Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008061.1 Hibiscus syriacus cultivar Beakdansim tig00110556_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: 5800122
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 26
Found at i:3755530 original size:42 final size:42
Alignment explanation
Indices: 3755444--3755656 Score: 316
Period size: 42 Copynumber: 5.2 Consensus size: 42
3755434 GACTATCGCA
3755444 TTGCGATAGTCGAAGTTCGCGTTGC-A--T-TTCCAAATT-G
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
3755481 TTGCGATAGTCGAAGTTCGCGTTACGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
3755523 TTGCGATAGTCCAAG-T-GCGTTGCGATTTATT-CAAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAA-TTCG
3755563 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
**
3755605 TTGCGATAGTCGAAGTTCGTATTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
3755647 TTACGATAGT
1 TTGCGATAGT
3755657 ACAAAATCGC
Statistics
Matches: 160, Mismatches: 7, Indels: 13
0.89 0.04 0.07
Matches are distributed among these distances:
37 24 0.15
38 1 0.01
39 4 0.03
40 33 0.21
41 11 0.07
42 83 0.52
43 4 0.03
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (42 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:3755572 original size:82 final size:81
Alignment explanation
Indices: 3755444--3755656 Score: 299
Period size: 82 Copynumber: 2.6 Consensus size: 81
3755434 GACTATCGCA
*
3755444 TTGCGATAGTCGAAGTTCGCGTTGC-A-TT-TCCAAATT-GTTGCGATAGTCGAAGTTCGCGTTA
1 TTGCGATAGTCGAAG-T-GCGTTGCGATTTATTCAAATTCGTTGCGATAGTCGAAGTTCGCGTTA
3755505 CGATTTATTCCAAATTCG
64 CGATTTATTCCAAATTCG
* *
3755523 TTGCGATAGTCCAAGTGCGTTGCGATTTATTCAAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGC
1 TTGCGATAGTCGAAGTGCGTTGCGATTTATTCAAA-TTCGTTGCGATAGTCGAAGTTCGCGTTAC
3755588 GATTTATTCCAAATTCG
65 GATTTATTCCAAATTCG
* *
3755605 TTGCGATAGTCGAAGTTCGTATTGCGATTTATTCCAAATTCGTTACGATAGT
1 TTGCGATAGTCGAAGTGCG--TTGCGATTTATT-CAAATTCGTTGCGATAGT
3755657 ACAAAATCGC
Statistics
Matches: 120, Mismatches: 6, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
77 7 0.06
78 2 0.02
79 16 0.13
80 5 0.04
81 2 0.02
82 59 0.49
84 25 0.21
85 4 0.03
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (81 bp):
TTGCGATAGTCGAAGTGCGTTGCGATTTATTCAAATTCGTTGCGATAGTCGAAGTTCGCGTTACG
ATTTATTCCAAATTCG
Found at i:3755632 original size:21 final size:19
Alignment explanation
Indices: 3755444--3755624 Score: 107
Period size: 21 Copynumber: 9.1 Consensus size: 19
3755434 GACTATCGCA
3755444 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCGAAGTT--CG
* * *
3755465 TTGC-AT-TTCCAAATT-G
1 TTGCGATAGTCGAAGTTCG
3755481 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCGAAGTT--CG
* * * *
3755502 TTACGATTTATTCCAAATTCG
1 TTGCGA--TAGTCGAAGTTCG
* *
3755523 TTGCGATAGTCCAAGTGCG
1 TTGCGATAGTCGAAGTTCG
* *
3755542 TTGCGATTTATTCAAAGTTCG
1 TTGCGA--TAGTCGAAGTTCG
3755563 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCGAAGTT--CG
* * *
3755584 TTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCGAAGTTCG
3755605 TTGCGATAGTCGAAGTTCG
1 TTGCGATAGTCGAAGTTCG
3755624 T
1 T
3755625 ATTGCGATTT
Statistics
Matches: 122, Mismatches: 25, Indels: 28
0.70 0.14 0.16
Matches are distributed among these distances:
16 5 0.04
17 2 0.02
18 6 0.05
19 42 0.34
20 2 0.02
21 49 0.40
23 16 0.13
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.35
Consensus pattern (19 bp):
TTGCGATAGTCGAAGTTCG
Found at i:3756400 original size:21 final size:21
Alignment explanation
Indices: 3756376--3756448 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
3756366 TTTTGAATAA
3756376 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* **
3756397 ATCGCAA--CGAA-TTTGAAA
1 ATCGCAACGCGAACTTCGACT
*
3756415 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
*
3756436 ATCGCAATGCGAA
1 ATCGCAACGCGAA
3756449 TATGTAAATC
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
18 11 0.26
19 4 0.10
20 4 0.10
21 23 0.55
ACGTcount: A:0.34, C:0.26, G:0.21, T:0.19
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:3756428 original size:39 final size:39
Alignment explanation
Indices: 3756351--3756464 Score: 156
Period size: 39 Copynumber: 2.8 Consensus size: 39
3756341 TGCGATTTTG
3756351 GACTATCGCAACGAATTTTGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAA-TTTG-A-AAATCGCAACGCGAACTTC
*
3756393 GACTATCGCAACGAATTTGAAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAATTTGAAAATCGCAACGCGAACTTC
* *
3756432 GACTATCGCAATGCGAATATGTAAATCGCAACG
1 GACTATCGCAA--CGAATTTGAAAATCGCAACG
3756465 ATAGTAAGTT
Statistics
Matches: 67, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
39 29 0.43
40 1 0.01
41 22 0.33
42 15 0.22
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (39 bp):
GACTATCGCAACGAATTTGAAAATCGCAACGCGAACTTC
Found at i:3756487 original size:19 final size:20
Alignment explanation
Indices: 3756463--3756505 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
3756453 TAAATCGCAA
*
3756463 CGATAGT-AAGTTCGTGTTG
1 CGATAGTCAAGTTCGCGTTG
3756482 CGATAGTCGAAGTTCGCGTTG
1 CGATAGTC-AAGTTCGCGTTG
3756503 CGA
1 CGA
3756506 ATCTGGAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
21 14 0.67
ACGTcount: A:0.21, C:0.16, G:0.33, T:0.30
Consensus pattern (20 bp):
CGATAGTCAAGTTCGCGTTG
Found at i:3756861 original size:27 final size:30
Alignment explanation
Indices: 3756827--3756896 Score: 124
Period size: 29 Copynumber: 2.3 Consensus size: 30
3756817 CCGAACCCAT
3756827 ATTATATATAATTAATATAAAAA-ATAAAA
1 ATTATATATAATTAATATAAAAATATAAAA
3756856 ATTATATATAATTAATATAAAAATATAAAA
1 ATTATATATAATTAATATAAAAATATAAAA
3756886 ATATATATATA
1 AT-TATATATA
3756897 TATAATCGGG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
29 23 0.59
30 8 0.21
31 8 0.21
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (30 bp):
ATTATATATAATTAATATAAAAATATAAAA
Found at i:3760533 original size:16 final size:17
Alignment explanation
Indices: 3760512--3760550 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
3760502 ATAATTATAA
3760512 ATTTTAAA-AAAAAAAT
1 ATTTTAAATAAAAAAAT
*
3760528 ATTTTAAATTAAAATAAT
1 ATTTTAAA-TAAAAAAAT
3760546 ATTTT
1 ATTTT
3760551 TGTTGGTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
18 12 0.60
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTTTAAATAAAAAAAT
Found at i:3761976 original size:17 final size:17
Alignment explanation
Indices: 3761935--3761979 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
3761925 CCCTACTTGA
3761935 TTAAATATTTAATAAAT
1 TTAAATATTTAATAAAT
** **
3761952 TTTTATATTTTTTAAAT
1 TTAAATATTTAATAAAT
3761969 TTAAATATTTA
1 TTAAATATTTA
3761980 TTGTTACATT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTAAATATTTAATAAAT
Found at i:3763048 original size:18 final size:19
Alignment explanation
Indices: 3763008--3763048 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3762998 ACATGATTTA
*
3763008 AAATTCAAACTACAGTCAT
1 AAATTCAAACTACAATCAT
*
3763027 AAATTCAAACT-CAATTAT
1 AAATTCAAACTACAATCAT
3763045 AAAT
1 AAAT
3763049 AATTGTCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.51, C:0.17, G:0.02, T:0.29
Consensus pattern (19 bp):
AAATTCAAACTACAATCAT
Found at i:3763278 original size:2 final size:2
Alignment explanation
Indices: 3763269--3763302 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3763259 AAAATATAAA
3763269 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3763303 ATCGGGGCGG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3770667 original size:21 final size:20
Alignment explanation
Indices: 3770643--3770696 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
3770633 ATTGAAATTA
3770643 ATAACAAATAAATATAATAAT
1 ATAA-AAATAAATATAATAAT
*
3770664 ATAATAAATAAATATAGTAAT
1 ATAA-AAATAAATATAATAAT
3770685 -TAAAATATAAAT
1 ATAAAA-ATAAAT
3770697 TTATAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 9 0.30
21 19 0.63
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (20 bp):
ATAAAAATAAATATAATAAT
Found at i:3773596 original size:64 final size:67
Alignment explanation
Indices: 3773528--3773655 Score: 210
Period size: 64 Copynumber: 2.0 Consensus size: 67
3773518 TTTAAAAAGA
3773528 AAACATCGAATAGGATTTATGCATCGATGCATAAG-G-AGTGCATCGATGCAT-CC-CCATTAAA
1 AAACATCGAATAGGATTTATGCATCGATGCAT-AGTGTAGTGCATCGATGCATACCTCCATTAAA
3773589 TAC
65 TAC
*
3773592 AAACATCGAATAGGATTTATGCATCGATGCATGGTGTAGTGCATCGATGCATACCTCCATTAAA
1 AAACATCGAATAGGATTTATGCATCGATGCATAGTGTAGTGCATCGATGCATACCTCCATTAAA
3773656 AGATGAAAAT
Statistics
Matches: 59, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
63 1 0.02
64 33 0.56
65 15 0.25
66 2 0.03
67 8 0.14
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (67 bp):
AAACATCGAATAGGATTTATGCATCGATGCATAGTGTAGTGCATCGATGCATACCTCCATTAAAT
AC
Found at i:3773962 original size:29 final size:29
Alignment explanation
Indices: 3773925--3773991 Score: 116
Period size: 29 Copynumber: 2.3 Consensus size: 29
3773915 TATGATATAT
* *
3773925 GACATGAATCCATACCTTATGCATTATGG
1 GACATGAATCCATACCCTATGAATTATGG
3773954 GACATGAATCCATACCCTATGAATTATGG
1 GACATGAATCCATACCCTATGAATTATGG
3773983 GACATGAAT
1 GACATGAAT
3773992 AAGCAAGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.28
Consensus pattern (29 bp):
GACATGAATCCATACCCTATGAATTATGG
Found at i:3774312 original size:103 final size:103
Alignment explanation
Indices: 3774133--3774343 Score: 386
Period size: 103 Copynumber: 2.0 Consensus size: 103
3774123 GTAGAGGGTC
* *
3774133 TATGTGGTCCTTCGGGACATATATGTATTATTTGGAACATGTGTGAGGTCTGGCGAGACACATAC
1 TATGTGGTCATTCAGGACATATATGTATTATTTGGAACATGTGTGAGGTCTGGCGAGACACATAC
3774198 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* *
3774236 TATGTGGTCATTCAGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCATTCAGGACATATATGTATTATTTGGAACATGTGTGAGGTCTGGCGAGACACATAC
3774301 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
3774339 TATGT
1 TATGT
3774344 AGTCCTTATG
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.27, C:0.13, G:0.25, T:0.36
Consensus pattern (103 bp):
TATGTGGTCATTCAGGACATATATGTATTATTTGGAACATGTGTGAGGTCTGGCGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:3774400 original size:23 final size:23
Alignment explanation
Indices: 3774367--3774429 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
3774357 ATTATTATAT
3774367 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
3774390 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
3774413 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
3774430 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:3780602 original size:64 final size:64
Alignment explanation
Indices: 3780534--3780676 Score: 175
Period size: 64 Copynumber: 2.2 Consensus size: 64
3780524 TGCACTGCAT
* *
3780534 GTGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAATAGGATTTATGCATCGATGCATAAG-G
1 GTGCATCGATGCATCCAA-TTAAAAA-AAAACATCAAATAGGATTTATGCATCGATGCAT-AGTG
3780597 -A
63 TA
* * * *
3780598 GTGCATCGATGCATCCCCATTAAATACAAACATCAAATAGGATTTATGCATCGATGCATGGTGTA
1 GTGCATCGATGCAT-CCAATTAAAAAAAAACATCAAATAGGATTTATGCATCGATGCATAGTGTA
3780663 GTGCATCGATGCAT
1 GTGCATCGATGCAT
3780677 ACCTCCATTA
Statistics
Matches: 69, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
63 1 0.01
64 46 0.67
65 21 0.30
66 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (64 bp):
GTGCATCGATGCATCCAATTAAAAAAAAACATCAAATAGGATTTATGCATCGATGCATAGTGTA
Found at i:3780994 original size:29 final size:29
Alignment explanation
Indices: 3780958--3781024 Score: 134
Period size: 29 Copynumber: 2.3 Consensus size: 29
3780948 TATGATATAT
3780958 GACATGAATCCATACCCTATGCATTATGG
1 GACATGAATCCATACCCTATGCATTATGG
3780987 GACATGAATCCATACCCTATGCATTATGG
1 GACATGAATCCATACCCTATGCATTATGG
3781016 GACATGAAT
1 GACATGAAT
3781025 AAGCAAGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (29 bp):
GACATGAATCCATACCCTATGCATTATGG
Found at i:3781349 original size:103 final size:103
Alignment explanation
Indices: 3781170--3781366 Score: 367
Period size: 103 Copynumber: 1.9 Consensus size: 103
3781160 AGGGTCTATG
3781170 TATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATACTTGATCCTTGGCATATGTATA
1 TATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATACTTGATCCTTGGCATATGTATA
* *
3781235 TGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATA
66 TGATTCTTAAGGAATGATACGTAGTCCTTCGGGACATA
3781273 TATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATACTTGATCCTTGGCATATGTATA
1 TATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATACTTGATCCTTGGCATATGTATA
*
3781338 TGATTCTTAAGGAATTATACGTAGTCCTT
66 TGATTCTTAAGGAATGATACGTAGTCCTT
3781367 ATGGACATTA
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 91 1.00
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATACTTGATCCTTGGCATATGTATA
TGATTCTTAAGGAATGATACGTAGTCCTTCGGGACATA
Found at i:3781410 original size:23 final size:22
Alignment explanation
Indices: 3781383--3781445 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 22
3781373 ATTATTATAT
3781383 GGCACTATGGTGCAATTCTACGC
1 GGCACT-TGGTGCAATTCTACGC
* *
3781406 GGCACTCCGGTGCAATTCTACGT
1 GGCACT-TGGTGCAATTCTACGC
3781429 GGCACTTAGGTGCAATT
1 GGCACTT-GGTGCAATT
3781446 ATATGAGTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.21, C:0.25, G:0.27, T:0.27
Consensus pattern (22 bp):
GGCACTTGGTGCAATTCTACGC
Found at i:3784509 original size:28 final size:27
Alignment explanation
Indices: 3784457--3784508 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
3784447 TTCAAAATAT
3784457 ATTATAATTATAATTATAATATTATTA
1 ATTATAATTATAATTATAATATTATTA
3784484 ATTATTAATTAT-ATT-TAATA-TATTA
1 ATTA-TAATTATAATTATAATATTATTA
3784509 TACATATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 5 0.21
26 5 0.21
27 7 0.29
28 7 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
ATTATAATTATAATTATAATATTATTA
Found at i:3784609 original size:16 final size:13
Alignment explanation
Indices: 3784575--3784607 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
3784565 GTATTCATTA
3784575 TTATTATATTTAT
1 TTATTATATTTAT
3784588 TTATTATATTTAT
1 TTATTATATTTAT
*
3784601 TTGTTAT
1 TTATTAT
3784608 TAATTTCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (13 bp):
TTATTATATTTAT
Found at i:3785194 original size:9 final size:9
Alignment explanation
Indices: 3785180--3785205 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
3785170 TTATTTCGAG
3785180 CCTTTGCTT
1 CCTTTGCTT
3785189 CCTTTGCTT
1 CCTTTGCTT
3785198 CCTTTGCT
1 CCTTTGCT
3785206 CAGTTTCACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.35, G:0.12, T:0.54
Consensus pattern (9 bp):
CCTTTGCTT
Found at i:3788189 original size:23 final size:23
Alignment explanation
Indices: 3788163--3788231 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
3788153 CACCACAGCT
* *
3788163 CGTATAAATGCACCGGAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
3788186 CGTAGAATTGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
* *
3788209 CGTAGAAATGCATCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
3788232 TATAAGATGT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.29, C:0.25, G:0.28, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:3789757 original size:20 final size:20
Alignment explanation
Indices: 3789729--3789780 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
3789719 TTCCCTTTGA
*
3789729 AGTGCATCGATGCATTCTAC
1 AGTGTATCGATGCATTCTAC
3789749 AGTGTATCGATGCATTCTAC
1 AGTGTATCGATGCATTCTAC
3789769 AGTGTATCGATG
1 AGTGTATCGATG
3789781 TATCCCTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (20 bp):
AGTGTATCGATGCATTCTAC
Found at i:3791251 original size:40 final size:39
Alignment explanation
Indices: 3791196--3791577 Score: 193
Period size: 40 Copynumber: 9.4 Consensus size: 39
3791186 GAAAAATAAT
3791196 GTACTTTAGT-G-GTTTTTATACAAACGCCGCTAAAGGTC
1 GTACTTTAGTGGCGTTTTTATACAAACGCCGCTAAA-GTC
* * * **
3791234 GTACTTTAGTGGCGTTTTAAGCACAAAAGCCGCTAATTACAC
1 GTACTTTAGTGGCGTTTTTA-TACAAACGCCGCTAA--AGTC
* * * * * *
3791276 GTATTTTAGTGGC-ATTTTACGCATAAACACCGCT-AATTAC
1 GTACTTTAGTGGCGTTTTTA--TACAAACGCCGCTAAAGT-C
* * * * *
3791316 ACTCACTATAGTGGCGTTTTTATATAAACGCTGATAAA-TAC
1 -GT-ACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGT-C
* * *
3791357 TGTACTTTAATGGCGTTTTTATACAAAAGCCGCTAAAGGTT
1 -GTACTTTAGTGGCGTTTTTATACAAACGCCGCTAAA-GTC
* * * *
3791398 GTACTTTAGTGGCGTTTTAAGCAAAAACGCCGCT-AATTAC
1 GTACTTTAGTGGCGTTTTTA-TACAAACGCCGCTAAAGT-C
* * **
3791438 ATGTTCTTTAGTGGCGTTTTATACACAAACGCCGCTAATTACAC
1 --GTACTTTAGTGGCGTTTT-TATACAAACGCCGCTAA--AGTC
* * ** * **
3791482 GTACTCTAGTTGTATTTTTATATAAACGCCGAGAAA-TAC
1 GTACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGT-C
* *
3791521 TATACTTTAGTGGCGTTTTTATACAAACGCCGCTAATGGTC
1 -GTACTTTAGTGGCGTTTTTATACAAACGCCGCTAA-AGTC
3791562 GTACTTTAGTGGCGTT
1 GTACTTTAGTGGCGTT
3791578 GCAAGCACAA
Statistics
Matches: 257, Mismatches: 62, Indels: 48
0.70 0.17 0.13
Matches are distributed among these distances:
38 10 0.04
39 5 0.02
40 97 0.38
41 56 0.22
42 79 0.31
43 8 0.03
44 1 0.00
45 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (39 bp):
GTACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGTC
Found at i:3791294 original size:42 final size:41
Alignment explanation
Indices: 3791233--3791654 Score: 243
Period size: 42 Copynumber: 10.2 Consensus size: 41
3791223 CGCTAAAGGT
3791233 CGTACTTTAGTGGCGTTTTAAGCACAAAAGCCGCTAATTACA
1 CGTACTTTAGTGGCGTTTTAA-CACAAAAGCCGCTAATTACA
* * * *
3791275 CGTATTTTAGTGGCATTTT-ACGCATAAACACCGCTAATTACA
1 CGTACTTTAGTGGCGTTTTAACACA-AAA-GCCGCTAATTACA
* * * * * * * *
3791317 C-TCACTATAGTGGCGTTTTTATATAAACGCTGATAAATAC-
1 CGT-ACTTTAGTGGCGTTTTAACACAAAAGCCGCTAATTACA
* * * * **
3791357 TGTACTTTAATGGCGTTTTTATACAAAAGCCGCTAA--AGGT
1 CGTACTTTAGTGGCGTTTTAACACAAAAGCCGCTAATTA-CA
*
3791397 TGTACTTTAGTGGCGTTTTAAGCA-AAAACGCCGCTAATTACA
1 CGTACTTTAGTGGCGTTTTAA-CACAAAA-GCCGCTAATTACA
* * *
3791439 TGTTCTTTAGTGGCGTTTTATACACAAACGCCGCTAATTACA
1 CGTACTTTAGTGGCGTTTTA-ACACAAAAGCCGCTAATTACA
* * ** * * * * ** *
3791481 CGTACTCTAGTTGTATTTTTATATAAACGCCGAGAAATACTA
1 CGTACTTTAGTGGCGTTTTAACACAAAAGCCGCTAATTAC-A
* * * ***
3791523 --TACTTTAGTGGCGTTTTTATACAAACGCCGCTAA-TGGT
1 CGTACTTTAGTGGCGTTTTAACACAAAAGCCGCTAATTACA
** *
3791561 CGTACTTTAGTGGCGTTGCAAGCACAAACA-CCACTAATTACA
1 CGTACTTTAGTGGCGTTTTAA-CACAAA-AGCCGCTAATTACA
* * * * *
3791603 CGTATTTTTGTGGCATTTTATGCACAAACGCCGCTAATTACA
1 CGTACTTTAGTGGCGTTTTA-ACACAAAAGCCGCTAATTACA
3791645 CGTACTTTAG
1 CGTACTTTAG
3791655 CGCCGCTAAA
Statistics
Matches: 288, Mismatches: 71, Indels: 42
0.72 0.18 0.10
Matches are distributed among these distances:
38 1 0.00
39 1 0.00
40 96 0.33
41 49 0.17
42 134 0.47
43 7 0.02
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (41 bp):
CGTACTTTAGTGGCGTTTTAACACAAAAGCCGCTAATTACA
Found at i:3791478 original size:164 final size:164
Alignment explanation
Indices: 3791179--3791650 Score: 657
Period size: 164 Copynumber: 2.9 Consensus size: 164
3791169 TTTTATGAGA
*
3791179 AAACGCCGAAAAATAATGTACTTTAGT-G-GTTTTTATACAAACGCCGCTAAAGGTCGTACTTTA
1 AAACGCCGAAAAATACTGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGGTCGTACTTTA
* * *
3791242 GTGGCGTTTTAAGCACAAAA-GCCGCTAATTACACGTATTTTAGTGGCATTTTACGCATAAACAC
66 GTGGCGTTTTAAGCA-AAAACGCCGCTAATTACACGTATTTTAGTGGCATTTTATGCACAAACGC
*
3791306 CGCTAATTACAC-TCACTATAGTGGCGTTTTTATAT
130 CGCTAATTACACGT-ACTATAGTGGCATTTTTATAT
* * * * *
3791341 AAACGCTGATAAATACTGTACTTTAATGGCGTTTTTATACAAAAGCCGCTAAAGGTTGTACTTTA
1 AAACGCCGAAAAATACTGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGGTCGTACTTTA
* * *
3791406 GTGGCGTTTTAAGCAAAAACGCCGCTAATTACATGT-TCTTTAGTGGCGTTTTATACACAAACGC
66 GTGGCGTTTTAAGCAAAAACGCCGCTAATTACACGTAT-TTTAGTGGCATTTTATGCACAAACGC
* * *
3791470 CGCTAATTACACGTACTCTAGTTGTATTTTTATAT
130 CGCTAATTACACGTACTATAGTGGCATTTTTATAT
* * *
3791505 AAACGCCGAGAAATACTATACTTTAGTGGCGTTTTTATACAAACGCCGCTAATGGTCGTACTTTA
1 AAACGCCGAAAAATACTGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGGTCGTACTTTA
** * * * *
3791570 GTGGCGTTGCAAGCACAAACACCACTAATTACACGTATTTTTGTGGCATTTTATGCACAAACGCC
66 GTGGCGTTTTAAGCAAAAACGCCGCTAATTACACGTATTTTAGTGGCATTTTATGCACAAACGCC
3791635 GCTAATTACACGTACT
131 GCTAATTACACGTACT
3791651 TTAGCGCCGC
Statistics
Matches: 272, Mismatches: 32, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
162 23 0.08
163 6 0.02
164 241 0.89
165 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (164 bp):
AAACGCCGAAAAATACTGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGGTCGTACTTTA
GTGGCGTTTTAAGCAAAAACGCCGCTAATTACACGTATTTTAGTGGCATTTTATGCACAAACGCC
GCTAATTACACGTACTATAGTGGCATTTTTATAT
Found at i:3791621 original size:122 final size:123
Alignment explanation
Indices: 3791399--3791621 Score: 265
Period size: 122 Copynumber: 1.8 Consensus size: 123
3791389 CTAAAGGTTG
* **
3791399 TACTTTAGTGGCGTTTTAAGCAAAAACGCCGCTAATTACATGTTCTTTAGTGGCGTTTTATACAC
1 TACTTTAGTGGCGTTTTAAGCAAAAACGCCGCTAATTACA-GTACTTTAGTGGCGTTGCATACAC
* * * *
3791464 AAACGCCGCTAATTACACGTACTCTAGTTGTATTTTTATATAAACGCCGAGAAATACTA
65 AAACACCACTAATTACACGTACTCTAGTGGCATTTTTATATAAACGCCGAGAAATACTA
* * *
3791523 TACTTTAGTGGCGTTTTTA-TACAAACGCCGCTAATGGT-C-GTACTTTAGTGGCGTTGCA-AGC
1 TACTTTAGTGGCGTTTTAAGCAAAAACGCCGCTAAT--TACAGTACTTTAGTGGCGTTGCATA-C
* * *
3791584 ACAAACACCACTAATTACACGTATTTTTGTGGCATTTT
63 ACAAACACCACTAATTACACGTACTCTAGTGGCATTTT
3791622 ATGCACAAAC
Statistics
Matches: 83, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
121 1 0.01
122 48 0.58
123 14 0.17
124 19 0.23
125 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (123 bp):
TACTTTAGTGGCGTTTTAAGCAAAAACGCCGCTAATTACAGTACTTTAGTGGCGTTGCATACACA
AACACCACTAATTACACGTACTCTAGTGGCATTTTTATATAAACGCCGAGAAATACTA
Found at i:3793153 original size:27 final size:29
Alignment explanation
Indices: 3793087--3793153 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 29
3793077 TAACATTAGT
* *
3793087 TATAAAGGAGTTAACACTGGTACTTTCAAAA
1 TATAAAGGAGTTAACACTAGTA-TAT-AAAA
3793118 TATAAAGGAGTTAACACTAGT-TAT-AAA
1 TATAAAGGAGTTAACACTAGTATATAAAA
3793145 TATAAAGGA
1 TATAAAGGA
3793154 CTTCCATTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 12 0.35
29 2 0.06
31 20 0.59
ACGTcount: A:0.46, C:0.09, G:0.16, T:0.28
Consensus pattern (29 bp):
TATAAAGGAGTTAACACTAGTATATAAAA
Found at i:3793779 original size:21 final size:20
Alignment explanation
Indices: 3793738--3793780 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
3793728 TCATTAGTCT
3793738 ATTTATGTTTCTTAACATCA
1 ATTTATGTTTCTTAACATCA
*
3793758 ATTT-TGTTTTTTATACTATCA
1 ATTTATGTTTCTTA-AC-ATCA
3793779 AT
1 AT
3793781 ATTACTTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 8 0.40
20 6 0.30
21 6 0.30
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.56
Consensus pattern (20 bp):
ATTTATGTTTCTTAACATCA
Found at i:3794951 original size:43 final size:43
Alignment explanation
Indices: 3794901--3795248 Score: 538
Period size: 43 Copynumber: 8.1 Consensus size: 43
3794891 ACGGTCATTA
* * * *
3794901 GCGGCGTTTGTATCAAAAAACGCCGCTATAGATCT-AACCTTTT
1 GCGGCGTTTGT-CCCAAAAACGCCGCTATAGATCTCGACCTATT
* * *
3794944 GTGGCGTTTGTTCCAAAAACGCCGCTATAAATCTCGACCTATT
1 GCGGCGTTTGTCCCAAAAACGCCGCTATAGATCTCGACCTATT
* * *
3794987 GCGGCATTTGTTCCAAAAACGTCGCTATAGATCTCGACCTATT
1 GCGGCGTTTGTCCCAAAAACGCCGCTATAGATCTCGACCTATT
3795030 GCGGCGTTTGTCCCAAAAACGCCGCTATAGATCTCGACCTATT
1 GCGGCGTTTGTCCCAAAAACGCCGCTATAGATCTCGACCTATT
*
3795073 GAGGCGTTTGT-CCAAAAACGCCGCTATAGATCTCGACCTATT
1 GCGGCGTTTGTCCCAAAAACGCCGCTATAGATCTCGACCTATT
* * *
3795115 GCGGCGTTTGTCCAAAAAATGCCGCTATAGATCTTGACCTATT
1 GCGGCGTTTGTCCCAAAAACGCCGCTATAGATCTCGACCTATT
*
3795158 GCGGCGTTTGTCCAAAAAACGCCGCTATAGATCTCGACCTATT
1 GCGGCGTTTGTCCCAAAAACGCCGCTATAGATCTCGACCTATT
3795201 GCGGCGTTTGTCCCAAAAACGCCGCTATAGATCTCGACCTATT
1 GCGGCGTTTGTCCCAAAAACGCCGCTATAGATCTCGACCTATT
3795244 GCGGC
1 GCGGC
3795249 ATTTTTTGTT
Statistics
Matches: 283, Mismatches: 20, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
42 62 0.22
43 221 0.78
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.28
Consensus pattern (43 bp):
GCGGCGTTTGTCCCAAAAACGCCGCTATAGATCTCGACCTATT
Found at i:3795133 original size:128 final size:128
Alignment explanation
Indices: 3794901--3795252 Score: 555
Period size: 128 Copynumber: 2.7 Consensus size: 128
3794891 ACGGTCATTA
* * * *
3794901 GCGGCGTTTGTATCAAAAAACGCCGCTATAGATCT-AACCTTTTGTGGCGTTTGTTCCAAAAACG
1 GCGGCGTTTGT-CCAAAAAACGCCGCTATAGATCTCGACCTATTGAGGCGTTTG-TCCAAAAACG
* *
3794965 CCGCTATAAATCTCGACCTATTGCGGCATTTGTTCCAAAAACGTCGCTATAGATCTCGACCTATT
64 CCGCTATAGATCTCGACCTATTGCGGCATTTGTTCCAAAAACGCCGCTATAGATCTCGACCTATT
*
3795030 GCGGCGTTTGTCCCAAAAACGCCGCTATAGATCTCGACCTATTGAGGCGTTTGTCCAAAAACGCC
1 GCGGCGTTTGTCCAAAAAACGCCGCTATAGATCTCGACCTATTGAGGCGTTTGTCCAAAAACGCC
* * *
3795095 GCTATAGATCTCGACCTATTGCGGCGTTTG-TCCAAAAAATGCCGCTATAGATCTTGACCTATT
66 GCTATAGATCTCGACCTATTGCGGCATTTGTTCC-AAAAACGCCGCTATAGATCTCGACCTATT
*
3795158 GCGGCGTTTGTCCAAAAAACGCCGCTATAGATCTCGACCTATTGCGGCGTTTGTCCCAAAAACGC
1 GCGGCGTTTGTCCAAAAAACGCCGCTATAGATCTCGACCTATTGAGGCGTTTGT-CCAAAAACGC
3795223 CGCTATAGATCTCGACCTATTGCGGCATTT
65 CGCTATAGATCTCGACCTATTGCGGCATTT
3795253 TTTGTTCACA
Statistics
Matches: 207, Mismatches: 13, Indels: 6
0.92 0.06 0.03
Matches are distributed among these distances:
127 3 0.01
128 139 0.67
129 65 0.31
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.28
Consensus pattern (128 bp):
GCGGCGTTTGTCCAAAAAACGCCGCTATAGATCTCGACCTATTGAGGCGTTTGTCCAAAAACGCC
GCTATAGATCTCGACCTATTGCGGCATTTGTTCCAAAAACGCCGCTATAGATCTCGACCTATT
Found at i:3797428 original size:23 final size:23
Alignment explanation
Indices: 3797402--3797470 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
3797392 CACCACATCT
* * *
3797402 CGTATAAATGCACCGGAGTGCCA
1 CGTAGAAATGCATCGAAGTGCCA
* *
3797425 CGTAGAATTGCATCGAAGTGCCG
1 CGTAGAAATGCATCGAAGTGCCA
*
3797448 CGTAGAAATGCATCGTAGTGCCA
1 CGTAGAAATGCATCGAAGTGCCA
3797471 TATCAGATGT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.29, C:0.23, G:0.28, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCATCGAAGTGCCA
Found at i:3801035 original size:18 final size:18
Alignment explanation
Indices: 3801012--3801047 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3801002 TCCTAACTTA
3801012 TAGAGATTCCTAATGTGG
1 TAGAGATTCCTAATGTGG
*
3801030 TAGAGATTCCTGATGTGG
1 TAGAGATTCCTAATGTGG
3801048 AAGCACCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.11, G:0.31, T:0.33
Consensus pattern (18 bp):
TAGAGATTCCTAATGTGG
Found at i:3802158 original size:22 final size:22
Alignment explanation
Indices: 3802130--3802198 Score: 138
Period size: 22 Copynumber: 3.1 Consensus size: 22
3802120 AAATACATCA
3802130 GCGACAAAACCTTTCGTTGGTG
1 GCGACAAAACCTTTCGTTGGTG
3802152 GCGACAAAACCTTTCGTTGGTG
1 GCGACAAAACCTTTCGTTGGTG
3802174 GCGACAAAACCTTTCGTTGGTG
1 GCGACAAAACCTTTCGTTGGTG
3802196 GCG
1 GCG
3802199 CCATATAATG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.26
Consensus pattern (22 bp):
GCGACAAAACCTTTCGTTGGTG
Found at i:3804067 original size:30 final size:30
Alignment explanation
Indices: 3804018--3804074 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
3804008 ATAAATAAAA
3804018 AAAATATTAAAGAAATAAAT-AAATTATTC
1 AAAATATTAAAGAAATAAATCAAATTATTC
3804047 AAAATGATTAAA-AAATTAAATCAAATTA
1 AAAAT-ATTAAAGAAA-TAAATCAAATTA
3804075 ATAAATAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
29 8 0.32
30 11 0.44
31 6 0.24
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.30
Consensus pattern (30 bp):
AAAATATTAAAGAAATAAATCAAATTATTC
Found at i:3805329 original size:14 final size:14
Alignment explanation
Indices: 3805310--3805341 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3805300 CGTTCGTGAA
*
3805310 CGTTCAGTTATGTT
1 CGTTCAATTATGTT
3805324 CGTTCAATTATGTT
1 CGTTCAATTATGTT
3805338 CGTT
1 CGTT
3805342 TCTGTTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.50
Consensus pattern (14 bp):
CGTTCAATTATGTT
Found at i:3805386 original size:24 final size:24
Alignment explanation
Indices: 3805317--3805386 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
3805307 GAACGTTCAG
*
3805317 TTATGTTCGTTCAATTATGTTCGT
1 TTATGTTCGTTCAATTATGTTTGT
* * **
3805341 TTCTGTTTGTTCGGTTATGTTTGT
1 TTATGTTCGTTCAATTATGTTTGT
* *
3805365 TTATGTTCATTCATTTATGTTT
1 TTATGTTCGTTCAATTATGTTT
3805387 AAGTCAATCT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.13, C:0.10, G:0.17, T:0.60
Consensus pattern (24 bp):
TTATGTTCGTTCAATTATGTTTGT
Found at i:3806053 original size:10 final size:10
Alignment explanation
Indices: 3806038--3806095 Score: 55
Period size: 10 Copynumber: 5.6 Consensus size: 10
3806028 GGTCTCCAAT
3806038 GTTTATGTTC
1 GTTTATGTTC
3806048 GTTTATGTTC
1 GTTTATGTTC
*
3806058 GTGTTCAT-TTAT
1 GT-TT-ATGTT-C
**
3806070 GTTCGTGTTC
1 GTTTATGTTC
3806080 GTTTATGTTC
1 GTTTATGTTC
3806090 GTTTAT
1 GTTTAT
3806096 TTATTAAATG
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
10 27 0.71
11 7 0.18
12 4 0.11
ACGTcount: A:0.10, C:0.10, G:0.21, T:0.59
Consensus pattern (10 bp):
GTTTATGTTC
Found at i:3806062 original size:16 final size:16
Alignment explanation
Indices: 3806043--3806091 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
3806033 CCAATGTTTA
3806043 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
3806059 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
3806075 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
3806091 T
1 T
3806092 TTATTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.08, C:0.12, G:0.22, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:3806186 original size:16 final size:16
Alignment explanation
Indices: 3806161--3806201 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
3806151 AAAAACATTT
3806161 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
3806177 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
3806193 T-TT-ATTTAT
1 TGTTCATTTAT
3806202 TAAATGAACG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 5 0.22
15 2 0.09
16 16 0.70
ACGTcount: A:0.12, C:0.10, G:0.17, T:0.61
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:3806352 original size:18 final size:19
Alignment explanation
Indices: 3806310--3806352 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
3806300 ATTGGTTTAC
* *
3806310 GGAATGTAAGATTACCAGT
1 GGAATATAAAATTACCAGT
3806329 GGAATATAAAATTACCAG-
1 GGAATATAAAATTACCAGT
3806347 GGAATA
1 GGAATA
3806353 GGATTACTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.44, C:0.09, G:0.23, T:0.23
Consensus pattern (19 bp):
GGAATATAAAATTACCAGT
Found at i:3809768 original size:19 final size:19
Alignment explanation
Indices: 3809730--3809767 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
3809720 CAAAAATTAT
3809730 TAAATAATAAAAATTAAAA
1 TAAATAATAAAAATTAAAA
*
3809749 TAAATAAATAAATATTAAA
1 TAAAT-AATAAAAATTAAA
3809768 TTAATCATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
TAAATAATAAAAATTAAAA
Found at i:3809850 original size:28 final size:30
Alignment explanation
Indices: 3809809--3809881 Score: 87
Period size: 31 Copynumber: 2.5 Consensus size: 30
3809799 AGAAATTGTT
* * *
3809809 AAATTGTTAAAAAATAAT-TTAGA-TTATC
1 AAATTATTACAAAATAATATTAAATTTATC
3809837 AAATTATTACAAAATAATAATTAAATTTATC
1 AAATTATTACAAAATAAT-ATTAAATTTATC
*
3809868 AAATTATTGCAAAA
1 AAATTATTACAAAA
3809882 AAAATCTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 16 0.42
30 4 0.11
31 18 0.47
ACGTcount: A:0.53, C:0.05, G:0.04, T:0.37
Consensus pattern (30 bp):
AAATTATTACAAAATAATATTAAATTTATC
Found at i:3813053 original size:14 final size:15
Alignment explanation
Indices: 3813034--3813081 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 15
3813024 TTTAATAAAT
*
3813034 AATATACAA-ACTAA
1 AATATAAAATACTAA
3813048 AATATAAAATACTAA
1 AATATAAAATACTAA
* *
3813063 AA-ATTAAATAATAA
1 AATATAAAATACTAA
3813077 AATAT
1 AATAT
3813082 TCACAATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
14 20 0.69
15 9 0.31
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (15 bp):
AATATAAAATACTAA
Found at i:3819543 original size:2 final size:2
Alignment explanation
Indices: 3819536--3819563 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3819526 CTTTGAGTGC
3819536 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
3819564 TGGTATTCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3820901 original size:46 final size:46
Alignment explanation
Indices: 3820834--3820929 Score: 147
Period size: 46 Copynumber: 2.1 Consensus size: 46
3820824 ATTTAATTAA
* *
3820834 TTTTTAATAGTATGTGATAATTACAATGTAATATATGTTTACAATT
1 TTTTTAATAGCATATGATAATTACAATGTAATATATGTTTACAATT
* * *
3820880 TTTTTAATAGCATATGGTAATTATAATGTAATATATGTTTATAATT
1 TTTTTAATAGCATATGATAATTACAATGTAATATATGTTTACAATT
3820926 TTTT
1 TTTT
3820930 AATCAATTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.51
Consensus pattern (46 bp):
TTTTTAATAGCATATGATAATTACAATGTAATATATGTTTACAATT
Found at i:3823157 original size:36 final size:36
Alignment explanation
Indices: 3823116--3823188 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
3823106 GTTAGTAAAC
* *
3823116 ATTATTCTATTAAATTCTCTTTGTACTGTAAACTTA
1 ATTATTCCATTAAATTCTCCTTGTACTGTAAACTTA
*
3823152 ATTATTCCATTAAATTCTCCTTGTACTGTAAATTTA
1 ATTATTCCATTAAATTCTCCTTGTACTGTAAACTTA
3823188 A
1 A
3823189 ATCCAACAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.32, C:0.15, G:0.05, T:0.48
Consensus pattern (36 bp):
ATTATTCCATTAAATTCTCCTTGTACTGTAAACTTA
Found at i:3831244 original size:31 final size:31
Alignment explanation
Indices: 3831198--3831272 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
3831188 AAGGCACCAC
* *
3831198 AGGATATAACATATACAGTTTCGAAATTTTA
1 AGGATAAAACATATACAGTTTCAAAATTTTA
*
3831229 AGGATAAAACGTATACAGTTTCAAAATTTTA
1 AGGATAAAACATATACAGTTTCAAAATTTTA
3831260 AGGATAAAACATA
1 AGGATAAAACATA
3831273 GATATTACAG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (31 bp):
AGGATAAAACATATACAGTTTCAAAATTTTA
Found at i:3832253 original size:146 final size:147
Alignment explanation
Indices: 3831989--3832288 Score: 586
Period size: 146 Copynumber: 2.1 Consensus size: 147
3831979 GTAGTCACAC
3831989 TGAGAG-AATGTGAAGCAGCTGGAGCAAAAGAATTGGGTGTGTTGGGGAGGGAATCAACGATGCC
1 TGAGAGCAATGTGAAGCAGCTGGAGCAAAAGAATTGGGTGTGTTGGGGAGGGAATCAACGATGCC
3832053 TTTTACTTTGGGTGCTCTTGATTTGTCTCTGGCGGTTTGAGTATTAGTACTGACACTCAAATTCC
66 TTTTACTTTGGGTGCTCTTGATTTGTCTCTGGCGGTTTGAGTATTAGTACTGACACTCAAATTCC
3832118 GCCATTTATCCTGCAAA
131 GCCATTTATCCTGCAAA
3832135 TGAGAGCAATGTGAAGCAGCTGGAGCAAAAG-ATTGGGTGTGTTGGGGAGGGAATCAACGATGCC
1 TGAGAGCAATGTGAAGCAGCTGGAGCAAAAGAATTGGGTGTGTTGGGGAGGGAATCAACGATGCC
3832199 TTTTACTTTGGGTGCTCTTGATTTGTCTCTGGCGGTTTGAGTATTAGTACTGACACTCAAATTCC
66 TTTTACTTTGGGTGCTCTTGATTTGTCTCTGGCGGTTTGAGTATTAGTACTGACACTCAAATTCC
3832264 GCCATTTATCCTGCAAA
131 GCCATTTATCCTGCAAA
3832281 TGAGAGCA
1 TGAGAGCA
3832289 GAAATGAGAA
Statistics
Matches: 153, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
146 129 0.84
147 24 0.16
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (147 bp):
TGAGAGCAATGTGAAGCAGCTGGAGCAAAAGAATTGGGTGTGTTGGGGAGGGAATCAACGATGCC
TTTTACTTTGGGTGCTCTTGATTTGTCTCTGGCGGTTTGAGTATTAGTACTGACACTCAAATTCC
GCCATTTATCCTGCAAA
Found at i:3832781 original size:18 final size:18
Alignment explanation
Indices: 3832755--3832796 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
3832745 AAAACGATTA
*
3832755 AAAAAAAACACTTATAA-C
1 AAAAAAAAC-CCTATAACC
*
3832773 AAAAGAAACCCTATAACC
1 AAAAAAAACCCTATAACC
3832791 AAAAAA
1 AAAAAA
3832797 GAAAACAGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.67, C:0.19, G:0.02, T:0.12
Consensus pattern (18 bp):
AAAAAAAACCCTATAACC
Found at i:3870168 original size:23 final size:23
Alignment explanation
Indices: 3870138--3870181 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
3870128 GTTTATTTAT
* *
3870138 TAAATAAACAAATATGAACAATA
1 TAAATAAACAAACATAAACAATA
3870161 TAAATAAACAAACATAAACAA
1 TAAATAAACAAACATAAACAA
3870182 ATTTTATGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.68, C:0.11, G:0.02, T:0.18
Consensus pattern (23 bp):
TAAATAAACAAACATAAACAATA
Found at i:3874350 original size:2 final size:2
Alignment explanation
Indices: 3874343--3874384 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3874333 TCATGCGTAC
3874343 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
3874385 CTCGTGAGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3874469 original size:2 final size:2
Alignment explanation
Indices: 3874462--3874489 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3874452 TATAATACCA
3874462 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
3874490 TAGACACATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3874850 original size:14 final size:14
Alignment explanation
Indices: 3874831--3874859 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3874821 CATGGCAACT
3874831 AAAATTAATACAAA
1 AAAATTAATACAAA
3874845 AAAATTAATACAAA
1 AAAATTAATACAAA
3874859 A
1 A
3874860 TACGGGACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (14 bp):
AAAATTAATACAAA
Found at i:3876200 original size:13 final size:12
Alignment explanation
Indices: 3876182--3876231 Score: 66
Period size: 13 Copynumber: 4.1 Consensus size: 12
3876172 CCTGCAAATG
3876182 TAATAAATAATAT
1 TAAT-AATAATAT
*
3876195 TAATAA-AATAA
1 TAATAATAATAT
3876206 TAATAATAATAT
1 TAATAATAATAT
3876218 ATAATAATAATAT
1 -TAATAATAATAT
3876231 T
1 T
3876232 TTTTAAAAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
11 10 0.30
12 7 0.21
13 16 0.48
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TAATAATAATAT
Found at i:3876207 original size:3 final size:3
Alignment explanation
Indices: 3876182--3876229 Score: 62
Period size: 3 Copynumber: 15.7 Consensus size: 3
3876172 CCTGCAAATG
*
3876182 TAA TAAA TAA TAT TAA TAA -AA TAA TAA TAA TAA TATA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
3876228 TA
1 TA
3876230 TTTTTTAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 32 0.80
4 6 0.15
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3876797 original size:129 final size:128
Alignment explanation
Indices: 3876424--3876836 Score: 293
Period size: 129 Copynumber: 3.2 Consensus size: 128
3876414 TGATCGTCTA
* *
3876424 AAGG-TGACA-AGACTCCTACATAAGGAG-AAGATCTAGTCAAGG-GATAACACTG-CTCATACG
1 AAGGTTGACATAG-CTCCTACATAAAGAGCAA-ATCTAGTC-AGGTGATGACAC-GACTCATACG
* * * * * *
3876484 TGATGAAGATTTCTTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGAC
62 TGATGAAGAGTGC-AGGCCATC--TA--AA-GGCGATAACACGGTTCCTACGTGATGAAGACGAC
3876549 TGGTTATC
121 TGGTTATC
* *
3876557 TAGGTTGACGTAGCTCCTACATAAAGAGCAAATCTAGTCAGGTGATGACACGACTCATACGTGAT
1 AAGGTTGACATAGCTCCTACATAAAGAGCAAATCTAGTCAGGTGATGACACGACTCATACGTGAT
* * * *** * **
3876622 GAAGAGTTCTGGCCATCTAAAGGTGATAACACAACTCATACGTGATGAAGA-GTTTTGGTTATC
66 GAAGAGTGCAGGCCATCTAAAGGCGATAACACGGTTCCTACGTGATGAAGACG-ACTGGTTATC
* * * * * * ** *
3876685 AAGGATTGACATTGCTCCTACATAATGAGGAGAT-TAGATCGGGTGATGATACGGTTCCTACGTG
1 AAGG-TTGACATAGCTCCTACATAAAGAGCAAATCTAG-TCAGGTGATGACACGACTCATACGTG
* * * * * *
3876749 ATGAGGACG-GCAGGCCATCTATAGGCGATAACACGGTTCCTACATGATGAGGACGGCTGTTTAT
64 ATGAAGA-GTGCAGGCCATCTAAAGGCGATAACACGGTTCCTACGTGATGAAGACGACTGGTTAT
3876813 C
128 C
** **
3876814 TGGGTTTGACACGGCTCCTACAT
1 AAGG-TTGACATAGCTCCTACAT
3876837 GATGAGGAGA
Statistics
Matches: 227, Mismatches: 43, Indels: 24
0.77 0.15 0.08
Matches are distributed among these distances:
127 1 0.00
128 38 0.17
129 112 0.49
130 2 0.01
131 2 0.01
133 15 0.07
134 53 0.23
135 4 0.02
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (128 bp):
AAGGTTGACATAGCTCCTACATAAAGAGCAAATCTAGTCAGGTGATGACACGACTCATACGTGAT
GAAGAGTGCAGGCCATCTAAAGGCGATAACACGGTTCCTACGTGATGAAGACGACTGGTTATC
Found at i:3877098 original size:90 final size:91
Alignment explanation
Indices: 3876991--3877164 Score: 242
Period size: 91 Copynumber: 1.9 Consensus size: 91
3876981 AAGTGTTGAA
* * * * * *
3876991 TTGAACAAGTTATTCTCATTATGAGCTTCTTGTCTCT-TTTGGATGAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTATTCTCATTATGAACTTATTCTCCCTCATTGGATGAATTCTTCTCATTATGAAC
*
3877055 TCTCAACTGGAAATCTTGAACTAAGG
66 TCTCAACTGAAAATCTTGAACTAAGG
* *
3877081 TTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATTGGTTGAATTCTTCTCATTATGAAC
1 TTGAACAAGTTATTCTCATTATGAACTTATTCTCCCTCATTGGATGAATTCTTCTCATTATGAAC
* *
3877146 TCTCCACTGAAAATGTTGA
66 TCTCAACTGAAAATCTTGA
3877165 TCCACCTCTT
Statistics
Matches: 72, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
90 32 0.44
91 40 0.56
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (91 bp):
TTGAACAAGTTATTCTCATTATGAACTTATTCTCCCTCATTGGATGAATTCTTCTCATTATGAAC
TCTCAACTGAAAATCTTGAACTAAGG
Found at i:3877880 original size:91 final size:90
Alignment explanation
Indices: 3877532--3878308 Score: 1178
Period size: 91 Copynumber: 8.6 Consensus size: 90
3877522 AAGGCTTACA
* * * * * * *
3877532 GATGACCCGAAGGATTTAAAAATCAAGAAACCCCAGAAGACTTAGTTTCTTAAAATCTCATTTGA
1 GATGGCCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTT-AGATTTCATTTGA
*
3877597 AAATATCCTGCACTGAAGGTCTTATG
65 AAACATCCTGCACTGAAGGTCTTATG
* *
3877623 GATGGCCCGAAGGACTTAGAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTAAATCTT-ATTTGA
1 GATGGCCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTAGAT-TTCATTTGA
3877687 AAACATCCTGCACTGAAGGTCTTATG
65 AAACATCCTGCACTGAAGGTCTTATG
* * * *
3877713 GATGACGCGAAGGACTTAAAAATTAAGAAACCCCCGAAGGCTCAGTTTCTTAGATCTCATTTGAA
1 GATGGCCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTAGATTTCATTTGAA
*
3877778 AACATCATGCACTGAAGGTCTTATG
66 AACATCCTGCACTGAAGGTCTTATG
*
3877803 GATGGCCCGAAGGACTTAAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTAGATTTAATTTGA
1 GATGGCCCGAAGGACTT-AAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTAGATTTCATTTGA
**
3877868 AAGTATCCTGCACTGAAGGTCTTATG
65 AAACATCCTGCACTGAAGGTCTTATG
* * *
3877894 GATGGCCCAAATGACTTAAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTAGATTTTATTTGA
1 GATGGCCCGAAGGACTT-AAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTAGATTTCATTTGA
3877959 AAACATCCTGCACTGAAGGTCTTATG
65 AAACATCCTGCACTGAAGGTCTTATG
* * *
3877985 GATGGCCCGAATGACTTAAAAAATCAAGAAACCCCCGAAGGCTCAGTTTTTTAGATTTAATTTGA
1 GATGGCCCGAAGGACTT-AAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTAGATTTCATTTGA
* *
3878050 AAGCATCATGCACTGAAGGTCTTATG
65 AAACATCCTGCACTGAAGGTCTTATG
* * *
3878076 GATGGCCCGAATGACTTAAAAAATCTAGAAACCCCCGAAGGCTCAGTTTCTTAGATTTTATTTGA
1 GATGGCCCGAAGGACTT-AAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTAGATTTCATTTGA
3878141 AAACATCCTGCACTGAAGGTCTTATG
65 AAACATCCTGCACTGAAGGTCTTATG
*
3878167 GATGGCCCGAAGGACTTAGAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTAGATTTCATTTGAA
1 GATGGCCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTAGATTTCATTTGAA
3878232 AACATCCTGCACTGAAGGTCTTATG
66 AACATCCTGCACTGAAGGTCTTATG
* * * * *
3878257 GATGACCCGAAGGACTTAGAAATCAAGAAACTCCCAAAAGCTCAGTTTCTTA
1 GATGGCCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTA
3878309 ATTGTCACCA
Statistics
Matches: 637, Mismatches: 46, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
89 1 0.00
90 249 0.39
91 387 0.61
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (90 bp):
GATGGCCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTAGATTTCATTTGAA
AACATCCTGCACTGAAGGTCTTATG
Found at i:3878425 original size:43 final size:43
Alignment explanation
Indices: 3878364--3878483 Score: 154
Period size: 43 Copynumber: 2.8 Consensus size: 43
3878354 TTCATCAAGT
*
3878364 TTGTCATCAAGGAACCCCTACATATCACGATGGTC-CTTCAAAC
1 TTGTCATCAAGAAACCCCTACATATCACGATGGTCTC-TCAAAC
* * *
3878407 TTGTCCTCAAGAAACCCCTGCATATCACGATGGTCTCTCAAGC
1 TTGTCATCAAGAAACCCCTACATATCACGATGGTCTCTCAAAC
* *
3878450 TTTTCATCAA-ATAACCCCTACATATCACGTTGGT
1 TTGTCATCAAGA-AACCCCTACATATCACGATGGT
3878484 TTCTAAAAAT
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
42 1 0.01
43 65 0.97
44 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.13, T:0.28
Consensus pattern (43 bp):
TTGTCATCAAGAAACCCCTACATATCACGATGGTCTCTCAAAC
Found at i:3878570 original size:40 final size:40
Alignment explanation
Indices: 3878526--3878632 Score: 142
Period size: 40 Copynumber: 2.6 Consensus size: 40
3878516 CTCAAGCGAG
3878526 ATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAACGAA
1 ATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAACGAA
* * * ** *
3878566 ATAAAATCTTTTGTTTCAAGGAAAATCCATCTTGATTGAG
1 ATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAACGAA
*
3878606 ATAAAATCTTCTGTTTCGAGTGAAAAA
1 ATAAAATCTTCTGTTTCAAG-GAAAAA
3878633 AAAAATGTCT
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
40 52 0.91
41 5 0.09
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (40 bp):
ATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAACGAA
Found at i:3878818 original size:75 final size:76
Alignment explanation
Indices: 3878676--3878820 Score: 190
Period size: 75 Copynumber: 1.9 Consensus size: 76
3878666 ACATGTAGTG
* * *
3878676 AAATGAAATGTCTTGTTTTGAATAAAACCTATCTCAAGCGAGACAAATCTTGTTTTGAGAAAAAC
1 AAATGAAATGTCTTGCTTTCAATAAAACCTATCTCAAGCGAGACAAATCTTGTTTTAAGAAAAAC
3878741 AATCTTGAGTC
66 AATCTTGAGTC
* *
3878752 AAATGAAATGTCTT-CTTTCAAGTAAAA-C-AGTCTCAAGTGAGATAAAT-TCTGTTTTAAGAAA
1 AAATGAAATGTCTTGCTTTCAA-TAAAACCTA-TCTCAAGCGAGACAAATCT-TGTTTTAAGAAA
3878813 AACAATCT
63 AACAATCT
3878821 CCAGTGAGAT
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
74 2 0.03
75 40 0.66
76 19 0.31
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (76 bp):
AAATGAAATGTCTTGCTTTCAATAAAACCTATCTCAAGCGAGACAAATCTTGTTTTAAGAAAAAC
AATCTTGAGTC
Found at i:3878833 original size:75 final size:76
Alignment explanation
Indices: 3878672--3878833 Score: 188
Period size: 75 Copynumber: 2.1 Consensus size: 76
3878662 AACAACATGT
* * *
3878672 AGTGAAATGAAATGTCTTGTTTTGAATAAAACCTATCTCAAGCGAGACAAATCTTGTTTTGAGAA
1 AGTGAAATGAAATGTCTTGCTTTCAATAAAACCTATCTCAAGCGAGACAAATCTTGTTTTAAGAA
**
3878737 AAACAATCTTG
66 AAACAATCTCC
* * *
3878748 AGTCAAATGAAATGTCTT-CTTTCAAGTAAAA-C-AGTCTCAAGTGAGATAAAT-TCTGTTTTAA
1 AGTGAAATGAAATGTCTTGCTTTCAA-TAAAACCTA-TCTCAAGCGAGACAAATCT-TGTTTTAA
3878809 GAAAAACAATCTCC
63 GAAAAACAATCTCC
*
3878823 AGTGAGATGAA
1 AGTGAAATGAA
3878834 TCCTCTGTAT
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
74 2 0.03
75 49 0.67
76 22 0.30
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.30
Consensus pattern (76 bp):
AGTGAAATGAAATGTCTTGCTTTCAATAAAACCTATCTCAAGCGAGACAAATCTTGTTTTAAGAA
AAACAATCTCC
Found at i:3880168 original size:28 final size:28
Alignment explanation
Indices: 3880128--3880185 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
3880118 CCAACCTTTT
3880128 CATGCTAGTGTGAGCCATCAAGATGCCC
1 CATGCTAGTGTGAGCCATCAAGATGCCC
* *
3880156 CATGCT-GATGTGAGCCTTCAATATGCCC
1 CATGCTAG-TGTGAGCCATCAAGATGCCC
3880184 CA
1 CA
3880186 CATGGATTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 1 0.04
28 26 0.96
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.24
Consensus pattern (28 bp):
CATGCTAGTGTGAGCCATCAAGATGCCC
Found at i:3881800 original size:9 final size:9
Alignment explanation
Indices: 3881762--3881869 Score: 94
Period size: 9 Copynumber: 12.9 Consensus size: 9
3881752 TTTTTTTTAT
3881762 TTTTTTTCTC
1 TTTTTTTC-C
3881772 TTTATTTT-C
1 TTT-TTTTCC
*
3881781 TTTATTT-C
1 TTTTTTTCC
3881789 TTTTTTTCC
1 TTTTTTTCC
3881798 --TTTTTCC
1 TTTTTTTCC
3881805 --TTTTTCC
1 TTTTTTTCC
3881812 TTTTTTTCC
1 TTTTTTTCC
3881821 TTTTTTTTCC
1 -TTTTTTTCC
3881831 TTTTTTT--
1 TTTTTTTCC
*
3881838 TTTCTTT--
1 TTTTTTTCC
3881845 TTTTTTT-C
1 TTTTTTTCC
3881853 TTTTTTTCC
1 TTTTTTTCC
3881862 TTTTTTTC
1 TTTTTTTC
3881870 TCTGATGGAT
Statistics
Matches: 87, Mismatches: 4, Indels: 15
0.82 0.04 0.14
Matches are distributed among these distances:
7 26 0.30
8 17 0.20
9 28 0.32
10 12 0.14
11 4 0.05
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTTCC
Found at i:3881803 original size:7 final size:7
Alignment explanation
Indices: 3881791--3881866 Score: 54
Period size: 7 Copynumber: 10.7 Consensus size: 7
3881781 TTTATTTCTT
3881791 TTTTTCC
1 TTTTTCC
3881798 TTTTTCC
1 TTTTTCC
3881805 TTTTTCC
1 TTTTTCC
3881812 TTTTTTTCC
1 --TTTTTCC
3881821 TTTTTTTTCC
1 ---TTTTTCC
3881831 TTTTT--
1 TTTTTCC
3881836 TTTTT-C
1 TTTTTCC
3881842 TTTTT--
1 TTTTTCC
*
3881847 TTTTTCTT
1 TTTTTC-C
3881855 TTTTTCC
1 TTTTTCC
3881862 TTTTT
1 TTTTT
3881867 TTCTCTGATG
Statistics
Matches: 61, Mismatches: 1, Indels: 14
0.80 0.01 0.18
Matches are distributed among these distances:
5 10 0.16
6 5 0.08
7 24 0.39
8 6 0.10
9 7 0.11
10 9 0.15
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTCC
Found at i:3881809 original size:50 final size:49
Alignment explanation
Indices: 3881755--3881872 Score: 116
Period size: 50 Copynumber: 2.4 Consensus size: 49
3881745 ATTTCATTTT
3881755 TTTTTATTTTTTTTCTCTTTATTTT-CTTTATTTCTTTT-TTTCCTTTTTCC
1 TTTTTATTTTTTTTCTCTTTATTTTCCTTT-TTT-TTTTCTTT-CTTTTTCC
** * * *
3881805 TTTTTCCTTTTTTTC-CTTTTTTTTCCTTTTTTTTTTCTTTTTTTTTTC
1 TTTTTATTTTTTTTCTCTTTATTTTCCTTTTTTTTTTCTTTCTTTTTCC
*
3881853 TTTTTTTCCTTTTTTTCTCT
1 TTTTTAT--TTTTTTTCTCT
3881873 GATGGATGAG
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
48 15 0.27
49 14 0.25
50 25 0.45
51 2 0.04
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.81
Consensus pattern (49 bp):
TTTTTATTTTTTTTCTCTTTATTTTCCTTTTTTTTTTCTTTCTTTTTCC
Found at i:3881818 original size:10 final size:10
Alignment explanation
Indices: 3881805--3881868 Score: 78
Period size: 10 Copynumber: 6.4 Consensus size: 10
3881795 TCCTTTTTCC
3881805 TTTTTCC-TT
1 TTTTTCCTTT
3881814 TTTTTCCTTT
1 TTTTTCCTTT
3881824 TTTTTCCTTTT
1 TTTTTCC-TTT
*
3881835 TTTTTTCTTT
1 TTTTTCCTTT
*
3881845 TTTTT-TTCTT
1 TTTTTCCT-TT
3881855 TTTTTCCTTT
1 TTTTTCCTTT
3881865 TTTT
1 TTTT
3881869 CTCTGATGGA
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
9 8 0.17
10 30 0.62
11 10 0.21
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTCCTTT
Found at i:3881835 original size:41 final size:41
Alignment explanation
Indices: 3881764--3881868 Score: 108
Period size: 41 Copynumber: 2.6 Consensus size: 41
3881754 TTTTTTATTT
* *
3881764 TTTTTCTCTTTATTTT-C-TTTATTTCTTTTTTTCCTTT-TTCC
1 TTTTTC-CTTT-TTTTCCTTTTTTTTCCTTTTTT-CTTTCTTCC
* **
3881805 TTTTTCCTTTTTTTCCTTTTTTTTCCTTTTTTTTTTCTTTT
1 TTTTTCCTTTTTTTCCTTTTTTTTCCTTTTTTCTTTCTTCC
*
3881846 TTTTTTCTTTTTTTCCTTTTTTT
1 TTTTTCCTTTTTTTCCTTTTTTT
3881869 CTCTGATGGA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
39 4 0.07
40 8 0.15
41 43 0.78
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (41 bp):
TTTTTCCTTTTTTTCCTTTTTTTTCCTTTTTTCTTTCTTCC
Found at i:3886844 original size:2 final size:2
Alignment explanation
Indices: 3886837--3886868 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3886827 TCATGCGTAC
3886837 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
3886869 CTCGTGAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3887328 original size:14 final size:14
Alignment explanation
Indices: 3887309--3887337 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3887299 CATGGTAACT
3887309 AAAATTAATACAAA
1 AAAATTAATACAAA
3887323 AAAATTAATACAAA
1 AAAATTAATACAAA
3887337 A
1 A
3887338 TATGGGACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (14 bp):
AAAATTAATACAAA
Found at i:3888683 original size:3 final size:3
Alignment explanation
Indices: 3888658--3888709 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
3888648 CCTGCAAATG
*
3888658 TAA TAAA TAA TAT TAA TAA -AA TAA TAA TAA TAA TAA TAA T-A TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3888702 TAA TAA TA
1 TAA TAA TA
3888710 TTTTTTAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
2 4 0.09
3 37 0.84
4 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3888685 original size:17 final size:18
Alignment explanation
Indices: 3888658--3888709 Score: 72
Period size: 17 Copynumber: 2.9 Consensus size: 18
3888648 CCTGCAAATG
*
3888658 TAATAAATAATATTAATAA
1 TAAT-AATAATAATAATAA
3888677 -AATAATAATAATAATAA
1 TAATAATAATAATAATAA
3888694 TAAT-ATAATAATAATA
1 TAATAATAATAATAATA
3888710 TTTTTTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 25 0.81
18 6 0.19
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TAATAATAATAATAATAA
Found at i:3888688 original size:20 final size:20
Alignment explanation
Indices: 3888658--3888711 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
3888648 CCTGCAAATG
3888658 TAATAAATAATATTAATAAAA
1 TAAT-AATAATATTAATAAAA
* *
3888679 TAATAATAATAATAATAATA
1 TAATAATAATATTAATAAAA
3888699 TAATAATAATATT
1 TAATAATAATATT
3888712 TTTTAAAAGC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 26 0.87
21 4 0.13
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
TAATAATAATATTAATAAAA
Found at i:3892671 original size:43 final size:44
Alignment explanation
Indices: 3892555--3893012 Score: 463
Period size: 43 Copynumber: 10.6 Consensus size: 44
3892545 TGAGAACCAA
* * *
3892555 AAACGCCGCTATAGTTCAAGATCTATAGCGGCGTTTTTGGA-AC
1 AAACGCCGCAAAAGGTCAAGATCTATAGCGGCGTTTTTGGATAC
* * * * * *
3892598 AAACGTCGCAAAAAGGTCGATATATATAGCGGCATTTTTAGA-AC
1 AAACGCCGC-AAAAGGTCAAGATCTATAGCGGCGTTTTTGGATAC
* *
3892642 AAACGCCGCAAAAGGTCAAGATCTCTAGCGGCGTTTATGGA-AC
1 AAACGCCGCAAAAGGTCAAGATCTATAGCGGCGTTTTTGGATAC
* * *
3892685 AAATGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGTA-AC
1 AAACGCCGCAAAAGGTCAAGATCTATAGCGGCGTTTTTGGATAC
* * * *
3892728 AAACGTCGCAAAAGGT-TAGATATTTAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAAGATCTATAGCGGCGTTTTTGGATAC
* * *
3892771 AAATGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGTA-AC
1 AAACGCCGCAAAAGGTCAAGATCTATAGCGGCGTTTTTGGATAC
** * * *
3892814 AAACGTTGCAAAAGGT-TAGATATTTAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAAGATCTATAGCGGCGTTTTTGGATAC
* * * * *
3892857 AAATGCTGCAAAAGGAC-AGATCTATAGTGGCGTTTTTGGACAC
1 AAACGCCGCAAAAGGTCAAGATCTATAGCGGCGTTTTTGGATAC
* * *
3892900 AAACGCCGCAAAAGGT-TAGATATTTAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAAGATCTATAGCGGCGTTTTTGGATAC
* * *
3892943 AAAACGCTGCAAAA-GT-ACGGATCTATAGCGGCGTTTTTGGACAC
1 -AAACGCCGCAAAAGGTCA-AGATCTATAGCGGCGTTTTTGGATAC
*
3892987 AAACGCCGCAAAAAGTC-AGATCTATA
1 AAACGCCGCAAAAGGTCAAGATCTATA
3893013 ATTACCATTC
Statistics
Matches: 342, Mismatches: 63, Indels: 20
0.80 0.15 0.05
Matches are distributed among these distances:
42 40 0.12
43 212 0.62
44 90 0.26
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (44 bp):
AAACGCCGCAAAAGGTCAAGATCTATAGCGGCGTTTTTGGATAC
Found at i:3892738 original size:86 final size:86
Alignment explanation
Indices: 3892580--3892999 Score: 571
Period size: 86 Copynumber: 4.9 Consensus size: 86
3892570 TCAAGATCTA
* * * * * *
3892580 TAGCGGCGTTTTTGGA-ACAAACGTCGCAAAAAGGTCGATATATATAGCGGCATTTTTAGAACAA
1 TAGCGGCGTTTTTGGATACAAATGCCGC-AAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAA
* * *
3892644 ACGCCGCAAAAGGTCAAGATCTC
65 ACGCCGCAAAAGGT-TAGATATT
* *
3892667 TAGCGGCGTTTATGGA-ACAAATGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGTAACAAA
1 TAGCGGCGTTTTTGGATACAAATGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAA
*
3892731 CGTCGCAAAAGGTTAGATATT
66 CGCCGCAAAAGGTTAGATATT
*
3892752 TAGCGGCGTTTTTGGATACAAATGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGTAACAAA
1 TAGCGGCGTTTTTGGATACAAATGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAA
**
3892817 CGTTGCAAAAGGTTAGATATT
66 CGCCGCAAAAGGTTAGATATT
* * *
3892838 TAGCGGCGTTTTTGGATACAAATGCTGCAAAAGGAC-AGATCTATAGTGGCGTTTTTGGACACAA
1 TAGCGGCGTTTTTGGATACAAATGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGA-ACAA
3892902 ACGCCGCAAAAGGTTAGATATT
65 ACGCCGCAAAAGGTTAGATATT
* *
3892924 TAGCGGCGTTTTTGGATACAAAACGCTGCAAAA-GTACG-GATCTATAGCGGCGTTTTTGGACAC
1 TAGCGGCGTTTTTGGATAC-AAATGCCGCAAAAGGT-CGAGATCTATAGCGGCGTTTTTGGA-AC
3892987 AAACGCCGCAAAA
63 AAACGCCGCAAAA
3893000 AGTCAGATCT
Statistics
Matches: 305, Mismatches: 23, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
85 41 0.13
86 190 0.62
87 74 0.24
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (86 bp):
TAGCGGCGTTTTTGGATACAAATGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAA
CGCCGCAAAAGGTTAGATATT
Found at i:3893888 original size:26 final size:26
Alignment explanation
Indices: 3893859--3893912 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
3893849 TAAAATAATT
3893859 AATGATTAAAATCACAAAATGCAGGG
1 AATGATTAAAATCACAAAATGCAGGG
3893885 AATGATTAAAATCACAAAATGCAGGG
1 AATGATTAAAATCACAAAATGCAGGG
3893911 AA
1 AA
3893913 ACAATATACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.52, C:0.11, G:0.19, T:0.19
Consensus pattern (26 bp):
AATGATTAAAATCACAAAATGCAGGG
Found at i:3894944 original size:20 final size:21
Alignment explanation
Indices: 3894909--3894951 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 21
3894899 ATCTTAAATC
3894909 CTACCTCGGTTTTTGAACTTT
1 CTACCTCGGTTTTTGAACTTT
3894930 CTACCTCGG-TTTTGAACTTT
1 CTACCTCGGTTTTTGAACTTT
3894950 CT
1 CT
3894952 TGGGTATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.14, C:0.26, G:0.14, T:0.47
Consensus pattern (21 bp):
CTACCTCGGTTTTTGAACTTT
Found at i:3895740 original size:14 final size:15
Alignment explanation
Indices: 3895710--3895740 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3895700 GCGTTTGCAT
3895710 AAAAACGCCACTAAA
1 AAAAACGCCACTAAA
*
3895725 AAAAACGCCGCTAAA
1 AAAAACGCCACTAAA
3895740 A
1 A
3895741 GTGCCGCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.26, G:0.10, T:0.06
Consensus pattern (15 bp):
AAAAACGCCACTAAA
Found at i:3896108 original size:29 final size:30
Alignment explanation
Indices: 3896039--3896097 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
3896029 AATTTAAGGC
3896039 AAAATGGTTTTTGGACTTGAATTGAATTTAA
1 AAAAT-GTTTTTGGACTTGAATTGAATTTAA
3896070 AAAATGTTTTTGGACTT-AATTGAATTTA
1 AAAATGTTTTTGGACTTGAATTGAATTTA
3896098 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.39
30 12 0.43
31 5 0.18
ACGTcount: A:0.36, C:0.03, G:0.17, T:0.44
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTAA
Found at i:3896322 original size:21 final size:21
Alignment explanation
Indices: 3896296--3896335 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3896286 TATCCTTCTG
3896296 TGCATCAATGCATCAAGGCCA
1 TGCATCAATGCATCAAGGCCA
*
3896317 TGCATCCATGCATCAAGGC
1 TGCATCAATGCATCAAGGC
3896336 TGCAACAGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (21 bp):
TGCATCAATGCATCAAGGCCA
Found at i:3897274 original size:23 final size:23
Alignment explanation
Indices: 3897248--3897292 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3897238 ATTTATTTTA
*
3897248 ATTATTTA-AAATAAATAATATTT
1 ATTAATTATAAATAAA-AATATTT
*
3897271 ATTAATTATATATAAAAATATT
1 ATTAATTATAAATAAAAATATT
3897293 AATAATGAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATTAATTATAAATAAAAATATTT
Found at i:3899883 original size:26 final size:29
Alignment explanation
Indices: 3899834--3899894 Score: 92
Period size: 26 Copynumber: 2.2 Consensus size: 29
3899824 AACGAGGAGA
*
3899834 TATATTATTGTGTTTATTAAATTTT-T-T
1 TATAATATTGTGTTTATTAAATTTTATGT
3899861 TATAATATTGTG-TTATTAAATTTTATGT
1 TATAATATTGTGTTTATTAAATTTTATGT
3899889 TATAAT
1 TATAAT
3899895 CATTAGATGA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
26 12 0.39
27 12 0.39
28 7 0.23
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (29 bp):
TATAATATTGTGTTTATTAAATTTTATGT
Found at i:3900201 original size:26 final size:26
Alignment explanation
Indices: 3900158--3900207 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
3900148 ATCATATTTT
*
3900158 TTAAAATAATTAAATAAATTTAATCA
1 TTAAAATAATTAAATAAATATAATCA
* **
3900184 TTAAAGTAATTATTTAAATATAAT
1 TTAAAATAATTAAATAAATATAAT
3900208 TTAATACATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (26 bp):
TTAAAATAATTAAATAAATATAATCA
Found at i:3916167 original size:26 final size:26
Alignment explanation
Indices: 3916120--3916169 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
3916110 GGTAATAATT
*
3916120 TTTTTAAAAATATATGAAATTTATAA
1 TTTTTAAAAATATATAAAATTTATAA
*
3916146 TTTTTAAAATTATA-AAATATTTAT
1 TTTTTAAAAATATATAAA-ATTTAT
3916170 TATCATCATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 2 0.10
26 19 0.90
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (26 bp):
TTTTTAAAAATATATAAAATTTATAA
Found at i:3916545 original size:340 final size:340
Alignment explanation
Indices: 3915901--3916531 Score: 944
Period size: 340 Copynumber: 1.9 Consensus size: 340
3915891 TGCTCTTCTC
* * * * *
3915901 AATATTTACCCTCAAAGTTTTTATATACTAGATTATATGTATTGTGTAATTTGAATGTAAAAATT
1 AATACTTACCCTCAAAGTTTTCATATACTAGATTATACGTATTGTGTAATTTGAATGCAAAAATC
* * *
3915966 TAAATAATTTTATTAAAAATGAATAAACATTATTAACTGCTGTTAAAAATTAAAAATTAATGAAT
66 AAAATAATTTTATTAAAAATAAATAAACATTATTAACTGCTGTTAAAAAATAAAAATTAATGAAT
* * * * *
3916031 AGTAATTCATTTGATCACTCAATTGTAATTAAAATTTTATTTTAATATTTTTTATATTTTTAAAC
131 AATAATTCATTTAATCACTCAATTGTAATTAAAAGTTTATTTTAATATATTTTATATGTTTAAAC
**
3916096 AATTAATTTTAAAAGGTAATAATTTTTTTAAAAATATATGAAATTTATAATTTTTAAAATTATAA
196 AATTAATTTTAAAAGAAAATAATTTTTTTAAAAATATATGAAATTTATAATTTTTAAAATTATAA
* ** * ** * * *
3916161 AATATTTATTATCATCATCATCATCATTTTGTAAAAGAAATACTAGTTATAAAACTTTTATAAAA
261 AAAAAATATTATCATAAAAATAAACATTGTGTAAAAGAAATACTAGTTATAAAACTTTTATAAAA
3916226 TTATTCATATTTTAA
326 TTATTCATATTTTAA
*
3916241 AATACTTACCCTCAAAGTTTTCATATACTAGATTATACGTATTGTGTAATTTTAATGCAAAAATC
1 AATACTTACCCTCAAAGTTTTCATATACTAGATTATACGTATTGTGTAATTTGAATGCAAAAATC
* *
3916306 AAAATAATTTTATTAAAAATAAATAAATATTATTAACTGTTGTTAAAAAATAAAAATTAATGAAT
66 AAAATAATTTTATTAAAAATAAATAAACATTATTAACTGCTGTTAAAAAATAAAAATTAATGAAT
*
3916371 AATAATTCATTTAATC-CTTTAATTGTAATTAAAAGTTTATTTTAATA-ATTTTATATGTTTAAA
131 AATAATTCATTTAATCAC-TCAATTGTAATTAAAAGTTTATTTTAATATATTTTATATGTTTAAA
*
3916434 CAATTAATTTTAAAAGAAAATAATTTTTTTTCAAAATATATGAAATTTATAATTTTTAAAATTAT
195 CAATTAATTTTAAAAGAAAATAA-TTTTTTTAAAAATATATGAAATTTATAATTTTTAAAATTAT
*
3916499 AAAAAAAATATTATTATAAAAAATAAAC-TTGTG
259 AAAAAAAATATTATCAT-AAAAATAAACATTGTG
3916532 ACACTAAAAT
Statistics
Matches: 258, Mismatches: 30, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
339 36 0.14
340 217 0.84
341 5 0.02
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (340 bp):
AATACTTACCCTCAAAGTTTTCATATACTAGATTATACGTATTGTGTAATTTGAATGCAAAAATC
AAAATAATTTTATTAAAAATAAATAAACATTATTAACTGCTGTTAAAAAATAAAAATTAATGAAT
AATAATTCATTTAATCACTCAATTGTAATTAAAAGTTTATTTTAATATATTTTATATGTTTAAAC
AATTAATTTTAAAAGAAAATAATTTTTTTAAAAATATATGAAATTTATAATTTTTAAAATTATAA
AAAAAATATTATCATAAAAATAAACATTGTGTAAAAGAAATACTAGTTATAAAACTTTTATAAAA
TTATTCATATTTTAA
Found at i:3922428 original size:15 final size:15
Alignment explanation
Indices: 3922408--3922459 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
3922398 AAGATACTAT
3922408 TTTTTATCCATATTA
1 TTTTTATCCATATTA
3922423 TTTTTATCCATATTA
1 TTTTTATCCATATTA
* **
3922438 TTGTTATTAATATTA
1 TTTTTATCCATATTA
*
3922453 TTATTAT
1 TTTTTAT
3922460 TATTATTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.62
Consensus pattern (15 bp):
TTTTTATCCATATTA
Found at i:3922439 original size:3 final size:3
Alignment explanation
Indices: 3922433--3922503 Score: 124
Period size: 3 Copynumber: 23.7 Consensus size: 3
3922423 TTTTTATCCA
* *
3922433 TAT TAT TGT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3922481 TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
3922504 ATTTATATTA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:3922460 original size:15 final size:15
Alignment explanation
Indices: 3922417--3922513 Score: 113
Period size: 15 Copynumber: 6.4 Consensus size: 15
3922407 TTTTTTATCC
* **
3922417 ATATTATTTTTATCC
1 ATATTATTATTATTA
*
3922432 ATATTATTGTTATTA
1 ATATTATTATTATTA
3922447 ATATTATTATTATTA
1 ATATTATTATTATTA
*
3922462 TTATTATTATTATTA
1 ATATTATTATTATTA
*
3922477 TTATTATTATTATTA
1 ATATTATTATTATTA
* *
3922492 TTATTATTATTAATTT
1 ATATTATTATT-ATTA
3922508 ATATTA
1 ATATTA
3922514 AATATATTAA
Statistics
Matches: 74, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
15 66 0.89
16 8 0.11
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (15 bp):
ATATTATTATTATTA
Found at i:3922969 original size:6 final size:6
Alignment explanation
Indices: 3922960--3922984 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3922950 AAAAAAAAAA
3922960 AGACAG AGACAG AGACAG AGACAG A
1 AGACAG AGACAG AGACAG AGACAG A
3922985 ACTGGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.32, T:0.00
Consensus pattern (6 bp):
AGACAG
Found at i:3935223 original size:16 final size:16
Alignment explanation
Indices: 3935202--3935233 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3935192 TATTATGCTT
3935202 AAAAAAAAAAAAAGAG
1 AAAAAAAAAAAAAGAG
*
3935218 AAAAAAGAAAAAAGAG
1 AAAAAAAAAAAAAGAG
3935234 GGTCAAGGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAGAG
Found at i:3935596 original size:19 final size:19
Alignment explanation
Indices: 3935568--3935604 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3935558 GTTCAACTTA
*
3935568 TTGGAGATTCAATTTATTT
1 TTGGAAATTCAATTTATTT
3935587 TTGGAAATTCAATTTATT
1 TTGGAAATTCAATTTATT
3935605 CTTTTATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.51
Consensus pattern (19 bp):
TTGGAAATTCAATTTATTT
Found at i:3936350 original size:52 final size:52
Alignment explanation
Indices: 3936267--3936615 Score: 680
Period size: 52 Copynumber: 6.7 Consensus size: 52
3936257 GAATATGCCA
* *
3936267 ATAGCATCTTCTGGAAGTGTTCTTTGTGTTATCTGATCTGGTTGGACAAAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
3936319 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
3936371 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
3936423 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
3936475 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
3936527 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
3936579 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
3936616 TGGACAGAAT
Statistics
Matches: 295, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 295 1.00
ACGTcount: A:0.23, C:0.15, G:0.24, T:0.38
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
Found at i:3936760 original size:130 final size:130
Alignment explanation
Indices: 3936527--3936824 Score: 569
Period size: 130 Copynumber: 2.3 Consensus size: 130
3936517 TGGACAGAAC
3936527 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
*
3936592 GAAGTGTTCTTTGAGTTATCTGATTGGACAGAATCAAGCATTGAATTTAGAATATGAATTTGCCA
66 GAAGTGTTCTTTGAGTTATCTGATTGGACAGAATCAAGCATTGAATTTAGAAGATGAATTTGCCA
3936657 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
3936722 GAAGTGTTCTTTGAGTTATCTGATTGGACAGAATCAAGCATTGAATTTAGAAGATGAATTTGCCA
66 GAAGTGTTCTTTGAGTTATCTGATTGGACAGAATCAAGCATTGAATTTAGAAGATGAATTTGCCA
* *
3936787 ATAGCATCTTCTGGAAGTGTTATTTGAGTTATTTGATC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
3936825 CGAAGAAGTG
Statistics
Matches: 165, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
130 165 1.00
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.37
Consensus pattern (130 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
GAAGTGTTCTTTGAGTTATCTGATTGGACAGAATCAAGCATTGAATTTAGAAGATGAATTTGCCA
Found at i:3936762 original size:47 final size:48
Alignment explanation
Indices: 3936657--3936762 Score: 153
Period size: 52 Copynumber: 2.1 Consensus size: 48
3936647 GAATTTGCCA
3936657 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGA----GTTGGACAGAAC
3936709 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGA-TTGGACAGAATC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAGTTGGACAGAA-C
3936757 A-AGCAT
1 ATAGCAT
3936763 TGAATTTAGA
Statistics
Matches: 53, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
47 15 0.28
48 2 0.04
52 36 0.68
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (48 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAGTTGGACAGAAC
Found at i:3937730 original size:112 final size:112
Alignment explanation
Indices: 3937420--3938282 Score: 1253
Period size: 112 Copynumber: 7.7 Consensus size: 112
3937410 GCAAGGTAGA
*
3937420 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
*** * * * * * * * *
3937485 ACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAAAAA
66 ACCTTTTGTTTAAATTCATCATTTGATGGATCAACATTACCAG-AGAG
*
3937533 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
*** * * * * * *
3937598 ACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAG
66 ACCTTTTGTTTAAATTCATCATTTGATGGATCAACATTACCAGAGAG
* *
3937645 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTATTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
*** * * * * * *
3937710 ACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAG
66 ACCTTTTGTTTAAATTCATCATTTGATGGATCAACATTACCAGAGAG
*
3937757 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAGGTTCATAATGAGAAGAACTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
*
3937822 ACTTTTTGTTTAAATTCATCATTTGATGGATCAACATTACCAGAGAG
66 ACCTTTTGTTTAAATTCATCATTTGATGGATCAACATTACCAGAGAG
*
3937869 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAGGTTCATAATGAGAAGAAC-TGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
*
3937933 ACTTTTTGTTTAAATTCATCATTTGATGGATCAACATTACCAGAGAAG
66 ACCTTTTGTTTAAATTCATCATTTGATGGATCAACATTACCAGAG-AG
*
3937981 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAGGTTCATAATGAGAAGAACTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
*
3938046 ACTTTTTGTTTAAATTCATCATTTGATGGATCAACATTACCAGAGAAG
66 ACCTTTTGTTTAAATTCATCATTTGATGGATCAACATTACCAGAG-AG
*
3938094 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAGGTTCATAATGAGAAGAACTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* * *
3938159 ACTTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCCAGAGAAA
66 ACCTTTTGTTTAAATTCATCATTTGATGGATCAACATTACCAGAG-AG
* * *
3938207 GTTCATGAATAAAAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
1 GTTCAT-AATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
3938272 AACC-TTTGTTT
65 AACCTTTTGTTT
3938283 GATATTATCT
Statistics
Matches: 724, Mismatches: 23, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
111 51 0.07
112 330 0.46
113 286 0.40
114 57 0.08
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.29
Consensus pattern (112 bp):
GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
ACCTTTTGTTTAAATTCATCATTTGATGGATCAACATTACCAGAGAG
Found at i:3938583 original size:15 final size:15
Alignment explanation
Indices: 3938563--3938614 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
3938553 AAGATACTAT
3938563 TTTTTATCCATATTA
1 TTTTTATCCATATTA
3938578 TTTTTATCCATATTA
1 TTTTTATCCATATTA
* **
3938593 TTGTTATTAATATTA
1 TTTTTATCCATATTA
*
3938608 TTATTAT
1 TTTTTAT
3938615 TATTATTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.62
Consensus pattern (15 bp):
TTTTTATCCATATTA
Found at i:3938594 original size:3 final size:3
Alignment explanation
Indices: 3938588--3938652 Score: 112
Period size: 3 Copynumber: 21.7 Consensus size: 3
3938578 TTTTTATCCA
* *
3938588 TAT TAT TGT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3938636 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
3938653 ATTTATATTA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:3938615 original size:15 final size:15
Alignment explanation
Indices: 3938572--3938652 Score: 99
Period size: 15 Copynumber: 5.4 Consensus size: 15
3938562 TTTTTTATCC
* **
3938572 ATATTATTTTTATCC
1 ATATTATTATTATTA
*
3938587 ATATTATTGTTATTA
1 ATATTATTATTATTA
3938602 ATATTATTATTATTA
1 ATATTATTATTATTA
*
3938617 TTATTATTATTATTA
1 ATATTATTATTATTA
*
3938632 TTATTATTATTATTA
1 ATATTATTATTATTA
*
3938647 TTATTA
1 ATATTA
3938653 ATTTATATTA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 61 1.00
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.63
Consensus pattern (15 bp):
ATATTATTATTATTA
Found at i:3939119 original size:6 final size:6
Alignment explanation
Indices: 3939110--3939140 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
3939100 AAAAAAAAAA
3939110 AGACAG AGACAG AGACAG AGACAG AGACAG A
1 AGACAG AGACAG AGACAG AGACAG AGACAG A
3939141 ACTGGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.52, C:0.16, G:0.32, T:0.00
Consensus pattern (6 bp):
AGACAG
Found at i:3940096 original size:24 final size:22
Alignment explanation
Indices: 3940048--3940096 Score: 53
Period size: 24 Copynumber: 2.1 Consensus size: 22
3940038 GTTTTAATAG
* *
3940048 TATTTTTATTTTTATGAATAAA
1 TATTTTTATTTTCATAAATAAA
*
3940070 TATTTTTATATATTCATAAATATA
1 TATTTTTAT-T-TTCATAAATAAA
3940094 TAT
1 TAT
3940097 ATAATAGTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 9 0.41
23 1 0.05
24 12 0.55
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
TATTTTTATTTTCATAAATAAA
Found at i:3944557 original size:36 final size:36
Alignment explanation
Indices: 3944510--3944594 Score: 143
Period size: 36 Copynumber: 2.4 Consensus size: 36
3944500 GATACAATCT
3944510 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
3944546 GTCCATCACCATTATCACGCCTATATCATTACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
3944582 TTCCATTACCATT
1 GTCCATCACCATT
3944595 TCATCACCAT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.29, C:0.34, G:0.05, T:0.32
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:3945552 original size:3 final size:3
Alignment explanation
Indices: 3945539--3945591 Score: 88
Period size: 3 Copynumber: 17.7 Consensus size: 3
3945529 TTTTTATCCA
* *
3945539 TAT TTT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3945587 TAT TA
1 TAT TA
3945592 ATAAATATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3945616 original size:17 final size:16
Alignment explanation
Indices: 3945591--3945629 Score: 71
Period size: 15 Copynumber: 2.5 Consensus size: 16
3945581 TATTATTATT
3945591 AATAAATATATAT-TA
1 AATAAATATATATATA
3945606 AATAAATATATATATA
1 AATAAATATATATATA
3945622 AATAAATA
1 AATAAATA
3945630 ATTACAGACC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AATAAATATATATATA
Found at i:3946067 original size:18 final size:16
Alignment explanation
Indices: 3946044--3946081 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 16
3946034 CCTGAAAAAA
3946044 AGAAAAAAAAACGGAGAC
1 AGAAAAAAAAA--GAGAC
3946062 AGAAAAAAAAAGAGAC
1 AGAAAAAAAAAGAGAC
3946078 AGAA
1 AGAA
3946082 CCGGAGAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 9 0.45
18 11 0.55
ACGTcount: A:0.71, C:0.08, G:0.21, T:0.00
Consensus pattern (16 bp):
AGAAAAAAAAAGAGAC
Found at i:3946086 original size:28 final size:28
Alignment explanation
Indices: 3946038--3946109 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
3946028 CCCCAACCTG
* * * *
3946038 AAAAAAAGAAAAAAAAACGGAGACAGAA
1 AAAAAAAGAGAAAGAACCGGAGAAAGAA
*
3946066 AAAAAAAGAGACAGAACCGGAGAAAGAA
1 AAAAAAAGAGAAAGAACCGGAGAAAGAA
*
3946094 AAAAACAGAGAAAGAA
1 AAAAAAAGAGAAAGAA
3946110 AAAAAAACTA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.71, C:0.08, G:0.21, T:0.00
Consensus pattern (28 bp):
AAAAAAAGAGAAAGAACCGGAGAAAGAA
Found at i:3958755 original size:16 final size:17
Alignment explanation
Indices: 3958736--3958781 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
3958726 CTATTTCAAG
*
3958736 TTCAATTTATT-GGAGA
1 TTCAATTTATTGGGAAA
3958752 TTCAATTTATTTTGGGAAA
1 TTCAATTTA--TTGGGAAA
3958771 TTCAATTTATT
1 TTCAATTTATT
3958782 CTTCTATGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 9 0.35
17 2 0.08
18 2 0.08
19 13 0.50
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (17 bp):
TTCAATTTATTGGGAAA
Found at i:3959675 original size:82 final size:82
Alignment explanation
Indices: 3959528--3960258 Score: 1066
Period size: 82 Copynumber: 8.9 Consensus size: 82
3959518 ATATCCTAGT
* * *
3959528 CCAAACATTAAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTAGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
3959593 TGATCTGGTTTGGTA-A-A
66 TGATCTGG-TTGG-ACAGA
* *
3959610 CCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAGGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTAGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
3959675 TGATCTGGTTTGG-CAGAA
66 TGATCTGG-TTGGACAG-A
* *
3959693 CCAATCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTAGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
3959758 TGATCTGGTTTGG-CAGAA
66 TGATCTGG-TTGGACAG-A
* *
3959776 CCAATCATTGAATTTGGAAGATGAATGTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTAGAAGATGAATTTG-TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
*
3959840 TTGATCTGGTTGGACAGA
65 CTGATCTGGTTGGACAGA
* * * *
3959858 ACAATCATTGAGTTTAGAAGATGAATGTGTTC-ATAGCATCTTCTAGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTAGAAGATGAATTTG-TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
3959922 CTGATCTGGTTGGACAGA
65 CTGATCTGGTTGGACAGA
* *
3959940 ACAATCATTGAGTTTAGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTAGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
3960005 TGATCTGGTTGGACAGA
66 TGATCTGGTTGGACAGA
* ** *
3960022 ACAATCATTGAATTCGGAAGATGAATGTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTAGAAGATGAATTTG-TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
3960086 CTGATCTGGTTGGACAGA
65 CTGATCTGGTTGGACAGA
* *
3960104 CCAATCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTAGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
3960169 TGATCTGGTTTGG-CAGAA
66 TGATCTGG-TTGGACAG-A
** *
3960187 CCAATCATTGAATTCGGAAGATGAATGTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTAGAAGATGAATTTG-TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
3960251 CTGATCTG
65 CTGATCTG
3960259 ATTCAGTAGG
Statistics
Matches: 606, Mismatches: 32, Indels: 21
0.92 0.05 0.03
Matches are distributed among these distances:
81 4 0.01
82 377 0.62
83 223 0.37
84 2 0.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.37
Consensus pattern (82 bp):
CCAATCATTGAATTTAGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
TGATCTGGTTGGACAGA
Found at i:3961177 original size:113 final size:114
Alignment explanation
Indices: 3961058--3961752 Score: 514
Period size: 117 Copynumber: 6.2 Consensus size: 114
3961048 TCTAAAGAAG
** * *
3961058 GAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGATGGATCAGTTTTTCCAGAGAAAGTT
1 GAAGAATTTGTTCAACCTTTTATTTGAATTCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTT
3961123 CATAATGAGAAGAA-CTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
66 CATAATGAGAAGAACCTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* *
3961171 GAAGAATTTGTTCAACCTTTTACTTGAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTT
1 GAAGAATTTGTTCAACCTTTTATTTGAATTCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTT
* * *** *
3961236 CATAATGAGAAGAA-CTCATCTAAAGAAGGAATAATTTGTTCA-AACCTTTTA
66 CATAATGAGAAGAACCTCATCTGAAGAAGGAAGAAGAAGTTCATAA----TGA
* * *** * * * *** * * * *
3961287 CATGAATCCATT--ACC--TGA--TGGA-GCATCATCCCCAGCGGA-AAG-TTCAT-AATGAGAA
1 GAAGAATTTGTTCAACCTTTTATTTGAATTCATCAT-TTGA-TGGATCAGCTT-TTCCA-GAGAA
**
3961342 GAACTCAT-AT--GAA-AA----A---G-A-AA-GAAGAAGAAGTTCATAATGA
62 -AGTTCATAATGAGAAGAACCTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* ** * * * * *
3961382 GAAGAACTTGTTCAATTTTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAG-GTAGAG
1 GAAGAATTTGTTCAACCTTTT-ATTTGAATTCATCATTTGATGGATCAGCTTTTCCAGAG-AAAG
* *
3961446 TTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAAAAGAAGTTCATAATAA
64 TTCATAATGAGAAGAAC-C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* * * * *
3961499 GAAGAACTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAG-GAAGAG
1 GAAGAATTTGTTCAACCTTTT-ATTTGAATTCATCATTTGATGGATCAGCTTTTCCAGAGAA-AG
3961563 TTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
64 TTCATAATGAGAAGAAC-C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* * * * *
3961616 GAAGAATTTGTTCAACCTTTTATCTGAATTCATCACTGGATGGATTA-TTTCTTCCAGAGAAAGT
1 GAAGAATTTGTTCAACCTTTTATTTGAATTCATCATTTGATGGATCAGCTT-TTCCAGAGAAAGT
* * *
3961680 TCATAATGAGAAGAACTCCTCATATGAAGAAGAAAGAAGAAGTTCATAATAA
65 TCATAATGAGAAGAA--CCTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* *
3961732 GAAGAACTTGTTCAACTTTTT
1 GAAGAATTTGTTCAACCTTTT
3961753 GCATAATTCT
Statistics
Matches: 461, Mismatches: 78, Indels: 83
0.74 0.13 0.13
Matches are distributed among these distances:
95 8 0.02
97 1 0.00
98 10 0.02
99 5 0.01
100 1 0.00
101 9 0.02
102 9 0.02
103 8 0.02
104 4 0.01
105 2 0.00
107 2 0.00
108 3 0.01
109 9 0.02
110 14 0.03
111 9 0.02
112 4 0.01
113 100 0.22
114 4 0.01
115 2 0.00
116 105 0.23
117 151 0.33
118 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (114 bp):
GAAGAATTTGTTCAACCTTTTATTTGAATTCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTT
CATAATGAGAAGAACCTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
Found at i:3961295 original size:94 final size:94
Alignment explanation
Indices: 3961175--3961349 Score: 244
Period size: 94 Copynumber: 1.9 Consensus size: 94
3961165 TAATGAGAAG
* ** * * **
3961175 AATTTGTTCAACCTTTTACTTGAATCCATCATTTGATGGATCAGCTTTTCCAG-AGAAAGTTCAT
1 AATTTGTTCAACCTTTTACATGAATCCATCACCTGATGGAGCAGCATCCCCAGCAGAAAGTTCAT
3961239 AATGAGAAGAACTCATCTAAAGAAGGAAT
66 AATGAGAAGAACTCATCTAAAGAAGGAAT
* * *
3961268 AATTTGTTCAAACCTTTTACATGAATCCATTACCTGATGGAGCATCATCCCCAGCGGAAAGTTCA
1 AATTTGTTC-AACCTTTTACATGAATCCATCACCTGATGGAGCAGCATCCCCAGCAGAAAGTTCA
3961333 TAATGAGAAGAACTCAT
65 TAATGAGAAGAACTCAT
3961350 ATGAAAAAGA
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
93 9 0.13
94 35 0.50
95 26 0.37
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (94 bp):
AATTTGTTCAACCTTTTACATGAATCCATCACCTGATGGAGCAGCATCCCCAGCAGAAAGTTCAT
AATGAGAAGAACTCATCTAAAGAAGGAAT
Found at i:3961477 original size:117 final size:116
Alignment explanation
Indices: 3961327--3961753 Score: 558
Period size: 117 Copynumber: 3.7 Consensus size: 116
3961317 CCCAGCGGAA
** *
3961327 AGTTCATAATGAGAAGAACTCAT-ATGAAAAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTT
1 AGTTCATAATGAGAAGAACTCATCAT-ATGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTT
**
3961391 GTTCAATTTTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAG
65 GTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAGG-AG
* * *
3961444 AGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAAAAGAAGTTCATAATAAGAAGAACTTG
1 AGTTCATAATGAGAAGAACTCATCATATGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTG
3961509 TTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGAAG
66 TTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAGG-AG
* * * * *
3961561 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTG
1 AGTTCATAATGAGAAGAACTCATCATATGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTG
* * * * * * *
3961626 TTCAACCTTTT-ATCTGAATTCATCACTGGATGGATTATTTC-TT-CCAGAGAA
66 TTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCA--ACATTGCCAG-GAG
*
3961677 AGTTCATAATGAGAAGAACTCCTCATATGAAG-AAGAAAGAAGAAGTTCATAATAAGAAGAACTT
1 AGTTCATAATGAGAAGAACTCATCATATGAAGAAAG-AAGAAGAAGTTCATAATAAGAAGAACTT
*
3961741 GTTCAACTTTTTG
65 GTTCAACCTTTTG
3961754 CATAATTCTA
Statistics
Matches: 278, Mismatches: 26, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
115 2 0.01
116 93 0.33
117 180 0.65
118 3 0.01
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (116 bp):
AGTTCATAATGAGAAGAACTCATCATATGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTG
TTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGAG
Found at i:3961731 original size:233 final size:233
Alignment explanation
Indices: 3961323--3961753 Score: 604
Period size: 233 Copynumber: 1.8 Consensus size: 233
3961313 CATCCCCAGC
3961323 GGAAAGTTCATAATGAGAAGAACTCATATGAAAAAGAAAGAAGAAGAAGTTCATAATGAGAAGAA
1 GGAAAGTTCATAATGAGAAGAACTCATATGAAAAAGAAAGAAGAAGAAGTTCATAATGAGAAGAA
** * * * * *
3961388 CTTGTTCAATTTTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAA
66 CTTGTTCAACCTTTTGATCTGAATTCATCACTGGATGGATCAACATTGCCAGGTAAAGTTCATAA
*
3961453 TGAGAAGAACTCATCATCTGAAGAAGGAAAAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTT
131 TGAGAAGAACTCATCATATGAAGAAGGAAAAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTT
3961518 TTGGTTTGAATTCATCATTTGATGGATCAACATTGCCA
196 TTGGTTTGAATTCATCATTTGATGGATCAACATTGCCA
* *** *
3961556 GGAAGAGTTCATAATGAGAAGAACTCGTCAT-CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAG
1 GGAA-AGTTCATAATGAGAAGAACTCAT-ATGAAAAAGAAAGAAGAAGAAGTTCATAATGAGAAG
* * *
3961620 AATTTGTTCAACCTTTT-ATCTGAATTCATCACTGGATGGATTATTTC-TT-CCAGAG-AAAGTT
64 AACTTGTTCAACCTTTTGATCTGAATTCATCACTGGATGGATCA--ACATTGCCAG-GTAAAGTT
*
3961681 CATAATGAGAAGAACTCCTCATATGAAGAA-GAAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
126 CATAATGAGAAGAACTCATCATATGAAGAAGGAAA-AAGAAGTTCATAATAAGAAGAACTTGTTC
*
3961745 AACTTTTTG
190 AACCTTTTG
3961754 CATAATTCTA
Statistics
Matches: 174, Mismatches: 18, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
232 4 0.02
233 99 0.57
234 68 0.39
235 3 0.02
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (233 bp):
GGAAAGTTCATAATGAGAAGAACTCATATGAAAAAGAAAGAAGAAGAAGTTCATAATGAGAAGAA
CTTGTTCAACCTTTTGATCTGAATTCATCACTGGATGGATCAACATTGCCAGGTAAAGTTCATAA
TGAGAAGAACTCATCATATGAAGAAGGAAAAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTT
TTGGTTTGAATTCATCATTTGATGGATCAACATTGCCA
Found at i:3961996 original size:3 final size:3
Alignment explanation
Indices: 3961988--3962023 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
3961978 CATATTTTAT
*
3961988 TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3962024 AATATATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:3962040 original size:13 final size:13
Alignment explanation
Indices: 3962022--3962056 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
3962012 TTATTATTAT
3962022 TAAATATATTAAA
1 TAAATATATTAAA
3962035 TAAATATA-TAAA
1 TAAATATATTAAA
3962047 TAAATA-ATTA
1 TAAATATATTA
3962057 CAGACCAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 1 0.05
12 12 0.57
13 8 0.38
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
TAAATATATTAAA
Found at i:3962491 original size:17 final size:17
Alignment explanation
Indices: 3962466--3962504 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
3962456 CCTGAAAAAA
*
3962466 AGAAAAAAAAACGGAGAC
1 AGAAAAAAAAA-AGAGAC
3962484 AGAAAAAAAAAAGAGAC
1 AGAAAAAAAAAAGAGAC
3962501 AGAA
1 AGAA
3962505 CCGGAGAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.72, C:0.08, G:0.21, T:0.00
Consensus pattern (17 bp):
AGAAAAAAAAAAGAGAC
Found at i:3962518 original size:28 final size:29
Alignment explanation
Indices: 3962460--3962532 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 29
3962450 CCCCAACCTG
* * * *
3962460 AAAAAAAGAAAAAAAAACGGAGACAGAAA
1 AAAAAAAGAGAAAGAACCGGAGAAAGAAA
*
3962489 AAAAAAAGAGACAGAACCGGAGAAAG-AA
1 AAAAAAAGAGAAAGAACCGGAGAAAGAAA
*
3962517 AAAAACAGAGAAAGAA
1 AAAAAAAGAGAAAGAA
3962533 AAAAAAACTA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
28 16 0.43
29 21 0.57
ACGTcount: A:0.71, C:0.08, G:0.21, T:0.00
Consensus pattern (29 bp):
AAAAAAAGAGAAAGAACCGGAGAAAGAAA
Found at i:3966125 original size:15 final size:15
Alignment explanation
Indices: 3966100--3966133 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
3966090 ATATTTTTTA
3966100 AAAAATAAAAATATTT
1 AAAAATAAAAATA-TT
3966116 AAAAAT-AAAATATT
1 AAAAATAAAAATATT
3966130 AAAA
1 AAAA
3966134 TATGTAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 6 0.33
16 6 0.33
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAAATAAAAATATT
Found at i:3971134 original size:31 final size:31
Alignment explanation
Indices: 3971089--3971164 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
3971079 AGTTAACTCG
* * *
3971089 AAGTGACCACATCTTAATTATATAAAAACGA
1 AAGTGACAATATCTTAATTAAATAAAAACGA
* *
3971120 AAGTGACTATATCTTAATTAAATAAAAATGA
1 AAGTGACAATATCTTAATTAAATAAAAACGA
3971151 AAGTGACAATATCT
1 AAGTGACAATATCT
3971165 CATTTTTTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.49, C:0.12, G:0.11, T:0.29
Consensus pattern (31 bp):
AAGTGACAATATCTTAATTAAATAAAAACGA
Done.