Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007886.1 Hibiscus syriacus cultivar Beakdansim tig00110266_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: 1254954
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 7
Found at i:951763 original size:22 final size:22
Alignment explanation
Indices: 951737--951787 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
951727 CTACGGCGAC
**
951737 ATCCGTCCCCATCTCTGACGAA
1 ATCCGTCCCCATCTCCAACGAA
*
951759 ATCCGTCCCCATTTCCAACGAA
1 ATCCGTCCCCATCTCCAACGAA
951781 ATCCGTC
1 ATCCGTC
951788 TATCTCCATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.24, C:0.41, G:0.12, T:0.24
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCAACGAA
Found at i:952085 original size:19 final size:20
Alignment explanation
Indices: 952047--952090 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
952037 AACACCAAAT
952047 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
* *
952067 TCGCAACG-GGAAATTAAAA
1 TCGCAACGCGAAAATGAAAA
952086 TCGCA
1 TCGCA
952091 TTGCGATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.14
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:955541 original size:14 final size:14
Alignment explanation
Indices: 955522--955561 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
955512 TTTTGATTAA
955522 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
** *
955536 TTGATTTGTTTAAT
1 TTGATTTGTAAAAG
955550 TTGATTTGTAAA
1 TTGATTTGTAAA
955562 TAAGAATTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:955554 original size:61 final size:66
Alignment explanation
Indices: 955471--955611 Score: 177
Period size: 66 Copynumber: 2.2 Consensus size: 66
955461 TTTTACATTG
955471 AAAGTTGATTTG-TTACAATTGATGAGGAAATAAG-A-T-TTATTTT-TTGATTAATTGATTTGT
1 AAAGTTGATTTGTTTACAATTGATGAGGAAATAAGAATTATTATTTTCTTGATTAATTGATTTGT
955531 A
66 A
* ** * * *
955532 AAAGTTGATTTGTTTA-ATTTGATTTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTG
1 AAAGTTGATTTGTTTACAATTGATGAGGAAATAAGAATTATTATTTT-CTTGATTAATTGATTTG
955596 TA
65 TA
955598 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
955612 GTTTCTAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
61 26 0.38
62 4 0.06
63 1 0.01
64 6 0.09
66 31 0.46
ACGTcount: A:0.31, C:0.01, G:0.17, T:0.50
Consensus pattern (66 bp):
AAAGTTGATTTGTTTACAATTGATGAGGAAATAAGAATTATTATTTTCTTGATTAATTGATTTGT
A
Found at i:955695 original size:20 final size:20
Alignment explanation
Indices: 955670--955707 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
955660 GTTGAAGGTA
955670 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
955690 CAAATTCGCAACGCGAAA
1 CAAATTCGCAACGCGAAA
955708 TAAGCATTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.26, G:0.18, T:0.13
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:955766 original size:34 final size:34
Alignment explanation
Indices: 955728--955800 Score: 96
Period size: 34 Copynumber: 2.1 Consensus size: 34
955718 GATAATCAAA
955728 TTCGCAACGC-GATTTT-CGGTTTGCGAATTTGACT
1 TTCGCAACGCTGATTTTGC-G-TTGCGAATTTGACT
* *
955762 TTCGCAACGCTTATTTTGCGTTGCGAATTTGGCT
1 TTCGCAACGCTGATTTTGCGTTGCGAATTTGACT
955796 TTCGC
1 TTCGC
955801 GTTGATCGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 28 0.80
35 6 0.17
36 1 0.03
ACGTcount: A:0.15, C:0.22, G:0.23, T:0.40
Consensus pattern (34 bp):
TTCGCAACGCTGATTTTGCGTTGCGAATTTGACT
Found at i:956029 original size:39 final size:39
Alignment explanation
Indices: 955978--956064 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
955968 TCAAGTTGTA
*
955978 GATTTTGATTTCCTTTTGCTTGGCACTATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
* *
956017 TATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
956056 GATTTTGAT
1 GATTTTGAT
956065 GAGCATCGGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.17, C:0.14, G:0.20, T:0.49
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:956393 original size:6 final size:6
Alignment explanation
Indices: 956368--956406 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
956358 CGAAATTTAT
* * *
956368 ATTGAA ATTCAA ACTCAA ATTGAA ATTGAA ATTGAA ATT
1 ATTGAA ATTGAA ATTGAA ATTGAA ATTGAA ATTGAA ATT
956407 CAAACTCCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.49, C:0.08, G:0.10, T:0.33
Consensus pattern (6 bp):
ATTGAA
Found at i:956429 original size:30 final size:30
Alignment explanation
Indices: 956359--956418 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
956349 TAGTGGAGCC
* *
956359 GAAATTTATATTGAAATTCAAACTCAAATT
1 GAAATTGAAATTGAAATTCAAACTCAAATT
*
956389 GAAATTGAAATTGAAATTCAAACTCCAATT
1 GAAATTGAAATTGAAATTCAAACTCAAATT
956419 ACATATGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.33
Consensus pattern (30 bp):
GAAATTGAAATTGAAATTCAAACTCAAATT
Found at i:956940 original size:20 final size:20
Alignment explanation
Indices: 956917--956978 Score: 79
Period size: 20 Copynumber: 3.1 Consensus size: 20
956907 AATAAGCGTT
*
956917 GCGATAGTTAAATTCGCAAC
1 GCGATAGTCAAATTCGCAAC
* * *
956937 GCGAAAGTCAAATTTGCTAC
1 GCGATAGTCAAATTCGCAAC
*
956957 GTGATAGTCAAATTCGCAAC
1 GCGATAGTCAAATTCGCAAC
956977 GC
1 GC
956979 TTATTTCGCG
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (20 bp):
GCGATAGTCAAATTCGCAAC
Found at i:957007 original size:20 final size:20
Alignment explanation
Indices: 956982--957027 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
956972 GCAACGCTTA
956982 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
*
957002 TTTCGCGTTTCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
*
957022 TATCGC
1 TTTCGC
957028 AACGCTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.41
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTGAC
Found at i:957040 original size:34 final size:34
Alignment explanation
Indices: 957002--957090 Score: 108
Period size: 34 Copynumber: 2.6 Consensus size: 34
956992 CGAATTTGAC
*
957002 TTTCGCGTTTCGAATTTGACTATCGCAACGCTTA
1 TTTCGCGTTTCGAATTTGACTACCGCAACGCTTA
* * * *
957036 TTTCGAGTTGT-AAATTTGACTACCGTAATGCTTA
1 TTTCGCGTT-TCGAATTTGACTACCGCAACGCTTA
*
957070 TTTCGCGTTGCGAATTTGACT
1 TTTCGCGTTTCGAATTTGACT
957091 TTCGTGTTGA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
34 44 0.98
35 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (34 bp):
TTTCGCGTTTCGAATTTGACTACCGCAACGCTTA
Found at i:957408 original size:18 final size:18
Alignment explanation
Indices: 957385--957420 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
957375 AAGCCGGTTG
*
957385 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
957403 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
957421 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:959680 original size:24 final size:24
Alignment explanation
Indices: 959646--959699 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
959636 CCATCACATC
*
959646 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
959670 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
959694 ATCAAA
1 ATCAAA
959700 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:959846 original size:12 final size:12
Alignment explanation
Indices: 959825--959858 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
959815 GGCTGTGGGT
*
959825 TTTGAGATTGTG
1 TTTGATATTGTG
959837 TTTGATATTGTG
1 TTTGATATTGTG
*
959849 TTTGGTATTG
1 TTTGATATTG
959859 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:960688 original size:20 final size:22
Alignment explanation
Indices: 960616--960734 Score: 82
Period size: 20 Copynumber: 5.8 Consensus size: 22
960606 GCGAAATTAA
960616 ATTCGCGTTGCGAATTTGAC-T
1 ATTCGCGTTGCGAATTTGACAT
960637 -TTCGCGTTGCGAATTTGGA-AT
1 ATTCGCGTTGCGAATTT-GACAT
**
960658 A-TCGCAATGCG-ATTT-ACAT
1 ATTCGCGTTGCGAATTTGACAT
*
960677 ATTCGCGTTGCGAAATTGGA-A-
1 ATTCGCGTTGCG-AATTTGACAT
* *
960698 ACT-GGGTTGCGAAATTTG--A-
1 ATTCGCGTTGCG-AATTTGACAT
960717 ATTCGCGTTGCGAATTTG
1 ATTCGCGTTGCGAATTTG
960735 TTGGTCATTT
Statistics
Matches: 79, Mismatches: 10, Indels: 20
0.72 0.09 0.18
Matches are distributed among these distances:
18 1 0.01
19 12 0.15
20 48 0.61
21 13 0.16
22 4 0.05
23 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (22 bp):
ATTCGCGTTGCGAATTTGACAT
Found at i:962043 original size:87 final size:86
Alignment explanation
Indices: 961880--962051 Score: 326
Period size: 87 Copynumber: 2.0 Consensus size: 86
961870 TTTCTCGTTC
961880 CGAATACTTTGTAGTCTTGTTGAATATGGTTCGACTCCATTTTCAACCAAATCCTTTGCAAGTTG
1 CGAATACTTTGTAGTCTTGTTGAATATGGTTCGACTCCATTTTCAACCAAATCCTTTGCAAGTTG
961945 TCTATTGGCTTTAAGGTTCGA
66 TCTATTGGCTTTAAGGTTCGA
*
961966 CGAATACTTTGTAGTCTTGTTGAATATGGTTCGACTCCGGTTTTCAACCAAATCCTTTGCAAGTT
1 CGAATACTTTGTAGTCTTGTTGAATATGGTTCGACTCC-ATTTTCAACCAAATCCTTTGCAAGTT
962031 GTCTATTGGCTTTAAGGTTCG
65 GTCTATTGGCTTTAAGGTTCG
962052 TGATTGGTTA
Statistics
Matches: 84, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
86 38 0.45
87 46 0.55
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.40
Consensus pattern (86 bp):
CGAATACTTTGTAGTCTTGTTGAATATGGTTCGACTCCATTTTCAACCAAATCCTTTGCAAGTTG
TCTATTGGCTTTAAGGTTCGA
Found at i:962608 original size:226 final size:225
Alignment explanation
Indices: 962187--962760 Score: 843
Period size: 226 Copynumber: 2.6 Consensus size: 225
962177 AATATTGACA
* * *
962187 ATAACATATCCGGTTATTTACTGAAAACATTATCAAGCATAATAACATATTAGGTAGCGCTTATG
1 ATAACATAACCAGTTAATTACTGAAAACATTATCAAGCATAATAACATATTAGGTAGCGCTTATG
* * **
962252 TAACGTAATAGATAGCGCCTTTTTAAAGCTGATGGG--TAAGAAATTTGACGATAACAAAATAGG
66 TAACGTAATAGGTAGCGCCTTTTTAAAGCTGATGGGCCTTAGAAATCCGACGATAACAAAATAGG
* *
962315 TTAATTACTTAATTTGTTATCAGTATTATCAACGTATTAGGTAAAGCCTAAAATGTTACCGAAGT
131 TTAATTACTTAATTTGTTATCAGTATTATCAACATATTAGGTAAAGCCTAAAATGTTACCAAAGT
* *
962380 TTAAGTTG-TCGGATCCTTAAAAATCCAACG
196 TTAAGCTGAT-GGAGCCTTAAAAATCCAACG
* * * *
962410 ATAATATAACC-GATTAATTACTGGAAACATTATCAAGCATAATAACATATTAGATAACGCTTAT
1 ATAACATAACCAG-TTAATTACTGAAAACATTATCAAGCATAATAACATATTAGGTAGCGCTTAT
*
962474 GTAACGTAATAGGTAGTGCCTTTTTAAAGCTGATGAGGCCTTAGAAATCCGACGATAACAAAATA
65 GTAACGTAATAGGTAGCGCCTTTTTAAAGCTGATG-GGCCTTAGAAATCCGACGATAACAAAATA
* * * *
962539 TGTTAATTACTTAATTTGTTATTAGTATTATCAACATATTATGTAACGCCTAAAATGTTACCAAA
129 GGTTAATTACTTAATTTGTTATCAGTATTATCAACATATTAGGTAAAGCCTAAAATGTTACCAAA
* * *
962604 GTTTAAGCTGATTGAGCCTTAGAAATCCGACG
194 GTTTAAGCTGATGGAGCCTTAAAAATCCAACG
962636 ATAACATAACCAGTTAATTACTGAAAACATTATCAAGCATAATAACATATTAGGTAGCGCTTATG
1 ATAACATAACCAGTTAATTACTGAAAACATTATCAAGCATAATAACATATTAGGTAGCGCTTATG
* * *
962701 TAACATAATAGGTAGCGCC-TTTTAAAGGTGATGGGGCCTTAGAAATCCAACGATAACAAA
66 TAACGTAATAGGTAGCGCCTTTTTAAAGCTGAT-GGGCCTTAGAAATCCGACGATAACAAA
962761 CAAGGCTGGT
Statistics
Matches: 314, Mismatches: 30, Indels: 12
0.88 0.08 0.03
Matches are distributed among these distances:
222 1 0.00
223 89 0.28
224 2 0.01
225 37 0.12
226 183 0.58
227 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (225 bp):
ATAACATAACCAGTTAATTACTGAAAACATTATCAAGCATAATAACATATTAGGTAGCGCTTATG
TAACGTAATAGGTAGCGCCTTTTTAAAGCTGATGGGCCTTAGAAATCCGACGATAACAAAATAGG
TTAATTACTTAATTTGTTATCAGTATTATCAACATATTAGGTAAAGCCTAAAATGTTACCAAAGT
TTAAGCTGATGGAGCCTTAAAAATCCAACG
Found at i:964357 original size:41 final size:41
Alignment explanation
Indices: 964284--964380 Score: 119
Period size: 41 Copynumber: 2.4 Consensus size: 41
964274 AATCATATAC
* *
964284 GCCC-CTCCAAA-CTGGGCCCCCTCCAAACATCAAAGTCATG
1 GCCCTCTCCAAACCTGAG-CCCCTCCAAACATCAAAGTCAGG
* *
964324 GCTCCT-TCTAAACCTGAGCCCCTCCAAATATCAAAGTCAGG
1 GC-CCTCTCCAAACCTGAGCCCCTCCAAACATCAAAGTCAGG
964365 GCCCTCTCCAAACCTG
1 GCCCTCTCCAAACCTG
964381 GGACCTAGGA
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
40 5 0.10
41 39 0.81
42 4 0.08
ACGTcount: A:0.27, C:0.40, G:0.14, T:0.19
Consensus pattern (41 bp):
GCCCTCTCCAAACCTGAGCCCCTCCAAACATCAAAGTCAGG
Found at i:970527 original size:40 final size:40
Alignment explanation
Indices: 970461--970610 Score: 237
Period size: 40 Copynumber: 3.8 Consensus size: 40
970451 ACCGTAGTGC
* **
970461 TACACATAAGGTCGTGCCCACTATATACAATGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* * *
970501 TACACATAAGGTCATGCACACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
970541 TACACATAAGGTCGTGCCCACCATATATACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
970581 TACACATAAGGTCGTGCCCACCATATACAC
1 TACACATAAGGTCGTGCCCACCATATACAC
970611 TTAGTGTCCT
Statistics
Matches: 99, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 99 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:970624 original size:40 final size:40
Alignment explanation
Indices: 970461--970629 Score: 225
Period size: 40 Copynumber: 4.2 Consensus size: 40
970451 ACCGTAGTGC
* *
970461 TACACATAAGGTCGTGCCCACTATATACA-ATGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCT-AAGTGTAT
* * *
970501 TACACATAAGGTCATGCACACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCTAAGTGTAT
* *
970541 TACACATAAGGTCGTGCCCACCATATATACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCTAAGTGTAT
* *
970581 TACACATAAGGTCGTGCCCACCATATACA-CTTAGTGTCCT
1 TACACATAAGGTCGTGCCCACCATATACACCTAAGTGT-AT
970621 TACACATAA
1 TACACATAA
970630 TAGTGTAATA
Statistics
Matches: 114, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
39 6 0.05
40 108 0.95
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCTAAGTGTAT
Found at i:971520 original size:29 final size:30
Alignment explanation
Indices: 971483--971540 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
971473 AACCCATCAA
*
971483 TTTTCC-AAAATTACTAAATTGATCCCCAAC
1 TTTTCCAAAAATTAC-AAAATGATCCCCAAC
*
971513 TTTT-CAAAAATTACAAAATGGTCCCCAA
1 TTTTCCAAAAATTACAAAATGATCCCCAA
971541 AATTTTCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.40, C:0.24, G:0.05, T:0.31
Consensus pattern (30 bp):
TTTTCCAAAAATTACAAAATGATCCCCAAC
Found at i:971547 original size:30 final size:30
Alignment explanation
Indices: 971481--971547 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
971471 ACAACCCATC
* *
971481 AATTTTCCAAAATTACTAAATTGATCCCCA
1 AATTTTCAAAAATTACTAAAATGATCCCCA
* *
971511 ACTTTTCAAAAATTAC-AAAATGGTCCCCAA
1 AATTTTCAAAAATTACTAAAATGATCCCC-A
971541 AATTTTC
1 AATTTTC
971548 TAAGGCTTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 10 0.32
30 21 0.68
ACGTcount: A:0.40, C:0.22, G:0.04, T:0.33
Consensus pattern (30 bp):
AATTTTCAAAAATTACTAAAATGATCCCCA
Found at i:979581 original size:6 final size:6
Alignment explanation
Indices: 979572--979618 Score: 60
Period size: 6 Copynumber: 7.7 Consensus size: 6
979562 GAAGATGAAA
*
979572 GAAAGT GAAAGT GAAAGT GAAAGT GAAAAG- GTAAAGT AAAAGT GAAA
1 GAAAGT GAAAGT GAAAGT GAAAGT G-AAAGT G-AAAGT GAAAGT GAAA
979619 AGAAGATAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
6 32 0.89
7 4 0.11
ACGTcount: A:0.55, C:0.00, G:0.30, T:0.15
Consensus pattern (6 bp):
GAAAGT
Found at i:979607 original size:19 final size:20
Alignment explanation
Indices: 979572--979620 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
979562 GAAGATGAAA
979572 GAAAGTG-AAA-GTGAAAGT
1 GAAAGTGAAAAGGTGAAAGT
979590 GAAAGTGAAAAGGT-AAAGT
1 GAAAGTGAAAAGGTGAAAGT
*
979609 AAAAGTGAAAAG
1 GAAAGTGAAAAG
979621 AAGATAAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 7 0.25
19 19 0.68
20 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.31, T:0.14
Consensus pattern (20 bp):
GAAAGTGAAAAGGTGAAAGT
Found at i:999897 original size:18 final size:19
Alignment explanation
Indices: 999854--999897 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
999844 TTTGGTTCAC
* *
999854 GGAATGTAAGATTACCAGTG
1 GGAATATAAGATTACCAG-A
999874 GGAATATAAGATTACCA-A
1 GGAATATAAGATTACCAGA
999892 GGAATA
1 GGAATA
999898 AGATTACTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.27
20 16 0.73
ACGTcount: A:0.43, C:0.09, G:0.25, T:0.23
Consensus pattern (19 bp):
GGAATATAAGATTACCAGA
Found at i:1001667 original size:18 final size:18
Alignment explanation
Indices: 1001644--1001679 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1001634 AGGTTTGATT
*
1001644 TCACATGAATTGATAGTC
1 TCACATGAATTCATAGTC
1001662 TCACATGAATTCATAGTC
1 TCACATGAATTCATAGTC
1001680 GAAACTGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (18 bp):
TCACATGAATTCATAGTC
Found at i:1002497 original size:22 final size:23
Alignment explanation
Indices: 1002466--1002512 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
1002456 TAATCGCGAG
1002466 TTTAGAAGATACGA-TTCTGGGC
1 TTTAGAAGATACGATTTCTGGGC
* *
1002488 TTTAGCAGATACGATTTTTGGGC
1 TTTAGAAGATACGATTTCTGGGC
1002511 TT
1 TT
1002513 ATTTAGGGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.38
Consensus pattern (23 bp):
TTTAGAAGATACGATTTCTGGGC
Found at i:1010995 original size:467 final size:468
Alignment explanation
Indices: 1010122--1011055 Score: 1802
Period size: 467 Copynumber: 2.0 Consensus size: 468
1010112 AATAGTCAAC
1010122 AATAGGTATGGAGCAAAAAGGGAGATTAATTAATTAAATTCTAATGTCTAAAGATGTTTTAAAAG
1 AATAGGTATGGAGCAAAAAGGGAGATTAATTAATTAAATTCTAATGTCTAAAGATGTTTTAAAAG
1010187 GATTAACACAAATTCTAAAAAATATAATTTTTTGGTTATACTGATAAGCAAGATCAAGACGATCA
66 GATTAACACAAATTCTAAAAAATATAATTTTTTGGTTATACTGATAAGCAAGATCAAGACGATCA
1010252 AGCTAGTTATATTTTATCAAAAAATAAAATTATGTGATATAAGATATTTAGTAGAATTTTCTAAA
131 AGCTAGTTATATTTTATCAAAAAATAAAATTATGTGATATAAGATATTTAGTAGAATTTTCTAAA
1010317 AAAAATTCTTCATGAATATCAAAAAAAAATGAAAAAAATAGAATTTTGGAAAAACTAATATTTCC
196 AAAAATTCTTCATGAATATCAAAAAAAAATGAAAAAAATAGAATTTTGGAAAAACTAATATTTCC
*
1010382 ATAAATTATCACCACCATGGGATGAGCTTTTTATAAACAAATATGAATCTTATCTTAAAAAACAT
261 ATAAATTATCACCACCATGGGATGACCTTTTTATAAACAAATATGAATCTTATCTTAAAAAACAT
*
1010447 AGTATATTATCTGGTGTGGAGATTAGTGGAATAGATTCTATAGAAAATAGAATTAATTTTGCTAG
326 AGTAGATTATCTGGTGTGGAGATTAGTGGAATAGATTCTATAGAAAATAGAATTAATTTTGCTAG
1010512 AGAAAGAATAACTAAAAATAGTATACAGGCTAAAGCCATTAAACAAGTG-AAAAATAAATTAAGT
391 AGAAAGAATAACTAAAAATAGTATACAGGCTAAAGCCATTAAACAAGTGAAAAAATAAATTAAGT
1010576 CTGATATAGAAAT
456 CTGATATAGAAAT
1010589 AATAGGTATGGAGCAAAAAGGGAGATTAATTAATTAAATTCTAATGTCTAAAGATGTTTTAAAAG
1 AATAGGTATGGAGCAAAAAGGGAGATTAATTAATTAAATTCTAATGTCTAAAGATGTTTTAAAAG
1010654 GATTAACACAAATTCTAAAAAATATAAATTTTTTGGTTATACTGATAAGCAAGATC-AGACGATC
66 GATTAACACAAATTCTAAAAAATAT-AATTTTTTGGTTATACTGATAAGCAAGATCAAGACGATC
1010718 AAGCTAGTTATATTTTATC-AAAAATAAAATTATGTGATATAAGATATTTAGTAGAATTTTCTAA
130 AAGCTAGTTATATTTTATCAAAAAATAAAATTATGTGATATAAGATATTTAGTAGAATTTTCTAA
1010782 AAAAAATTCTTCATGAATATCAAAAAAAAATGAAAAAAAATAGAATTTTGGAAAAACTAATATTT
195 AAAAAATTCTTCATGAATATCAAAAAAAAATG-AAAAAAATAGAATTTTGGAAAAACTAATATTT
*
1010847 CTATAAATTATCACCACCATGGGATGACCTTTTTATAAACAAATATGAATCTTATCTTAAAAAAC
259 CCATAAATTATCACCACCATGGGATGACCTTTTTATAAACAAATATGAATCTTATCTTAAAAAAC
1010912 ATAGTAGATTATCTGGTGTGGAGATTAGTGGAATAGATTCTATAGAAAATAGAATTAATTTTGCT
324 ATAGTAGATTATCTGGTGTGGAGATTAGTGGAATAGATTCTATAGAAAATAGAATTAATTTTGCT
1010977 AGAGAAAGAATAACTAAAAATAGTATACAGGCTAAAGCCATTAAACAAGTGAAAAAATAAATTAA
389 AGAGAAAGAATAACTAAAAATAGTATACAGGCTAAAGCCATTAAACAAGTGAAAAAATAAATTAA
1011042 GTCTGATATAGAAA
454 GTCTGATATAGAAA
1011056 ATATTAAATC
Statistics
Matches: 461, Mismatches: 3, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
466 77 0.17
467 327 0.71
468 57 0.12
ACGTcount: A:0.46, C:0.09, G:0.14, T:0.31
Consensus pattern (468 bp):
AATAGGTATGGAGCAAAAAGGGAGATTAATTAATTAAATTCTAATGTCTAAAGATGTTTTAAAAG
GATTAACACAAATTCTAAAAAATATAATTTTTTGGTTATACTGATAAGCAAGATCAAGACGATCA
AGCTAGTTATATTTTATCAAAAAATAAAATTATGTGATATAAGATATTTAGTAGAATTTTCTAAA
AAAAATTCTTCATGAATATCAAAAAAAAATGAAAAAAATAGAATTTTGGAAAAACTAATATTTCC
ATAAATTATCACCACCATGGGATGACCTTTTTATAAACAAATATGAATCTTATCTTAAAAAACAT
AGTAGATTATCTGGTGTGGAGATTAGTGGAATAGATTCTATAGAAAATAGAATTAATTTTGCTAG
AGAAAGAATAACTAAAAATAGTATACAGGCTAAAGCCATTAAACAAGTGAAAAAATAAATTAAGT
CTGATATAGAAAT
Found at i:1013718 original size:42 final size:42
Alignment explanation
Indices: 1013661--1013772 Score: 170
Period size: 42 Copynumber: 2.7 Consensus size: 42
1013651 GGTTCTACGT
*
1013661 GGTCCTTCGGGACATATATGTGATCCTTTGGAACATATATGC
1 GGTCCTTCGGGACATATATGTGGTCCTTTGGAACATATATGC
* * * * *
1013703 GGTCTTTCGAGACATATATTTGGTCATTTGGAACATATATGT
1 GGTCCTTCGGGACATATATGTGGTCCTTTGGAACATATATGC
1013745 GGTCCTTCGGGACATATATGTGGTCCTT
1 GGTCCTTCGGGACATATATGTGGTCCTT
1013773 CGGGACAATT
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 60 1.00
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (42 bp):
GGTCCTTCGGGACATATATGTGGTCCTTTGGAACATATATGC
Found at i:1013773 original size:21 final size:21
Alignment explanation
Indices: 1013659--1013779 Score: 152
Period size: 21 Copynumber: 5.8 Consensus size: 21
1013649 AGGGTTCTAC
1013659 GTGGTCCTTCGGGACATATAT
1 GTGGTCCTTCGGGACATATAT
* * *
1013680 GTGATCCTTTGGAACATATAT
1 GTGGTCCTTCGGGACATATAT
* * *
1013701 GCGGTCTTTCGAGACATATAT
1 GTGGTCCTTCGGGACATATAT
* * * *
1013722 TTGGTCATTTGGAACATATAT
1 GTGGTCCTTCGGGACATATAT
1013743 GTGGTCCTTCGGGACATATAT
1 GTGGTCCTTCGGGACATATAT
1013764 GTGGTCCTTCGGGACA
1 GTGGTCCTTCGGGACA
1013780 ATTCTACGAG
Statistics
Matches: 81, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 81 1.00
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (21 bp):
GTGGTCCTTCGGGACATATAT
Found at i:1014668 original size:14 final size:15
Alignment explanation
Indices: 1014648--1014681 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1014638 TCAAATATTA
1014648 ATATTTTAAAATAAT
1 ATATTTTAAAATAAT
*
1014663 -TATTTTATAATAAT
1 ATATTTTAAAATAAT
1014677 ATATT
1 ATATT
1014682 ATATTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATTTTAAAATAAT
Found at i:1014718 original size:24 final size:27
Alignment explanation
Indices: 1014691--1014741 Score: 72
Period size: 24 Copynumber: 2.0 Consensus size: 27
1014681 TATATTATTT
1014691 TTATATTTAAAT-GTT-AATAA-ATAA
1 TTATATTTAAATAGTTAAATAATATAA
*
1014715 TTATATTTTAATAGTTAAATAATATAA
1 TTATATTTAAATAGTTAAATAATATAA
1014742 AAATAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 11 0.48
25 3 0.13
26 5 0.22
27 4 0.17
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (27 bp):
TTATATTTAAATAGTTAAATAATATAA
Found at i:1016107 original size:18 final size:18
Alignment explanation
Indices: 1016086--1016133 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
1016076 AGAAGATCGA
*
1016086 AAGAATGCATCATCAATG
1 AAGAATACATCATCAATG
*
1016104 AAGAATATATCATCAATG
1 AAGAATACATCATCAATG
*
1016122 AAGAATATATCA
1 AAGAATACATCA
1016134 ATAATGGAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.25
Consensus pattern (18 bp):
AAGAATACATCATCAATG
Found at i:1016139 original size:18 final size:18
Alignment explanation
Indices: 1016094--1016133 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
1016084 GAAAGAATGC
1016094 ATCATCAATGAAGAATAT
1 ATCATCAATGAAGAATAT
1016112 ATCATCAATGAAGAATAT
1 ATCATCAATGAAGAATAT
1016130 ATCA
1 ATCA
1016134 ATAATGGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (18 bp):
ATCATCAATGAAGAATAT
Found at i:1020267 original size:159 final size:159
Alignment explanation
Indices: 1019978--1020282 Score: 585
Period size: 159 Copynumber: 1.9 Consensus size: 159
1019968 AACCTCAGAC
1019978 ATACGGACAGCCAAAATGTGTCATCCAGACCTTAAAGGATATGCTTAGGTGCACCATTATAGACC
1 ATACGGACAGCCAAAATGTGTCATCCAGACCTTAAAGGATATGCTTAGGTGCACCATTATAGACC
*
1020043 TCGAGGGTAGTTGTGAGGACCACCTGTCATTGTTGGAGTTTACGTAAAATAGAATTTTTCAGTCG
66 TCGAGGGTAGTTGTGAGGACCACCTGCCATTGTTGGAGTTTACGTAAAATAGAATTTTTCAGTCG
1020108 AGCATTTAGATGGCTCCGTAAGAGGCCTT
131 AGCATTTAGATGGCTCCGTAAGAGGCCTT
1020137 ATACGGACAGCCAAAATGTGTCATCCAGACCTTAAAGGATATGCTTAGGTGCACCATTATAGACC
1 ATACGGACAGCCAAAATGTGTCATCCAGACCTTAAAGGATATGCTTAGGTGCACCATTATAGACC
1020202 TCGAGGGTAGTTGTGAGGACCACCTGCCATTGTTGGAGTTTACGTAAAATAGCAA-TTTTCAGTC
66 TCGAGGGTAGTTGTGAGGACCACCTGCCATTGTTGGAGTTTACGTAAAATAG-AATTTTTCAGTC
1020266 GAGCATTTAGATGGCTC
130 GAGCATTTAGATGGCTC
1020283 TACTTTATTA
Statistics
Matches: 144, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
159 142 0.99
160 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (159 bp):
ATACGGACAGCCAAAATGTGTCATCCAGACCTTAAAGGATATGCTTAGGTGCACCATTATAGACC
TCGAGGGTAGTTGTGAGGACCACCTGCCATTGTTGGAGTTTACGTAAAATAGAATTTTTCAGTCG
AGCATTTAGATGGCTCCGTAAGAGGCCTT
Found at i:1021489 original size:20 final size:21
Alignment explanation
Indices: 1021464--1021517 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1021454 CAATTTTCCC
*
1021464 AATCGCAATGCGAA-TAAGTA
1 AATCGCAATGCGAATTAAGAA
* **
1021484 AATCGCAACGCGAATTGGGAA
1 AATCGCAATGCGAATTAAGAA
1021505 AATCGCAATGCGA
1 AATCGCAATGCGA
1021518 TACTGACTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.41, C:0.19, G:0.24, T:0.17
Consensus pattern (21 bp):
AATCGCAATGCGAATTAAGAA
Found at i:1021531 original size:20 final size:20
Alignment explanation
Indices: 1021506--1021600 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
1021496 AATTGGGAAA
*
1021506 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
1021526 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
1021547 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
1021567 TTCGCAGCGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1021587 TTCGCAACGCGATA
1 ATCGCAACGCGATA
1021601 ATACATAATC
Statistics
Matches: 59, Mismatches: 15, Indels: 2
0.78 0.20 0.03
Matches are distributed among these distances:
20 45 0.76
21 14 0.24
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1021579 original size:41 final size:41
Alignment explanation
Indices: 1021503--1021580 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
1021493 GCGAATTGGG
* * *
1021503 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
* * *
1021544 AAAATCGCAACGAGATACTTACTTTCGCAGCGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA
1021581 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
Found at i:1021808 original size:22 final size:22
Alignment explanation
Indices: 1021780--1021823 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1021770 CACTCTCTCA
1021780 CCCATCTCCAACGAAATCCGTC
1 CCCATCTCCAACGAAATCCGTC
**
1021802 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCAACGAAATCCGTC
1021824 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCAACGAAATCCGTC
Found at i:1022106 original size:20 final size:20
Alignment explanation
Indices: 1022057--1022109 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
1022047 AAATCGCAAC
1022057 GCGATTTT-ATTTTCACGTT
1 GCGATTTTCATTTTCACGTT
** **
1022076 GCGATAGTCATTTTCGTGTT
1 GCGATTTTCATTTTCACGTT
1022096 GCGATTTTCATTTT
1 GCGATTTTCATTTT
1022110 TAGAAACTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 6 0.22
20 21 0.78
ACGTcount: A:0.15, C:0.15, G:0.19, T:0.51
Consensus pattern (20 bp):
GCGATTTTCATTTTCACGTT
Found at i:1023451 original size:18 final size:18
Alignment explanation
Indices: 1023430--1023474 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1023420 TCCACTTCGG
*
1023430 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1023448 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1023466 GAGCCATCA
1 GAGCCATCA
1023475 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1024010 original size:19 final size:20
Alignment explanation
Indices: 1023967--1024022 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
1023957 CGCAACACAA
*
1023967 AAATGACTATCGTAACGCGG
1 AAATGACTATCGCAACGCGG
* *
1023987 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
**
1024006 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
1024023 ACAAAATCGC
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:1024030 original size:14 final size:14
Alignment explanation
Indices: 1024011--1024068 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1024001 ATGCGAAATG
1024011 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1024025 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
1024041 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1024057 AAAATCGCAACG
1 AAAATCGCAACG
1024069 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1024053 original size:32 final size:33
Alignment explanation
Indices: 1023995--1024085 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
1023985 GGAAATGGCT
1023995 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1024028 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1024060 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
1024086 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1024160 original size:19 final size:19
Alignment explanation
Indices: 1024134--1024200 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
1024124 GCGATTTTGT
**
1024134 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
1024153 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
*
1024173 CGTTGCGATAGTCATTTAG
1 CGTTGCGATAGTCATTTCG
1024192 CGTTGCGAT
1 CGTTGCGAT
1024201 TTTAAGTTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 23 0.57
20 17 0.43
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.37
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:1024180 original size:20 final size:19
Alignment explanation
Indices: 1024146--1024200 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
1024136 TTGCGATTTT
*
1024146 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1024165 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
1024185 CATTTAGCGTTGCGAT
1 CATTTCGCGTTGCGAT
1024201 TTTAAGTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1026064 original size:14 final size:14
Alignment explanation
Indices: 1026045--1026080 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1026035 ATTGTTTAAT
1026045 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1026059 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1026073 TGATTTGT
1 TGATTTGT
1026081 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1026218 original size:19 final size:19
Alignment explanation
Indices: 1026196--1026282 Score: 139
Period size: 19 Copynumber: 4.8 Consensus size: 19
1026186 ATCGCAACGA
1026196 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1026215 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1026234 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1026253 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
1026267 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
1026283 TTTTCATTTC
Statistics
Matches: 65, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
14 11 0.17
15 1 0.02
16 2 0.03
17 2 0.03
19 49 0.75
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:1026247 original size:38 final size:33
Alignment explanation
Indices: 1026167--1026282 Score: 151
Period size: 33 Copynumber: 3.4 Consensus size: 33
1026157 AAAACAGACT
* ***
1026167 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1026200 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAA
1026238 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1026271 ATCGCAATGCGA
1 ATCGCAATGCGA
1026283 TTTTCATTTC
Statistics
Matches: 74, Mismatches: 4, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
33 38 0.51
34 1 0.01
35 2 0.03
36 2 0.03
37 1 0.01
38 30 0.41
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:1026358 original size:20 final size:20
Alignment explanation
Indices: 1026301--1026358 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
1026291 TCGCATTGCG
* * *
1026301 ATTTTCTCGTTGTGATAACC
1 ATTTTCGCGTTGCGATAGCC
1026321 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
1026341 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
1026359 TCAAATGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.40
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:1027446 original size:24 final size:24
Alignment explanation
Indices: 1027419--1027472 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1027409 GTATTCGAAA
* *
1027419 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
1027443 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
1027467 TTTGAT
1 TTTGAT
1027473 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:1027664 original size:12 final size:12
Alignment explanation
Indices: 1027647--1027671 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1027637 ATATAATCCT
1027647 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1027659 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1027671 G
1 G
1027672 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1028452 original size:31 final size:31
Alignment explanation
Indices: 1028414--1028569 Score: 242
Period size: 31 Copynumber: 5.0 Consensus size: 31
1028404 CCCGAAGGAC
* * *
1028414 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
1028445 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
1028476 CAGTCCGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1028507 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1028538 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1028569 C
1 C
1028570 CCTCGACCCT
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 114 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1028830 original size:24 final size:22
Alignment explanation
Indices: 1028785--1028830 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1028775 ATATACTTGT
*
1028785 TTTCACATATATATTCATATCA
1 TTTCACATATACATTCATATCA
1028807 TTTCACATATACACTTTCATATCA
1 TTTCACATATACA--TTCATATCA
1028831 CATGCCATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 12 0.57
24 9 0.43
ACGTcount: A:0.35, C:0.22, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTCACATATACATTCATATCA
Found at i:1029491 original size:21 final size:21
Alignment explanation
Indices: 1029461--1029505 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1029451 ATTCTGTCGT
* *
1029461 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1029482 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1029503 TTG
1 TTG
1029506 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1032512 original size:31 final size:31
Alignment explanation
Indices: 1032474--1032629 Score: 242
Period size: 31 Copynumber: 5.0 Consensus size: 31
1032464 CCCGAAGGAC
* * *
1032474 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
1032505 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
1032536 CAGTCCGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1032567 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1032598 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1032629 C
1 C
1032630 CCTCGACCCT
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 114 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1032845 original size:23 final size:24
Alignment explanation
Indices: 1032819--1032865 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
1032809 ATATACTTGT
*
1032819 TTTCACATATATA-TTTCATATCA
1 TTTCACATATACACTTTCATATCA
1032842 TTTCACATATACACTTTCATATCA
1 TTTCACATATACACTTTCATATCA
1032866 CATGCCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTCACATATACACTTTCATATCA
Found at i:1033525 original size:21 final size:21
Alignment explanation
Indices: 1033495--1033539 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1033485 ATTCTGTCGT
* *
1033495 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1033516 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1033537 TTG
1 TTG
1033540 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1036544 original size:33 final size:33
Alignment explanation
Indices: 1036502--1036628 Score: 184
Period size: 33 Copynumber: 3.8 Consensus size: 33
1036492 GGAAATTACT
*
1036502 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
**
1036535 ATCGCAATGCGAAATGAAAATCACAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
* *
1036567 TTTCGCAATGCGAAATGAAAATCACAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCACAACGAGAGA
*
1036601 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCACAACG
1036629 CGAATTTAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
32 1 0.01
33 81 0.98
34 1 0.01
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCACAACGAGAGA
Found at i:1036609 original size:66 final size:66
Alignment explanation
Indices: 1036503--1036635 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
1036493 GAAATTACTA
* *
1036503 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCACAACGCTAAT
1 TCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCACAACGCGAAT
1036568 T
66 T
* *
1036569 TCGCAATGCGAAATGAAAATCACAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCACAACGCGAAT
1036634 T
66 T
1036635 T
1 T
1036636 AATTTCGCGT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCACAACGCGAAT
T
Found at i:1036650 original size:19 final size:19
Alignment explanation
Indices: 1036628--1036669 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1036618 AAATCGCAAC
*
1036628 GCGAATTTAATTTCGCGTT
1 GCGAATTTAATTTCGCATT
* *
1036647 GCGATTTTCATTTCGCATT
1 GCGAATTTAATTTCGCATT
1036666 GCGA
1 GCGA
1036670 TAGTACTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (19 bp):
GCGAATTTAATTTCGCATT
Found at i:1036796 original size:14 final size:14
Alignment explanation
Indices: 1036777--1036813 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1036767 CATCAATTAA
1036777 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1036791 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1036805 ACAAATCAA
1 ACAAATCAA
1036814 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:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1038254 original size:42 final size:42
Alignment explanation
Indices: 1038208--1038291 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
1038198 CGATGACAGT
* * * *
1038208 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCAAGGAATGATAGG
* * *
1038250 GGCCTCTTCAACGATAGGAGTGGACTCTTAAGGGATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCAAGGAATGATAGG
1038292 CGAGTCGGGC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.24, C:0.17, G:0.38, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCAAGGAATGATAGG
Found at i:1040362 original size:34 final size:33
Alignment explanation
Indices: 1040319--1040423 Score: 111
Period size: 39 Copynumber: 3.0 Consensus size: 33
1040309 ACGAGATAAT
**
1040319 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGAAAATCGCAACGA
1040353 GAGAATCGCAACGCGAAATGAAAATCGCAACCGCGAAA
1 GAGAATCGCAACGCGAAATGAAAATCGCAA---CG--A
* *
1040391 TAAAAATCGCAACGCGAAATGAAAATCGCAACG
1 -GAGAATCGCAACGCGAAATGAAAATCGCAACG
1040424 CGAAATGAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
33 14 0.23
34 14 0.23
36 4 0.07
38 1 0.02
39 28 0.46
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.10
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGAAAATCGCAACGA
Found at i:1040380 original size:19 final size:19
Alignment explanation
Indices: 1040294--1040445 Score: 161
Period size: 19 Copynumber: 8.1 Consensus size: 19
1040284 TCTTTTGGTT
* *
1040294 GAAATGAAAATCGTAACGA
1 GAAATGAAAATCGCAACGC
*
1040313 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
1040333 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
1040351 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1040367 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
1040387 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1040406 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
* *
1040425 GAAATGAAAATTGCAATGC
1 GAAATGAAAATCGCAACGC
1040444 GA
1 GA
1040446 TTTTGGTTTC
Statistics
Matches: 113, Mismatches: 12, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
14 9 0.08
15 1 0.01
16 2 0.02
17 1 0.01
18 2 0.02
19 52 0.46
20 44 0.39
21 2 0.02
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1040410 original size:39 final size:38
Alignment explanation
Indices: 1040356--1040445 Score: 144
Period size: 39 Copynumber: 2.3 Consensus size: 38
1040346 GCAACGAGAG
1040356 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAA-CGCGAAATAAA
*
1040395 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
* *
1040433 AATTGCAATGCGA
1 AATCGCAACGCGA
1040446 TTTTGGTTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
38 21 0.44
39 27 0.56
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.12
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
Found at i:1040463 original size:19 final size:18
Alignment explanation
Indices: 1040441--1040507 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 18
1040431 AAAATTGCAA
*
1040441 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-ATTTCGCGT
1040460 TGCGATTTTTATTTCGCGT
1 TGCGA-TTTTATTTCGCGT
*
1040479 TGCGATAGTTATTTCCGCGT
1 TGCGAT-TTTATTT-CGCGT
1040499 TGCGATTTT
1 TGCGATTTT
1040508 CATTCTCGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
18 1 0.02
19 26 0.62
20 15 0.36
ACGTcount: A:0.10, C:0.16, G:0.25, T:0.48
Consensus pattern (18 bp):
TGCGATTTTATTTCGCGT
Found at i:1041110 original size:20 final size:20
Alignment explanation
Indices: 1041025--1041138 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
1041015 CGCTATGTAA
* * *
1041025 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
1041045 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
1041065 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
1041086 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1041106 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1041126 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1041139 TTTCCCAATT
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
19 3 0.04
20 65 0.79
21 12 0.15
22 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1041123 original size:61 final size:61
Alignment explanation
Indices: 1041025--1041141 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 61
1041015 CGCTATGTAA
* * * *
1041025 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
1041086 ATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
1041142 CCCAATTCGC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:1041157 original size:61 final size:61
Alignment explanation
Indices: 1041025--1041159 Score: 164
Period size: 61 Copynumber: 2.2 Consensus size: 61
1041015 CGCTATGTAA
* * * * ** *
1041025 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
1041086 ATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
1041148 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
1041160 TTACTTATTC
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
61 60 0.97
62 2 0.03
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:1041249 original size:21 final size:21
Alignment explanation
Indices: 1041209--1041249 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1041199 ATTGTATACC
**
1041209 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
1041230 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
1041250 GCGAATTTGC
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:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:1042902 original size:23 final size:23
Alignment explanation
Indices: 1042876--1042925 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
1042866 GTCATGTTAT
1042876 TTGTGGTTAATTGCCAAGTGCAA
1 TTGTGGTTAATTGCCAAGTGCAA
*
1042899 TTGTGGTTAATTGCTAAGTGCAA
1 TTGTGGTTAATTGCCAAGTGCAA
1042922 TTGT
1 TTGT
1042926 TATTCAGGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.24, C:0.10, G:0.26, T:0.40
Consensus pattern (23 bp):
TTGTGGTTAATTGCCAAGTGCAA
Found at i:1045564 original size:22 final size:22
Alignment explanation
Indices: 1045536--1045579 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1045526 ATATATATCC
* *
1045536 TATAAAATAGTTGTTCGAATTT
1 TATAAAATAGTTATTCAAATTT
1045558 TATAAAATAGTTATTCAAATTT
1 TATAAAATAGTTATTCAAATTT
1045580 CAAACTCAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (22 bp):
TATAAAATAGTTATTCAAATTT
Found at i:1046220 original size:6 final size:7
Alignment explanation
Indices: 1046204--1046240 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
1046194 CTAGGCAAGA
1046204 AAAAATG
1 AAAAATG
1046211 AAAAAT-
1 AAAAATG
1046217 AAAAATG
1 AAAAATG
1046224 AAAAAT-
1 AAAAATG
1046230 -AAAATG
1 AAAAATG
1046236 AAAAA
1 AAAAA
1046241 AACATCATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
5 5 0.19
6 6 0.22
7 16 0.59
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:1046227 original size:12 final size:11
Alignment explanation
Indices: 1046203--1046242 Score: 53
Period size: 12 Copynumber: 3.4 Consensus size: 11
1046193 GCTAGGCAAG
1046203 AAAAAATGAAAA
1 AAAAAATG-AAA
1046215 ATAAAAATGAAA
1 A-AAAAATGAAA
1046227 AATAAAATGAAA
1 AA-AAAATGAAA
1046239 AAAA
1 AAAA
1046243 CATCATTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 3 0.12
12 16 0.62
13 7 0.27
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.12
Consensus pattern (11 bp):
AAAAAATGAAA
Found at i:1046241 original size:13 final size:13
Alignment explanation
Indices: 1046204--1046240 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1046194 CTAGGCAAGA
1046204 AAAAATGAAAAAT
1 AAAAATGAAAAAT
1046217 AAAAATGAAAAAT
1 AAAAATGAAAAAT
1046230 -AAAATGAAAAA
1 AAAAATGAAAAA
1046241 AACATCATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (13 bp):
AAAAATGAAAAAT
Found at i:1055705 original size:21 final size:21
Alignment explanation
Indices: 1055676--1055719 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
1055666 TAATGACCTT
1055676 ACAACTGACACATTAAAAATC
1 ACAACTGACACATTAAAAATC
*
1055697 ACAATTGACACATTAAAAATC
1 ACAACTGACACATTAAAAATC
1055718 AC
1 AC
1055720 TACGAATATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.52, C:0.23, G:0.05, T:0.20
Consensus pattern (21 bp):
ACAACTGACACATTAAAAATC
Found at i:1060903 original size:20 final size:20
Alignment explanation
Indices: 1060878--1060991 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
1060868 AATTGGGAAA
*
1060878 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1060898 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * * *
1060918 ATCACAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
1060939 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1060959 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
1060979 TTCGCAACGCGAT
1 ATCGCAACGCGAT
1060992 TTACATAGCG
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 63 0.80
21 12 0.15
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1060991 original size:61 final size:61
Alignment explanation
Indices: 1060875--1060991 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
1060865 GCAAATTGGG
* * * * *
1060875 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCACAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCACAACGCGATAATAC
* * * *
1060936 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCACAACGCGAT
1060992 TTACATAGCG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCACAACGCGATAATAC
Found at i:1061570 original size:19 final size:19
Alignment explanation
Indices: 1061510--1061590 Score: 55
Period size: 19 Copynumber: 4.5 Consensus size: 19
1061500 TTCGAGAATG
1061510 AAAATCGCAACGCGAAAATA
1 AAAATCGCAACGCG-AAATA
** *
1061530 ACTATCGCAA--CGAGAT-
1 AAAATCGCAACGCGAAATA
1061546 --AATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
** **
1061563 AAAATCGCATTGCGAAACC
1 AAAATCGCAACGCGAAATA
1061582 AAAATCGCA
1 AAAATCGCA
1061591 TTGCGATTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 11
0.70 0.13 0.16
Matches are distributed among these distances:
14 7 0.15
16 5 0.11
17 3 0.06
18 2 0.04
19 22 0.47
20 8 0.17
ACGTcount: A:0.47, C:0.23, G:0.16, T:0.14
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:1061608 original size:19 final size:19
Alignment explanation
Indices: 1061586--1061736 Score: 168
Period size: 19 Copynumber: 8.1 Consensus size: 19
1061576 GAAACCAAAA
*
1061586 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1061605 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1061624 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1061643 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
1061659 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
**
1061676 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
1061695 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
1061715 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1061735 TC
1 TC
1061737 AACCAAAAGA
Statistics
Matches: 116, Mismatches: 9, Indels: 14
0.83 0.06 0.10
Matches are distributed among these distances:
14 10 0.09
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 69 0.59
20 32 0.28
21 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1061614 original size:38 final size:38
Alignment explanation
Indices: 1061567--1061654 Score: 97
Period size: 38 Copynumber: 2.3 Consensus size: 38
1061557 GAAATAAAAA
*
1061567 TCGCATTGCGA-AACCAAAATCGCATTGCGATTTTCATT
1 TCGCGTTGCGATAACC-AAATCGCATTGCGATTTTCATT
*** ** *
1061605 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATAACCAAATCGCATTGCGATTTTCATT
1061643 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1061655 TGTCTGGTCG
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
38 41 0.98
39 1 0.02
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (38 bp):
TCGCGTTGCGATAACCAAATCGCATTGCGATTTTCATT
Found at i:1063798 original size:42 final size:42
Alignment explanation
Indices: 1063738--1063860 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
1063728 GCCCGACTCG
* * *
1063738 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
1063780 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
1063822 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
1063861 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:1063818 original size:21 final size:21
Alignment explanation
Indices: 1063794--1063860 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1063784 TCATTCCTCG
1063794 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1063815 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1063836 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1063857 AGAG
1 AGAG
1063861 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1065236 original size:14 final size:14
Alignment explanation
Indices: 1065217--1065252 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1065207 ATTGTTTAAT
1065217 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1065231 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1065245 TGATTTGT
1 TGATTTGT
1065253 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1065374 original size:19 final size:19
Alignment explanation
Indices: 1065350--1065442 Score: 80
Period size: 19 Copynumber: 5.4 Consensus size: 19
1065340 GTTGAAGGCA
1065350 ATTGCGATTTTCATTTCGC
1 ATTGCGATTTTCATTTCGC
* *
1065369 ATTGCGA-----AATTAGC
1 ATTGCGATTTTCATTTCGC
*
1065383 GTTGCGATTTTCATTTCGC
1 ATTGCGATTTTCATTTCGC
*
1065402 ATTGCGA--TTC-TCTCG-
1 ATTGCGATTTTCATTTCGC
1065417 -TTGCGATTTTCATTTCGC
1 ATTGCGATTTTCATTTCGC
1065435 ATTGCGAT
1 ATTGCGAT
1065443 AGTAATTTCC
Statistics
Matches: 56, Mismatches: 8, Indels: 20
0.67 0.10 0.24
Matches are distributed among these distances:
14 17 0.30
16 7 0.12
17 7 0.12
19 25 0.45
ACGTcount: A:0.17, C:0.20, G:0.19, T:0.43
Consensus pattern (19 bp):
ATTGCGATTTTCATTTCGC
Found at i:1065388 original size:33 final size:34
Alignment explanation
Indices: 1065351--1065441 Score: 141
Period size: 33 Copynumber: 2.7 Consensus size: 34
1065341 TTGAAGGCAA
1065351 TTGCGATTTTCATTTCGCATTGCGAAAT-TAGCG
1 TTGCGATTTTCATTTCGCATTGCGAAATCTAGCG
* **
1065384 TTGCGATTTTCATTTCGCATTGCG-ATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGAAATCTAGCG
1065417 TTGCGATTTTCATTTCGCATTGCGA
1 TTGCGATTTTCATTTCGCATTGCGA
1065442 TAGTAATTTC
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
32 2 0.04
33 51 0.96
ACGTcount: A:0.16, C:0.21, G:0.20, T:0.43
Consensus pattern (34 bp):
TTGCGATTTTCATTTCGCATTGCGAAATCTAGCG
Found at i:1066612 original size:20 final size:19
Alignment explanation
Indices: 1066577--1066643 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
1066567 GAAACTTAAA
1066577 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
1066596 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
1066616 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
1066635 ATCGCAACG
1 ATCGCAACG
1066644 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1066651 original size:14 final size:14
Alignment explanation
Indices: 1066632--1066694 Score: 74
Period size: 14 Copynumber: 4.3 Consensus size: 14
1066622 ATGCGAAATG
1066632 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1066646 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
1066662 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1066678 AAAATCGCAACG-C
1 AAAATCGCAACGAC
1066691 AAAA
1 AAAA
1066695 CACAAATCGC
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
13 5 0.12
14 21 0.49
16 8 0.19
18 9 0.21
ACGTcount: A:0.51, C:0.25, G:0.16, T:0.08
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1066674 original size:32 final size:33
Alignment explanation
Indices: 1066616--1066690 Score: 134
Period size: 32 Copynumber: 2.3 Consensus size: 33
1066606 GGAAATGGCT
*
1066616 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1066649 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1066681 ATCGCAACGC
1 ATCGCAACGC
1066691 AAAACACAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
32 26 0.63
33 15 0.37
ACGTcount: A:0.45, C:0.25, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:1066723 original size:19 final size:19
Alignment explanation
Indices: 1066701--1066782 Score: 104
Period size: 18 Copynumber: 4.6 Consensus size: 19
1066691 AAAACACAAA
1066701 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1066720 TCGCGTTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
*
1066738 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
1066754 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1066771 TCGCATTGCGAT
1 TCGCATTGCGAT
1066783 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
14 6 0.11
15 3 0.06
16 4 0.07
17 4 0.07
18 20 0.37
19 17 0.31
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1066801 original size:20 final size:19
Alignment explanation
Indices: 1066767--1066821 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1066757 TTGCGATTTT
*
1066767 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1066786 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
1066806 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
1066822 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1066810 original size:39 final size:34
Alignment explanation
Indices: 1066701--1066802 Score: 102
Period size: 33 Copynumber: 2.8 Consensus size: 34
1066691 AAAACACAAA
1066701 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTCATT
1 TCGCATTGCGA---TCATTTCGCGTTGCGATTTCATT
1066738 TCGCATTGCGAT--TTT-GTCGTTGCGATTTTCATT
1 TCGCATTGCGATCATTTCG-CGTTGCGA-TTTCATT
1066771 TCGCATTGCGATAGCCATTTCCGCGTTGCGAT
1 TCGCATTGCGAT---CATTT-CGCGTTGCGAT
1066803 AGTCATTTTC
Statistics
Matches: 56, Mismatches: 0, Indels: 17
0.77 0.00 0.23
Matches are distributed among these distances:
31 1 0.02
32 11 0.20
33 19 0.34
34 1 0.02
37 11 0.20
38 4 0.07
39 8 0.14
40 1 0.02
ACGTcount: A:0.14, C:0.23, G:0.22, T:0.42
Consensus pattern (34 bp):
TCGCATTGCGATCATTTCGCGTTGCGATTTCATT
Found at i:1067329 original size:18 final size:18
Alignment explanation
Indices: 1067303--1067347 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1067293 GTCGATCAGA
1067303 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGTGAGG
* *
1067321 TGATAGCTCTGGGTGAGG
1 TGATGGCTCTAGGTGAGG
1067339 TGATGGCTC
1 TGATGGCTC
1067348 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.16, C:0.13, G:0.42, T:0.29
Consensus pattern (18 bp):
TGATGGCTCTAGGTGAGG
Found at i:1068691 original size:20 final size:20
Alignment explanation
Indices: 1068666--1068703 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1068656 AATAGTTTCT
1068666 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
1068686 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
1068704 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:1068994 original size:22 final size:22
Alignment explanation
Indices: 1068967--1069010 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1068957 GATGGAGATA
1068967 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1068989 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
1069011 TGAGAGAGCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1069223 original size:20 final size:20
Alignment explanation
Indices: 1069198--1069291 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
1069188 GATTATGTAT
1069198 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1069218 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
1069238 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
1069259 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1069279 TATCGCATTGCGA
1 TATCGCGTTGCGA
1069292 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1069292 original size:20 final size:20
Alignment explanation
Indices: 1069178--1069292 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
1069168 CGCTTTGAAA
*
1069178 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
1069199 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
1069219 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
1069239 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
1069260 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1069280 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1069293 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1069310 original size:21 final size:21
Alignment explanation
Indices: 1069281--1069356 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
1069271 ATAGTCAGTA
1069281 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
1069302 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
1069322 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* *
1069343 TCGCGTTACGATTT
1 TCGCATTGCGATTT
1069357 ACTTATTCAC
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 16 0.36
21 28 0.64
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:1069311 original size:41 final size:41
Alignment explanation
Indices: 1069220--1069354 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
1069210 AAAGTCAGTA
* * * ** *
1069220 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
1069260 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
1069302 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
*
1069343 TCGCGTTACGAT
1 TCGCGTTGCGAT
1069355 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:1069325 original size:20 final size:20
Alignment explanation
Indices: 1069300--1069364 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
1069290 GATTTTCCCA
1069300 ATTCGCGTTGCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
* * **
1069320 ATTCGCATTGCGATTTTCCCA
1 ATTCGCGTTGCGA-TTTACTT
*
1069341 ATTCGCGTTACGATTTACTT
1 ATTCGCGTTGCGATTTACTT
1069361 ATTC
1 ATTC
1069365 ACATTGCGAA
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 20 0.57
21 15 0.43
ACGTcount: A:0.18, C:0.23, G:0.15, T:0.43
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTACTT
Found at i:1069355 original size:41 final size:41
Alignment explanation
Indices: 1069281--1069373 Score: 168
Period size: 41 Copynumber: 2.3 Consensus size: 41
1069271 ATAGTCAGTA
*
1069281 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTACGATTTACTTAT
1069322 TCGCATTGCGATTTTCCCAATTCGCGTTACGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTACGATTTACTTAT
*
1069363 TCACATTGCGA
1 TCGCATTGCGA
1069374 ATTGGGAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.19, C:0.25, G:0.16, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTACGATTTACTTAT
Found at i:1075522 original size:19 final size:20
Alignment explanation
Indices: 1075479--1075522 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
1075469 TAAAGTTTCA
* * *
1075479 AAACTCTTGAGATAGTTTTG
1 AAACTCTTGAGAAAGTATCG
1075499 AAACTCTTGA-AAAGTATCG
1 AAACTCTTGAGAAAGTATCG
1075518 AAACT
1 AAACT
1075523 TTTTTGGGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (20 bp):
AAACTCTTGAGAAAGTATCG
Found at i:1076763 original size:18 final size:20
Alignment explanation
Indices: 1076722--1076764 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
1076712 CATTTTGCCA
* *
1076722 TTTTTAAACATAATGAGTTG
1 TTTTTAAACATAATGAATTC
1076742 TTTTTAAA-A-AATGAATTC
1 TTTTTAAACATAATGAATTC
1076760 TTTTT
1 TTTTT
1076765 CTTTTGTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 12 0.57
19 1 0.05
20 8 0.38
ACGTcount: A:0.35, C:0.05, G:0.09, T:0.51
Consensus pattern (20 bp):
TTTTTAAACATAATGAATTC
Found at i:1082199 original size:190 final size:191
Alignment explanation
Indices: 1081930--1082333 Score: 560
Period size: 191 Copynumber: 2.1 Consensus size: 191
1081920 AATAGATAAC
* * * * * **
1081930 AATATATTTTAATTTGAAATATTCAAAAGATAAAACTCTTTTTACCATTCAACCTTAAATATGTA
1 AATATA-TTTAATTTGCAATATTAAAAAGATAAAACTCCTTTTACCATTCAAACTTAAAAAAATA
* *
1081995 TTATTTTAATTTGAAATATACAAAAGTATATAAATATC-TTCAATATTCAAAGTTAAAAAGGTAA
65 TTATTTTAATTTGAAATATACAAAAGTATATAAATATCTTTCAATATTCAAAATTAAAAAGATAA
* * * *
1082059 CAAATATATTTTTAAGTTGACATATTCAAAGAGTAATTATCCTACTAATATTCAAATTAAAT
130 CAAATACATTTTTAAATTGACATATTAAAAGAGTAATTATCCTACTAATATTCAAATTAAAA
* * *
1082121 AATATATTTAATTTGCAATGGTTAAAAAGGT-AAACTCCTTTTACTATTCAAACTTAAAAAAATA
1 AATATATTTAATTTGCAAT-ATTAAAAAGATAAAACTCCTTTTACCATTCAAACTTAAAAAAATA
* *
1082185 TTATTTTAATTTGAAATATACAAAAGTATATAATTATCTTTTAATATTCAAAATTAAAAAGATAA
65 TTATTTTAATTTGAAATATACAAAAGTATATAAATATCTTTCAATATTCAAAATTAAAAAGATAA
* * *
1082250 CAAATACATTTTTAAATTGACTTATTAAAAGAGTAATTATTCTACTAGTATTCAAATTAAAA
130 CAAATACATTTTTAAATTGACATATTAAAAGAGTAATTATCCTACTAATATTCAAATTAAAA
*
1082312 AATTATCTTTTAATTTGCAATA
1 AA-TAT-ATTTAATTTGCAATA
1082334 GACAAAAGGA
Statistics
Matches: 186, Mismatches: 23, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
190 76 0.41
191 94 0.51
192 3 0.02
193 13 0.07
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.39
Consensus pattern (191 bp):
AATATATTTAATTTGCAATATTAAAAAGATAAAACTCCTTTTACCATTCAAACTTAAAAAAATAT
TATTTTAATTTGAAATATACAAAAGTATATAAATATCTTTCAATATTCAAAATTAAAAAGATAAC
AAATACATTTTTAAATTGACATATTAAAAGAGTAATTATCCTACTAATATTCAAATTAAAA
Found at i:1083961 original size:2 final size:2
Alignment explanation
Indices: 1083915--1083946 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1083905 TTTTTAACTA
1083915 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
1083947 TAATTTTCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1084737 original size:61 final size:59
Alignment explanation
Indices: 1084642--1084777 Score: 200
Period size: 61 Copynumber: 2.3 Consensus size: 59
1084632 ATATGTGTAT
* *
1084642 TAAGTTTTGGTAACTTTCCTTTCACATTTGTACACTTTTGCTCACTAAATTCAAAAAAACA
1 TAAGTTTTGGTCACTTTCCTTTCACATTTGTACACTTTT-CTCACCAAATTC-AAAAAACA
* **
1084703 TAAGTTTTGGTCACTTTCCTTTTATTTTTGTACACTTTTCTCACCAAATTCAAAAAACA
1 TAAGTTTTGGTCACTTTCCTTTCACATTTGTACACTTTTCTCACCAAATTCAAAAAACA
*
1084762 TAAGTTTTGATCACTT
1 TAAGTTTTGGTCACTT
1084778 ACGTTATTGT
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
59 23 0.33
60 11 0.16
61 35 0.51
ACGTcount: A:0.30, C:0.19, G:0.08, T:0.43
Consensus pattern (59 bp):
TAAGTTTTGGTCACTTTCCTTTCACATTTGTACACTTTTCTCACCAAATTCAAAAAACA
Found at i:1084839 original size:31 final size:31
Alignment explanation
Indices: 1084762--1084831 Score: 122
Period size: 31 Copynumber: 2.3 Consensus size: 31
1084752 TCAAAAAACA
*
1084762 TAAGTTTTGATCACTTACGTTATTGTTTTAT
1 TAAGTTTTGATCACTTACGTTATTATTTTAT
*
1084793 TAAGTTTTGATCACTTATGTTATTATTTTAT
1 TAAGTTTTGATCACTTACGTTATTATTTTAT
1084824 TAAGTTTT
1 TAAGTTTT
1084832 TTTCACTTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.24, C:0.07, G:0.11, T:0.57
Consensus pattern (31 bp):
TAAGTTTTGATCACTTACGTTATTATTTTAT
Found at i:1088343 original size:19 final size:19
Alignment explanation
Indices: 1088319--1088357 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1088309 GGACTTATTC
1088319 ATAAGACTTTGAAAAATTA
1 ATAAGACTTTGAAAAATTA
1088338 ATAAGACTTTGAAAAATTA
1 ATAAGACTTTGAAAAATTA
1088357 A
1 A
1088358 GGTATGTAAC
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:0.54, C:0.05, G:0.10, T:0.31
Consensus pattern (19 bp):
ATAAGACTTTGAAAAATTA
Found at i:1096236 original size:18 final size:18
Alignment explanation
Indices: 1096209--1096244 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1096199 TGACCGGTCA
1096209 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
*
1096227 CGACCTGACCCGTTGACC
1 CGACCCGACCCGTTGACC
1096245 GGTGACCGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.47, G:0.22, T:0.14
Consensus pattern (18 bp):
CGACCCGACCCGTTGACC
Found at i:1096317 original size:29 final size:29
Alignment explanation
Indices: 1096252--1096348 Score: 95
Period size: 29 Copynumber: 3.3 Consensus size: 29
1096242 ACCGGTGACC
* * * ** *
1096252 GGTGCTATTCTGGGAATTTATTCGATTTT
1 GGTGCTATTATGGGAATTAATTCAAAATG
*
1096281 GGTACTATTATGGGAATTAATTCAAAATG
1 GGTGCTATTATGGGAATTAATTCAAAATG
* * *
1096310 GGTGCTATTTTGGTAATTAATTCAAAAAGG
1 GGTGCTATTATGGGAATTAATTC-AAAATG
1096340 GGTGCTATT
1 GGTGCTATT
1096349 TTTGTAAAAT
Statistics
Matches: 56, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
29 42 0.75
30 14 0.25
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40
Consensus pattern (29 bp):
GGTGCTATTATGGGAATTAATTCAAAATG
Found at i:1096345 original size:30 final size:29
Alignment explanation
Indices: 1096285--1096355 Score: 97
Period size: 30 Copynumber: 2.4 Consensus size: 29
1096275 GATTTTGGTA
* * *
1096285 CTATTATGGGAATTAATTCAAAATGGGTG
1 CTATTTTGGTAATTAATTCAAAAGGGGTG
1096314 CTATTTTGGTAATTAATTCAAAAAGGGGTG
1 CTATTTTGGTAATTAATTC-AAAAGGGGTG
*
1096344 CTATTTTTGTAA
1 CTATTTTGGTAA
1096356 AATGGTTGAC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 17 0.46
30 20 0.54
ACGTcount: A:0.32, C:0.07, G:0.21, T:0.39
Consensus pattern (29 bp):
CTATTTTGGTAATTAATTCAAAAGGGGTG
Found at i:1098555 original size:19 final size:19
Alignment explanation
Indices: 1098485--1098557 Score: 67
Period size: 20 Copynumber: 3.7 Consensus size: 19
1098475 CGTCGGAAAC
*
1098485 AAAGTATCGAAACT-TTAGGT
1 AAAGTATCGAAACTCTT--GA
* *
1098505 AAAGTTTCAAAACTCTTGA
1 AAAGTATCGAAACTCTTGA
* *
1098524 GATAGTTTCGAAACTCTTGA
1 -AAAGTATCGAAACTCTTGA
1098544 AAAGTATCGAAACT
1 AAAGTATCGAAACT
1098558 TTTTTGGGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
19 13 0.30
20 29 0.66
21 2 0.05
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
AAAGTATCGAAACTCTTGA
Found at i:1101856 original size:19 final size:20
Alignment explanation
Indices: 1101815--1101858 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
1101805 TAAAGTTTCA
* *
1101815 AAACTCTTGAGATATTTTCG
1 AAACTCTTGAGAAATTATCG
1101835 AAACTCTTGA-AAATTATCG
1 AAACTCTTGAGAAATTATCG
1101854 AAACT
1 AAACT
1101859 TTTTGGGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (20 bp):
AAACTCTTGAGAAATTATCG
Found at i:1112276 original size:22 final size:23
Alignment explanation
Indices: 1112234--1112276 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
1112224 AATGTAACTC
*
1112234 ATTTTATAATGATATTTAATTCT
1 ATTTTATAATGATATTAAATTCT
1112257 ATTTT-TAATAGA-ATTAAATT
1 ATTTTATAAT-GATATTAAATT
1112277 ATGCATTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (23 bp):
ATTTTATAATGATATTAAATTCT
Found at i:1119640 original size:23 final size:21
Alignment explanation
Indices: 1119614--1119664 Score: 50
Period size: 22 Copynumber: 2.4 Consensus size: 21
1119604 TTGGAACATA
1119614 TATGTGGTTCTTAGGGACAATT
1 TATGTGGTTCTTAGGGA-AATT
* * *
1119636 CTATG-GGGTCTTCGGGATATT
1 -TATGTGGTTCTTAGGGAAATT
1119657 TATGTGGT
1 TATGTGGT
1119665 CCTTCGGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
20 4 0.17
21 5 0.22
22 10 0.43
23 4 0.17
ACGTcount: A:0.18, C:0.10, G:0.31, T:0.41
Consensus pattern (21 bp):
TATGTGGTTCTTAGGGAAATT
Found at i:1119671 original size:21 final size:21
Alignment explanation
Indices: 1119512--1119690 Score: 119
Period size: 21 Copynumber: 8.5 Consensus size: 21
1119502 AGGGTTCTAC
* *
1119512 GTGGTTCTTCGGGATATATAT
1 GTGGTCCTTCGGGACATATAT
* * * * *
1119533 GTGATCTTTTGGAATATATAT
1 GTGGTCCTTCGGGACATATAT
* * *
1119554 GTGGTCTTTTGGAACATATAT
1 GTGGTCCTTCGGGACATATAT
*
1119575 TTGGTCCTTCGGGACATATAT
1 GTGGTCCTTCGGGACATATAT
* * * *
1119596 TTGGTCATTTGGAACATATAT
1 GTGGTCCTTCGGGACATATAT
* * *
1119617 GTGGTTCTTAGGGACAATTCTAT
1 GTGGTCCTTCGGGAC-A-TATAT
* * *
1119640 GGGGT-CTTCGGGATATTTAT
1 GTGGTCCTTCGGGACATATAT
1119660 GTGGTCCTTC-GGACATATAT
1 GTGGTCCTTCGGGACATATAT
**
1119680 GCAGTCCTTCG
1 GTGGTCCTTCG
1119691 AGATATTTTA
Statistics
Matches: 125, Mismatches: 29, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
20 24 0.19
21 85 0.68
22 8 0.06
23 8 0.06
ACGTcount: A:0.21, C:0.13, G:0.25, T:0.40
Consensus pattern (21 bp):
GTGGTCCTTCGGGACATATAT
Found at i:1119937 original size:23 final size:23
Alignment explanation
Indices: 1119911--1119966 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
1119901 CAGGTAAGAG
* *
1119911 ATGAAAGTATGTGATTGTATGAT
1 ATGAAAGTATGTAAATGTATGAT
* *
1119934 ATGAAAGTATGTAAATGTGTGTT
1 ATGAAAGTATGTAAATGTATGAT
1119957 ATGAAAGTAT
1 ATGAAAGTAT
1119967 ATAACTGCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.25, T:0.38
Consensus pattern (23 bp):
ATGAAAGTATGTAAATGTATGAT
Found at i:1119979 original size:23 final size:23
Alignment explanation
Indices: 1119933--1119979 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1119923 GATTGTATGA
* **
1119933 TATGAAAGTATGTAAATGTGTGT
1 TATGAAAGTATATAAATGCATGT
*
1119956 TATGAAAGTATATAACTGCATGT
1 TATGAAAGTATATAAATGCATGT
1119979 T
1 T
1119980 TCAGTAGTTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.38
Consensus pattern (23 bp):
TATGAAAGTATATAAATGCATGT
Done.