Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397256.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_56.0, 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: 13963513
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 99179 characters in sequence are not A, C, G, or T
File 10 of 29
Found at i:3570987 original size:96 final size:96
Alignment explanation
Indices: 3570823--3571018 Score: 374
Period size: 96 Copynumber: 2.0 Consensus size: 96
3570813 CACTAAAAGT
3570823 TGTTTGAACATGGTTATTGATGATTTGGTCCACAACTCCCTTAGCCACACTTTTTCCTTTTTGTA
1 TGTTTGAACATGGTTATTGATGATTTGGTCCACAACTCCCTTAGCCACACTTTTTCCTTTTTGTA
*
3570888 GATTATTCAGGTCTCTTTTTTACGCTTTGCA
66 GATTATTCAGGTCTCTTTTTTACACTTTGCA
*
3570919 TGTTTGAACATGGTTATTGATGATTTGGTCCACAACTCCCTTGGCCACACTTTTTCCTTTTTGTA
1 TGTTTGAACATGGTTATTGATGATTTGGTCCACAACTCCCTTAGCCACACTTTTTCCTTTTTGTA
3570984 GATTATTCAGGTCTCTTTTTTACACTTTGCA
66 GATTATTCAGGTCTCTTTTTTACACTTTGCA
3571015 TGTT
1 TGTT
3571019 GATTAAAACA
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 98 1.00
ACGTcount: A:0.18, C:0.20, G:0.16, T:0.45
Consensus pattern (96 bp):
TGTTTGAACATGGTTATTGATGATTTGGTCCACAACTCCCTTAGCCACACTTTTTCCTTTTTGTA
GATTATTCAGGTCTCTTTTTTACACTTTGCA
Found at i:3573586 original size:30 final size:30
Alignment explanation
Indices: 3573552--3573622 Score: 106
Period size: 30 Copynumber: 2.4 Consensus size: 30
3573542 TTGGAGTAAC
* *
3573552 GTTGTTGAAAGCATGACTTTGGCTAAAAAT
1 GTTGTTGAAAACATGACTTTGACTAAAAAT
*
3573582 GTTGTTGAAAACATGACTTTGACTGAAAAT
1 GTTGTTGAAAACATGACTTTGACTAAAAAT
*
3573612 GTTGTTAAAAA
1 GTTGTTGAAAA
3573623 TATTGAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.34
Consensus pattern (30 bp):
GTTGTTGAAAACATGACTTTGACTAAAAAT
Found at i:3574079 original size:64 final size:65
Alignment explanation
Indices: 3574010--3574133 Score: 198
Period size: 64 Copynumber: 1.9 Consensus size: 65
3574000 CATATAATGA
*
3574010 AATTGTT-GGATTTTCATATGTTATTTGTAACATATTATTACTATAAAT-CCAAAAAAAGATAAA
1 AATTGTTGGGA-TTGCATATGTTATTTGTAACATATTATTACTATAAATCCCAAAAAAAGATAAA
3574073 C
65 C
* *
3574074 AATTGTTGGGATTGCATATGTTATTTGTAGCATATTATTACTCTAAATCCCAAAAAAAGA
1 AATTGTTGGGATTGCATATGTTATTTGTAACATATTATTACTATAAATCCCAAAAAAAGA
3574134 GGATATAACT
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
64 41 0.75
65 14 0.25
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (65 bp):
AATTGTTGGGATTGCATATGTTATTTGTAACATATTATTACTATAAATCCCAAAAAAAGATAAAC
Found at i:3581290 original size:8 final size:8
Alignment explanation
Indices: 3581279--3581364 Score: 56
Period size: 8 Copynumber: 11.1 Consensus size: 8
3581269 TTAAAAAATT
3581279 ATATTTTA
1 ATATTTTA
3581287 ATATTTTA
1 ATATTTTA
*
3581295 ATAGTATTAA
1 ATA-T-TTTA
*
3581305 ATAATTTA
1 ATATTTTA
*
3581313 A-ATATTA
1 ATATTTTA
3581320 ATATTTT-
1 ATATTTTA
*
3581327 -TA-GTTA
1 ATATTTTA
*
3581333 A-ATATTA
1 ATATTTTA
*
3581340 ATTTTTTA
1 ATATTTTA
*
3581348 ATTTTTTA
1 ATATTTTA
3581356 ATATTTTA
1 ATATTTTA
3581364 A
1 A
3581365 GTTAAATATT
Statistics
Matches: 60, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
5 2 0.03
6 3 0.05
7 9 0.15
8 39 0.65
9 1 0.02
10 6 0.10
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (8 bp):
ATATTTTA
Found at i:3581335 original size:20 final size:20
Alignment explanation
Indices: 3581310--3581378 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
3581300 ATTAAATAAT
3581310 TTAAATATTAATATTTTTAG
1 TTAAATATTAATATTTTTAG
*
3581330 TTAAATATTAAT-TTTTTAA
1 TTAAATATTAATATTTTTAG
* *
3581349 TT---TTTTAATATTTTAAG
1 TTAAATATTAATATTTTTAG
3581366 TTAAATATTAATA
1 TTAAATATTAATA
3581379 ATCTTCAAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
16 6 0.15
17 7 0.17
19 8 0.20
20 19 0.47
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (20 bp):
TTAAATATTAATATTTTTAG
Found at i:3587217 original size:33 final size:32
Alignment explanation
Indices: 3587174--3587472 Score: 123
Period size: 33 Copynumber: 9.4 Consensus size: 32
3587164 TTTAAAATGT
3587174 TATAAT-TAAAATAAAAATATTAAAATAAAATA
1 TATAATATAAAATAAAAA-ATTAAAATAAAATA
*
3587206 TATAATATAAAAATCAAAAATTAAAAT-AAA-A
1 TATAATAT-AAAATAAAAAATTAAAATAAAATA
*
3587237 TA-AA-AT---ATAAAAAATTAAAAT---TTA
1 TATAATATAAAATAAAAAATTAAAATAAAATA
*
3587261 TATAATAT-AAATAAAACAAATTAAAGTAAAATA
1 TATAATATAAAAT-AAA-AAATTAAAATAAAATA
* ** *
3587294 TATAATATAAAAATATATTATATAAAATTATAATA
1 TATAATAT-AAAATAAAAAAT-TAAAA-TAAAATA
* * *
3587329 -ATAA-ATAAAAATAAAATATATGATATTAAAA-A
1 TATAATAT-AAAATAAAA-A-ATTAAAATAAAATA
* ** * *
3587361 TAT-ATTTAAGAA-ATGATATT-ATATAAAA-A
1 TATAATATAA-AATAAAAAATTAAAATAAAATA
*
3587390 TTAATAATATAAATATAAATATATTAAAAATAAAATA
1 -T-ATAATATAAA-ATAAA-AAATT-AAAATAAAATA
* * * *
3587427 TATAAAATTATAATAATAAATAAAAATAAAATA
1 TATAATA-TAAAATAAAAAATTAAAATAAAATA
3587460 TATAATATTAAAA
1 TATAATA-TAAAA
3587473 ATATATTTAA
Statistics
Matches: 200, Mismatches: 36, Indels: 61
0.67 0.12 0.21
Matches are distributed among these distances:
24 3 0.01
25 16 0.08
26 2 0.01
28 2 0.01
29 11 0.05
30 14 0.07
31 6 0.03
32 21 0.10
33 63 0.31
34 29 0.14
35 21 0.10
36 11 0.05
37 1 0.00
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (32 bp):
TATAATATAAAATAAAAAATTAAAATAAAATA
Found at i:3587218 original size:15 final size:15
Alignment explanation
Indices: 3587184--3587478 Score: 121
Period size: 15 Copynumber: 20.8 Consensus size: 15
3587174 TATAATTAAA
*
3587184 ATAAAAATAT-TAAA
1 ATAAAAATATATAAT
3587198 AT-AAAATATATAAT
1 ATAAAAATATATAAT
*
3587212 ATAAAAATCA-AAAAT
1 ATAAAAAT-ATATAAT
* *
3587227 -TAAAATAAAATAAAAT
1 AT-AAA-AATATATAAT
*
3587243 ATAAAAA-ATTAAAAT
1 ATAAAAATA-TATAAT
* *
3587258 TTATATAATATA-AAT
1 ATA-AAAATATATAAT
3587273 A-AAACAA-AT-TAA-
1 ATAAA-AATATATAAT
3587285 AGT-AAAATATATAAT
1 A-TAAAAATATATAAT
*
3587300 ATAAAAATATATTAT
1 ATAAAAATATATAAT
3587315 AT-AAAAT-TATAAT
1 ATAAAAATATATAAT
*
3587328 A-ATAAATA-A-AA-
1 ATAAAAATATATAAT
*
3587339 AT-AAAATATATGAT
1 ATAAAAATATATAAT
3587353 ATTAAAAATATAT--T
1 A-TAAAAATATATAAT
*
3587367 -TAAGAAATGATATTAT
1 ATAA-AAAT-ATATAAT
3587383 ATAAAAAT-TAATAAT
1 ATAAAAATAT-ATAAT
* *
3587398 ATAAATATAAAT-AT
1 ATAAAAATATATAAT
3587412 ATTAAAAATA-A-AAT
1 A-TAAAAATATATAAT
3587426 ATATAAAAT-TATAAT
1 ATA-AAAATATATAAT
*
3587441 A-ATAAATA-A-AA-
1 ATAAAAATATATAAT
3587452 AT-AAAATATATAAT
1 ATAAAAATATATAAT
3587466 ATTAAAAATATAT
1 A-TAAAAATATAT
3587479 TTAAGAGATG
Statistics
Matches: 218, Mismatches: 18, Indels: 88
0.67 0.06 0.27
Matches are distributed among these distances:
11 12 0.06
12 12 0.06
13 41 0.19
14 43 0.20
15 66 0.30
16 39 0.18
17 5 0.02
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (15 bp):
ATAAAAATATATAAT
Found at i:3587267 original size:24 final size:25
Alignment explanation
Indices: 3587221--3587346 Score: 85
Period size: 29 Copynumber: 4.7 Consensus size: 25
3587211 TATAAAAATC
3587221 AAAAATTAAAATAAAATAAAATATA
1 AAAAATTAAAATAAAATAAAATATA
3587246 AAAAATTAAAATTTATATAATATAAATA-A
1 AAAAATTAAAA--TA-A-AATA-AAATATA
*
3587275 AACAAATTAAAGTAAAATATATAATATA
1 AA-AAATTAAAATAAAATA-A-AATATA
* * * *
3587303 AAAATATATTATATAAAATTATA-ATA
1 AAAA-AT-TAAAATAAAATAAAATATA
* *
3587329 ATAAATAAAAATAAAATA
1 AAAAATTAAAATAAAATA
3587347 TATGATATTA
Statistics
Matches: 80, Mismatches: 11, Indels: 21
0.71 0.10 0.19
Matches are distributed among these distances:
24 8 0.10
25 13 0.16
26 12 0.15
27 10 0.12
28 9 0.11
29 15 0.19
30 13 0.16
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (25 bp):
AAAAATTAAAATAAAATAAAATATA
Found at i:3587322 original size:64 final size:66
Alignment explanation
Indices: 3587252--3587431 Score: 190
Period size: 68 Copynumber: 2.7 Consensus size: 66
3587242 TATAAAAAAT
* * *
3587252 TAAAATTTATATAATATAAATAAAACAAATTAAAGTAAAATATATAATATAA-AAAT-ATATTAT
1 TAAAATTTATATAATATAAATAAAATATATTAAAATAAAATATATAATATAAGAAATGATATTAT
3587315 A
66 A
* * * * *
3587316 TAAAATTATAATAATAAATAAAAATAAAATATATGATATTAAAA-ATAT-ATTTAAGAAATGATA
1 TAAAATT-T-AT-AT-AATATAAATAAAATATATTAAAATAAAATATATAATATAAGAAATGATA
3587379 TTATA
62 TTATA
*
3587384 TAAAAATTA-ATAATATAAATATAAATATATTAAAAATAAAATATATAA
1 TAAAATTTATATAATATAAATA-AAATATATT-AAAATAAAATATATAA
3587432 AATTATAATA
Statistics
Matches: 94, Mismatches: 12, Indels: 17
0.76 0.10 0.14
Matches are distributed among these distances:
63 9 0.10
64 17 0.18
65 8 0.09
66 12 0.13
67 12 0.13
68 36 0.38
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (66 bp):
TAAAATTTATATAATATAAATAAAATATATTAAAATAAAATATATAATATAAGAAATGATATTAT
A
Found at i:3587417 original size:9 final size:9
Alignment explanation
Indices: 3587380--3587478 Score: 56
Period size: 9 Copynumber: 11.6 Consensus size: 9
3587370 GAAATGATAT
3587380 TATATAAAA
1 TATATAAAA
3587389 -AT-TAATAA
1 TATATAA-AA
3587397 TATAAATATAAA
1 TAT--ATA-AAA
*
3587409 TATATTAAA
1 TATATAAAA
3587418 -A-ATAAAA
1 TATATAAAA
3587425 TATATAAAA
1 TATATAAAA
3587434 T-TATAATAA
1 TATATAA-AA
*
3587443 TAAAT-AAA
1 TATATAAAA
3587451 -A-ATAAAA
1 TATATAAAA
*
3587458 TATATAATA
1 TATATAAAA
3587467 T-TA-AAAA
1 TATATAAAA
3587474 TATAT
1 TATAT
3587479 TTAAGAGATG
Statistics
Matches: 70, Mismatches: 5, Indels: 30
0.67 0.05 0.29
Matches are distributed among these distances:
6 2 0.03
7 16 0.23
8 18 0.26
9 22 0.31
10 4 0.06
12 7 0.10
13 1 0.01
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
TATATAAAA
Found at i:3587686 original size:2 final size:2
Alignment explanation
Indices: 3587679--3587705 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3587669 AATTATCCAA
3587679 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 A
3587706 AACCCAAGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3601108 original size:14 final size:14
Alignment explanation
Indices: 3601083--3601195 Score: 106
Period size: 14 Copynumber: 7.9 Consensus size: 14
3601073 GAAACTAAGA
3601083 GAGGGGGAGGGGGAGG
1 GAGGGGG-GGGGG-GG
3601099 G-GGGGGGGGGGGG
1 GAGGGGGGGGGGGG
3601112 GAGGGGGGGGGGGG
1 GAGGGGGGGGGGGG
3601126 G-GGGGGGGGGGGG
1 GAGGGGGGGGGGGG
* ***
3601139 G-GGGGGAGGGTAT
1 GAGGGGGGGGGGGG
3601152 GAGGTGTGGGGGGGGAG
1 GAGG-G-GGGGGGGG-G
*
3601169 GTGAGGGGGGGGGGG
1 GAG-GGGGGGGGGGG
3601184 GAGGGGGGGGGG
1 GAGGGGGGGGGG
3601196 TGGGTCTTTT
Statistics
Matches: 81, Mismatches: 10, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
13 25 0.31
14 29 0.36
15 9 0.11
16 14 0.17
17 3 0.04
18 1 0.01
ACGTcount: A:0.09, C:0.00, G:0.87, T:0.04
Consensus pattern (14 bp):
GAGGGGGGGGGGGG
Found at i:3601211 original size:1 final size:1
Alignment explanation
Indices: 3601085--3601195 Score: 96
Period size: 1 Copynumber: 111.0 Consensus size: 1
3601075 AACTAAGAGA
* * * * *
3601085 GGGGGAGGGGGAGGGGGGGGGGGGGGGGAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGAGGGT
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
** * * * * * * *
3601150 ATGAGGTGTGGGGGGGGAGGTGAGGGGGGGGGGGGAGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
3601196 TGGGTCTTTT
Statistics
Matches: 84, Mismatches: 26, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 84 1.00
ACGTcount: A:0.08, C:0.00, G:0.87, T:0.05
Consensus pattern (1 bp):
G
Found at i:3619853 original size:15 final size:15
Alignment explanation
Indices: 3619829--3619858 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3619819 CTGGAATTTG
*
3619829 AATTAGAATTTTAAA
1 AATTAAAATTTTAAA
3619844 AATTAAAATTTTAAA
1 AATTAAAATTTTAAA
3619859 TTGACATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (15 bp):
AATTAAAATTTTAAA
Found at i:3620752 original size:18 final size:19
Alignment explanation
Indices: 3620718--3620754 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
3620708 TCGACTTCGG
3620718 ATATTATCTTATTAATTAA
1 ATATTATCTTATTAATTAA
*
3620737 ATATTAT-TTTTTAATTAA
1 ATATTATCTTATTAATTAA
3620755 TTTTAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
ATATTATCTTATTAATTAA
Found at i:3628343 original size:17 final size:16
Alignment explanation
Indices: 3628316--3628351 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
3628306 CCTATATATA
*
3628316 TAATAATAATATTTTG
1 TAATAATAATATTATG
3628332 TAATAGATAATATTATG
1 TAATA-ATAATATTATG
3628349 TAA
1 TAA
3628352 ATATATATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.44
Consensus pattern (16 bp):
TAATAATAATATTATG
Found at i:3629051 original size:22 final size:21
Alignment explanation
Indices: 3629023--3629078 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
3629013 TTTAGGGTTA
* *
3629023 AACTTATAATATGCATATATTT
1 AACTTATAATAAGCAT-TACTT
*
3629045 AATTTATATATAAGCATTACTT
1 AACTTATA-ATAAGCATTACTT
3629067 AACTTATAATAA
1 AACTTATAATAA
3629079 ACTTCAAGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 4 0.14
22 18 0.62
23 7 0.24
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.43
Consensus pattern (21 bp):
AACTTATAATAAGCATTACTT
Found at i:3633921 original size:110 final size:110
Alignment explanation
Indices: 3633788--3634002 Score: 299
Period size: 110 Copynumber: 2.0 Consensus size: 110
3633778 ATGTTAGAAC
* * * *
3633788 GGCATGTTTTTGTTAATGATTTTTATTGTAAACATGTATAAGAATTAGTCTT-GATTATTACATT
1 GGCATGTTTGTGTTAATCATTTTTATTGTAAACATGAATAAGAATTAATCTTAG-TTATTACATT
*
3633852 TTGATGATGATTTTCATAATTTGTTTCTATTTCTTTTAGCTCTTAT
65 TTGATGATGATTTTCATAATTTGTTTCAATTTCTTTTAGCTCTTAT
* * * *
3633898 GGCATGTTTGTGTTAA-CATTTTTTATTGTTAACATGAATGAGAATTAATCTTAGTTTTTATATT
1 GGCATGTTTGTGTTAATCA-TTTTTATTGTAAACATGAATAAGAATTAATCTTAGTTATTACATT
* *
3633962 TTGATGATGATTTTGATAGTTTGTTTCAATTTCTTTTAGCT
65 TTGATGATGATTTTCATAATTTGTTTCAATTTCTTTTAGCT
3634003 TATGTATGAA
Statistics
Matches: 92, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
109 1 0.01
110 90 0.98
111 1 0.01
ACGTcount: A:0.25, C:0.07, G:0.15, T:0.53
Consensus pattern (110 bp):
GGCATGTTTGTGTTAATCATTTTTATTGTAAACATGAATAAGAATTAATCTTAGTTATTACATTT
TGATGATGATTTTCATAATTTGTTTCAATTTCTTTTAGCTCTTAT
Found at i:3634662 original size:19 final size:19
Alignment explanation
Indices: 3634622--3634668 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
3634612 TAACTTTTTG
*
3634622 TTTTTATTTATGTATTAAAT
1 TTTTTATTTATATATT-AAT
3634642 TTTTTATTTACTATATT-AT
1 TTTTTATTTA-TATATTAAT
3634661 TTTATTAT
1 TTT-TTAT
3634669 AGGAAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 5 0.21
20 14 0.58
21 5 0.21
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTTTATTTATATATTAAT
Found at i:3636077 original size:38 final size:37
Alignment explanation
Indices: 3636035--3636124 Score: 101
Period size: 38 Copynumber: 2.4 Consensus size: 37
3636025 TTTCATTGCA
*
3636035 AATTTCCAACAGAAAATC-CTATTGAAAACTTTGTTCGT
1 AATTTCCAAC-GAAAATCTC-ATTGAAAACTCTGTTCGT
** * *
3636073 AATTTCCATTGAAAAATCTCATTGGAAACTCTGTTGGT
1 AATTTCCAACG-AAAATCTCATTGAAAACTCTGTTCGT
3636111 AATTTCCAACGAAA
1 AATTTCCAACGAAA
3636125 GTTTCTGCCG
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
37 4 0.09
38 38 0.88
39 1 0.02
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (37 bp):
AATTTCCAACGAAAATCTCATTGAAAACTCTGTTCGT
Found at i:3637082 original size:87 final size:84
Alignment explanation
Indices: 3636913--3637082 Score: 189
Period size: 87 Copynumber: 2.0 Consensus size: 84
3636903 CATATGTTTC
* * * * *
3636913 TAGAATTGTAAAGTTGCCACACTATTTTTTTTTTCCAGAATAGCTGCAAAGGTTCTATTAATTAC
1 TAGAATTGAAAAGTTACCACACTATTTTTTTTTTCCAAAATACCT-CAAAGGTTCTACTAATTAC
* *
3636978 ATCTTGACCCCATAAATTTT
65 AGCTTGACCCCAGAAATTTT
* *
3636998 TAGAATTGAAAAGTTACCACACTATTTTCTTTTTTTTCAAAATCACC-CTAAAGGTTCTGCTAAT
1 TAGAATTGAAAAGTTACCACACTA-TTT-TTTTTTTCCAAAAT-ACCTC-AAAGGTTCTACTAAT
**
3637062 TACAGCTTGACCTTAGAAATT
62 TACAGCTTGACCCCAGAAATT
3637083 ATTACATAAA
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
85 22 0.31
86 4 0.06
87 42 0.60
88 2 0.03
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (84 bp):
TAGAATTGAAAAGTTACCACACTATTTTTTTTTTCCAAAATACCTCAAAGGTTCTACTAATTACA
GCTTGACCCCAGAAATTTT
Found at i:3645607 original size:16 final size:16
Alignment explanation
Indices: 3645586--3645617 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3645576 CCTTTACGTA
3645586 AATATTCAAAATATTT
1 AATATTCAAAATATTT
*
3645602 AATATTTAAAATATTT
1 AATATTCAAAATATTT
3645618 TTACTCATGA
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
AATATTCAAAATATTT
Found at i:3650614 original size:30 final size:29
Alignment explanation
Indices: 3650580--3650654 Score: 89
Period size: 30 Copynumber: 2.6 Consensus size: 29
3650570 TGATTAACAC
**
3650580 AAATATAAAAATTTATTTAGTTTAAAATAA
1 AAATATAAAAATTTATTT-GAATAAAATAA
* * *
3650610 AAATATAAAAGTTTAATTGAATATAATAA
1 AAATATAAAAATTTATTTGAATAAAATAA
3650639 AAA-ATAAAAATTTATT
1 AAATATAAAAATTTATT
3650655 CAAATTTTCT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
28 11 0.29
29 11 0.29
30 16 0.42
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (29 bp):
AAATATAAAAATTTATTTGAATAAAATAA
Found at i:3650682 original size:21 final size:22
Alignment explanation
Indices: 3650643--3650688 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
3650633 TAATAAAAAA
3650643 TAAAAATTTATTCAAATTTTCT
1 TAAAAATTTATTCAAATTTTCT
*
3650665 TAAATAATTTA-T-AAATTTTTT
1 TAAA-AATTTATTCAAATTTTCT
3650686 TAA
1 TAA
3650689 GTATTATCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 11 0.50
22 5 0.23
23 6 0.27
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (22 bp):
TAAAAATTTATTCAAATTTTCT
Found at i:3674741 original size:103 final size:104
Alignment explanation
Indices: 3674553--3674748 Score: 272
Period size: 103 Copynumber: 1.9 Consensus size: 104
3674543 ATAATGGAGT
3674553 GGTGAAGTCTCGGCTTGCACCTTGTTTGGAAGATGGAGTGGAGCTTTGTTAAATGGTGAAGTATG
1 GGTGAAGTCTCGGCTTGCACCTTGTTTGGAAGATGGAGTGGAGCTTTGTTAAATGGTGAAGTATG
* *
3674618 ACACTTGTAGTCCTAATGAATGGCATTTTCGTAGTTATG
66 ACACTTATAGTCATAATGAATGGCATTTTCGTAGTTATG
* * *
3674657 GGTGAAGTCTTGAG-TTGCACCTTG-TTGGAA-AGTGGAGTGGGGCTTTGTTAAATGGTTAAGTA
1 GGTGAAGTCTCG-GCTTGCACCTTGTTTGGAAGA-TGGAGTGGAGCTTTGTTAAATGGTGAAGTA
* * * *
3674719 TGGCACTTATAGTTATACTGAATGTCATTT
64 TGACACTTATAGTCATAATGAATGGCATTT
3674749 CCATTATTTA
Statistics
Matches: 81, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
102 1 0.01
103 58 0.72
104 21 0.26
105 1 0.01
ACGTcount: A:0.23, C:0.11, G:0.30, T:0.36
Consensus pattern (104 bp):
GGTGAAGTCTCGGCTTGCACCTTGTTTGGAAGATGGAGTGGAGCTTTGTTAAATGGTGAAGTATG
ACACTTATAGTCATAATGAATGGCATTTTCGTAGTTATG
Found at i:3674766 original size:103 final size:104
Alignment explanation
Indices: 3674567--3674769 Score: 259
Period size: 103 Copynumber: 2.0 Consensus size: 104
3674557 AAGTCTCGGC
* *
3674567 TTGCACCTTGTTTGGAAGATGGAGTGGAGCTTTGTTAAATGGTGAAGTATGACACTTGTAGTCCT
1 TTGCACCTTGTTTGGAAGATGGAGTGGAGCTTTGTTAAATGGTGAAGTATGACACTTATAGTCAT
* *
3674632 AATGAATGGCATTTTCGTAGTTATGGGTGAAGTCTTGAG
66 AATGAATGGCATTTCCGTAGTTATGGCTGAAGTCTTGAG
* * * *
3674671 TTGCACCTTG-TTGGAA-AGTGGAGTGGGGCTTTGTTAAATGGTTAAGTATGGCACTTATAGTTA
1 TTGCACCTTGTTTGGAAGA-TGGAGTGGAGCTTTGTTAAATGGTGAAGTATGACACTTATAGTCA
* * * *
3674734 TACTGAATGTCATTTCCATTATTTAT-GCTGAAGTCT
65 TAATGAATGGCATTTCC-GTAGTTATGGCTGAAGTCT
3674770 GGGGTTGAAT
Statistics
Matches: 85, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
102 1 0.01
103 68 0.80
104 16 0.19
ACGTcount: A:0.24, C:0.11, G:0.27, T:0.37
Consensus pattern (104 bp):
TTGCACCTTGTTTGGAAGATGGAGTGGAGCTTTGTTAAATGGTGAAGTATGACACTTATAGTCAT
AATGAATGGCATTTCCGTAGTTATGGCTGAAGTCTTGAG
Found at i:3678618 original size:94 final size:94
Alignment explanation
Indices: 3678455--3678721 Score: 240
Period size: 94 Copynumber: 2.9 Consensus size: 94
3678445 TAATCGATAG
* * * * *
3678455 AATTTATAGTGAGATTTTCTTCTCTCATAGAGGTTCGTAAGACGATTAAGGAAAAATGTATATAT
1 AATTTATAGTGAGATTTTCTTCTCTCATAGAGGTTCATAAAACGATTAAGGAAAAATATACATAC
3678520 ATGGTAACATATATAACAAATTTTTACAA
66 ATGGTAACATATATAACAAATTTTTACAA
* ** * *
3678549 AATTTATAGT-AGATTTTCTCTCTTTCATAGAGGTTCATAAAATTATTTAA-GAAGAATATGCAT
1 AATTTATAGTGAGATTTTCT-TCTCTCATAGAGGTTCATAAAACGA-TTAAGGAAAAATATACAT
* *
3678612 ACATGGTAACATATATAGCAAA--TTTGCAA
64 ACATGGTAACATATATAACAAATTTTTACAA
* * * * * * * * * *
3678641 GTAGA-TCATAGTAAAATTTTCTTCTCTCACATAGGTTTATAAGACAACTAA-GAAAAATTTACA
1 --A-ATTTATAGTGAGATTTTCTTCTCTCATAGAGGTTCATAAAACGATTAAGGAAAAATATACA
*
3678704 TACATGGTAATATATATA
63 TACATGGTAACATATATA
3678722 GCCTTACTGT
Statistics
Matches: 141, Mismatches: 26, Indels: 13
0.78 0.14 0.07
Matches are distributed among these distances:
92 6 0.04
93 38 0.27
94 84 0.60
95 13 0.09
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (94 bp):
AATTTATAGTGAGATTTTCTTCTCTCATAGAGGTTCATAAAACGATTAAGGAAAAATATACATAC
ATGGTAACATATATAACAAATTTTTACAA
Found at i:3681498 original size:107 final size:107
Alignment explanation
Indices: 3681291--3681485 Score: 282
Period size: 107 Copynumber: 1.8 Consensus size: 107
3681281 CATGTTCAAG
* * *
3681291 CTTAATATTAATAAGAATACTATCAGTTCTACTTATTTTGATGCCTTATTTAATGTTTATGATAG
1 CTTAATATTAATAAAAATACTATCAATTCTACTTATATTGATGCCTTATTTAATGTTTATGATAG
**
3681356 TAAAGTAGCATCATTTAATCTATAGCATAATAGATTCATGTC
66 TAAAGTAGCATCATCAAATCTATAGCATAATAGATTCATGTC
** * * * *
3681398 CTTAATATTAATAAAAATGTTATTAATTCTGCTTGTATTGATGCCTTATTTAGTGTTTATGATAG
1 CTTAATATTAATAAAAATACTATCAATTCTACTTATATTGATGCCTTATTTAATGTTTATGATAG
*
3681463 TAAGGTAGCATCATCAAATCTAT
66 TAAAGTAGCATCATCAAATCTAT
3681486 GGTGTAATAG
Statistics
Matches: 76, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
107 76 1.00
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.43
Consensus pattern (107 bp):
CTTAATATTAATAAAAATACTATCAATTCTACTTATATTGATGCCTTATTTAATGTTTATGATAG
TAAAGTAGCATCATCAAATCTATAGCATAATAGATTCATGTC
Found at i:3690785 original size:20 final size:20
Alignment explanation
Indices: 3690754--3690815 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
3690744 AACTCAAAAT
*
3690754 TGATAACTTTTTATGAATAA
1 TGATAACTTTTCATGAATAA
* * *
3690774 TGATGATCTTTTCATAAATAG
1 TGAT-AACTTTTCATGAATAA
*
3690795 TGATAACTTTTGATGAATAA
1 TGATAACTTTTCATGAATAA
3690815 T
1 T
3690816 AATTTTATGA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
20 17 0.52
21 16 0.48
ACGTcount: A:0.37, C:0.06, G:0.13, T:0.44
Consensus pattern (20 bp):
TGATAACTTTTCATGAATAA
Found at i:3708847 original size:100 final size:99
Alignment explanation
Indices: 3708730--3708931 Score: 368
Period size: 100 Copynumber: 2.0 Consensus size: 99
3708720 GTTGATAACG
3708730 GGTCTAAAATTCTCTCCATTATTGCAAGCTTGTTTTGTGTTTGACGCATTGAGCAATAATGGTAG
1 GGTCTAAAATTCTCTCCATTATTGCAAGCTTGTTTTGTGTTTGACGCATTGAGCAATAATGGTAG
*
3708795 GGTTTGGGTTTTTCTTTGACTTGTTATTTGTGGAA
66 GGTTTGGG-TTTCCTTTGACTTGTTATTTGTGGAA
* *
3708830 GGTCTAAAATTCTCTCCATTGTTGCAAGCTTGTTTTGTGTTTGACGCGTTGAGCAATAATGGTAG
1 GGTCTAAAATTCTCTCCATTATTGCAAGCTTGTTTTGTGTTTGACGCATTGAGCAATAATGGTAG
3708895 GGTTTGGGTTTCCTTTGACTTGTTATTTGTGGAA
66 GGTTTGGGTTTCCTTTGACTTGTTATTTGTGGAA
3708929 GGT
1 GGT
3708932 TGGGAGATGG
Statistics
Matches: 99, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
99 28 0.28
100 71 0.72
ACGTcount: A:0.19, C:0.12, G:0.26, T:0.43
Consensus pattern (99 bp):
GGTCTAAAATTCTCTCCATTATTGCAAGCTTGTTTTGTGTTTGACGCATTGAGCAATAATGGTAG
GGTTTGGGTTTCCTTTGACTTGTTATTTGTGGAA
Found at i:3711596 original size:78 final size:76
Alignment explanation
Indices: 3711460--3711616 Score: 253
Period size: 78 Copynumber: 2.0 Consensus size: 76
3711450 GTGAACTTGA
*
3711460 GTAGATAATTGTTAGATGATTGCCACCGGTTGTGGGAATTACTTTCTCTTTACTTTTTCAGATCT
1 GTAGATAATTGTTAGATGATTGCCACCAGTTGTGGGAATTACTTTCTCTTTACTTTTTCAGATC-
3711525 ATATGCTTGATAT
65 -TATGCTTGATAT
* *
3711538 GTAGATTATTGTTAGATGATTGCCACTAGTTGTGGGAATTACTTTCTCTTT-CTCTTTTCAGATC
1 GTAGATAATTGTTAGATGATTGCCACCAGTTGTGGGAATTACTTTCTCTTTACT-TTTTCAGATC
3711602 TATGCTTGATAT
65 TATGCTTGATAT
3711614 GTA
1 GTA
3711617 TCATGAACTT
Statistics
Matches: 75, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
76 15 0.20
77 2 0.03
78 58 0.77
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.45
Consensus pattern (76 bp):
GTAGATAATTGTTAGATGATTGCCACCAGTTGTGGGAATTACTTTCTCTTTACTTTTTCAGATCT
ATGCTTGATAT
Found at i:3712091 original size:2 final size:2
Alignment explanation
Indices: 3712084--3712108 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3712074 TAAATTCTGA
3712084 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
3712109 TTCTAAACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3715916 original size:14 final size:14
Alignment explanation
Indices: 3715887--3715939 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
3715877 TTTTTATTTT
*
3715887 TTATATTAATATTA
1 TTATATTAATAATA
*
3715901 TTATATTAAAAATA
1 TTATATTAATAATA
*
3715915 TTTTAATTAATAATAA
1 TTAT-ATTAATAAT-A
3715931 TTA-ATTAAT
1 TTATATTAAT
3715940 CATTACTTAC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
14 21 0.66
15 8 0.25
16 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TTATATTAATAATA
Found at i:3716191 original size:2 final size:2
Alignment explanation
Indices: 3716184--3716216 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3716174 CCACAGCAGA
3716184 AT AT 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 A
3716217 GATTAAAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3718553 original size:2 final size:2
Alignment explanation
Indices: 3718546--3718571 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3718536 GGACAAAAAG
3718546 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3718572 AATTAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3718588 original size:16 final size:16
Alignment explanation
Indices: 3718569--3718602 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3718559 ATATATATAT
*
3718569 ATAAATTAATTAATTA
1 ATAAATTAATGAATTA
3718585 ATAAATTAATGAATTA
1 ATAAATTAATGAATTA
3718601 AT
1 AT
3718603 TTCGTTCAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
ATAAATTAATGAATTA
Found at i:3726001 original size:18 final size:19
Alignment explanation
Indices: 3725960--3726003 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
3725950 TCCACCATTC
3725960 TAAT-TTTTTATTTATATT
1 TAATATTTTTATTTATATT
* *
3725978 TTATATTTTTATTT-TGTT
1 TAATATTTTTATTTATATT
3725996 TAATATTT
1 TAATATTT
3726004 CAAATTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (19 bp):
TAATATTTTTATTTATATT
Found at i:3726346 original size:108 final size:109
Alignment explanation
Indices: 3726202--3726405 Score: 338
Period size: 108 Copynumber: 1.9 Consensus size: 109
3726192 TATAAGAAAT
* *
3726202 TTTGAGTAAATTTAAATAAAAAAGTAAATTGGGTAAGAGTTAAATAGTTACAAAAGAATGTGTAT
1 TTTGAGTAAATTTAAATAAAAAAGTAAATTGGGTAAGAGTTAAATAATTACAAAAGAATATGTAT
* *
3726267 TTGTAAATTGTGAAAGTTATAACTAAATCAAAATATTTTGCTAA
66 TTATAAATTGTGAAAATTATAACTAAATCAAAATATTTTGCTAA
* *
3726311 TTTGAGTAAATTTAAAT-AAAAAGTAAATTGGGTAAGAGTTGAATAATTTCAAAAGAATATGTAT
1 TTTGAGTAAATTTAAATAAAAAAGTAAATTGGGTAAGAGTTAAATAATTACAAAAGAATATGTAT
*
3726375 TTATAAATTGTGAAAATTTTAACTAAATCAA
66 TTATAAATTGTGAAAATTATAACTAAATCAA
3726406 CATAGTTAGT
Statistics
Matches: 88, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
108 71 0.81
109 17 0.19
ACGTcount: A:0.47, C:0.03, G:0.15, T:0.35
Consensus pattern (109 bp):
TTTGAGTAAATTTAAATAAAAAAGTAAATTGGGTAAGAGTTAAATAATTACAAAAGAATATGTAT
TTATAAATTGTGAAAATTATAACTAAATCAAAATATTTTGCTAA
Found at i:3728455 original size:14 final size:13
Alignment explanation
Indices: 3728436--3728484 Score: 57
Period size: 14 Copynumber: 3.7 Consensus size: 13
3728426 TTCAAAGCAC
3728436 AAAAAAAATGATAG
1 AAAAAAAATGA-AG
3728450 AAAAAAAATG-A-
1 AAAAAAAATGAAG
3728461 AAAAAAAATAGAAAG
1 AAAAAAAAT-G-AAG
3728476 AAAAAAAAT
1 AAAAAAAAT
3728485 AATACTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
11 9 0.29
12 2 0.06
14 11 0.35
15 9 0.29
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (13 bp):
AAAAAAAATGAAG
Found at i:3728463 original size:22 final size:23
Alignment explanation
Indices: 3728436--3728480 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
3728426 TTCAAAGCAC
3728436 AAAAAAAATGATAGAAA-AAAAATG
1 AAAAAAAA--ATAGAAAGAAAAATG
3728460 AAAAAAAAATAGAAAGAAAAA
1 AAAAAAAAATAGAAAGAAAAA
3728481 AAATAATACT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 7 0.35
23 5 0.25
24 8 0.40
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (23 bp):
AAAAAAAAATAGAAAGAAAAATG
Found at i:3728477 original size:26 final size:25
Alignment explanation
Indices: 3728436--3728484 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
3728426 TTCAAAGCAC
*
3728436 AAAAAAAATGATAGAAAAAAAATGA
1 AAAAAAAATGAAAGAAAAAAAATGA
3728461 AAAAAAAATAGAAAGAAAAAAAAT
1 AAAAAAAAT-GAAAGAAAAAAAAT
3728485 AATACTTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (25 bp):
AAAAAAAATGAAAGAAAAAAAATGA
Found at i:3728759 original size:17 final size:16
Alignment explanation
Indices: 3728731--3728768 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
3728721 TTTTTAAAGC
3728731 TTTTTTTATAAAAATTT
1 TTTTTTTAT-AAAATTT
3728748 TATTTTTT-TAAAATTT
1 T-TTTTTTATAAAATTT
3728764 TTTTT
1 TTTTT
3728769 AGAGTTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 4 0.20
16 8 0.40
17 2 0.10
18 6 0.30
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTTTTATAAAATTT
Found at i:3731191 original size:16 final size:16
Alignment explanation
Indices: 3731172--3731210 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
3731162 AAAAGAAGTT
3731172 AATAAAATAGAAAAAG-
1 AATAAAAT-GAAAAAGA
*
3731188 AATAAAATGAAAATGA
1 AATAAAATGAAAAAGA
3731204 AATAAAA
1 AATAAAA
3731211 AGGGAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.15
Consensus pattern (16 bp):
AATAAAATGAAAAAGA
Found at i:3731233 original size:15 final size:15
Alignment explanation
Indices: 3731213--3731241 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3731203 AAATAAAAAG
3731213 GGAAAATAATAATAT
1 GGAAAATAATAATAT
3731228 GGAAAATAATAATA
1 GGAAAATAATAATA
3731242 ACAATGAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.14, T:0.24
Consensus pattern (15 bp):
GGAAAATAATAATAT
Found at i:3737217 original size:42 final size:42
Alignment explanation
Indices: 3737085--3737225 Score: 144
Period size: 42 Copynumber: 3.4 Consensus size: 42
3737075 TGTTATGAAT
* ** * *
3737085 GTGGATTGAGAAGGTCTCCACATTCCCATGATTTTGTTAT-GA
1 GTGGATTGAGTAGGTCTCCAC-TTTTCATGGTTTTGTTGTAGA
* * * *
3737127 TGTGGATTGAGTATGTCTCCA-TTTCTCAT-GATTTGTGGTAAA
1 -GTGGATTGAGTAGGTCTCCACTTT-TCATGGTTTTGTTGTAGA
*
3737169 ATGGATTGAGTAGGTCTCCACTTTTCATGGTTTTGTTGTAGA
1 GTGGATTGAGTAGGTCTCCACTTTTCATGGTTTTGTTGTAGA
3737211 GTGGATTGAGTAGGT
1 GTGGATTGAGTAGGT
3737226 GTCTTCTTCC
Statistics
Matches: 79, Mismatches: 15, Indels: 9
0.77 0.15 0.09
Matches are distributed among these distances:
41 30 0.38
42 31 0.39
43 18 0.23
ACGTcount: A:0.21, C:0.12, G:0.27, T:0.40
Consensus pattern (42 bp):
GTGGATTGAGTAGGTCTCCACTTTTCATGGTTTTGTTGTAGA
Found at i:3737240 original size:83 final size:83
Alignment explanation
Indices: 3737086--3737243 Score: 196
Period size: 83 Copynumber: 1.9 Consensus size: 83
3737076 GTTATGAATG
3737086 TGGATTGAGAAGGTCTCCACATTCCCATGATTTTGTTATGATGTGGATTGAGTATGTCTCCATTT
1 TGGATTGAGAAGGTCTCCACATTCCCATGATTTTGTTATGATGTGGATTGAGTATGTCTCCA-TT
*
3737151 CTCATGATTTGTGGTAAAA
65 CCCATGATTTGTGGTAAAA
* ** * * *
3737170 TGGATTGAGTAGGTCTCCAC-TTTTCATGGTTTTGTTGTAGA-GTGGATTGAGTAGGTGTCTTC-
1 TGGATTGAGAAGGTCTCCACATTCCCATGATTTTGTTAT-GATGTGGATTGAGTA--TGTCTCCA
3737232 TTCCCATGATTT
63 TTCCCATGATTT
3737244 TGTTGTGATT
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
83 37 0.58
84 21 0.33
85 6 0.09
ACGTcount: A:0.20, C:0.14, G:0.25, T:0.41
Consensus pattern (83 bp):
TGGATTGAGAAGGTCTCCACATTCCCATGATTTTGTTATGATGTGGATTGAGTATGTCTCCATTC
CCATGATTTGTGGTAAAA
Found at i:3737245 original size:42 final size:42
Alignment explanation
Indices: 3737085--3737249 Score: 136
Period size: 42 Copynumber: 3.9 Consensus size: 42
3737075 TGTTATGAAT
* * * *
3737085 GTGGATTGAGAAGGTCTCCACATTCCCATGATTTTGTTAT-GA
1 GTGGATTGAGTAGGTGTCTAC-TTCCCATGATTTTGTTGTAGA
* * * * * * *
3737127 TGTGGATTGAGTATGTCTCCATTTCTCATGA-TTTGTGGTAAA
1 -GTGGATTGAGTAGGTGTCTACTTCCCATGATTTTGTTGTAGA
* * * ** *
3737169 ATGGATTGAGTAGGTCTCCACTTTTCATGGTTTTGTTGTAGA
1 GTGGATTGAGTAGGTGTCTACTTCCCATGATTTTGTTGTAGA
*
3737211 GTGGATTGAGTAGGTGTCTTCTTCCCATGATTTTGTTGT
1 GTGGATTGAGTAGGTGTCTACTTCCCATGATTTTGTTGT
3737250 GATTGGGTCT
Statistics
Matches: 99, Mismatches: 21, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
41 31 0.31
42 50 0.51
43 18 0.18
ACGTcount: A:0.19, C:0.13, G:0.25, T:0.42
Consensus pattern (42 bp):
GTGGATTGAGTAGGTGTCTACTTCCCATGATTTTGTTGTAGA
Found at i:3740504 original size:21 final size:21
Alignment explanation
Indices: 3740478--3740519 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3740468 TGCTCACTAC
3740478 CTTAAAAGTATCGATACATTT
1 CTTAAAAGTATCGATACATTT
* *
3740499 CTTAAATGTATTGATACATTT
1 CTTAAAAGTATCGATACATTT
3740520 TCAACTGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.43
Consensus pattern (21 bp):
CTTAAAAGTATCGATACATTT
Found at i:3749232 original size:15 final size:13
Alignment explanation
Indices: 3749214--3749273 Score: 50
Period size: 15 Copynumber: 4.3 Consensus size: 13
3749204 ATTCAATGCT
3749214 AACTAAACTAAAAGC
1 AACTAAA-TAAAA-C
* *
3749229 AACTTAATATAA-
1 AACTAAATAAAAC
3749241 AACTAAAATAAAAC
1 AACT-AAATAAAAC
3749255 AACTTAAATTAAAAC
1 AAC-TAAA-TAAAAC
3749270 AACT
1 AACT
3749274 CGACATGATT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
12 4 0.11
13 6 0.16
14 11 0.30
15 16 0.43
ACGTcount: A:0.62, C:0.15, G:0.02, T:0.22
Consensus pattern (13 bp):
AACTAAATAAAAC
Found at i:3749245 original size:27 final size:26
Alignment explanation
Indices: 3749214--3749269 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 26
3749204 ATTCAATGCT
*
3749214 AACTAAACTAAAAGCAACTT-AATATAA
1 AACTAAAATAAAA-CAACTTAAAT-TAA
3749241 AACTAAAATAAAACAACTTAAATTAA
1 AACTAAAATAAAACAACTTAAATTAA
3749267 AAC
1 AAC
3749270 AACTCGACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 12 0.44
27 15 0.56
ACGTcount: A:0.62, C:0.14, G:0.02, T:0.21
Consensus pattern (26 bp):
AACTAAAATAAAACAACTTAAATTAA
Found at i:3749267 original size:26 final size:27
Alignment explanation
Indices: 3749214--3749269 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
3749204 ATTCAATGCT
*
3749214 AACTAAACTAAAAGCAACTTAATATAA
1 AACTAAAATAAAAGCAACTTAATATAA
3749241 AACTAAAATAAAA-CAACTTAA-ATTAA
1 AACTAAAATAAAAGCAACTTAATA-TAA
3749267 AAC
1 AAC
3749270 AACTCGACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 1 0.04
26 14 0.52
27 12 0.44
ACGTcount: A:0.62, C:0.14, G:0.02, T:0.21
Consensus pattern (27 bp):
AACTAAAATAAAAGCAACTTAATATAA
Found at i:3753591 original size:15 final size:16
Alignment explanation
Indices: 3753562--3753594 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3753552 CTTGTGGATG
3753562 ATGCAATTTGCTTTTA
1 ATGCAATTTGCTTTTA
*
3753578 ATGC-ATTTGTTTTTA
1 ATGCAATTTGCTTTTA
3753593 AT
1 AT
3753595 TTAGGGATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.24, C:0.09, G:0.12, T:0.55
Consensus pattern (16 bp):
ATGCAATTTGCTTTTA
Found at i:3762471 original size:2 final size:2
Alignment explanation
Indices: 3762464--3762500 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3762454 TATTATTTTC
*
3762464 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3762501 AGGCTGAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3763681 original size:2 final size:2
Alignment explanation
Indices: 3763676--3763707 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3763666 ACACACATAC
3763676 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
3763708 CCCAAATCCT
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:3767005 original size:15 final size:15
Alignment explanation
Indices: 3766981--3767022 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
3766971 ACTTTACAAT
3766981 GTAATGTGATTGCAA
1 GTAATGTGATTGCAA
*
3766996 GTAATATGATTGCAA
1 GTAATGTGATTGCAA
3767011 GTAATGTGATTG
1 GTAATGTGATTG
3767023 TAGAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.36
Consensus pattern (15 bp):
GTAATGTGATTGCAA
Found at i:3767295 original size:24 final size:24
Alignment explanation
Indices: 3767238--3767321 Score: 86
Period size: 24 Copynumber: 3.5 Consensus size: 24
3767228 TTTTAATGTC
3767238 ATATATTT-TAT-TTTTATTTATTA
1 ATATATTTATATATTTTATTT-TTA
*
3767261 TTATAATTTTATATATTTTATTTTTA
1 ATAT-ATTT-ATATATTTTATTTTTA
* *
3767287 ATATATTTATATTTTTTATTATTA
1 ATATATTTATATATTTTATTTTTA
3767311 AT-T-TTTATATA
1 ATATATTTATATA
3767322 ATATCATCTC
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
22 7 0.13
23 4 0.08
24 20 0.38
25 4 0.08
26 9 0.17
27 8 0.15
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (24 bp):
ATATATTTATATATTTTATTTTTA
Found at i:3767301 original size:31 final size:31
Alignment explanation
Indices: 3767238--3767542 Score: 99
Period size: 33 Copynumber: 10.0 Consensus size: 31
3767228 TTTTAATGTC
*
3767238 ATATATTTTATTTTT-ATTTATTATTATAATTTT
1 ATATATTTTATTTTTAATATA-T-TTAT-ATTTT
3767271 ATATATTTTATTTTTAATATATTTATATTTT
1 ATATATTTTATTTTTAATATATTTATATTTT
*
3767302 -T-TATTATTAATTTTT-ATATA-ATATCATCTCTT
1 ATATATT-TT-ATTTTTAATATATTTAT-AT-T-TT
* * *
3767334 A-A-A-TATATTTTTAATGTCA--TATA-CTT
1 ATATATTTTATTTTTAATAT-ATTTATATTTT
* *
3767360 -TAT-TTTCATTTATTATTATAATCTTATATGTTT
1 ATATATTTTATTT-TTAATAT-AT-TTATAT-TTT
* *
3767393 -TAT-TTTTATTTCTTTAATATATTTTTTATATT
1 ATATATTTTA-TT-TTTAATATA-TTTATATTTT
*
3767425 ATATATTTTA-TTTTAATTTATTTTACCTATATTAT
1 ATATATTTTATTTTTAATATA-TTTA--TAT-TT-T
*
3767460 ATAAATTTTAATTTTT-A-ATATTT-TA-TTT
1 ATATATTTT-ATTTTTAATATATTTATATTTT
* *
3767488 -TAT-TTTAATTTTTGAT-TA-TTATA--TT
1 ATATATTTTATTTTTAATATATTTATATTTT
3767513 ATATATTTTA-TTTTAATATATTT-TATTTT
1 ATATATTTTATTTTTAATATATTTATATTTT
3767542 A
1 A
3767543 ATTATAACAG
Statistics
Matches: 209, Mismatches: 24, Indels: 82
0.66 0.08 0.26
Matches are distributed among these distances:
25 10 0.05
26 20 0.10
27 15 0.07
28 9 0.04
29 19 0.09
30 17 0.08
31 32 0.15
32 10 0.05
33 37 0.18
34 22 0.11
35 12 0.06
36 2 0.01
37 4 0.02
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (31 bp):
ATATATTTTATTTTTAATATATTTATATTTT
Found at i:3767371 original size:114 final size:114
Alignment explanation
Indices: 3767169--3767400 Score: 428
Period size: 114 Copynumber: 2.0 Consensus size: 114
3767159 AAAATACAAG
3767169 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAA
1 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAA
* * *
3767234 TGTCATATATTTTATTTTTATTTATTATTATAATTTTATATATTTTATT
66 TGTCATATACTTTATTTTCATTTATTATTATAATCTTATATATTTTATT
3767283 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAA
1 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAA
*
3767348 TGTCATATACTTTATTTTCATTTATTATTATAATCTTATATGTTTTATT
66 TGTCATATACTTTATTTTCATTTATTATTATAATCTTATATATTTTATT
3767397 TTTA
1 TTTA
3767401 TTTCTTTAAT
Statistics
Matches: 114, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
114 114 1.00
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.62
Consensus pattern (114 bp):
TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAA
TGTCATATACTTTATTTTCATTTATTATTATAATCTTATATATTTTATT
Found at i:3767446 original size:15 final size:15
Alignment explanation
Indices: 3767428--3767545 Score: 59
Period size: 15 Copynumber: 8.0 Consensus size: 15
3767418 TTATATTATA
3767428 TATTTTATTTTAATT
1 TATTTTATTTTAATT
**
3767443 TATTTTA-CCT-ATAT
1 TATTTTATTTTAAT-T
**
3767457 TATATAAATTTTAATT
1 TAT-TTTATTTTAATT
* *
3767473 T-TTAATATTTTATTT
1 TATT-TTATTTTAATT
*
3767488 TATTTTAATTT--TT
1 TATTTTATTTTAATT
* * *
3767501 GATTATTATATT-ATA
1 TATT-TTATTTTAATT
*
3767516 TATTTTATTTTAATA
1 TATTTTATTTTAATT
3767531 TATTTTATTTTAATT
1 TATTTTATTTTAATT
3767546 ATAACAGTAT
Statistics
Matches: 77, Mismatches: 17, Indels: 18
0.69 0.15 0.16
Matches are distributed among these distances:
13 7 0.09
14 17 0.22
15 46 0.60
16 5 0.06
17 2 0.03
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.66
Consensus pattern (15 bp):
TATTTTATTTTAATT
Found at i:3767482 original size:35 final size:32
Alignment explanation
Indices: 3767419--3767484 Score: 80
Period size: 35 Copynumber: 1.9 Consensus size: 32
3767409 ATATATTTTT
3767419 TATATTATATATTTTATTTTAATTTATTTTACC
1 TATATTATATATTTTATTTTAA-TTATTTTACC
3767452 TATATTATATAAATTTTAATTTTTAA-TATTTTA
1 TATATTATAT--ATTTT-A-TTTTAATTATTTTA
3767485 TTTTATTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
33 10 0.34
35 12 0.41
36 1 0.03
37 6 0.21
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (32 bp):
TATATTATATATTTTATTTTAATTATTTTACC
Found at i:3767488 original size:5 final size:5
Alignment explanation
Indices: 3767478--3767542 Score: 51
Period size: 5 Copynumber: 12.4 Consensus size: 5
3767468 TAATTTTTAA
* *
3767478 TATTT TATTT TATTT TAATTTT TGATTAT TATAT TA-TA TATTT TATTT
1 TATTT TATTT TATTT T-A-TTT T-ATT-T TATTT TATTT TATTT TATTT
* *
3767526 TAATA TATTT TATTT TA
1 TATTT TATTT TATTT TA
3767543 ATTATAACAG
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
4 2 0.04
5 33 0.70
6 5 0.11
7 7 0.15
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (5 bp):
TATTT
Found at i:3767494 original size:55 final size:51
Alignment explanation
Indices: 3767412--3767542 Score: 147
Period size: 55 Copynumber: 2.4 Consensus size: 51
3767402 TTCTTTAATA
*
3767412 TATTTTTTATATTATATATTTTATTTTAATTTATT-TTACCTATATTATATAAATTT
1 TATTTTTAATATT-T-TATTTTATTTTAATTT-TTATTA-CTATATTATAT--ATTT
*
3767468 TAATTTTTAATATTTTATTTTATTTTAATTTTTGATTATTATATTATATATTT
1 T-ATTTTTAATATTTTATTTTATTTTAATTTTT-ATTACTATATTATATATTT
*
3767521 TATTTTAATATATTTTATTTTA
1 TATTTTTA-ATATTTTATTTTA
3767543 ATTATAACAG
Statistics
Matches: 68, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
52 6 0.09
53 18 0.26
54 2 0.03
55 26 0.38
56 5 0.07
57 11 0.16
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.66
Consensus pattern (51 bp):
TATTTTTAATATTTTATTTTATTTTAATTTTTATTACTATATTATATATTT
Found at i:3767514 original size:24 final size:25
Alignment explanation
Indices: 3767452--3767545 Score: 74
Period size: 25 Copynumber: 3.8 Consensus size: 25
3767442 TTATTTTACC
*
3767452 TATATTATATAAATTTTAATTTTTAA
1 TATATTATAT-TATTTTAATTTTTAA
* *
3767478 TATTTTATTTTATTTTAATTTTTGATTA
1 TATATTATATTATTTTAATTTTT-A--A
3767506 TTATATTATA-TATTTT-A-TTTTAA
1 -TATATTATATTATTTTAATTTTTAA
3767529 TATA-T-T-TTATTTTAATT
1 TATATTATATTATTTTAATT
3767546 ATAACAGTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 18
0.71 0.06 0.23
Matches are distributed among these distances:
20 7 0.12
21 2 0.04
22 5 0.09
23 1 0.02
25 13 0.23
26 13 0.23
27 1 0.02
28 7 0.12
29 7 0.12
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (25 bp):
TATATTATATTATTTTAATTTTTAA
Found at i:3771289 original size:17 final size:17
Alignment explanation
Indices: 3771248--3771280 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3771238 CTCTAAATAT
3771248 AATCACAACAAGACAAG
1 AATCACAACAAGACAAG
*
3771265 AATCACAACACGACAA
1 AATCACAACAAGACAA
3771281 TCATCACAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.27, G:0.09, T:0.06
Consensus pattern (17 bp):
AATCACAACAAGACAAG
Found at i:3771515 original size:2 final size:2
Alignment explanation
Indices: 3771508--3771538 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3771498 CAAACACATC
3771508 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3771539 TCACAACACT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3775247 original size:362 final size:364
Alignment explanation
Indices: 3774580--3775257 Score: 972
Period size: 362 Copynumber: 1.9 Consensus size: 364
3774570 AGACCCTTTT
* * * * *
3774580 TTTTTTCTTTTTTTTAATTGTTAATGAAATGTTATGTTATAATTTAATTTTATTTTAAAACTAAT
1 TTTTTTCTATATTTAAATTGTTAATAAAATGTTATGTTATAATTTAATTTTATTTCAAAACTAAT
* * * * *
3774645 TAAATTTTTACCTCGAATCGAATTATTGACCCGATCCATGACCTTGTATGATTACTCTGTAACCA
66 TAAATTTTTACCTCAAATCGAATGATTGACCCGATCCATAACCATATATGATTACTCTGTAACCA
*
3774710 TATCTCATACAAAATCTTATATATATATATATATATATGTTTGATTTTATTTATTTATTTGCAAG
131 CATCTCATACAAAATCTTATATATATATATATATATATGTTTGATTTTATTTATTTATTTGCAAG
** * * *
3774775 GAATAGGTTAAAGTTTCTATCCTTATCATTAACTGTGATTCATGTGCAAATAAAAGCTAAAGTCG
196 GAATAAATAAAAGTTTCTATCCTTATCATTAACTGTGATTCATGTGCAAATAAAAGCTAAAATAG
** * *
3774840 AAAACAAAATGTGATAAAGTACAAAACTTCTTTCACATGGACTCTATTATGCAATTGGCCTTTCT
261 AAAACAAAACATGACAAAATACAAAACTTCTTTCACATGGACTCTATTATGCAATTGGCCTTTCT
3774905 TCTTTGCTATGAGTGCCACCTCCAAAACTTTTTTCTCTC
326 TCTTTGCTATGAGTGCCACCTCCAAAACTTTTTTCTCTC
* * *
3774944 TTTTTTCTATATTTAAATTGTTAATAAAATTTTATGTTATAATTTTATTTTATTTCAAAACTGAT
1 TTTTTTCTATATTTAAATTGTTAATAAAATGTTATGTTATAATTTAATTTTATTTCAAAACTAAT
* * *
3775009 TAATTTTTTA-CTCCAAATCGAATGATTGACCCTATCCATAACCATATA-GAATTACTCTTTAAC
66 TAAATTTTTACCT-CAAATCGAATGATTGACCCGATCCATAACCATATATG-ATTACTCTGTAAC
* *
3775072 CAC-CCTTCATATAAAATCTT-T-TATATATATATATATATGTTTGATTTTATTTATTTATTTGC
129 CACATC-TCATACAAAATCTTATATATATATATATATATATGTTTGATTTTATTTATTTATTTGC
* * *
3775134 AAGGAATAAATAAAAGCTTT-TGTCTTTATCATTAATTGTGATTCATGTGCAAATAAAAGCTAAA
193 AAGGAATAAATAAAAG-TTTCTATCCTTATCATTAACTGTGATTCATGTGCAAATAAAAGCTAAA
* * *
3775198 ATAGAAAATAAAGCATGACAAAATACAAAACTTCTTTCACGTGGACTCTATTATGCAATT
257 ATAGAAAACAAAACATGACAAAATACAAAACTTCTTTCACATGGACTCTATTATGCAATT
3775258 ATTCTTTCTT
Statistics
Matches: 276, Mismatches: 34, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
362 146 0.53
363 8 0.03
364 122 0.44
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (364 bp):
TTTTTTCTATATTTAAATTGTTAATAAAATGTTATGTTATAATTTAATTTTATTTCAAAACTAAT
TAAATTTTTACCTCAAATCGAATGATTGACCCGATCCATAACCATATATGATTACTCTGTAACCA
CATCTCATACAAAATCTTATATATATATATATATATATGTTTGATTTTATTTATTTATTTGCAAG
GAATAAATAAAAGTTTCTATCCTTATCATTAACTGTGATTCATGTGCAAATAAAAGCTAAAATAG
AAAACAAAACATGACAAAATACAAAACTTCTTTCACATGGACTCTATTATGCAATTGGCCTTTCT
TCTTTGCTATGAGTGCCACCTCCAAAACTTTTTTCTCTC
Found at i:3776159 original size:17 final size:18
Alignment explanation
Indices: 3776133--3776168 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
3776123 AATTGTAATG
3776133 ATTTTCATTA-AAATATT
1 ATTTTCATTATAAATATT
*
3776150 ATTTTTATTATAAATATT
1 ATTTTCATTATAAATATT
3776168 A
1 A
3776169 ATAGATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTTCATTATAAATATT
Found at i:3777173 original size:25 final size:25
Alignment explanation
Indices: 3777139--3777187 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
3777129 GCCTAGGGTC
3777139 TGTTTCAAATGTGGGGTTTATGGTT
1 TGTTTCAAATGTGGGGTTTATGGTT
3777164 TGTTTCAAATGTGGGGTTTATGGT
1 TGTTTCAAATGTGGGGTTTATGGT
3777188 CATACAAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.16, C:0.04, G:0.33, T:0.47
Consensus pattern (25 bp):
TGTTTCAAATGTGGGGTTTATGGTT
Found at i:3788868 original size:17 final size:18
Alignment explanation
Indices: 3788833--3788877 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
3788823 TTTTGAGAAG
3788833 TTTTTAAAAAATAAGTTT
1 TTTTTAAAAAATAAGTTT
*
3788851 TTTTTAAAGAATAA--TT
1 TTTTTAAAAAATAAGTTT
3788867 TTTTTAAAAAA
1 TTTTTAAAAAA
3788878 AAAAAGCTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 12 0.48
18 13 0.52
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (18 bp):
TTTTTAAAAAATAAGTTT
Found at i:3796104 original size:8 final size:8
Alignment explanation
Indices: 3796091--3796124 Score: 68
Period size: 8 Copynumber: 4.2 Consensus size: 8
3796081 AGTCAATCTT
3796091 TAGGCTCA
1 TAGGCTCA
3796099 TAGGCTCA
1 TAGGCTCA
3796107 TAGGCTCA
1 TAGGCTCA
3796115 TAGGCTCA
1 TAGGCTCA
3796123 TA
1 TA
3796125 CTTCCTTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (8 bp):
TAGGCTCA
Found at i:3797862 original size:28 final size:28
Alignment explanation
Indices: 3797822--3797895 Score: 105
Period size: 28 Copynumber: 2.6 Consensus size: 28
3797812 TTCAATACAA
*
3797822 TGCCTTTTAAAGGTTCAAACATAACTAT
1 TGCCTTTTCAAGGTTCAAACATAACTAT
**
3797850 TGCCTTTTCAAGGGTT-AAGTATAACTAT
1 TGCCTTTTCAA-GGTTCAAACATAACTAT
3797878 TGCCTTTTCAAGGTTCAA
1 TGCCTTTTCAAGGTTCAA
3797896 GCACAACCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
27 4 0.10
28 33 0.80
29 4 0.10
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.38
Consensus pattern (28 bp):
TGCCTTTTCAAGGTTCAAACATAACTAT
Found at i:3798673 original size:21 final size:21
Alignment explanation
Indices: 3798649--3798713 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
3798639 ATGAAGGTTT
3798649 AAAACTTATTTAACAATTTCA
1 AAAACTTATTTAACAATTTCA
*
3798670 AAAAC-TATTTAAACAAGTTC-
1 AAAACTTATTT-AACAATTTCA
* *
3798690 AAAACTCATTGAAGCAATTTCA
1 AAAACTTATTTAA-CAATTTCA
3798712 AA
1 AA
3798714 CAATTTTGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
20 12 0.33
21 22 0.61
22 2 0.06
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.31
Consensus pattern (21 bp):
AAAACTTATTTAACAATTTCA
Found at i:3798840 original size:21 final size:21
Alignment explanation
Indices: 3798788--3798842 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
3798778 ATTAAGTTCT
*
3798788 AAAACTCATTCAAACAACTTC
1 AAAAGTCATTCAAACAACTTC
* * *
3798809 AAAAGTAATTCAAATAAGTTC
1 AAAAGTCATTCAAACAACTTC
3798830 -AAAGTTCATTCAA
1 AAAAG-TCATTCAA
3798843 GCAATTTTGA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 4 0.14
21 24 0.86
ACGTcount: A:0.49, C:0.18, G:0.05, T:0.27
Consensus pattern (21 bp):
AAAAGTCATTCAAACAACTTC
Found at i:3801983 original size:23 final size:23
Alignment explanation
Indices: 3801956--3802002 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
3801946 AGAGAGATTT
*
3801956 GGAAGAAATGAAAG-GAAAGGAAG
1 GGAAGAAA-CAAAGAGAAAGGAAG
*
3801979 GGAAGAGACAAAGAGAAAGGAAG
1 GGAAGAAACAAAGAGAAAGGAAG
3802002 G
1 G
3802003 CAGATAATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.55, C:0.02, G:0.40, T:0.02
Consensus pattern (23 bp):
GGAAGAAACAAAGAGAAAGGAAG
Found at i:3811335 original size:2 final size:2
Alignment explanation
Indices: 3811328--3811369 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3811318 CTTTGTGAAG
3811328 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
3811370 TGATAACTAA
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:3812418 original size:38 final size:38
Alignment explanation
Indices: 3812347--3812420 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 38
3812337 TCCGATAAAT
* *
3812347 TTTATGTACAATTAATTCATATTTCACCAAAGATTTAC
1 TTTATGTACAATTAATTCATACTTAACCAAAGATTTAC
*
3812385 TTTATGTATAATTAATTCATACTTAACTC-AAGATTT
1 TTTATGTACAATTAATTCATACTTAAC-CAAAGATTT
3812421 GTTATAATTG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 31 0.97
39 1 0.03
ACGTcount: A:0.36, C:0.14, G:0.05, T:0.45
Consensus pattern (38 bp):
TTTATGTACAATTAATTCATACTTAACCAAAGATTTAC
Found at i:3832370 original size:10 final size:10
Alignment explanation
Indices: 3832355--3832383 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
3832345 AGAAGATAAC
3832355 ATGGAAGAAG
1 ATGGAAGAAG
3832365 ATGGAAGAAG
1 ATGGAAGAAG
3832375 ATGGAAGAA
1 ATGGAAGAA
3832384 AATAAAGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.38, T:0.10
Consensus pattern (10 bp):
ATGGAAGAAG
Found at i:3832715 original size:103 final size:105
Alignment explanation
Indices: 3832589--3832800 Score: 311
Period size: 110 Copynumber: 2.0 Consensus size: 105
3832579 TATGTTAGAA
* * * *
3832589 TGGCATGTTTTTGTTAACTTTTTTTATTGT-T-ATGGGAATTAGTCTTGATTCTTACATTTTGAT
1 TGGCATATTTTTGTTAACATTTTTTATTGTATAATGGGAATTAGTCTTAATTCTTACATTTTAAT
*
3832652 GATGATTTTGATAGTTTGTTTCAATTTCTTTTAGCTTATT
66 GATGATTTTGATAGTTTGTTTCAATTGCTTTTAGCTTATT
*
3832692 TGGCATATTTTTGTTAACATTTTTTATTGTAAACATGAATGGGAATTAGTCTTAATTCTTATATT
1 TGGCATATTTTTGTTAACATTTTTTATTGT----AT-AATGGGAATTAGTCTTAATTCTTACATT
3832757 TTAATGATGATTTTGATAGTTTGTTTCAATTGCTTTTAGCTTAT
61 TTAATGATGATTTTGATAGTTTGTTTCAATTGCTTTTAGCTTAT
3832801 GTATGAATAT
Statistics
Matches: 96, Mismatches: 6, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
103 28 0.29
108 1 0.01
110 67 0.70
ACGTcount: A:0.23, C:0.08, G:0.16, T:0.54
Consensus pattern (105 bp):
TGGCATATTTTTGTTAACATTTTTTATTGTATAATGGGAATTAGTCTTAATTCTTACATTTTAAT
GATGATTTTGATAGTTTGTTTCAATTGCTTTTAGCTTATT
Found at i:3832814 original size:110 final size:109
Alignment explanation
Indices: 3832620--3832822 Score: 320
Period size: 110 Copynumber: 1.9 Consensus size: 109
3832610 TTTTATTGTT
* * *
3832620 ATGGGAATTAGTCTTGATTCTTACATTTTGATGATGATTTTGATAGTTTGTTTCAATTTCTTTTA
1 ATGGGAATTAGTCTTAATTCTTACATTTTAATGATGATTTTGATAGTTTGTTTCAATTGCTTTTA
*
3832685 GCTTATTTGGCATATTTTTGTTAACATTTTTTATTGTAAACATGA
66 GCTTATTTGGAATATTTTTGTT-ACATTTTTTATTGTAAACATGA
*
3832730 ATGGGAATTAGTCTTAATTCTTATATTTTAATGATGATTTTGATAGTTTGTTTCAATTGCTTTTA
1 ATGGGAATTAGTCTTAATTCTTACATTTTAATGATGATTTTGATAGTTTGTTTCAATTGCTTTTA
3832795 GCTTATGTAT-GAATA-TTTTGTTACATTT
66 GCTTAT-T-TGGAATATTTTTGTTACATTT
3832823 CAAGAATGCT
Statistics
Matches: 86, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
109 6 0.07
110 74 0.86
111 5 0.06
112 1 0.01
ACGTcount: A:0.25, C:0.07, G:0.15, T:0.52
Consensus pattern (109 bp):
ATGGGAATTAGTCTTAATTCTTACATTTTAATGATGATTTTGATAGTTTGTTTCAATTGCTTTTA
GCTTATTTGGAATATTTTTGTTACATTTTTTATTGTAAACATGA
Found at i:3838815 original size:261 final size:264
Alignment explanation
Indices: 3838306--3838828 Score: 998
Period size: 261 Copynumber: 2.0 Consensus size: 264
3838296 TACAAGAAAA
3838306 TATGTGAAATACTTAGTCCTTGCTCTAACAAAGATCAGTAAAGAAATATTGTCTGGCGAAAGCAC
1 TATGTGAAATACTTAGTCCTTGCTCTAACAAAGATCAGTAAAGAAATATTGTCTGGCGAAAGCAC
*
3838371 TGACCATGAAATAAAGGAGATTGTAAGGTATGAAGTGGATATGGCATTGGCGTTATCGGCTGAAG
66 TGACCATGAAATAAA-GAGATTGTAAGGTATGAAGTGGATATGGCATTGGCGTTATCGACTGAAG
3838436 GCTTTGCGTGGAGCCATGCCTTGAAAGACAAGCTTTGATTAAATGTCAATGTAGCTAGATTTCAA
130 GCTTTGCGTGGAGCCATGCCTTGAAAGACAAGCTTTGATTAAATGTCAATGTAGCTAGATTTCAA
3838501 AGCTCTTTAGCTCATCACCAGCTCCCATCCTTCAAAATTTCTTCGTCAACTTATAGTCCAAACTG
195 AGCTCTTTAGCTCATCACCAGCTCCCATCCTTCAAAATTTCTTCGTCAACTTATAGTCCAAACTG
3838566 TGAGG
260 TGAGG
3838571 TATGTGAAATACTTAGTCCTTGCTCTAACAAAGATCAGTAAAGAAATATTGTCTGGCGAAAGCAC
1 TATGTGAAATACTTAGTCCTTGCTCTAACAAAGATCAGTAAAGAAATATTGTCTGGCGAAAGCAC
*
3838636 TGACCATGAAATAAA-AGATTGTGAGGTATGAAGTGGATATGGCATTGGCGTTATCGACTGAAGG
66 TGACCATGAAATAAAGAGATTGTAAGGTATGAAGTGGATATGGCATTGGCGTTATCGACTGAAGG
3838700 CTTTGCGTGGAGCCATG-CTTGAAAGACAAGCTTTGA-TAAATGTCAATGTAGCTAGATTTCAAA
131 CTTTGCGTGGAGCCATGCCTTGAAAGACAAGCTTTGATTAAATGTCAATGTAGCTAGATTTCAAA
3838763 GCTCTTTAGCTCATCACCAGCTCCCATCCTTCAAAATTTCTTCGTCAACTTATAGTCCAAACTGT
196 GCTCTTTAGCTCATCACCAGCTCCCATCCTTCAAAATTTCTTCGTCAACTTATAGTCCAAACTGT
3838828 G
261 G
3838829 GGAACATGAT
Statistics
Matches: 256, Mismatches: 2, Indels: 4
0.98 0.01 0.02
Matches are distributed among these distances:
261 93 0.36
262 19 0.07
263 64 0.25
265 80 0.31
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (264 bp):
TATGTGAAATACTTAGTCCTTGCTCTAACAAAGATCAGTAAAGAAATATTGTCTGGCGAAAGCAC
TGACCATGAAATAAAGAGATTGTAAGGTATGAAGTGGATATGGCATTGGCGTTATCGACTGAAGG
CTTTGCGTGGAGCCATGCCTTGAAAGACAAGCTTTGATTAAATGTCAATGTAGCTAGATTTCAAA
GCTCTTTAGCTCATCACCAGCTCCCATCCTTCAAAATTTCTTCGTCAACTTATAGTCCAAACTGT
GAGG
Found at i:3842476 original size:24 final size:24
Alignment explanation
Indices: 3842426--3842480 Score: 69
Period size: 22 Copynumber: 2.3 Consensus size: 24
3842416 CCAGCCACAC
3842426 AAAAAAAATCAAAAGAAAACAGTAA
1 AAAAAAAATCAAAAGAAAACAG-AA
* *
3842451 AACAAAAATC-AAAGAAAA-ACAA
1 AAAAAAAATCAAAAGAAAACAGAA
3842473 AAAAAAAA
1 AAAAAAAA
3842481 GAAATGTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 9 0.33
23 1 0.04
24 8 0.30
25 9 0.33
ACGTcount: A:0.80, C:0.09, G:0.05, T:0.05
Consensus pattern (24 bp):
AAAAAAAATCAAAAGAAAACAGAA
Found at i:3842477 original size:25 final size:25
Alignment explanation
Indices: 3842429--3842477 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
3842419 GCCACACAAA
**
3842429 AAAAATCAAAAGAAAACAGTAAAAC
1 AAAAATCAAAAGAAAACAAAAAAAC
3842454 AAAAATC-AAAGAAAAACAAAAAAA
1 AAAAATCAAAAG-AAAACAAAAAAA
3842478 AAAGAAATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.78, C:0.10, G:0.06, T:0.06
Consensus pattern (25 bp):
AAAAATCAAAAGAAAACAAAAAAAC
Found at i:3842481 original size:17 final size:17
Alignment explanation
Indices: 3842429--3842484 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
3842419 GCCACACAAA
*
3842429 AAAAATCAAAAGAAAACAG
1 AAAAA-CAAAA-AAAAAAG
* **
3842448 TAAAACAAAAATCAAAG
1 AAAAACAAAAAAAAAAG
3842465 AAAAACAAAAAAAAAAG
1 AAAAACAAAAAAAAAAG
3842482 AAA
1 AAA
3842485 TGTATACATT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 21 0.70
18 5 0.17
19 4 0.13
ACGTcount: A:0.79, C:0.09, G:0.07, T:0.05
Consensus pattern (17 bp):
AAAAACAAAAAAAAAAG
Found at i:3844513 original size:21 final size:21
Alignment explanation
Indices: 3844484--3844526 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3844474 GAATAGTTAA
3844484 TTTAAGTTATTTTATTTAAAT
1 TTTAAGTTATTTTATTTAAAT
* *
3844505 TTTACGTTATTTTTTTTAAAT
1 TTTAAGTTATTTTATTTAAAT
3844526 T
1 T
3844527 ACTTTAGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65
Consensus pattern (21 bp):
TTTAAGTTATTTTATTTAAAT
Found at i:3847516 original size:21 final size:21
Alignment explanation
Indices: 3847468--3847516 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
3847458 TGATAACATT
*
3847468 ATACAGAGTCAAGCAGCTATC
1 ATACAAAGTCAAGCAGCTATC
*
3847489 ATTCAAAGTCAAGCAGC-ATC
1 ATACAAAGTCAAGCAGCTATC
3847509 AATACAAA
1 -ATACAAA
3847517 ACCTTGAGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.45, C:0.22, G:0.14, T:0.18
Consensus pattern (21 bp):
ATACAAAGTCAAGCAGCTATC
Found at i:3858643 original size:62 final size:62
Alignment explanation
Indices: 3858546--3858666 Score: 224
Period size: 62 Copynumber: 2.0 Consensus size: 62
3858536 AATAGACAGA
*
3858546 CACTCTCCATATAAAGCTAATATGAGAATATTCTAGTTTTCGATAAACCTATCCCTTTTAAG
1 CACTCTCCATATAAAGCTAATATGAGAATATTCTAGTTTTCGAAAAACCTATCCCTTTTAAG
*
3858608 CACTCTCCATATAAAGCTAATATGAGAATATTCTAGTTTTTGAAAAACCTATCCCTTTT
1 CACTCTCCATATAAAGCTAATATGAGAATATTCTAGTTTTCGAAAAACCTATCCCTTTT
3858667 GGGCAAACAG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (62 bp):
CACTCTCCATATAAAGCTAATATGAGAATATTCTAGTTTTCGAAAAACCTATCCCTTTTAAG
Found at i:3860284 original size:2 final size:2
Alignment explanation
Indices: 3860277--3860304 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3860267 GGGACCTAGC
3860277 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3860305 ATAAACAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3860986 original size:53 final size:53
Alignment explanation
Indices: 3860924--3861143 Score: 149
Period size: 53 Copynumber: 4.2 Consensus size: 53
3860914 ACCTAAAGAT
3860924 AAAAATAAAATAATTAGATATAAAAAATAGATTTAGATAGATAGAAAAATAAA-
1 AAAAATAAAATAATTAGATATAAAAAATAGATTTAGATAGATA-AAAAATAAAG
* ** * * *
3860977 AAAAATAAAAATATTTATTTGTAAGAAA-AGATTTAGGTAGATAAAAAGA-AATAG
1 AAAAAT-AAAATAATTAGATATAAAAAATAGATTTAGATAGATAAAAA-ATAA-AG
* * * *
3861031 AAAAATAAAA-AAATAGTTATAAAAACAT--ATTTAGGTAAATAAAAAAATAAAG
1 AAAAATAAAATAATTAGATATAAAAA-ATAGATTTAGATAGAT-AAAAAATAAAG
*
3861083 AAATAA-ATAAAT-ATGT-GACTA-AAAAAATAGATTTAGGA-AGATAAAAAAGAAA-
1 AAA-AATA-AAATAAT-TAGA-TATAAAAAATAGATTTA-GATAGATAAAAAATAAAG
*
3861135 AATAATAAA
1 AAAAATAAA
3861144 GTATTTAGTT
Statistics
Matches: 132, Mismatches: 18, Indels: 36
0.71 0.10 0.19
Matches are distributed among these distances:
51 4 0.03
52 39 0.30
53 55 0.42
54 33 0.25
55 1 0.01
ACGTcount: A:0.64, C:0.01, G:0.11, T:0.24
Consensus pattern (53 bp):
AAAAATAAAATAATTAGATATAAAAAATAGATTTAGATAGATAAAAAATAAAG
Found at i:3860988 original size:54 final size:52
Alignment explanation
Indices: 3860924--3861143 Score: 152
Period size: 54 Copynumber: 4.2 Consensus size: 52
3860914 ACCTAAAGAT
*
3860924 AAAAATAAAATAATTAGATATAAAAAATAGATTTAGATAGATAGAAAAATAAA
1 AAAAATAAAAAAATTAGATATAAAAAATAGATTTAGATAGATA-AAAAATAAA
* ** * * *
3860977 AAAAATAAAAATATTTATTTGTAAGAAA-AGATTTAGGTAGATAAAAAGA-AATA
1 AAAAATAAAAA-AATTAGATATAAAAAATAGATTTAGATAGATAAAAA-ATAA-A
* * *
3861030 GAAAAATAAAAAAA-TAGTTATAAAAACAT--ATTTAGGTAAATAAAAAA-ATAA
1 -AAAAATAAAAAAATTAGATATAAAAA-ATAGATTTAGATAGATAAAAAATA-AA
* *
3861081 AGAAATAAATAAATATGT-GACTA-AAAAAATAGATTTAGGA-AGATAAAAAAGAAA
1 AAAAATAAA-AAA-AT-TAGA-TATAAAAAATAGATTTA-GATAGATAAAAAATAAA
*
3861135 AATAATAAA
1 AAAAATAAA
3861144 GTATTTAGTT
Statistics
Matches: 133, Mismatches: 18, Indels: 31
0.73 0.10 0.17
Matches are distributed among these distances:
50 8 0.06
51 6 0.05
52 35 0.26
53 34 0.26
54 48 0.36
55 2 0.02
ACGTcount: A:0.64, C:0.01, G:0.11, T:0.24
Consensus pattern (52 bp):
AAAAATAAAAAAATTAGATATAAAAAATAGATTTAGATAGATAAAAAATAAA
Found at i:3861106 original size:52 final size:51
Alignment explanation
Indices: 3861007--3861130 Score: 128
Period size: 52 Copynumber: 2.4 Consensus size: 51
3860997 GTAAGAAAAG
* * *
3861007 ATTTAGGTAGATAAAAAGAAATAGAAAAATAAAAAAATAGTTATAAAAACAT-
1 ATTTAGGTAAAT-AAAA-AAATAGAAAAATAAAAAAATAGTGATAAAAAAATA
*
3861059 ATTTAGGTAAATAAAAAAATA-AAGAAATAAATAAATATGTGACTAAAAAAATA
1 ATTTAGGTAAATAAAAAAATAGAA-AAATAAAAAAATA-GTGA-TAAAAAAATA
3861112 GATTTAGG-AAGATAAAAAA
1 -ATTTAGGTAA-ATAAAAAA
3861131 GAAAAATAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
49 2 0.03
50 17 0.27
51 7 0.11
52 19 0.31
53 2 0.03
54 15 0.24
ACGTcount: A:0.63, C:0.02, G:0.12, T:0.23
Consensus pattern (51 bp):
ATTTAGGTAAATAAAAAAATAGAAAAATAAAAAAATAGTGATAAAAAAATA
Found at i:3868771 original size:3 final size:3
Alignment explanation
Indices: 3868756--3868794 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
3868746 GCCCTTTAAT
*
3868756 AAG AAG CAG AAG AAG AAG AAG AAG AAG AAG AAGG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA-G AAG AA
3868795 ATGGCTATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.64, C:0.03, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3873969 original size:2 final size:2
Alignment explanation
Indices: 3873962--3873989 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3873952 AAATAAATAA
3873962 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
3873990 CAGTTCGGTC
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:3877843 original size:4 final size:4
Alignment explanation
Indices: 3877834--3877860 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3877824 TATTAAGCAA
3877834 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
3877861 GTCCACCTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:3878966 original size:14 final size:14
Alignment explanation
Indices: 3878947--3878977 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3878937 CAGAGGTATT
3878947 TGACATGAACATTC
1 TGACATGAACATTC
*
3878961 TGACATTAACATTC
1 TGACATGAACATTC
3878975 TGA
1 TGA
3878978 TACTTCCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (14 bp):
TGACATGAACATTC
Found at i:3887783 original size:2 final size:2
Alignment explanation
Indices: 3887776--3887804 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3887766 CTTAATCCTC
3887776 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 A
3887805 GAGTTGGGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3890150 original size:25 final size:24
Alignment explanation
Indices: 3890107--3890162 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
3890097 TATTTTTTAA
* * *
3890107 AAATATATAAATATTTTTATTATAT
1 AAATA-ATTAATATATTTATTAAAT
3890132 AACATAATTAATATATTTATTAAAT
1 AA-ATAATTAATATATTTATTAAAT
3890157 AAATAA
1 AAATAA
3890163 AACTTAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 4 0.15
25 20 0.74
26 3 0.11
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
AAATAATTAATATATTTATTAAAT
Found at i:3891549 original size:21 final size:20
Alignment explanation
Indices: 3891533--3891572 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3891523 TTTAAAATAA
3891533 ATTTTTAGA-AATATAAAAGT
1 ATTTTTAGATAATATAAAA-T
*
3891553 ATTTTTATATAATATAAAAT
1 ATTTTTAGATAATATAAAAT
3891573 TTATAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
ATTTTTAGATAATATAAAAT
Found at i:3891556 original size:20 final size:21
Alignment explanation
Indices: 3891533--3891571 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3891523 TTTAAAATAA
3891533 ATTTTTAGA-AATATAAAAGT
1 ATTTTTAGATAATATAAAAGT
*
3891553 ATTTTTATATAATATAAAA
1 ATTTTTAGATAATATAAAA
3891572 TTTATAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (21 bp):
ATTTTTAGATAATATAAAAGT
Found at i:3897409 original size:18 final size:18
Alignment explanation
Indices: 3897386--3897422 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
3897376 TAAAGATAAA
*
3897386 TGATAAATTTGATTCATC
1 TGATAAATTTGATTAATC
3897404 TGATAAATTTGATTAATC
1 TGATAAATTTGATTAATC
3897422 T
1 T
3897423 TTTTAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.46
Consensus pattern (18 bp):
TGATAAATTTGATTAATC
Found at i:3911561 original size:17 final size:18
Alignment explanation
Indices: 3911529--3911564 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
3911519 TGTAGATACA
3911529 AAAGAAAATAATTTTTTT
1 AAAGAAAATAATTTTTTT
*
3911547 AAAGAATAT-ATTTTTTT
1 AAAGAAAATAATTTTTTT
3911564 A
1 A
3911565 TTAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (18 bp):
AAAGAAAATAATTTTTTT
Found at i:3912217 original size:3 final size:3
Alignment explanation
Indices: 3912209--3912233 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3912199 AACAATAGAC
3912209 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
3912234 CGAAATGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:3913402 original size:25 final size:25
Alignment explanation
Indices: 3913348--3913423 Score: 75
Period size: 25 Copynumber: 3.0 Consensus size: 25
3913338 TTGGTCATAT
* *
3913348 TATTATATCAAATTATCATATTAAGT-
1 TATTATATAAAATAAT-ATATTAA-TA
*
3913374 TATTAT-TAATTATAATATATTAATA
1 TATTATATAA-AATAATATATTAATA
*
3913399 TATTATATAAAATAATATTTTAATA
1 TATTATATAAAATAATATATTAATA
3913424 AAATTATTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
24 1 0.02
25 28 0.67
26 13 0.31
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (25 bp):
TATTATATAAAATAATATATTAATA
Found at i:3913414 original size:17 final size:16
Alignment explanation
Indices: 3913394--3913427 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3913384 TATAATATAT
3913394 TAATATATTATATAAAA
1 TAATATATTA-ATAAAA
*
3913411 TAATATTTTAATAAAA
1 TAATATATTAATAAAA
3913427 T
1 T
3913428 TATTTAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATATATTAATAAAA
Found at i:3913446 original size:19 final size:19
Alignment explanation
Indices: 3913424--3913464 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
3913414 TATTTTAATA
3913424 AAATTATTTAATTTAAAAT
1 AAATTATTTAATTTAAAAT
3913443 AAATTATTTAATTTAAAAT
1 AAATTATTTAATTTAAAAT
3913462 AAA
1 AAA
3913465 AATATAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AAATTATTTAATTTAAAAT
Found at i:3915043 original size:3 final size:3
Alignment explanation
Indices: 3915035--3915068 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3915025 TATTGATATC
3915035 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3915069 CTACTACTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3921850 original size:33 final size:34
Alignment explanation
Indices: 3921787--3921857 Score: 94
Period size: 33 Copynumber: 2.1 Consensus size: 34
3921777 AATATTTTAT
3921787 AATATTATAATTAAAATAAAAAATATTAAAATAA
1 AATATTATAATTAAAATAAAAAATATTAAAATAA
*
3921821 AATA-TATAATGTAAGAATCAAAAA-A-TAAAATAA
1 AATATTATAAT-TAA-AATAAAAAATATTAAAATAA
3921854 AATA
1 AATA
3921858 AAATATAAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
33 18 0.53
34 8 0.24
35 8 0.24
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (34 bp):
AATATTATAATTAAAATAAAAAATATTAAAATAA
Found at i:3921909 original size:15 final size:15
Alignment explanation
Indices: 3921795--3921912 Score: 66
Period size: 15 Copynumber: 8.0 Consensus size: 15
3921785 ATAATATTAT
3921795 AATTAAAATAAAA-A
1 AATTAAAATAAAATA
3921809 ATATTAAAATAAAATA
1 A-ATTAAAATAAAATA
* ** *
3921825 TA-TAATGTAAGAATC
1 AATTAAAATAA-AATA
3921840 AA--AAAATAAAATA
1 AATTAAAATAAAATA
* * *
3921853 AAATAAAATATAAGA
1 AATTAAAATAAAATA
**
3921868 AATTAAAAT-TTATA
1 AATTAAAATAAAATA
* **
3921882 TAATTTAGGTAAAATA
1 -AATTAAAATAAAATA
3921898 AATTAAAATAAAATA
1 AATTAAAATAAAATA
3921913 TAGAATATAA
Statistics
Matches: 76, Mismatches: 21, Indels: 13
0.69 0.19 0.12
Matches are distributed among these distances:
13 5 0.07
14 15 0.20
15 52 0.68
16 4 0.05
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (15 bp):
AATTAAAATAAAATA
Found at i:3922751 original size:16 final size:17
Alignment explanation
Indices: 3922721--3922753 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3922711 TTATACATAC
3922721 TTAATTATTAATTTATT
1 TTAATTATTAATTTATT
*
3922738 TTAA-TATTATTTTATT
1 TTAATTATTAATTTATT
3922754 ATAAAAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTAATTATTAATTTATT
Found at i:3922941 original size:1 final size:1
Alignment explanation
Indices: 3922935--3922962 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
3922925 TGTTATAGGA
3922935 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
3922963 AAGTTGGACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:3932567 original size:21 final size:22
Alignment explanation
Indices: 3932538--3932581 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
3932528 AAGTGATTAA
3932538 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
* *
3932559 TTTAGGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
3932581 T
1 T
3932582 ACTTTAAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:3955072 original size:10 final size:10
Alignment explanation
Indices: 3955044--3955073 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
3955034 ATTTGTTTCA
*
3955044 ATATATATAT
1 ATATATATTT
3955054 ATATATATTT
1 ATATATATTT
3955064 ATATATATTT
1 ATATATATTT
3955074 TTTAGCTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
ATATATATTT
Found at i:3955257 original size:27 final size:27
Alignment explanation
Indices: 3955226--3955286 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
3955216 AGTTATAGTA
*
3955226 GTTAAATGAATTCATTCACTGTTAGAG
1 GTTAAATGAATTCATCCACTGTTAGAG
* * * *
3955253 GTTAAACGTATTCATCCACTTTTAGTG
1 GTTAAATGAATTCATCCACTGTTAGAG
*
3955280 GTCAAAT
1 GTTAAAT
3955287 TTATTTTTAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (27 bp):
GTTAAATGAATTCATCCACTGTTAGAG
Found at i:3960350 original size:22 final size:22
Alignment explanation
Indices: 3960322--3960392 Score: 133
Period size: 22 Copynumber: 3.2 Consensus size: 22
3960312 GATAGGGCAT
3960322 TGACTAGCTAGTAAGCATTGCG
1 TGACTAGCTAGTAAGCATTGCG
*
3960344 TGACTAGCTAATAAGCATTGCG
1 TGACTAGCTAGTAAGCATTGCG
3960366 TGACTAGCTAGTAAGCATTGCG
1 TGACTAGCTAGTAAGCATTGCG
3960388 TGACT
1 TGACT
3960393 TAGGGTTTGT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.28
Consensus pattern (22 bp):
TGACTAGCTAGTAAGCATTGCG
Found at i:3963829 original size:296 final size:296
Alignment explanation
Indices: 3963269--3964457 Score: 1231
Period size: 296 Copynumber: 4.0 Consensus size: 296
3963259 GCTTGTCTTC
* * * **
3963269 GGCATTACA-TGACTTGTTTGTTGAAGCATGAGAAGGC-AATTTAGATGAACATCTATTGATAAA
1 GGCATTA-AGTGACTTATTTGTTGAAGCATGTGAA-GCAAATTTGGATGAACATCTATCAATAAA
* *
3963332 TTCCACTATCTATCAATAGATGACCACTCGAGAACTTTGCAAATCAAAGAGGCCCGAGAACTA-T
64 TTCCACTATCTATCAATAGATGACCACTCAAGAACTTTGCAAATCAAAGAGGCCCGAAAACTACT
* * * *
3963396 CGATAGATAACACTATCTATTAATAGGGCATTACGTGTCT-GATTGATAGTCATTGCATAACTAA
129 -GATAGATACCACTATCTATTCATAGAGCATTACGTGCCTAG-TTGATAGTCATTGCATAACTAA
* * * * * * * *
3963460 AGCATTGTCTAGTTGGTTTTTAGTCATTGCGTAACTTA-AGCATTGCGTGAAT-GAGGTGTAGCC
192 GGCATTGTGTGGCTAGTTTTTAATCATTGCATAACTTAGA-CATTGCGTGAATAG-GGTGTAGTC
* *
3963523 ATTATGTGACTTGTTGATAGGGTATCGCATGACTAGTTGGTA
255 ATTGTGTGACTTGTTGATAAGGTATCGCATGACTAGTTGGTA
* * *
3963565 GGCATTAAGTGACTTATTTGTTGAAGCATGTGAAGCAAATTTGGATTAACATTTATCGATAAATT
1 GGCATTAAGTGACTTATTTGTTGAAGCATGTGAAGCAAATTTGGATGAACATCTATCAATAAATT
* * * **
3963630 CCACTATCTATAAATAGATGACCAC-CTAAGAACTTTGCAACTCAAATAGGCCTAAAAACTA-TG
66 CCACTATCTATCAATAGATGACCACTC-AAGAACTTTGCAAATCAAAGAGGCCCGAAAACTACTG
* * * * ** *
3963693 AACAAATACCATTATCTATTCATAGAGCATTACGTGCCTAGTTGATAGTTATCACATAACTAATG
130 -ATAGATACCACTATCTATTCATAGAGCATTACGTGCCTAGTTGATAGTCATTGCATAACTAAGG
* * * * *
3963758 TATTGTGTGGCTGGTTTTTAGTCATTGCATAACTTAGACATTGCATGAATAGGGTGAAGTCATTG
194 CATTGTGTGGCTAGTTTTTAATCATTGCATAACTTAGACATTGCGTGAATAGGGTGTAGTCATTG
3963823 TGTGACTTGTTGATAAGGTATCGCATGACTAGTTGGTA
259 TGTGACTTGTTGATAAGGTATCGCATGACTAGTTGGTA
** * * * * *
3963861 AACATTAAGTAACTTGTTTATTGAAGCATGTGAA-AACAATTTGGATCAACATCTA-CTAATAAA
1 GGCATTAAGTGACTTATTTGTTGAAGCATGTGAAGCA-AATTTGGATGAACATCTATC-AATAAA
* * ** * * * *
3963924 TTCCACTATTTGTCGCTAGATGACCACCCAAGAACTTTGCAAATCAAAGAAGCCTGAAAACTATT
64 TTCCACTATCTATCAATAGATGACCACTCAAGAACTTTGCAAATCAAAGAGGCCCGAAAACTACT
* * * *
3963989 GATAGATATCACTATCTATTGATAGGGCATTACGTGCCTAGTTGAGAGTCATTGCATAACTAAGG
129 GATAGATACCACTATCTATTCATAGAGCATTACGTGCCTAGTTGATAGTCATTGCATAACTAAGG
* * * * * *
3964054 CATTGTGTGGCCAGTTTTTAATCATTACATAACTTAGGCATTGTGTGAAT-GAAGAGTAGTCATT
194 CATTGTGTGGCTAGTTTTTAATCATTGCATAACTTAGACATTGCGTGAATAG-GGTGTAGTCATT
** * *
3964118 GTGTTTCTTGTTGATAGGGTATCGCGA-CACTAGTTGGTA
258 GTGTGACTTGTTGATAAGGTATCGC-ATGACTAGTTGGTA
** * * * * ** * * *
3964157 AACGTTACGTGACTTATTTGTTAAAGCATGTAAAGGTAATTTGGATGAATATTTATCAATAGA-T
1 GGCATTAAGTGACTTATTTGTTGAAGCATGTGAAGCAAATTTGGATGAACATCTATCAATAAATT
* * * * * *
3964221 CCACTATTTATCGATAGATGAGCACTCGAGAACTTTGCAAATCAAAGAGGCCCGGAAACTACCGA
66 CCACTATCTATCAATAGATGACCACTCAAGAACTTTGCAAATCAAAGAGGCCCGAAAACTACTGA
* * * *
3964286 TAGATACCACAATCTA-TCGATA-AGGCATTACGTGCCTGGTTGATAATCATTGCGTAACTAAGG
131 TAGATACCACTATCTATTC-ATAGA-GCATTACGTGCCTAGTTGATAGTCATTGCATAACTAAGG
* * * * *
3964349 CATTGTGTGGCTAGTTTTTAATCATTGCGTAACTTAGGCATTGTGTGAATATGGTGTAGTTATTG
194 CATTGTGTGGCTAGTTTTTAATCATTGCATAACTTAGACATTGCGTGAATAGGGTGTAGTCATTG
** * *
3964414 CATGACTTGTTGATAAGGTATCG-AGTGATTAATTGGTA
259 TGTGACTTGTTGATAAGGTATCGCA-TGACTAGTTGGTA
3964452 GGCATT
1 GGCATT
3964458 GTGTGTTTTA
Statistics
Matches: 746, Mismatches: 127, Indels: 41
0.82 0.14 0.04
Matches are distributed among these distances:
293 1 0.00
294 1 0.00
295 203 0.27
296 533 0.71
297 8 0.01
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.33
Consensus pattern (296 bp):
GGCATTAAGTGACTTATTTGTTGAAGCATGTGAAGCAAATTTGGATGAACATCTATCAATAAATT
CCACTATCTATCAATAGATGACCACTCAAGAACTTTGCAAATCAAAGAGGCCCGAAAACTACTGA
TAGATACCACTATCTATTCATAGAGCATTACGTGCCTAGTTGATAGTCATTGCATAACTAAGGCA
TTGTGTGGCTAGTTTTTAATCATTGCATAACTTAGACATTGCGTGAATAGGGTGTAGTCATTGTG
TGACTTGTTGATAAGGTATCGCATGACTAGTTGGTA
Found at i:3966657 original size:22 final size:22
Alignment explanation
Indices: 3966624--3966775 Score: 116
Period size: 22 Copynumber: 7.0 Consensus size: 22
3966614 GCTTTAACTT
* *
3966624 CATA-TAAGGCATTGCATGACTG
1 CATATTAA-GCATTGCGTGACTC
*
3966646 GATATTAAGCATTGCGTGACTC
1 CATATTAAGCATTGCGTGACTC
**
3966668 CATAGCAAGCATTGCGTGAC-C
1 CATATTAAGCATTGCGTGACTC
* * *
3966689 TTATATT-AGACATT-TGTGACTG
1 -CATATTAAG-CATTGCGTGACTC
*
3966711 GATATTAAGCATTGCGTGACTC
1 CATATTAAGCATTGCGTGACTC
*
3966733 CATAGTAAGCATTGCGTGAC-C
1 CATATTAAGCATTGCGTGACTC
* * *
3966754 TTATATTAGGCATTGTGTGACT
1 -CATATTAAGCATTGCGTGACT
3966776 AGTTATTATG
Statistics
Matches: 102, Mismatches: 20, Indels: 15
0.74 0.15 0.11
Matches are distributed among these distances:
21 18 0.18
22 81 0.79
23 3 0.03
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (22 bp):
CATATTAAGCATTGCGTGACTC
Found at i:3966744 original size:65 final size:66
Alignment explanation
Indices: 3966640--3966775 Score: 247
Period size: 65 Copynumber: 2.1 Consensus size: 66
3966630 AGGCATTGCA
3966640 TGACTGGATATTAAGCATTGCGTGACTCCATAGCAAGCATTGCGTGACCTTATATTAGACATT-T
1 TGACTGGATATTAAGCATTGCGTGACTCCATAGCAAGCATTGCGTGACCTTATATTAGACATTGT
3966704 G
66 G
* *
3966705 TGACTGGATATTAAGCATTGCGTGACTCCATAGTAAGCATTGCGTGACCTTATATTAGGCATTGT
1 TGACTGGATATTAAGCATTGCGTGACTCCATAGCAAGCATTGCGTGACCTTATATTAGACATTGT
3966770 G
66 G
3966771 TGACT
1 TGACT
3966776 AGTTATTATG
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
65 61 0.90
66 7 0.10
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (66 bp):
TGACTGGATATTAAGCATTGCGTGACTCCATAGCAAGCATTGCGTGACCTTATATTAGACATTGT
G
Found at i:3969419 original size:42 final size:42
Alignment explanation
Indices: 3969344--3969426 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
3969334 GTATATTGGA
* *
3969344 TCATTGCATTGAACATCTTCTAAAATAACAGTTGTAGCATGG
1 TCATCGCATTGAACATCTTCTAAAACAACAGTTGTAGCATGG
* * * * *
3969386 TCATCGCATTGAACATTTTTTAACACAATAGTTGTGGCATG
1 TCATCGCATTGAACATCTTCTAAAACAACAGTTGTAGCATG
3969427 TTTTGTACTG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (42 bp):
TCATCGCATTGAACATCTTCTAAAACAACAGTTGTAGCATGG
Found at i:3970352 original size:22 final size:22
Alignment explanation
Indices: 3970320--3970396 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 22
3970310 AAACTAGTCA
3970320 CGTAATGCCTAAAAATCAATCT
1 CGTAATGCCTAAAAATCAATCT
* * *
3970342 CGTAATTCCT-AGAATCTAGTCAT
1 CGTAATGCCTAAAAATC-AATC-T
*
3970365 -GCAATGCCTAAAAATCAATCT
1 CGTAATGCCTAAAAATCAATCT
*
3970386 TGTAATGCCTA
1 CGTAATGCCTA
3970397 TAACTTAATC
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
21 6 0.14
22 31 0.72
23 6 0.14
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (22 bp):
CGTAATGCCTAAAAATCAATCT
Found at i:3970376 original size:44 final size:44
Alignment explanation
Indices: 3970313--3970396 Score: 132
Period size: 44 Copynumber: 1.9 Consensus size: 44
3970303 GCCTAACAAA
* *
3970313 CTAGTCACGTAATGCCTAAAAATCAATCTCGTAATTCCTAGAAT
1 CTAGTCACGCAATGCCTAAAAATCAATCTCGTAATGCCTAGAAT
* *
3970357 CTAGTCATGCAATGCCTAAAAATCAATCTTGTAATGCCTA
1 CTAGTCACGCAATGCCTAAAAATCAATCTCGTAATGCCTA
3970397 TAACTTAATC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.30
Consensus pattern (44 bp):
CTAGTCACGCAATGCCTAAAAATCAATCTCGTAATGCCTAGAAT
Found at i:3971886 original size:19 final size:19
Alignment explanation
Indices: 3971862--3971907 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
3971852 AATAAGATTT
3971862 CTTTCTCTCCCCTTAAATA
1 CTTTCTCTCCCCTTAAATA
* *
3971881 CTTTCTTTCCCTTTAAATA
1 CTTTCTCTCCCCTTAAATA
3971900 CTTTCTCT
1 CTTTCTCT
3971908 TATATTTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.17, C:0.33, G:0.00, T:0.50
Consensus pattern (19 bp):
CTTTCTCTCCCCTTAAATA
Done.