Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008755.1 Hibiscus syriacus cultivar Beakdansim tig00111847_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: 3030620
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 14
Found at i:2561552 original size:18 final size:17
Alignment explanation
Indices: 2561453--2561555 Score: 72
Period size: 18 Copynumber: 6.1 Consensus size: 17
2561443 TGAACTATAT
*
2561453 ATATAAACTATATA-T-
1 ATATAAAATATATATTA
* **
2561468 ATATAAAGTATATGGTA
1 ATATAAAATATATATTA
* *
2561485 TATATAAACTATATAGTA
1 -ATATAAAATATATATTA
2561503 TATATAAAATATATATT-
1 -ATATAAAATATATATTA
*
2561520 ATATATTAAT-T-TATTA
1 ATATA-AAATATATATTA
2561536 ATATAAACATATATATTA
1 ATATAAA-ATATATATTA
2561554 AT
1 AT
2561556 TGAAAGATTT
Statistics
Matches: 72, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
15 17 0.24
16 14 0.19
17 4 0.06
18 37 0.51
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (17 bp):
ATATAAAATATATATTA
Found at i:2561724 original size:61 final size:61
Alignment explanation
Indices: 2561584--2561724 Score: 196
Period size: 61 Copynumber: 2.3 Consensus size: 61
2561574 TATAAGGATC
* *
2561584 AAATTGAACAAATTTTTAATATGAAGCTTAAATTAATAAATTGCAACATTAAATTTGGTCT
1 AAATTGAACAAATTTTAAATATGAAGCTTAAATTAATAAATTGCAACATTAAATTTGGACT
* * * *
2561645 AAATTGAACCAATTTTAAATATGAAGCTTAAATTAAATACATTGTATCATTAAATTTGGACT
1 AAATTGAACAAATTTTAAATATGAAGCTTAAATT-AATAAATTGCAACATTAAATTTGGACT
2561707 AAATT-AA-AAATATTTAAA
1 AAATTGAACAAAT-TTTAAA
2561725 ACTAGAAGAG
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
60 3 0.04
61 40 0.56
62 28 0.39
ACGTcount: A:0.47, C:0.08, G:0.09, T:0.37
Consensus pattern (61 bp):
AAATTGAACAAATTTTAAATATGAAGCTTAAATTAATAAATTGCAACATTAAATTTGGACT
Found at i:2562087 original size:102 final size:101
Alignment explanation
Indices: 2561942--2562124 Score: 269
Period size: 102 Copynumber: 1.8 Consensus size: 101
2561932 AAAACCCTCC
* * *
2561942 TTTGATATTCACAAACACCAAAACCCAAACCATTTCGTGTTTTTTTGTATCAAACACCCAAAAAT
1 TTTGATATTCACAAACACCAAAACCCAAACCATTTCCTATTTTTTCG-ATCAAACACCCAAAAAT
*
2562007 TCAACCCTTGTTAATCCAGTTCTTCTCCAAACCATTA
65 TAAACCCTTGTTAATCCAGTTCTTCTCCAAACCATTA
* *
2562044 TTTGATCTTCACAAACACCAAAACCTAAACTCA-TTCCTATTTTTTCGATCAAACACCCAAAAAT
1 TTTGATATTCACAAACACCAAAACCCAAAC-CATTTCCTATTTTTTCGATCAAACACCCAAAAAT
* *
2562108 TAAACTCTTGTTCATCC
65 TAAACCCTTGTTAATCC
2562125 TTGTTCATCC
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
101 31 0.43
102 39 0.54
103 2 0.03
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.32
Consensus pattern (101 bp):
TTTGATATTCACAAACACCAAAACCCAAACCATTTCCTATTTTTTCGATCAAACACCCAAAAATT
AAACCCTTGTTAATCCAGTTCTTCTCCAAACCATTA
Found at i:2562399 original size:18 final size:18
Alignment explanation
Indices: 2562334--2562409 Score: 91
Period size: 18 Copynumber: 4.3 Consensus size: 18
2562324 CCTAAACCCT
* *
2562334 AACCCTAACCCAAATCCA
1 AACCCGAACCCGAATCCA
* * *
2562352 AACCCAAATCTGAATCCA
1 AACCCGAACCCGAATCCA
2562370 AACCCGAACCCGAATCCA
1 AACCCGAACCCGAATCCA
*
2562388 AACCCGAACCCG-ATTCA
1 AACCCGAACCCGAATCCA
2562405 AACCC
1 AACCC
2562410 AAAACCAAAC
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
17 9 0.18
18 41 0.82
ACGTcount: A:0.41, C:0.42, G:0.07, T:0.11
Consensus pattern (18 bp):
AACCCGAACCCGAATCCA
Found at i:2562412 original size:6 final size:6
Alignment explanation
Indices: 2562316--2562398 Score: 58
Period size: 6 Copynumber: 13.8 Consensus size: 6
2562306 TCCTAACTTG
* * * * * **
2562316 AACCCA AACCTA AACCCT AACCCT AACCCA AATCCA AACCCA AATCTG
1 AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA
* * * * *
2562364 AATCCA AACCCG AACCCG AATCCA AACCCG AACCC
1 AACCCA AACCCA AACCCA AACCCA AACCCA AACCC
2562399 GATTCAAACC
Statistics
Matches: 60, Mismatches: 17, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 60 1.00
ACGTcount: A:0.42, C:0.43, G:0.05, T:0.10
Consensus pattern (6 bp):
AACCCA
Found at i:2562523 original size:20 final size:21
Alignment explanation
Indices: 2562487--2562529 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
2562477 ATATCCAGGT
*
2562487 TTTTTAATTCTTTTTTTCATA
1 TTTTTAATTCTTTTTTTAATA
2562508 TTTTT-ATT-TTTATTTTAATA
1 TTTTTAATTCTTT-TTTTAATA
2562528 TT
1 TT
2562530 CGAACTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 3 0.15
20 12 0.60
21 5 0.25
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTTAATTCTTTTTTTAATA
Found at i:2563697 original size:6 final size:5
Alignment explanation
Indices: 2563654--2563695 Score: 66
Period size: 5 Copynumber: 8.2 Consensus size: 5
2563644 GTCTCATCTT
*
2563654 GGCTC GGCTC GGCTC GGCTC GACTC GGCTC GGCTC GTGCTC G
1 GGCTC GGCTC GGCTC GGCTC GGCTC GGCTC GGCTC G-GCTC G
2563696 TGGTCGTGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
5 29 0.85
6 5 0.15
ACGTcount: A:0.02, C:0.38, G:0.38, T:0.21
Consensus pattern (5 bp):
GGCTC
Found at i:2563702 original size:6 final size:6
Alignment explanation
Indices: 2563687--2563717 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
2563677 TCGGCTCGGC
*
2563687 TCGTGC TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
2563718 AATACATGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.19, G:0.45, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:2582341 original size:2 final size:2
Alignment explanation
Indices: 2582334--2582383 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
2582324 AATCTGTTAA
2582334 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2582376 AT AT -T AT A
1 AT AT AT AT A
2582384 CTCATTAAGT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2583717 original size:16 final size:17
Alignment explanation
Indices: 2583692--2583725 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2583682 CCAATGTGTC
2583692 ACATTGAC-TTTACAAA
1 ACATTGACTTTTACAAA
*
2583708 ACATTTACTTTTACAAA
1 ACATTGACTTTTACAAA
2583725 A
1 A
2583726 GAATGAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.44, C:0.18, G:0.03, T:0.35
Consensus pattern (17 bp):
ACATTGACTTTTACAAA
Found at i:2584547 original size:21 final size:21
Alignment explanation
Indices: 2584453--2584548 Score: 75
Period size: 21 Copynumber: 4.6 Consensus size: 21
2584443 ACCACTCCTT
* *
2584453 AAGGATCACATATATATTCCA
1 AAGGACCACATATATATCCCA
* * * *
2584474 AATGACCAAATATGTGTCCCA
1 AAGGACCACATATATATCCCA
* * * *
2584495 AAGAACCGCATATATGTTCCA
1 AAGGACCACATATATATCCCA
**
2584516 AAGGATTACATATATATCCCA
1 AAGGACCACATATATATCCCA
*
2584537 CAGGACCACATA
1 AAGGACCACATA
2584549 GAACCCTCGA
Statistics
Matches: 54, Mismatches: 21, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.41, C:0.23, G:0.12, T:0.24
Consensus pattern (21 bp):
AAGGACCACATATATATCCCA
Found at i:2588544 original size:5 final size:5
Alignment explanation
Indices: 2588534--2588563 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
2588524 TCGTAGCCCT
*
2588534 TTCTC TTCTC TTCTC TTCTA TTCTC TTCTC
1 TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC
2588564 ATTTTTCTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.03, C:0.37, G:0.00, T:0.60
Consensus pattern (5 bp):
TTCTC
Found at i:2592824 original size:13 final size:13
Alignment explanation
Indices: 2592808--2592867 Score: 75
Period size: 13 Copynumber: 4.6 Consensus size: 13
2592798 TCAATGAACG
2592808 TCATAAATGTGCA
1 TCATAAATGTGCA
*
2592821 TCATAAATGTGTA
1 TCATAAATGTGCA
* **
2592834 TCATAAATGAGTG
1 TCATAAATGTGCA
*
2592847 TCATAAATGTGCG
1 TCATAAATGTGCA
2592860 TCATAAAT
1 TCATAAAT
2592868 TTATGACGCA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 42 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (13 bp):
TCATAAATGTGCA
Found at i:2593466 original size:37 final size:36
Alignment explanation
Indices: 2593388--2593466 Score: 88
Period size: 37 Copynumber: 2.2 Consensus size: 36
2593378 TCATATATTT
* * *
2593388 TATAGTCACATGGCTTATCTCATAGACATGTATTCA
1 TATAGTCACATAGCTCATCACATAGACATGTATTCA
* *
2593424 CATAGTCACATAGCTCATTCACATATACATGT-TATCA
1 TATAGTCACATAGCTCA-TCACATAGACATGTAT-TCA
2593461 TATAGT
1 TATAGT
2593467 TCATATCCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
36 15 0.43
37 20 0.57
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.35
Consensus pattern (36 bp):
TATAGTCACATAGCTCATCACATAGACATGTATTCA
Found at i:2595336 original size:18 final size:17
Alignment explanation
Indices: 2595315--2595349 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2595305 AAATTTGTTG
2595315 TTTTAATTAAAATTGATA
1 TTTTAATTAAAA-TGATA
*
2595333 TTTTTATTAAAATGATA
1 TTTTAATTAAAATGATA
2595350 AATATGTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (17 bp):
TTTTAATTAAAATGATA
Found at i:2597901 original size:20 final size:20
Alignment explanation
Indices: 2597876--2597956 Score: 90
Period size: 20 Copynumber: 4.0 Consensus size: 20
2597866 CAATAGTTGG
*
2597876 TGCTTGATTCTGCTTGACAT
1 TGCTTGATTCTGCTTGATAT
* * *
2597896 TGCTTGATTATGTTTTATAT
1 TGCTTGATTCTGCTTGATAT
* * *
2597916 TGTTTGCTTCTGTTTGATAT
1 TGCTTGATTCTGCTTGATAT
*
2597936 TGCTTTATTCTGCTTGATAT
1 TGCTTGATTCTGCTTGATAT
2597956 T
1 T
2597957 TGTAAGGGTT
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.15, C:0.12, G:0.17, T:0.56
Consensus pattern (20 bp):
TGCTTGATTCTGCTTGATAT
Found at i:2598077 original size:23 final size:23
Alignment explanation
Indices: 2598043--2598103 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
2598033 TACTTTCTGA
2598043 ATGCAA-GATGCTTGCTAAATTG
1 ATGCAATGATGCTTGCTAAATTG
*
2598065 ATGCAATGATGCTTACTAAATTG
1 ATGCAATGATGCTTGCTAAATTG
* *
2598088 ATACAGTGATGCTTGC
1 ATGCAATGATGCTTGC
2598104 CGGTTGCTAC
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:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (23 bp):
ATGCAATGATGCTTGCTAAATTG
Found at i:2599991 original size:44 final size:44
Alignment explanation
Indices: 2599942--2600195 Score: 400
Period size: 44 Copynumber: 5.8 Consensus size: 44
2599932 CGGCTCTAAA
* * * *
2599942 ATAAATGAAAATACATAACGGCGCATTATTGGCATAAATGTGCA
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAATGTGCC
*
2599986 ATAAATGAAAATGCATAACGGTGCATTATTGGTAGAAATGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAATGTGCC
* *
2600030 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGTC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAATGTGCC
* * *
2600074 ATAAATGAAAATGCATAACGGTGTATTATTGACAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAATGTGCC
*
2600118 ATAAATGAAAATGCATAACAGTGCATTATTGGCAGAAATGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAATGTGCC
*
2600162 ATAAATGAAAATGCATAACAGTGCATTATTGGCA
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCA
2600196 TAAAAGGTGT
Statistics
Matches: 195, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 195 1.00
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.26
Consensus pattern (44 bp):
ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAATGTGCC
Found at i:2615757 original size:44 final size:44
Alignment explanation
Indices: 2615708--2615871 Score: 249
Period size: 44 Copynumber: 3.7 Consensus size: 44
2615698 CTGCTCTAAA
* *
2615708 ATAAATGAAAATGCATAACGGTGCATTATTGGAAGAAATATATC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGTAGAAATGTATC
* * * *
2615752 ATAAATGAAAATGTATAATGGTGCATTATTGGTAGAAAGGTGTC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGTAGAAATGTATC
*
2615796 ATAAATGAAAATGCATAATGGTGCATTATTGGTAGAAATGTGA-C
1 ATAAATGAAAATGCATAACGGTGCATTATTGGTAGAAATGT-ATC
2615840 ATAAATGAAAATGCATAACGGTGCATTATTGG
1 ATAAATGAAAATGCATAACGGTGCATTATTGG
2615872 CATAAAAGGT
Statistics
Matches: 109, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
44 109 1.00
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.29
Consensus pattern (44 bp):
ATAAATGAAAATGCATAACGGTGCATTATTGGTAGAAATGTATC
Found at i:2616642 original size:18 final size:18
Alignment explanation
Indices: 2616621--2616682 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
2616611 TAAAATTTAC
*
2616621 AATATAAGAATTATAAAT
1 AATATAAGAATTAGAAAT
* * *
2616639 AATAAAAGAATTGGAATT
1 AATATAAGAATTAGAAAT
* *
2616657 AATATAAAGAATTGGAATT
1 AATAT-AAGAATTAGAAAT
2616676 AATATAA
1 AATATAA
2616683 AAATCAAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
18 20 0.53
19 18 0.47
ACGTcount: A:0.58, C:0.00, G:0.11, T:0.31
Consensus pattern (18 bp):
AATATAAGAATTAGAAAT
Found at i:2616667 original size:19 final size:19
Alignment explanation
Indices: 2616638--2616683 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
2616628 GAATTATAAA
2616638 TAATA-AAAGAATTGGAAT
1 TAATATAAAGAATTGGAAT
2616656 TAATATAAAGAATTGGAAT
1 TAATATAAAGAATTGGAAT
2616675 TAATATAAA
1 TAATATAAA
2616684 AATCAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 5 0.19
19 22 0.81
ACGTcount: A:0.57, C:0.00, G:0.13, T:0.30
Consensus pattern (19 bp):
TAATATAAAGAATTGGAAT
Found at i:2618230 original size:13 final size:13
Alignment explanation
Indices: 2618186--2618230 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
2618176 TACTTTTTAT
2618186 ATTAATTATAATC
1 ATTAATTATAATC
*
2618199 CTTATATTATAAATC
1 ATTA-ATTAT-AATC
2618214 -TTAATTATAATC
1 ATTAATTATAATC
2618226 ATTAA
1 ATTAA
2618231 ATTAATTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
12 4 0.14
13 12 0.43
14 8 0.29
15 4 0.14
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTAATTATAATC
Found at i:2618352 original size:23 final size:24
Alignment explanation
Indices: 2618322--2618371 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
2618312 TTTTTATGTA
2618322 ATAATTAA-TTAATAA-TTT-AAAT
1 ATAATTAACTTAA-AATTTTAAAAT
2618344 ATAATTTAACTTAAAATTTTAAAAT
1 ATAA-TTAACTTAAAATTTTAAAAT
2618369 ATA
1 ATA
2618372 TGTAAAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.17
23 6 0.25
24 7 0.29
25 7 0.29
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
ATAATTAACTTAAAATTTTAAAAT
Found at i:2618442 original size:2 final size:2
Alignment explanation
Indices: 2618435--2618465 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2618425 ACTTTATACT
2618435 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2618466 TCACATGAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2618816 original size:8 final size:8
Alignment explanation
Indices: 2618805--2618847 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
2618795 CGCGCACGCG
2618805 CACGCACA
1 CACGCACA
2618813 CACGCACA
1 CACGCACA
* *
2618821 CACACCCA
1 CACGCACA
*
2618829 CGCGCACA
1 CACGCACA
*
2618837 CACACACA
1 CACGCACA
2618845 CAC
1 CAC
2618848 ACATACATAT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.37, C:0.53, G:0.09, T:0.00
Consensus pattern (8 bp):
CACGCACA
Found at i:2618816 original size:14 final size:14
Alignment explanation
Indices: 2618777--2618843 Score: 71
Period size: 14 Copynumber: 4.8 Consensus size: 14
2618767 ATAATTACTT
*
2618777 CACACACACGCGCG
1 CACACACACACGCG
* * *
2618791 CACGCGCGCACGCG
1 CACACACACACGCG
* *
2618805 CACGCACACACGCA
1 CACACACACACGCG
*
2618819 CACACACCCACGCG
1 CACACACACACGCG
2618833 CACACACACAC
1 CACACACACAC
2618844 ACACACATAC
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 42 1.00
ACGTcount: A:0.30, C:0.52, G:0.18, T:0.00
Consensus pattern (14 bp):
CACACACACACGCG
Found at i:2618972 original size:2 final size:2
Alignment explanation
Indices: 2618854--2618964 Score: 131
Period size: 2 Copynumber: 56.5 Consensus size: 2
2618844 ACACACATAC
2618854 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
2618896 AT AT AT AT AT AT AT -T AT GT AT GT AT AT ACT -T AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
* *
2618937 AT ACT -T AT AC AT A- AT AT AT AT AA AT AT A
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT A
2618965 AGTATATACA
Statistics
Matches: 93, Mismatches: 10, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
1 4 0.04
2 87 0.94
3 2 0.02
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2619020 original size:11 final size:11
Alignment explanation
Indices: 2619004--2619070 Score: 50
Period size: 11 Copynumber: 6.1 Consensus size: 11
2618994 TTAATGTATA
2619004 ATATACATTAT
1 ATATACATTAT
*
2619015 ATATACATGA-
1 ATATACATTAT
*
2619025 AT-TATATTAT
1 ATATACATTAT
2619035 CATA-ACATTCAT
1 -ATATACATT-AT
* *
2619047 CATACATATTAT
1 -ATATACATTAT
2619059 ATATACATTAT
1 ATATACATTAT
2619070 A
1 A
2619071 AATATATGTA
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
9 5 0.11
10 2 0.05
11 25 0.57
12 8 0.18
13 4 0.09
ACGTcount: A:0.45, C:0.12, G:0.01, T:0.42
Consensus pattern (11 bp):
ATATACATTAT
Found at i:2619111 original size:16 final size:13
Alignment explanation
Indices: 2619079--2619117 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 13
2619069 TAAATATATG
2619079 TATACTTATATTA
1 TATACTTATATTA
2619092 TATACTTATATAAGTA
1 TATACTTATAT---TA
2619108 TATACTTATA
1 TATACTTATA
2619118 ATGTATGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 11 0.48
16 12 0.52
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.49
Consensus pattern (13 bp):
TATACTTATATTA
Found at i:2620085 original size:65 final size:64
Alignment explanation
Indices: 2619937--2620096 Score: 173
Period size: 65 Copynumber: 2.5 Consensus size: 64
2619927 TGCACTAAGA
* *
2619937 GTGCATCGATGCATAAAATGCATTCGATG-TTTCAAAATTGCCTAAGTGCATCGATGCATGGCTT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAAAT-CCTAAGTGCATCGATGCATGACTT
* * * * * *
2620001 GTGTATCGATACATCAAATGCATTCGATGTTTTCATAAAAAT-CTGAGTGCATTGATGCAT-ATT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTC--AAAAATCCTAAGTGCATCGATGCATGACT
2620064 AT
64 -T
* *
2620066 GTGCATCGTTGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATAAAATGCATTCGATGTT
2620097 CAATTTATTC
Statistics
Matches: 80, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
64 27 0.34
65 48 0.60
67 5 0.06
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAAATCCTAAGTGCATCGATGCATGACTT
Found at i:2620601 original size:2 final size:2
Alignment explanation
Indices: 2620594--2620631 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2620584 TTATATGTAC
2620594 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2620632 CTTAAACTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2621320 original size:38 final size:39
Alignment explanation
Indices: 2621269--2621345 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
2621259 AGGAGGAGGA
*
2621269 GCACGAGAGGAGCTA-GAGCAGCTCGTGAAGAACTCGCT
1 GCACGAGAAGAGCTAGGAGCAGCTCGTGAAGAACTCGCT
2621307 GCACGAGAAGAGCTAGGAGCAGCTCGTGAAGAACTCGCT
1 GCACGAGAAGAGCTAGGAGCAGCTCGTGAAGAACTCGCT
2621346 CTCGAAGTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 14 0.38
39 23 0.62
ACGTcount: A:0.30, C:0.23, G:0.34, T:0.13
Consensus pattern (39 bp):
GCACGAGAAGAGCTAGGAGCAGCTCGTGAAGAACTCGCT
Found at i:2622903 original size:23 final size:22
Alignment explanation
Indices: 2622876--2622955 Score: 90
Period size: 22 Copynumber: 3.6 Consensus size: 22
2622866 GCATGACCTT
2622876 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
2622898 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
2622920 GTGTATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* *
2622942 ATGTATCGATGCAC
1 GTGCATCGATGCAC
2622956 TGTTAGGTGT
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
21 15 0.31
22 17 0.35
23 16 0.33
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:2622929 original size:44 final size:42
Alignment explanation
Indices: 2622880--2622974 Score: 120
Period size: 44 Copynumber: 2.2 Consensus size: 42
2622870 GACCTTGTGC
* *
2622880 ATCGATGCACATTCAAGGCGTGCATCGGTGCACCT-TCATGGTGT
1 ATCGATGCACATTCAAGG-ATGCATCGATGCA-CTGTCA-GGTGT
* *
2622924 ATCGATGCACATTCAAGGATGTATCGATGCACTGTTAGGTGT
1 ATCGATGCACATTCAAGGATGCATCGATGCACTGTCAGGTGT
2622966 ATCGATGCA
1 ATCGATGCA
2622975 TTAAGCACAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
42 16 0.35
43 12 0.26
44 18 0.39
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.28
Consensus pattern (42 bp):
ATCGATGCACATTCAAGGATGCATCGATGCACTGTCAGGTGT
Found at i:2622968 original size:20 final size:21
Alignment explanation
Indices: 2622880--2622974 Score: 95
Period size: 21 Copynumber: 4.4 Consensus size: 21
2622870 GACCTTGTGC
*
2622880 ATCGATGCACATTCAAGGCGTGC
1 ATCGATGCACATTCAA-G-GTGT
* * *
2622903 ATCGGTGCACCTTCATGGTGT
1 ATCGATGCACATTCAAGGTGT
2622924 ATCGATGCACATTCAAGGATGT
1 ATCGATGCACATTCAAGG-TGT
*
2622946 ATCGATGCAC-TGT-TAGGTGT
1 ATCGATGCACAT-TCAAGGTGT
2622966 ATCGATGCA
1 ATCGATGCA
2622975 TTAAGCACAA
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
20 12 0.19
21 22 0.35
22 15 0.24
23 13 0.21
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.28
Consensus pattern (21 bp):
ATCGATGCACATTCAAGGTGT
Found at i:2628680 original size:21 final size:21
Alignment explanation
Indices: 2628625--2628673 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
2628615 GGGAGCGTCA
2628625 GTGCATCGATGCATACCCAAG
1 GTGCATCGATGCATACCCAAG
2628646 GTGCATCGATGCATACCCAAG
1 GTGCATCGATGCATACCCAAG
2628667 GTGCATC
1 GTGCATC
2628674 AGTGCATCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (21 bp):
GTGCATCGATGCATACCCAAG
Found at i:2628793 original size:27 final size:26
Alignment explanation
Indices: 2628757--2628839 Score: 65
Period size: 27 Copynumber: 3.4 Consensus size: 26
2628747 ATGCATAAAA
2628757 TGCATTCGATGTTTCAAAATAGCATGAG
1 TGCA-TCGATGTTTCAAAATAGC-TGAG
**
2628785 TGCATCGATGCAT-AAAAT-GC--A-
1 TGCATCGATGTTTCAAAATAGCTGAG
2628806 T---TCGATGTTTCAAAATAGCCTGAG
1 TGCATCGATGTTTCAAAATAG-CTGAG
2628830 TGCATCGATG
1 TGCATCGATG
2628840 CATGGCTGGT
Statistics
Matches: 42, Mismatches: 4, Indels: 19
0.65 0.06 0.29
Matches are distributed among these distances:
18 7 0.17
19 5 0.12
20 1 0.02
21 2 0.05
22 1 0.02
23 1 0.02
24 1 0.02
25 2 0.05
26 5 0.12
27 13 0.31
28 4 0.10
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (26 bp):
TGCATCGATGTTTCAAAATAGCTGAG
Found at i:2628801 original size:45 final size:45
Alignment explanation
Indices: 2628737--2628842 Score: 203
Period size: 45 Copynumber: 2.4 Consensus size: 45
2628727 GGTGCACTAA
2628737 GAGTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCAT
1 GAGTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCAT
*
2628782 GAGTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCCT
1 GAGTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCAT
2628827 GAGTGCATCGATGCAT
1 GAGTGCATCGATGCAT
2628843 GGCTGGTGCA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 60 1.00
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (45 bp):
GAGTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCAT
Found at i:2628852 original size:64 final size:63
Alignment explanation
Indices: 2628784--2628973 Score: 217
Period size: 65 Copynumber: 3.0 Consensus size: 63
2628774 AATAGCATGA
2628784 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCCTGAGTGCATCGATGCATGGCT-G
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATA-CCTGAGTGCATCGATGCATGG-TAG
* *
2628848 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ACTCTGAGTGCATCGATGCATAGTA
1 GTGCATCGATGCATAAAATGCATTCGATG-TTTCA-AAATAC-CTGAGTGCATCGATGCATGGTA
*
2628912 T
63 G
* * * *
2628913 GTGCATCGATGCATGAAATGAATTCGATG-TTCAATTTATTCCATG-GTGCATCGATGCATGG
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAA--AATACC-TGAGTGCATCGATGCATGG
2628974 ATTGGTGAAT
Statistics
Matches: 110, Mismatches: 8, Indels: 16
0.82 0.06 0.12
Matches are distributed among these distances:
62 1 0.01
63 4 0.04
64 47 0.43
65 55 0.50
66 3 0.03
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATACCTGAGTGCATCGATGCATGGTAG
Found at i:2628917 original size:65 final size:65
Alignment explanation
Indices: 2628775--2628943 Score: 220
Period size: 65 Copynumber: 2.6 Consensus size: 65
2628765 ATGTTTCAAA
2628775 ATAGCATGAGTGCATCGATGCATAAAATGCATTCGATG-TTTCAAAATAGCCTGAGTGCATCGAT
1 ATAGC-TG-GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCTGAGTGCATCGAT
2628839 GC
64 GC
* *
2628841 ATGGCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-A-CTCTGAGTGCATCGAT
1 ATAGCTGGTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATAGC-CTGAGTGCATCGAT
2628904 GC
64 GC
* * *
2628906 ATAG-TATGTGCATCGATGCATGAAATGAATTCGATGTT
1 ATAGCT-GGTGCATCGATGCATAAAATGCATTCGATGTT
2628944 CAATTTATTC
Statistics
Matches: 93, Mismatches: 6, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
64 30 0.32
65 56 0.60
66 7 0.08
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (65 bp):
ATAGCTGGTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCTGAGTGCATCGATGC
Found at i:2629244 original size:2 final size:2
Alignment explanation
Indices: 2629237--2629261 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2629227 AATGTTTTCA
2629237 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
2629262 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2629266 original size:2 final size:2
Alignment explanation
Indices: 2629261--2629338 Score: 126
Period size: 2 Copynumber: 40.0 Consensus size: 2
2629251 ACACACACAC
2629261 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2629303 AT AT AT AT AT AT AT AT AT -T AT AT CA- AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT
2629339 TTACAATTTT
Statistics
Matches: 72, Mismatches: 0, Indels: 8
0.90 0.00 0.10
Matches are distributed among these distances:
1 3 0.04
2 68 0.94
3 1 0.01
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2629594 original size:53 final size:52
Alignment explanation
Indices: 2629475--2629594 Score: 118
Period size: 53 Copynumber: 2.2 Consensus size: 52
2629465 TGGCCCATAC
* * *
2629475 TTATTTATATTTTTGTAATTATTTTTTATTTGATCCCTCATCCATTTTTATAT
1 TTATTTA-AATTTTATAATTATTTTTGATTTGATCCCTCATCCATTTTTATAT
** * *
2629528 TTATTTCGTATTTTATAATTA-TTTTGATTTGATGCCTCATTCATATTGTT-TAGT
1 TTATTT-AAATTTTATAATTATTTTTGATTTGATCCCTCATCCAT-TT-TTATA-T
2629582 TTATTTAAATTTT
1 TTATTTAAATTTT
2629595 GTTGTAATTT
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
52 20 0.37
53 25 0.46
54 9 0.17
ACGTcount: A:0.23, C:0.09, G:0.07, T:0.61
Consensus pattern (52 bp):
TTATTTAAATTTTATAATTATTTTTGATTTGATCCCTCATCCATTTTTATAT
Found at i:2632323 original size:29 final size:30
Alignment explanation
Indices: 2632262--2632329 Score: 120
Period size: 29 Copynumber: 2.3 Consensus size: 30
2632252 ACTAATTTTC
2632262 AATTATCAAAATTATAATAAAATCAATCGT
1 AATTATCAAAATTATAATAAAATCAATCGT
*
2632292 AATTATCAAAATTATAAT-AAATCTATCGT
1 AATTATCAAAATTATAATAAAATCAATCGT
2632321 AATTATCAA
1 AATTATCAA
2632330 TTAAATTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 19 0.51
30 18 0.49
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.35
Consensus pattern (30 bp):
AATTATCAAAATTATAATAAAATCAATCGT
Found at i:2637599 original size:31 final size:31
Alignment explanation
Indices: 2637470--2637599 Score: 145
Period size: 31 Copynumber: 4.2 Consensus size: 31
2637460 AGAAAAATGG
2637470 TCACTTTCATTTTTATTTAATTAAGATTTGA
1 TCACTTTCATTTTTATTTAATTAAGATTTGA
* * * *
2637501 TAACATTCATATTTATTTCAA-TAAGATTTTA
1 TCACTTTCATTTTTATTT-AATTAAGATTTGA
* * *
2637532 TTACATTCATTTTTAATTTAATTAAGATTTGG
1 TCACTTTCATTTTT-ATTTAATTAAGATTTGA
** *
2637564 TCACTTTTGTTTTTATTTAATTAAGATGTGA
1 TCACTTTCATTTTTATTTAATTAAGATTTGA
2637595 TCACT
1 TCACT
2637600 AAACATTTTA
Statistics
Matches: 82, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
31 58 0.71
32 24 0.29
ACGTcount: A:0.31, C:0.09, G:0.08, T:0.52
Consensus pattern (31 bp):
TCACTTTCATTTTTATTTAATTAAGATTTGA
Found at i:2637987 original size:231 final size:224
Alignment explanation
Indices: 2637599--2638023 Score: 730
Period size: 231 Copynumber: 1.9 Consensus size: 224
2637589 ATGTGATCAC
2637599 TAAACATTTTAAGGATTGCTGACATGACGTTAATATTTGAGTAAATTTTCATTTTGTCCATTGAA
1 TAAACATTTTAAGGATTGCTGACATGACGTTAATATTTGAGTAAATTTTCATTTTGTCCATTGAA
2637664 GTTTCAAAAAAAAAAATTAGTCACTAAAATAGATCTTTGAACAATAATTTTATATCTAATTTATA
66 GTTTCAAAAAAAAAAATTAGTCACTAAAATAGATCTTTGAACAATAATTTTATATCTAATTTATA
2637729 GTAAATTACACCATTCATCACTCAATTCTCTTCTCACA-CTA-TTCAGTCACTAAAGTTTTATTT
131 GTAAATTACACCATTCATCACTCAATTCTCTTCTCACAGCTATTTCAGTCACTAAAG-TTTATTT
2637792 AAGATGTGATCACTAATTGTTAATTATCGT
195 AAGATGTGATCACTAATTGTTAATTATCGT
2637822 TAAACA-TTTAACGGATTGCTGACATGACGTTAATATTTGAGTAAATTTTCATTTTGTCCATTGA
1 TAAACATTTTAA-GGATTGCTGACATGACGTTAATATTTGAGTAAATTTTCATTTTGTCCATTGA
2637886 AGTTTCAAAAAAAAAAAATTAGTCACTAAAACATTATATAGATCTTTGAACAATAATTTTATATC
65 AGTTTC-AAAAAAAAAAATTAGTCACT---A-A--A-ATAGATCTTTGAACAATAATTTTATATC
*
2637951 TAATTTATAGTAAATTACACCATTCATCATTCAATTCTCTTCTCACAGCTATTTCAGTCACTAAA
122 TAATTTATAGTAAATTACACCATTCATCACTCAATTCTCTTCTCACAGCTATTTCAGTCACTAAA
2638016 GTTTATTT
187 GTTTATTT
2638024 TTTTTAATTT
Statistics
Matches: 190, Mismatches: 1, Indels: 13
0.93 0.00 0.06
Matches are distributed among these distances:
222 5 0.03
223 64 0.34
224 20 0.11
227 1 0.01
228 1 0.01
230 1 0.01
231 74 0.39
232 10 0.05
233 14 0.07
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (224 bp):
TAAACATTTTAAGGATTGCTGACATGACGTTAATATTTGAGTAAATTTTCATTTTGTCCATTGAA
GTTTCAAAAAAAAAAATTAGTCACTAAAATAGATCTTTGAACAATAATTTTATATCTAATTTATA
GTAAATTACACCATTCATCACTCAATTCTCTTCTCACAGCTATTTCAGTCACTAAAGTTTATTTA
AGATGTGATCACTAATTGTTAATTATCGT
Found at i:2639165 original size:179 final size:179
Alignment explanation
Indices: 2638923--2639257 Score: 545
Period size: 179 Copynumber: 1.9 Consensus size: 179
2638913 ATTAAATTTT
* *
2638923 AAATATTAAATATATTATATATAACATATGGGTTCAACCCAAATCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAAACCCAATTAATAA
*
2638988 TTTAAGATCCAATAAATTTTAAACTTAAATCAATATTAATTAATT-AAAAA-TTATATAAATTTT
66 TTTAAGATCCAATAAATTTTAAACTTAAATCAA-ATTAATTAATTAAAAAATTTATATAAA-ATT
2639051 TTATTTTATAATTATATATTATTTAAATTATTTGTAAATTGTTTTTTAATTAA
129 TTATTTTATAA-T-TATATTATTTAAATTATTTGTAAATTGTTTTTTAATTAA
2639104 AAATATT-AA-ATATTATATATAACATATGGGCT-AAGCCCAAACCATTTAAAACCCAATTAATA
1 AAATATTAAATATATTATATATAACATATGGGCTCAA-CCCAAACCATTTAAAACCCAATTAATA
* *
2639166 ATTTAAGATCCAATAACTTTTAAACTTAAATCAAATTAATTAATTAAAAAATTTATCTAAAATTT
65 ATTTAAGATCCAATAAATTTTAAACTTAAATCAAATTAATTAATTAAAAAATTTATATAAAATTT
2639231 TATTTTATAATTATATTATTTAAATTA
130 TATTTTATAATTATATTATTTAAATTA
2639258 ATTATAAACT
Statistics
Matches: 146, Mismatches: 5, Indels: 10
0.91 0.03 0.06
Matches are distributed among these distances:
177 16 0.11
178 14 0.10
179 99 0.68
180 10 0.07
181 7 0.05
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (179 bp):
AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAAATTTTAAACTTAAATCAAATTAATTAATTAAAAAATTTATATAAAATTTT
ATTTTATAATTATATTATTTAAATTATTTGTAAATTGTTTTTTAATTAA
Found at i:2639311 original size:30 final size:30
Alignment explanation
Indices: 2639270--2639338 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
2639260 TATAAACTTT
*
2639270 TTCGGTTAATATGTTCGAAAAAAAATTCGG
1 TTCGATTAATATGTTCGAAAAAAAATTCGG
2639300 TTCGATTAATATGTTCGAAAAAAAATTCGG
1 TTCGATTAATATGTTCGAAAAAAAATTCGG
*
2639330 TTCGTTTAA
1 TTCGATTAA
2639339 CGGTTAAAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.36
Consensus pattern (30 bp):
TTCGATTAATATGTTCGAAAAAAAATTCGG
Found at i:2639351 original size:31 final size:30
Alignment explanation
Indices: 2639270--2639355 Score: 84
Period size: 30 Copynumber: 2.8 Consensus size: 30
2639260 TATAAACTTT
* * *
2639270 TTCGGTTAATATGTTCGAAAAAAAATTCGG
1 TTCGATTAATAGGTTAGAAAAAAAATTCGG
* *
2639300 TTCGATTAATATGTTCGAAAAAAAATTCGG
1 TTCGATTAATAGGTTAGAAAAAAAATTCGG
* *
2639330 TTCGTTTAA-CGGTTAAAGAAAAAAAA
1 TTCGATTAATAGGTT--AGAAAAAAAA
2639356 GTTTAATTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
29 3 0.06
30 37 0.76
31 9 0.18
ACGTcount: A:0.42, C:0.09, G:0.17, T:0.31
Consensus pattern (30 bp):
TTCGATTAATAGGTTAGAAAAAAAATTCGG
Found at i:2639382 original size:15 final size:14
Alignment explanation
Indices: 2639362--2639391 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
2639352 AAAAGTTTAA
2639362 TTAATTCGGTTATGG
1 TTAATTCGGTT-TGG
2639377 TTAATTCGGTTTGG
1 TTAATTCGGTTTGG
2639391 T
1 T
2639392 CGGCCACCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.17, C:0.07, G:0.27, T:0.50
Consensus pattern (14 bp):
TTAATTCGGTTTGG
Found at i:2646793 original size:2 final size:2
Alignment explanation
Indices: 2646788--2646841 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
2646778 ACACACACAA
2646788 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2646830 AT AT AT AT AT AT
1 AT AT AT AT AT AT
2646842 CTTCCATTCG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2647902 original size:19 final size:19
Alignment explanation
Indices: 2647878--2647921 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
2647868 TTGCTTAAGC
*
2647878 ACTAGTGAATGTATCTTGA
1 ACTAGTGAACGTATCTTGA
2647897 ACTAGTGAACGTATCTTGA
1 ACTAGTGAACGTATCTTGA
2647916 ACTAGT
1 ACTAGT
2647922 ACATAGTGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (19 bp):
ACTAGTGAACGTATCTTGA
Found at i:2651434 original size:24 final size:24
Alignment explanation
Indices: 2651414--2651498 Score: 134
Period size: 24 Copynumber: 3.5 Consensus size: 24
2651404 TGAATTCAGT
2651414 TATGATACTTGACATGGATTCTGA
1 TATGATACTTGACATGGATTCTGA
* *
2651438 TATGATACATGACCTGGATTCTGA
1 TATGATACTTGACATGGATTCTGA
* *
2651462 TCTGATACTTGACATGAATTCTGA
1 TATGATACTTGACATGGATTCTGA
2651486 TATGATACTTGAC
1 TATGATACTTGAC
2651499 TTGAATTATG
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.36
Consensus pattern (24 bp):
TATGATACTTGACATGGATTCTGA
Found at i:2651503 original size:24 final size:24
Alignment explanation
Indices: 2651404--2651510 Score: 133
Period size: 24 Copynumber: 4.5 Consensus size: 24
2651394 ATTTCCGATT
* *
2651404 TGAATTCAGTTATGATACTTGACA
1 TGAATTCTGATATGATACTTGACA
* * *
2651428 TGGATTCTGATATGATACATGACC
1 TGAATTCTGATATGATACTTGACA
* *
2651452 TGGATTCTGATCTGATACTTGACA
1 TGAATTCTGATATGATACTTGACA
*
2651476 TGAATTCTGATATGATACTTGACT
1 TGAATTCTGATATGATACTTGACA
*
2651500 TGAATTATGAT
1 TGAATTCTGAT
2651511 TTTATTTTTG
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 71 1.00
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.38
Consensus pattern (24 bp):
TGAATTCTGATATGATACTTGACA
Found at i:2652801 original size:19 final size:19
Alignment explanation
Indices: 2652777--2652821 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
2652767 GCTTCATTTC
*
2652777 TGAATTTCTATGATTTGAG
1 TGAATTTCTATGACTTGAG
*
2652796 TGAATTTCTCTGACTTGAG
1 TGAATTTCTATGACTTGAG
2652815 TGAATTT
1 TGAATTT
2652822 TGTGGATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.24, C:0.09, G:0.20, T:0.47
Consensus pattern (19 bp):
TGAATTTCTATGACTTGAG
Found at i:2655554 original size:20 final size:19
Alignment explanation
Indices: 2655524--2655599 Score: 91
Period size: 20 Copynumber: 3.9 Consensus size: 19
2655514 TTTGTGAAGG
*
2655524 TATGCACCGATGCACTCAT
1 TATGCATCGATGCACTCAT
*
2655543 TGATGCATCGATGCACTCTT
1 T-ATGCATCGATGCACTCAT
*
2655563 TCATGCATCGATGCACTTA-
1 T-ATGCATCGATGCACTCAT
*
2655582 TATGAATCGATGCACTCA
1 TATGCATCGATGCACTCA
2655600 GGATTTTATG
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
18 15 0.31
19 2 0.04
20 32 0.65
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (19 bp):
TATGCATCGATGCACTCAT
Found at i:2655643 original size:28 final size:28
Alignment explanation
Indices: 2655587--2655647 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
2655577 ACTTATATGA
*
2655587 ATCGATGCACTCAGGATTTTATGGAAAC
1 ATCGATGCACTCAGGATTTTATAGAAAC
*
2655615 ATCGATGCACTCCAGGCTTGTT-TAG-AAC
1 ATCGATGCACT-CAGGATT-TTATAGAAAC
2655643 ATCGA
1 ATCGA
2655648 ATGTATTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 19 0.66
29 8 0.28
30 2 0.07
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (28 bp):
ATCGATGCACTCAGGATTTTATAGAAAC
Found at i:2663219 original size:20 final size:20
Alignment explanation
Indices: 2663182--2663240 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
2663172 CAGAACCCCA
* *
2663182 GGGGGTATCGATTCCC-CTGT
1 GGGGGGATCGATTCCCTC-AT
*
2663202 GGGGGGAATCGGTTCCCTCAT
1 GGGGGG-ATCGATTCCCTCAT
2663223 GGGGGGATCGATTCCCTC
1 GGGGGGATCGATTCCCTC
2663241 TGCACCAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 16 0.48
21 16 0.48
22 1 0.03
ACGTcount: A:0.12, C:0.25, G:0.37, T:0.25
Consensus pattern (20 bp):
GGGGGGATCGATTCCCTCAT
Found at i:2671028 original size:21 final size:21
Alignment explanation
Indices: 2671002--2671123 Score: 86
Period size: 21 Copynumber: 5.6 Consensus size: 21
2670992 TTGTGCATAA
2671002 TGCATCGATACACTATGAAGG
1 TGCATCGATACACTATGAAGG
* * *
2671023 TGCATCAATGCATCCCTATGAATG
1 TGCATCGAT--A-CACTATGAAGG
*
2671047 TGCATCGATACACCATGAAGG
1 TGCATCGATACACTATGAAGG
* * * *
2671068 TGCACCGATGCACTCCTTGAATG
1 TGCATCGATACACT--ATGAAGG
* *
2671091 TGCATCGATGCACTCA-GCA-G
1 TGCATCGATACACT-ATGAAGG
2671111 TGCATCGATACAC
1 TGCATCGATACAC
2671124 CAGTCGGGAT
Statistics
Matches: 80, Mismatches: 16, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
20 13 0.16
21 29 0.36
22 2 0.03
23 19 0.24
24 17 0.21
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (21 bp):
TGCATCGATACACTATGAAGG
Found at i:2671066 original size:45 final size:44
Alignment explanation
Indices: 2671002--2671099 Score: 144
Period size: 45 Copynumber: 2.2 Consensus size: 44
2670992 TTGTGCATAA
* *
2671002 TGCATCGATACACTATGAAGGTGCATCAATGCA-TCCCTATGAATG
1 TGCATCGATACACCATGAAGGTGCACCAATGCACT-CCT-TGAATG
*
2671047 TGCATCGATACACCATGAAGGTGCACCGATGCACTCCTTGAATG
1 TGCATCGATACACCATGAAGGTGCACCAATGCACTCCTTGAATG
2671091 TGCATCGAT
1 TGCATCGAT
2671100 GCACTCAGCA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
44 15 0.31
45 33 0.67
46 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (44 bp):
TGCATCGATACACCATGAAGGTGCACCAATGCACTCCTTGAATG
Found at i:2671093 original size:23 final size:23
Alignment explanation
Indices: 2671002--2671105 Score: 92
Period size: 21 Copynumber: 4.7 Consensus size: 23
2670992 TTGTGCATAA
* *
2671002 TGCATCGATACACT--ATGAAGG
1 TGCATCGATGCACTCCATGAATG
*
2671023 TGCATCAATGCA-TCCCTATGAATG
1 TGCATCGATGCACT-CC-ATGAATG
* *
2671047 TGCATCGAT--ACACCATGAAGG
1 TGCATCGATGCACTCCATGAATG
* *
2671068 TGCACCGATGCACTCCTTGAATG
1 TGCATCGATGCACTCCATGAATG
2671091 TGCATCGATGCACTC
1 TGCATCGATGCACTC
2671106 AGCAGTGCAT
Statistics
Matches: 65, Mismatches: 11, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
20 1 0.02
21 24 0.37
22 3 0.05
23 23 0.35
24 14 0.22
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (23 bp):
TGCATCGATGCACTCCATGAATG
Found at i:2675577 original size:24 final size:24
Alignment explanation
Indices: 2675466--2675570 Score: 111
Period size: 24 Copynumber: 4.4 Consensus size: 24
2675456 ATTTCTGATT
* * *
2675466 TGAATTTTGTTATGATACCTGACA
1 TGAATTATGATATGATACTTGACA
* *
2675490 TGGATTATGATATGATACTTGACC
1 TGAATTATGATATGATACTTGACA
* * **
2675514 TGGATTCTGATCCGATACTTGACA
1 TGAATTATGATATGATACTTGACA
* *
2675538 TGAATTCTGATATGATACTTGACT
1 TGAATTATGATATGATACTTGACA
2675562 TGAATTATG
1 TGAATTATG
2675571 TTTTGATTTT
Statistics
Matches: 67, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 67 1.00
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (24 bp):
TGAATTATGATATGATACTTGACA
Found at i:2676263 original size:23 final size:23
Alignment explanation
Indices: 2676233--2676276 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
2676223 ACATGTTTTA
2676233 ATAAAAGTTTTAAATCTTCCGCT
1 ATAAAAGTTTTAAATCTTCCGCT
*
2676256 ATAAAAGTTTTAAATTTTCCG
1 ATAAAAGTTTTAAATCTTCCG
2676277 TCCTCGTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (23 bp):
ATAAAAGTTTTAAATCTTCCGCT
Found at i:2681284 original size:31 final size:32
Alignment explanation
Indices: 2681236--2681318 Score: 116
Period size: 32 Copynumber: 2.6 Consensus size: 32
2681226 CAGTGCTCGA
2681236 CTCGTTAA-AAAATTTTGTTGCTCGAGTCG-TG
1 CTCGTTAAGAAAA-TTTGTTGCTCGAGTCGTTG
* *
2681267 CTTGTTAAGAAAATTTGTTGCTCGATTCGTTG
1 CTCGTTAAGAAAATTTGTTGCTCGAGTCGTTG
*
2681299 CTCATTAAGAAAATTTGTTG
1 CTCGTTAAGAAAATTTGTTG
2681319 TTCCCCTCGT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
31 22 0.48
32 24 0.52
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.41
Consensus pattern (32 bp):
CTCGTTAAGAAAATTTGTTGCTCGAGTCGTTG
Found at i:2681329 original size:32 final size:32
Alignment explanation
Indices: 2681271--2681338 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
2681261 GTCGTGCTTG
* * *
2681271 TTAAGAAAATTTGTTGCTCGATTCGTTGCTCA
1 TTAAGAAAATTTGTTGCTCCACTCGTTACTCA
* * *
2681303 TTAAGAAAATTTGTTGTTCCCCTCGTTACTCG
1 TTAAGAAAATTTGTTGCTCCACTCGTTACTCA
2681335 TTAA
1 TTAA
2681339 CCTTACTGAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Consensus pattern (32 bp):
TTAAGAAAATTTGTTGCTCCACTCGTTACTCA
Found at i:2681556 original size:8 final size:8
Alignment explanation
Indices: 2681543--2681576 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
2681533 AAAATAATAA
*
2681543 TTATTAAT
1 TTATTATT
2681551 TTATTATT
1 TTATTATT
2681559 TTATTATT
1 TTATTATT
2681567 TTATTATT
1 TTATTATT
2681575 TT
1 TT
2681577 TAACTATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
TTATTATT
Found at i:2686647 original size:20 final size:20
Alignment explanation
Indices: 2686622--2686674 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
2686612 TAGAAATACT
*
2686622 CCATACTAAAAATTTATAAA
1 CCATACTGAAAATTTATAAA
2686642 CCATACTGAAAATTTATAAA
1 CCATACTGAAAATTTATAAA
*
2686662 TCATACTGAAAAT
1 CCATACTGAAAAT
2686675 AAAATGAGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.51, C:0.15, G:0.04, T:0.30
Consensus pattern (20 bp):
CCATACTGAAAATTTATAAA
Found at i:2691916 original size:22 final size:22
Alignment explanation
Indices: 2691891--2691938 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
2691881 ATTTTGTCGT
*
2691891 AAAAACTCAACCATCAAAAAAC
1 AAAAAATCAACCATCAAAAAAC
* * *
2691913 AAAAAATTAACCATTAAATAAC
1 AAAAAATCAACCATCAAAAAAC
2691935 AAAA
1 AAAA
2691939 TATGAAACAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.67, C:0.19, G:0.00, T:0.15
Consensus pattern (22 bp):
AAAAAATCAACCATCAAAAAAC
Found at i:2704762 original size:22 final size:20
Alignment explanation
Indices: 2704719--2704756 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2704709 TTCAGACTGA
*
2704719 ATAGTATCGGTACCTCTCCT
1 ATAGTATCGATACCTCTCCT
*
2704739 ATAGTATCGATACTTCTC
1 ATAGTATCGATACCTCTC
2704757 TTCTATGGTA
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:0.24, C:0.26, G:0.13, T:0.37
Consensus pattern (20 bp):
ATAGTATCGATACCTCTCCT
Found at i:2704771 original size:22 final size:22
Alignment explanation
Indices: 2704732--2704773 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2704722 GTATCGGTAC
*
2704732 CTCTCCTATAGTATCGATACTT
1 CTCTCCTATAGTACCGATACTT
* *
2704754 CTCTTCTATGGTACCGATAC
1 CTCTCCTATAGTACCGATAC
2704774 CCACTTCGGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.21, C:0.29, G:0.12, T:0.38
Consensus pattern (22 bp):
CTCTCCTATAGTACCGATACTT
Found at i:2711531 original size:31 final size:29
Alignment explanation
Indices: 2711474--2711541 Score: 91
Period size: 31 Copynumber: 2.3 Consensus size: 29
2711464 AAGCCTTAGA
* *
2711474 AAAATTTGGGGACCATTCAATAATTTTTG
1 AAAAGTTGGGGACCATTCAATAATTTTGG
*
2711503 AAAAGTTGGGGAACCAATTCGATAATTTTGG
1 AAAAGTTGGGG-ACC-ATTCAATAATTTTGG
2711534 AAAAGTTG
1 AAAAGTTG
2711542 TGAATGGTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 10 0.29
30 3 0.09
31 21 0.62
ACGTcount: A:0.37, C:0.09, G:0.22, T:0.32
Consensus pattern (29 bp):
AAAAGTTGGGGACCATTCAATAATTTTGG
Found at i:2718819 original size:30 final size:31
Alignment explanation
Indices: 2718785--2718842 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
2718775 AAAATTTTAA
* *
2718785 GGACC-ATTTTATAATTTTTGAAAAGTTGGG
1 GGACCAATTTGATAATTTTGGAAAAGTTGGG
*
2718815 GGACCAATTTGGTAATTTTGGAAAAGTT
1 GGACCAATTTGATAATTTTGGAAAAGTT
2718843 ATGAATGGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 5 0.21
31 19 0.79
ACGTcount: A:0.31, C:0.07, G:0.24, T:0.38
Consensus pattern (31 bp):
GGACCAATTTGATAATTTTGGAAAAGTTGGG
Found at i:2723116 original size:2 final size:2
Alignment explanation
Indices: 2723109--2723153 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
2723099 AATAGATTGT
2723109 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2723149 TA TA T
1 TA TA T
2723154 TGGATCATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2730908 original size:25 final size:27
Alignment explanation
Indices: 2730873--2730934 Score: 101
Period size: 27 Copynumber: 2.3 Consensus size: 27
2730863 AGAACTGGAC
2730873 TTAGATGACAA-AA-AATTTTGAGATTT
1 TTAG-TGACAATAAGAATTTTGAGATTT
2730899 TTAGTGACAATAAGAATTTTGAGATTT
1 TTAGTGACAATAAGAATTTTGAGATTT
2730926 TTAGTGACA
1 TTAGTGACA
2730935 GTCAATCAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
25 6 0.18
26 6 0.18
27 22 0.65
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.39
Consensus pattern (27 bp):
TTAGTGACAATAAGAATTTTGAGATTT
Found at i:2731725 original size:30 final size:30
Alignment explanation
Indices: 2731689--2731758 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 30
2731679 TGTTTTAGCT
*
2731689 GGTCTCCTAGAAACAAGAGAAGCAGGAGCA
1 GGTCTCCCAGAAACAAGAGAAGCAGGAGCA
**
2731719 GGTCTCCCAGAAACCGGAGAAGCAGGAGCA
1 GGTCTCCCAGAAACAAGAGAAGCAGGAGCA
2731749 GGTCTCCCAG
1 GGTCTCCCAG
2731759 TTTTTCTGCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.33, C:0.26, G:0.31, T:0.10
Consensus pattern (30 bp):
GGTCTCCCAGAAACAAGAGAAGCAGGAGCA
Found at i:2732615 original size:23 final size:24
Alignment explanation
Indices: 2732589--2732633 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2732579 AGTACCCCTT
2732589 CCCTTAA-TAAAATCCCTAACCTC
1 CCCTTAATTAAAATCCCTAACCTC
* *
2732612 CCCTTAATTGAAATTCCTAACC
1 CCCTTAATTAAAATCCCTAACC
2732634 CTATTTCCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.33, C:0.36, G:0.02, T:0.29
Consensus pattern (24 bp):
CCCTTAATTAAAATCCCTAACCTC
Found at i:2735346 original size:24 final size:24
Alignment explanation
Indices: 2735319--2735368 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
2735309 TGGCAGTACC
2735319 CCTCCCCTTAATTAAAATCCCTAA
1 CCTCCCCTTAATTAAAATCCCTAA
*
2735343 CCTCCCCTTAATTGAAATCCCTAA
1 CCTCCCCTTAATTAAAATCCCTAA
2735367 CC
1 CC
2735369 CTATTCCAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.30, C:0.40, G:0.02, T:0.28
Consensus pattern (24 bp):
CCTCCCCTTAATTAAAATCCCTAA
Found at i:2742756 original size:11 final size:11
Alignment explanation
Indices: 2742742--2742808 Score: 50
Period size: 11 Copynumber: 6.2 Consensus size: 11
2742732 AAAACACACA
2742742 AAAAAAGAAAG
1 AAAAAAGAAAG
*
2742753 AAAAAAAACAAG
1 AAAAAAGA-AAG
2742765 AAAAACAG-AAG
1 AAAAA-AGAAAG
*
2742776 -AAAAA-AAAT
1 AAAAAAGAAAG
* *
2742785 AAAAAATAAAA
1 AAAAAAGAAAG
*
2742796 AAAAAATAAAG
1 AAAAAAGAAAG
2742807 AA
1 AA
2742809 TAAATAGACA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
9 3 0.07
10 9 0.20
11 25 0.54
12 8 0.17
13 1 0.02
ACGTcount: A:0.84, C:0.03, G:0.09, T:0.04
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:2742756 original size:12 final size:12
Alignment explanation
Indices: 2742741--2742782 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
2742731 AAAAACACAC
2742741 AAAAAAAGAAAG
1 AAAAAAAGAAAG
2742753 AAAAAAA-ACAAG
1 AAAAAAAGA-AAG
*
2742765 AAAAACAG-AAG
1 AAAAAAAGAAAG
2742776 AAAAAAA
1 AAAAAAA
2742783 ATAAAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 10 0.38
12 16 0.62
ACGTcount: A:0.83, C:0.05, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAG
Found at i:2742768 original size:23 final size:25
Alignment explanation
Indices: 2742715--2742783 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 25
2742705 ACACAGAGAG
2742715 AAAAAGAAGAGATATAAAAAACACACAA
1 AAAAAGAA-AGA-A-AAAAAACACACAA
*
2742743 AAAAAGAAAGAAAAAAAACA-AGAA
1 AAAAAGAAAGAAAAAAAACACACAA
*
2742767 AAACAG-AAGAAAAAAAA
1 AAAAAGAAAGAAAAAAAA
2742784 TAAAAAATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.28
24 8 0.21
25 8 0.21
26 1 0.03
27 3 0.08
28 8 0.21
ACGTcount: A:0.78, C:0.07, G:0.12, T:0.03
Consensus pattern (25 bp):
AAAAAGAAAGAAAAAAAACACACAA
Found at i:2742799 original size:18 final size:18
Alignment explanation
Indices: 2742753--2742812 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
2742743 AAAAAGAAAG
* *
2742753 AAAAAAAACAAGAAAAACAG
1 AAAAAAAA-AATAAAAA-AT
2742773 AAGAAAAAAAATAAAAAAT
1 AA-AAAAAAAATAAAAAAT
*
2742792 AAAAAAAAAATAAAGAAT
1 AAAAAAAAAATAAAAAAT
2742810 AAA
1 AAA
2742813 TAGACAGATC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 18 0.50
19 3 0.08
20 9 0.25
21 6 0.17
ACGTcount: A:0.83, C:0.03, G:0.07, T:0.07
Consensus pattern (18 bp):
AAAAAAAAAATAAAAAAT
Found at i:2744549 original size:4 final size:4
Alignment explanation
Indices: 2744540--2749721 Score: 7105
Period size: 4 Copynumber: 1318.2 Consensus size: 4
2744530 TAAGTGCATT
* * *
2744540 CATA CATA CATA CATA CATA CATA CATA CGTA CGTA CGTA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * *
2744588 CATA CATA CATA CATA CGTA CCTA CGTA CATA CGTA CGTA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2744636 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * *
2744684 CATA CATA CATA CATA CGTA CATA CATA CATA CATA CGTA CATA CGTA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * *
2744732 CGTA CATA CATA CATA CGTA CATA CATA CGTA CATA CGTA CGTA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * ** * *
2744780 CATA CGTA CATA CGTA TGTA CATA CATA CATA CATA CATA CGTA CGTA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
2744828 CATA CATA CATA CATA CATA CATA CCTA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2744876 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2744924 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
2744972 CATA CATA CATA CATA CATA CGTA CGTA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * *
2745020 CATA CATA CATA CGTA CATA CATA CGTA CATA CATA CATA CATA CGTA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
** * * * * *
2745068 CATA TGTA CATA CGTA CATA CGTA CCTA CGTA CGTA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * *
2745116 CGTA CATA CATA CATA CATA TATA CATG CATA CATA CATA TATA CGTA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * *
2745164 CATA CATA CATA CATA CGTA CATA CGTA CGTA CATA TATA CATA CGTA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * *
2745212 CATA CGTA CGTA CATA CGTA CGTA CATA CATA CGTA CATA CGTA CGTA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * *
2745260 CATA CATA CCTA CATA CATA CATA CGTA CGTA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
2745308 CATA CATA CATA CGTA CGTA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2745356 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CA-A CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2745403 CA-A C-TA CATA CATA CATA CATA C-TA CATA CATA CATA CAT- CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
2745447 CATA CATA CATA CATA CATA CATA C--A CATA CATA C-TA CCTA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
2745492 CATA CATA CATA CATA CATA CATA CATA CATA CATA CCTA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
2745540 CATA CATA CATA CATA CCTA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
2745588 CATA CATA CATA CATA CATA CATA CATA CATA CGTA CATA CGTA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * * * *
2745636 CGTA CATA CGTA CATA CGTA CCTA CGTA CCTA CGTA CCTA CGTA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * *
2745684 CGTA CCTA CGTA CATA CGTA CATA TATA CATA CATA CGTA CATA CGTA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * *
2745732 CATA CGTA CATA CGTA CGTA CCTA CGTA CATA CATA CGTA CATA CGTA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * *
2745780 CATA CGTA CATA CGTA CCTA CATA CATA CGTA CATA CGTA CATA CGTA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2745828 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2745876 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA C--A
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
2745922 CATA CATA CATA CATA CATA CATA -AGTG CATA C-TA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CA-TA CATA CATA CATA CATA CATA
2745969 C-TA CATA CATA CATA CATA CATA CATA -ATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2746015 CATA CATA CATA CATA CATA C--A CATA CATA -ATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2746060 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
2746108 CATA CATA CATA CATA CGTA CATA CATA CGTA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * *
2746156 CGTA TATA CGTA CATA CGTA CATA CGTA CGTA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * *
2746204 CATA CATA CATA TATA CGTA CATA CATA CATA CATA CGTA CATA CGTA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * *
2746252 CGTA CATA TATA CATA CGTATA CGTA CACGTA CGTA CATA CATA CGTA
1 CATA CATA CATA CATA C--ATA CATA CA--TA CATA CATA CATA CATA
* * * * *
2746300 CA-A CATA CGTA CATA CATA CCTA TATA CATA CATA C-GA CGTA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * *
2746346 CATA CATA CATA CCTA CATA CGTA CGTA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
2746394 CATA CATA CATA CCTA CATA CATA CATA CATA CATA CATA CATA C--A
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2746440 CATA CATA CATA CATA CATA CATA CATA CAT- CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2746487 CAT- CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
2746534 CCTA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
2746582 CCTA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * *
2746630 CATA CATA CATA CATA CATA CATA CGTA CATA CGTA CATA CGTA CCTA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * *
2746678 CGTA CATA CGTA CATA CGTA CATA CGTA CGTA CGTA CATA CGTA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * *
2746726 CGTA CCTA CATA CATA CGTA CATA CGTA CATA CGTA CCTA CGTA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * *
2746774 CGTA CATA CGTA CATA CGTA CATA CGTA CATA CATA CATA CGTA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * ** * * *
2746822 CGTA CATA CGTA CCTA TGTA CATA CGTA CATA CGTA CATA CGTA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * *
2746870 CGTA CATA CGTA CATA CATA CATA CGTA CATA CGTA CATA CGTA CCTA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * *
2746918 CATA CATA CGTA CATA CGTA CATA CGTA CATA CGTA CATA CGTA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * *
2746966 CGTA CATA CGTA CATA CGTA CATA CATA CGTA CATA CATA CATA CGTA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
2747014 CATA CGTA CATA CGTA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2747062 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * *
2747110 CATA CATA CATA CATA CTTA CATA CATA CATA CGTA CATA CGTA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * * *
2747158 CGTA CCTA CGTA CCTA CGTA CATA CGTA CATA CGTA CATA CGTA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * *
2747206 CGTA CCTA CGTA CATA CGTA CATA CGTA CATA CGTA CATA CGTA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * *
2747254 CGTA CATA CATA CATA CATA CATA CATA CGTA CATA CGTA CATA CGTA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
2747302 CATA CGTA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2747350 CATA CATA CAT- -ATA CATA CATA CATA C-TA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2747395 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2747443 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
2747491 CATA CATA CATA CATA -AGTG CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CA-TA CATA CATA CATA CATA CATA CATA CATA
* *
2747539 CATA CAT- CATA CATA CATA TATA CAT- -ATA CATA TATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
2747584 CATA CTACA CATA CATA CATA CATA CATA CCTA CATA CATA CATA CATA
1 CATA C-ATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2747633 CATA CATA CATA CATA CAT- CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2747680 C-TA CATA CATA CAT- CATA CATA CATA CATA CATA CATA CATA C-TA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * *
2747725 CAT- CGTA CATA C-TA CA-A C-TA CATA CATA CGTA CATA CGTA C-TA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * *
2747768 CGTA CATA CGTA CATA CATA CATA TATA CATA C-TA TATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2747815 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * *
2747863 CATA CATA CATA TATA CATA CGTA CATA CGTA CCTA CGTA CATA CGTA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * *
2747911 CATA CGTA CATA CATA CATA CGTA CATA CGTA CATA CGTA CATA CGTA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * *
2747959 CATA CGTA CCTA CGTA CATA CGTA CATA CGTA CATA CGTA CATA CGTA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * *
2748007 CATA CGTA CAGA CGTA CATA CGTA CATA CGTA CATA CGTA CATA CGTA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * *
2748055 CACGTA C-TA CGTA CATA C-GA CATA CGTA CATA CGTA CATA CGTA CATA
1 CA--TA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
2748103 CATA CTCTA CATA CATA CATA CGTA CATA CA-A C-TA CATA CATA CATA
1 CATA C-ATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * *
2748150 CGTA CATA CGTA CATA CGTA CATA CATA C-TA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2748197 CATA CATA CATA CATA CA-A CATA CATA CATA C-TA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2748243 CAT- CATA CATA CATA CATA CATA CATA C-TA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2748289 CAT- CATA CATA CAT- CATA CATA CATCA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CAT-A CATA CATA CATA CATA CATA
*
2748336 CATA CATA CATA CATA CATA CATA CATA CAGA CATA CATA CA-A CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2748383 CATA CATA CATA CATA CATA CATA CATA C-TA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
2748430 CATA CATA CATA CATA CAGA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2748478 CATA CATA CATA CATA CATA CATA CATA CATA C--A CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2748524 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2748572 CATA CATA CATA CATA CATA CACCTA CATA CATA CA-A CATA CATA CATA
1 CATA CATA CATA CATA CATA CA--TA CATA CATA CATA CATA CATA CATA
2748621 CATA C--A CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
2748667 CATA CATA CAT- CATA CA-A CATA CATA CGTA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
2748713 CGTATA CAT- -ATA CGTA CACGTA CATA CATA CAT- CGTA CATA C-TA
1 C--ATA CATA CATA CATA CA--TA CATA CATA CATA CATA CATA CATA
*
2748757 CATA CATA CAT- -ATA CATA CATA CATA CATA CATA CGTA CATA C--A
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2748801 CATA CATA CATA CATA C-TA CATA CACTA CATA C-TA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CA-TA CATA CATA CATA CATA CATA
2748848 CATA CATA CATA CATA TCATA CATA CATA CATA CATA CATA C--A CATA
1 CATA CATA CATA CATA -CATA CATA CATA CATA CATA CATA CATA CATA
2748895 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CA-A
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2748942 CATA CATA CATA CATA CATA CA-A CATA CATA C--A CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2748987 CATA CATA CATA C--A CATA CATA CATA CATA CATA C-TA CAT- CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
2749031 CATA CAGA CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT-
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * *
2749078 CATA CATA CATA CATA C--A CATA CATA CTTA TTATA CGTA CATA CGTA
1 CATA CATA CATA CATA CATA CATA CATA CATA -CATA CATA CATA CATA
*
2749125 CAT- -ATA CATA CATA TATA CATA CATA CATA C-TA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
2749170 CATA CATA CATA CATA C--A CATA CATA CATA CATA -ATA CCTA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2749215 CATA CATA C-TA CATA CATA CATA CAT- CATA CATA CATA CA-A CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2749260 CATA CATA CATA CATAA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CAT-A CATA CATA CATA CATA CATA CATA CATA CATA
2749309 CATA CATA CATA CATA CATA CATA CATA CATA C-T- CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2749355 CATA CATA CATA CA-A CATA CATA CATA CATA CATA CA-A CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2749401 CATA CATA C-TA CATA CATA CATA CATA CAT- CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2749447 CATA C-TA CATA CATA CATA CATA CATA C-TA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
2749493 CATA CATA C-CA CATA CA-A CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2749539 CATA C--A CATA CATA CATA CATA CA-A CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
2749584 CATA CATA CATA CATA CATA CATA C--A CATA CATA CATC CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2749630 CATA CATA CATA CATA C-TA CATA -ATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2749676 CATA CATA CATA C-TA CATA C-TA CATA CATA CAT- CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2749721 C
1 C
2749722 TTCTTACAGA
Statistics
Matches: 4617, Mismatches: 428, Indels: 266
0.87 0.08 0.05
Matches are distributed among these distances:
2 39 0.01
3 202 0.04
4 4328 0.94
5 26 0.01
6 22 0.00
ACGTcount: A:0.45, C:0.26, G:0.04, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:2750145 original size:52 final size:53
Alignment explanation
Indices: 2749929--2750185 Score: 242
Period size: 53 Copynumber: 4.9 Consensus size: 53
2749919 TCTTGACGAT
* * * * * **
2749929 TTTTTAAATGAGTTTAAAGAAA-CTAAGTCTGATTTTCAGAAGTTTCTTGATG
1 TTTTCAAATGAATTTAAAGAAATCTAAGCCTAATTTTTAGGGGTTTCTTGATG
* * **
2749981 ATTTTTAAAAGAACTTTCAAAGAAAT-TAAGCCTAA-TTTTAGGGGTTTTCTTGACA
1 -TTTTCAAATGAA-TTT-AAAGAAATCTAAGCCTAATTTTTAGGGG-TTTCTTGATG
* * * * *
2750036 TTTTCAAATGAATTTGAAAG-AAGCTAAGCTTGATTTTCAGGAGTTTCTT-AT-
1 TTTTCAAATGAATTT-AAAGAAATCTAAGCCTAATTTTTAGGGGTTTCTTGATG
*
2750087 TGTTTCAAATGAATTTTAAGAAATC-AAGCCTAATTTTTAGGGGTTTCTTGATG
1 T-TTTCAAATGAATTTAAAGAAATCTAAGCCTAATTTTTAGGGGTTTCTTGATG
2750140 TTTTCAAATGAATATTAAAGAAA-CTAAGCCTAATTTTTAGGGGTTT
1 TTTTCAAATGAAT-TTAAAGAAATCTAAGCCTAATTTTTAGGGGTTT
2750186 GATGATAACT
Statistics
Matches: 167, Mismatches: 25, Indels: 24
0.77 0.12 0.11
Matches are distributed among these distances:
51 24 0.14
52 35 0.21
53 60 0.36
54 26 0.16
55 22 0.13
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.40
Consensus pattern (53 bp):
TTTTCAAATGAATTTAAAGAAATCTAAGCCTAATTTTTAGGGGTTTCTTGATG
Found at i:2750146 original size:104 final size:107
Alignment explanation
Indices: 2749917--2750176 Score: 302
Period size: 104 Copynumber: 2.4 Consensus size: 107
2749907 TTTTCAGAAG
* *
2749917 TTTCTTGACGATTTTTTAAATGAGTTTAAAGAAACTAAG-TCTGATTTTCAGAAGTTTCTTGATG
1 TTTCTTGAC-A-TTTTCAAATGAATTTAAAGAAACTAAGCTCTGATTTTCAGAAGTTTCTTGATG
* *
2749981 ATTTTTAAAAGAACTTTCAAAGAAATTAAGCCTAATTTTAGGGGT
64 A-TTTCAAAAGAACTTTCAAAGAAATCAAGCCTAATTTTAGGGGT
* *
2750026 TTTCTTGACATTTTCAAATGAATTTGAAAGAAGCTAAGCT-TGATTTTCAGGAGTTTCTT-ATTG
1 TTTCTTGACATTTTCAAATGAATTT-AAAGAAACTAAGCTCTGATTTTCAGAAGTTTCTTGA-TG
* *
2750089 -TTTCAAATGAA-TTT-TAAGAAATCAAGCCTAATTTTTAGGGG-
64 ATTTCAAAAGAACTTTCAAAGAAATCAAGCCTAA-TTTTAGGGGT
** *
2750130 TTTCTTGATGTTTTCAAATGAATATTAAAGAAACTAAGC-CTAATTTT
1 TTTCTTGACATTTTCAAATGAAT-TTAAAGAAACTAAGCTCTGATTTT
2750177 TAGGGGTTTG
Statistics
Matches: 133, Mismatches: 12, Indels: 17
0.82 0.07 0.10
Matches are distributed among these distances:
104 54 0.41
105 14 0.11
106 9 0.07
107 14 0.11
108 32 0.24
109 10 0.08
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (107 bp):
TTTCTTGACATTTTCAAATGAATTTAAAGAAACTAAGCTCTGATTTTCAGAAGTTTCTTGATGAT
TTCAAAAGAACTTTCAAAGAAATCAAGCCTAATTTTAGGGGT
Found at i:2750355 original size:41 final size:41
Alignment explanation
Indices: 2750244--2750355 Score: 129
Period size: 41 Copynumber: 2.7 Consensus size: 41
2750234 AGCGTTTCTT
* *
2750244 GATGAGTAAGTCCTTTGGGCCAT-CAGTAAGTCTTTCGAGCAT
1 GATGA-TAAGTCCTTCGGGCCATCCA-TAAGTCTTTCGAGCAA
* * * *
2750286 GATGCTTAAATCCTTC-GGTCATCTATAAGTCTTTCGAGCAA
1 GATG-ATAAGTCCTTCGGGCCATCCATAAGTCTTTCGAGCAA
2750327 GATGATAAGTCCTTCGGGCCATCCATAAG
1 GATGATAAGTCCTTCGGGCCATCCATAAG
2750356 ACCTTCAGGC
Statistics
Matches: 57, Mismatches: 10, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
40 9 0.16
41 35 0.61
42 13 0.23
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.30
Consensus pattern (41 bp):
GATGATAAGTCCTTCGGGCCATCCATAAGTCTTTCGAGCAA
Found at i:2751644 original size:136 final size:135
Alignment explanation
Indices: 2751394--2751753 Score: 577
Period size: 136 Copynumber: 2.7 Consensus size: 135
2751384 GGTAAATTAG
* * *
2751394 TCAACATTTCCAGTGGAGATTTCATAATGAAAGAACTCATCCGTTGAGAGAGAAGAAGTTCATAA
1 TCAACATTTCCAGTGGAGAGTTCATAATG-AAGAACTCATCCGATGAGGGAGAAGAAGTTCATAA
*
2751459 TGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAATACCTTAC
65 TGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACC--AC
*
2751524 TTGAGGGA
128 TCGAGGGA
*
2751532 TCACCATTTCCAGTGGAGAGTTCATAATG-AGAACTCATCCGATGAGGGAGAAGAAGTTCATAAT
1 TCAACATTTCCAGTGGAGAGTTCATAATGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAAT
2751596 GAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCACTCG
66 GAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCACTCG
2751661 AGGGA
131 AGGGA
*
2751666 TCAACATTTTCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAG-AG-T--TA
1 TCAACATTTCCAGTGGAGAGTTCATAAT--GAAGAACTCATCCGATGAGGGAGAAGAAGTTCATA
2751727 ATGAGAAGAACTTGTTCAACCTTAGCT
64 ATGAGAAGAACTTGTTCAACCTTAGCT
2751754 TGTTTTCCAT
Statistics
Matches: 211, Mismatches: 8, Indels: 11
0.92 0.03 0.05
Matches are distributed among these distances:
133 29 0.14
134 35 0.17
135 1 0.00
136 95 0.45
137 24 0.11
138 27 0.13
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (135 bp):
TCAACATTTCCAGTGGAGAGTTCATAATGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAAT
GAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCACTCG
AGGGA
Found at i:2752544 original size:21 final size:21
Alignment explanation
Indices: 2752519--2752568 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
2752509 AGGAGAAAAA
2752519 AGGAGAAAGAATGAGGTTAGG
1 AGGAGAAAGAATGAGGTTAGG
2752540 AGGAGAAAGAATGAGGTTAGG
1 AGGAGAAAGAATGAGGTTAGG
2752561 AGGA-AAAG
1 AGGAGAAAG
2752569 GGGTCCGGCC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 4 0.14
21 25 0.86
ACGTcount: A:0.46, C:0.00, G:0.42, T:0.12
Consensus pattern (21 bp):
AGGAGAAAGAATGAGGTTAGG
Found at i:2758617 original size:195 final size:194
Alignment explanation
Indices: 2758191--2758774 Score: 577
Period size: 192 Copynumber: 3.0 Consensus size: 194
2758181 TACAAGTTTG
* *
2758191 GAGGTAGCATTGGGCAACAGCACATGCACTGAATCTGATCTCAAAGAAAGAAAAAGAAAGAAACG
1 GAGGTAGCATTGGGCAACAGCACAGGCACTGAATCTGATCTCAAAGGAAGAAAAAG--A-AAA--
* * * *
2758256 AAAGAATTCAAAGGGGTCTTTGTGCAAAGATGAAGACCGAAAGGATGTGGAGATTA-AAACCAAT
61 AAA-CA---AAAGGGGTCTTTGTGCAAGGATGAAGACCAAAAGGATGTCGAGA-TAGAAACCAA-
* * * * * * *
2758320 GA-GGAGGAAGTTGTTCCCT-TCAACTT-GA-TT-GTTG-CA-AAAGATGATGTTGCACTAACAG
120 GATGGAAGAAGTTATTCCTTCTCCA-TTGGACTTGGCTGTCACAAAGACGATGTTACACTAACAG
*
2758378 CTAAGGTTTCG
184 CTAAGGTTTCA
* * * *
2758389 GAGGTAGCACTAGGCAACAGAACAGGCACTGAATCTGATCTCAAAGGAAGTAAAAGAAAAAAACA
1 GAGGTAGCATTGGGCAACAGCACAGGCACTGAATCTGATCTCAAAGGAAGAAAAAGAAAAAAACA
* *
2758454 AAAGGGGTCTTTGTGCAAGGATGAATACCAAAAGGATGTTGAGATAGAAACCAAGATGGAAGAAG
66 AAAGGGGTCTTTGTGCAAGGATGAAGACCAAAAGGATGTCGAGATAGAAACCAAGATGGAAGAAG
*
2758519 TTATTCCTTCTCCATTGGACTTGGCTGTCACAACAGACGATGTTACACTAATAGCTAAGGTTTCA
131 TTATTCCTTCTCCATTGGACTTGGCTGTCACAA-AGACGATGTTACACTAACAGCTAAGGTTTCA
* **
2758584 GAGGTAGCATTGGGCAAGAGCACAGGCACTGAATCTGATC-CGAAAGGAAGAAAAAGAAAGAAGT
1 GAGGTAGCATTGGGCAACAGCACAGGCACTGAATCTGATCTC-AAAGGAAGAAAAAGAAA-AAAA
* ** * * *
2758648 C-GAAGAAG---TTGTGCAAGGATGGAGACCAAACA-GATGTCGAGATAGGAACTAAGATGGAAG
64 CAAAAGGGGTCTTTGTGCAAGGATGAAGACCAAA-AGGATGTCGAGATAGAAACCAAGATGGAAG
* * * * * *
2758708 AAGTTATCCCTTCTCCCTTGAACTTGGCTGTTGCA-AAAGACCATGATACACTAACAGCTAATGT
128 AAGTTATTCCTTCTCCATTGGACTTGGCTG-T-CACAAAGACGATGTTACACTAACAGCTAAGGT
2758772 TTC
191 TTC
2758775 TCCTTCGATC
Statistics
Matches: 330, Mismatches: 42, Indels: 34
0.81 0.10 0.08
Matches are distributed among these distances:
188 4 0.01
189 63 0.19
190 5 0.02
191 2 0.01
192 102 0.31
193 9 0.03
194 5 0.02
195 86 0.26
196 4 0.01
198 50 0.15
ACGTcount: A:0.38, C:0.16, G:0.25, T:0.21
Consensus pattern (194 bp):
GAGGTAGCATTGGGCAACAGCACAGGCACTGAATCTGATCTCAAAGGAAGAAAAAGAAAAAAACA
AAAGGGGTCTTTGTGCAAGGATGAAGACCAAAAGGATGTCGAGATAGAAACCAAGATGGAAGAAG
TTATTCCTTCTCCATTGGACTTGGCTGTCACAAAGACGATGTTACACTAACAGCTAAGGTTTCA
Found at i:2758972 original size:246 final size:246
Alignment explanation
Indices: 2758537--2759039 Score: 916
Period size: 246 Copynumber: 2.0 Consensus size: 246
2758527 TCTCCATTGG
* *
2758537 ACTTGGCTGTCACAACAGACGATGTTACACTAATAGCTAAGGTTTCAGAGGTAGCATTGGGCAAG
1 ACTTGGCTGTCACAACAGACGATGTTACACGAATAGCTAAGGTTTCAGAGGTAGCATTGGGCAAC
* *
2758602 AGCACAGGCACTGAATCTGATCCGAAAGGAAGAAAAAGAAAGAAGTCGAAGAAGTTGTGCAAGGA
66 AGCACAGGCACTGAATCTGACCCGAAAGGAAGAAAAAGAAAGAAGTCAAAGAAGTTGTGCAAGGA
*
2758667 TGGAGACCAAACAGATGTCGAGATAGGAACTAAGATGGAAGAAGTTATCCCTTCTCCCTTGAACT
131 TGGAGACCAAACAGATGTCGAGATAGGAACTAAGATGGAAGAAGTAATCCCTTCTCCCTTGAACT
2758732 TGGCTGTTGCAAAAGACCATGATACACTAACAGCTAATGTTTCTCCTTCGA
196 TGGCTGTTGCAAAAGACCATGATACACTAACAGCTAATGTTTCTCCTTCGA
*
2758783 TCTTGGCTGTCACAACAGACGATGTTACACGAATAGCTAAGGTTTCAGAGGTAGCATTGGGCAAC
1 ACTTGGCTGTCACAACAGACGATGTTACACGAATAGCTAAGGTTTCAGAGGTAGCATTGGGCAAC
* *
2758848 AGCACAGGCACTGAATCTGACCCGAAAGGAAGAAAAAGAAAGAATTCAAAGAAGTTGTGGAAGGA
66 AGCACAGGCACTGAATCTGACCCGAAAGGAAGAAAAAGAAAGAAGTCAAAGAAGTTGTGCAAGGA
*
2758913 TGGAGACCAAACAGATGTTGAGATAGGAACTAAGATGGAAGAAGTAATCCCTTCTCCCTTGAACT
131 TGGAGACCAAACAGATGTCGAGATAGGAACTAAGATGGAAGAAGTAATCCCTTCTCCCTTGAACT
*
2758978 TGGCTGTTGCAAAATACCATGATACACTAACAGCTAATGTTTCTCCTTCGA
196 TGGCTGTTGCAAAAGACCATGATACACTAACAGCTAATGTTTCTCCTTCGA
2759029 ACTTGGCTGTC
1 ACTTGGCTGTC
2759040 GCAAAAGATG
Statistics
Matches: 246, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
246 246 1.00
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22
Consensus pattern (246 bp):
ACTTGGCTGTCACAACAGACGATGTTACACGAATAGCTAAGGTTTCAGAGGTAGCATTGGGCAAC
AGCACAGGCACTGAATCTGACCCGAAAGGAAGAAAAAGAAAGAAGTCAAAGAAGTTGTGCAAGGA
TGGAGACCAAACAGATGTCGAGATAGGAACTAAGATGGAAGAAGTAATCCCTTCTCCCTTGAACT
TGGCTGTTGCAAAAGACCATGATACACTAACAGCTAATGTTTCTCCTTCGA
Found at i:2759031 original size:54 final size:54
Alignment explanation
Indices: 2758964--2759068 Score: 140
Period size: 54 Copynumber: 1.9 Consensus size: 54
2758954 AAGTAATCCC
* * *
2758964 TTCTCCCTTGAACTTGGCTGTTGCAAAATACCATGATACACTAACAGCTAATGT
1 TTCTCCCTTGAACTTGGCTGTCGCAAAAGACCATGACACACTAACAGCTAATGT
** *
2759018 TTCT-CCTTCGAACTTGGCTGTCGCAAAAGATGATGCCACACTAACAGCTAA
1 TTCTCCCTT-GAACTTGGCTGTCGCAAAAGACCATGACACACTAACAGCTAA
2759069 AGCTAGAGAG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
53 4 0.09
54 40 0.91
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.29
Consensus pattern (54 bp):
TTCTCCCTTGAACTTGGCTGTCGCAAAAGACCATGACACACTAACAGCTAATGT
Found at i:2764636 original size:23 final size:22
Alignment explanation
Indices: 2764571--2764637 Score: 91
Period size: 22 Copynumber: 3.0 Consensus size: 22
2764561 TCCAAACCGA
*
2764571 TTTGATCAGTCAGACCGTTGAC
1 TTTGACCAGTCAGACCGTTGAC
*
2764593 TTTGACCAGTCAGACCATTGAC
1 TTTGACCAGTCAGACCGTTGAC
2764615 TTTGACCGAGTCA-ACCCGTTGAC
1 TTTGACC-AGTCAGA-CCGTTGAC
2764638 CGTTGACTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
22 28 0.70
23 12 0.30
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (22 bp):
TTTGACCAGTCAGACCGTTGAC
Found at i:2767007 original size:54 final size:54
Alignment explanation
Indices: 2766873--2767264 Score: 509
Period size: 54 Copynumber: 7.2 Consensus size: 54
2766863 TACCAAATAG
** * * **
2766873 GCACTAAACGTGCATTTCACGGAATTCATCCTTTGTGGATTGAAAAACTATTTC-
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGA-TGAATAACCGTTTCA
* *
2766927 GACACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAATCATTTCA
1 G-CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
* * *
2766982 GCACTAAGTGTACATTTCACAGAATTCATCCTATGTGGATGAATAATCGTTTCA
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
* * *
2767036 ACACTAAGTGTGCATTTCACAGAATTCATCTTATGTGGATGAATAACCGTTTC-
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
* * * ** *
2767089 GATACTAAGTGTGTATTTCACGAAATTCATCCTATGTGGATGAATAATTGTTTCG
1 G-CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
* * *
2767144 GCACTAAGTTTGCATTTCACGGAATTCATCCTATGGGGATGAATAACCGTTTCT
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
*
2767198 GTACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
* *
2767252 GCCCTATGTGTGC
1 GCACTAAGTGTGC
2767265 GAAACACAAA
Statistics
Matches: 298, Mismatches: 36, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
54 261 0.88
55 37 0.12
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (54 bp):
GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
Found at i:2767311 original size:162 final size:162
Alignment explanation
Indices: 2766882--2767311 Score: 459
Period size: 162 Copynumber: 2.6 Consensus size: 162
2766872 GGCACTAAAC
* * * ** * **
2766882 GTGCATTTCACGGAATTCATCCTTTGTGGATTGAAAAACTATTTCGACACTAAGTGTGCATTTCA
1 GTGCATTTCACAGAATTCATCCTATGTGGA-TGAATAACCGTTTCGACACTAAGTGTGGATAACA
** ** * * *
2766947 CGGAATTCATCCTATGTGGATGAATAATCATTTCAGCACTAAGTGTACATTTCACAGAATTCATC
65 CAAAATTCATAATATGTGGATGAATAATCGTATCGGCACTAAGTGTACATTTCACAGAATTCATC
* *
2767012 CTATGTGGATGAATAATCGTTTCAACACTAAGT
130 CTATGGGGATGAATAACCGTTTCAACACTAAGT
* * * **
2767045 GTGCATTTCACAGAATTCATCTTATGTGGATGAATAACCGTTTCGATACTAAGTGTGTATTTCAC
1 GTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCGACACTAAGTGTGGATAACAC
* ** * * * * *
2767110 GAAATTCATCCTATGTGGATGAATAATTGTTTCGGCACTAAGTTTGCATTTCACGGAATTCATCC
66 AAAATTCATAATATGTGGATGAATAATCGTATCGGCACTAAGTGTACATTTCACAGAATTCATCC
***
2767175 TATGGGGATGAATAACCGTTTCTGTACTAAGT
131 TATGGGGATGAATAACCGTTTCAACACTAAGT
* * *
2767207 GTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC-AGCCCTATGTGTGCGA-AAC
1 GTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCGA-CACTAAGTGTG-GATAAC
** * *
2767270 ACAAAATTCATAATATGTTTATGAATGATCGTATGGGCACTA
64 ACAAAATTCATAATATGTGGATGAATAATCGTATCGGCACTA
2767312 CGGGTGTATT
Statistics
Matches: 228, Mismatches: 37, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
161 1 0.00
162 199 0.87
163 28 0.12
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Consensus pattern (162 bp):
GTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCGACACTAAGTGTGGATAACAC
AAAATTCATAATATGTGGATGAATAATCGTATCGGCACTAAGTGTACATTTCACAGAATTCATCC
TATGGGGATGAATAACCGTTTCAACACTAAGT
Found at i:2772153 original size:30 final size:30
Alignment explanation
Indices: 2772117--2772189 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
2772107 TAAGGTGACC
*
2772117 CTTGGGTAGGCTCTGCAACCTCAAGATCTT
1 CTTGGGTAGGCTCTGCAACCCCAAGATCTT
* * * *
2772147 CTTGGGTAGGCCCTGCAGCCCCAATATTTT
1 CTTGGGTAGGCTCTGCAACCCCAAGATCTT
2772177 CTTGGGTAGGCTC
1 CTTGGGTAGGCTC
2772190 ACAGGCCCTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.16, C:0.27, G:0.26, T:0.30
Consensus pattern (30 bp):
CTTGGGTAGGCTCTGCAACCCCAAGATCTT
Found at i:2774462 original size:29 final size:29
Alignment explanation
Indices: 2774422--2774479 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
2774412 ATTTTTAATA
*
2774422 TTTTCTTTTGTAAATAAAATTTAATATAT
1 TTTTATTTTGTAAATAAAATTTAATATAT
2774451 TTTTATTTTGTAAATAAAATTTAATATAT
1 TTTTATTTTGTAAATAAAATTTAATATAT
2774480 ATATATCCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (29 bp):
TTTTATTTTGTAAATAAAATTTAATATAT
Found at i:2785728 original size:56 final size:56
Alignment explanation
Indices: 2785629--2785820 Score: 325
Period size: 56 Copynumber: 3.4 Consensus size: 56
2785619 AGAAATGTAA
*
2785629 ATAAT-AGTTTATTAATTT-CGTATGGGCACTTTGTGTGCAAAAAACTAAGAAATTT
1 ATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGC-AAAAACTAAGAAATTT
2785684 ATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAACTAAGAAATTT
1 ATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAACTAAGAAATTT
* *
2785740 ATAATAAGTTTATGAATTTCCGTATAGGCACTTTGTGTGCAAAAACTAAGAAATTC
1 ATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAACTAAGAAATTT
*
2785796 ATAATAAGTTTATGAATTTTCGTAT
1 ATAATAAGTTTATGAATTTCCGTAT
2785821 TGGTAATGGG
Statistics
Matches: 131, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
55 5 0.04
56 106 0.81
57 20 0.15
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (56 bp):
ATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAACTAAGAAATTT
Found at i:2791985 original size:41 final size:41
Alignment explanation
Indices: 2791940--2792032 Score: 109
Period size: 41 Copynumber: 2.3 Consensus size: 41
2791930 TGCCAAAATG
* * *
2791940 GTATCGATACCGAAATG-GAG-TATCGGTACCATAGTGTAGTA
1 GTATCGATACCGAAA-GAAAGCTATCGGTACCATAGTATA-AA
* *
2791981 GTATCGATACTGAGAGAAAGCTATCGGTACCATAGTATAAA
1 GTATCGATACCGAAAGAAAGCTATCGGTACCATAGTATAAA
2792022 GTATCGATACC
1 GTATCGATACC
2792033 ATGGTAAGGG
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
40 1 0.02
41 26 0.59
42 17 0.39
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (41 bp):
GTATCGATACCGAAAGAAAGCTATCGGTACCATAGTATAAA
Found at i:2792429 original size:56 final size:56
Alignment explanation
Indices: 2792357--2792473 Score: 207
Period size: 56 Copynumber: 2.1 Consensus size: 56
2792347 ATGTATGGTG
2792357 ATTTCCGTATGGGCACTTTGTGTGCAAAAACTAAGAAATTCATAATAAGTTTATAA
1 ATTTCCGTATGGGCACTTTGTGTGCAAAAACTAAGAAATTCATAATAAGTTTATAA
* * *
2792413 ATTTTCGTATGGGCACTTTGTGTGTAAAAACTAAGAAATTCATAATAAGTTTATGA
1 ATTTCCGTATGGGCACTTTGTGTGCAAAAACTAAGAAATTCATAATAAGTTTATAA
2792469 ATTTC
1 ATTTC
2792474 ATATTGGTAG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (56 bp):
ATTTCCGTATGGGCACTTTGTGTGCAAAAACTAAGAAATTCATAATAAGTTTATAA
Found at i:2795704 original size:13 final size:14
Alignment explanation
Indices: 2795674--2795701 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2795664 TTTAATAAAA
2795674 TAAAAAATAATTTT
1 TAAAAAATAATTTT
2795688 TAAAAAATAATTTT
1 TAAAAAATAATTTT
2795702 AAATAACTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAAAAAATAATTTT
Found at i:2797244 original size:23 final size:23
Alignment explanation
Indices: 2797218--2797293 Score: 98
Period size: 23 Copynumber: 3.2 Consensus size: 23
2797208 AATAACATAT
2797218 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATGTAA
2797241 TAGGTAGAGCGCTTATATAATGTAA
1 TAGGT--AGCGCTTATATAATGTAA
* * **
2797266 TAGGTAACACTTATATAATAAAA
1 TAGGTAGCGCTTATATAATGTAA
2797289 TAGGT
1 TAGGT
2797294 TAATTACTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
23 24 0.51
25 23 0.49
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.33
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATGTAA
Found at i:2797257 original size:25 final size:24
Alignment explanation
Indices: 2797218--2797293 Score: 102
Period size: 25 Copynumber: 3.2 Consensus size: 24
2797208 AATAACATAT
2797218 TAGGT-AGCGCTTATATAATGTAA
1 TAGGTAAGCGCTTATATAATGTAA
2797241 TAGGTAGAGCGCTTATATAATGTAA
1 TAGGTA-AGCGCTTATATAATGTAA
* **
2797266 TAGGTAA-CACTTATATAATAAAA
1 TAGGTAAGCGCTTATATAATGTAA
2797289 TAGGT
1 TAGGT
2797294 TAATTACTTA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
23 23 0.48
24 1 0.02
25 24 0.50
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.33
Consensus pattern (24 bp):
TAGGTAAGCGCTTATATAATGTAA
Found at i:2797418 original size:23 final size:23
Alignment explanation
Indices: 2797392--2797441 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
2797382 ATCAAGAACA
* *
2797392 ATAACATATTAGTTAGCGCTTAT
1 ATAACATAATAGCTAGCGCTTAT
* *
2797415 ATAACGTAATAGCTAGCTCTTAT
1 ATAACATAATAGCTAGCGCTTAT
2797438 ATAA
1 ATAA
2797442 TAAAATAGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (23 bp):
ATAACATAATAGCTAGCGCTTAT
Found at i:2797685 original size:157 final size:158
Alignment explanation
Indices: 2797248--2797734 Score: 760
Period size: 158 Copynumber: 3.1 Consensus size: 158
2797238 TAATAGGTAG
* *
2797248 AGCGCTTATATAATGTAATAGGTAACACTTATATAATAAAATAGGTTAATTACTTAATTTGTTAT
1 AGCGCTTATATAACGTAATAGATAACACTTATATAATAAAATAGGTTAATTACTTAATTTGTTAT
* ** *
2797313 TACAACATATTAGGTAAATGCCTAAAATGTTATCAATGATAACATAACCGGTTAATTACTATAAA
66 TACAACATATTAGGTAAATGCCTAAAATGTTACCAATGATAACATAACCAATTAATTACTAGAAA
* *
2797378 CATTATCAAGAACAATAACATATTAGTT
131 CATTATCAAGCACAATAACATATTAGGT
* * * *
2797406 AGCGCTTATATAACGTAATAGCTAGCTCTTATATAATAAAATAGGTTAATTATTTAATTTGTTAT
1 AGCGCTTATATAACGTAATAGATAACACTTATATAATAAAATAGGTTAATTACTTAATTTGTTAT
**
2797471 TACAACATATTAGGTAAATGCCTAAAATGTTACCAACAATAACATAACCAATTAATTACTAGAAA
66 TACAACATATTAGGTAAATGCCTAAAATGTTACCAATGATAACATAACCAATTAATTACTAGAAA
*
2797536 CATTATCAAGCACAATAACATTTTAGGT
131 CATTATCAAGCACAATAACATATTAGGT
* *
2797564 AGCGCTTATATAACGTAATAGATAACGCTTATATAATAAAATA-ATTAATTACTTAATTTGTTAT
1 AGCGCTTATATAACGTAATAGATAACACTTATATAATAAAATAGGTTAATTACTTAATTTGTTAT
* *
2797628 TACAACATATTAGGTAAACGCTTAAAATGTTACCAATGATAACATAACCAATTAATTACTAGAAA
66 TACAACATATTAGGTAAATGCCTAAAATGTTACCAATGATAACATAACCAATTAATTACTAGAAA
* * *
2797693 CATTATCAAACATAATAATATATTAGGT
131 CATTATCAAGCACAATAACATATTAGGT
*
2797721 AGCGCTTATGTAAC
1 AGCGCTTATATAAC
2797735 AAAATATACT
Statistics
Matches: 301, Mismatches: 28, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
157 117 0.39
158 184 0.61
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (158 bp):
AGCGCTTATATAACGTAATAGATAACACTTATATAATAAAATAGGTTAATTACTTAATTTGTTAT
TACAACATATTAGGTAAATGCCTAAAATGTTACCAATGATAACATAACCAATTAATTACTAGAAA
CATTATCAAGCACAATAACATATTAGGT
Found at i:2798058 original size:74 final size:72
Alignment explanation
Indices: 2797807--2798046 Score: 355
Period size: 74 Copynumber: 3.4 Consensus size: 72
2797797 AAAATTTAAA
* *
2797807 CTACCTATTACATTAAAATACC-ACCG--TTTTT-AAGGTTGTTAATAATGTAAACGGT-AAGAA
1 CTACCTATTACATTAAAATACCTACCGATTTTTTGAAGGTTGCTAATAATGTAAACGGTAAAAAA
2797867 AATAGCG
66 AATAGCG
*
2797874 CTACCTATTACATTAAAATACCTATCGATTTTTTGAAGGTTGCTAATAATGTAAACGGTAAAAAA
1 CTACCTATTACATTAAAATACCTACCGATTTTTTGAAGGTTGCTAATAATGTAAACGGT-AAAAA
*
2797939 AAATAGTG
65 AAATAGCG
* *
2797947 CTACATATTACATTAAAATACCTACCGGTTTTTTTGAAGGTTGCTAATAATGTAAACGGTAAAAA
1 CTACCTATTACATTAAAATACCTACC-GATTTTTTGAAGGTTGCTAATAATGTAAACGGTAAAAA
2798012 AAATAGACG
65 AAATAG-CG
*
2798021 CTACCTATTACATTAAACTACCTACC
1 CTACCTATTACATTAAAATACCTACC
2798047 AGATATGTTG
Statistics
Matches: 155, Mismatches: 10, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
67 22 0.14
68 3 0.02
70 5 0.03
71 23 0.15
73 45 0.29
74 57 0.37
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.32
Consensus pattern (72 bp):
CTACCTATTACATTAAAATACCTACCGATTTTTTGAAGGTTGCTAATAATGTAAACGGTAAAAAA
AATAGCG
Found at i:2798265 original size:21 final size:20
Alignment explanation
Indices: 2798236--2798274 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
2798226 CTGATATGTT
2798236 AAAAGTATCGATACTTTATA
1 AAAAGTATCGATACTTTATA
2798256 AAAATGTATCGATACTTTA
1 AAAA-GTATCGATACTTTA
2798275 CAATATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (20 bp):
AAAAGTATCGATACTTTATA
Found at i:2798591 original size:114 final size:114
Alignment explanation
Indices: 2798126--2798807 Score: 995
Period size: 113 Copynumber: 6.1 Consensus size: 114
2798116 TAGCGCCTAT
*
2798126 AAAGTATCGATAC--TTTATAAAAATGTATCGATACTTTACAATATAACA-GTAAAAATATGACA
1 AAAGTATCGATCCTTTTTATAAAAATGTATCGATACTTTACAATATAACATGTAAAAATATGACA
* *
2798188 AAACCAATTTCATTATGACAAAACCGGTAAAGAGCTACCTGATATGTTA
66 AAACCAGTTTCATTATGACAAAACCGGTAAAGAGCTACCTGATATGTTG
* * *
2798237 AAAGTATCGATAC--TTTATAAAAATGTATCGATACTTTACAATATAAAAGGTAAAAATATGACA
1 AAAGTATCGATCCTTTTTATAAAAATGTATCGATACTTTACAATATAACATGTAAAAATATGACA
* *
2798300 AAACCAGTTT-ATTATGACAAAA-CGGTAAAGAGTTACCTAATATGTTG
66 AAACCAGTTTCATTATGACAAAACCGGTAAAGAGCTACCTGATATGTTG
* *
2798347 AAAGTATCGATCCATTTTATAAAAATGTATTGATACTTTACAATATAACATGTAAAAATATGACA
1 AAAGTATCGATCCTTTTTATAAAAATGTATCGATACTTTACAATATAACATGTAAAAATATGACA
*
2798412 AAACCA-TTTCATTATGACAAAACCGGTAAAGAGCTACTTGATATGTTG
66 AAACCAGTTTCATTATGACAAAACCGGTAAAGAGCTACCTGATATGTTG
* * * * *
2798460 AAATTATCGATCATTTTTATAAAAATATATCGATACTTTACAATATAACATGTAAAAATAAGATA
1 AAAGTATCGATCCTTTTTATAAAAATGTATCGATACTTTACAATATAACATGTAAAAATATGACA
* *
2798525 AAACCAGTTTTATTATGACAAAACCGGTAAAGAACTACCTGATATGTTG
66 AAACCAGTTTCATTATGACAAAACCGGTAAAGAGCTACCTGATATGTTG
* ** *
2798574 AAAGTATCGATCCTTTTTATAAAAATCTATCGATACTTTACAATATAACAAATAAAAATAAGA-A
1 AAAGTATCGATCCTTTTTATAAAAATGTATCGATACTTTACAATATAACATGTAAAAATATGACA
* * *
2798638 AAACCAGCTTCATTATGACAAAACCGGTAAAGAGCTACTTTATATGTTG
66 AAACCAGTTTCATTATGACAAAACCGGTAAAGAGCTACCTGATATGTTG
** *
2798687 AAAGTATCGATTTTTTTTATAAAAATATATCGATACTTTACAATATAACATGTAAAAATATGACA
1 AAAGTATCGATCCTTTTTATAAAAATGTATCGATACTTTACAATATAACATGTAAAAATATGACA
* * * * * *
2798752 AAACCGGTTTCATTATGACAACATCAGAAAAGAGCTACCTAATATGTTG
66 AAACCAGTTTCATTATGACAAAACCGGTAAAGAGCTACCTGATATGTTG
2798801 AAAGTAT
1 AAAGTAT
2798808 AAATAATTTT
Statistics
Matches: 518, Mismatches: 46, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
110 34 0.07
111 62 0.12
112 88 0.17
113 188 0.36
114 146 0.28
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.31
Consensus pattern (114 bp):
AAAGTATCGATCCTTTTTATAAAAATGTATCGATACTTTACAATATAACATGTAAAAATATGACA
AAACCAGTTTCATTATGACAAAACCGGTAAAGAGCTACCTGATATGTTG
Found at i:2798619 original size:227 final size:223
Alignment explanation
Indices: 2798126--2798807 Score: 1021
Period size: 227 Copynumber: 3.0 Consensus size: 223
2798116 TAGCGCCTAT
*
2798126 AAAGTATCGATAC-TTTATAAAAATGTATCGATACTTTACAATATAACAGTAAAAATATGACAAA
1 AAAGTATCGATCCTTTTATAAAAATGTATCGATACTTTACAATATAACAGTAAAAATATGACAAA
* * *
2798190 ACCAATTTCATTATGACAAAACCGGTAAAGAGCTACCTGATATGTTAAAAGTATCGATA-CTTTA
66 ACC-ATTTCATTATGACAAAACCGGTAAAGAGCTACTTGATATGTTGAAAGTATCGATATTTTTA
* * *
2798254 TAAAAATGTATCGATACTTTACAATATAAAAGGTAAAAATATGACAAAACCAG-TTTATTATGAC
130 TAAAAATATATCGATACTTTACAATATAACATGTAAAAATATGACAAAACCAGTTTTATTATGAC
*
2798318 AAAACGGTAAAGAGTTACCTAATATGTTG
195 AAAACGGTAAAGAGCTACCTAATATGTTG
*
2798347 AAAGTATCGATCCATTTTATAAAAATGTATTGATACTTTACAATATAACATGTAAAAATATGACA
1 AAAGTATCGATCC-TTTTATAAAAATGTATCGATACTTTACAATATAACA-GTAAAAATATGACA
*
2798412 AAACCATTTCATTATGACAAAACCGGTAAAGAGCTACTTGATATGTTGAAATTATCGATCATTTT
64 AAACCATTTCATTATGACAAAACCGGTAAAGAGCTACTTGATATGTTGAAAGTATCGAT-ATTTT
* *
2798477 TATAAAAATATATCGATACTTTACAATATAACATGTAAAAATAAGATAAAACCAGTTTTATTATG
128 TATAAAAATATATCGATACTTTACAATATAACATGTAAAAATATGACAAAACCAGTTTTATTATG
* *
2798542 ACAAAACCGGTAAAGAACTACCTGATATGTTG
193 ACAAAA-CGGTAAAGAGCTACCTAATATGTTG
* * *
2798574 AAAGTATCGATCCTTTTTATAAAAATCTATCGATACTTTACAATATAACAAATAAAAATAAGA-A
1 AAAGTATCGATCC-TTTTATAAAAATGTATCGATACTTTACAATATAAC-AGTAAAAATATGACA
* * *
2798638 AAACCAGCTTCATTATGACAAAACCGGTAAAGAGCTACTTTATATGTTGAAAGTATCGATTTTTT
64 AAACCA-TTTCATTATGACAAAACCGGTAAAGAGCTACTTGATATGTTGAAAGTATCGA-TATTT
* *
2798703 TTATAAAAATATATCGATACTTTACAATATAACATGTAAAAATATGACAAAACCGGTTTCATTAT
127 TTATAAAAATATATCGATACTTTACAATATAACATGTAAAAATATGACAAAACCAGTTTTATTAT
* * *
2798768 GACAACATCAGAAAAGAGCTACCTAATATGTTG
192 GACAA-AACGGTAAAGAGCTACCTAATATGTTG
2798801 AAAGTAT
1 AAAGTAT
2798808 AAATAATTTT
Statistics
Matches: 418, Mismatches: 32, Indels: 16
0.90 0.07 0.03
Matches are distributed among these distances:
221 12 0.03
223 85 0.20
224 20 0.05
225 52 0.12
226 22 0.05
227 224 0.54
228 3 0.01
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.31
Consensus pattern (223 bp):
AAAGTATCGATCCTTTTATAAAAATGTATCGATACTTTACAATATAACAGTAAAAATATGACAAA
ACCATTTCATTATGACAAAACCGGTAAAGAGCTACTTGATATGTTGAAAGTATCGATATTTTTAT
AAAAATATATCGATACTTTACAATATAACATGTAAAAATATGACAAAACCAGTTTTATTATGACA
AAACGGTAAAGAGCTACCTAATATGTTG
Found at i:2799457 original size:2 final size:2
Alignment explanation
Indices: 2799422--2799446 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2799412 CACATCTCAC
2799422 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
2799447 ATTTTTCTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2805210 original size:29 final size:29
Alignment explanation
Indices: 2805153--2805239 Score: 124
Period size: 29 Copynumber: 3.0 Consensus size: 29
2805143 ATTTTCACCT
* *
2805153 AACTAAATTGATGT-AGCAATGCTATCAA
1 AACTAAATTGATATAAGAAATGCTATCAA
*
2805181 AACTAAATTGATATAAGTAATGCTATCAA
1 AACTAAATTGATATAAGAAATGCTATCAA
2805210 AACTAAATTGATATAAGAAATGAC-ATCAA
1 AACTAAATTGATATAAGAAATG-CTATCAA
2805239 A
1 A
2805240 TTAATTTAGG
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
28 13 0.24
29 40 0.74
30 1 0.02
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.28
Consensus pattern (29 bp):
AACTAAATTGATATAAGAAATGCTATCAA
Found at i:2818202 original size:29 final size:29
Alignment explanation
Indices: 2818160--2818218 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
2818150 ATTTTCACCT
2818160 AACTAAACTAATGTAAGCAATGACATCAA
1 AACTAAACTAATGTAAGCAATGACATCAA
* *
2818189 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAACTAATGTAAGCAATGACATCAA
2818218 A
1 A
2818219 TTAATTTAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.51, C:0.15, G:0.12, T:0.22
Consensus pattern (29 bp):
AACTAAACTAATGTAAGCAATGACATCAA
Found at i:2827308 original size:2 final size:2
Alignment explanation
Indices: 2827301--2827328 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2827291 TTTTCAAACT
2827301 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
2827329 AAGACCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2836751 original size:18 final size:19
Alignment explanation
Indices: 2836713--2836753 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
2836703 TTAAAGTCAA
* *
2836713 CGGCTCAGTCGGCTTGGCT
1 CGGCTCAGTCGGCTCGACT
2836732 CGGCTCAGT-GGCTCGACT
1 CGGCTCAGTCGGCTCGACT
2836750 CGGC
1 CGGC
2836754 GGGGCGGCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.07, C:0.34, G:0.37, T:0.22
Consensus pattern (19 bp):
CGGCTCAGTCGGCTCGACT
Found at i:2843263 original size:21 final size:21
Alignment explanation
Indices: 2843238--2843278 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2843228 TGGGGCTTCT
2843238 TTGTATAAGTGGACATTCTCC
1 TTGTATAAGTGGACATTCTCC
*
2843259 TTGTATAGGTGGACATTCTC
1 TTGTATAAGTGGACATTCTC
2843279 GTATGCGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (21 bp):
TTGTATAAGTGGACATTCTCC
Found at i:2850369 original size:29 final size:29
Alignment explanation
Indices: 2850327--2850506 Score: 172
Period size: 29 Copynumber: 6.3 Consensus size: 29
2850317 AGAAATGTGA
* *
2850327 TTATTGTAATTTCTATGAAGTTTTTTATT
1 TTATTGTAATTTCTATAAAGTTTTGTATT
*
2850356 TTATTGTAATTTCTATGAAGTTTTGTATT
1 TTATTGTAATTTCTATAAAGTTTTGTATT
* * *
2850385 TTATTGTAATTTATA-AAATATTTTGTA-C
1 TTATTGTAATTTCTATAAA-GTTTTGTATT
* *
2850413 TTATTGTAAATTCTAAAAAGTTTTGTATT
1 TTATTGTAATTTCTATAAAGTTTTGTATT
* *
2850442 TTATTGTAA-TTCCAAAAAGTTTTGTCA--
1 TTATTGTAATTTCTATAAAGTTTTGT-ATT
* * * **
2850469 TTATTGTAAATTCCAAAAAGTTTTGTCCT
1 TTATTGTAATTTCTATAAAGTTTTGTATT
2850498 TTATTGTAA
1 TTATTGTAA
2850507 ATTACAATTA
Statistics
Matches: 133, Mismatches: 11, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
27 9 0.07
28 53 0.40
29 71 0.53
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.53
Consensus pattern (29 bp):
TTATTGTAATTTCTATAAAGTTTTGTATT
Found at i:2850427 original size:57 final size:56
Alignment explanation
Indices: 2850356--2850547 Score: 201
Period size: 57 Copynumber: 3.4 Consensus size: 56
2850346 GTTTTTTATT
* **
2850356 TTATTGTAATTTCTATGAAGTTTTGTATTTTATTGTAATTTATAAAATATTTTGT-A
1 TTATTGTAAATTCTAAAAAGTTTTGTATTTTATTGTAATTTA-AAAATATTTTGTCA
* *
2850412 CTTATTGTAAATTCTAAAAAGTTTTGTATTTTATTGTAATTCCAAAAA-GTTTTGTCA
1 -TTATTGTAAATTCTAAAAAGTTTTGTATTTTATTGTAATT-TAAAAATATTTTGTCA
* ** * * * * *
2850469 TTATTGTAAATTCCAAAAAGTTTTGTCCTTTATTGTAAATTACAATTAGTTTGTTCT
1 TTATTGTAAATTCTAAAAAGTTTTGTATTTTATTGTAATTTAAAAATATTTTG-TCA
2850526 TTATTGTAAATT-TCAAAAAGTT
1 TTATTGTAAATTCT-AAAAAGTT
2850548 ATCCTTTATT
Statistics
Matches: 114, Mismatches: 16, Indels: 10
0.81 0.11 0.07
Matches are distributed among these distances:
55 3 0.03
56 46 0.40
57 64 0.56
58 1 0.01
ACGTcount: A:0.32, C:0.07, G:0.10, T:0.51
Consensus pattern (56 bp):
TTATTGTAAATTCTAAAAAGTTTTGTATTTTATTGTAATTTAAAAATATTTTGTCA
Found at i:2850507 original size:29 final size:29
Alignment explanation
Indices: 2850344--2850574 Score: 206
Period size: 28 Copynumber: 8.2 Consensus size: 29
2850334 AATTTCTATG
* * * * **
2850344 AAGTTTTTTATTTTATTGTAATTTCTATG
1 AAGTTTTGTACTTTATTGTAAATTCCAAA
* * **
2850373 AAGTTTTGTATTTTATTGTAATTTATAAA
1 AAGTTTTGTACTTTATTGTAAATTCCAAA
*
2850402 ATA-TTTTGTAC-TTATTGTAAATTCTAAA
1 A-AGTTTTGTACTTTATTGTAAATTCCAAA
*
2850430 AAGTTTTGTATTTTATTGT-AATTCCAAA
1 AAGTTTTGTACTTTATTGTAAATTCCAAA
*
2850458 AAGTTTTGT-CATTATTGTAAATTCCAAA
1 AAGTTTTGTACTTTATTGTAAATTCCAAA
* * *
2850486 AAGTTTTGTCCTTTATTGTAAATTACAAT
1 AAGTTTTGTACTTTATTGTAAATTCCAAA
* * *
2850515 TAG-TTTGTTCTTTATTGTAAATTTCAAA
1 AAGTTTTGTACTTTATTGTAAATTCCAAA
* * *
2850543 AAG--TTATCCTTTATTGTAAATTTCAAA
1 AAGTTTTGTACTTTATTGTAAATTCCAAA
2850570 AAGTT
1 AAGTT
2850575 ATGCCTTTTA
Statistics
Matches: 174, Mismatches: 21, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
27 33 0.19
28 82 0.47
29 58 0.33
30 1 0.01
ACGTcount: A:0.32, C:0.07, G:0.10, T:0.51
Consensus pattern (29 bp):
AAGTTTTGTACTTTATTGTAAATTCCAAA
Found at i:2852502 original size:7 final size:7
Alignment explanation
Indices: 2852492--2852527 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
2852482 GTTTTTTTTC
2852492 TTTTCAG
1 TTTTCAG
*
2852499 TTTTCAC
1 TTTTCAG
2852506 TTTTCAG
1 TTTTCAG
*
2852513 TTTTCAC
1 TTTTCAG
2852520 TTTTCAG
1 TTTTCAG
2852527 T
1 T
2852528 ATACTTATGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.14, C:0.19, G:0.08, T:0.58
Consensus pattern (7 bp):
TTTTCAG
Found at i:2852508 original size:14 final size:14
Alignment explanation
Indices: 2852491--2852527 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
2852481 TGTTTTTTTT
2852491 CTTTTCAGTTTTCA
1 CTTTTCAGTTTTCA
2852505 CTTTTCAGTTTTCA
1 CTTTTCAGTTTTCA
2852519 CTTTTCAGT
1 CTTTTCAGT
2852528 ATACTTATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.14, C:0.22, G:0.08, T:0.57
Consensus pattern (14 bp):
CTTTTCAGTTTTCA
Found at i:2853219 original size:27 final size:27
Alignment explanation
Indices: 2853183--2853247 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
2853173 TTACGTAATG
2853183 AAGATTGCTTTCAACTTCATGGCTAAGA
1 AAGA-TGCTTTCAACTTCATGGCTAAGA
2853211 AAGATGCTTTCAACTTCATGGCTAAGA
1 AAGATGCTTTCAACTTCATGGCTAAGA
2853238 AAGATGCTTT
1 AAGATGCTTT
2853248 ATGGGTACGC
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 33 0.89
28 4 0.11
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Consensus pattern (27 bp):
AAGATGCTTTCAACTTCATGGCTAAGA
Found at i:2856201 original size:23 final size:22
Alignment explanation
Indices: 2856159--2856201 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
2856149 ACTAATTTAT
*
2856159 AATAATTATATTTAAATAAATA
1 AATAATTAAATTTAAATAAATA
*
2856181 AATAACTTAAATTTAATTAAA
1 AATAA-TTAAATTTAAATAAA
2856202 ATTTATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
AATAATTAAATTTAAATAAATA
Done.