCACGTATGAGCCGTGTTATCACC-TTAGATGG
* * *
994246 CCAGAACTCTTCACCACGTATGAGCCGTGTCATTC-CC--CGA---
1 CCAGAACTCTTCATCACGTATGAGCCGTGTTA-TCACCTTAGATGG
* * * * **
994286 CCAGATCTCTTCATCACGTAGGAGCCGTGTCA--ACCATAGATAA
1 CCAGAACTCTTCATCACGTATGAGCCGTGTTATCACCTTAGATGG
994329 CCA-AACTCTTCATCACGTATGAGC
1 CCAGAACTCTTCATCACGTATGAGC
994353 AGTGGCGTCC
Statistics
Matches: 220, Mismatches: 38, Indels: 47
0.72 0.12 0.15
Matches are distributed among these distances:
37 1 0.00
38 4 0.02
39 3 0.01
40 59 0.27
41 1 0.00
42 43 0.20
43 33 0.15
45 10 0.05
46 62 0.28
47 4 0.02
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.25
Consensus pattern (45 bp):
CCAGAACTCTTCATCACGTATGAGCCGTGTTATCACCTTAGATGG
Found at i:994142 original size:89 final size:83
Alignment explanation
Indices: 993989--994331 Score: 227
Period size: 86 Copynumber: 4.0 Consensus size: 83
993979 CTAAAGATGG
* * *
993989 CCAGTCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCTTCATCACGTATGAGC
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGAACTCTTCATCACGTATGAGC
994054 CGTGTCAACCATAGATAA
66 CGTGTCAACCATAGATAA
* *
994072 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTCATC-CC--CAGA---CCAGAACTCTTCATCACGT
* *
994137 ATGAGCCGTGTCATTCC-TCG---A
60 ATGAGCCGTGTCA-ACCATAGATAA
* * * * * * *
994158 CCAGATC-TCTTCATCACGTATGAGCCGTGTCA-CCCTAGATAACCAG-CCGTCCTCATCACGTA
1 CCAG-CCGTCCTCATCACGTAGGAACCGTGTCATCCCCAG---ACCAGAAC-TCTTCATCACGTA
* * * * **
994220 GGAACCGTGTTATCACCTTTAGATGG
61 TGAGCCGTGTCA--ACC-ATAGATAA
* * * * * * *
994246 CCAGAAC-TCTTCACCACGTATGAGCCGTGTCATTCCCC-GACCAGATCTCTTCATCACGTAGGA
1 CCAG-CCGTCCTCATCACGTAGGAACCGTGTCA-TCCCCAGACCAGAACTCTTCATCACGTATGA
994309 GCCGTGTCAACCATAGATAA
64 GCCGTGTCAACCATAGATAA
994329 CCA
1 CCA
994332 AACTCTTCAT
Statistics
Matches: 208, Mismatches: 31, Indels: 42
0.74 0.11 0.15
Matches are distributed among these distances:
81 1 0.00
82 28 0.13
83 41 0.20
84 7 0.03
85 4 0.02
86 56 0.27
87 2 0.01
88 30 0.14
89 34 0.16
90 5 0.02
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.25
Consensus pattern (83 bp):
CCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGAACTCTTCATCACGTATGAGC
CGTGTCAACCATAGATAA
Found at i:994250 original size:128 final size:129
Alignment explanation
Indices: 993999--994331 Score: 580
Period size: 128 Copynumber: 2.6 Consensus size: 129
993989 CCAGTCGTCC
* * *
993999 TCATCATGTAGGAACCGTGTCA-TCCCCAGACCAGATCTCTTCATCACGTATGAGCCGTGTCAAC
1 TCATCACGTATGAGCCGTGTCATTCCCC-GACCAGATCTCTTCATCACGTATGAGCCGTGTCAAC
994063 CATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
65 CATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
*
994128 TCATCACGTATGAGCCGTGTCATTCCTCGACCAGATCTCTTCATCACGTATGAGCCGTGTC-ACC
1 TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACC
*
994192 CTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
66 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
* *
994256 TCACCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACC
1 TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACC
994321 ATAGATAACCA
66 ATAGATAACCA
994332 AACTCTTCAT
Statistics
Matches: 193, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
128 124 0.64
129 65 0.34
130 4 0.02
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (129 bp):
TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACC
ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
Found at i:994522 original size:3 final size:3
Alignment explanation
Indices: 994514--994570 Score: 69
Period size: 3 Copynumber: 18.7 Consensus size: 3
994504 CTTTTTTGTA
** *
994514 TAT TAT TAT TAT CGT TAT TTT TAT TAT TAT TAT TAT TAT TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
*
994560 TAT TAA TAT TA
1 TAT TAT TAT TA
994571 CATTTTACAT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:994640 original size:11 final size:10
Alignment explanation
Indices: 994604--994641 Score: 58
Period size: 11 Copynumber: 3.6 Consensus size: 10
994594 AAGCCCAATA
994604 CAACAAGGCC
1 CAACAAGGCC
994614 CAACCAAGGCC
1 CAA-CAAGGCC
994625 CAACAGAGGCC
1 CAACA-AGGCC
994636 CAACAA
1 CAACAA
994642 CCCATCAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 6 0.23
11 20 0.77
ACGTcount: A:0.42, C:0.39, G:0.18, T:0.00
Consensus pattern (10 bp):
CAACAAGGCC
Found at i:994674 original size:25 final size:25
Alignment explanation
Indices: 994645--994719 Score: 123
Period size: 25 Copynumber: 3.0 Consensus size: 25
994635 CCAACAACCC
*
994645 ATCAGTTTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
994670 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
* *
994695 AACAAATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
994720 TCCCCTATCC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:998729 original size:30 final size:31
Alignment explanation
Indices: 998693--998752 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
998683 TCTTGCTTGC
998693 ACTAACTC-GTTTCTCT-ATTTTGTTTGTGTT
1 ACTAACTCAGTTTCTCTCA-TTTGTTTGTGTT
* *
998723 ACTAACTCATTTTTTCTCATTTGTTTGTGT
1 ACTAACTCAGTTTCTCTCATTTGTTTGTGT
998753 CATTTTTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 8 0.31
31 17 0.65
32 1 0.04
ACGTcount: A:0.15, C:0.17, G:0.12, T:0.57
Consensus pattern (31 bp):
ACTAACTCAGTTTCTCTCATTTGTTTGTGTT
Found at i:1001867 original size:11 final size:11
Alignment explanation
Indices: 1001839--1001876 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
1001829 AAGAGCAAAG
1001839 AGAAAAATCAA
1 AGAAAAATCAA
1001850 AGCAAAAATCAA
1 AG-AAAAATCAA
*
1001862 AGAAAAAGCAA
1 AGAAAAATCAA
1001873 AGAA
1 AGAA
1001877 CAAAAGAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.71, C:0.11, G:0.13, T:0.05
Consensus pattern (11 bp):
AGAAAAATCAA
Found at i:1003093 original size:28 final size:29
Alignment explanation
Indices: 1003061--1003138 Score: 95
Period size: 28 Copynumber: 2.6 Consensus size: 29
1003051 ATTGAGAAAC
* *
1003061 ATACATCAACTCATACATATATATATATATA
1 ATACATCAACTCATAC--ATACATATATACA
1003092 CATACATCAACTCATACATACATATATAC-
1 -ATACATCAACTCATACATACATATATACA
*
1003121 ATACATCAACACATACAT
1 ATACATCAACTCATACAT
1003139 GCATGTTACA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
28 17 0.40
30 10 0.23
32 16 0.37
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.29
Consensus pattern (29 bp):
ATACATCAACTCATACATACATATATACA
Found at i:1003098 original size:32 final size:32
Alignment explanation
Indices: 1003059--1003126 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
1003049 AGATTGAGAA
* *
1003059 ACATACATCAACTCATACATATATATATATAT
1 ACATACATCAACTCATACATACATATATACAT
1003091 ACATACATCAACTCATACATACATATATACAT
1 ACATACATCAACTCATACATACATATATACAT
1003123 ACAT
1 ACAT
1003127 CAACACATAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (32 bp):
ACATACATCAACTCATACATACATATATACAT
Found at i:1003605 original size:36 final size:36
Alignment explanation
Indices: 1003510--1003608 Score: 171
Period size: 36 Copynumber: 2.8 Consensus size: 36
1003500 GATTTTTCTA
*
1003510 AAAACAAATTTTGTCTCGCTGGAGACAATTTATTTC
1 AAAACAAATTTTGTCTCGCTTGAGACAATTTATTTC
1003546 AAAACAAATTTTGTCTCGCTTGAGACAATTTATTTC
1 AAAACAAATTTTGTCTCGCTTGAGACAATTTATTTC
**
1003582 AAAACAAATTTTGTCTCATTTGAGACA
1 AAAACAAATTTTGTCTCGCTTGAGACA
1003609 TTTTCCCTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 60 1.00
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.36
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCGCTTGAGACAATTTATTTC
Found at i:1003937 original size:101 final size:100
Alignment explanation
Indices: 1003731--1003959 Score: 248
Period size: 101 Copynumber: 2.3 Consensus size: 100
1003721 TGAGAATTTT
** * *
1003731 AAAACAAATTGCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCACT
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
* * * *
1003796 AAAAACAAAATCTCACCTTAGTTTGTTGTTTCTTTC
66 AAAAACAAAATCTCACCTCACTTAGTCGTTTC-TTC
* * *
1003832 AAAACAAATTTTGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTGTTTCAC-
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
* * * *
1003896 ATTAAACAAAGT-TGATCTCACTTGAGATCGTTTC-TC
66 A-AAAACAAAATCTCACCTCACTT-AG-TCGTTTCTTC
*
1003932 AAAAACAAACTTTGTCTCGCTTGAGACA
1 -AAAACAAATTTTGTCTCGCTTGAGACA
1003960 ATTGCTCTAA
Statistics
Matches: 107, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
100 10 0.09
101 91 0.85
102 6 0.06
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.37
Consensus pattern (100 bp):
AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
AAAAACAAAATCTCACCTCACTTAGTCGTTTCTTC
Found at i:1003975 original size:36 final size:34
Alignment explanation
Indices: 1003932--1004029 Score: 101
Period size: 36 Copynumber: 2.8 Consensus size: 34
1003922 ATCGTTTCTC
1003932 AAAAACAAACTTTGTCTCGCTTGAGACAAT-TGCTCT
1 AAAAACAAA-TTTGTCTCGCTTGAGACAATAT-CT-T
** *
1003968 AAAAACAAATTTTGTCTCATTTGAGACTATATCTT
1 AAAAACAAA-TTTGTCTCGCTTGAGACAATATCTT
*
1004003 -AAAGCAAATTTCGTCTCGCTTGAGACA
1 AAAAACAAATTT-GTCTCGCTTGAGACA
1004030 TCATTTTCTC
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
33 3 0.06
34 19 0.37
35 1 0.02
36 28 0.54
37 1 0.02
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (34 bp):
AAAAACAAATTTGTCTCGCTTGAGACAATATCTT
Found at i:1004321 original size:29 final size:28
Alignment explanation
Indices: 1004273--1004375 Score: 127
Period size: 29 Copynumber: 3.6 Consensus size: 28
1004263 TCTGGAGACA
* * *
1004273 GTTTCTCTTGAGATAAATCTTTGAGTCT
1 GTTTCTTTTGAAAAAAATCTTTGAGTCT
*
1004301 GTTCCTTTTGAATAAAAATCTTTGAGT-T
1 GTTTCTTTTGAA-AAAAATCTTTGAGTCT
1004329 GTTTCTTTTGAAACAAATATCTTTGAGTCT
1 GTTTCTTTTGAAA-AAA-ATCTTTGAGTCT
*
1004359 ATTTCTTTTGAAAAAAA
1 GTTTCTTTTGAAAAAAA
1004376 ATTTATCTCC
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
27 1 0.02
28 25 0.38
29 26 0.40
30 13 0.20
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.46
Consensus pattern (28 bp):
GTTTCTTTTGAAAAAAATCTTTGAGTCT
Found at i:1004432 original size:62 final size:63
Alignment explanation
Indices: 1004330--1004469 Score: 151
Period size: 62 Copynumber: 2.2 Consensus size: 63
1004320 CTTTGAGTTG
**
1004330 TTTCTTTTGAAACAAATATCTTTGAGTCTATTTCTTTTGAAAAAAAATTTATCTC-CTAAAGACA
1 TTTCTTTTG-AA-AAATATCTTTGAGTCTATTTCCCTTGAAAAAAAATTT-TCTCTCTAAAGACA
1004394 A
63 A
* * * **
1004395 TTTCTTTTGAAAAA-ATCTTTGAGT-TGGTTTCCCTTGAAACAAAATTTTGTCTCTCGAGACAA
1 TTTCTTTTGAAAAATATCTTTGAGTCT-ATTTCCCTTGAAAAAAAATTTTCTCTCTAAAGACAA
*
1004457 CTTCTTTTGAAAA
1 TTTCTTTTGAAAA
1004470 TACCCACCTT
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
61 4 0.06
62 47 0.72
63 3 0.05
64 2 0.03
65 9 0.14
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (63 bp):
TTTCTTTTGAAAAATATCTTTGAGTCTATTTCCCTTGAAAAAAAATTTTCTCTCTAAAGACAA
Found at i:1004609 original size:15 final size:15
Alignment explanation
Indices: 1004586--1004629 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
1004576 TTTTGAGTCG
*
1004586 TTTCACTTGAAACAT
1 TTTCTCTTGAAACAT
1004601 TTTCTCTTGAAACAT
1 TTTCTCTTGAAACAT
*
1004616 TTTCTCTTAAAACA
1 TTTCTCTTGAAACA
1004630 AGATCATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (15 bp):
TTTCTCTTGAAACAT
Found at i:1005038 original size:40 final size:40
Alignment explanation
Indices: 1004980--1005333 Score: 223
Period size: 40 Copynumber: 8.4 Consensus size: 40
1004970 CCAGTCGTCC
* * * * *
1004980 TCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCT
1 TCATCACGTATGAGCCGTGTCATCCCTAGACCAGAACTCT
* * * *
1005020 TCATCACGTATGAGCCGTGTCAACCATAGATAACCAG-CCGTCC
1 TCATCACGTATGAGCCGTGTCATCCCTAG---ACCAGAAC-TCT
* * *
1005063 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTATGAGCCGTGTCATC-CC--TAGA---CCAGAACTCT
* * *
1005109 TCATCACGTATGAGCCGTGTCATTCCTCGACCAGATCTCT
1 TCATCACGTATGAGCCGTGTCATCCCTAGACCAGAACTCT
* *
1005149 TCATCACGTATGAGCCGTGTCA-CCCTAGATAACCAG-CCGTCC
1 TCATCACGTATGAGCCGTGTCATCCCTAG---ACCAGAAC-TCT
* * *
1005191 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTATGAGCCGTGTCATC-CC--TAGA---CCAGAACTCT
* * *
1005237 TCACCACGTATGAGCCGTGTCATTCCC-CGACCAGATCTCT
1 TCATCACGTATGAGCCGTGTCA-TCCCTAGACCAGAACTCT
* * *
1005277 TCATCACGTAGGAGCCGTGTCAACCATAGATAACCA-AACTCT
1 TCATCACGTATGAGCCGTGTCATCCCTAG---ACCAGAACTCT
1005319 TCATCACGTATGAGC
1 TCATCACGTATGAGC
1005334 AGTGGCGTCC
Statistics
Matches: 243, Mismatches: 43, Indels: 54
0.71 0.13 0.16
Matches are distributed among these distances:
39 6 0.02
40 84 0.35
41 1 0.00
42 46 0.19
43 39 0.16
44 3 0.01
45 2 0.01
46 58 0.24
47 4 0.02
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.25
Consensus pattern (40 bp):
TCATCACGTATGAGCCGTGTCATCCCTAGACCAGAACTCT
Found at i:1005115 original size:46 final size:45
Alignment explanation
Indices: 1005010--1005333 Score: 195
Period size: 46 Copynumber: 7.6 Consensus size: 45
1005000 CATCCCCAGA
* * * **
1005010 CCAGATCTCTTCATCACGTATGAGCCGTGTCA--ACCATAGATAA
1 CCAGAACTCTTCATCACGTATGAGCCGTGTTATCACCTTAGATGG
* * * *
1005053 CCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGG
1 CCAGAAC-TCTTCATCACGTATGAGCCGTGTTATCACC-TTAGATGG
* * *
1005099 CCAGAACTCTTCATCACGTATGAGCCGTGTCAT-TCC-TCGA---
1 CCAGAACTCTTCATCACGTATGAGCCGTGTTATCACCTTAGATGG
* * **
1005139 CCAGATCTCTTCATCACGTATGAGCCGTG---TCACCCTAGATAA
1 CCAGAACTCTTCATCACGTATGAGCCGTGTTATCACCTTAGATGG
* * * *
1005181 CCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGG
1 CCAGAAC-TCTTCATCACGTATGAGCCGTGTTATCACC-TTAGATGG
* * *
1005227 CCAGAACTCTTCACCACGTATGAGCCGTGTCATTC-CC--CGA---
1 CCAGAACTCTTCATCACGTATGAGCCGTGTTA-TCACCTTAGATGG
* * * * **
1005267 CCAGATCTCTTCATCACGTAGGAGCCGTGTCA--ACCATAGATAA
1 CCAGAACTCTTCATCACGTATGAGCCGTGTTATCACCTTAGATGG
1005310 CCA-AACTCTTCATCACGTATGAGC
1 CCAGAACTCTTCATCACGTATGAGC
1005334 AGTGGCGTCC
Statistics
Matches: 220, Mismatches: 38, Indels: 47
0.72 0.12 0.15
Matches are distributed among these distances:
37 1 0.00
38 4 0.02
39 3 0.01
40 59 0.27
41 1 0.00
42 43 0.20
43 33 0.15
45 10 0.05
46 62 0.28
47 4 0.02
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.25
Consensus pattern (45 bp):
CCAGAACTCTTCATCACGTATGAGCCGTGTTATCACCTTAGATGG
Found at i:1005123 original size:89 final size:83
Alignment explanation
Indices: 1004970--1005312 Score: 227
Period size: 86 Copynumber: 4.0 Consensus size: 83
1004960 CTAAAGATGG
* * *
1004970 CCAGTCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCTTCATCACGTATGAGC
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGAACTCTTCATCACGTATGAGC
1005035 CGTGTCAACCATAGATAA
66 CGTGTCAACCATAGATAA
* *
1005053 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTCATC-CC--CAGA---CCAGAACTCTTCATCACGT
* *
1005118 ATGAGCCGTGTCATTCC-TCG---A
60 ATGAGCCGTGTCA-ACCATAGATAA
* * * * * * *
1005139 CCAGATC-TCTTCATCACGTATGAGCCGTGTCA-CCCTAGATAACCAG-CCGTCCTCATCACGTA
1 CCAG-CCGTCCTCATCACGTAGGAACCGTGTCATCCCCAG---ACCAGAAC-TCTTCATCACGTA
* * * * **
1005201 GGAACCGTGTTATCACCTTTAGATGG
61 TGAGCCGTGTCA--ACC-ATAGATAA
* * * * * * *
1005227 CCAGAAC-TCTTCACCACGTATGAGCCGTGTCATTCCCC-GACCAGATCTCTTCATCACGTAGGA
1 CCAG-CCGTCCTCATCACGTAGGAACCGTGTCA-TCCCCAGACCAGAACTCTTCATCACGTATGA
1005290 GCCGTGTCAACCATAGATAA
64 GCCGTGTCAACCATAGATAA
1005310 CCA
1 CCA
1005313 AACTCTTCAT
Statistics
Matches: 208, Mismatches: 31, Indels: 42
0.74 0.11 0.15
Matches are distributed among these distances:
81 1 0.00
82 28 0.13
83 41 0.20
84 7 0.03
85 4 0.02
86 56 0.27
87 2 0.01
88 30 0.14
89 34 0.16
90 5 0.02
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.25
Consensus pattern (83 bp):
CCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGAACTCTTCATCACGTATGAGC
CGTGTCAACCATAGATAA
Found at i:1005231 original size:128 final size:129
Alignment explanation
Indices: 1004980--1005312 Score: 580
Period size: 128 Copynumber: 2.6 Consensus size: 129
1004970 CCAGTCGTCC
* * *
1004980 TCATCATGTAGGAACCGTGTCA-TCCCCAGACCAGATCTCTTCATCACGTATGAGCCGTGTCAAC
1 TCATCACGTATGAGCCGTGTCATTCCCC-GACCAGATCTCTTCATCACGTATGAGCCGTGTCAAC
1005044 CATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
65 CATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
*
1005109 TCATCACGTATGAGCCGTGTCATTCCTCGACCAGATCTCTTCATCACGTATGAGCCGTGTC-ACC
1 TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACC
*
1005173 CTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
66 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
* *
1005237 TCACCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACC
1 TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACC
1005302 ATAGATAACCA
66 ATAGATAACCA
1005313 AACTCTTCAT
Statistics
Matches: 193, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
128 124 0.64
129 65 0.34
130 4 0.02
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (129 bp):
TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACC
ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
Found at i:1005502 original size:3 final size:3
Alignment explanation
Indices: 1005494--1005547 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
1005484 TCTTTTTGTA
** *
1005494 TAT TAT TAT TAT CGT TAT TTT TAT TAT TAT TAT TAT TATT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
*
1005540 TAA TAT TA
1 TAT TAT TA
1005548 CATTTTACAT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1005554 original size:19 final size:18
Alignment explanation
Indices: 1005512--1005554 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
1005502 TTATCGTTAT
* *
1005512 TTTTATTATTATTATTAT
1 TTTTATTATTAATATTAA
1005530 TATTTATTATTAATATTACA
1 T-TTTATTATTAATATTA-A
1005550 TTTTA
1 TTTTA
1005555 CATATTTTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 19 0.90
20 1 0.05
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTATTATTAATATTAA
Found at i:1005617 original size:11 final size:10
Alignment explanation
Indices: 1005581--1005618 Score: 58
Period size: 11 Copynumber: 3.6 Consensus size: 10
1005571 AAGCCCAATA
1005581 CAACAAGGCC
1 CAACAAGGCC
1005591 CAACCAAGGCC
1 CAA-CAAGGCC
1005602 CAACAGAGGCC
1 CAACA-AGGCC
1005613 CAACAA
1 CAACAA
1005619 CCCATCAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 6 0.23
11 20 0.77
ACGTcount: A:0.42, C:0.39, G:0.18, T:0.00
Consensus pattern (10 bp):
CAACAAGGCC
Found at i:1005651 original size:25 final size:25
Alignment explanation
Indices: 1005622--1005696 Score: 123
Period size: 25 Copynumber: 3.0 Consensus size: 25
1005612 CCAACAACCC
*
1005622 ATCAGTTTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
1005647 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
* *
1005672 AACAAATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
1005697 TCCCTATCCA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:1009885 original size:4 final size:4
Alignment explanation
Indices: 1009876--1009901 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1009866 GCACGTAATG
1009876 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
1009902 GAGATAACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1013801 original size:16 final size:16
Alignment explanation
Indices: 1013775--1013815 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
1013765 AGATTAGATG
1013775 AAAAT-AAAAGAAACA
1 AAAATAAAAAGAAACA
1013790 AAAATAAAAAGAAACA
1 AAAATAAAAAGAAACA
*
1013806 AAAACAAAAA
1 AAAATAAAAA
1013816 CAAAAACCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 5 0.21
16 19 0.79
ACGTcount: A:0.83, C:0.07, G:0.05, T:0.05
Consensus pattern (16 bp):
AAAATAAAAAGAAACA
Found at i:1017325 original size:13 final size:15
Alignment explanation
Indices: 1017301--1017332 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1017291 TTTAGCTGGA
1017301 CGGGCGGATGT-GGG
1 CGGGCGGATGTGGGG
1017315 CGGGC-GATGTGGGG
1 CGGGCGGATGTGGGG
1017329 CGGG
1 CGGG
1017333 TAATGTCTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.06, C:0.16, G:0.66, T:0.12
Consensus pattern (15 bp):
CGGGCGGATGTGGGG
Found at i:1017520 original size:2 final size:2
Alignment explanation
Indices: 1017515--1017604 Score: 173
Period size: 2 Copynumber: 45.5 Consensus size: 2
1017505 ATAAAGTTGC
1017515 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1017557 A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1017598 AT AT AT A
1 AT AT AT A
1017605 AGGAAGTTCT
Statistics
Matches: 87, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 86 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1030208 original size:2 final size:2
Alignment explanation
Indices: 1030203--1030230 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1030193 TGTGTGTGTG
1030203 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1030231 CATAAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1032282 original size:40 final size:40
Alignment explanation
Indices: 1032238--1032326 Score: 169
Period size: 40 Copynumber: 2.2 Consensus size: 40
1032228 GTGGGTTACA
1032238 GCTGCTATTAATGGGTAGCGGCCAATCGCGGCAATAGCGG
1 GCTGCTATTAATGGGTAGCGGCCAATCGCGGCAATAGCGG
1032278 GCTGCTATTAATGGGTAGCGGCCAATCGCGGCAATAGCGG
1 GCTGCTATTAATGGGTAGCGGCCAATCGCGGCAATAGCGG
*
1032318 ACTGCTATT
1 GCTGCTATT
1032327 CCATTATTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.22, C:0.22, G:0.33, T:0.22
Consensus pattern (40 bp):
GCTGCTATTAATGGGTAGCGGCCAATCGCGGCAATAGCGG
Found at i:1034266 original size:32 final size:31
Alignment explanation
Indices: 1034195--1034268 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
1034185 ATTTACCAGT
*
1034195 GGTGATCACATCTTAAATAAATAAAAACAAA
1 GGTGATCATATCTTAAATAAATAAAAACAAA
** * * *
1034226 ATTAATCATATCTTAAGTAAATAAAAAACGAA
1 GGTGATCATATCTTAAATAAAT-AAAAACAAA
1034258 GGTGATCATAT
1 GGTGATCATAT
1034269 TTTATGTATT
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
31 17 0.52
32 16 0.48
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.27
Consensus pattern (31 bp):
GGTGATCATATCTTAAATAAATAAAAACAAA
Found at i:1045783 original size:14 final size:14
Alignment explanation
Indices: 1045764--1045801 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
1045754 ATGTATTTTA
1045764 CAGAAAATAAATTT
1 CAGAAAATAAATTT
1045778 CAGAAAATAAATTT
1 CAGAAAATAAATTT
* *
1045792 AATAAAATAA
1 CAGAAAATAA
1045802 TTCTATTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.26
Consensus pattern (14 bp):
CAGAAAATAAATTT
Found at i:1046342 original size:18 final size:18
Alignment explanation
Indices: 1046316--1046355 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1046306 TCATATCCGG
1046316 ATATAAATACGGATATCA
1 ATATAAATACGGATATCA
* * *
1046334 ATATCAATATGGATATGA
1 ATATAAATACGGATATCA
1046352 ATAT
1 ATAT
1046356 GGGTATCGAA
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:0.47, C:0.07, G:0.12, T:0.33
Consensus pattern (18 bp):
ATATAAATACGGATATCA
Found at i:1052018 original size:28 final size:28
Alignment explanation
Indices: 1051982--1052079 Score: 115
Period size: 30 Copynumber: 3.4 Consensus size: 28
1051972 AAAAAGTTTG
* * * *
1051982 AATAGTTTAGGTATCAATTTTGATATAA
1 AATACTTTAGGCATCTATTTTGATAAAA
*
1052010 AATACTTTAGGCACCTATTTTGATTAAAA
1 AATACTTTAGGCATCTATTTTGA-TAAAA
*
1052039 AATAACTTTAGGCATTTATTTTGATCAAAA
1 AAT-ACTTTAGGCATCTATTTTGAT-AAAA
1052069 AATACTTTAGG
1 AATACTTTAGG
1052080 TACTTAAATA
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
28 19 0.32
29 16 0.27
30 25 0.42
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (28 bp):
AATACTTTAGGCATCTATTTTGATAAAA
Found at i:1052068 original size:29 final size:28
Alignment explanation
Indices: 1051998--1052079 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 28
1051988 TTAGGTATCA
1051998 ATTTTGATATAAAAT-ACTTTAGGCACCT
1 ATTTTGATA-AAAATAACTTTAGGCACCT
**
1052026 ATTTTGATTAAAAAATAACTTTAGGCATTT
1 ATTTTGA-T-AAAAATAACTTTAGGCACCT
1052056 ATTTTGATCAAAAA-ATACTTTAGG
1 ATTTTGAT-AAAAATA-ACTTTAGG
1052080 TACTTAAATA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
28 8 0.17
29 20 0.43
30 19 0.40
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.40
Consensus pattern (28 bp):
ATTTTGATAAAAATAACTTTAGGCACCT
Found at i:1052411 original size:34 final size:34
Alignment explanation
Indices: 1052373--1052461 Score: 106
Period size: 34 Copynumber: 2.5 Consensus size: 34
1052363 AACACGCTGG
* *
1052373 GCATCTGAGGCCATCCGACCGAGGCCATCCGAGA
1 GCATCCGAGGCCATCCGACCGAGACCATCCGAGA
*
1052407 GCATCCGAGGCCATTCGACCGAGACCATCCGAACGA
1 GCATCCGAGGCCATCCGACCGAGACCATCCG-A-GA
* *
1052443 GCTATGCGAGGGCATCCGA
1 GC-ATCCGAGGCCATCCGA
1052462 GGGCAACCGA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
34 28 0.61
35 1 0.02
36 4 0.09
37 13 0.28
ACGTcount: A:0.25, C:0.34, G:0.29, T:0.12
Consensus pattern (34 bp):
GCATCCGAGGCCATCCGACCGAGACCATCCGAGA
Found at i:1059997 original size:2 final size:2
Alignment explanation
Indices: 1059990--1060019 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1059980 TTGTTTAGTT
1059990 TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1060020 TAGATTCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1063936 original size:29 final size:30
Alignment explanation
Indices: 1063903--1063974 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
1063893 TTTTAGAAGT
1063903 TAGTTTTTTATTATATTATAATTATT-TAA
1 TAGTTTTTTATTATATTATAATTATTGTAA
* * * *
1063932 TAGTTTATTATTTTATTATATTTATTGTAG
1 TAGTTTTTTATTATATTATAATTATTGTAA
*
1063962 TAATTTTTTATTA
1 TAGTTTTTTATTA
1063975 CTTTTTACAA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
29 23 0.66
30 12 0.34
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.64
Consensus pattern (30 bp):
TAGTTTTTTATTATATTATAATTATTGTAA
Found at i:1066054 original size:24 final size:23
Alignment explanation
Indices: 1066022--1066098 Score: 65
Period size: 24 Copynumber: 3.4 Consensus size: 23
1066012 TAGACTTGTT
1066022 TTTTATTTATTTGTTTCTTAATG
1 TTTTATTTATTTGTTTCTTAATG
* *
1066045 ATTTTATTTA----ATTATTAACT-
1 -TTTTATTTATTTGTTTCTTAA-TG
1066065 TTTTATTTATTTTGTTTCTTAATG
1 TTTTATTTA-TTTGTTTCTTAATG
1066089 TTTTTATTTA
1 -TTTTATTTA
1066099 ATTATGGACT
Statistics
Matches: 41, Mismatches: 4, Indels: 15
0.68 0.07 0.25
Matches are distributed among these distances:
19 9 0.22
20 6 0.15
21 1 0.02
23 1 0.02
24 15 0.37
25 9 0.22
ACGTcount: A:0.22, C:0.04, G:0.05, T:0.69
Consensus pattern (23 bp):
TTTTATTTATTTGTTTCTTAATG
Found at i:1066083 original size:44 final size:44
Alignment explanation
Indices: 1066021--1066121 Score: 168
Period size: 44 Copynumber: 2.3 Consensus size: 44
1066011 ATAGACTTGT
*
1066021 TTTTTATTTA-TTTGTTTCTTAATGATTTTATTTAATTATTAAC
1 TTTTTATTTATTTTGTTTCTTAATGATTTTATTTAATTATGAAC
* *
1066064 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGGAC
1 TTTTTATTTATTTTGTTTCTTAATGATTTTATTTAATTATGAAC
1066108 TTTTTATTTATTTT
1 TTTTTATTTATTTT
1066122 TTCTTATTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 10 0.19
44 44 0.81
ACGTcount: A:0.22, C:0.04, G:0.06, T:0.68
Consensus pattern (44 bp):
TTTTTATTTATTTTGTTTCTTAATGATTTTATTTAATTATGAAC
Found at i:1066128 original size:10 final size:9
Alignment explanation
Indices: 1066108--1066142 Score: 52
Period size: 10 Copynumber: 3.7 Consensus size: 9
1066098 AATTATGGAC
1066108 TTTTTATTTA
1 TTTTT-TTTA
1066118 TTTTTTCTTA
1 TTTTTT-TTA
1066128 TTTTTTTTA
1 TTTTTTTTA
1066137 TTTTTT
1 TTTTTT
1066143 AATTGTTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 10 0.42
10 14 0.58
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:1069619 original size:44 final size:43
Alignment explanation
Indices: 1069506--1069624 Score: 119
Period size: 37 Copynumber: 2.9 Consensus size: 43
1069496 AAAATAATAC
*
1069506 AAAAT-AATTAATATAATAAAATTTGGTTAAATAATTAAATAT
1 AAAATAAATTAATATAATAAAATTTGGTTAAATAATTAAACAT
** *
1069548 AAAATAAATATAATATAATAAAA-------AAATAATTTTACCT
1 AAAATAAAT-TAATATAATAAAATTTGGTTAAATAATTAAACAT
*
1069585 TAAATAAAATTAATATAATAAAATTTGGTTAAATAATTAA
1 AAAAT-AAATTAATATAATAAAATTTGGTTAAATAATTAA
1069625 TAATGTAATG
Statistics
Matches: 60, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
37 27 0.45
38 4 0.07
42 5 0.08
43 3 0.05
44 21 0.35
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (43 bp):
AAAATAAATTAATATAATAAAATTTGGTTAAATAATTAAACAT
Found at i:1070068 original size:3 final size:3
Alignment explanation
Indices: 1070062--1070100 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1070052 GAACAACAAC
1070062 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1070101 TTTCTTTCGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1074996 original size:21 final size:21
Alignment explanation
Indices: 1074970--1075010 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1074960 GACTATTGCA
1074970 TTGCGATTTTCCAAATTCGCG
1 TTGCGATTTTCCAAATTCGCG
*
1074991 TTGCGATTTTCCTAATTCGC
1 TTGCGATTTTCCAAATTCGC
1075011 AATGCGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.41
Consensus pattern (21 bp):
TTGCGATTTTCCAAATTCGCG
Found at i:1075016 original size:21 final size:21
Alignment explanation
Indices: 1074971--1075017 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1074961 ACTATTGCAT
**
1074971 TGCGATTTTCCAAATTCGCGT
1 TGCGATTTTCCAAATTCGCAA
*
1074992 TGCGATTTTCCTAATTCGCAA
1 TGCGATTTTCCAAATTCGCAA
1075013 TGCGA
1 TGCGA
1075018 ATACGTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.36
Consensus pattern (21 bp):
TGCGATTTTCCAAATTCGCAA
Found at i:1078521 original size:20 final size:19
Alignment explanation
Indices: 1078478--1078635 Score: 129
Period size: 19 Copynumber: 8.7 Consensus size: 19
1078468 GCAACGAGAG
*
1078478 AATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
1078497 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAA-ATGAA
* * *
1078517 TATCGTAACGCGGAAATGAC
1 AATCGCAACGC-GAAATGAA
* *
1078537 TATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1078556 AATCGCAA--CG--A-GAT
1 AATCGCAACGCGAAATGAA
*
1078570 AATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
**
1078589 AATCGCAA--CG--A-GGG
1 AATCGCAACGCGAAATGAA
*
1078603 AATCGCAAAGCGAAATGAA
1 AATCGCAACGCGAAATGAA
1078622 AATCGCAACGCGAA
1 AATCGCAACGCGAA
1078636 TTTAGTTTCG
Statistics
Matches: 112, Mismatches: 15, Indels: 24
0.74 0.10 0.16
Matches are distributed among these distances:
14 19 0.17
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 51 0.46
20 27 0.24
21 3 0.03
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.15
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:1078544 original size:40 final size:39
Alignment explanation
Indices: 1078478--1078633 Score: 122
Period size: 33 Copynumber: 4.3 Consensus size: 39
1078468 GCAACGAGAG
*
1078478 AATCGCAATGC-GAAATGAAAATCGCAACGCGAATATGAA
1 AATCGCAACGCGGAAATGAAAATCGCAACGCGAA-ATGAA
* * ** *
1078517 TATCGTAACGCGGAAATGACTATCGCAATGCGAAATGAA
1 AATCGCAACGCGGAAATGAAAATCGCAACGCGAAATGAA
* *
1078556 AATCGCAA--C-G--A-GATAATCGCAATGCGAAATGAA
1 AATCGCAACGCGGAAATGAAAATCGCAACGCGAAATGAA
* *
1078589 AATCGCAACGAGG----G--AATCGCAAAGCGAAATGAA
1 AATCGCAACGCGGAAATGAAAATCGCAACGCGAAATGAA
1078622 AATCGCAACGCG
1 AATCGCAACGCG
1078634 AATTTAGTTT
Statistics
Matches: 100, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
33 57 0.57
34 1 0.01
35 1 0.01
36 2 0.02
37 1 0.01
39 19 0.19
40 19 0.19
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.15
Consensus pattern (39 bp):
AATCGCAACGCGGAAATGAAAATCGCAACGCGAAATGAA
Found at i:1078580 original size:33 final size:33
Alignment explanation
Indices: 1078538--1078631 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
1078528 GGAAATGACT
*
1078538 ATCGCAATGCGAAATGAAAATCGCAACGAGATA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1078571 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1078604 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1078632 CGAATTTAGT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1078714 original size:19 final size:19
Alignment explanation
Indices: 1078641--1078706 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
1078631 GCGAATTTAG
*
1078641 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
1078660 TTTCGCATTGCGA--TTC-
1 TTTCGCATTGCGATTTTCA
* *
1078676 TCTCG--TTGCGATTTTTA
1 TTTCGCATTGCGATTTTCA
1078693 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
1078707 AGTCATTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
14 6 0.16
16 6 0.16
17 7 0.18
19 19 0.50
ACGTcount: A:0.12, C:0.21, G:0.20, T:0.47
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:1078832 original size:14 final size:14
Alignment explanation
Indices: 1078813--1078849 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1078803 CATCAATTAA
1078813 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1078827 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1078841 ACAAATCAA
1 ACAAATCAA
1078850 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1081442 original size:14 final size:15
Alignment explanation
Indices: 1081425--1081453 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1081415 TATATGATAT
1081425 GCATA-AACATAAGA
1 GCATATAACATAAGA
1081439 GCATATAACATAAGA
1 GCATATAACATAAGA
1081454 TATGTGATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.55, C:0.14, G:0.14, T:0.17
Consensus pattern (15 bp):
GCATATAACATAAGA
Found at i:1081716 original size:15 final size:15
Alignment explanation
Indices: 1081698--1081745 Score: 96
Period size: 15 Copynumber: 3.2 Consensus size: 15
1081688 CGAGGGTTCT
1081698 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
1081713 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
1081728 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
1081743 GTA
1 GTA
1081746 ATGGTCCTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.15, C:0.25, G:0.33, T:0.27
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:1081780 original size:22 final size:19
Alignment explanation
Indices: 1081730--1081782 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
1081720 TTCGGGACGT
*
1081730 AGTCCTTCGGGACGTAATG
1 AGTCCTTCGGGACATAATG
*
1081749 -GTCCTACGGGACATATATAG
1 AGTCCTTCGGGACATA-AT-G
1081769 CAGTCCTTCGGGAC
1 -AGTCCTTCGGGAC
1081783 GAATACTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 13 0.48
19 2 0.07
20 1 0.04
22 11 0.41
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.25
Consensus pattern (19 bp):
AGTCCTTCGGGACATAATG
Found at i:1082991 original size:94 final size:93
Alignment explanation
Indices: 1082826--1082998 Score: 301
Period size: 94 Copynumber: 1.8 Consensus size: 93
1082816 AATATGTTTC
* *
1082826 AAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAAC
1 AAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAATTTAGCAGAATTGGCAGCAAC
1082891 CGAATAAATTTACTTCAACCAAAAGATA
66 CGAATAAATTTACTTCAACCAAAAGATA
* *
1082919 AAACAAAAGACAAATACTAACTTCACAGTGTTAAATAATAAACAATTTAGCAGTATTGGCAGCAA
1 AAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAATTTAGCAGAATTGGCAGCAA
1082984 CCGAATAAATTTACT
65 CCGAATAAATTTACT
1082999 AAGCAATCTA
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
93 4 0.05
94 71 0.95
ACGTcount: A:0.47, C:0.17, G:0.12, T:0.23
Consensus pattern (93 bp):
AAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAATTTAGCAGAATTGGCAGCAAC
CGAATAAATTTACTTCAACCAAAAGATA
Found at i:1084741 original size:19 final size:19
Alignment explanation
Indices: 1084677--1084804 Score: 166
Period size: 19 Copynumber: 6.6 Consensus size: 19
1084667 TCTTTTGGTT
*
1084677 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
**
1084696 GAAAATGACTATCGCAACGC
1 G-AAATGAAAATCGCAACGC
**
1084716 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
*
1084736 GAAATGAAAATCACAACGC
1 GAAATGAAAATCGCAACGC
*
1084755 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1084774 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1084793 GAAATGAAAATC
1 GAAATGAAAATC
1084805 ACAGTGCGAT
Statistics
Matches: 98, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
19 64 0.65
20 33 0.34
21 1 0.01
ACGTcount: A:0.47, C:0.20, G:0.19, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1084889 original size:20 final size:20
Alignment explanation
Indices: 1084850--1084896 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
1084840 GTTGCGATAG
* *
1084850 TCATTTTCGTGTTGCGATTT
1 TCATTTTCATGTTGCAATTT
* *
1084870 TTATTTTCATGTTGTAATTT
1 TCATTTTCATGTTGCAATTT
1084890 TCATTTT
1 TCATTTT
1084897 AGAAACTATT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.15, C:0.11, G:0.13, T:0.62
Consensus pattern (20 bp):
TCATTTTCATGTTGCAATTT
Found at i:1085473 original size:20 final size:20
Alignment explanation
Indices: 1085448--1085661 Score: 182
Period size: 20 Copynumber: 10.6 Consensus size: 20
1085438 CTTTAAAAAT
*
1085448 CGCGTTGCGATTTATGGATA
1 CGCGTTGCGATTTACGGATA
* *
1085468 CGCGTTGCGCTTTTTC--ATA
1 CGCGTTGCG-ATTTACGGATA
* *
1085487 TTGTCGTTGCAATTTACGGATA
1 -CG-CGTTGCGATTTACGGATA
* * * *
1085509 CACATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
1085529 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* * *
1085549 CGCGTTGTGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
1085569 CTCGTTGCGATTTACGGATG
1 CGCGTTGCGATTTACGGATA
*
1085589 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
1085609 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
1085630 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
1085651 CTCGTTGCGAT
1 CGCGTTGCGAT
1085662 AGTCAGAATC
Statistics
Matches: 152, Mismatches: 33, Indels: 18
0.75 0.16 0.09
Matches are distributed among these distances:
19 3 0.02
20 101 0.66
21 45 0.30
22 3 0.02
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1085604 original size:81 final size:80
Alignment explanation
Indices: 1085450--1085702 Score: 271
Period size: 81 Copynumber: 3.1 Consensus size: 80
1085440 TTAAAAATCG
* * * * * * * *
1085450 CGTTGCGATTTATGGATACGCGTTGCGCTTTTTCATATTGTCGTTGCAATTTACGGATACACATT
1 CGTTGCGATTTACGGATACGCGTTGCG-ATTTACGTATTCTCGTTGCGATTTACGGAT-CGCGTT
1085515 GCGA-TTTACGTATTCT
64 GCGATTTTACGTATTCT
* *
1085531 CGTTGCGATTTACAGATACGCGTTGTGATTTACGTATTCTCGTTGCGATTTACGGATGCGCGTTG
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGAT-CGCGTTG
*
1085596 CGATTTTACGTATTGT
65 CGATTTTACGTATTCT
* * * *
1085612 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGATAGT-CAGAATCGCGT
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCTCGTTGCGAT-TTAC-GGATCGCGT
*
1085676 TGCGATTTTTA--TATTCG
63 TGCGA-TTTTACGTATTCT
1085693 CGTTGCGATT
1 CGTTGCGATT
1085703 CTGGAAAATC
Statistics
Matches: 147, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
80 33 0.22
81 75 0.51
82 30 0.20
83 9 0.06
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.39
Consensus pattern (80 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATCGCGTTGC
GATTTTACGTATTCT
Found at i:1085644 original size:41 final size:41
Alignment explanation
Indices: 1085450--1085702 Score: 284
Period size: 41 Copynumber: 6.2 Consensus size: 41
1085440 TTAAAAATCG
* * * * *
1085450 CGTTGCGATTTATGGATACGCGTTGCGCTTTTTCATATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * *
1085491 CGTTGCAATTTACGGATACACATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
1085531 CGTTGCGATTTACAGATACGCGTTGTGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
1085571 CGTTGCGATTTACGGATGCGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
1085612 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * *
1085653 CGTTGCGATAGT-CAGA-ATCGCGTTGCGATTTTTA--TATTCG
1 CGTTGCGAT-TTACGGATA-CGCGTTGCGA-TTTTACGTATTCT
1085693 CGTTGCGATT
1 CGTTGCGATT
1085703 CTGGAAAATC
Statistics
Matches: 181, Mismatches: 27, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
40 82 0.45
41 93 0.51
42 6 0.03
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.39
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:1085720 original size:21 final size:21
Alignment explanation
Indices: 1085696--1085748 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
1085686 ATATTCGCGT
1085696 TGCGATTCTGGAAAATCGCAA
1 TGCGATTCTGGAAAATCGCAA
* ** *
1085717 TGCGAATT-TGTACTATCGCAT
1 TGCG-ATTCTGGAAAATCGCAA
1085738 TGCGATTCTGG
1 TGCGATTCTGG
1085749 GAACTGATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
20 3 0.12
21 19 0.76
22 3 0.12
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (21 bp):
TGCGATTCTGGAAAATCGCAA
Found at i:1089323 original size:44 final size:44
Alignment explanation
Indices: 1089230--1089413 Score: 137
Period size: 44 Copynumber: 4.2 Consensus size: 44
1089220 ATATTTTAAG
* * *
1089230 TTTTTTCCAATAT-ATCTATCTATCTTTTCAACTT-AGGCCCCTAA
1 TTTTTTTCAATATCA-CTTTCTATCTTTTCAA-TTGAGGTCCCTAA
* * * *
1089274 GTTTTTTCAATATCTCTTTCTACCTTTTCAATTGAGGTCTCTAA
1 TTTTTTTCAATATCACTTTCTATCTTTTCAATTGAGGTCCCTAA
* * *
1089318 TTTTTTT-AATCTCAATTTCTATCTTTAT-AATTGAGG-CTCTTAA
1 TTTTTTTCAATATCACTTTCTATCTTT-TCAATTGAGGTC-CCTAA
* * * *
1089361 GTTTTTTTTAATCTCACTTTCTAAC-TTTCTTATTGAGGTCCCTAA
1 -TTTTTTTCAATATCACTTTCTATCTTTTC-AATTGAGGTCCCTAA
*
1089406 ATTTTTTC
1 TTTTTTTC
1089414 GATCTTAATT
Statistics
Matches: 111, Mismatches: 20, Indels: 18
0.74 0.13 0.12
Matches are distributed among these distances:
42 1 0.01
43 29 0.26
44 55 0.50
45 25 0.23
46 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.07, T:0.51
Consensus pattern (44 bp):
TTTTTTTCAATATCACTTTCTATCTTTTCAATTGAGGTCCCTAA
Found at i:1089324 original size:45 final size:43
Alignment explanation
Indices: 1089248--1089412 Score: 131
Period size: 43 Copynumber: 3.8 Consensus size: 43
1089238 AATATATCTA
* * *
1089248 TCTATCTTTTCAACTT-AGGCCCCTAAGTTTTTTCAATATCTCTT
1 TCTATCTTTTCAA-TTGAGGTCCCTAA-TTTTTTTAATATCACTT
* * * *
1089292 TCTACCTTTTCAATTGAGGTCTCTAATTTTTTTAATCTCAATT
1 TCTATCTTTTCAATTGAGGTCCCTAATTTTTTTAATATCACTT
* *
1089335 TCTATCTTTAT-AATTGAGG-CTCTTAAGTTTTTTTTAATCTCACTT
1 TCTATCTTT-TCAATTGAGGTC-CCTAA--TTTTTTTAATATCACTT
* * *
1089380 TCTAAC-TTTCTTATTGAGGTCCCTAAATTTTTT
1 TCTATCTTTTC-AATTGAGGTCCCTAATTTTTTT
1089413 CGATCTTAAT
Statistics
Matches: 98, Mismatches: 15, Indels: 17
0.75 0.12 0.13
Matches are distributed among these distances:
42 1 0.01
43 41 0.42
44 23 0.23
45 32 0.33
46 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.08, T:0.51
Consensus pattern (43 bp):
TCTATCTTTTCAATTGAGGTCCCTAATTTTTTTAATATCACTT
Found at i:1089337 original size:43 final size:43
Alignment explanation
Indices: 1089290--1089497 Score: 160
Period size: 43 Copynumber: 4.8 Consensus size: 43
1089280 TCAATATCTC
1089290 TTTCTACCTTTTCAATTGAGGTCTCTAATTTTTTTAATCTCAA
1 TTTCTACCTTTTCAATTGAGGTCTCTAATTTTTTTAATCTCAA
* *
1089333 TTTCTATCTTTAT-AATTGAGG-CTCTTAAGTTTTTTTTAATCTCAC
1 TTTCTACCTTT-TCAATTGAGGTCTC-TAA--TTTTTTTAATCTCAA
* * * ** *
1089378 TTTCTAAC-TTTCTTATTGAGGTCCCTAAATTTTTTCGATCTTAA
1 TTTCTACCTTTTC-AATTGAGGTCTCT-AATTTTTTTAATCTCAA
* * ** *
1089422 -TTATACATTTAT-AATTGAGACCTCT-ATTTTTTTAATCTCGA
1 TTTCTACCTTT-TCAATTGAGGTCTCTAATTTTTTTAATCTCAA
* * *
1089463 TTTCTACCTTTACAATTAACGTCTCT-ATTTTTTTA
1 TTTCTACCTTTTCAATTGAGGTCTCTAATTTTTTTA
1089498 CAATTTCATA
Statistics
Matches: 126, Mismatches: 27, Indels: 25
0.71 0.15 0.14
Matches are distributed among these distances:
41 12 0.10
42 29 0.23
43 35 0.28
44 16 0.13
45 30 0.24
46 4 0.03
ACGTcount: A:0.24, C:0.17, G:0.07, T:0.51
Consensus pattern (43 bp):
TTTCTACCTTTTCAATTGAGGTCTCTAATTTTTTTAATCTCAA
Found at i:1090319 original size:17 final size:17
Alignment explanation
Indices: 1090291--1090332 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
1090281 ATTCGATTTG
1090291 ATTTAAAA-TTTTAGAT
1 ATTTAAAATTTTTAGAT
1090307 ATTTAAAATTTTTAGAT
1 ATTTAAAATTTTTAGAT
1090324 ATTTAAAAT
1 ATTTAAAAT
1090333 GGTGATATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 8 0.32
17 17 0.68
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (17 bp):
ATTTAAAATTTTTAGAT
Found at i:1093812 original size:18 final size:18
Alignment explanation
Indices: 1093789--1093824 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1093779 ATCACCTATG
1093789 ACGCTGATCTATTTTACT
1 ACGCTGATCTATTTTACT
1093807 ACGCTGATCTATTTTACT
1 ACGCTGATCTATTTTACT
1093825 GACTAAGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.44
Consensus pattern (18 bp):
ACGCTGATCTATTTTACT
Found at i:1094339 original size:96 final size:96
Alignment explanation
Indices: 1094175--1094376 Score: 264
Period size: 96 Copynumber: 2.1 Consensus size: 96
1094165 TTGAAGTGGA
* * * *
1094175 TTCATCTACCTTGTTACCGCTAGAAATGACTTTCTTTGATGACTTCTACAGTGATTTTGCCTCTG
1 TTCATCTACATTGTTACCGCTAGAAATGACCTTCTTCGATGACTTATACAGTGATTTTGCCTCTG
*
1094240 AATCA-CTGCCCGTGTCACCTTCTTTCATAGT
66 AATCATCTG-CAGTGTCACCTTCTTTCATAGT
* * * *
1094271 TTCATCTGCATTGTTATCGCTAG-AATCTACCTTCTTCGATGACTTATTCAGTGATTTTGCCTCT
1 TTCATCTACATTGTTACCGCTAGAAAT-GACCTTCTTCGATGACTTATACAGTGATTTTGCCTCT
* * *
1094335 GAATCATTTGCAGTGTCACTTTCTTTCTTAGT
65 GAATCATCTGCAGTGTCACCTTCTTTCATAGT
1094367 TTCATCTACA
1 TTCATCTACA
1094377 CCAACTGGAG
Statistics
Matches: 91, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
95 3 0.03
96 86 0.95
97 2 0.02
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.42
Consensus pattern (96 bp):
TTCATCTACATTGTTACCGCTAGAAATGACCTTCTTCGATGACTTATACAGTGATTTTGCCTCTG
AATCATCTGCAGTGTCACCTTCTTTCATAGT
Found at i:1103413 original size:21 final size:21
Alignment explanation
Indices: 1103371--1103429 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
1103361 GCAACAAAGT
**
1103371 CTTGCAACAACTTCATGTCAG
1 CTTGCAACAACTTCATCCCAG
*
1103392 CTTGCAACACCTTCATCCCAG
1 CTTGCAACAACTTCATCCCAG
* * *
1103413 CCTGTAACATCTTCATC
1 CTTGCAACAACTTCATC
1103430 TCAACATGTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.36, G:0.10, T:0.29
Consensus pattern (21 bp):
CTTGCAACAACTTCATCCCAG
Found at i:1103439 original size:21 final size:21
Alignment explanation
Indices: 1103397--1103440 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1103387 GTCAGCTTGC
* *
1103397 AACACCTTCATCCCAGCCTGT
1 AACACCTTCATCCCAACATGT
* *
1103418 AACATCTTCATCTCAACATGT
1 AACACCTTCATCCCAACATGT
1103439 AA
1 AA
1103441 AAATGATGCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.34, G:0.07, T:0.27
Consensus pattern (21 bp):
AACACCTTCATCCCAACATGT
Found at i:1104131 original size:22 final size:22
Alignment explanation
Indices: 1104106--1104147 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1104096 TTTTTATAAA
* *
1104106 ATTTTTGGATTTTTAAATATAT
1 ATTTTTGAAATTTTAAATATAT
*
1104128 ATTTTTTAAATTTTAAATAT
1 ATTTTTGAAATTTTAAATAT
1104148 TTTTTAAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (22 bp):
ATTTTTGAAATTTTAAATATAT
Found at i:1105061 original size:10 final size:10
Alignment explanation
Indices: 1105046--1105080 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
1105036 TTTATCACAC
1105046 CAAATTCTCT
1 CAAATTCTCT
1105056 CAAATTCTCT
1 CAAATTCTCT
1105066 -AAATTTCTCT
1 CAAA-TTCTCT
1105076 CAAAT
1 CAAAT
1105081 ACTCAATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 3 0.13
10 17 0.74
11 3 0.13
ACGTcount: A:0.34, C:0.26, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:1112505 original size:60 final size:60
Alignment explanation
Indices: 1112432--1112557 Score: 225
Period size: 60 Copynumber: 2.1 Consensus size: 60
1112422 AGCCACCATC
* *
1112432 ATCAGAAATGTAACTTCCCTGTGGCATCGGTTGGACAATAAGATAGTCTTCCTTTTCAAT
1 ATCAGAAATGTAACTTCCCTGTAGCATCGGTTGGACAATAAGATAGCCTTCCTTTTCAAT
*
1112492 ATCAGAAATGTAACTTCCCTGTAGCATCGGTTGGACCATAAGATAGCCTTCCTTTTCAAT
1 ATCAGAAATGTAACTTCCCTGTAGCATCGGTTGGACAATAAGATAGCCTTCCTTTTCAAT
1112552 ATCAGA
1 ATCAGA
1112558 TGGCTCCGTA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 63 1.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.32
Consensus pattern (60 bp):
ATCAGAAATGTAACTTCCCTGTAGCATCGGTTGGACAATAAGATAGCCTTCCTTTTCAAT
Found at i:1118166 original size:12 final size:12
Alignment explanation
Indices: 1118149--1118175 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1118139 CAATTACACC
1118149 CTCCCTCTCTCT
1 CTCCCTCTCTCT
1118161 CTCCCTCTCTCT
1 CTCCCTCTCTCT
1118173 CTC
1 CTC
1118176 ACTCACCAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (12 bp):
CTCCCTCTCTCT
Found at i:1124594 original size:21 final size:21
Alignment explanation
Indices: 1124569--1124616 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
1124559 TTTAGTACTT
1124569 AAACTTTCAAATTTTTCTTTA
1 AAACTTTCAAATTTTTCTTTA
1124590 AAACTTTCAAATTTTTCTTTA
1 AAACTTTCAAATTTTTCTTTA
1124611 AAACTT
1 AAACTT
1124617 AACGTTACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (21 bp):
AAACTTTCAAATTTTTCTTTA
Found at i:1125975 original size:22 final size:23
Alignment explanation
Indices: 1125933--1125975 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1125923 GGATGGAGGA
*
1125933 TTAAAATAAAATACATTATTATT
1 TTAAAATAAAATACATAATTATT
*
1125956 TTAAAAT-AATTACATAATTA
1 TTAAAATAAAATACATAATTA
1125976 AAAAAACATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (23 bp):
TTAAAATAAAATACATAATTATT
Found at i:1144741 original size:17 final size:16
Alignment explanation
Indices: 1144710--1144740 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1144700 AATATTGAAA
*
1144710 CTTGAACTCAAAAAAG
1 CTTGAACTAAAAAAAG
1144726 CTTGAACTAAAAAAA
1 CTTGAACTAAAAAAA
1144741 AATTAGAAGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.16, G:0.10, T:0.19
Consensus pattern (16 bp):
CTTGAACTAAAAAAAG
Found at i:1151876 original size:12 final size:12
Alignment explanation
Indices: 1151861--1151901 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
1151851 TGATGACGAC
1151861 GAAGAAGAGGAG
1 GAAGAAGAGGAG
*
1151873 GAAGAAGAGGAA
1 GAAGAAGAGGAG
*
1151885 GAGGAAGAGGAG
1 GAAGAAGAGGAG
*
1151897 AAAGA
1 GAAGA
1151902 GCTTCAGCCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (12 bp):
GAAGAAGAGGAG
Found at i:1153709 original size:15 final size:15
Alignment explanation
Indices: 1153689--1153718 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1153679 ATTTTCTTAC
1153689 GCATTCTAATAGTTT
1 GCATTCTAATAGTTT
1153704 GCATTCTAATAGTTT
1 GCATTCTAATAGTTT
1153719 AAGCTTCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (15 bp):
GCATTCTAATAGTTT
Found at i:1158959 original size:21 final size:21
Alignment explanation
Indices: 1158935--1158982 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
1158925 TTGTAACCTT
*
1158935 TGTAATTACTCATGTAACTGG
1 TGTAATTACACATGTAACTGG
*
1158956 TGTAATTACACTTGTAACTGG
1 TGTAATTACACATGTAACTGG
1158977 TGTAAT
1 TGTAAT
1158983 AAACAGTCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (21 bp):
TGTAATTACACATGTAACTGG
Found at i:1164900 original size:16 final size:16
Alignment explanation
Indices: 1164869--1164898 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1164859 TCAAATGATA
1164869 TTTTAATTATTAAAAT
1 TTTTAATTATTAAAAT
1164885 TTTTAATT-TTAAAA
1 TTTTAATTATTAAAA
1164899 ATGATAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTTAATTATTAAAAT
Found at i:1164914 original size:19 final size:20
Alignment explanation
Indices: 1164887--1164928 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1164877 ATTAAAATTT
*
1164887 TTAATTTTA-AAAATGATAA
1 TTAAATTTATAAAATGATAA
* *
1164906 TTAAATTTATCAAATGATTA
1 TTAAATTTATAAAATGATAA
1164926 TTA
1 TTA
1164929 TAATAACATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (20 bp):
TTAAATTTATAAAATGATAA
Found at i:1166517 original size:14 final size:14
Alignment explanation
Indices: 1166498--1166525 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1166488 GTCCTTACCT
1166498 GCATTCAGTCACCC
1 GCATTCAGTCACCC
1166512 GCATTCAGTCACCC
1 GCATTCAGTCACCC
1166526 ATTGTCAGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.43, G:0.14, T:0.21
Consensus pattern (14 bp):
GCATTCAGTCACCC
Found at i:1169139 original size:277 final size:277
Alignment explanation
Indices: 1168645--1169199 Score: 1110
Period size: 277 Copynumber: 2.0 Consensus size: 277
1168635 GAGAATGAAA
1168645 ATAAGCATTTAGAATTCAGTAATGCTATATTGTTTATTATTCATAGGTCGTTGTAAGGTAAAATA
1 ATAAGCATTTAGAATTCAGTAATGCTATATTGTTTATTATTCATAGGTCGTTGTAAGGTAAAATA
1168710 CAGTGAGATACAATTCTGTAATGGGCTACCATCCTTGAAACTGCGAAGACTAGCACAAAAACTTC
66 CAGTGAGATACAATTCTGTAATGGGCTACCATCCTTGAAACTGCGAAGACTAGCACAAAAACTTC
1168775 AAAACACAACACATAAAAAAATTAACCTGCAGTCCATCTTCATGGGCTCTTTGCTCAATTTCAAG
131 AAAACACAACACATAAAAAAATTAACCTGCAGTCCATCTTCATGGGCTCTTTGCTCAATTTCAAG
1168840 CACGGTTGCAACATCCTGATCTGTAGGCCCTTCTTCTTGAAGACGTACTACTTCATCCAAAGCAA
196 CACGGTTGCAACATCCTGATCTGTAGGCCCTTCTTCTTGAAGACGTACTACTTCATCCAAAGCAA
1168905 GATCAACCTGTTCCGCG
261 GATCAACCTGTTCCGCG
1168922 ATAAGCATTTAGAATTCAGTAATGCTATATTGTTTATTATTCATAGGTCGTTGTAAGGTAAAATA
1 ATAAGCATTTAGAATTCAGTAATGCTATATTGTTTATTATTCATAGGTCGTTGTAAGGTAAAATA
1168987 CAGTGAGATACAATTCTGTAATGGGCTACCATCCTTGAAACTGCGAAGACTAGCACAAAAACTTC
66 CAGTGAGATACAATTCTGTAATGGGCTACCATCCTTGAAACTGCGAAGACTAGCACAAAAACTTC
1169052 AAAACACAACACATAAAAAAATTAACCTGCAGTCCATCTTCATGGGCTCTTTGCTCAATTTCAAG
131 AAAACACAACACATAAAAAAATTAACCTGCAGTCCATCTTCATGGGCTCTTTGCTCAATTTCAAG
1169117 CACGGTTGCAACATCCTGATCTGTAGGCCCTTCTTCTTGAAGACGTACTACTTCATCCAAAGCAA
196 CACGGTTGCAACATCCTGATCTGTAGGCCCTTCTTCTTGAAGACGTACTACTTCATCCAAAGCAA
1169182 GATCAACCTGTTCCGCG
261 GATCAACCTGTTCCGCG
1169199 A
1 A
1169200 CAGATTTTTT
Statistics
Matches: 278, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
277 278 1.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (277 bp):
ATAAGCATTTAGAATTCAGTAATGCTATATTGTTTATTATTCATAGGTCGTTGTAAGGTAAAATA
CAGTGAGATACAATTCTGTAATGGGCTACCATCCTTGAAACTGCGAAGACTAGCACAAAAACTTC
AAAACACAACACATAAAAAAATTAACCTGCAGTCCATCTTCATGGGCTCTTTGCTCAATTTCAAG
CACGGTTGCAACATCCTGATCTGTAGGCCCTTCTTCTTGAAGACGTACTACTTCATCCAAAGCAA
GATCAACCTGTTCCGCG
Found at i:1173570 original size:3 final size:3
Alignment explanation
Indices: 1173562--1173594 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
1173552 GACCAGAAAT
1173562 GAA GAA GAA GAA GAA GAA GAA -AA GAGA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA-A GAA GAA
1173595 AGAAAAACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 23 0.82
4 3 0.11
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1173579 original size:12 final size:11
Alignment explanation
Indices: 1173556--1173595 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
1173546 ACAAATGACC
*
1173556 AGAAATGAAGA
1 AGAAAAGAAGA
1173567 AGAAGAAGAAGA
1 AGAA-AAGAAGA
1173579 AGAAAAGAGAGA
1 AGAAAAGA-AGA
1173591 AGAAA
1 AGAAA
1173596 GAAAAACAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 8 0.31
12 18 0.69
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.03
Consensus pattern (11 bp):
AGAAAAGAAGA
Found at i:1177163 original size:198 final size:198
Alignment explanation
Indices: 1176825--1177306 Score: 768
Period size: 198 Copynumber: 2.4 Consensus size: 198
1176815 ATCCCTCCCC
**
1176825 AACTGAA-TTTCTAGCCTTTGAACTTTTGGCACCACCTGATGTTGTACTCTTCCAGACAGGAGCA
1 AACTGAAGTTT-TAGCCTTCAAACTTTTGGCACCACCTGATGTTGTACTCTTCCAGACAGGAGCA
* *
1176889 GGCTGTTGTTCCTTTTCTGATGACTTCAAAGTTCCACCAACTGAAGAGCCTTTGGACTCCGAAAA
65 GACTGTTGTTCCTTTTCTGATGACTTCAAAGTTCCACCAACCGAAGAGCCTTTGGACTCCGAAAA
* *
1176954 TGGCTTTGAAGGAGGTTGAGGAACCAACCGAGAATGTTGGGAACTTTCCTGGTGATCTAAGTCCT
130 TGGCCTTGAAGGAGGTTGAGGAACCAACCGAGAATGTTGGGAACTTTCCTGGTGATCCAAGTCCT
1177019 CAGA
195 CAGA
1177023 AACTGAAGTTTTAGCCTTCAAACTTTTGGCACCACCTGATGTTGTACTCTTCCAGACAGGAGCAG
1 AACTGAAGTTTTAGCCTTCAAACTTTTGGCACCACCTGATGTTGTACTCTTCCAGACAGGAGCAG
* *
1177088 ACTGTTGTTCCTTTTCTGATGACTTCAAAGTTCCACCAACCGAAGAGCCTTTGGCCTCTGAAAAT
66 ACTGTTGTTCCTTTTCTGATGACTTCAAAGTTCCACCAACCGAAGAGCCTTTGGACTCCGAAAAT
* ** *
1177153 GGCCTTGAAGGTGGTTGAGGTGCCAACTGAGAATGTTGGGAACTTTCCTGGTGATCCAAGTCCTC
131 GGCCTTGAAGGAGGTTGAGGAACCAACCGAGAATGTTGGGAACTTTCCTGGTGATCCAAGTCCTC
1177218 AGA
196 AGA
* * * * * *
1177221 AACTGAAGTTTTAGCCTTCAAACTTTTGGAACCACCTGACGATGTACCCCTCCAGACAGAAGCAG
1 AACTGAAGTTTTAGCCTTCAAACTTTTGGCACCACCTGATGTTGTACTCTTCCAGACAGGAGCAG
**
1177286 ACTGCCGTTCCTTTTCTGATG
66 ACTGTTGTTCCTTTTCTGATG
1177307 GCACCACCTG
Statistics
Matches: 263, Mismatches: 20, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
198 260 0.99
199 3 0.01
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (198 bp):
AACTGAAGTTTTAGCCTTCAAACTTTTGGCACCACCTGATGTTGTACTCTTCCAGACAGGAGCAG
ACTGTTGTTCCTTTTCTGATGACTTCAAAGTTCCACCAACCGAAGAGCCTTTGGACTCCGAAAAT
GGCCTTGAAGGAGGTTGAGGAACCAACCGAGAATGTTGGGAACTTTCCTGGTGATCCAAGTCCTC
AGA
Found at i:1178212 original size:21 final size:21
Alignment explanation
Indices: 1178186--1178233 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
1178176 CTAGGGCCAT
1178186 AATCATCAAAAGTTGCAGGCA
1 AATCATCAAAAGTTGCAGGCA
1178207 AATCATCAAAAGTTGCAGGCA
1 AATCATCAAAAGTTGCAGGCA
*
1178228 AGTCAT
1 AATCAT
1178234 TCACGTTAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.21
Consensus pattern (21 bp):
AATCATCAAAAGTTGCAGGCA
Found at i:1184734 original size:23 final size:23
Alignment explanation
Indices: 1184704--1184751 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
1184694 TATGTGCAAA
1184704 CATAAAACGGAGAGCAATTGGGG
1 CATAAAACGGAGAGCAATTGGGG
1184727 CATAAAACGGAGAGCAATTGGGG
1 CATAAAACGGAGAGCAATTGGGG
1184750 CA
1 CA
1184752 CTACAATGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.40, C:0.15, G:0.33, T:0.12
Consensus pattern (23 bp):
CATAAAACGGAGAGCAATTGGGG
Found at i:1185743 original size:29 final size:29
Alignment explanation
Indices: 1185701--1185789 Score: 124
Period size: 29 Copynumber: 3.1 Consensus size: 29
1185691 TACCGGGGGT
*
1185701 AGGTCGCCATGCACGCCCGGCGACCTACC
1 AGGTCGCCATGCACGCCCAGCGACCTACC
***
1185730 AGGTCGCCATGCACGCCCAGCGACCTGGT
1 AGGTCGCCATGCACGCCCAGCGACCTACC
* *
1185759 AGGTCGCCATGCATGCCCTGCGACCTACC
1 AGGTCGCCATGCACGCCCAGCGACCTACC
1185788 AG
1 AG
1185790 CCAACGACCT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.18, C:0.40, G:0.28, T:0.13
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCAGCGACCTACC
Found at i:1186057 original size:29 final size:29
Alignment explanation
Indices: 1185996--1186079 Score: 96
Period size: 29 Copynumber: 2.9 Consensus size: 29
1185986 ATGAATCCTT
** * **
1185996 GGTCGCCCCGAGTGCATGGCGACCTCCTT
1 GGTCGCCGGGAGTGCATGGCGACCTACGA
* *
1186025 GGTCGCCGGGCGTGCATGGCGACCTAGGA
1 GGTCGCCGGGAGTGCATGGCGACCTACGA
*
1186054 GGTCGCTGGGAGTGCATGGCGACCTA
1 GGTCGCCGGGAGTGCATGGCGACCTA
1186080 TGGTTGGGTT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.13, C:0.30, G:0.39, T:0.18
Consensus pattern (29 bp):
GGTCGCCGGGAGTGCATGGCGACCTACGA
Found at i:1186813 original size:19 final size:18
Alignment explanation
Indices: 1186786--1186843 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 18
1186776 CCGATAAATC
1186786 AAACCGAACCGAACCAAA
1 AAACCGAACCGAACCAAA
*
1186804 AAACCCGAACCGTTA--AAA
1 AAA-CCGAACCG-AACCAAA
1186822 AAACCGAACCGAACCGAAA
1 AAACCGAACCGAACC-AAA
1186841 AAA
1 AAA
1186844 TCAGTTTTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
16 1 0.03
17 8 0.24
18 9 0.27
19 14 0.42
20 1 0.03
ACGTcount: A:0.55, C:0.29, G:0.12, T:0.03
Consensus pattern (18 bp):
AAACCGAACCGAACCAAA
Found at i:1186841 original size:17 final size:17
Alignment explanation
Indices: 1186786--1186842 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 17
1186776 CCGATAAATC
1186786 AAACCGAACCGAACCAAA
1 AAACCGAACCGAACC-AA
1186804 AAACCCGAACCGTTAA--AA
1 AAA-CCGAACCG--AACCAA
1186822 AAACCGAACCGAACCGAA
1 AAACCGAACCGAACC-AA
1186840 AAA
1 AAA
1186843 ATCAGTTTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
15 2 0.06
17 8 0.24
18 13 0.39
19 8 0.24
21 2 0.06
ACGTcount: A:0.54, C:0.30, G:0.12, T:0.04
Consensus pattern (17 bp):
AAACCGAACCGAACCAA
Found at i:1191759 original size:19 final size:19
Alignment explanation
Indices: 1191731--1191769 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1191721 TATCATCTTA
*
1191731 ATATTGTTTATAAAATTAT
1 ATATTGTTTACAAAATTAT
* *
1191750 ATATTTTTTACCAAATTAT
1 ATATTGTTTACAAAATTAT
1191769 A
1 A
1191770 ACATTATGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (19 bp):
ATATTGTTTACAAAATTAT
Found at i:1199039 original size:21 final size:21
Alignment explanation
Indices: 1199013--1199069 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
1199003 CATATGAAAT
* *
1199013 TTGTCCCGAAGGATCACTGTA
1 TTGTCCCGAAGGACCACTATA
1199034 TTGTCCCGAAGGACCACTATA
1 TTGTCCCGAAGGACCACTATA
*
1199055 TTATCCCGAAGGACC
1 TTGTCCCGAAGGACC
1199070 TATGAAACCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (21 bp):
TTGTCCCGAAGGACCACTATA
Found at i:1205381 original size:13 final size:13
Alignment explanation
Indices: 1205360--1205404 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
1205350 TTTTAAATAC
*
1205360 ATAAATATTTAAT
1 ATAATTATTTAAT
1205373 ATAATTATTTAAT
1 ATAATTATTTAAT
1205386 ATAA-TATTTAAT
1 ATAATTATTTAAT
*
1205398 ATTATTA
1 ATAATTA
1205405 GTTATAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
ATAATTATTTAAT
Found at i:1205395 original size:12 final size:12
Alignment explanation
Indices: 1205363--1205399 Score: 65
Period size: 12 Copynumber: 3.0 Consensus size: 12
1205353 TAAATACATA
1205363 AATATTTAATAT
1 AATATTTAATAT
1205375 AATTATTTAATAT
1 AA-TATTTAATAT
1205388 AATATTTAATAT
1 AATATTTAATAT
1205400 TATTAGTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 12 0.50
13 12 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
AATATTTAATAT
Done.