Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001838.1 Hibiscus syriacus cultivar Beakdansim tig00003721_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: 3924084
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 18
Found at i:3270957 original size:41 final size:41
Alignment explanation
Indices: 3270915--3270993 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 41
3270905 AACATTTATA
* *
3270915 TTTAATAAAATAAT-TATGTAAAACATAATATATAAAAAATAT
1 TTTAA-AAAATAATATATATAAAA-AAAATATATAAAAAATAT
*
3270957 TTTAAAAAATAATATATATAAAAAAAATATTTAAAAA
1 TTTAAAAAATAATATATATAAAAAAAATATATAAAAA
3270994 GAATAAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
41 20 0.61
42 13 0.39
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (41 bp):
TTTAAAAAATAATATATATAAAAAAAATATATAAAAAATAT
Found at i:3270999 original size:31 final size:30
Alignment explanation
Indices: 3270942--3271007 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
3270932 GTAAAACATA
* * *
3270942 ATATATAAAAAATATTTTAAAAAATAATAT
1 ATATAAAAAAAATATTTAAAAAAATAAAAT
3270972 ATATAAAAAAAATATTTAAAAAGAATAAAAT
1 ATATAAAAAAAATATTTAAAAA-AATAAAAT
3271003 ATATA
1 ATATA
3271008 TTTAATTAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 20 0.62
31 12 0.38
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (30 bp):
ATATAAAAAAAATATTTAAAAAAATAAAAT
Found at i:3272766 original size:3 final size:3
Alignment explanation
Indices: 3272758--3272876 Score: 161
Period size: 3 Copynumber: 39.7 Consensus size: 3
3272748 GTTCACATTT
* **
3272758 TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA ATA -TA TTA TTA TTA AGA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
3272804 TTA TTA TTA ATA TTA ATA TTA TATA TTA TATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA T-TA TTA TTA TTA TTA TTA
3272851 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
3272877 TAAATATATA
Statistics
Matches: 103, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
2 4 0.04
3 93 0.90
4 6 0.06
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:3274287 original size:2 final size:2
Alignment explanation
Indices: 3274275--3274319 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
3274265 TTATTTTTAT
* * *
3274275 TA TA TA AA TA TA TG TA TG TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3274317 TA T
1 TA T
3274320 GTAAATTATT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3275793 original size:9 final size:10
Alignment explanation
Indices: 3275768--3275792 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3275758 TTTCATAATA
3275768 TTTTTTATTT
1 TTTTTTATTT
3275778 TTTTTTATTT
1 TTTTTTATTT
3275788 TTTTT
1 TTTTT
3275793 ACTTTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTATTT
Found at i:3283247 original size:70 final size:73
Alignment explanation
Indices: 3283081--3283254 Score: 194
Period size: 70 Copynumber: 2.4 Consensus size: 73
3283071 ATCAACAAGA
* * *
3283081 AGCAAATGTTGGGGTATGCTGAAAACCCATTTCAATCATAATCAGGAATATTGACGAGTTTTGAA
1 AGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAAAATCAGGAATA-T-ACGAGTTTTGAA
* *
3283146 TATTCACGTC
64 CATTCACATC
* * *
3283156 AACAAATGTTGGGGCATGCTGAAAGCCCATTTTAATCAGAAAT-TGGAATA-AC-A-TTTTGAAC
1 AGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCA-AAATCAGGAATATACGAGTTTTGAAC
* *
3283217 GTTCATATC
65 ATTCACATC
*
3283226 AGCAAATGTTGGGGCATGCTGAAGGCCCA
1 AGCAAATGTTGGGGCATGCTGAAAGCCCA
3283255 CATCATTATG
Statistics
Matches: 86, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
70 40 0.47
71 1 0.01
72 2 0.02
75 40 0.47
76 3 0.03
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (73 bp):
AGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAAAATCAGGAATATACGAGTTTTGAACA
TTCACATC
Found at i:3284562 original size:20 final size:22
Alignment explanation
Indices: 3284516--3284573 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
3284506 TACATCTACA
3284516 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
3284538 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
* *
3284560 CTTTTCGAAGATGA
1 CTCTTCAAAGATGA
3284574 CAGCTTTATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (22 bp):
CTCTTCAAAGATGATAGATTCT
Found at i:3286013 original size:73 final size:73
Alignment explanation
Indices: 3285244--3285986 Score: 1209
Period size: 73 Copynumber: 10.0 Consensus size: 73
3285234 CTATTTCCCA
* *
3285244 CATCTGTAAGTCCTACAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGACCTACAGTGCATGATGTTTT-CAAAAAGCCTTCGGGAGCTTTTTGA--TCTT-A
*
3285309 AAGCCTCAGGTT
62 AAGCCTCAGGGT
* *
3285321 CATCTATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAATC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
3285386 CTCAGGGT
66 CTCAGGGT
*
3285394 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAATC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
3285459 CTCAGGGT
66 CTCAGGGT
*
3285467 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAACC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
3285532 CTCAGGGT
66 CTCAGGGT
*
3285540 CATCTGTAAGACCAACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAG-TATTTTGATCTTAAAG
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCT-TTTTGATCTTAAAG
*
3285604 CCTCAGGAT
65 CCTCAGGGT
*
3285613 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAATC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
3285678 CTCAGGGT
66 CTCAGGGT
* *
3285686 CATCTATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAATC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
*
3285751 CTCGGGGT
66 CTCAGGGT
* *
3285759 CATCTGTAAGACCTACAGTGCATGATATTTTCAAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTT
1 CATCTGTAAGACCTACAGTGCATGATGTTTTC--AAAAAGCCTTCGGGAGCTTTTTGA---TCTT
*
3285824 AAACCCTCAGGGT
61 AAAGCCTCAGGGT
3285837 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
*
3285902 CTCAGTGT
66 CTCAGGGT
* *
3285910 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAACTTTTTGATTTTAAAAG
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTT-AAAG
3285975 CCTCAGGGT
65 CCTCAGGGT
3285984 CAT
1 CAT
3285987 TCATAAGACC
Statistics
Matches: 631, Mismatches: 27, Indels: 19
0.93 0.04 0.03
Matches are distributed among these distances:
72 1 0.00
73 464 0.74
74 19 0.03
75 24 0.04
76 49 0.08
77 29 0.05
78 45 0.07
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (73 bp):
CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
CTCAGGGT
Found at i:3286152 original size:3 final size:3
Alignment explanation
Indices: 3286146--3286223 Score: 124
Period size: 3 Copynumber: 26.7 Consensus size: 3
3286136 CACATTTTTT
**
3286146 TTA TTA TTA TTA TTA TT- TTA TTA TTA TTA TTA AGA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3286193 TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3286224 TAAATATATA
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
2 4 0.06
3 65 0.94
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:3286276 original size:22 final size:23
Alignment explanation
Indices: 3286246--3286288 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
3286236 ACAAATTATA
*
3286246 ATCAGACCCAGA-AGGCCCAAAT
1 ATCAAACCCAGACAGGCCCAAAT
*
3286268 ATCAAACCCAGACTGGCCCAA
1 ATCAAACCCAGACAGGCCCAA
3286289 CAATAAACCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.40, C:0.35, G:0.16, T:0.09
Consensus pattern (23 bp):
ATCAAACCCAGACAGGCCCAAAT
Found at i:3286882 original size:28 final size:28
Alignment explanation
Indices: 3286840--3286902 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
3286830 GAGGGTTATT
*
3286840 AGGAAAAACTGGGCTTGGATTTAGGACA
1 AGGAAAAACTGGGCTTCGATTTAGGACA
*
3286868 AGGGAAAA-TCGGGCTTCGATTTAGGACA
1 AGGAAAAACT-GGGCTTCGATTTAGGACA
3286896 AGGAAAA
1 AGGAAAA
3286903 GAGGAAAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 1 0.03
28 30 0.97
ACGTcount: A:0.38, C:0.11, G:0.32, T:0.19
Consensus pattern (28 bp):
AGGAAAAACTGGGCTTCGATTTAGGACA
Found at i:3287481 original size:14 final size:14
Alignment explanation
Indices: 3287462--3287491 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3287452 TTATTTTTAT
3287462 TATATAAATATATG
1 TATATAAATATATG
*
3287476 TATATATATATATG
1 TATATAAATATATG
3287490 TA
1 TA
3287492 AATTATTACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (14 bp):
TATATAAATATATG
Found at i:3294774 original size:2 final size:2
Alignment explanation
Indices: 3294769--3294794 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3294759 AAAACAATCA
3294769 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
3294795 TTATCGGCTA
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):
AT
Found at i:3320502 original size:78 final size:77
Alignment explanation
Indices: 3320356--3320505 Score: 221
Period size: 78 Copynumber: 1.9 Consensus size: 77
3320346 AAGGTAATGG
* * *
3320356 TATATAAAAGACTTTTAAGATGATGCAATGAATATCATCTATAGCTGTTACCAAGGTAATTAATG
1 TATATAAAAGACCTTTAAGATGATACAATGAATATCATCTATAGCTGTTACCAAGGCAATTAATG
3320421 GTAGAGTCGTTT
66 GTAGAGTCGTTT
* * *
3320433 TATATTAAATGACCTTTGAGATGATACAATGAATCTCATCTACT-GCTGTTACCAAGGCAATTAA
1 TATA-TAAAAGACCTTTAAGATGATACAATGAATATCATCTA-TAGCTGTTACCAAGGCAATTAA
3320497 TGGTAGAGT
64 TGGTAGAGT
3320506 TAGTAGCACA
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
77 4 0.06
78 60 0.92
79 1 0.02
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (77 bp):
TATATAAAAGACCTTTAAGATGATACAATGAATATCATCTATAGCTGTTACCAAGGCAATTAATG
GTAGAGTCGTTT
Found at i:3321508 original size:14 final size:15
Alignment explanation
Indices: 3321474--3321516 Score: 70
Period size: 14 Copynumber: 2.9 Consensus size: 15
3321464 ATAGTATTCA
3321474 GTAGAAAACAGACTGT
1 GTAGAAAACAGAC-GT
3321490 GTAGAAAACAGAC-T
1 GTAGAAAACAGACGT
3321504 GTAGAAAACAGAC
1 GTAGAAAACAGAC
3321517 AAGTCTGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 14 0.52
16 13 0.48
ACGTcount: A:0.49, C:0.14, G:0.23, T:0.14
Consensus pattern (15 bp):
GTAGAAAACAGACGT
Found at i:3325572 original size:14 final size:14
Alignment explanation
Indices: 3325553--3325580 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3325543 CCTTATACCA
3325553 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
3325567 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
3325581 AAGTCTGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.21, T:0.14
Consensus pattern (14 bp):
TGTAGAAAACAGAC
Found at i:3326620 original size:138 final size:138
Alignment explanation
Indices: 3326363--3326626 Score: 492
Period size: 138 Copynumber: 1.9 Consensus size: 138
3326353 CTTTATTGGG
*
3326363 TAAACTAGGTGAATGGGTCATTAAAATTTGAGTAAATTTTCAATTGTTCCACTTTACTTTCAAAA
1 TAAACTAGGTGAATGGGTCATTAAAATTTGAGTAAATTTTCAATTGTTCCACTTAACTTTCAAAA
*
3326428 GTTATAAATTAATTACTAATGTTAAATATTTGTAACAAAATAATCATTCATAGTTAACCTTCAAA
66 GTTATAAATTAATTACTAATGTTAAAGATTTGTAACAAAATAATCATTCATAGTTAACCTTCAAA
3326493 ATAATCAT
131 ATAATCAT
*
3326501 TAAATTAGGTGAATGGGTCATTAAAATTTGAGTAAATTTTCAATTGTTCCACTTAACTTTCAAAA
1 TAAACTAGGTGAATGGGTCATTAAAATTTGAGTAAATTTTCAATTGTTCCACTTAACTTTCAAAA
*
3326566 GTTATAAATTAATTACTAATGTTAAAGATTTGTAACAAAATAATCATTCGTAGTTAACCTT
66 GTTATAAATTAATTACTAATGTTAAAGATTTGTAACAAAATAATCATTCATAGTTAACCTT
3326627 GTTAACAACG
Statistics
Matches: 122, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
138 122 1.00
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.39
Consensus pattern (138 bp):
TAAACTAGGTGAATGGGTCATTAAAATTTGAGTAAATTTTCAATTGTTCCACTTAACTTTCAAAA
GTTATAAATTAATTACTAATGTTAAAGATTTGTAACAAAATAATCATTCATAGTTAACCTTCAAA
ATAATCAT
Found at i:3331832 original size:40 final size:40
Alignment explanation
Indices: 3331770--3331847 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
3331760 GACAATGAAA
3331770 AAAATACAGATCCAGTAAATCCTACTAAAAGAAAAGTACT
1 AAAATACAGATCCAGTAAATCCTACTAAAAGAAAAGTACT
* * * *
3331810 AAAATATAGATCCCGTAGATCCTACTCAAAGAAAAGTA
1 AAAATACAGATCCAGTAAATCCTACTAAAAGAAAAGTA
3331848 AAACACTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.50, C:0.18, G:0.12, T:0.21
Consensus pattern (40 bp):
AAAATACAGATCCAGTAAATCCTACTAAAAGAAAAGTACT
Found at i:3340277 original size:25 final size:25
Alignment explanation
Indices: 3340249--3340306 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
3340239 GAATAATACC
3340249 AAAGGTCAATGGGATAGTTAATATT
1 AAAGGTCAATGGGATAGTTAATATT
3340274 AAAGGTCAATGGGATAGTTAATATT
1 AAAGGTCAATGGGATAGTTAATATT
3340299 AAAGGTCA
1 AAAGGTCA
3340307 TGTTTTGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.41, C:0.05, G:0.24, T:0.29
Consensus pattern (25 bp):
AAAGGTCAATGGGATAGTTAATATT
Found at i:3349871 original size:15 final size:17
Alignment explanation
Indices: 3349851--3349884 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
3349841 TAATTTATTT
3349851 TAATTT-TAAAT-TAAA
1 TAATTTATAAATATAAA
3349866 TAATTTATAAATATAAA
1 TAATTTATAAATATAAA
3349883 TA
1 TA
3349885 TCCCATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 5 0.29
17 6 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTTATAAATATAAA
Found at i:3353323 original size:21 final size:21
Alignment explanation
Indices: 3353286--3353327 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3353276 TTTTCTTTTT
*
3353286 AAAGCAAAATTGGATTTTGAA
1 AAAGCAAAATTGAATTTTGAA
3353307 AAAGCAAAA-TGAAATTTTGAA
1 AAAGCAAAATTG-AATTTTGAA
3353328 CAATGGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.52, C:0.05, G:0.17, T:0.26
Consensus pattern (21 bp):
AAAGCAAAATTGAATTTTGAA
Found at i:3355151 original size:35 final size:35
Alignment explanation
Indices: 3355110--3355205 Score: 117
Period size: 34 Copynumber: 2.8 Consensus size: 35
3355100 TATTAATTTG
* * *
3355110 TATCTGATAACTGTAAAACATATGATATTTGTAAA
1 TATCTGATAACTGTAAAACATCTGATATCTATAAA
*
3355145 TATCTGATAA-T-TATAATCATCTGATATCTATAAA
1 TATCTGATAACTGTA-AAACATCTGATATCTATAAA
3355179 TATCTGATAACTG-AAAATCATCTGATA
1 TATCTGATAACTGTAAAA-CATCTGATA
3355206 ACAGTAAACA
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
33 2 0.04
34 29 0.56
35 21 0.40
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (35 bp):
TATCTGATAACTGTAAAACATCTGATATCTATAAA
Found at i:3355166 original size:17 final size:17
Alignment explanation
Indices: 3355146--3355206 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
3355136 ATTTGTAAAT
3355146 ATCTGATAATTATAATC
1 ATCTGATAATTATAATC
3355163 ATCTGAT-ATCTATAAAT-
1 ATCTGATAAT-TAT-AATC
* *
3355180 ATCTGATAACTGAAAATC
1 ATCTGATAA-TTATAATC
3355198 ATCTGATAA
1 ATCTGATAA
3355207 CAGTAAACAT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
16 2 0.05
17 20 0.54
18 14 0.38
19 1 0.03
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.36
Consensus pattern (17 bp):
ATCTGATAATTATAATC
Found at i:3364372 original size:64 final size:66
Alignment explanation
Indices: 3364218--3364377 Score: 202
Period size: 65 Copynumber: 2.5 Consensus size: 66
3364208 AATTAAATTG
* * *
3364218 AACATCGAATGCATTTCATGCATCGATGCA-CATACCATACACCGATGCATTGAGGATTTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACCATACCATACACCGATGCACTCAGGATTTTATGA
3364282 A
66 A
* * * * *
3364283 AACATCGAATGCATTTGATGCATCGATGCACCA-GCCATGCATCGATGCACTCTGGCTATTT-TG
1 AACATCGAATGCATTTGATGCATCGATGCACCATACCATACACCGATGCACTCAGGAT-TTTATG
3364346 -A
65 AA
*
3364347 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
3364378 TCTTAGTGCA
Statistics
Matches: 84, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 31 0.37
65 48 0.57
66 5 0.06
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.27
Consensus pattern (66 bp):
AACATCGAATGCATTTGATGCATCGATGCACCATACCATACACCGATGCACTCAGGATTTTATGA
A
Found at i:3365721 original size:21 final size:22
Alignment explanation
Indices: 3365680--3365721 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
3365670 ATGTAGTCTT
*
3365680 GAAGTACACTTCTCATGCACTA
1 GAAGTACACTTCTCATACACTA
3365702 GAAGT-CACTTCTTCA-ACACT
1 GAAGTACACTTC-TCATACACT
3365722 GACTCTTCGC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.29
Consensus pattern (22 bp):
GAAGTACACTTCTCATACACTA
Found at i:3372386 original size:20 final size:21
Alignment explanation
Indices: 3372358--3372398 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
3372348 GGTTGTGGCT
*
3372358 ATTTTTAGCC-ATTGGGGATG
1 ATTTCTAGCCTATTGGGGATG
*
3372378 ATTTCTAGCCTTTTGGGGATG
1 ATTTCTAGCCTATTGGGGATG
3372399 TTTTATCTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.17, C:0.12, G:0.29, T:0.41
Consensus pattern (21 bp):
ATTTCTAGCCTATTGGGGATG
Found at i:3372458 original size:21 final size:21
Alignment explanation
Indices: 3372426--3372465 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
3372416 AACTGCCCAA
3372426 TATAGAGGGTATCGATACTTC
1 TATAGAGGGTATCGATACTTC
3372447 TATAG-GGAGTATCGATACT
1 TATAGAGG-GTATCGATACT
3372466 ACCTTTGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (21 bp):
TATAGAGGGTATCGATACTTC
Found at i:3396125 original size:11 final size:11
Alignment explanation
Indices: 3396109--3396165 Score: 57
Period size: 11 Copynumber: 5.4 Consensus size: 11
3396099 AAAATTATAT
3396109 TATTAAAAATA
1 TATTAAAAATA
3396120 TATTAAAAATA
1 TATTAAAAATA
* **
3396131 CATTATTAATA
1 TATTAAAAATA
3396142 -ATTATAAAAT-
1 TATTA-AAAATA
3396152 T-TTAAAAATA
1 TATTAAAAATA
3396162 TATT
1 TATT
3396166 TTTAAATATA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
9 5 0.14
10 8 0.22
11 24 0.65
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:3396125 original size:25 final size:24
Alignment explanation
Indices: 3396097--3396152 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
3396087 TTTAAATTTT
*
3396097 TTAAAATTATATTATTAAAAATATA
1 TTAAAATTACATTATTAAAAAT-TA
* *
3396122 TTAAAAATACATTATTAATAATTA
1 TTAAAATTACATTATTAAAAATTA
3396146 -TAAAATT
1 TTAAAATT
3396153 TTAAAAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 6 0.22
24 2 0.07
25 19 0.70
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
TTAAAATTACATTATTAAAAATTA
Found at i:3396170 original size:14 final size:14
Alignment explanation
Indices: 3396094--3396171 Score: 54
Period size: 14 Copynumber: 5.6 Consensus size: 14
3396084 AATTTTAAAT
*
3396094 TTTTTAAAATTATA
1 TTTTTAAAAATATA
*
3396108 TTATTAAAAATATA
1 TTTTTAAAAATATA
*
3396122 ---TTAAAAATACA
1 TTTTTAAAAATATA
* *
3396133 TTATTAATAATTATAAA
1 TTTTTAA-AA--ATATA
*
3396150 ATTTTAAAAATATA
1 TTTTTAAAAATATA
3396164 TTTTTAAA
1 TTTTTAAA
3396172 TATAATATAA
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
11 10 0.20
14 27 0.54
15 2 0.04
16 2 0.04
17 9 0.18
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (14 bp):
TTTTTAAAAATATA
Found at i:3396181 original size:33 final size:31
Alignment explanation
Indices: 3396122--3396187 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
3396112 TAAAAATATA
*
3396122 TTAAAAATACATTATTAATAATTATAAAATT
1 TTAAAAATACATTATTAATAAATATAAAATT
* * *
3396153 TTAAAAATATATTTTTAAATATAATATAAGATT
1 TTAAAAATACATTATT-AATA-AATATAAAATT
3396186 TT
1 TT
3396188 TGTATGTTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 14 0.48
32 4 0.14
33 11 0.38
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (31 bp):
TTAAAAATACATTATTAATAAATATAAAATT
Found at i:3396235 original size:17 final size:17
Alignment explanation
Indices: 3396210--3396244 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3396200 TTCGAGTTTA
*
3396210 AGTTCGAGCTTGAATCG
1 AGTTCGAGCTTCAATCG
*
3396227 AGTTTGAGCTTCAATCG
1 AGTTCGAGCTTCAATCG
3396244 A
1 A
3396245 ACTCAAAATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (17 bp):
AGTTCGAGCTTCAATCG
Found at i:3398990 original size:40 final size:35
Alignment explanation
Indices: 3398946--3399375 Score: 269
Period size: 37 Copynumber: 11.8 Consensus size: 35
3398936 AGTTTGAAGT
3398946 CATTTTGAAATTATATAATATATAGTTTTGTAAAACAAAA
1 CATTTTGAAATTATATAATATATAGTTTTGT-----AAAA
* *
3398986 CATTTTGAAAGTATATAATATATGGTTTT-TAAAA
1 CATTTTGAAATTATATAATATATAGTTTTGTAAAA
*
3399020 CATTTTGAAAATTTATATAATATATAGTTTTG-AAAT
1 CATTTTG-AAA-TTATATAATATATAGTTTTGTAAAA
3399056 CATTTTGAAAATATATATATAATATATAGTTTT-TAAAA
1 CATTTTG--AA-AT-TATATAATATATAGTTTTGTAAAA
*
3399094 CATTTTTTTAAAAACTTATATAATATATAGTTTT-TAAAA
1 CA---TTTT-GAAA-TTATATAATATATAGTTTTGTAAAA
*
3399133 CATTTTAAAAAACTTATATAATATATAGTTTT-TAAAA
1 CATTTT--GAAA-TTATATAATATATAGTTTTGTAAAA
*
3399170 CATTTTGAAAAACTTATATAATATATAGTTTT-AAAAA
1 CATTTTG--AAA-TTATATAATATATAGTTTTGTAAAA
* * *
3399207 CATTTTTAAAAAATTATATAATATATAGATTT-AAAAA
1 CA-TTTT--GAAATTATATAATATATAGTTTTGTAAAA
* * * *
3399244 TATTTTTAAA--A-ACTTATATAATA-TTTT-TAAAT
1 CATTTTGAAATTATA-TAATAT-ATAGTTTTGTAAAA
* *
3399276 CATTTTTACAAAACTATATAATATATAGTTTTG-AAAA
1 CA-TTTT--GAAATTATATAATATATAGTTTTGTAAAA
* ** * *
3399313 C-TTTTTAAAAAATTTAATATATAGTTTT-AAAAA
1 CATTTTGAAATTATATAATATATAGTTTTGTAAAA
* *
3399346 TAATTTTGAAATATATATATTATATAGTTT
1 -CATTTTGAAAT-TATATAATATATAGTTT
3399376 ATGTTATATT
Statistics
Matches: 327, Mismatches: 31, Indels: 68
0.77 0.07 0.16
Matches are distributed among these distances:
31 1 0.00
32 13 0.04
33 30 0.09
34 14 0.04
35 17 0.05
36 52 0.16
37 107 0.33
38 32 0.10
39 27 0.08
40 30 0.09
41 4 0.01
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (35 bp):
CATTTTGAAATTATATAATATATAGTTTTGTAAAA
Found at i:3399036 original size:76 final size:72
Alignment explanation
Indices: 3398946--3399375 Score: 334
Period size: 74 Copynumber: 5.9 Consensus size: 72
3398936 AGTTTGAAGT
*
3398946 CATTTTG-AAA-TTATATAATATATAGTTTTGTAAAACAAAACATTTTGAAA-GTATATAATATA
1 CATTTTGAAAACTTATATAATATATAGTTTTGT-----AAAACATTTTGAAACATATATAATATA
*
3399008 TGGTTTTTAAAA
61 TAGTTTTTAAAA
* * *
3399020 CATTTTGAAAATTTATATAATATATAGTTTTG-AAATCATTTTGAAAATATATATATAATATATA
1 CATTTTGAAAACTTATATAATATATAGTTTTGTAAAACATTTTG--AA-ACATATATAATATATA
3399084 GTTTTTAAAA
63 GTTTTTAAAA
* * *
3399094 CATTTTTTTAAAAACTTATATAATATATAGTTTT-TAAAACATTTTAAAAAACTTATATAATATA
1 CA---TTTTGAAAACTTATATAATATATAGTTTTGTAAAACATTTT--GAAACATATATAATATA
3399158 TAGTTTTTAAAA
61 TAGTTTTTAAAA
* * *
3399170 CATTTTGAAAAACTTATATAATATATAGTTTT-AAAAACATTTTTAAAAAATTATATAATATATA
1 CATTTTG-AAAACTTATATAATATATAGTTTTGTAAAACA-TTTTGAAACA-TATATAATATATA
* *
3399234 GATTTAAAAA
63 GTTTTTAAAA
* * * * *
3399244 TATTTTTAAAAAC-T-TAT-ATA-ATA-TTTT-TAAATCATTTTTACAAAACTATATAATATATA
1 CA-TTTTGAAAACTTATATAATATATAGTTTTGTAAAACATTTTGA-AACA-TATATAATATATA
*
3399303 GTTTTGAAAA
63 GTTTTTAAAA
* * * * * * *
3399313 C-TTTTTAAAA--AATTTAATATATAGTTTT-AAAAATAATTTTGAAATATATATATTATATAGT
1 CATTTTGAAAACTTATATAATATATAGTTTTGTAAAA-CATTTTGAAACATATATAATATATAGT
3399374 TT
65 TT
3399376 ATGTTATATT
Statistics
Matches: 301, Mismatches: 33, Indels: 49
0.79 0.09 0.13
Matches are distributed among these distances:
67 10 0.03
68 8 0.03
69 53 0.18
70 23 0.08
71 9 0.03
72 5 0.02
73 10 0.03
74 88 0.29
75 11 0.04
76 46 0.15
77 38 0.13
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (72 bp):
CATTTTGAAAACTTATATAATATATAGTTTTGTAAAACATTTTGAAACATATATAATATATAGTT
TTTAAAA
Found at i:3399144 original size:37 final size:37
Alignment explanation
Indices: 3398997--3399375 Score: 392
Period size: 37 Copynumber: 10.5 Consensus size: 37
3398987 ATTTTGAAAG
* * *
3398997 TATATAATATATGGTTTTTAAAACATTTT-GAAAATT
1 TATATAATATATAGTTTTTAAAACATTTTAAAAAACT
* * *
3399033 TATATAATATATAGTTTTGAAATCATTTTGAAAATA-T
1 TATATAATATATAGTTTTTAAAACATTTT-AAAAAACT
*
3399070 ATATATAATATATAGTTTTTAAAACATTTTTTTAAAAACT
1 -TATATAATATATAGTTTTTAAAACA--TTTTAAAAAACT
3399110 TATATAATATATAGTTTTTAAAACATTTTAAAAAACT
1 TATATAATATATAGTTTTTAAAACATTTTAAAAAACT
*
3399147 TATATAATATATAGTTTTTAAAACATTTTGAAAAACT
1 TATATAATATATAGTTTTTAAAACATTTTAAAAAACT
*
3399184 TATATAATATATAGTTTTAAAAACATTTTTAAAAAA-T
1 TATATAATATATAGTTTTTAAAACA-TTTTAAAAAACT
* * * *
3399221 TATATAATATATAGATTTAAAAATATTTTTAAAAAC-
1 TATATAATATATAGTTTTTAAAACATTTTAAAAAACT
* *
3399257 T-TAT-ATA-ATA-TTTTTAAATCATTTTTACAAAAC-
1 TATATAATATATAGTTTTTAAAACA-TTTTAAAAAACT
* *
3399290 TATATAATATATAGTTTTGAAAACTTTTTAAAAAA--
1 TATATAATATATAGTTTTTAAAACATTTTAAAAAACT
* * * *
3399325 T-T-TAATATATAGTTTTAAAAATAATTTTGAAATA--
1 TATATAATATATAGTTTTTAAAA-CATTTTAAAAAACT
*
3399359 TATATATTATATAGTTT
1 TATATAATATATAGTTT
3399376 ATGTTATATT
Statistics
Matches: 295, Mismatches: 32, Indels: 32
0.82 0.09 0.09
Matches are distributed among these distances:
32 7 0.02
33 31 0.11
34 16 0.05
35 8 0.03
36 60 0.20
37 104 0.35
38 35 0.12
39 29 0.10
40 5 0.02
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (37 bp):
TATATAATATATAGTTTTTAAAACATTTTAAAAAACT
Found at i:3399385 original size:19 final size:17
Alignment explanation
Indices: 3399361--3399427 Score: 59
Period size: 19 Copynumber: 3.8 Consensus size: 17
3399351 TTGAAATATA
3399361 TATATTATATAGTTTATGT
1 TATATTAT-TA-TTTATGT
3399380 TATATTATTA-TTA-G-
1 TATATTATTATTTATGT
*
3399394 TATATTATTTATTTTATTT
1 TATATTA-TTA-TTTATGT
3399413 TATATTATTCATTTA
1 TATATTATT-ATTTA
3399428 ATTTTATTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 13
0.75 0.02 0.24
Matches are distributed among these distances:
14 7 0.17
15 4 0.10
16 3 0.07
17 3 0.07
18 8 0.20
19 16 0.39
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.63
Consensus pattern (17 bp):
TATATTATTATTTATGT
Found at i:3399431 original size:19 final size:19
Alignment explanation
Indices: 3399394--3399440 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
3399384 TTATTATTAG
* *
3399394 TATATTATTTATTTTATTT
1 TATATTATTCATTTAATTT
3399413 TATATTATTCATTTAATTT
1 TATATTATTCATTTAATTT
*
3399432 TATTTTATT
1 TATATTATT
3399441 TTTTCAGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (19 bp):
TATATTATTCATTTAATTT
Found at i:3399443 original size:6 final size:5
Alignment explanation
Indices: 3399401--3399442 Score: 50
Period size: 5 Copynumber: 8.6 Consensus size: 5
3399391 TAGTATATTA
* * *
3399401 TTTAT TTTAT TTTAT ATTA- TTCAT TTAAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
3399443 TTCAGTTTAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
4 2 0.06
5 29 0.94
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (5 bp):
TTTAT
Found at i:3399451 original size:24 final size:24
Alignment explanation
Indices: 3399396--3399439 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
3399386 ATTATTAGTA
3399396 TATT-ATTT-ATTTTATTTTATAT
1 TATTCATTTAATTTTATTTTATAT
3399418 TATTCATTTAATTTTATTTTAT
1 TATTCATTTAATTTTATTTTAT
3399440 TTTTTCAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 4 0.20
23 4 0.20
24 12 0.60
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (24 bp):
TATTCATTTAATTTTATTTTATAT
Found at i:3400522 original size:2 final size:2
Alignment explanation
Indices: 3400515--3400541 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3400505 TTTATTTTAT
3400515 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3400542 GTTTTTTCGG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3400590 original size:18 final size:18
Alignment explanation
Indices: 3400567--3400635 Score: 50
Period size: 18 Copynumber: 3.6 Consensus size: 18
3400557 TTAATTTATT
3400567 TTTTTTTATTTGTATTTG
1 TTTTTTTATTTGTATTTG
* *
3400585 TTTTTTCATTTTGT-TTTT
1 TTTTTTTA-TTTGTATTTG
*
3400603 TCCTTTGATTTATTTTTATTTG
1 T--TTT--TTTATTTGTATTTG
*
3400625 TTTATTTATTT
1 TTTTTTTATTT
3400636 TTAATTTGGT
Statistics
Matches: 39, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
18 18 0.46
19 5 0.13
20 5 0.13
21 4 0.10
22 7 0.18
ACGTcount: A:0.12, C:0.04, G:0.07, T:0.77
Consensus pattern (18 bp):
TTTTTTTATTTGTATTTG
Found at i:3400597 original size:19 final size:16
Alignment explanation
Indices: 3400563--3400653 Score: 55
Period size: 15 Copynumber: 5.6 Consensus size: 16
3400553 TTATTTAATT
3400563 TATTTTTTTTTATTTG
1 TATTTTTTTTTATTTG
3400579 TATTTGTTTTTTCA-TT-
1 TATTT-TTTTTT-ATTTG
* **
3400595 T-TGTTTTTTCCTTTG
1 TATTTTTTTTTATTTG
*
3400610 -ATTTATTTTTATTTG
1 TATTTTTTTTTATTTG
*
3400625 TTTATTTATTTTTAATTTGG
1 --TATTT-TTTTTTATTT-G
3400645 TATTTTTTT
1 TATTTTTTT
3400654 AAAAAAATTA
Statistics
Matches: 56, Mismatches: 9, Indels: 19
0.67 0.11 0.23
Matches are distributed among these distances:
14 7 0.12
15 12 0.21
16 6 0.11
17 12 0.21
18 10 0.18
19 8 0.14
20 1 0.02
ACGTcount: A:0.13, C:0.03, G:0.08, T:0.76
Consensus pattern (16 bp):
TATTTTTTTTTATTTG
Found at i:3400648 original size:18 final size:18
Alignment explanation
Indices: 3400610--3400653 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
3400600 TTTTCCTTTG
*
3400610 ATTTATTTTTATTTGTTT
1 ATTTATTTTTATTTGTGT
3400628 ATTTATTTTTAATTTG-GT
1 ATTTATTTTT-ATTTGTGT
3400646 ATTT-TTTT
1 ATTTATTTT
3400654 AAAAAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 15 0.62
19 5 0.21
ACGTcount: A:0.18, C:0.00, G:0.07, T:0.75
Consensus pattern (18 bp):
ATTTATTTTTATTTGTGT
Found at i:3403571 original size:95 final size:95
Alignment explanation
Indices: 3403382--3403564 Score: 312
Period size: 95 Copynumber: 1.9 Consensus size: 95
3403372 ATTATATATA
* * * *
3403382 TATATACAATAAAGCTTGAGTTGTCCTTCTAGAGTAATTGGTTTAACGCCCCGGCTTTATGGATA
1 TATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAGCTTTATGGATA
*
3403447 AGATTCAGCTAGCCTGATAAAGGCTATTAT
66 AGATTCAACTAGCCTGATAAAGGCTATTAT
3403477 TATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAGCTTTATGGATA
1 TATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAGCTTTATGGATA
*
3403542 ATATTCAACTAGCCTGATAAAGG
66 AGATTCAACTAGCCTGATAAAGG
3403565 TGATTATAAT
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
95 82 1.00
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (95 bp):
TATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAGCTTTATGGATA
AGATTCAACTAGCCTGATAAAGGCTATTAT
Found at i:3404878 original size:80 final size:81
Alignment explanation
Indices: 3404532--3405554 Score: 1176
Period size: 80 Copynumber: 12.4 Consensus size: 81
3404522 ACGAATCCAG
* * * ** * *
3404532 TACATCATAACTCAAGGCGAGAAGGTTTATCTGTCAACCAAGACCTTCGAGTTCAATTACACTCA
1 TACAGCATAGCTCAAGGCAAGAAGGGCTATCTG-C-ACAAAGACCTTCGAGTTCGATTACACTCA
*
3404597 GCTCAAAGGTACATCATT
64 GCTCAAAGGCACATCATT
* * * * *
3404615 TGCAGCATAGCTCAAGCCAATG-AGAGATATCTTCCAACAAAGACCTTCGAGTTCGATTACACTC
1 TACAGCATAGCTCAAGGCAA-GAAGGGCTATC-TGC-ACAAAGACCTTCGAGTTCGATTACACTC
3404679 AGCTCAAAGGCACATCATT
63 AGCTCAAAGGCACATCATT
* * * * *
3404698 TATAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCA
1 TACAGCATAGCTCAAGGCAAGAAGGGCTATCTG-C-ACAAAGACCTTCGAGTTCGATTACACTCA
*
3404763 GCT-AAAGGCATATCATT
64 GCTCAAAGGCACATCATT
* *
3404780 TGCAGCATAGCTCAAGGCAATAAGGGCTATCTGC-CAAAGACCTTCGAGTTCGATTACACTCAGC
1 TACAGCATAGCTCAAGGCAAGAAGGGCTATCTGCACAAAGACCTTCGAGTTCGATTACACTCAGC
* *
3404844 TCAAAGGTAAATCATT
66 TCAAAGGCACATCATT
* * * *
3404860 TGCAACATAGCTCAAGGCAAGAAGGGCTATTTACCAACAAAAGACCTTCGAGTTCGATTACACTC
1 TACAGCATAGCTCAAGGCAAGAAGGGCTATCT-GC-AC-AAAGACCTTCGAGTTCGATTACACTC
* * *
3404925 AACTTAAAGACACATCATT
63 AGCTCAAAGGCACATCATT
* * *
3404944 TACAGCATAGTTCAAGGCAAGAAGGGTTATCTGC-CAAAGACCTTCGAGTTCGATTACACTCAAC
1 TACAGCATAGCTCAAGGCAAGAAGGGCTATCTGCACAAAGACCTTCGAGTTCGATTACACTCAGC
3405008 TCAAAGGCACATCATT
66 TCAAAGGCACATCATT
* * * *
3405024 TATAGTATAGCTCAAGGCAAGAAGGGCTATCTACCAACAAAAGACCTTCGAGTTTGATTACACTC
1 TACAGCATAGCTCAAGGCAAGAAGGGCTATCT-GC-AC-AAAGACCTTCGAGTTCGATTACACTC
*
3405089 AGCTCAAAGGTACATCATT
63 AGCTCAAAGGCACATCATT
* * * * * * *
3405108 TACAGTATAACTCAAGGCTAGAAGGGTTATCCGTCAACAAAGACCTTCAAGTTTGATTACACTCA
1 TACAGCATAGCTCAAGGCAAGAAGGGCTATCTG-C-ACAAAGACCTTCGAGTTCGATTACACTCA
3405173 GCTCAAAGGCACATCATT
64 GCTCAAAGGCACATCATT
** * *
3405191 TGTAGCATAGCTCAAGGCAAGAAGGGCTACCTG-TCAAAGACCTTCGAGTTCGATTACACTCAGC
1 TACAGCATAGCTCAAGGCAAGAAGGGCTATCTGCACAAAGACCTTCGAGTTCGATTACACTCAGC
3405255 TCAAAGGCACATCATT
66 TCAAAGGCACATCATT
* * * * * * *
3405271 TGCAACATAGCTCAAGGTAAGAAGGGTTATTTACCAACAAAAGACCTTCGAGTTTGATTACACTC
1 TACAGCATAGCTCAAGGCAAGAAGGGCTATCT-GC-AC-AAAGACCTTCGAGTTCGATTACACTC
* *
3405336 AGCTTAAAGACACATCATT
63 AGCTCAAAGGCACATCATT
* * *
3405355 TACAACATAGTTCAAGGCAAGAAGGGCTATCTGC-CAAAGACCTTCGAGTTCGATTACACTCAAC
1 TACAGCATAGCTCAAGGCAAGAAGGGCTATCTGCACAAAGACCTTCGAGTTCGATTACACTCAGC
3405419 TCAAAGGCACATCATT
66 TCAAAGGCACATCATT
* * *
3405435 TATAGCATAGCTCAAGGCAAGAAGGGCTATCTACCAACAAAATACCTTCGAGTTCGATTACACTC
1 TACAGCATAGCTCAAGGCAAGAAGGGCTATCT-GC-AC-AAAGACCTTCGAGTTCGATTACACTC
* *
3405500 AGCTTAAAGGCATATCAAATTT
63 AGCTCAAAGGCACATC--A-TT
* *
3405522 TACAGCATATCTCAGGGCAAGAAGGGCTATCTG
1 TACAGCATAGCTCAAGGCAAGAAGGGCTATCTG
3405555 TCAACAAAAT
Statistics
Matches: 807, Mismatches: 108, Indels: 47
0.84 0.11 0.05
Matches are distributed among these distances:
79 30 0.04
80 252 0.31
81 6 0.01
82 42 0.05
83 196 0.24
84 249 0.31
86 1 0.00
87 31 0.04
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (81 bp):
TACAGCATAGCTCAAGGCAAGAAGGGCTATCTGCACAAAGACCTTCGAGTTCGATTACACTCAGC
TCAAAGGCACATCATT
Found at i:3405005 original size:164 final size:164
Alignment explanation
Indices: 3404532--3405578 Score: 1200
Period size: 164 Copynumber: 6.4 Consensus size: 164
3404522 ACGAATCCAG
* * * ** ** * *
3404532 TACATCATAACTCAAGGCGAGAAGGTTTATCTGTCAACCAAGACCTTCGAGTTCAATTACACTCA
1 TACAGCATAGCTCAAGGCAAGAAGGGCTATCTACCAACAAAGACCTTCGAGTTCGATTACACTCA
* * * * *
3404597 GCTCAAAGGTACATCATTTGCAGCATAGCTCAAGCCAATG-AGAGATATCTTCCAACAAAGACCT
66 GCTCAAAGGCACATCATTTACAGCATAGCTCAAGGCAA-GAAGGGTTATC-TCC-ACAAAGACCT
3404661 TCGAGTTCGATTACACTCAGCTCAAAGGCACATCATT
128 TCGAGTTCGATTACACTCAGCTCAAAGGCACATCATT
* * * * ** *
3404698 TATAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCA
1 TACAGCATAGCTCAAGGCAAGAAGGGCTATCTACCAACAAAGACCTTCGAGTTCGATTACACTCA
* * * * *
3404763 GCT-AAAGGCATATCATTTGCAGCATAGCTCAAGGCAATAAGGGCTATCTGC-CAAAGACCTTCG
66 GCTCAAAGGCACATCATTTACAGCATAGCTCAAGGCAAGAAGGGTTATCTCCACAAAGACCTTCG
* *
3404826 AGTTCGATTACACTCAGCTCAAAGGTAAATCATT
131 AGTTCGATTACACTCAGCTCAAAGGCACATCATT
* * *
3404860 TGCAACATAGCTCAAGGCAAGAAGGGCTATTTACCAACAAAAGACCTTCGAGTTCGATTACACTC
1 TACAGCATAGCTCAAGGCAAGAAGGGCTATCTACCAAC-AAAGACCTTCGAGTTCGATTACACTC
* * * * *
3404925 AACTTAAAGACACATCATTTACAGCATAGTTCAAGGCAAGAAGGGTTATCTGC-CAAAGACCTTC
65 AGCTCAAAGGCACATCATTTACAGCATAGCTCAAGGCAAGAAGGGTTATCTCCACAAAGACCTTC
*
3404989 GAGTTCGATTACACTCAACTCAAAGGCACATCATT
130 GAGTTCGATTACACTCAGCTCAAAGGCACATCATT
* * *
3405024 TATAGTATAGCTCAAGGCAAGAAGGGCTATCTACCAACAAAAGACCTTCGAGTTTGATTACACTC
1 TACAGCATAGCTCAAGGCAAGAAGGGCTATCTACCAAC-AAAGACCTTCGAGTTCGATTACACTC
* * * * *
3405089 AGCTCAAAGGTACATCATTTACAGTATAACTCAAGGCTAGAAGGGTTATCCGTCAACAAAGACCT
65 AGCTCAAAGGCACATCATTTACAGCATAGCTCAAGGCAAGAAGGGTTAT-C-TCCACAAAGACCT
* *
3405154 TCAAGTTTGATTACACTCAGCTCAAAGGCACATCATT
128 TCGAGTTCGATTACACTCAGCTCAAAGGCACATCATT
** ***
3405191 TGTAGCATAGCTCAAGGCAAGAAGGGCTA-C--CTGTCAAAGACCTTCGAGTTCGATTACACTCA
1 TACAGCATAGCTCAAGGCAAGAAGGGCTATCTACCAACAAAGACCTTCGAGTTCGATTACACTCA
* * * *
3405253 GCTCAAAGGCACATCATTTGCAACATAGCTCAAGGTAAGAAGGGTTATTTACCAACAAAAGACCT
66 GCTCAAAGGCACATCATTTACAGCATAGCTCAAGGCAAGAAGGGTTATCT-CC-AC-AAAGACCT
* * *
3405318 TCGAGTTTGATTACACTCAGCTTAAAGACACATCATT
128 TCGAGTTCGATTACACTCAGCTCAAAGGCACATCATT
* * *
3405355 TACAACATAGTTCAAGGCAAGAAGGGCTATCT-GC--CAAAGACCTTCGAGTTCGATTACACTCA
1 TACAGCATAGCTCAAGGCAAGAAGGGCTATCTACCAACAAAGACCTTCGAGTTCGATTACACTCA
* * * *
3405417 ACTCAAAGGCACATCATTTATAGCATAGCTCAAGGCAAGAAGGGCTATCTACCAACAAAATACCT
66 GCTCAAAGGCACATCATTTACAGCATAGCTCAAGGCAAGAAGGGTTATCT-CC-AC-AAAGACCT
* *
3405482 TCGAGTTCGATTACACTCAGCTTAAAGGCATATCAAATTT
128 TCGAGTTCGATTACACTCAGCTCAAAGGCACATC--A-TT
* * ** *
3405522 TACAGCATATCTCAGGGCAAGAAGGGCTATCTGTCAACAAA-A-TTATCGAGTTCGATT
1 TACAGCATAGCTCAAGGCAAGAAGGGCTATCTACCAACAAAGACCT-TCGAGTTCGATT
3405579 CCATTAAGCT
Statistics
Matches: 769, Mismatches: 94, Indels: 33
0.86 0.10 0.04
Matches are distributed among these distances:
161 1 0.00
162 74 0.10
163 97 0.13
164 372 0.48
165 40 0.05
166 66 0.09
167 100 0.13
168 2 0.00
169 13 0.02
170 4 0.01
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.25
Consensus pattern (164 bp):
TACAGCATAGCTCAAGGCAAGAAGGGCTATCTACCAACAAAGACCTTCGAGTTCGATTACACTCA
GCTCAAAGGCACATCATTTACAGCATAGCTCAAGGCAAGAAGGGTTATCTCCACAAAGACCTTCG
AGTTCGATTACACTCAGCTCAAAGGCACATCATT
Found at i:3405332 original size:411 final size:410
Alignment explanation
Indices: 3404543--3405562 Score: 1585
Period size: 411 Copynumber: 2.5 Consensus size: 410
3404533 ACATCATAAC
* * * * * *
3404543 TCAAGGCGAGAAGGTTTATCTGTCAACCAAGACCTTCGAGTTCAATTACACTCAGCTCAAAGGTA
1 TCAAGGCAAGAAGGGTTATCTG-C--CAAAGACCTTCGAGTTCGATTACACTCAACTCAAAGGCA
** * * * *
3404608 CATCATTTGCAGCATAGCTCAAGCCAATG-AGAGATATCTTCCAAC-AAAGACCTTCGAGTTCGA
63 CATCATTTATAGCATAGCTCAAGGCAA-GAAGGGCTATCTACCAACAAAAGACCTTCGAGTTCGA
*
3404671 TTACACTCAGCTCAAAGGCACATCATTTATAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAAC
127 TTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAAC
* * * *
3404736 CAAGACCTTCGAGTTCGATTACACTCAGCTAAAGGCATATCATTTGCAGCATAGCTCAAGGCAAT
192 AAAGACCTTCAAGTTCGATTACACTCAGCTAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAG
* *
3404801 AAGGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGTAAATCATTTGCAAC
257 AAGGGCTACCTGCCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCAAATCATTTGCAAC
3404866 ATAGCTCAAGGCAAGAAGGGCTATTTACCAACAAAAGACCTTCGAGTTCGATTACACTCAACTTA
322 ATAGCTCAAGGCAAGAAGGGCTATTTACCAACAAAAGACCTTCGAGTTCGATTACACTCAACTTA
*
3404931 AAGACACATCATTTACAGCATAGT
387 AAGACACATCATTTACAACATAGT
3404955 TCAAGGCAAGAAGGGTTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAACTCAAAGGCACAT
1 TCAAGGCAAGAAGGGTTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAACTCAAAGGCACAT
* *
3405020 CATTTATAGTATAGCTCAAGGCAAGAAGGGCTATCTACCAACAAAAGACCTTCGAGTTTGATTAC
66 CATTTATAGCATAGCTCAAGGCAAGAAGGGCTATCTACCAACAAAAGACCTTCGAGTTCGATTAC
* * *
3405085 ACTCAGCTCAAAGGTACATCATTTACAGTATAACTCAAGGCTAGAAGGGTTATCCGTCAACAAAG
131 ACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAG
* *
3405150 ACCTTCAAGTTTGATTACACTCAGCTCAAAGGCACATCATTTGTAGCATAGCTCAAGGCAAGAAG
196 ACCTTCAAGTTCGATTACACTCAGCT-AAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAG
* *
3405215 GGCTACCTGTCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAACATA
260 GGCTACCTGCCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCAAATCATTTGCAACATA
* * * *
3405280 GCTCAAGGTAAGAAGGGTTATTTACCAACAAAAGACCTTCGAGTTTGATTACACTCAGCTTAAAG
325 GCTCAAGGCAAGAAGGGCTATTTACCAACAAAAGACCTTCGAGTTCGATTACACTCAACTTAAAG
3405345 ACACATCATTTACAACATAGT
390 ACACATCATTTACAACATAGT
*
3405366 TCAAGGCAAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAACTCAAAGGCACAT
1 TCAAGGCAAGAAGGGTTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAACTCAAAGGCACAT
*
3405431 CATTTATAGCATAGCTCAAGGCAAGAAGGGCTATCTACCAACAAAATACCTTCGAGTTCGATTAC
66 CATTTATAGCATAGCTCAAGGCAAGAAGGGCTATCTACCAACAAAAGACCTTCGAGTTCGATTAC
* * * * * *
3405496 ACTCAGCTTAAAGGCATATCAAATTTTACAGCATATCTCAGGGCAAGAAGGGCTATCTGTCAACA
131 ACTCAGCTCAAAGGCACATC--A-TTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACA
3405561 AA
193 AA
3405563 ATTATCGAGT
Statistics
Matches: 556, Mismatches: 46, Indels: 10
0.91 0.08 0.02
Matches are distributed among these distances:
408 1 0.00
409 71 0.13
410 105 0.19
411 321 0.58
412 20 0.04
413 1 0.00
414 37 0.07
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (410 bp):
TCAAGGCAAGAAGGGTTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAACTCAAAGGCACAT
CATTTATAGCATAGCTCAAGGCAAGAAGGGCTATCTACCAACAAAAGACCTTCGAGTTCGATTAC
ACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAG
ACCTTCAAGTTCGATTACACTCAGCTAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAGG
GCTACCTGCCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCAAATCATTTGCAACATAG
CTCAAGGCAAGAAGGGCTATTTACCAACAAAAGACCTTCGAGTTCGATTACACTCAACTTAAAGA
CACATCATTTACAACATAGT
Found at i:3406161 original size:37 final size:35
Alignment explanation
Indices: 3406120--3406248 Score: 142
Period size: 35 Copynumber: 3.6 Consensus size: 35
3406110 TTTGAAGTCA
3406120 TTTTGAAAATATATAATATATAGTTTTGTAAACAAAT
1 TTTTGAAAATATATAATATATAGTTTTGTAAAC--AT
*
3406157 TTTTGAAAGTATATAATATAT-GATTTT-TAAACAT
1 TTTTGAAAATATATAATATATAG-TTTTGTAAACAT
3406191 TTTT-AAAACTTATATAATATATAGTTTTG-AAATCA-
1 TTTTGAAAA--TATATAATATATAGTTTTGTAAA-CAT
*
3406226 TTTTGAATATATATATATATATA
1 TTTTGAAAATATATA-ATATATA
3406249 ATATATATAT
Statistics
Matches: 81, Mismatches: 3, Indels: 18
0.79 0.03 0.18
Matches are distributed among these distances:
33 3 0.04
34 12 0.15
35 30 0.37
36 12 0.15
37 24 0.30
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (35 bp):
TTTTGAAAATATATAATATATAGTTTTGTAAACAT
Found at i:3406205 original size:35 final size:34
Alignment explanation
Indices: 3406118--3406487 Score: 204
Period size: 37 Copynumber: 10.9 Consensus size: 34
3406108 AGTTTGAAGT
*
3406118 CATTTTGAAAA-TATATAATATATAGTTTTGTAAA
1 CATTTTTAAAAGTATATAATATATAGTTTT-TAAA
*
3406152 CAAATTTTTGAAAGTATATAATATAT-GATTTTTAAA
1 C--ATTTTTAAAAGTATATAATATATAG-TTTTTAAA
* *
3406188 CATTTTTAAAACTTATATAATATATAGTTTTGAAA
1 CATTTTTAAAA-GTATATAATATATAGTTTTTAAA
* *
3406223 TCA-TTTT-GAA-TATAT-ATATATA-----TATA
1 -CATTTTTAAAAGTATATAATATATAGTTTTTAAA
* * *
3406249 -ATATAT-ATA-TATAT-ATATATAGTTTTTAAAA
1 CATTTTTAAAAGTATATAATATATAGTTTTT-AAA
*
3406280 CATTTTTTAAAACTTATATAATATATAGTTTTTAAAA
1 CA-TTTTTAAAA-GTATATAATATATAGTTTTT-AAA
* * *
3406317 CATTTTGAAAAACTTATATAATATATAGTTTTAAAAA
1 CATTTT-TAAAA-GTATATAATATATAGTTTT-TAAA
* * *
3406354 CATTTTTAAAAAATTATATAATTTATAGTTTTAAAAA
1 CATTTTT--AAAAGTATATAATATATAGTTTT-TAAA
* *
3406391 TATTTTTAAAAACTTATATAATAT-T--TTTTTAAA
1 CATTTTT-AAAA-GTATATAATATATAGTTTTTAAA
* * *
3406424 TAATTTTTGCAAAACTATATAATATATAGTTTTGAAA
1 -CATTTTT--AAAAGTATATAATATATAGTTTTTAAA
* *
3406461 -ACTTTTAAAA-AATATAATATATAGTTT
1 CATTTTTAAAAGTATATAATATATAGTTT
3406488 GAAAAATAAT
Statistics
Matches: 277, Mismatches: 29, Indels: 62
0.75 0.08 0.17
Matches are distributed among these distances:
24 1 0.00
25 15 0.05
26 2 0.01
30 1 0.00
31 9 0.03
32 22 0.08
33 10 0.04
34 34 0.12
35 33 0.12
36 32 0.12
37 114 0.41
38 4 0.01
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (34 bp):
CATTTTTAAAAGTATATAATATATAGTTTTTAAA
Found at i:3406239 original size:2 final size:2
Alignment explanation
Indices: 3406232--3406269 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3406222 ATCATTTTGA
3406232 AT AT AT AT AT AT AT AT A- 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 AT AT A
3406270 GTTTTTAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3406270 original size:128 final size:129
Alignment explanation
Indices: 3406128--3406359 Score: 339
Period size: 128 Copynumber: 1.8 Consensus size: 129
3406118 CATTTTGAAA
*
3406128 ATATATAATATATAGTTTTGT-AAACAAATTTTTGAAA-GTATATAATATAT-GATTTTT-AAAC
1 ATATATAATATATAGTTTT-TAAAAC-AATTTTTAAAACGTATATAATATATAG-TTTTTAAAAC
* * *
3406189 ATTTT-TAAAACTTATATAATATATAGTTTTGAAATCATTTTGAATATATATATATATATAATAT
63 ATTTTGAAAAACTTATATAATATATAGTTTTAAAAACATTTTGAATATATATATATATATAATAT
3406253 AT
128 AT
* *
3406255 ATATATATATATATAGTTTTTAAAACATTTTTTAAAACTTATATAATATATAGTTTTTAAAACAT
1 ATATATA-ATATATAGTTTTTAAAACAATTTTTAAAACGTATATAATATATAGTTTTTAAAACAT
3406320 TTTGAAAAACTTATATAATATATAGTTTTAAAAACATTTT
65 TTTGAAAAACTTATATAATATATAGTTTTAAAAACATTTT
3406360 TAAAAAATTA
Statistics
Matches: 93, Mismatches: 6, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
127 17 0.18
128 33 0.35
129 10 0.11
130 33 0.35
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (129 bp):
ATATATAATATATAGTTTTTAAAACAATTTTTAAAACGTATATAATATATAGTTTTTAAAACATT
TTGAAAAACTTATATAATATATAGTTTTAAAAACATTTTGAATATATATATATATATAATATAT
Found at i:3406307 original size:37 final size:37
Alignment explanation
Indices: 3406256--3406487 Score: 286
Period size: 37 Copynumber: 6.5 Consensus size: 37
3406246 ATAATATATA
*
3406256 TATATATATATATAGTTTTTAAAACATTTTTTAAAACT
1 TATATA-ATATATAGTTTTTAAAACATTTTTAAAAACT
*
3406294 TATATAATATATAGTTTTTAAAACATTTTGAAAAACT
1 TATATAATATATAGTTTTTAAAACATTTTTAAAAACT
* *
3406331 TATATAATATATAGTTTTAAAAACATTTTTAAAAAAT
1 TATATAATATATAGTTTTTAAAACATTTTTAAAAACT
* * *
3406368 TATATAATTTATAGTTTTAAAAATATTTTTAAAAACT
1 TATATAATATATAGTTTTTAAAACATTTTTAAAAACT
*
3406405 TATATAATAT-T--TTTTTAAATA-ATTTTTGCAAAAC-
1 TATATAATATATAGTTTTTAAA-ACATTTTT-AAAAACT
*
3406439 TATATAATATATAGTTTTGAAAAC--TTTTAAAAA--
1 TATATAATATATAGTTTTTAAAACATTTTTAAAAACT
3406472 -ATATAATATATAGTTT
1 TATATAATATATAGTTT
3406488 GAAAAATAAT
Statistics
Matches: 175, Mismatches: 13, Indels: 18
0.85 0.06 0.09
Matches are distributed among these distances:
32 16 0.09
34 27 0.15
35 11 0.06
36 2 0.01
37 113 0.65
38 6 0.03
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (37 bp):
TATATAATATATAGTTTTTAAAACATTTTTAAAAACT
Found at i:3406519 original size:36 final size:37
Alignment explanation
Indices: 3406256--3406523 Score: 229
Period size: 37 Copynumber: 7.5 Consensus size: 37
3406246 ATAATATATA
* * **
3406256 TATATATATATATAGTTTTTAAAA-CATTTTTTAAAAC
1 TATATA-ATATATAGTTTTAAAAATAATTTTGAAAAAC
* *
3406293 TTATATAATATATAGTTTTTAAAA-CATTTTGAAAAAC
1 -TATATAATATATAGTTTTAAAAATAATTTTGAAAAAC
* * * *
3406330 TTATATAATATATAGTTTTAAAAACATTTTTAAAAAAT
1 -TATATAATATATAGTTTTAAAAATAATTTTGAAAAAC
* *
3406368 TATATAATTTATAGTTTTAAAAAT-ATTTTTAAAAAC
1 TATATAATATATAGTTTTAAAAATAATTTTGAAAAAC
* *
3406404 TTATATAATAT-T--TTTT-TAAATAATTTTTGCAAAAC
1 -TATATAATATATAGTTTTAAAAATAA-TTTTGAAAAAC
* *
3406439 TATATAATATATAGTTTT-GAAA-ACTTTT-AAAAA-
1 TATATAATATATAGTTTTAAAAATAATTTTGAAAAAC
* *
3406472 -ATATAATATATAGTTTGAAAAATAATTTTGAAATA-
1 TATATAATATATAGTTTTAAAAATAATTTTGAAAAAC
*
3406507 TATATATTATATAGTTT
1 TATATAATATATAGTTT
3406524 ATATTATATT
Statistics
Matches: 195, Mismatches: 24, Indels: 24
0.80 0.10 0.10
Matches are distributed among these distances:
32 16 0.08
33 7 0.04
34 24 0.12
35 18 0.09
36 26 0.13
37 89 0.46
38 15 0.08
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (37 bp):
TATATAATATATAGTTTTAAAAATAATTTTGAAAAAC
Found at i:3406554 original size:5 final size:5
Alignment explanation
Indices: 3406546--3406591 Score: 58
Period size: 5 Copynumber: 9.4 Consensus size: 5
3406536 TGTTAGTATA
* * *
3406546 TTATT TTATT TTATT TTATT TTA-T TCATT TAATT GTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TT
3406592 TCGGTTCAGG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
4 3 0.09
5 32 0.91
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (5 bp):
TTATT
Found at i:3406575 original size:24 final size:23
Alignment explanation
Indices: 3406544--3406591 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
3406534 ATTGTTAGTA
* *
3406544 TATTATTTTATTTTATTTTATTT
1 TATTATTTAATTGTATTTTATTT
3406567 TATTCATTTAATTGTATTTTATTT
1 TATT-ATTTAATTGTATTTTATTT
3406591 T
1 T
3406592 TCGGTTCAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (23 bp):
TATTATTTAATTGTATTTTATTT
Found at i:3407689 original size:2 final size:2
Alignment explanation
Indices: 3407682--3407711 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3407672 TTTATTTCAT
3407682 TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3407712 GTTTTTGGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3409609 original size:70 final size:71
Alignment explanation
Indices: 3409496--3409636 Score: 275
Period size: 70 Copynumber: 2.0 Consensus size: 71
3409486 TCCTTAACGT
3409496 GTATATCGATACACTGCTTATGTATCGATACACAAATTACATTTGATGTTTTCATTTTAA-GGGT
1 GTATATCGATACACTGCTTATGTATCGATACACAAATTACATTTGATGTTTTCATTTTAAGGGGT
3409560 GTACGA
66 GTACGA
3409566 GTATATCGATACACTGCTTATGTATCGATACACAAATTACATTTGATGTTTTCATTTTAAGGGGT
1 GTATATCGATACACTGCTTATGTATCGATACACAAATTACATTTGATGTTTTCATTTTAAGGGGT
3409631 GTACGA
66 GTACGA
3409637 TACACTTCCT
Statistics
Matches: 70, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
70 60 0.86
71 10 0.14
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (71 bp):
GTATATCGATACACTGCTTATGTATCGATACACAAATTACATTTGATGTTTTCATTTTAAGGGGT
GTACGA
Found at i:3410367 original size:33 final size:33
Alignment explanation
Indices: 3410330--3410396 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
3410320 ATAACAGACC
3410330 TGTCCTTCACTGCCTGAACCGAGAGAAAATATT
1 TGTCCTTCACTGCCTGAACCGAGAGAAAATATT
3410363 TGTCCTTCACTGCCTGAACCGAGAGAAAATATT
1 TGTCCTTCACTGCCTGAACCGAGAGAAAATATT
3410396 T
1 T
3410397 CTTCAATTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (33 bp):
TGTCCTTCACTGCCTGAACCGAGAGAAAATATT
Found at i:3416123 original size:22 final size:22
Alignment explanation
Indices: 3416091--3416167 Score: 115
Period size: 22 Copynumber: 3.6 Consensus size: 22
3416081 AGCACTTGAT
3416091 GAACAATATCGATATTGATGAA
1 GAACAATATCGATATTGATGAA
*
3416113 GAATAATATCGATATTGATGAA
1 GAACAATATCGATATTGATGAA
3416135 GAACAATATCGAT-TTGA--AA
1 GAACAATATCGATATTGATGAA
*
3416154 GAACAATATTGATA
1 GAACAATATCGATA
3416168 CTAAATGAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 14 0.27
21 4 0.08
22 33 0.65
ACGTcount: A:0.47, C:0.08, G:0.17, T:0.29
Consensus pattern (22 bp):
GAACAATATCGATATTGATGAA
Found at i:3416336 original size:14 final size:14
Alignment explanation
Indices: 3416304--3416345 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
3416294 GAGGTGTATG
3416304 AAAATA-TTCAG-A
1 AAAATATTTCAGTA
*
3416316 TAAATATTTCAGTA
1 AAAATATTTCAGTA
3416330 AAAATATTTCA-TA
1 AAAATATTTCAGTA
3416343 AAA
1 AAA
3416346 CATGCTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 5 0.19
13 10 0.38
14 11 0.42
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (14 bp):
AAAATATTTCAGTA
Found at i:3418865 original size:92 final size:92
Alignment explanation
Indices: 3418748--3418953 Score: 324
Period size: 92 Copynumber: 2.2 Consensus size: 92
3418738 CGCGATTCTC
* *
3418748 CAAAATCGCAACGCGAATTTCGTTTTCGCAA-TGCGAATTTCACAACGCTAATTACCGATATAGG
1 CAAATTCGCAACGCGAATTTTGTTTTCGCAACT-CGAATTTCACAACGCTAATTACCGATATAGG
*
3418812 TAAACACAACTATTTACAACCCAGTTTT
65 TAAACACAACTATTCACAACCCAGTTTT
* *
3418840 CAAATTCGCAACGCAAATTTTGTTTTCGCAACTCGAATTTCGCAACGCTAATTACCGATATAGGT
1 CAAATTCGCAACGCGAATTTTGTTTTCGCAACTCGAATTTCACAACGCTAATTACCGATATAGGT
* *
3418905 AATCACAACTATTCACAACTCAGTTTT
66 AAACACAACTATTCACAACCCAGTTTT
*
3418932 CAAATTCGCAACTCGAATTTTG
1 CAAATTCGCAACGCGAATTTTG
3418954 CAACGCTAAT
Statistics
Matches: 104, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
92 103 0.99
93 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.30
Consensus pattern (92 bp):
CAAATTCGCAACGCGAATTTTGTTTTCGCAACTCGAATTTCACAACGCTAATTACCGATATAGGT
AAACACAACTATTCACAACCCAGTTTT
Found at i:3418960 original size:164 final size:164
Alignment explanation
Indices: 3418772--3419078 Score: 481
Period size: 164 Copynumber: 1.9 Consensus size: 164
3418762 GAATTTCGTT
*
3418772 TTCGCAATGCGAATTTCACAACGCTAATTACCGATATAGGTAAACACAACTATTTACAACCCAGT
1 TTCGCAATGCGAATTTCACAACGCTAATTACCGATATAGGTAAACACAACTATTCACAACCCAGT
* * *
3418837 TTTCAAATTCGCAACGCAAATTTTGTTTTCGCAACTCGAATTTCGCAACGCTAATTACCGATATA
66 TTTCAAATTCGCAACGCAAATTTCGTTTTCGCAACTCGAATTTCACAACGCTAATTACCGATAAA
* *
3418902 GGTAATCACAACTATTCACAACTCAGTTTTCAAA
131 CGTAAACACAACTATTCACAACTCAGTTTTCAAA
** * * *
3418936 TTCGCAACT-CGAATTTTGCAACGCTAATTACCGATATAGGTAAACAGAACTATTCGCAACTCAG
1 TTCGCAA-TGCGAATTTCACAACGCTAATTACCGATATAGGTAAACACAACTATTCACAACCCAG
* *
3419000 TTTTCAAATTCGCAACGCGAATTTCGTTTTCGCGACTCGAATTTCACAACGCTAATTACCGATAA
65 TTTTCAAATTCGCAACGCAAATTTCGTTTTCGCAACTCGAATTTCACAACGCTAATTACCGATAA
3419065 ACGTAAACACAACT
130 ACGTAAACACAACT
3419079 CAGTTTTCAA
Statistics
Matches: 129, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
164 128 0.99
165 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.29
Consensus pattern (164 bp):
TTCGCAATGCGAATTTCACAACGCTAATTACCGATATAGGTAAACACAACTATTCACAACCCAGT
TTTCAAATTCGCAACGCAAATTTCGTTTTCGCAACTCGAATTTCACAACGCTAATTACCGATAAA
CGTAAACACAACTATTCACAACTCAGTTTTCAAA
Found at i:3418987 original size:72 final size:72
Alignment explanation
Indices: 3418864--3419025 Score: 279
Period size: 72 Copynumber: 2.2 Consensus size: 72
3418854 AAATTTTGTT
*
3418864 TTCGCAACTCGAATTTCGCAACGCTAATTACCGATATAGGTAATCACAACTATTCACAACTCAGT
1 TTCGCAACTCGAATTTCGCAACGCTAATTACCGATATAGGTAAACACAACTATTCACAACTCAGT
3418929 TTTCAAA
66 TTTCAAA
* * *
3418936 TTCGCAACTCGAATTTTGCAACGCTAATTACCGATATAGGTAAACAGAACTATTCGCAACTCAGT
1 TTCGCAACTCGAATTTCGCAACGCTAATTACCGATATAGGTAAACACAACTATTCACAACTCAGT
3419001 TTTCAAA
66 TTTCAAA
*
3419008 TTCGCAACGCGAATTTCG
1 TTCGCAACTCGAATTTCG
3419026 TTTTCGCGAC
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 84 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (72 bp):
TTCGCAACTCGAATTTCGCAACGCTAATTACCGATATAGGTAAACACAACTATTCACAACTCAGT
TTTCAAA
Found at i:3420062 original size:24 final size:24
Alignment explanation
Indices: 3420008--3420062 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
3419998 TTCCTCAAAG
* *
3420008 TATTTTCTTCATCTCAATATCATT
1 TATTTTTTTCAGCTCAATATCATT
*
3420032 TAATTTTTTCAGCTCAATATCA--
1 TATTTTTTTCAGCTCAATATCATT
3420054 TATTTTTTT
1 TATTTTTTT
3420063 AACTTAAACA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 8 0.30
24 19 0.70
ACGTcount: A:0.25, C:0.16, G:0.02, T:0.56
Consensus pattern (24 bp):
TATTTTTTTCAGCTCAATATCATT
Found at i:3420352 original size:83 final size:82
Alignment explanation
Indices: 3420265--3420426 Score: 238
Period size: 83 Copynumber: 2.0 Consensus size: 82
3420255 TTTATATATG
*
3420265 TTTAATATTTTAAATTTAAAATATATTATTAT-CTGTTTAAATTTAGATATTAAAAGA-TATATG
1 TTTAATATTTTAAATTTAAAAGATATTATTATACTGTTTAAA-TTAGATATTAAAAGAGTATA-G
*
3420328 ATTGGAGTAAATCTCTCAGA
64 A-TGGAGTAAAACTCTCAGA
* * *
3420348 TTTAATATTTTAAATTTAAAAGATATTATTATATTTTTTAAATTAGATATTAAAAGAGTTTAGAT
1 TTTAATATTTTAAATTTAAAAGATATTATTATACTGTTTAAATTAGATATTAAAAGAGTATAGAT
3420413 GGAGTAAAACTCTC
66 GGAGTAAAACTCTC
3420427 TTGAAATTCC
Statistics
Matches: 72, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
82 14 0.19
83 48 0.67
84 10 0.14
ACGTcount: A:0.41, C:0.04, G:0.10, T:0.44
Consensus pattern (82 bp):
TTTAATATTTTAAATTTAAAAGATATTATTATACTGTTTAAATTAGATATTAAAAGAGTATAGAT
GGAGTAAAACTCTCAGA
Found at i:3427898 original size:43 final size:43
Alignment explanation
Indices: 3427835--3427942 Score: 146
Period size: 43 Copynumber: 2.5 Consensus size: 43
3427825 TATGATTTAC
* * *
3427835 AGTGGCATTTTTGTCGACAAACGACACTAATTTTCTTGTCTTT
1 AGTGGCGTTTTTGTCAACAAACGACACTAATTCTCTTGTCTTT
* * *
3427878 AGTGGCGTTTTTGTCTACAAACGCCGCTAATTCTCTTGTCTTT
1 AGTGGCGTTTTTGTCAACAAACGACACTAATTCTCTTGTCTTT
*
3427921 AGTAGCGTTTTTG-CAACAAACG
1 AGTGGCGTTTTTGTCAACAAACG
3427943 CTTATCTTGT
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
42 8 0.14
43 50 0.86
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (43 bp):
AGTGGCGTTTTTGTCAACAAACGACACTAATTCTCTTGTCTTT
Found at i:3432673 original size:29 final size:29
Alignment explanation
Indices: 3432640--3432708 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 29
3432630 TATTTTAATT
3432640 ACTTAACTTTGAGAAATTATAAAATGATC
1 ACTTAACTTTGAGAAATTATAAAATGATC
* * **
3432669 ACTTATACTATCGATAAATTATAATGTGATC
1 ACTTA-ACT-TTGAGAAATTATAAAATGATC
3432700 ACTT-ACTTT
1 ACTTAACTTT
3432709 ATTGATAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
28 1 0.03
29 8 0.24
30 3 0.09
31 21 0.64
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (29 bp):
ACTTAACTTTGAGAAATTATAAAATGATC
Found at i:3432688 original size:31 final size:31
Alignment explanation
Indices: 3432653--3432737 Score: 93
Period size: 31 Copynumber: 2.7 Consensus size: 31
3432643 TAACTTTGAG
3432653 AAATTATAAAATGATCACTTA-TACTATCGAT
1 AAATTATAAAATGATCACTTACT-CTATCGAT
** * *
3432684 AAATTATAATGTGATCACTTACTTTATTGAT
1 AAATTATAAAATGATCACTTACTCTATCGAT
*
3432715 AAATCATAAAAT-AGTCACTTACT
1 AAATTATAAAATGA-TCACTTACT
3432738 ACCGATGATG
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
30 1 0.02
31 43 0.96
32 1 0.02
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.38
Consensus pattern (31 bp):
AAATTATAAAATGATCACTTACTCTATCGAT
Found at i:3433616 original size:27 final size:27
Alignment explanation
Indices: 3433560--3433612 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
3433550 TTTATAATAT
* **
3433560 TTTTTTTGAAATAATAATAGATTTACA
1 TTTTTCTGAAATAATAATAGATCAACA
*
3433587 TTTTTCTGAAATAA-AATATATCAACA
1 TTTTTCTGAAATAATAATAGATCAACA
3433613 ATTTCATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (27 bp):
TTTTTCTGAAATAATAATAGATCAACA
Found at i:3434703 original size:29 final size:28
Alignment explanation
Indices: 3434654--3434806 Score: 146
Period size: 29 Copynumber: 5.1 Consensus size: 28
3434644 AAACTATTTT
3434654 TTATCTTAACTTATTAAATATATTTTATTC
1 TTATCTTAACTTA--AAATATATTTTATTC
* *
3434684 TTTTCATAACCTTAAAATATATTTTATTC
1 TTATCTTAA-CTTAAAATATATTTTATTC
* * *
3434713 TTATTTTAATTTAAAAATATATTTTACTC
1 TTATCTTAACTT-AAAATATATTTTATTC
*
3434742 TTATCTTAAATTTAAAA-ATAATATTTATTC
1 TTATCTT-AACTTAAAATAT-AT-TTTATTC
*
3434772 TTATCTTAACTTAAATATTTATATTTTATTA
1 TTATCTTAACTTAAA-A--TATATTTTATTC
3434803 TTAT
1 TTAT
3434807 AATATTTTAA
Statistics
Matches: 103, Mismatches: 11, Indels: 17
0.79 0.08 0.13
Matches are distributed among these distances:
28 4 0.04
29 55 0.53
30 26 0.25
31 14 0.14
32 2 0.02
33 2 0.02
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (28 bp):
TTATCTTAACTTAAAATATATTTTATTC
Found at i:3434786 original size:59 final size:58
Alignment explanation
Indices: 3434654--3434786 Score: 160
Period size: 59 Copynumber: 2.3 Consensus size: 58
3434644 AAACTATTTT
* * * *
3434654 TTATCTTAACTTATTAAATATATTTTATTCTTTTCATAACCTTAAAATATATTTTATTC
1 TTATCTTAACTTA-AAAATATATTTTACTCTTATCATAAACTTAAAATATATTTTATTC
* * * *
3434713 TTATTTTAATTTAAAAATATATTTTACTCTTATCTTAAATTTAAAA-ATAATATTTATTC
1 TTATCTTAACTTAAAAATATATTTTACTCTTATCATAAACTTAAAATAT-AT-TTTATTC
3434772 TTATCTTAACTTAAA
1 TTATCTTAACTTAAA
3434787 TATTTATATT
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
57 2 0.03
58 29 0.47
59 31 0.50
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53
Consensus pattern (58 bp):
TTATCTTAACTTAAAAATATATTTTACTCTTATCATAAACTTAAAATATATTTTATTC
Found at i:3434894 original size:24 final size:25
Alignment explanation
Indices: 3434852--3434940 Score: 74
Period size: 25 Copynumber: 3.4 Consensus size: 25
3434842 TAGTTAAGAT
*
3434852 AAATATAAAATATATTTTTGT-AGTTA
1 AAATA-AAAAAATATTTTT-TAAGTTA
3434878 AAATAAAAAAATA-TTTTTAAGTTAA
1 AAATAAAAAAATATTTTTTAAGTT-A
* *
3434903 GATAAGAATAGAAAATATGTTTTAAGTTA
1 -A-AATAA-A-AAAATATTTTTTAAGTTA
3434932 AAATAAAAA
1 AAATAAAAA
3434941 TTAATTATAT
Statistics
Matches: 52, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
23 1 0.02
24 8 0.15
25 10 0.19
26 7 0.13
27 8 0.15
28 2 0.04
29 7 0.13
30 9 0.17
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (25 bp):
AAATAAAAAAATATTTTTTAAGTTA
Found at i:3434928 original size:30 final size:28
Alignment explanation
Indices: 3434807--3435171 Score: 224
Period size: 30 Copynumber: 12.6 Consensus size: 28
3434797 TTATTATTAT
* * * *
3434807 AATATTTTAAATTTAAGATAAAAAT-AT
1 AATATTTTTAAGTTAAGATAAGAATAAA
3434834 AATATTTTT-AGTTAAGATAA-ATATAAA
1 AATATTTTTAAGTTAAGATAAGA-ATAAA
* *
3434861 ATATATTTTTGTAGTT-A-A-AATAA-AAA
1 A-ATATTTTT-AAGTTAAGATAAGAATAAA
3434887 AATATTTTTAAGTTAAGATAAGAATAGAA
1 AATATTTTTAAGTTAAGATAAGAATA-AA
* * *
3434916 AATATGTTTTAAGTTAAAATAAAAATTAAT
1 AATAT-TTTTAAGTTAAGATAAGAA-TAAA
* * * *
3434946 TATATTTAATAATTTAAGGTAAGAATTAAA
1 AATATTT-TTAAGTTAAGATAAGAA-TAAA
* * ** **
3434976 TATATTTAATACTTTAATTTAAGAATATAA
1 AATATTT-TTAAGTTAAGATAAGAATA-AA
** **
3435006 TTTATGTAATAAGTTAAGATAAGAATAAA
1 AATAT-TTTTAAGTTAAGATAAGAATAAA
*
3435035 ATATATTTTTAAAGTTAAGATAAAGACTAAA
1 A-ATATTTTT-AAGTTAAGAT-AAGAATAAA
*
3435066 ATATATTTTTAAGTTAAAATAAGAATAAA
1 A-ATATTTTTAAGTTAAGATAAGAATAAA
*
3435095 ATATATTTTTAAGTTAAGACAAGAATAAA
1 A-ATATTTTTAAGTTAAGATAAGAATAAA
* **
3435124 ATATATTTAATAAGTTAATTTAA-AACTAAA
1 A-ATATTT-TTAAGTTAAGATAAGAA-TAAA
3435154 AGATATTTTTAATGTTAA
1 A-ATATTTTTAA-GTTAA
3435172 AATGTAAAAT
Statistics
Matches: 277, Mismatches: 39, Indels: 41
0.78 0.11 0.11
Matches are distributed among these distances:
24 4 0.01
25 10 0.04
26 17 0.06
27 17 0.06
28 11 0.04
29 64 0.23
30 133 0.48
31 21 0.08
ACGTcount: A:0.51, C:0.01, G:0.08, T:0.39
Consensus pattern (28 bp):
AATATTTTTAAGTTAAGATAAGAATAAA
Found at i:3434931 original size:54 final size:53
Alignment explanation
Indices: 3434834--3434940 Score: 148
Period size: 54 Copynumber: 2.0 Consensus size: 53
3434824 ATAAAAATAT
*
3434834 AATATTTTTAGTTAAGATAAATATAAAATATATTTTTGTAGTTAAAATAAAAA
1 AATATTTTTAGTTAAGATAAATATAAAATATATTTTTGAAGTTAAAATAAAAA
3434887 AATATTTTTAAGTTAAGATAAGA-ATAGAAA-ATATGTTTT-AAGTTAAAATAAAAA
1 AATATTTTT-AGTTAAGATAA-ATATA-AAATATAT-TTTTGAAGTTAAAATAAAAA
3434941 TTAATTATAT
Statistics
Matches: 49, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
53 9 0.18
54 32 0.65
55 8 0.16
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.38
Consensus pattern (53 bp):
AATATTTTTAGTTAAGATAAATATAAAATATATTTTTGAAGTTAAAATAAAAA
Found at i:3434969 original size:60 final size:59
Alignment explanation
Indices: 3434843--3435186 Score: 278
Period size: 60 Copynumber: 5.8 Consensus size: 59
3434833 TAATATTTTT
*
3434843 AGTTAAGATAA-ATATAAAATATATTTTTGTAGTTAAAATAAAAA--AA-TAT-TTT--TA
1 AGTTAAGATAAGA-ATAAAATATATTTTT-AAGTTAAAATAAAAATTAATTATATTTAATA
3434897 AGTTAAGATAAGAATAGAAA-ATATGTTTTAAGTTAAAATAAAAATTAATTATATTTAATA
1 AGTTAAGATAAGAATA-AAATATAT-TTTTAAGTTAAAATAAAAATTAATTATATTTAATA
* * * * ** ** * *
3434957 ATTTAAGGTAAGAATTAAATATATTTAATACTTTAATTTAAGAATATAATT-TATGTAATA
1 AGTTAAGATAAGAATAAAATATATTT-TTAAGTTAAAATAAAAAT-TAATTATATTTAATA
* * * * *
3435017 AGTTAAGATAAGAATAAAATATATTTTTAAAGTTAAGATAAAGACTAAAATATATTT-TTA
1 AGTTAAGATAAGAATAAAATATATTTTT-AAGTTAAAATAAA-AATTAATTATATTTAATA
* * * * * *
3435077 AGTTAAAATAAGAATAAAATATATTTTTAAGTTAAGACAAGAATAAAATATATTTAATA
1 AGTTAAGATAAGAATAAAATATATTTTTAAGTTAAAATAAAAATTAATTATATTTAATA
** * *
3435136 AGTTAATTTAA-AACTAAAAGATATTTTTAATGTTAAAATGTAAAATTAATT
1 AGTTAAGATAAGAA-TAAAATATATTTTTAA-GTTAAAAT-AAAAATTAATT
3435187 TAATATGGAA
Statistics
Matches: 232, Mismatches: 39, Indels: 31
0.77 0.13 0.10
Matches are distributed among these distances:
54 32 0.14
55 8 0.03
56 2 0.01
57 3 0.01
58 18 0.08
59 43 0.19
60 108 0.47
61 18 0.08
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.39
Consensus pattern (59 bp):
AGTTAAGATAAGAATAAAATATATTTTTAAGTTAAAATAAAAATTAATTATATTTAATA
Found at i:3435729 original size:2 final size:2
Alignment explanation
Indices: 3435722--3435750 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3435712 TCAGCCTTTA
3435722 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
3435751 ATTTTTAATA
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:3436996 original size:20 final size:20
Alignment explanation
Indices: 3436952--3437163 Score: 226
Period size: 20 Copynumber: 10.4 Consensus size: 20
3436942 GATTCTGACT
3436952 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGAGTATCCGT-AA
3436973 ATCGCAACGAGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
** *
3436993 ATCGCAACGACAATACGTAAA
1 ATCGCAACGAGTATCCGT-AA
* *
3437014 ATTGCAACGCGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
* * *
3437034 ATCGCAACGAGAATACATAA
1 ATCGCAACGAGTATCCGTAA
* *
3437054 ATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGTATCCGTAA
* *
3437074 ATCGCAACGAGAATACGTAA
1 ATCGCAACGAGTATCCGTAA
* *
3437094 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
** *
3437114 ATCGCAACGACAATACGTAAA
1 ATCGCAACGAGTATCCGT-AA
* *
3437135 ATCACAACGCGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
3437155 ATCGCAACG
1 ATCGCAACG
3437164 CGATTTTTAA
Statistics
Matches: 152, Mismatches: 37, Indels: 5
0.78 0.19 0.03
Matches are distributed among these distances:
20 104 0.68
21 48 0.32
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
ATCGCAACGAGTATCCGTAA
Found at i:3437074 original size:40 final size:41
Alignment explanation
Indices: 3436952--3437163 Score: 320
Period size: 41 Copynumber: 5.2 Consensus size: 41
3436942 GATTCTGACT
* * *
3436952 ATCGCAACGAGTATCCGTAAAATCGCAACGAGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
3436993 ATCGCAACGACAATACGTAAAATTGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
3437034 ATCGCAACGAGAATACAT-AAATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
3437074 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
3437114 ATCGCAACGACAATACGTAAAATCACAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
3437155 ATCGCAACG
1 ATCGCAACG
3437164 CGATTTTTAA
Statistics
Matches: 155, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 74 0.48
41 81 0.52
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.19
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:3437786 original size:21 final size:21
Alignment explanation
Indices: 3437725--3437817 Score: 106
Period size: 20 Copynumber: 4.6 Consensus size: 21
3437715 TTCTAAACTT
*
3437725 AAAATCGCAAC-ATGAAAATG
1 AAAATCGCAACGACGAAAATG
3437745 AAAATCGCAAC-ACGAAAATG
1 AAAATCGCAACGACGAAAATG
**
3437765 ACTATCGCAACGA-GAGAAATG
1 AAAATCGCAACGACGA-AAATG
3437786 AAAATCGCAACG-CG-AAATG
1 AAAATCGCAACGACGAAAATG
*
3437805 AAAAACGCAACGA
1 AAAATCGCAACGA
3437818 GATAATCGCA
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
19 16 0.25
20 30 0.48
21 17 0.27
ACGTcount: A:0.52, C:0.19, G:0.18, T:0.11
Consensus pattern (21 bp):
AAAATCGCAACGACGAAAATG
Found at i:3437804 original size:40 final size:40
Alignment explanation
Indices: 3437725--3437819 Score: 122
Period size: 40 Copynumber: 2.4 Consensus size: 40
3437715 TTCTAAACTT
3437725 AAAATCGCAAC-ATGAAAATGAAAATCGCAACACGAAAATG
1 AAAATCGCAACGA-GAAAATGAAAATCGCAACACGAAAATG
** *
3437765 ACTATCGCAACGAGAGAAATGAAAATCGCAACGCG-AAATG
1 AAAATCGCAACGAGA-AAATGAAAATCGCAACACGAAAATG
*
3437805 AAAAACGCAACGAGA
1 AAAATCGCAACGAGA
3437820 TAATCGCAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
40 28 0.60
41 19 0.40
ACGTcount: A:0.52, C:0.19, G:0.19, T:0.11
Consensus pattern (40 bp):
AAAATCGCAACGAGAAAATGAAAATCGCAACACGAAAATG
Found at i:3437905 original size:20 final size:20
Alignment explanation
Indices: 3437880--3437926 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
3437870 GATTCTCTCA
*
3437880 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTCTCGCG
* *
3437900 TTGCGATAGTTATTCTCTCG
1 TTGCGATAGTCATTCTCGCG
3437920 TTGCGAT
1 TTGCGAT
3437927 TTTTATTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.19, G:0.23, T:0.43
Consensus pattern (20 bp):
TTGCGATAGTCATTCTCGCG
Found at i:3439781 original size:94 final size:94
Alignment explanation
Indices: 3439620--3439999 Score: 638
Period size: 94 Copynumber: 4.1 Consensus size: 94
3439610 TAGATTGCTT
* * *
3439620 AGTAAATTTATTCGGTTGCTGCAAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
3439685 ATTTGTCTTTTATTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
3439714 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
3439779 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
3439808 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
3439873 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * * * *
3439902 ACTAAATTTGTTCAGTTGCTGTCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
3439967 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
3439995 AGTAA
1 AGTAA
3440000 TGCAATCCAT
Statistics
Matches: 274, Mismatches: 11, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
93 24 0.09
94 250 0.91
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:3440121 original size:14 final size:14
Alignment explanation
Indices: 3440102--3440159 Score: 71
Period size: 14 Copynumber: 3.8 Consensus size: 14
3440092 AACGCGAAAT
3440102 GAATCGCAACGAGA
1 GAATCGCAACGAGA
3440116 GAATCGCAACGAGAAA
1 GAATCGCAACGAG--A
3440132 TGAAAATCGCAACGAGA
1 -G--AATCGCAACGAGA
3440149 GAATCGCAACG
1 GAATCGCAACG
3440160 CGAAATGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
14 23 0.59
16 2 0.05
17 2 0.05
19 12 0.31
ACGTcount: A:0.45, C:0.21, G:0.26, T:0.09
Consensus pattern (14 bp):
GAATCGCAACGAGA
Found at i:3440141 original size:19 final size:19
Alignment explanation
Indices: 3440117--3440176 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
3440107 GCAACGAGAG
3440117 AATCGCAACGAGAAATGAA
1 AATCGCAACGAGAAATGAA
3440136 AATCGCAACGAG--A-G--
1 AATCGCAACGAGAAATGAA
*
3440150 AATCGCAACGCGAAATGAA
1 AATCGCAACGAGAAATGAA
3440169 AATCGCAA
1 AATCGCAA
3440177 TGACAAAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 11 0.31
16 2 0.06
17 2 0.06
19 20 0.57
ACGTcount: A:0.48, C:0.20, G:0.22, T:0.10
Consensus pattern (19 bp):
AATCGCAACGAGAAATGAA
Found at i:3440145 original size:33 final size:33
Alignment explanation
Indices: 3440090--3440211 Score: 167
Period size: 33 Copynumber: 3.8 Consensus size: 33
3440080 AATGACTATT
3440090 GCAACGCGAAATG--AATCGCAACGAGAGAATC
1 GCAACGCGAAATGAAAATCGCAACGAGAGAATC
*
3440121 GCAACGAGAAATGAAAATCGCAACGAGAGAATC
1 GCAACGCGAAATGAAAATCGCAACGAGAGAATC
* * *
3440154 GCAACGCGAAATGAAAATCGCAATGACAAAATC
1 GCAACGCGAAATGAAAATCGCAACGAGAGAATC
* **
3440187 ACAACGCGAAACCAAAATCGCAACG
1 GCAACGCGAAATGAAAATCGCAACG
3440212 CGAAACTATA
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
31 12 0.15
33 68 0.85
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (33 bp):
GCAACGCGAAATGAAAATCGCAACGAGAGAATC
Found at i:3440226 original size:19 final size:19
Alignment explanation
Indices: 3440180--3440217 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
3440170 ATCGCAATGA
*
3440180 CAAAATCACAACGCGAAAC
1 CAAAATCGCAACGCGAAAC
3440199 CAAAATCGCAACGCGAAAC
1 CAAAATCGCAACGCGAAAC
3440218 TATAATCGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.32, G:0.13, T:0.05
Consensus pattern (19 bp):
CAAAATCGCAACGCGAAAC
Found at i:3440337 original size:20 final size:20
Alignment explanation
Indices: 3440259--3440327 Score: 120
Period size: 20 Copynumber: 3.5 Consensus size: 20
3440249 GCGATTCTCT
**
3440259 CATTGCGATAGTCAAATTCG
1 CATTGCGATAGTCATTTTCG
3440279 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
3440299 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
3440319 CATTGCGAT
1 CATTGCGAT
3440328 TTTAAGTTTC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTGCGATAGTCATTTTCG
Found at i:3440852 original size:18 final size:19
Alignment explanation
Indices: 3440813--3440854 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
3440803 CTCACCTGTC
3440813 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
3440834 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
3440852 ATC
1 ATC
3440855 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:3440908 original size:42 final size:42
Alignment explanation
Indices: 3440838--3440929 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
3440828 TCCCCTATCG
* *
3440838 TTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCACCA
1 TTCAAGAGGCCACTATCATCCCTCAAGAGGT-CCCTCCCAACA
* ** *
3440880 TTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCAACA
1 TTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAACA
*
3440922 TTCTAGAG
1 TTCAAGAG
3440930 CCCGATTCAC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 40 0.95
43 2 0.05
ACGTcount: A:0.25, C:0.36, G:0.17, T:0.22
Consensus pattern (42 bp):
TTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAACA
Found at i:3442288 original size:14 final size:14
Alignment explanation
Indices: 3442269--3442304 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3442259 ATTGTTTAAT
3442269 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
3442283 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
3442297 TGATTTGT
1 TGATTTGT
3442305 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3442509 original size:19 final size:19
Alignment explanation
Indices: 3442487--3442593 Score: 125
Period size: 19 Copynumber: 5.8 Consensus size: 19
3442477 TGCGAAACTA
* *
3442487 ATTTCGCGTTGCGATTTTT
1 ATTTCGCATTGCGATTTTC
*
3442506 ATTTTCGTATTGCGA--TTC
1 A-TTTCGCATTGCGATTTTC
*
3442524 A-CTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
*
3442540 ATTTCACATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
3442559 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
3442578 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
3442594 CTCTCGTTGC
Statistics
Matches: 75, Mismatches: 7, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 2 0.03
18 3 0.04
19 46 0.61
20 11 0.15
ACGTcount: A:0.16, C:0.20, G:0.17, T:0.48
Consensus pattern (19 bp):
ATTTCGCATTGCGATTTTC
Found at i:3442604 original size:33 final size:33
Alignment explanation
Indices: 3442493--3442626 Score: 133
Period size: 34 Copynumber: 3.8 Consensus size: 33
3442483 ACTAATTTCG
* * *
3442493 CGTTGCGATTTTTATTTTCGTATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
* *
3442527 CGTTGCGATTTTCATTTCACATTGCGATTTTCATTT
1 CGTTGCGATTTTCATTTCGCATTGCGA--TTC-TCT
3442563 CGCATTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CG--TTGCGATTTTCATTTCGCATTGCGATTCTCT
** *
3442598 CGTTGCGATAGTCAATTCCGCATTGCGAT
1 CGTTGCGATTTTC-ATTTCGCATTGCGAT
3442627 AGTCATTTCC
Statistics
Matches: 84, Mismatches: 10, Indels: 12
0.79 0.09 0.11
Matches are distributed among these distances:
33 20 0.24
34 27 0.32
35 7 0.08
36 6 0.07
38 24 0.29
ACGTcount: A:0.16, C:0.22, G:0.18, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:3442622 original size:72 final size:72
Alignment explanation
Indices: 3442487--3442635 Score: 192
Period size: 72 Copynumber: 2.1 Consensus size: 72
3442477 TGCGAAACTA
* * * ** *
3442487 ATTTCGCGTTGCGATTTTTATTTTCGTATTGCGATTCACTCGTTGCGATTTTCATTTCACATTGC
1 ATTTCGCATTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATAGTCATTCCACATTGC
**
3442552 GATTTTC
66 GATAGTC
* *
3442559 ATTTCGCATTGCGATTTTCA-TTTCGCATTGCGATTCTCTCGTTGCGATAGTCAATTCCGCATTG
1 ATTTCGCATTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATAGTC-ATTCCACATTG
3442623 CGATAGTC
65 CGATAGTC
3442631 ATTTC
1 ATTTC
3442636 CGTGTTGCGA
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
71 28 0.42
72 38 0.58
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.44
Consensus pattern (72 bp):
ATTTCGCATTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATAGTCATTCCACATTGC
GATAGTC
Found at i:3442659 original size:20 final size:21
Alignment explanation
Indices: 3442599--3442671 Score: 98
Period size: 20 Copynumber: 3.6 Consensus size: 21
3442589 CGATTCTCTC
*
3442599 GTTGCGATAGTCA-ATTCCGC
1 GTTGCGATAGTCATATTCCGT
*
3442619 ATTGCGATAGTCAT-TTCCGT
1 GTTGCGATAGTCATATTCCGT
3442639 GTTGCGATAGTCATATT-CGT
1 GTTGCGATAGTCATATTCCGT
*
3442659 GTTGCTATAGTCA
1 GTTGCGATAGTCA
3442672 AATGAATGTC
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
20 45 0.96
21 2 0.04
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (21 bp):
GTTGCGATAGTCATATTCCGT
Found at i:3444705 original size:12 final size:13
Alignment explanation
Indices: 3444673--3444706 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
3444663 TTCCCGTGGC
3444673 ATTTTCTTCGGGG
1 ATTTTCTTCGGGG
*
3444686 ATTTTCTTTGGGG
1 ATTTTCTTCGGGG
3444699 A-TTTCTTC
1 ATTTTCTTC
3444707 TTCTTCTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.09, C:0.15, G:0.24, T:0.53
Consensus pattern (13 bp):
ATTTTCTTCGGGG
Found at i:3444836 original size:87 final size:88
Alignment explanation
Indices: 3444738--3444912 Score: 327
Period size: 87 Copynumber: 2.0 Consensus size: 88
3444728 ATATGAATTA
3444738 CAGAATGGATGTTCAATATGTTCATTTACAGTCG-AACTTCCTCCTCATTATCA-CAATAACATC
1 CAGAATGGATGTTCAATATGTTCATTTACAGTCGTAACTT-CTCCTCATTATCATCAATAACATC
3444801 TTCCTCGGCAACGGCTGTTTCATC
65 TTCCTCGGCAACGGCTGTTTCATC
3444825 CAGAATGGATGTTCAATATGTTCATTTACAGTCGTAACTTCTCCTCATTATCATCAATAACATCT
1 CAGAATGGATGTTCAATATGTTCATTTACAGTCGTAACTTCTCCTCATTATCATCAATAACATCT
3444890 TCCTCGGCAACGGCTGTTTCATC
66 TCCTCGGCAACGGCTGTTTCATC
3444913 ATCAAAATTC
Statistics
Matches: 86, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
87 47 0.55
88 39 0.45
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.34
Consensus pattern (88 bp):
CAGAATGGATGTTCAATATGTTCATTTACAGTCGTAACTTCTCCTCATTATCATCAATAACATCT
TCCTCGGCAACGGCTGTTTCATC
Found at i:3445917 original size:20 final size:20
Alignment explanation
Indices: 3445892--3445937 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
3445882 ATCTCGTTGC
3445892 GATTTATAG-ATTCGCATTGT
1 GATTTAT-GTATTCGCATTGT
3445912 GATTTATGTATTCGCATTGT
1 GATTTATGTATTCGCATTGT
3445932 GATTTA
1 GATTTA
3445938 CATAATCACA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.24, C:0.09, G:0.20, T:0.48
Consensus pattern (20 bp):
GATTTATGTATTCGCATTGT
Found at i:3445971 original size:20 final size:20
Alignment explanation
Indices: 3445903--3445973 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
3445893 ATTTATAGAT
* * *
3445903 TCGCATTGTGATTTATGTAT
1 TCGCATTGCGATTTACGTAA
* *
3445923 TCGCATTGTGATTTACATAA
1 TCGCATTGCGATTTACGTAA
*
3445943 TCACATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGTAA
*
3445963 TCGCGTTGCGA
1 TCGCATTGCGA
3445974 ATTAGGAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAA
Found at i:3446110 original size:20 final size:20
Alignment explanation
Indices: 3446066--3446257 Score: 183
Period size: 20 Copynumber: 9.6 Consensus size: 20
3446056 TACCGGAGAT
*
3446066 CGCGTTGCGAATTATC-GAT-
1 CGCGTTGCGATTTA-CGGATA
**
3446085 CGCGTTATGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3446105 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
3446125 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
3446146 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* **
3446166 CTCGTTGCGATTTATAGATA
1 CGCGTTGCGATTTACGGATA
* *
3446186 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
3446206 CTCGTTGCGATTTATGGATA
1 CGCGTTGCGATTTACGGATA
3446226 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
3446247 CTCGTTGCGAT
1 CGCGTTGCGAT
3446258 AGTCAGAATC
Statistics
Matches: 137, Mismatches: 30, Indels: 11
0.77 0.17 0.06
Matches are distributed among these distances:
18 1 0.01
19 14 0.10
20 87 0.64
21 35 0.26
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:3446134 original size:60 final size:58
Alignment explanation
Indices: 3446068--3446280 Score: 189
Period size: 61 Copynumber: 3.5 Consensus size: 58
3446058 CCGGAGATCG
* ** *
3446068 CGTTGCGAATTATCGATCGCGTTATGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTA-CGATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACG-ATAGT
* * * *
3446128 CGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCTCGTTGCGATTTATA-GATACG-
1 CGTTGCGATTTAC-GAT-CGCGTTGCGATTTACGGATACGCGTTGCGATTT-TACGATA-GT
* * *
3446188 CGTTGCGATTTACGTATTCTCGTTGCGATTTATGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACG-A-TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTAC-GATAGT
*
3446249 CGTTGCGATAGT-CAGAATCGCGTTGCGATTTA
1 CGTTGCGAT-TTAC-G-ATCGCGTTGCGATTTA
3446281 TATGTTCACG
Statistics
Matches: 124, Mismatches: 18, Indels: 21
0.76 0.11 0.13
Matches are distributed among these distances:
59 4 0.03
60 57 0.46
61 58 0.47
62 5 0.04
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (58 bp):
CGTTGCGATTTACGATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGATAGT
Found at i:3446171 original size:40 final size:41
Alignment explanation
Indices: 3446093--3446257 Score: 253
Period size: 40 Copynumber: 4.1 Consensus size: 41
3446083 ATCGCGTTAT
*
3446093 GATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGC
1 GATTTACGGATACGCGTTGCGATTTTACGTATTCTCGTTGC
*
3446134 GATTTACGGATACGCATTGCGA-TTTACGTATTCTCGTTGC
1 GATTTACGGATACGCGTTGCGATTTTACGTATTCTCGTTGC
**
3446174 GATTTATAGATACGCGTTGCGA-TTTACGTATTCTCGTTGC
1 GATTTACGGATACGCGTTGCGATTTTACGTATTCTCGTTGC
* * *
3446214 GATTTATGGATACGCGTTGCGATTTTACGGATACTCGTTGC
1 GATTTACGGATACGCGTTGCGATTTTACGTATTCTCGTTGC
3446255 GAT
1 GAT
3446258 AGTCAGAATC
Statistics
Matches: 115, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
40 75 0.65
41 40 0.35
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (41 bp):
GATTTACGGATACGCGTTGCGATTTTACGTATTCTCGTTGC
Found at i:3446271 original size:81 final size:79
Alignment explanation
Indices: 3446101--3446299 Score: 249
Period size: 81 Copynumber: 2.5 Consensus size: 79
3446091 ATGATTTACG
* * *
3446101 GATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCATTGCGATTTACGTATT
1 GATACGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATACGCATTGCGATTTACGGATA
3446166 CTCGTTGCGATTTATA
65 CTCGTTGCGA-TTATA
* *
3446182 GATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTATGGATACGCGTTGCGATTTTACGGATA
1 GATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCATTGCGA-TTTACGGATA
3446247 CTCGTTGCGA-TAGTCA
65 CTCGTTGCGATTA-T-A
** * *
3446263 GA-ATCGCGTTGCGATTTATATGTTCACGTTGCGATTT
1 GATA-CGCGTTGCGATTTACGTATTCTCGTTGCGATTT
3446300 TCATATTCAC
Statistics
Matches: 105, Mismatches: 9, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
79 2 0.02
80 39 0.37
81 64 0.61
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.38
Consensus pattern (79 bp):
GATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCATTGCGATTTACGGATAC
TCGTTGCGATTATA
Found at i:3446292 original size:20 final size:20
Alignment explanation
Indices: 3446269--3446318 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
3446259 GTCAGAATCG
*
3446269 CGTTGCGATTTAT-ATGTTCA
1 CGTTGCGATTT-TCATATTCA
3446289 CGTTGCGATTTTCATATTCA
1 CGTTGCGATTTTCATATTCA
3446309 CGTTGCGATT
1 CGTTGCGATT
3446319 CTGGAAAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTTTCATATTCA
Found at i:3446420 original size:20 final size:19
Alignment explanation
Indices: 3446368--3446421 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
3446358 ATTCTTCATA
3446368 ATCGCGTTACGATTCTGGG
1 ATCGCGTTACGATTCTGGG
* ** *
3446387 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTACGATTCTGG-G
3446408 ATCGCGTTACGATT
1 ATCGCGTTACGATT
3446422 TTTATTTCGC
Statistics
Matches: 25, Mismatches: 8, Indels: 3
0.69 0.22 0.08
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.33
Consensus pattern (19 bp):
ATCGCGTTACGATTCTGGG
Found at i:3452999 original size:21 final size:21
Alignment explanation
Indices: 3452961--3453000 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3452951 CCCCCTTTGA
* *
3452961 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGAATACCCCCAC
*
3452982 AGGGGAATCGAATACCCCC
1 AGGGGAACCGAATACCCCC
3453001 TGGGGTTCTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.38, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGAATACCCCCAC
Found at i:3462918 original size:21 final size:21
Alignment explanation
Indices: 3462892--3462936 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
3462882 AATATTTTTT
3462892 AATATTTCAAACATTTG-AAAA
1 AATATTT-AAACATTTGTAAAA
*
3462913 AATATTTTAACATTTGTAAAA
1 AATATTTAAACATTTGTAAAA
3462934 AAT
1 AAT
3462937 GCATTGAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (21 bp):
AATATTTAAACATTTGTAAAA
Found at i:3464513 original size:20 final size:19
Alignment explanation
Indices: 3464488--3464528 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
3464478 AAAACAAAAA
3464488 TCCCGGTTTTTCCCAGATTT
1 TCCCGGTTTTTCCC-GATTT
*
3464508 TCCCGGTTTTTTCCGATTT
1 TCCCGGTTTTTCCCGATTT
3464527 TC
1 TC
3464529 AATCGGTCCG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.07, C:0.29, G:0.15, T:0.49
Consensus pattern (19 bp):
TCCCGGTTTTTCCCGATTT
Found at i:3468887 original size:60 final size:58
Alignment explanation
Indices: 3468761--3468906 Score: 159
Period size: 60 Copynumber: 2.4 Consensus size: 58
3468751 GAATTTTAAT
*
3468761 AAATAAATTTAACAATTTATTTCTTTCTTACAAAATAGAATCATACTTGACTCTCAAGA
1 AAATAAATTTAA-AATTTATTTCTTTCTTACAAAATAGAATCATACTTAACTCTCAAGA
* * * * * *
3468820 AAGTAAATTTAATAATTTATTTCATTTTTTTA-AAACTATAATCATACTTAATTTTCAAGA
1 AAATAAATTTAA-AATTTATTTC--TTTCTTACAAAATAGAATCATACTTAACTCTCAAGA
*
3468880 AAATAAATTCAAAATTTTATTTTCTTT
1 AAATAAATTTAAAA-TTTA-TTTCTTT
3468907 TATAAAATAG
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
59 26 0.36
60 37 0.51
61 10 0.14
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.44
Consensus pattern (58 bp):
AAATAAATTTAAAATTTATTTCTTTCTTACAAAATAGAATCATACTTAACTCTCAAGA
Found at i:3469028 original size:39 final size:38
Alignment explanation
Indices: 3468975--3469125 Score: 187
Period size: 39 Copynumber: 3.9 Consensus size: 38
3468965 ATTATCAAGA
* *
3468975 AAAATAAATCCAATGGTTTATTTTCTTTTACAAAACTGG
1 AAAATAAATCCAATGATTTATTTCCTTTTACAAAACT-G
*
3469014 AAAATAAATCCAATGATTTATTTCCTTTTACAAATCATG
1 AAAATAAATCCAATGATTTATTTCCTTTTACAAAAC-TG
* * *
3469053 AAAACAAATTCAATGATTTATTTCATTTTACAAAA-TAAG
1 AAAATAAATCCAATGATTTATTTCCTTTTACAAAACT--G
* *
3469092 AAAATAAATCAAACGATTTATTTCCTTTTACAAA
1 AAAATAAATCCAATGATTTATTTCCTTTTACAAA
3469126 TCAGAATCAT
Statistics
Matches: 97, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
37 1 0.01
39 95 0.98
40 1 0.01
ACGTcount: A:0.44, C:0.13, G:0.06, T:0.37
Consensus pattern (38 bp):
AAAATAAATCCAATGATTTATTTCCTTTTACAAAACTG
Found at i:3469114 original size:78 final size:78
Alignment explanation
Indices: 3468975--3469128 Score: 222
Period size: 78 Copynumber: 2.0 Consensus size: 78
3468965 ATTATCAAGA
* * * * *
3468975 AAAATAAATCCAATGGTTTATTTTCTTTTACAAAACTGGAAAATAAATCCAATGATTTATTTCCT
1 AAAACAAATCCAATGATTTATTTTCTTTTACAAAACTAGAAAATAAATCAAACGATTTATTTCCT
3469040 TTTACAAATCATG
66 TTTACAAATCATG
*
3469053 AAAACAAATTCAATGATTTA-TTTCATTTTACAAAA-TAAGAAAATAAATCAAACGATTTATTTC
1 AAAACAAATCCAATGATTTATTTTC-TTTTACAAAACT-AGAAAATAAATCAAACGATTTATTTC
3469116 CTTTTACAAATCA
64 CTTTTACAAATCA
3469129 GAATCATGTG
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
77 5 0.07
78 63 0.93
ACGTcount: A:0.44, C:0.14, G:0.06, T:0.37
Consensus pattern (78 bp):
AAAACAAATCCAATGATTTATTTTCTTTTACAAAACTAGAAAATAAATCAAACGATTTATTTCCT
TTTACAAATCATG
Found at i:3469180 original size:136 final size:135
Alignment explanation
Indices: 3469013--3469256 Score: 364
Period size: 136 Copynumber: 1.8 Consensus size: 135
3469003 TACAAAACTG
*
3469013 GAAAATAAATCCAATGATTTATTTCCTTTTACAA-ATCATGAAAACAAATTCAATGATTTATTTC
1 GAAAATAAATCCAATGATTTATTTCCTTTTACAAGA-CATGAAAACAAATTAAATGATTTATTTC
3469077 ATTTTACAAAATAAGAAAATAAATCAAACGATTTATTTCCTTTTACAAATCAGAATCATGTGAGA
65 ATTTTACAAAA-AAGAAAATAAATCAAACGATTTATTTCCTTTTACAAATCAGAATCATGTGAGA
3469142 GTCTCAT
129 GTCTCAT
* * * * *
3469149 GAAAATAATTTCACTGATTTATTTCCTTTTACAAGACATGAAAATAAATTAAATGATTTATTTCC
1 GAAAATAAATCCAATGATTTATTTCCTTTTACAAGACATGAAAACAAATTAAATGATTTATTTCA
* * * * *
3469214 TTTTACAAGACATAAAATAAATCCAATGATTTATTTCCTTTTA
66 TTTTACAAAAAAGAAAATAAATCAAACGATTTATTTCCTTTTA
3469257 AAAAATAGAA
Statistics
Matches: 96, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
135 29 0.30
136 66 0.69
137 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (135 bp):
GAAAATAAATCCAATGATTTATTTCCTTTTACAAGACATGAAAACAAATTAAATGATTTATTTCA
TTTTACAAAAAAGAAAATAAATCAAACGATTTATTTCCTTTTACAAATCAGAATCATGTGAGAGT
CTCAT
Found at i:3469194 original size:175 final size:175
Alignment explanation
Indices: 3468922--3469293 Score: 473
Period size: 175 Copynumber: 2.1 Consensus size: 175
3468912 AATAGTAATT
* * *
3468922 AATCCAACAATTTATTTTCTTTTACAACCCAGAATCATATAAGATTATCAAGAAAAATAAATCCA
1 AATCCAACGATTTATTTTCTTTTACAAACCAGAATCATATAAGAGTATCAAGAAAAATAAATCCA
* * *
3468987 ATGGTTTATTTTCTTTTACAAAACTGGAAAATAAATCCAATGATTTATTTCCTTTTACAA-ATCA
66 ATGATTTATTTCCTTTTACAAAACTGGAAAATAAATCAAATGATTTATTTCCTTTTACAAGA-CA
* *
3469051 TGAAAACAAATTCAATGATTTATTTCATTTTACAAAATAAGAAAAT-A
130 T-AAAACAAATCCAATGATTTATTTCATTTTAAAAAAT-AGAAAATAA
* * * * * * * * *
3469098 AATCAAACGATTTATTTCCTTTTACAAATCAGAATCATGTGAGAGTCTCATG-AAAATAATTTCA
1 AATCCAACGATTTATTTTCTTTTACAAACCAGAATCATATAAGAGTATCAAGAAAAATAAATCCA
* * *
3469162 CTGATTTATTTCCTTTTACAAGACAT-GAAAATAAATTAAATGATTTATTTCCTTTTACAAGACA
66 ATGATTTATTTCCTTTTACAAAAC-TGGAAAATAAATCAAATGATTTATTTCCTTTTACAAGACA
* *
3469226 TAAAATAAATCCAATGATTTATTTCCTTTTAAAAAATAGAAAATAA
130 TAAAACAAATCCAATGATTTATTTCATTTTAAAAAATAGAAAATAA
*
3469272 AATCCAACGATCTATTTTCTTT
1 AATCCAACGATTTATTTTCTTT
3469294 CTTTTACAAA
Statistics
Matches: 168, Mismatches: 25, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
173 7 0.04
174 52 0.31
175 65 0.39
176 44 0.26
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (175 bp):
AATCCAACGATTTATTTTCTTTTACAAACCAGAATCATATAAGAGTATCAAGAAAAATAAATCCA
ATGATTTATTTCCTTTTACAAAACTGGAAAATAAATCAAATGATTTATTTCCTTTTACAAGACAT
AAAACAAATCCAATGATTTATTTCATTTTAAAAAATAGAAAATAA
Found at i:3469206 original size:39 final size:39
Alignment explanation
Indices: 3469146--3469272 Score: 179
Period size: 39 Copynumber: 3.3 Consensus size: 39
3469136 GTGAGAGTCT
* *
3469146 CATGAAAATAATTTCACTGATTTATTTCCTTTTACAAGA
1 CATGAAAATAAATTCAATGATTTATTTCCTTTTACAAGA
*
3469185 CATGAAAATAAATTAAATGATTTATTTCCTTTTACAAGA
1 CATGAAAATAAATTCAATGATTTATTTCCTTTTACAAGA
*
3469224 CAT-AAAATAAATCCAATGATTTATTTCCTTTTA-AA-A
1 CATGAAAATAAATTCAATGATTTATTTCCTTTTACAAGA
*
3469260 AATAGAAAATAAA
1 CAT-GAAAATAAA
3469273 ATCCAACGAT
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
36 3 0.04
37 2 0.03
38 36 0.45
39 39 0.49
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.37
Consensus pattern (39 bp):
CATGAAAATAAATTCAATGATTTATTTCCTTTTACAAGA
Found at i:3469242 original size:38 final size:38
Alignment explanation
Indices: 3469163--3469293 Score: 163
Period size: 39 Copynumber: 3.4 Consensus size: 38
3469153 ATAATTTCAC
**
3469163 TGATTTATTTCCTTTTACAAGACATGAAAATAAATTAAA
1 TGATTTATTTCCTTTTACAAGACAT-AAAATAAATCCAA
3469202 TGATTTATTTCCTTTTACAAGACATAAAATAAATCCAA
1 TGATTTATTTCCTTTTACAAGACATAAAATAAATCCAA
* * * *
3469240 TGATTTATTTCCTTTTAAAAAATAGAAAATAAAATCCAA
1 TGATTTATTTCCTTTTACAAGACATAAAAT-AAATCCAA
* * *
3469279 CGATCTATTTTCTTT
1 TGATTTATTTCCTTT
3469294 CTTTTACAAA
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
38 37 0.45
39 45 0.55
ACGTcount: A:0.41, C:0.13, G:0.06, T:0.40
Consensus pattern (38 bp):
TGATTTATTTCCTTTTACAAGACATAAAATAAATCCAA
Found at i:3470856 original size:21 final size:21
Alignment explanation
Indices: 3470832--3470875 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3470822 GATAAAAAAA
3470832 TATTTAAAATATT-ATTATTTT
1 TATTTAAAATATTAATT-TTTT
*
3470853 TATTTAAAATTTTAATTTTTT
1 TATTTAAAATATTAATTTTTT
3470874 TA
1 TA
3470876 ATATTTTCGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TATTTAAAATATTAATTTTTT
Found at i:3470881 original size:17 final size:18
Alignment explanation
Indices: 3470839--3470882 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
3470829 AAATATTTAA
*
3470839 AATATTATTATTTTTATTT
1 AATATT-TTAATTTTATTT
*
3470858 AAAATTTTAATTTT-TTT
1 AATATTTTAATTTTATTT
3470875 AATATTTT
1 AATATTTT
3470883 CGGTAAAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 10 0.45
18 7 0.32
19 5 0.23
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
AATATTTTAATTTTATTT
Found at i:3475080 original size:36 final size:36
Alignment explanation
Indices: 3475040--3475153 Score: 196
Period size: 36 Copynumber: 3.2 Consensus size: 36
3475030 CAAAATGGTC
3475040 ATTTCCAATACTAGTGGAATAACCTAATTTGAGCAT
1 ATTTCCAATACTAGTGGAATAACCTAATTTGAGCAT
3475076 ATTTCCAATACTAGTGGAATAACCTAATTTGAGCAT
1 ATTTCCAATACTAGTGGAATAACCTAATTTGAGCAT
* *
3475112 ATTTCCAATACTAGTGGGATAACCTAA-CT-AGCAT
1 ATTTCCAATACTAGTGGAATAACCTAATTTGAGCAT
3475146 ATTTCCAA
1 ATTTCCAA
3475154 CATTCAATTG
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
34 13 0.17
35 1 0.01
36 62 0.82
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.32
Consensus pattern (36 bp):
ATTTCCAATACTAGTGGAATAACCTAATTTGAGCAT
Found at i:3475761 original size:31 final size:31
Alignment explanation
Indices: 3475726--3475784 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
3475716 AATTCGATGA
*
3475726 ATTCAATATGTCCTTCTCACTAGAAACTTTC
1 ATTCAATATGTCATTCTCACTAGAAACTTTC
*
3475757 ATTCAATATGTCATTCTCACTAGGAACT
1 ATTCAATATGTCATTCTCACTAGAAACT
3475785 CCCAAACTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.31, C:0.24, G:0.08, T:0.37
Consensus pattern (31 bp):
ATTCAATATGTCATTCTCACTAGAAACTTTC
Found at i:3479228 original size:18 final size:18
Alignment explanation
Indices: 3479205--3479239 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3479195 AAAAAACACT
3479205 AATATTTATATAGCTATA
1 AATATTTATATAGCTATA
3479223 AATATTTATATAGCTAT
1 AATATTTATATAGCTAT
3479240 TTAATAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.46
Consensus pattern (18 bp):
AATATTTATATAGCTATA
Found at i:3481977 original size:21 final size:21
Alignment explanation
Indices: 3481953--3482000 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
3481943 GGGGCATGAG
3481953 ACGACCATCTCAAGGCACATC
1 ACGACCATCTCAAGGCACATC
*
3481974 ACGACCATCTTAAGGCACATC
1 ACGACCATCTCAAGGCACATC
3481995 ACGACC
1 ACGACC
3482001 TACAGTCAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.38, G:0.15, T:0.15
Consensus pattern (21 bp):
ACGACCATCTCAAGGCACATC
Done.