Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009624.1 Hibiscus syriacus cultivar Beakdansim tig00117016_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: 8249038
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 38
Found at i:1048485 original size:30 final size:30
Alignment explanation
Indices: 1048451--1048520 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
1048441 TCCCAACTTT
* *
1048451 TTTTTCCAAAATTACAAATTGGTCCCTCAA
1 TTTTTCCAAAATTACAAAATGGTCCCTAAA
* *
1048481 TTTTTCAAAAATTATAAAATGGTCCCTAAA
1 TTTTTCCAAAATTACAAAATGGTCCCTAAA
1048511 TTTTTCCAAA
1 TTTTTCCAAA
1048521 GCTTGTAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.06, T:0.39
Consensus pattern (30 bp):
TTTTTCCAAAATTACAAAATGGTCCCTAAA
Found at i:1049505 original size:30 final size:30
Alignment explanation
Indices: 1049469--1049526 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
1049459 TTTAGTCCCT
* *
1049469 AAACTTTTC-TAAGTTTATACTTTGGTCATC
1 AAACTTTACTTAA-TTTATAATTTGGTCATC
1049499 AAACTTTACTTAATTTATAATTTGGTCA
1 AAACTTTACTTAATTTATAATTTGGTCA
1049527 CTAAATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.88
31 3 0.12
ACGTcount: A:0.31, C:0.14, G:0.09, T:0.47
Consensus pattern (30 bp):
AAACTTTACTTAATTTATAATTTGGTCATC
Found at i:1057530 original size:27 final size:28
Alignment explanation
Indices: 1057490--1057555 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 28
1057480 GATTAAATAA
*
1057490 AAATAAAAATAGAAACAAAATAAAACAT
1 AAATAAAAATAGAAACAAAAAAAAACAT
* *
1057518 AAATATAAA-AGAAACAAAAAAAAACGT
1 AAATAAAAATAGAAACAAAAAAAAACAT
1057545 AAA-AGAAAATA
1 AAATA-AAAATA
1057556 TACAAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 1 0.03
27 22 0.69
28 9 0.28
ACGTcount: A:0.76, C:0.06, G:0.06, T:0.12
Consensus pattern (28 bp):
AAATAAAAATAGAAACAAAAAAAAACAT
Found at i:1057553 original size:26 final size:27
Alignment explanation
Indices: 1057490--1057563 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
1057480 GATTAAATAA
* *
1057490 AAATAAAAATAGAAACAAAATAAAACAT
1 AAATAGAAA-AGAAACAAAAAAAAACAT
* *
1057518 AAATATAAAAGAAACAAAAAAAAACGT
1 AAATAGAAAAGAAACAAAAAAAAACAT
* *
1057545 AAA-AGAAAATATACAAAAA
1 AAATAGAAAAGAAACAAAAA
1057564 GAATGCGAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
26 13 0.32
27 19 0.47
28 8 0.20
ACGTcount: A:0.76, C:0.07, G:0.05, T:0.12
Consensus pattern (27 bp):
AAATAGAAAAGAAACAAAAAAAAACAT
Found at i:1057656 original size:21 final size:21
Alignment explanation
Indices: 1057600--1057658 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
1057590 AAATAAAAGC
* * *
1057600 AAGAAGAAAATAACAAATAAG
1 AAGAAAAAAATAATAAATAAA
* *
1057621 TAGATAAATAA-AATAAATAAA
1 AAGA-AAAAAATAATAAATAAA
1057642 AAGAAAAAAATAATAAA
1 AAGAAAAAAATAATAAA
1057659 AAACAAACGA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
20 5 0.17
21 20 0.69
22 4 0.14
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (21 bp):
AAGAAAAAAATAATAAATAAA
Found at i:1057846 original size:3 final size:3
Alignment explanation
Indices: 1057838--1057863 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1057828 ATATAAAGAA
1057838 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1057864 CAAGTATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1057857 original size:24 final size:23
Alignment explanation
Indices: 1057805--1057857 Score: 54
Period size: 24 Copynumber: 2.2 Consensus size: 23
1057795 AAACAAGTAA
*
1057805 AATAATGAAAACAAAATATATAT
1 AATAAAGAAAACAAAATATATAT
*
1057828 ATATAAAGAAAATAATAATA-ATAAT
1 A-ATAAAGAAAACAA-AATATAT-AT
1057853 AATAA
1 AATAA
1057858 TAATAACAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 1 0.04
24 17 0.68
25 7 0.28
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (23 bp):
AATAAAGAAAACAAAATATATAT
Found at i:1057924 original size:22 final size:21
Alignment explanation
Indices: 1057872--1057924 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
1057862 AACAAGTATA
*
1057872 AAAAAAATAAAGACAAAATAT
1 AAAAAAATAAAGACAAAAAAT
*
1057893 ATAAAAAATAAATA-AATAAAAT
1 A-AAAAAATAAAGACAA-AAAAT
1057915 AAAAAGAATA
1 AAAAA-AATA
1057925 TAATTATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 7 0.26
22 20 0.74
ACGTcount: A:0.77, C:0.02, G:0.04, T:0.17
Consensus pattern (21 bp):
AAAAAAATAAAGACAAAAAAT
Found at i:1058964 original size:2 final size:2
Alignment explanation
Indices: 1058957--1058988 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1058947 TAATAAAATA
1058957 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
1058989 GTTAAATAAA
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:1061693 original size:21 final size:21
Alignment explanation
Indices: 1061667--1061844 Score: 218
Period size: 21 Copynumber: 8.5 Consensus size: 21
1061657 GTTTCCAGAT
* *
1061667 TCGCAACGCGAACTTTGACTA
1 TCGCAATGCGAACTTGGACTA
1061688 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
*
1061709 TCGCAATACGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* *
1061730 TCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* *
1061750 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
* * *
1061771 TTGTAATACGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
1061792 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
*
1061813 TCGCAATGTGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
1061834 TCGCAATGCGA
1 TCGCAATGCGA
1061845 TTTACATATT
Statistics
Matches: 133, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
20 16 0.12
21 117 0.88
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:1061963 original size:21 final size:21
Alignment explanation
Indices: 1061853--1061956 Score: 190
Period size: 21 Copynumber: 5.0 Consensus size: 21
1061843 GATTTACATA
1061853 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
1061874 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
1061895 TTCTCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
1061916 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
1061937 TTCGCATTGCGATAGTCCAA
1 TTCGCATTGCGATAGTCCAA
1061957 AATCGCAACG
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 79 1.00
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:1062591 original size:6 final size:6
Alignment explanation
Indices: 1062581--1062613 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
1062571 TCTCGTCTCG
*
1062581 GGTCGG GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1062614 AATACGTGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.15, G:0.55, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:1062732 original size:21 final size:21
Alignment explanation
Indices: 1062706--1062808 Score: 120
Period size: 21 Copynumber: 4.8 Consensus size: 21
1062696 ATTTTGGACT
*
1062706 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
1062727 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
1062748 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
1062769 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
1062790 AACGCAACGCGAACTTGGA
1 ATCGCAA--CGAACTTGGA
1062809 CTATCGCAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
19 10 0.14
21 40 0.57
23 20 0.29
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.18
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:1062815 original size:63 final size:62
Alignment explanation
Indices: 1062702--1062823 Score: 174
Period size: 63 Copynumber: 1.9 Consensus size: 62
1062692 TGCGATTTTG
* *
1062702 GACTATCGCAACGAATTTGGAATAAATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAAACGCAACGAACTTGGAAT-AATCGCAACGCGAACTTC
* *
1062765 GACTATCGCAACGAACTTGGAATAAAACGCAACGCGAACTTGGACT-ATCGCAATGCGAA
1 GACTATCGCAACGAACTTGGAATAAAACGCAA--CGAACTTGGAATAATCGCAACGCGAA
1062824 TATGTAAATC
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
63 42 0.79
65 11 0.21
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (62 bp):
GACTATCGCAACGAACTTGGAATAAAACGCAACGAACTTGGAATAATCGCAACGCGAACTTC
Found at i:1069809 original size:13 final size:12
Alignment explanation
Indices: 1069772--1069810 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
1069762 CAAAATATTA
*
1069772 TAAAAAAAATCAA
1 TAAAAAAAAT-AT
1069785 TAAAAAAAATAT
1 TAAAAAAAATAT
1069797 TAAAAAATAATAT
1 TAAAAAA-AATAT
1069810 T
1 T
1069811 TTAACCTACG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (12 bp):
TAAAAAAAATAT
Found at i:1074697 original size:21 final size:20
Alignment explanation
Indices: 1074631--1074768 Score: 73
Period size: 21 Copynumber: 6.8 Consensus size: 20
1074621 AAATGACCAA
**
1074631 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ** *
1074650 AAAAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1074670 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1074691 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1074712 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
1074732 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1074753 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1074769 ACACATAAAT
Statistics
Matches: 86, Mismatches: 27, Indels: 11
0.69 0.22 0.09
Matches are distributed among these distances:
18 1 0.01
19 11 0.13
20 28 0.33
21 46 0.53
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1074808 original size:20 final size:20
Alignment explanation
Indices: 1074736--1074944 Score: 217
Period size: 20 Copynumber: 10.4 Consensus size: 20
1074726 GATTTTCCAG
* ** *
1074736 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1074756 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1074776 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1074796 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1074816 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1074836 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1074856 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1074876 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1074896 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1074916 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1074936 AATCACAAC
1 AATCGCAAC
1074945 ACTGAAATTT
Statistics
Matches: 161, Mismatches: 22, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.01
20 157 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1075662 original size:24 final size:24
Alignment explanation
Indices: 1075623--1075669 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1075613 AAATTTGGTC
1075623 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1075647 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1075670 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1075861 original size:12 final size:12
Alignment explanation
Indices: 1075844--1075868 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1075834 ATATAATCCT
1075844 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1075856 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1075868 G
1 G
1075869 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:1078205 original size:20 final size:19
Alignment explanation
Indices: 1078154--1078383 Score: 265
Period size: 19 Copynumber: 12.7 Consensus size: 19
1078144 GCAACGAGAG
1078154 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1078173 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1078187 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
1078207 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1078226 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
1078246 AATTGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1078265 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1078279 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
1078299 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
1078318 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1078332 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
1078352 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1078371 AATCGCATTGCGA
1 AATCGCAATGCGA
1078384 TTCTCTCGTT
Statistics
Matches: 181, Mismatches: 11, Indels: 38
0.79 0.05 0.17
Matches are distributed among these distances:
14 31 0.17
15 2 0.01
16 3 0.02
17 7 0.04
19 78 0.43
20 60 0.33
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1078217 original size:53 final size:53
Alignment explanation
Indices: 1078154--1078383 Score: 241
Period size: 53 Copynumber: 4.2 Consensus size: 53
1078144 GCAACGAGAG
*
1078154 AATCGCAATGCGA-AAT-GAAAAT-CCCAACATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAGAATCG-AAATGCGCAA-ATGAAAATCGCAATGC-GAAATGAA
* * *
1078207 AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATTGCAATGCGAAATGAA
1 AATCGCAATGCG--A-G--AATCGAAATGCGCAAATGAAAATCGCAATGCGAAATGAA
* * * * *
1078265 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAGAATCGAAATGCGCAAATGAAAATCGCAATGCGAAATGAA
* * * *
1078318 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAGAATCGAAATGCGCAAATGAAAATCGCAATGCGAAATGAA
*
1078371 AATCGCATTGCGA
1 AATCGCAATGCGA
1078384 TTCTCTCGTT
Statistics
Matches: 157, Mismatches: 12, Indels: 16
0.85 0.06 0.09
Matches are distributed among these distances:
53 111 0.71
55 2 0.01
56 1 0.01
58 18 0.11
59 21 0.13
60 4 0.03
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.16
Consensus pattern (53 bp):
AATCGCAATGCGAGAATCGAAATGCGCAAATGAAAATCGCAATGCGAAATGAA
Found at i:1078236 original size:39 final size:39
Alignment explanation
Indices: 1078154--1078382 Score: 269
Period size: 39 Copynumber: 6.3 Consensus size: 39
1078144 GCAACGAGAG
*
1078154 AATCGCAATGC-GAAATGAAAATCCCAA--C---ATGAA
1 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1078187 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
*
1078226 AATCGCAATGCGGAAATGAAAATTGCAATGCGAAATGAA
1 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
*
1078265 AATCGCAA--C-G--A-GAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGGAAATGAAAATCGCAATGC-GAAATGAA
* *
1078299 AATCGCAATGC-GAAATTAAAATCGCAA--CG--A-GAG
1 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1078332 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
*
1078371 AATCGCATTGCG
1 AATCGCAATGCG
1078383 ATTCTCTCGT
Statistics
Matches: 168, Mismatches: 10, Indels: 30
0.81 0.05 0.14
Matches are distributed among these distances:
33 36 0.21
34 48 0.29
36 7 0.04
37 2 0.01
38 2 0.01
39 73 0.43
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.16
Consensus pattern (39 bp):
AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
Found at i:1078375 original size:92 final size:87
Alignment explanation
Indices: 1078132--1078382 Score: 326
Period size: 92 Copynumber: 2.8 Consensus size: 87
1078122 TCGCAACACG
* *
1078132 GAAATTACAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAAT
1 GAAATTAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGATGAAAATCGCAAT
1078196 GCGGAAATGAAAATCGCAATGC
66 GCGGAAATGAAAATCGCAATGC
* * * *
1078218 GAAATGAAAATCGCAATGCGGAAATGAAAATTGCAATGCGAAATGAAAATCGCAACGA-GAGAAT
1 GAAATTAAAATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAACGATGAAAAT
1078282 CGCAATGCGGAAATGAAAATCGCAATGC
60 CGCAATGCGGAAATGAAAATCGCAATGC
1078310 GAAATTAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATC
1 GAAATTAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAA--CG--ATGAAAATC
*
1078375 GCATTGCG
61 GCAATGCG
1078383 ATTCTCTCGT
Statistics
Matches: 141, Mismatches: 11, Indels: 20
0.82 0.06 0.12
Matches are distributed among these distances:
86 26 0.18
87 17 0.12
88 1 0.01
89 4 0.03
90 1 0.01
91 2 0.01
92 89 0.63
93 1 0.01
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.16
Consensus pattern (87 bp):
GAAATTAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGATGAAAATCGCAAT
GCGGAAATGAAAATCGCAATGC
Found at i:1078397 original size:14 final size:14
Alignment explanation
Indices: 1078378--1078446 Score: 50
Period size: 14 Copynumber: 4.6 Consensus size: 14
1078368 GAAAATCGCA
1078378 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
1078392 TTGCGATTTTCAT-G
1 TTGCGATTCTC-TCG
* *
1078406 TTGGGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
1078423 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
1078439 TTGCGATT
1 TTGCGATT
1078447 TTCATTTCGC
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
14 24 0.57
15 1 0.02
16 7 0.17
17 5 0.12
19 5 0.12
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:1078429 original size:33 final size:34
Alignment explanation
Indices: 1078392--1078470 Score: 126
Period size: 33 Copynumber: 2.4 Consensus size: 34
1078382 GATTCTCTCG
*
1078392 TTGCGATTTTCAT-GTTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATCGTTGCGATTTTCATTTCGCA
*
1078425 TTGCGATTCTC-TCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATCGTTGCGATTTTCATTTCGCA
1078458 TTGCGATTTTCAT
1 TTGCGATTTTCAT
1078471 TTCCGCATTG
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
32 1 0.02
33 39 0.95
34 1 0.02
ACGTcount: A:0.14, C:0.19, G:0.19, T:0.48
Consensus pattern (34 bp):
TTGCGATTTTCATCGTTGCGATTTTCATTTCGCA
Found at i:1078442 original size:47 final size:50
Alignment explanation
Indices: 1078373--1078484 Score: 167
Period size: 47 Copynumber: 2.2 Consensus size: 50
1078363 GAAATGAAAA
*
1078373 TCGCATTGCGATTCTCTCGTTGCGATTTTCA-T-G-TTGGGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTCGATTGCGATTTTCATT
1078420 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCA-TTCG-ATTGCGATTTTCATT
1078472 TCCGCATTGCGAT
1 T-CGCATTGCGAT
1078485 AGTCATTTTT
Statistics
Matches: 58, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
47 31 0.53
49 1 0.02
50 1 0.02
52 14 0.24
53 11 0.19
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (50 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTCGATTGCGATTTTCATT
Found at i:1078479 original size:20 final size:19
Alignment explanation
Indices: 1078410--1078484 Score: 97
Period size: 19 Copynumber: 4.2 Consensus size: 19
1078400 TTCATGTTGG
1078410 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
*
1078429 GA--TTC-TCTCG--TTGC
1 GATTTTCATTTCGCATTGC
1078443 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
1078462 GATTTTCATTTCCGCATTGC
1 GATTTTCATTT-CGCATTGC
1078482 GAT
1 GAT
1078485 AGTCATTTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
14 6 0.12
16 7 0.15
17 7 0.15
19 17 0.35
20 11 0.23
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
GATTTTCATTTCGCATTGC
Found at i:1078490 original size:20 final size:19
Alignment explanation
Indices: 1078415--1078492 Score: 67
Period size: 20 Copynumber: 4.3 Consensus size: 19
1078405 GTTGGGATTT
1078415 TCATTTCGCATTGCGAT--
1 TCATTTCGCATTGCGATAG
* **
1078432 TC-TCTCG--TTGCGATTT
1 TCATTTCGCATTGCGATAG
**
1078448 TCATTTCGCATTGCGATTT
1 TCATTTCGCATTGCGATAG
1078467 TCATTTCCGCATTGCGATAG
1 TCATTT-CGCATTGCGATAG
1078487 TCATTT
1 TCATTT
1078493 TTGCCTTCAA
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
14 7 0.14
16 6 0.12
17 6 0.12
19 15 0.29
20 17 0.33
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:1078611 original size:14 final size:14
Alignment explanation
Indices: 1078587--1078626 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
1078577 TTCGCATCAA
1078587 TTACAAAATCAACTT
1 TTAC-AAATCAACTT
*
1078602 TTACAAATCATCTT
1 TTACAAATCAACTT
1078616 TTACAAATCAA
1 TTACAAATCAA
1078627 TTAAACAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 19 0.83
15 4 0.17
ACGTcount: A:0.45, C:0.20, G:0.00, T:0.35
Consensus pattern (14 bp):
TTACAAATCAACTT
Found at i:1080531 original size:19 final size:19
Alignment explanation
Indices: 1080489--1080661 Score: 150
Period size: 19 Copynumber: 9.6 Consensus size: 19
1080479 TAGTTTACTT
* *
1080489 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
1080509 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
1080528 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
**
1080547 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1080566 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
* *
1080585 TCACAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1080599 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1080618 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
1080632 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1080651 TCGCAATGCGA
1 TCGCAACGCGA
1080662 TTTTGGTTTC
Statistics
Matches: 126, Mismatches: 17, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
14 17 0.13
15 1 0.01
16 7 0.06
17 7 0.06
18 1 0.01
19 81 0.64
20 12 0.10
ACGTcount: A:0.46, C:0.24, G:0.20, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1080618 original size:71 final size:66
Alignment explanation
Indices: 1080524--1080652 Score: 159
Period size: 71 Copynumber: 1.9 Consensus size: 66
1080514 ACGCGAAATG
1080524 AGAATCGCAACGAGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCAC
1 AGAATCGCAACGAGAAACCAAAATCGCAA--CG--A-CAAAATCGCAACGCGAAATGAAAATCAC
1080589 AACGAC
61 AACGAC
* * ** * *
1080595 AGAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATC
1 AGAATCGCAACGAGAAACCAAAATCGCAACGACAAAATCGCAACGCGAAATGAAAATC
1080653 GCAATGCGAT
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
66 24 0.46
67 1 0.02
69 2 0.04
71 25 0.48
ACGTcount: A:0.48, C:0.23, G:0.19, T:0.09
Consensus pattern (66 bp):
AGAATCGCAACGAGAAACCAAAATCGCAACGACAAAATCGCAACGCGAAATGAAAATCACAACGA
C
Found at i:1080653 original size:33 final size:33
Alignment explanation
Indices: 1080564--1080656 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
1080554 GCGAAACCAA
*
1080564 AATCGCAACGCGAAATGAAAATCACAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* *
1080597 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1080630 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1080657 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:1080653 original size:52 final size:52
Alignment explanation
Indices: 1080523--1080661 Score: 140
Period size: 52 Copynumber: 2.7 Consensus size: 52
1080513 AACGCGAAAT
* * * *
1080523 GAGAATCGCAACGAGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACGC
1 GAGAATCGCAACGCGAAACGAAAATCGCAATGCGAAACCAAAATCGCAACGA
* ** **
1080575 GA-AAT-GAAAATC-ACAACGACAGAATCGCAATGCGAAATGAAAATCGCAACGA
1 GAGAATCGCAACGCGA-AACGA-A-AATCGCAATGCGAAACCAAAATCGCAACGA
*
1080627 GAGAATCGCAACGCGAAATGAAAATCGCAATGCGA
1 GAGAATCGCAACGCGAAACGAAAATCGCAATGCGA
1080662 TTTTGGTTTC
Statistics
Matches: 68, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
49 1 0.01
50 7 0.10
51 4 0.06
52 43 0.63
53 4 0.06
54 8 0.12
55 1 0.01
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (52 bp):
GAGAATCGCAACGCGAAACGAAAATCGCAATGCGAAACCAAAATCGCAACGA
Found at i:1080692 original size:14 final size:14
Alignment explanation
Indices: 1080673--1080731 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
1080663 TTTGGTTTCG
1080673 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
1080687 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
1080704 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
1080720 CGTTGCGATTTT
1 CGTTGCGATTTT
1080732 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1080699 original size:33 final size:33
Alignment explanation
Indices: 1080657--1080780 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
1080647 AAAATCGCAA
*
1080657 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1080690 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
1080723 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* *
1080756 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
1080781 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1080711 original size:19 final size:18
Alignment explanation
Indices: 1080657--1080748 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 18
1080647 AAAATCGCAA
1080657 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
1080676 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
1080690 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
1080709 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
1080723 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
1080742 TGCGATT
1 TGCGATT
1080749 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 23 0.38
15 1 0.02
16 2 0.03
17 2 0.03
18 2 0.03
19 30 0.50
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:1080758 original size:14 final size:14
Alignment explanation
Indices: 1080706--1080762 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1080696 TTTGGTTTCG
*
1080706 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
1080720 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1080739 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1080753 CGTTGCGATT
1 CGTTGCGATT
1080763 TTAAGTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1082654 original size:20 final size:20
Alignment explanation
Indices: 1082623--1082686 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
1082613 TTTTGGTTGA
1082623 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
1082643 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
1082663 AAATGAAAATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
1082684 AAT
1 AAT
1082687 CGCAACGCGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.47, C:0.16, G:0.25, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:1082675 original size:21 final size:21
Alignment explanation
Indices: 1082621--1082685 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
1082611 TCTTTTGGTT
1082621 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
1082642 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
1082662 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
1082683 GAA
1 GAA
1082686 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:1082746 original size:14 final size:14
Alignment explanation
Indices: 1082727--1082783 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1082717 TTTGGTTTCG
1082727 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1082741 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1082760 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1082774 CGTTACGATT
1 CGTTGCGATT
1082784 TTCATTTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1082759 original size:33 final size:33
Alignment explanation
Indices: 1082711--1082790 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
1082701 AAAATCGCAA
**
1082711 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1082744 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
1082777 TACGATTTTCATTT
1 TGCGATTTTCATTT
1082791 TTCTCGTTGC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.10, C:0.21, G:0.21, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1082796 original size:21 final size:21
Alignment explanation
Indices: 1082771--1082844 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
1082761 GTTGCGATTC
*
1082771 TCTCGTTACGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
1082792 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
1082813 TCACGTTGCGATTTTCATTTC
1 TCTCGTTGCGATTTTCATTTT
1082834 TCTCGTTGCGA
1 TCTCGTTGCGA
1082845 CTCTTCTGAA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
20 6 0.14
21 31 0.72
22 6 0.14
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:1082966 original size:33 final size:33
Alignment explanation
Indices: 1082924--1082994 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1082914 AATACTAACT
1082924 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
1082957 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1082990 TGAAA
1 TGAAA
1082995 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:1083399 original size:20 final size:20
Alignment explanation
Indices: 1083374--1083566 Score: 228
Period size: 20 Copynumber: 9.6 Consensus size: 20
1083364 CTTTAAAAAT
1083374 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1083394 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
1083414 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* *
1083435 CGCGTTGCGATATATGGATA
1 CGCGTTGCGATTTACGGATA
*
1083455 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
1083475 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1083495 CACGTTGCGGTTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1083515 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1083535 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1083555 CGCGTTGCGATT
1 CGCGTTGCGATT
1083567 CTGGAAAATC
Statistics
Matches: 148, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
20 130 0.88
21 18 0.12
ACGTcount: A:0.18, C:0.19, G:0.28, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1085723 original size:18 final size:19
Alignment explanation
Indices: 1085688--1085724 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1085678 CACGGAATGT
1085688 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
1085708 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
1085725 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:1086872 original size:14 final size:14
Alignment explanation
Indices: 1086826--1086863 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
1086816 CGTTGGGCAT
*
1086826 CCGAAGCCATCCGA
1 CCGAGGCCATCCGA
*
1086840 CCGAGGGCATCCGA
1 CCGAGGCCATCCGA
1086854 CCGAGGCCAT
1 CCGAGGCCAT
1086864 TCGAGCGAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.24, C:0.39, G:0.29, T:0.08
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:1086963 original size:29 final size:30
Alignment explanation
Indices: 1086919--1086997 Score: 115
Period size: 31 Copynumber: 2.6 Consensus size: 30
1086909 GAAGAGCAGG
1086919 AGGAGTGCATGACGACCTAC-AAGGTCGCC
1 AGGAGTGCATGACGACCTACAAAGGTCGCC
*
1086948 AGGAGTGCATGTCGACCTACAAAAGGTCGCC
1 AGGAGTGCATGACGACCTAC-AAAGGTCGCC
* *
1086979 CGGAGTGCATGGCGACCTA
1 AGGAGTGCATGACGACCTA
1086998 TGCTGGGAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 19 0.42
31 26 0.58
ACGTcount: A:0.27, C:0.27, G:0.32, T:0.15
Consensus pattern (30 bp):
AGGAGTGCATGACGACCTACAAAGGTCGCC
Found at i:1095707 original size:29 final size:28
Alignment explanation
Indices: 1095675--1095735 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
1095665 ATTAAAAAAT
*
1095675 AAATAAATATTAATA-AAATATTTATATAA
1 AAATAAA-ATTAATATAAATAATT-TATAA
*
1095704 AAAT-AAATTAATATATATAATTTATAA
1 AAATAAAATTAATATAAATAATTTATAA
1095731 AAATA
1 AAATA
1095736 GGATATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
27 16 0.57
28 8 0.29
29 4 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (28 bp):
AAATAAAATTAATATAAATAATTTATAA
Found at i:1095720 original size:18 final size:17
Alignment explanation
Indices: 1095660--1095717 Score: 57
Period size: 16 Copynumber: 3.4 Consensus size: 17
1095650 ATCCCATTTC
1095660 TTAATATTAAAAAATAAA
1 TTAATATT-AAAAATAAA
* *
1095678 TAAATATTAATAAA-ATA
1 TTAATATTAA-AAATAAA
*
1095695 TTTATA-TAAAAATAAA
1 TTAATATTAAAAATAAA
1095711 TTAATAT
1 TTAATAT
1095718 ATATAATTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
15 3 0.10
16 10 0.32
17 8 0.26
18 10 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAATATTAAAAATAAA
Found at i:1095863 original size:15 final size:16
Alignment explanation
Indices: 1095843--1095873 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1095833 ATTTTTTTTC
1095843 TAAAATT-AATTTATA
1 TAAAATTAAATTTATA
1095858 TAAAATTAAATTTATA
1 TAAAATTAAATTTATA
1095874 AATAGGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAAATTAAATTTATA
Found at i:1095875 original size:14 final size:15
Alignment explanation
Indices: 1095843--1095875 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1095833 ATTTTTTTTC
*
1095843 TAAAATTAATTTATA
1 TAAAATTAAATTATA
1095858 TAAAATTAAATT-TA
1 TAAAATTAAATTATA
1095872 TAAA
1 TAAA
1095876 TAGGATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAAAATTAAATTATA
Found at i:1097315 original size:3 final size:3
Alignment explanation
Indices: 1097307--1097368 Score: 81
Period size: 3 Copynumber: 21.0 Consensus size: 3
1097297 GCCTGAAATG
* * * *
1097307 TAA TAA TAA TAA T-T TAT TAT TAA TAA TAA TAA TGA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1097354 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
1097369 ACAAATAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
2 1 0.02
3 53 0.98
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:1097840 original size:105 final size:106
Alignment explanation
Indices: 1097671--1097871 Score: 284
Period size: 105 Copynumber: 1.9 Consensus size: 106
1097661 TCTTTTTTAG
* ** * *
1097671 ATGAGTTCTTCTCATTTTGAACTTCTTCTGGAAATGTTGATGTTGATCTATCTCCTTCTATGATA
1 ATGAGTTCTTCTCATTATGAACTTCTTCTGGAAATGTTGATACTAATCTATCTCATTCTATGATA
1097736 GTA-T-TAAGCAAAAGGTTGAACAAATTCTTCTTCCTCTTCAT
66 G-AGTCT-AGCAAAAGGTTGAACAAATTCTTCTTCCTCTTCAT
*
1097777 ATGAGTTCTTCTCATTATGAAC-TCTTCCT-GAAATGTTGATACTAATCTATCTCATTCTGTGAT
1 ATGAGTTCTTCTCATTATGAACTTCTT-CTGGAAATGTTGATACTAATCTATCTCATTCTATGAT
*
1097840 AGAGTCTAGCAAAAGGTTGAACAAGTTCTTCT
65 AGAGTCTAGCAAAAGGTTGAACAAATTCTTCT
1097872 CATTATGAAC
Statistics
Matches: 85, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
104 1 0.01
105 60 0.71
106 24 0.28
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (106 bp):
ATGAGTTCTTCTCATTATGAACTTCTTCTGGAAATGTTGATACTAATCTATCTCATTCTATGATA
GAGTCTAGCAAAAGGTTGAACAAATTCTTCTTCCTCTTCAT
Found at i:1098059 original size:113 final size:113
Alignment explanation
Indices: 1097847--1098409 Score: 923
Period size: 113 Copynumber: 5.0 Consensus size: 113
1097837 GATAGAGTCT
*
1097847 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTC-TC-TCTAGATGAGTTCTTC
1 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC-AGATGAGTTCTTC
* * *
1097910 TCATTATGAACTCTACCTGGCAATGTTGATCCATCGAATGATGAATTTG
65 TCATTATGAACCCTACCTGGCAATGCTGATCCATCGAATGATGAATTCG
* *
1097959 AGCAAAAGGTTGAACACGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * *
1098024 CATTATAAACCCTACCTGGTAATGATGATCCATCGAATGATGAATTCG
66 CATTATGAACCCTACCTGGCAATGCTGATCCATCGAATGATGAATTCG
1098072 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* *
1098137 TATTATGAACCCTACCTGGCAATGTTGATCCATCGAATGATGAATTCG
66 CATTATGAACCCTACCTGGCAATGCTGATCCATCGAATGATGAATTCG
* *
1098185 AGCAAAATGTTGAACAAGTTCTTCTCATTATTAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1098250 CATTATGAACCCTACCTGGCAATGCTGATCCATCGAATGATGAATTCG
66 CATTATGAACCCTACCTGGCAATGCTGATCCATCGAATGATGAATTCG
* *
1098298 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTTCTCCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * * * *
1098363 CATTATGAACTCTACCTTGAAATGCTGATCCATCGAGTGATGGATTC
66 CATTATGAACCCTACCTGGCAATGCTGATCCATCGAATGATGAATTC
1098410 TAATATTTGC
Statistics
Matches: 422, Mismatches: 27, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
112 42 0.10
113 378 0.90
114 2 0.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.36
Consensus pattern (113 bp):
AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
CATTATGAACCCTACCTGGCAATGCTGATCCATCGAATGATGAATTCG
Found at i:1098802 original size:22 final size:22
Alignment explanation
Indices: 1098775--1098816 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1098765 CATCTTTAAA
1098775 AGAGAATCTATCATATTTGAAG
1 AGAGAATCTATCATATTTGAAG
*
1098797 AGAGAATCTATCATCTTTGA
1 AGAGAATCTATCATATTTGA
1098817 GGAATGTAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (22 bp):
AGAGAATCTATCATATTTGAAG
Found at i:1105985 original size:35 final size:34
Alignment explanation
Indices: 1105916--1105990 Score: 87
Period size: 35 Copynumber: 2.2 Consensus size: 34
1105906 GCAAAGATGC
* * *
1105916 AAATGCAAAAATGAAAATGTAAATACAAACGTAA
1 AAATGTAAAAATCAAAATGCAAATACAAACGTAA
* *
1105950 AAATGTAAAAATACAAAATGCAAATGCAAATGTAA
1 AAATGTAAAAAT-CAAAATGCAAATACAAACGTAA
*
1105985 ATATGT
1 AAATGT
1105991 GAATGTAACA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
34 11 0.32
35 23 0.68
ACGTcount: A:0.59, C:0.08, G:0.12, T:0.21
Consensus pattern (34 bp):
AAATGTAAAAATCAAAATGCAAATACAAACGTAA
Found at i:1106214 original size:43 final size:43
Alignment explanation
Indices: 1106153--1106238 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
1106143 CCGTGCATCA
*
1106153 AACAAAACTTTACATATAGGGGACAACTTTCAGTCCTAACTTC
1 AACAAAACTTTACATATAGGGGACAACTTTCACTCCTAACTTC
* *
1106196 AACAAAACTTTACATATAGGGGATAACTTTCCCTCCTAACTTC
1 AACAAAACTTTACATATAGGGGACAACTTTCACTCCTAACTTC
1106239 TCTAAAGCCA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.29
Consensus pattern (43 bp):
AACAAAACTTTACATATAGGGGACAACTTTCACTCCTAACTTC
Found at i:1108675 original size:2 final size:2
Alignment explanation
Indices: 1108668--1108698 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1108658 AATTTTAAGA
*
1108668 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1108699 AGAAATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1108973 original size:15 final size:16
Alignment explanation
Indices: 1108953--1108985 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1108943 TGATTTTTTT
1108953 TATAAAAGT-AATTTA
1 TATAAAAGTAAATTTA
*
1108968 TATAAAATTAAATTTA
1 TATAAAAGTAAATTTA
1108984 TA
1 TA
1108986 AATAAGATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
TATAAAAGTAAATTTA
Found at i:1109068 original size:14 final size:14
Alignment explanation
Indices: 1109023--1109073 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
1109013 GATATTATTT
*
1109023 ATTATATATATTAA
1 ATTAAATATATTAA
* *
1109037 ATAATAATA-ATAATA
1 ATTA-AATATATTA-A
1109052 ATTAAATATATTAA
1 ATTAAATATATTAA
1109066 ATTAAATA
1 ATTAAATA
1109074 ATAACAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
14 19 0.66
15 10 0.34
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATTAAATATATTAA
Found at i:1109096 original size:37 final size:34
Alignment explanation
Indices: 1109032--1109108 Score: 84
Period size: 37 Copynumber: 2.2 Consensus size: 34
1109022 TATTATATAT
* * *
1109032 ATTAAATAATAATAATAATAATTAAATATATTAA
1 ATTAAATAATAACAATAATAATTAAATAGATAAA
1109066 ATTAAATAATAACAA-AATAATGACTAAAATAGATAAA
1 ATTAAATAATAACAATAATAAT---T-AAATAGATAAA
1109103 ATTAAA
1 ATTAAA
1109109 ACTATTGTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
33 6 0.17
34 14 0.39
36 1 0.03
37 15 0.42
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (34 bp):
ATTAAATAATAACAATAATAATTAAATAGATAAA
Found at i:1109928 original size:22 final size:22
Alignment explanation
Indices: 1109900--1109955 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
1109890 GGTGAAGTTC
1109900 GGTGAGTCACCGAACTTCCAGT
1 GGTGAGTCACCGAACTTCCAGT
1109922 GGTGAGTCACCGAACTTCCAGT
1 GGTGAGTCACCGAACTTCCAGT
*
1109944 GGTGACTCACCG
1 GGTGAGTCACCG
1109956 TTGGGGGCGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.21, C:0.29, G:0.29, T:0.21
Consensus pattern (22 bp):
GGTGAGTCACCGAACTTCCAGT
Found at i:1110289 original size:3 final size:3
Alignment explanation
Indices: 1110281--1110343 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
1110271 GCCTGAAATG
* * * * *
1110281 TAA TAA TAA TAA T-T TAT TAT TAA TAA TAA TCA TGA TAA TAA TTAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
1110326 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
1110344 ACAAATAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
2 1 0.02
3 49 0.92
4 3 0.06
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:1110327 original size:22 final size:22
Alignment explanation
Indices: 1110281--1110343 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
1110271 GCCTGAAATG
* *
1110281 TAATAATAATAATTTATTATTAA
1 TAATAATAATAA-TAATAATTAA
* *
1110304 TAATAATCATGATAATAATTAA
1 TAATAATAATAATAATAATTAA
1110326 TAATAATAATAATAATAA
1 TAATAATAATAATAATAA
1110344 ACAAATAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
22 24 0.71
23 10 0.29
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
TAATAATAATAATAATAATTAA
Found at i:1112447 original size:30 final size:29
Alignment explanation
Indices: 1112406--1112501 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 29
1112396 ATAGTTATTA
*
1112406 TATTTTATATTAATATAATTATATAAAT-AT
1 TATTTTTTATTAA-ATAATTAT-TAAATAAT
*
1112436 TATTTTTTATTAAAATAA-TATTTATATAAT
1 TATTTTTTATT-AAATAATTA-TTAAATAAT
* * *
1112466 TATTATTTATTGAA-AATTATTAATTAAT
1 TATTTTTTATTAAATAATTATTAAATAAT
1112494 TATTTTTT
1 TATTTTTT
1112502 GTGCTAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
28 16 0.29
29 10 0.18
30 27 0.49
31 2 0.04
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (29 bp):
TATTTTTTATTAAATAATTATTAAATAAT
Found at i:1112470 original size:33 final size:31
Alignment explanation
Indices: 1112381--1112473 Score: 89
Period size: 32 Copynumber: 2.9 Consensus size: 31
1112371 ATTTTTCAGT
* * * *
1112381 TATTATTATTTTTAAATAGTTATTATATTTTA
1 TATTAATATATTTATATAATTATTAT-TTTTA
* *
1112413 TATTAATATAATTATATAAATATTATTTTT-
1 TATTAATATATTTATATAATTATTATTTTTA
1112443 TATTAAAATAATATTTATATAATTATTATTT
1 TATT--AAT-ATATTTATATAATTATTATTT
1112474 ATTGAAAATT
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
30 4 0.08
31 4 0.08
32 23 0.46
33 19 0.38
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (31 bp):
TATTAATATATTTATATAATTATTATTTTTA
Found at i:1114877 original size:34 final size:34
Alignment explanation
Indices: 1114834--1114940 Score: 160
Period size: 34 Copynumber: 3.1 Consensus size: 34
1114824 ATAAATGTTT
*
1114834 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
1 TTAAAATACAAATTATATTATTCGAAATTTAAAA
* *
1114868 TTAAAATACAAATAATATTATTCGAAATTTAAAT
1 TTAAAATACAAATTATATTATTCGAAATTTAAAA
* * *
1114902 TTAAAATATAAATTATATTATTCAAAATTTAACA
1 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1114936 TTAAA
1 TTAAA
1114941 TTCAACTTAA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 65 1.00
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (34 bp):
TTAAAATACAAATTATATTATTCGAAATTTAAAA
Found at i:1114954 original size:34 final size:33
Alignment explanation
Indices: 1114834--1114954 Score: 113
Period size: 34 Copynumber: 3.6 Consensus size: 33
1114824 ATAAATGTTT
* *
1114834 TTAAAATACAAATT-ATAGTATTCGAAATTTAAAA
1 TTAAAATTC-AATTAATATTATTCGAAATTT-AAA
* *
1114868 TTAAAATACAAATAATATTATTCGAAATTTAAA
1 TTAAAATTCAATTAATATTATTCGAAATTTAAA
* *
1114901 TTTAAAATATAAATT-ATATTATTCAAAATTTAACA
1 -TTAAAAT-TCAATTAATATTATTCGAAATTTAA-A
1114936 TT-AAATTCAACTTAATATT
1 TTAAAATTCAA-TTAATATT
1114955 CCAATTGTAT
Statistics
Matches: 74, Mismatches: 7, Indels: 12
0.80 0.08 0.13
Matches are distributed among these distances:
32 3 0.04
33 12 0.16
34 55 0.74
35 4 0.05
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (33 bp):
TTAAAATTCAATTAATATTATTCGAAATTTAAA
Found at i:1115663 original size:127 final size:127
Alignment explanation
Indices: 1115363--1115742 Score: 618
Period size: 127 Copynumber: 3.0 Consensus size: 127
1115353 GTGCTTTAAA
* * * * *
1115363 GTCCCCTAAGAAACAGTAGGTATTGACATGAATAGTTCTCGGGGGACATAAGTGATATAATAGGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGG
* *
1115428 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGC-CCCCCGGGAACGCACCTTCACA
66 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
*
1115489 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGAG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGG
* *
1115554 CAATGATAACATATTCTCTGACAAAATAATAGAAGGCGCGCCCCCGAGAACGCGCCTTCACG
66 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
* * *
1115616 GTCCCCTAAGGAATAATAAGTATTGATATAAATAGTTCCCGGGGGACATAAGTGACATAATAGGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGG
* *
1115681 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGTGCCCCCGGGAATGCGCCTTCACG
66 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
1115743 TGAATAATAC
Statistics
Matches: 235, Mismatches: 18, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
126 97 0.41
127 138 0.59
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.22
Consensus pattern (127 bp):
GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGG
CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
Found at i:1120084 original size:21 final size:21
Alignment explanation
Indices: 1120060--1120123 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
1120050 GCAAATTCGC
1120060 GTTGCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* **
1120081 GTTGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
1120101 TTTTCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
1120122 GT
1 GT
1120124 CTACAGTTGT
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
20 15 0.45
21 18 0.55
ACGTcount: A:0.17, C:0.17, G:0.27, T:0.39
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGATA
Found at i:1120146 original size:41 final size:41
Alignment explanation
Indices: 1120064--1120187 Score: 130
Period size: 41 Copynumber: 3.0 Consensus size: 41
1120054 ATTCGCGTTG
* * *
1120064 CATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTT
1 CATTTCGCGTTGCGATAGTCT-ACAGTTGTCGTTGCGA-TTTT
*
1120105 CATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGTGATTTT
1 CATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTT
* *
1120146 CCAAATT--CGTTGCGATAGTCTACAGTTGTCGTTACGATTTT
1 -C-ATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTT
1120187 C
1 C
1120188 CAAATTCGTT
Statistics
Matches: 72, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
40 1 0.01
41 59 0.82
42 9 0.12
43 3 0.04
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.40
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTT
Found at i:1120177 original size:22 final size:22
Alignment explanation
Indices: 1120112--1120183 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 22
1120102 TTTCATTTCG
1120112 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * * **
1120134 CGTTGTGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
1120153 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
*
1120175 CGTTACGAT
1 CGTTGCGAT
1120184 TTTCCAAATT
Statistics
Matches: 36, Mismatches: 11, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
19 9 0.25
20 5 0.14
21 5 0.14
22 17 0.47
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:1120188 original size:41 final size:41
Alignment explanation
Indices: 1120112--1120201 Score: 162
Period size: 41 Copynumber: 2.2 Consensus size: 41
1120102 TTTCATTTCG
**
1120112 CGTTGCGATAGTCTACAGTTGTCGTTGTGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTACGATTTTCCAAATT
1120153 CGTTGCGATAGTCTACAGTTGTCGTTACGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTACGATTTTCCAAATT
1120194 CGTTGCGA
1 CGTTGCGA
1120202 AAATTCGTTG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTTGTCGTTACGATTTTCCAAATT
Found at i:1120527 original size:6 final size:6
Alignment explanation
Indices: 1120516--1120548 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
1120506 TCTCGTCTCG
*
1120516 GGTCGT GGTCGT GGTCGT GGTCGT TGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1120549 AATACGTGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.15, G:0.48, T:0.36
Consensus pattern (6 bp):
GGTCGT
Found at i:1120667 original size:19 final size:19
Alignment explanation
Indices: 1120643--1120711 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
1120633 CAACGAATTT
1120643 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
* * * **
1120662 TCGCAACAACAACTGTAGACTA
1 TCGCAAC--GAA-TTTGGAAAA
1120684 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
1120703 TCGCAACGA
1 TCGCAACGA
1120712 CAACTGTAGA
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 21 0.57
20 2 0.05
21 2 0.05
22 12 0.32
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.19
Consensus pattern (19 bp):
TCGCAACGAATTTGGAAAA
Found at i:1120688 original size:41 final size:41
Alignment explanation
Indices: 1120643--1120732 Score: 171
Period size: 41 Copynumber: 2.2 Consensus size: 41
1120633 CAACGAATTT
1120643 TCGCAACGAATTTGGAAAATCGCAACAACAACTGTAGACTA
1 TCGCAACGAATTTGGAAAATCGCAACAACAACTGTAGACTA
*
1120684 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTGGAAAATCGCAACAACAACTGTAGACTA
1120725 TCGCAACG
1 TCGCAACG
1120733 TCAAATGGAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (41 bp):
TCGCAACGAATTTGGAAAATCGCAACAACAACTGTAGACTA
Found at i:1120732 original size:22 final size:22
Alignment explanation
Indices: 1120661--1120732 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
1120651 AATTTGGAAA
*
1120661 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
1120683 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
1120702 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
1120724 ATCGCAACG
1 ATCGCAACG
1120733 TCAAATGGAA
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 13 0.34
20 2 0.05
21 2 0.05
22 21 0.55
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:1120766 original size:41 final size:41
Alignment explanation
Indices: 1120721--1120857 Score: 169
Period size: 41 Copynumber: 3.5 Consensus size: 41
1120711 ACAACTGTAG
*
1120721 ACTATCGCAACGTCAAATGGAAAATCGAAACGCGATTTTCA
1 ACTATCGCAACGTCAAATGGAAAATCGCAACGCGATTTTCA
* *
1120762 ACTATCGCAAC-ACGAAATGGAAAAGCGCAACGCGATTTTCA
1 ACTATCGCAACGTC-AAATGGAAAATCGCAACGCGATTTTCA
* *
1120803 ACTATCGCAACG-C-GAT---AAATCGCAACGCGATTTTTA
1 ACTATCGCAACGTCAAATGGAAAATCGCAACGCGATTTTCA
*
1120839 ACTATCGCAACGTGAAATG
1 ACTATCGCAACGTCAAATG
1120858 CAACGCGAAT
Statistics
Matches: 83, Mismatches: 8, Indels: 12
0.81 0.08 0.12
Matches are distributed among these distances:
36 30 0.36
38 2 0.02
39 2 0.02
40 1 0.01
41 48 0.58
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (41 bp):
ACTATCGCAACGTCAAATGGAAAATCGCAACGCGATTTTCA
Found at i:1120768 original size:21 final size:21
Alignment explanation
Indices: 1120744--1120850 Score: 84
Period size: 21 Copynumber: 5.4 Consensus size: 21
1120734 CAAATGGAAA
*
1120744 ATCGAAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
* ** ** *
1120765 ATCGCAACACGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
*
1120785 AGCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
1120806 ATCGCAACGCGA---T-AA--
1 ATCGCAACGCGATTTTCAACT
*
1120821 ATCGCAACGCGATTTTTAACT
1 ATCGCAACGCGATTTTCAACT
1120842 ATCGCAACG
1 ATCGCAACG
1120851 TGAAATGCAA
Statistics
Matches: 64, Mismatches: 15, Indels: 14
0.69 0.16 0.15
Matches are distributed among these distances:
15 12 0.19
17 2 0.03
18 2 0.03
19 2 0.03
20 13 0.20
21 33 0.52
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:1120834 original size:36 final size:34
Alignment explanation
Indices: 1120787--1120865 Score: 115
Period size: 36 Copynumber: 2.3 Consensus size: 34
1120777 AATGGAAAAG
1120787 CGCAACGCGATTTTCAACTATCGCAACGCGATAAAT
1 CGCAACGCGATTTTCAACTATCGCAACGCG--AAAT
* *
1120823 CGCAACGCGATTTTTAACTATCGCAACGTGAAAT
1 CGCAACGCGATTTTCAACTATCGCAACGCGAAAT
1120857 -GCAACGCGA
1 CGCAACGCGA
1120866 ATTTGCGATA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
33 9 0.22
34 4 0.10
36 28 0.68
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.22
Consensus pattern (34 bp):
CGCAACGCGATTTTCAACTATCGCAACGCGAAAT
Found at i:1128206 original size:30 final size:30
Alignment explanation
Indices: 1128148--1128207 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1128138 GAGGTATAAT
*
1128148 AATAATTTTATTAAAATATTTCATATAAAA
1 AATAATTTTATTAAAATATTTAATATAAAA
* *
1128178 AATACATTTT-TTAATATTTTTAATATAAAA
1 AATA-ATTTTATTAAAATATTTAATATAAAA
1128208 TTATTACAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (30 bp):
AATAATTTTATTAAAATATTTAATATAAAA
Found at i:1132508 original size:191 final size:193
Alignment explanation
Indices: 1132094--1132516 Score: 480
Period size: 191 Copynumber: 2.2 Consensus size: 193
1132084 ACACATGGTC
* * ** * * *
1132094 ACCTATTAGTAGTATAAATGACGTTTATACATAACGTCACTTTATAA-TTGATACT-CGATGACA
1 ACCTAATAGTATTATAAATGACACTTATGCATAACGTCATTTTATAACTT-ATATTGC-ATGACA
** *
1132157 ACTAGTTACGTAATTAAATTATATAAAATTTTGTTATTAATAATTCATATAGTCACGAATAATAC
64 GTTAGTTACGTAACTAAATTATATAAAATTTTGTTATTAATAATTCATATAGTCACGAATAATAC
* * * * * * *
1132222 ATTAAAATCAATCTATATGTGACGAAATAAATATTGTCACATTTTCAGTGACGTAATGTAGCGTT
129 AATAAAATCAACCTATATGTGACGAAAGAAATATTGTCAAATTTTCAGTGACATAATATAACGTT
* *
1132287 ACCTAATATTATTATAAATGACACTTATGCATAATGTCATTTTATAACTTATATTGCATGACAGT
1 ACCTAATAGTATTATAAATGACACTTATGCATAACGTCATTTTATAACTTATATTGCATGACAGT
* * * *
1132352 TAGTTACGTCACTAAATTATATAATA-TTT-TTATTAATAATTTATATCA-TCACGAATACTACA
66 TAGTTACGTAACTAAATTATATAAAATTTTGTTATTAATAATTCATAT-AGTCACGAATAATACA
* * * *
1132414 ATAAAATCAACCTATATGTTACGAAAGAGATATTGTCAAATTTTTAGTGACATAATATAATGTT
130 ATAAAATCAACCTATATGTGACGAAAGAAATATTGTCAAATTTTCAGTGACATAATATAACGTT
** * * *
1132478 ATGTAATAGTATTTTGAATGATGA-TTATGCATAACGTCA
1 ACCTAATAGTATTATAAATGA-CACTTATGCATAACGTCA
1132517 ACTTATACAA
Statistics
Matches: 192, Mismatches: 34, Indels: 10
0.81 0.14 0.04
Matches are distributed among these distances:
191 112 0.58
192 5 0.03
193 72 0.38
194 3 0.02
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (193 bp):
ACCTAATAGTATTATAAATGACACTTATGCATAACGTCATTTTATAACTTATATTGCATGACAGT
TAGTTACGTAACTAAATTATATAAAATTTTGTTATTAATAATTCATATAGTCACGAATAATACAA
TAAAATCAACCTATATGTGACGAAAGAAATATTGTCAAATTTTCAGTGACATAATATAACGTT
Found at i:1133006 original size:33 final size:33
Alignment explanation
Indices: 1132961--1133034 Score: 132
Period size: 33 Copynumber: 2.2 Consensus size: 33
1132951 AACAAAGCAG
1132961 ATCTCATA-ATCTCCATTTAAGTTTGACGAAACC
1 ATCTCA-ACATCTCCATTTAAGTTTGACGAAACC
1132994 ATCTCAACATCTCCATTTAAGTTTGACGAAACC
1 ATCTCAACATCTCCATTTAAGTTTGACGAAACC
1133027 ATCTCAAC
1 ATCTCAAC
1133035 TATATAAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
32 1 0.03
33 39 0.98
ACGTcount: A:0.34, C:0.27, G:0.08, T:0.31
Consensus pattern (33 bp):
ATCTCAACATCTCCATTTAAGTTTGACGAAACC
Found at i:1133348 original size:26 final size:26
Alignment explanation
Indices: 1133319--1133394 Score: 129
Period size: 24 Copynumber: 3.0 Consensus size: 26
1133309 ATATAACTCT
1133319 AAAACAAGATTATTTCAAAAGTAAAA
1 AAAACAAGATTATTTCAAAAGTAAAA
*
1133345 AAAACAATATTATTTCAAAAGT--AA
1 AAAACAAGATTATTTCAAAAGTAAAA
1133369 AAAACAAGATTATTTCAAAAGTAAAA
1 AAAACAAGATTATTTCAAAAGTAAAA
1133395 TACATAAAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
24 23 0.50
26 23 0.50
ACGTcount: A:0.61, C:0.08, G:0.07, T:0.25
Consensus pattern (26 bp):
AAAACAAGATTATTTCAAAAGTAAAA
Found at i:1133893 original size:12 final size:12
Alignment explanation
Indices: 1133876--1133914 Score: 71
Period size: 12 Copynumber: 3.3 Consensus size: 12
1133866 AATAAAATAG
1133876 TAAAAAAATTAA
1 TAAAAAAATTAA
1133888 TAAAAAAATTAA
1 TAAAAAAATTAA
1133900 T-AAAAAATTAA
1 TAAAAAAATTAA
1133911 TAAA
1 TAAA
1133915 TTTAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 11 0.42
12 15 0.58
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
TAAAAAAATTAA
Found at i:1136556 original size:56 final size:56
Alignment explanation
Indices: 1136482--1136589 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 56
1136472 CACCTCTGTG
* * * *
1136482 AAAAAAAAAGGATTGAGCATCTCTGTGTTGTAATCAAATATTTGGCACCTCTATTT
1 AAAAAAAAAAGATTGAGCACCTCTGTGCTGTAATCAAATATTTGACACCTCTATTT
** *
1136538 AAAAAAAAAAGATTGAGCACCTCTGTGCTGTAATTGAATGTTTGACACCTCT
1 AAAAAAAAAAGATTGAGCACCTCTGTGCTGTAATCAAATATTTGACACCTCT
1136590 GTGCTTAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
56 45 1.00
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (56 bp):
AAAAAAAAAAGATTGAGCACCTCTGTGCTGTAATCAAATATTTGACACCTCTATTT
Found at i:1136600 original size:56 final size:56
Alignment explanation
Indices: 1136483--1136707 Score: 167
Period size: 54 Copynumber: 4.1 Consensus size: 56
1136473 ACCTCTGTGA
* * * * *
1136483 AAAAAAAAGGATTGAGCATCTCTGTGTTGTAATCAAATATTTGGCACCTCTAT--TT
1 AAAAAAAA-GATTGAGCACCTCTGTGCTGCAATCGAATATTTGACACCTCTATGCTT
* * * *
1136538 AAAAAAAAAAGATTGAGCACCTCTGTGCTGTAATTGAATGTTTGACACCTCTGTGCTT
1 --AAAAAAAAGATTGAGCACCTCTGTGCTGCAATCGAATATTTGACACCTCTATGCTT
* * * * * *
1136596 --AAAAAGGATTGAGCACATCTCTGTTGCACTCGAATATCTGACACCTCTATGCTT
1 AAAAAAAAGATTGAGCACCTCTGTGCTGCAATCGAATATTTGACACCTCTATGCTT
* * * * * * * *
1136650 ---AAAAGGATTAAGCACTTTTGTGCTGCAATAGAATATGTGGCACCTCTGTGCTT
1 AAAAAAAAGATTGAGCACCTCTGTGCTGCAATCGAATATTTGACACCTCTATGCTT
1136703 AAAAA
1 AAAAA
1136708 GGGTTGAGTA
Statistics
Matches: 136, Mismatches: 27, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
53 43 0.32
54 44 0.32
56 39 0.29
57 8 0.06
58 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (56 bp):
AAAAAAAAGATTGAGCACCTCTGTGCTGCAATCGAATATTTGACACCTCTATGCTT
Found at i:1136684 original size:53 final size:53
Alignment explanation
Indices: 1136543--1136715 Score: 175
Period size: 54 Copynumber: 3.2 Consensus size: 53
1136533 TATTTAAAAA
* * * * * *
1136543 AAAAAGATTGAGCACCTCTGTGCTGTAATTGAATGTTTGACACCTCTGTGCTT
1 AAAAGGATTGAGCACATCTGTGCTGCAATAGAATATCTGACACCTCTGTGCTT
* * * * *
1136596 AAAAAGGATTGAGCACATCTCTGTTGCACTCGAATATCTGACACCTCTATGCTT
1 -AAAAGGATTGAGCACATCTGTGCTGCAATAGAATATCTGACACCTCTGTGCTT
* * * * *
1136650 AAAAGGATTAAGCACTTTTGTGCTGCAATAGAATATGTGGCACCTCTGTGCTT
1 AAAAGGATTGAGCACATCTGTGCTGCAATAGAATATCTGACACCTCTGTGCTT
*
1136703 AAAAAGGGTTGAG
1 -AAAAGGATTGAG
1136716 TACCTCTATA
Statistics
Matches: 96, Mismatches: 22, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
53 43 0.45
54 53 0.55
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.31
Consensus pattern (53 bp):
AAAAGGATTGAGCACATCTGTGCTGCAATAGAATATCTGACACCTCTGTGCTT
Found at i:1140170 original size:2 final size:2
Alignment explanation
Indices: 1140165--1140261 Score: 97
Period size: 2 Copynumber: 47.0 Consensus size: 2
1140155 TTGAAACAAT
1140165 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
1140207 T- TA TG TA TA AA CTA TA TA GTG TA TA TA TA AA GTG TA TA TA TA
1 TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA
*
1140249 AA CTA TA TA TA TA
1 TA -TA TA TA TA TA
1140262 AATTTTATAG
Statistics
Matches: 78, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
1 1 0.01
2 74 0.95
3 3 0.04
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1140240 original size:13 final size:13
Alignment explanation
Indices: 1140219--1140263 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
1140209 ATGTATAAAC
*
1140219 TATATAGTGTATA
1 TATAAAGTGTATA
1140232 TATAAAGTGTATA
1 TATAAAGTGTATA
* *
1140245 TATAAACTATATA
1 TATAAAGTGTATA
1140258 TATAAA
1 TATAAA
1140264 TTTTATAGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (13 bp):
TATAAAGTGTATA
Found at i:1140249 original size:33 final size:30
Alignment explanation
Indices: 1140165--1140261 Score: 108
Period size: 33 Copynumber: 3.2 Consensus size: 30
1140155 TTGAAACAAT
* *
1140165 TATATATATATATA-TATATATATA-TATA
1 TATATATATATAAATTATATATAAACTATA
* *
1140193 TATATATATATATATTATGTATAAACTATA
1 TATATATATATAAATTATATATAAACTATA
*
1140223 TAGTGTATATATAAAGTGTATATATAAACTATA
1 TA-TATATATATAAA-T-TATATATAAACTATA
1140256 TATATA
1 TATATA
1140262 AATTTTATAG
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
28 14 0.24
29 8 0.14
30 6 0.10
31 10 0.17
32 4 0.07
33 16 0.28
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.45
Consensus pattern (30 bp):
TATATATATATAAATTATATATAAACTATA
Found at i:1140270 original size:13 final size:13
Alignment explanation
Indices: 1140165--1140263 Score: 60
Period size: 13 Copynumber: 7.8 Consensus size: 13
1140155 TTGAAACAAT
*
1140165 TATATATATA-TA
1 TATATATAAACTA
*
1140177 TATATATATA-TA
1 TATATATAAACTA
*
1140189 TATATATATA-TA
1 TATATATAAACTA
* **
1140201 TATATATTATGTA
1 TATATATAAACTA
* * * *
1140214 TAAACTATATAGTG
1 TATA-TATAAACTA
* *
1140228 TATATATAAAGTG
1 TATATATAAACTA
1140241 TATATATAAACTA
1 TATATATAAACTA
1140254 TATATATAAA
1 TATATATAAA
1140264 TTTTATAGTT
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
12 31 0.42
13 34 0.47
14 8 0.11
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.44
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:1140278 original size:33 final size:33
Alignment explanation
Indices: 1140165--1140278 Score: 98
Period size: 33 Copynumber: 3.6 Consensus size: 33
1140155 TTGAAACAAT
* *
1140165 TATATA-TATATA-TATATATATATA-TATATA
1 TATATATTATATAGTTTATATATAAACTATATA
*
1140195 TATATA-TATATA--TTATGTATAAACTATATA
1 TATATATTATATAGTTTATATATAAACTATATA
* * *
1140225 GTGTATA-TATAAAGTGTATATATAAACTATATA
1 -TATATATTATATAGTTTATATATAAACTATATA
* *
1140258 TATAAATTTTATAGTTTATAT
1 TATATATTATATAGTTTATAT
1140279 TTATATTATT
Statistics
Matches: 67, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
29 8 0.12
30 18 0.27
31 10 0.15
32 4 0.06
33 27 0.40
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (33 bp):
TATATATTATATAGTTTATATATAAACTATATA
Found at i:1140352 original size:11 final size:11
Alignment explanation
Indices: 1140338--1140413 Score: 52
Period size: 11 Copynumber: 7.3 Consensus size: 11
1140328 TATACAGTTA
1140338 ATATATAAATT
1 ATATATAAATT
* *
1140349 ATATATGAATC
1 ATATATAAATT
*
1140360 ATATTTAAA-T
1 ATATATAAATT
* *
1140370 ATATACAACTT
1 ATATATAAATT
* *
1140381 ATATTTATA-T
1 ATATATAAATT
*
1140391 AT-TATATATT
1 ATATATAAATT
1140401 ATATAT-AATT
1 ATATATAAATT
1140411 ATA
1 ATA
1140414 AATTATATAT
Statistics
Matches: 48, Mismatches: 14, Indels: 7
0.70 0.20 0.10
Matches are distributed among these distances:
9 5 0.10
10 18 0.38
11 25 0.52
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (11 bp):
ATATATAAATT
Found at i:1140405 original size:22 final size:22
Alignment explanation
Indices: 1140381--1140423 Score: 52
Period size: 24 Copynumber: 1.9 Consensus size: 22
1140371 TATACAACTT
*
1140381 ATAT-TTATATATTATATATTAT
1 ATATATTATAAATTATATATT-T
1140403 ATATAATTATAAATTATATAT
1 ATAT-ATTATAAATTATATAT
1140424 ACTATGTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 4 0.22
24 14 0.78
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATATATTATAAATTATATATTT
Found at i:1140435 original size:20 final size:19
Alignment explanation
Indices: 1140386--1140502 Score: 89
Period size: 20 Copynumber: 6.1 Consensus size: 19
1140376 AACTTATATT
*
1140386 TATATAT-TATATATTATA
1 TATATATGTATAAATTATA
1140404 TATA-AT-TATAAATTATA
1 TATATATGTATAAATTATA
*
1140421 TATACTATGTATAAATTGTA
1 TATA-TATGTATAAATTATA
* * * *
1140441 TTGTTTATTAATATAAACTATA
1 -TATATA-T-GTATAAATTATA
**
1140463 TATA-AACTATAAATTATA
1 TATATATGTATAAATTATA
1140481 TATACTATGTATAAATTATA
1 TATA-TATGTATAAATTATA
1140501 TA
1 TA
1140503 ATTTATATAG
Statistics
Matches: 77, Mismatches: 14, Indels: 14
0.73 0.13 0.13
Matches are distributed among these distances:
17 16 0.21
18 18 0.23
19 2 0.03
20 27 0.35
21 5 0.06
22 9 0.12
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.47
Consensus pattern (19 bp):
TATATATGTATAAATTATA
Found at i:1140481 original size:27 final size:29
Alignment explanation
Indices: 1140451--1140511 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 29
1140441 TTGTTTATTA
1140451 ATATAAACTATATATAAACTATA-AA-TT
1 ATATAAACTATATATAAACTATATAATTT
* * *
1140478 ATATATACTATGTATAAATTATATAATTT
1 ATATAAACTATATATAAACTATATAATTT
1140507 ATATA
1 ATATA
1140512 GTTTAAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 20 0.69
28 2 0.07
29 7 0.24
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (29 bp):
ATATAAACTATATATAAACTATATAATTT
Found at i:1140530 original size:9 final size:9
Alignment explanation
Indices: 1140518--1140548 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
1140508 TATAGTTTAA
1140518 ATATAAAGT
1 ATATAAAGT
1140527 ATATAAAGT
1 ATATAAAGT
1140536 ATAT-AAGT
1 ATATAAAGT
1140544 ATATA
1 ATATA
1140549 TTAAATTGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (9 bp):
ATATAAAGT
Found at i:1140545 original size:17 final size:15
Alignment explanation
Indices: 1140515--1140548 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
1140505 TTATATAGTT
1140515 TAAATATAAAGTATA
1 TAAATATAAAGTATA
1140530 TAAAGTATATAAGTATA
1 TAAA-TATA-AAGTATA
1140547 TA
1 TA
1140549 TTAAATTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 4 0.24
17 9 0.53
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (15 bp):
TAAATATAAAGTATA
Found at i:1140623 original size:13 final size:13
Alignment explanation
Indices: 1140607--1140726 Score: 88
Period size: 13 Copynumber: 9.2 Consensus size: 13
1140597 AATATAAGTT
1140607 TATATATAAACTA
1 TATATATAAACTA
1140620 TATATATAAACTA
1 TATATATAAACTA
*
1140633 TATTTATATAA-TA
1 TATATATA-AACTA
*
1140646 AACTATAT-AA-T-
1 TA-TATATAAACTA
*
1140657 TAT-TATAAGCTA
1 TATATATAAACTA
*
1140669 TATATATAAATTA
1 TATATATAAACTA
* *
1140682 TGTTTATATGAACTA
1 --TATATATAAACTA
*
1140697 TATAGATAAACTA
1 TATATATAAACTA
1140710 TATATGTATAAACTA
1 TATA--TATAAACTA
1140725 TA
1 TA
1140727 GAAAGTATAT
Statistics
Matches: 83, Mismatches: 14, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
9 3 0.04
10 2 0.02
11 2 0.02
12 6 0.07
13 44 0.53
14 6 0.07
15 20 0.24
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:1140625 original size:15 final size:15
Alignment explanation
Indices: 1140607--1140726 Score: 81
Period size: 15 Copynumber: 8.0 Consensus size: 15
1140597 AATATAAGTT
1140607 TATATATAAAC--TA
1 TATATATAAACTATA
1140620 TATATATAAACTATA
1 TATATATAAACTATA
1140635 TTTATATAATAAACTATA
1 --TATAT-ATAAACTATA
*
1140653 TAATTATTATAAGC--TA
1 T-A-TA-TATAAACTATA
* *
1140669 TATATATAAATTATG
1 TATATATAAACTATA
* *
1140684 TTTATATGAAC--TA
1 TATATATAAACTATA
*
1140697 TATAGATAAACTATA
1 TATATATAAACTATA
*
1140712 TATGTATAAACTATA
1 TATATATAAACTATA
1140727 GAAAGTATAT
Statistics
Matches: 82, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
13 25 0.30
14 2 0.02
15 27 0.33
16 4 0.05
17 6 0.07
18 17 0.21
19 1 0.01
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (15 bp):
TATATATAAACTATA
Found at i:1140664 original size:18 final size:18
Alignment explanation
Indices: 1140620--1140673 Score: 67
Period size: 18 Copynumber: 3.0 Consensus size: 18
1140610 ATATAAACTA
1140620 TATATATAAACTATAT-T
1 TATATATAAACTATATAT
1140637 TATATAATAAACTATATAAT
1 TATAT-ATAAACTATAT-AT
*
1140657 TAT-TATAAGCTATATAT
1 TATATATAAACTATATAT
1140674 ATAAATTATG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
17 7 0.21
18 21 0.64
19 1 0.03
20 4 0.12
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (18 bp):
TATATATAAACTATATAT
Found at i:1140723 original size:28 final size:26
Alignment explanation
Indices: 1140637--1140726 Score: 74
Period size: 28 Copynumber: 3.2 Consensus size: 26
1140627 AAACTATATT
1140637 TATATAATAAACTATATAATTATTATAAGC
1 TATATAATAAACTATAT-ATTA-TA-AA-C
* *
1140667 TATATATATAAATTATGT-TTATATGAAC
1 TATATA-ATAAACTATATATTATA--AAC
1140695 TATATAGATAAACTATATATGTATAAAC
1 TATATA-ATAAACTATATAT-TATAAAC
1140723 TATA
1 TATA
1140727 GAAAGTATAT
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
28 25 0.50
29 6 0.12
30 10 0.20
31 9 0.18
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.41
Consensus pattern (26 bp):
TATATAATAAACTATATATTATAAAC
Found at i:1140767 original size:40 final size:39
Alignment explanation
Indices: 1140723--1140863 Score: 104
Period size: 40 Copynumber: 3.3 Consensus size: 39
1140713 ATGTATAAAC
1140723 TATAGAAAGTATATAGTTTATAAAATATAATTTATATTTA
1 TATAGAAA-TATATAGTTTATAAAATATAATTTATATTTA
* * **
1140763 TATAGTGTATATATATATGTGTGTATATAAACTATATATGTATAAACTA
1 TATA--G-AAATATATA-GT-T-TATA-AAA-TATA-ATTTAT-ATTTA
* *
1140812 TATA-AAATATATAGTTTATAAATTATAATTTATATTAA
1 TATAGAAATATATAGTTTATAAAATATAATTTATATTTA
*
1140850 TATAGTATATATAT
1 TATAG-AAATATAT
1140864 GTATGTATAA
Statistics
Matches: 78, Mismatches: 11, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
38 6 0.08
39 5 0.06
40 15 0.19
41 2 0.03
42 11 0.14
43 5 0.06
44 3 0.04
45 12 0.15
46 3 0.04
47 4 0.05
48 5 0.06
49 7 0.09
ACGTcount: A:0.45, C:0.01, G:0.08, T:0.45
Consensus pattern (39 bp):
TATAGAAATATATAGTTTATAAAATATAATTTATATTTA
Found at i:1140775 original size:2 final size:2
Alignment explanation
Indices: 1140755--1140925 Score: 65
Period size: 2 Copynumber: 87.0 Consensus size: 2
1140745 AAATATAATT
* * * * * *
1140755 TA TA TT TA TA TA GTG TA TA TA TA TA TG TG TG TA TA TA AA CTA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * * *
1140799 TA TG TA TA AA CTA TA TA -A AA TA TA TA GTT TA TA AA T- TA TA -A
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * *
1140840 TT TA TA T- TA -A TA TA GTA TA TA TA TG TA TG TA TA -A CTA -A TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA
* *
1140880 TA -A GTA -A TC TA TA GA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1140920 TA TA TA
1 TA TA TA
1140926 GTTTATAGAA
Statistics
Matches: 126, Mismatches: 26, Indels: 34
0.68 0.14 0.18
Matches are distributed among these distances:
1 10 0.08
2 108 0.86
3 8 0.06
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1140806 original size:87 final size:87
Alignment explanation
Indices: 1140702--1140869 Score: 282
Period size: 87 Copynumber: 1.9 Consensus size: 87
1140692 AACTATATAG
* *
1140702 ATAAACTATATATGTATAAACTATAGAAAGTATATAGTTTATAAAATATAATTTATATTTATATA
1 ATAAACTATATATGTATAAACTATAGAAAATATATAGTTTATAAAATATAATTTATATTAATATA
*
1140767 GTGTATATATATATGTGTGTAT
66 GTATATATATATATGTGTGTAT
* *
1140789 ATAAACTATATATGTATAAACTATATAAAATATATAGTTTATAAATTATAATTTATATTAATATA
1 ATAAACTATATATGTATAAACTATAGAAAATATATAGTTTATAAAATATAATTTATATTAATATA
*
1140854 GTATATATATGTATGT
66 GTATATATATATATGT
1140870 ATAACTAATA
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 75 1.00
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.44
Consensus pattern (87 bp):
ATAAACTATATATGTATAAACTATAGAAAATATATAGTTTATAAAATATAATTTATATTAATATA
GTATATATATATATGTGTGTAT
Found at i:1140992 original size:7 final size:7
Alignment explanation
Indices: 1140982--1141027 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
1140972 TATTTTATAA
1140982 AAACCCT
1 AAACCCT
1140989 AAACCCT
1 AAACCCT
1140996 AAACCCT
1 AAACCCT
*
1141003 AAACCAT
1 AAACCCT
* *
1141010 AAGCCAT
1 AAACCCT
*
1141017 AAGCCCT
1 AAACCCT
1141024 AAAC
1 AAAC
1141028 ACTATGCATA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.46, C:0.37, G:0.04, T:0.13
Consensus pattern (7 bp):
AAACCCT
Found at i:1141132 original size:57 final size:58
Alignment explanation
Indices: 1141060--1141213 Score: 181
Period size: 55 Copynumber: 2.7 Consensus size: 58
1141050 TATATGTAAC
* *
1141060 CTATAGTATATGTATACATGTAAACTATATATGTAACTTATAATACATGTATGTATA-AAT
1 CTAT-GTATATGTAT--ATATAAACTATATATGTAACTTATAATACATGTATATATACAAT
* * * *
1141120 -TATGTATA-GTATATATAAGCTATATATATAACTTATAGTATATGTATATATACAAT
1 CTATGTATATGTATATATAAACTATATATGTAACTTATAATACATGTATATATACAAT
* *
1141176 CTATTTATATGT-TATATAAACTATATATGTAACCTATA
1 CTATGTATATGTATATATAAACTATATATGTAACTTATA
1141214 GTTTATAAAC
Statistics
Matches: 81, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
55 34 0.42
56 3 0.04
57 34 0.42
58 7 0.09
59 3 0.04
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (58 bp):
CTATGTATATGTATATATAAACTATATATGTAACTTATAATACATGTATATATACAAT
Found at i:1141234 original size:21 final size:20
Alignment explanation
Indices: 1141210--1141300 Score: 67
Period size: 21 Copynumber: 4.3 Consensus size: 20
1141200 ATATGTAACC
1141210 TATAGTTTATAAACAATAGTT
1 TATA-TTTATAAACAATAGTT
**
1141231 TATA-TTAGTGTACTATATAGTT
1 TATATTTA-TAAAC-A-ATAGTT
* * *
1141253 TATACTTTATAACCTATAGTA
1 TATA-TTTATAAACAATAGTT
*
1141274 TATAATTTATAAACTATAGTT
1 TAT-ATTTATAAACAATAGTT
1141295 TATATT
1 TATATT
1141301 AATGTAGTAT
Statistics
Matches: 55, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
19 3 0.05
20 6 0.11
21 30 0.55
22 11 0.20
23 2 0.04
24 3 0.05
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.47
Consensus pattern (20 bp):
TATATTTATAAACAATAGTT
Found at i:1141267 original size:57 final size:58
Alignment explanation
Indices: 1141205--1141320 Score: 144
Period size: 64 Copynumber: 1.9 Consensus size: 58
1141195 ACTATATATG
*
1141205 TAACCTATAG-TTTATAAACAATAGTTTATATTAGTGTACTATATAGTTTATACTTTA
1 TAACCTATAGATTTATAAACAATAGTTTATATTAATGTACTATATAGTTTATACTTTA
* *
1141262 TAACCTATAGTATATAATTTATAAACTATAGTTTATATTAATGTAGTATATAGTTTATA
1 TAACCTATAG------ATTTATAAACAATAGTTTATATTAATGTACTATATAGTTTATA
1141321 TTAATGTTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
57 10 0.20
64 39 0.80
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.46
Consensus pattern (58 bp):
TAACCTATAGATTTATAAACAATAGTTTATATTAATGTACTATATAGTTTATACTTTA
Found at i:1141481 original size:31 final size:31
Alignment explanation
Indices: 1141432--1141492 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
1141422 TACTATATAA
1141432 TTTATAACATATAGTTTATATTAATATTAAC
1 TTTATAACATATAGTTTATATTAATATTAAC
*
1141463 TTTATAGAC-TATATTTTATATTAATATTAA
1 TTTATA-ACATATAGTTTATATTAATATTAA
1141493 TTACAAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 26 0.93
32 2 0.07
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (31 bp):
TTTATAACATATAGTTTATATTAATATTAAC
Found at i:1141549 original size:21 final size:20
Alignment explanation
Indices: 1141509--1141549 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1141499 ATTATAAAAT
* *
1141509 ATATTATTATAATTATTTTA
1 ATATTATTATAAATAGTTTA
1141529 ATATTAATTATAAATAGTTTA
1 ATATT-ATTATAAATAGTTTA
1141550 TTAATGTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
ATATTATTATAAATAGTTTA
Found at i:1144377 original size:23 final size:23
Alignment explanation
Indices: 1144343--1144403 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
1144333 TGCTTTCTTA
1144343 ATGCAA-GATGCTTGCAGAATTG
1 ATGCAATGATGCTTGCAGAATTG
*
1144365 ATGCAATGATGCTTGCTGAATTG
1 ATGCAATGATGCTTGCAGAATTG
* * *
1144388 GTACATTGATGCTTGC
1 ATGCAATGATGCTTGC
1144404 CGGTTGGTGC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 6 0.18
23 28 0.82
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (23 bp):
ATGCAATGATGCTTGCAGAATTG
Found at i:1144997 original size:13 final size:13
Alignment explanation
Indices: 1144978--1145015 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
1144968 TAATTTAGTG
1144978 ATTATAAATAA-A
1 ATTATAAATAAGA
1144990 ATTTATAATATAAGA
1 A-TTATAA-ATAAGA
1145005 ATTATAAATAA
1 ATTATAAATAA
1145016 TATAAAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (13 bp):
ATTATAAATAAGA
Found at i:1145053 original size:70 final size:70
Alignment explanation
Indices: 1144979--1145121 Score: 222
Period size: 70 Copynumber: 2.0 Consensus size: 70
1144969 AATTTAGTGA
1144979 TTATAA-ATA-AAATTTATAATATAAGAATTATAAATAATATAAAGAATT-TGAATTAATAT-AA
1 TTATAATATACAAA-TTATAATATAAGAATTATAAA-AATATAAAGAATTGT-AATTAATATAAA
1145040 AAATCAAAT
63 AAAT-AAAT
1145049 TTATAATATACAAATTATAATATAAGAATTATAAAAATATAAAGAATTGTAATTAATATAAAAAA
1 TTATAATATACAAATTATAATATAAGAATTATAAAAATATAAAGAATTGTAATTAATATAAAAAA
1145114 TAAAT
66 TAAAT
1145119 TTA
1 TTA
1145122 ATTATCATAA
Statistics
Matches: 69, Mismatches: 0, Indels: 8
0.90 0.00 0.10
Matches are distributed among these distances:
70 35 0.51
71 31 0.45
72 3 0.04
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (70 bp):
TTATAATATACAAATTATAATATAAGAATTATAAAAATATAAAGAATTGTAATTAATATAAAAAA
TAAAT
Found at i:1145068 original size:14 final size:14
Alignment explanation
Indices: 1145044--1145082 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
1145034 ATATAAAAAT
1145044 CAAATTTATAATATA
1 CAAA-TTATAATATA
1145059 CAAATTATAATATA
1 CAAATTATAATATA
1145073 -AGAATTATAA
1 CA-AATTATAA
1145083 AAATATAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.04
14 18 0.78
15 4 0.17
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (14 bp):
CAAATTATAATATA
Found at i:1145165 original size:27 final size:26
Alignment explanation
Indices: 1145113--1145166 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
1145103 AATATAAAAA
* *
1145113 ATAAATTTAATTATCATAAGTTTATT
1 ATAAATTTAAATAACATAAGTTTATT
1145139 ATAAATTTAAAATAACATAA-TTATATT
1 ATAAATTT-AAATAACATAAGTT-TATT
1145166 A
1 A
1145167 ATTGTAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 10 0.42
27 14 0.58
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (26 bp):
ATAAATTTAAATAACATAAGTTTATT
Found at i:1145356 original size:26 final size:26
Alignment explanation
Indices: 1145320--1145382 Score: 126
Period size: 26 Copynumber: 2.4 Consensus size: 26
1145310 TAAATCTCGG
1145320 GTTCGGGTTCATATCATTCGGATGCA
1 GTTCGGGTTCATATCATTCGGATGCA
1145346 GTTCGGGTTCATATCATTCGGATGCA
1 GTTCGGGTTCATATCATTCGGATGCA
1145372 GTTCGGGTTCA
1 GTTCGGGTTCA
1145383 GGTATCATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.17, C:0.19, G:0.29, T:0.35
Consensus pattern (26 bp):
GTTCGGGTTCATATCATTCGGATGCA
Found at i:1148597 original size:20 final size:20
Alignment explanation
Indices: 1148567--1148614 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1148557 AATAATTTTC
*
1148567 TTTTG-AAAGCAAAATTG-GA
1 TTTTGAAAAGCAAAA-TGAAA
1148586 TTTTGAAAAGCAAAATGAAA
1 TTTTGAAAAGCAAAATGAAA
1148606 TTTTGAAAA
1 TTTTGAAAA
1148615 ATGATTTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.48, C:0.04, G:0.17, T:0.31
Consensus pattern (20 bp):
TTTTGAAAAGCAAAATGAAA
Found at i:1165191 original size:26 final size:26
Alignment explanation
Indices: 1165155--1165222 Score: 127
Period size: 26 Copynumber: 2.6 Consensus size: 26
1165145 CTACAATGAG
*
1165155 TGACATTCATTGAAATGCACCACTAA
1 TGACATGCATTGAAATGCACCACTAA
1165181 TGACATGCATTGAAATGCACCACTAA
1 TGACATGCATTGAAATGCACCACTAA
1165207 TGACATGCATTGAAAT
1 TGACATGCATTGAAAT
1165223 TATAAAATAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (26 bp):
TGACATGCATTGAAATGCACCACTAA
Done.