Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009610.1 Hibiscus syriacus cultivar Beakdansim tig00116996_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: 3811333
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 18
Found at i:1315915 original size:16 final size:17
Alignment explanation
Indices: 1315896--1315932 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1315886 TAAAATATTA
1315896 TTTTA-AATAATTAC-AT
1 TTTTACAATAA-TACTAT
1315912 TTTTACAATAATACTAT
1 TTTTACAATAATACTAT
1315929 TTTT
1 TTTT
1315933 TTCATCCCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTTACAATAATACTAT
Found at i:1315984 original size:15 final size:15
Alignment explanation
Indices: 1315942--1315987 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1315932 TTTCATCCCA
*
1315942 TAAAAT-TATAAATAG
1 TAAAATATA-AAATAT
*
1315957 TAAAATATTAAATAT
1 TAAAATATAAAATAT
1315972 TAAAATATAAAATAT
1 TAAAATATAAAATAT
1315987 T
1 T
1315988 TTAAATTCTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 26 0.96
16 1 0.04
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (15 bp):
TAAAATATAAAATAT
Found at i:1318472 original size:17 final size:18
Alignment explanation
Indices: 1318424--1318472 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 18
1318414 AATTCATCTT
*
1318424 TGTTTTTATCAGTTTTAG
1 TGTTTTTATAAGTTTTAG
* *
1318442 T-TTCTAATAA-TTTT-G
1 TGTTTTTATAAGTTTTAG
1318457 TGTTTTTATAAGTTTT
1 TGTTTTTATAAGTTTT
1318473 TTTTTTCTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 5
0.71 0.15 0.15
Matches are distributed among these distances:
15 2 0.08
16 11 0.46
17 10 0.42
18 1 0.04
ACGTcount: A:0.20, C:0.04, G:0.12, T:0.63
Consensus pattern (18 bp):
TGTTTTTATAAGTTTTAG
Found at i:1320060 original size:32 final size:30
Alignment explanation
Indices: 1320018--1320090 Score: 94
Period size: 32 Copynumber: 2.4 Consensus size: 30
1320008 ATAAACAAGG
*
1320018 TAAAGAAAAAAATAAAATAAAGAGAATAAAA
1 TAAAGGAAAAAATAAAATAAAGA-AATAAAA
* *
1320049 TAAAAGGAAAAAATAAAATAAATAAATAAGA
1 T-AAAGGAAAAAATAAAATAAAGAAATAAAA
1320080 T-AAGGAAAAAA
1 TAAAGGAAAAAA
1320091 ATAGTAAAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 10 0.26
31 8 0.21
32 20 0.53
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (30 bp):
TAAAGGAAAAAATAAAATAAAGAAATAAAA
Found at i:1320063 original size:13 final size:15
Alignment explanation
Indices: 1320028--1320066 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
1320018 TAAAGAAAAA
1320028 AATAAAAT-AAAGAG
1 AATAAAATAAAAGAG
1320042 AATAAAATAAAAG-G
1 AATAAAATAAAAGAG
1320056 AA-AAAATAAAA
1 AATAAAATAAAA
1320067 TAAATAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.38
14 11 0.46
15 4 0.17
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (15 bp):
AATAAAATAAAAGAG
Found at i:1320142 original size:2 final size:2
Alignment explanation
Indices: 1320135--1320163 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1320125 AACAAGGAAA
1320135 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
1320164 CATCAAAGTA
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:1320219 original size:36 final size:38
Alignment explanation
Indices: 1320154--1320229 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 38
1320144 TATATATATA
*
1320154 TATATATATACATCAAAGTATTAATAAAATA-AATAAGC
1 TATATATATACAACAAAGTATTAATAAAATAGAA-AAGC
*
1320192 TATATATATACAACAAA-TATTTA-AAAATAGAAAAGC
1 TATATATATACAACAAAGTATTAATAAAATAGAAAAGC
1320228 TA
1 TA
1320230 CCCTCTCACT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 12 0.34
37 7 0.20
38 16 0.46
ACGTcount: A:0.57, C:0.08, G:0.05, T:0.30
Consensus pattern (38 bp):
TATATATATACAACAAAGTATTAATAAAATAGAAAAGC
Found at i:1321382 original size:64 final size:65
Alignment explanation
Indices: 1321314--1321434 Score: 154
Period size: 64 Copynumber: 1.9 Consensus size: 65
1321304 GGAACACTTA
* **
1321314 ATGCAGCGGTGCACCAAGTGTGCATCGATGCATGTAATGCATTCGATG-TTTGAAAAATAGCTTG
1 ATGCAGCGATGCACCAAGTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAAATAGCTTG
* *****
1321378 ATGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAA
1 ATGCAGCGATGCACCAAGTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAA
1321435 TATTCAGAGT
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
64 39 0.83
65 8 0.17
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (65 bp):
ATGCAGCGATGCACCAAGTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAAATAGCTTG
Found at i:1321403 original size:19 final size:20
Alignment explanation
Indices: 1321373--1321410 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
1321363 TTGAAAAATA
1321373 GCTTGATGCATCGATGCATG
1 GCTTGATGCATCGATGCATG
1321393 GCTTG-TGCATCGATGCAT
1 GCTTGATGCATCGATGCAT
1321411 CAAATGCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (20 bp):
GCTTGATGCATCGATGCATG
Found at i:1321435 original size:64 final size:65
Alignment explanation
Indices: 1321330--1321492 Score: 208
Period size: 65 Copynumber: 2.5 Consensus size: 65
1321320 CGGTGCACCA
*
1321330 AGTGTGCATCGATGCATGTAATGCATTCGATG-TTTGAAAAATAGCTT-GA-TGCATCGATGCAT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATA--TTAGAGTGCATCGATGCAT
1321392 GG
64 GG
** *
1321394 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATATT-AGAGTGCATCGATGCATG
1321458 G
65 G
* * *
1321459 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
1321493 CAATTAATTC
Statistics
Matches: 85, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
62 2 0.02
64 36 0.42
65 47 0.55
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.31
Consensus pattern (65 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATATTAGAGTGCATCGATGCATGG
Found at i:1321464 original size:19 final size:19
Alignment explanation
Indices: 1321440--1321490 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1321430 GAAAATATTC
1321440 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
1321459 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
1321478 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
1321491 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:1321532 original size:65 final size:63
Alignment explanation
Indices: 1321334--1321541 Score: 201
Period size: 65 Copynumber: 3.2 Consensus size: 63
1321324 GCACCAAGTG
* * * *
1321334 TGCATCGATGCATGTAATGCATTCGATGTTTGAAAAATAGCTTGATGCATCGATGCATGGCTTG-
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAAT-TCATGATGCATCGATGCATGAC-TGA
*
1321398 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGGA--
1 TGCATCGATGCATGAAATGCATTCGATG-TTTGAAAA-ATTCATGA-TGCATCGATGCAT-GACT
1321460 GA
62 GA
* * * *
1321462 GTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTAATTCATCGATGCATCGATGCATGTACT
1 -TGCATCGATGCATGAAATGCATTCGATGTTTGAA-AAATTCAT-GATGCATCGATGCATG-ACT
1321526 GA
62 GA
*
1321528 TGCATCGGTGCATG
1 TGCATCGATGCATG
1321542 CCTTTGAATA
Statistics
Matches: 122, Mismatches: 10, Indels: 23
0.79 0.06 0.15
Matches are distributed among these distances:
63 11 0.09
64 43 0.35
65 63 0.52
66 5 0.04
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (63 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATTCATGATGCATCGATGCATGACTGA
Found at i:1327976 original size:22 final size:21
Alignment explanation
Indices: 1327934--1327973 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1327924 GAGTTTGTTT
*
1327934 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1327955 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1327974 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1329966 original size:64 final size:64
Alignment explanation
Indices: 1329898--1330078 Score: 220
Period size: 64 Copynumber: 2.8 Consensus size: 64
1329888 TTGGAACACT
* ***
1329898 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTT-GAAAAATAGCC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTCG-AAAATAGCC
** * **
1329962 TGATGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTCGAAAATATTC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTCGAAAATAGCC
* * * *
1330026 AGAGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 TGA-TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTT
1330079 CAATTAATTC
Statistics
Matches: 99, Mismatches: 16, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
64 55 0.56
65 44 0.44
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (64 bp):
TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTCGAAAATAGCC
Found at i:1330050 original size:19 final size:19
Alignment explanation
Indices: 1330026--1330076 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1330016 GAAAATATTC
1330026 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
1330045 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
1330064 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
1330077 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:1330118 original size:65 final size:64
Alignment explanation
Indices: 1329920--1330127 Score: 228
Period size: 65 Copynumber: 3.2 Consensus size: 64
1329910 GCACCAAGTG
* * * *
1329920 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTGATGCATCGATGCATGGCTTG-
1 TGCATCGATGCATGAAATGCATTCGATGTTTCAAAAAT-TCATGATGCATCGATGCATGGATTGA
*
1329984 TGCATCGATGCATCAAATGCATTCGATGTTTCGAAAATATTCA-GAGTGCATCGATGCATGGA--
1 TGCATCGATGCATGAAATGCATTCGATGTTTC-AAAA-ATTCATGA-TGCATCGATGCATGGATT
1330046 GA
63 GA
* * * *
1330048 GTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTAATTCATCGATGCATCGATGCATGTATT
1 -TGCATCGATGCATGAAATGCATTCGATGTTTCAA-AAATTCAT-GATGCATCGATGCATGGATT
1330112 GA
63 GA
*
1330114 TGCATCGGTGCATG
1 TGCATCGATGCATG
1330128 CCTTTGAATA
Statistics
Matches: 124, Mismatches: 10, Indels: 19
0.81 0.07 0.12
Matches are distributed among these distances:
63 8 0.06
64 51 0.41
65 61 0.49
66 4 0.03
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (64 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTCAAAAATTCATGATGCATCGATGCATGGATTGA
Found at i:1330414 original size:2 final size:2
Alignment explanation
Indices: 1330407--1330485 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
1330397 AATATTAAAG
1330407 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1330449 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1330486 GTAAAAAATC
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1332050 original size:106 final size:106
Alignment explanation
Indices: 1331860--1332391 Score: 752
Period size: 106 Copynumber: 5.0 Consensus size: 106
1331850 AGTATTGTTC
* * *
1331860 CGAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGATTCT-AGAACTGGGAAATTGTTTGTTGA
1 CGAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGTTCTGA-AATTGGGAAATTGTTTGTTGA
* *
1331923 CAACCAGCCGTCCCTTTGTTGTGAAGTTGAACTTGTGTTGTCT
64 CAACCATCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
1331966 CGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGTTCTAAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACA
*
1332031 ACCATCCGTCCTTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCATCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
** * *
1332072 CGAGTCCAATGCCCTTCGCTGTGAAGTTGAAATT-CTCTCTGAAATTGGGAAATTATTTGTTGAC
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGT-TCTGAAATTGGGAAATTGTTTGTTGAC
1332136 AACCAAT-CGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
65 AACC-ATCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
1332178 CGAGTCCAAT-GCTCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGAC
1 CGAGTCCAATATC-CTTCGCTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGAC
* *
1332242 AACCAGCCGTCCATTCGTTGTGAAGTTGAACTTGTGTTGTCT
65 AACCATCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * * *
1332284 TGAGTCCAATATCCTTTGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGAAA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACA
*
1332349 ACCAGT-CGTCCCTTCGTTGTGAAGTTGAACTTGTCTTGTCT
66 ACCA-TCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
1332390 CG
1 CG
1332392 GGTGGCGCGA
Statistics
Matches: 385, Mismatches: 32, Indels: 18
0.89 0.07 0.04
Matches are distributed among these distances:
105 3 0.01
106 377 0.98
107 5 0.01
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACA
ACCATCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:1333104 original size:37 final size:37
Alignment explanation
Indices: 1333022--1333106 Score: 91
Period size: 37 Copynumber: 2.3 Consensus size: 37
1333012 GTTTCATGGG
* * * * **
1333022 AAACGGTCTCAAGTGAGACAAAATTTTGTTTTAAGAA
1 AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAGAA
1333059 AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAA-AA
1 AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAGAA
*
1333095 GAAATTGTCTCA
1 -AAACTGTCTCA
1333107 CGGGGAGAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
36 2 0.05
37 38 0.95
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.26
Consensus pattern (37 bp):
AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAGAA
Found at i:1334920 original size:8 final size:8
Alignment explanation
Indices: 1334909--1334949 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
1334899 TCTTTTGATT
1334909 TTTTCTTC
1 TTTTCTTC
1334917 TTTTCTT-
1 TTTTCTTC
1334924 TTTTGCTTC
1 TTTT-CTTC
1334933 TTTTCTT-
1 TTTTCTTC
*
1334940 TTTTATTC
1 TTTTCTTC
1334948 TT
1 TT
1334950 GATTGAATCT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
7 10 0.34
8 15 0.52
9 4 0.14
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.78
Consensus pattern (8 bp):
TTTTCTTC
Found at i:1334927 original size:15 final size:15
Alignment explanation
Indices: 1334907--1334949 Score: 68
Period size: 16 Copynumber: 2.8 Consensus size: 15
1334897 TTTCTTTTGA
1334907 TTTTTTCTTCTTTTC
1 TTTTTTCTTCTTTTC
1334922 TTTTTTGCTTCTTTTC
1 TTTTTT-CTTCTTTTC
*
1334938 TTTTTTATTCTT
1 TTTTTTCTTCTT
1334950 GATTGAATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 11 0.42
16 15 0.58
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.79
Consensus pattern (15 bp):
TTTTTTCTTCTTTTC
Found at i:1339321 original size:14 final size:14
Alignment explanation
Indices: 1339265--1339323 Score: 59
Period size: 14 Copynumber: 4.3 Consensus size: 14
1339255 ATAAACAAGG
*
1339265 TAAAA-AAAACAAA
1 TAAAATAAAAGAAA
*
1339278 TAAGAT-AAAGAGAA
1 TAAAATAAAAGA-AA
*
1339292 TAAAATAAAAGGAA
1 TAAAATAAAAGAAA
*
1339306 TAAAATAAAATAAA
1 TAAAATAAAAGAAA
1339320 TAAA
1 TAAA
1339324 TAAGATAAGG
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
13 8 0.22
14 25 0.68
15 4 0.11
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (14 bp):
TAAAATAAAAGAAA
Found at i:1339441 original size:40 final size:39
Alignment explanation
Indices: 1339390--1339466 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 39
1339380 GAAAAAATAT
*
1339390 ATATATATATATACATCAAAGTATTAATAAAATA-AATAAG
1 ATATATATATATACAACAAA-TATTAA-AAAATAGAATAAG
*
1339430 ATATATATATATACAACAAATATTTAAAAATAGAATA
1 ATATATATATATACAACAAATATTAAAAAATAGAATA
1339467 GCTACCCTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
38 6 0.18
39 9 0.26
40 19 0.56
ACGTcount: A:0.58, C:0.05, G:0.04, T:0.32
Consensus pattern (39 bp):
ATATATATATATACAACAAATATTAAAAAATAGAATAAG
Found at i:1339680 original size:23 final size:23
Alignment explanation
Indices: 1339633--1339681 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1339623 ACAAGATTTT
* **
1339633 TAAAAAAATAATATAATAATGAA
1 TAAAAAAATAAAATAATAAAAAA
*
1339656 TAAAAAACTAAAATAATAAAAAA
1 TAAAAAAATAAAATAATAAAAAA
1339679 TAA
1 TAA
1339682 TATATATATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (23 bp):
TAAAAAAATAAAATAATAAAAAA
Found at i:1339800 original size:2 final size:2
Alignment explanation
Indices: 1339751--1339784 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1339741 ATAATTAAGA
1339751 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1339785 TAATAATAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1340439 original size:14 final size:14
Alignment explanation
Indices: 1340417--1340451 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
1340407 TCCTTGCTCG
*
1340417 GTTGTTGCACCTTT
1 GTTGGTGCACCTTT
1340431 GTTGGTGCACCTTT
1 GTTGGTGCACCTTT
1340445 GTTGGTG
1 GTTGGTG
1340452 TGGTTGTTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.06, C:0.17, G:0.31, T:0.46
Consensus pattern (14 bp):
GTTGGTGCACCTTT
Found at i:1348639 original size:2 final size:2
Alignment explanation
Indices: 1348632--1348662 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1348622 ATCTCCAAAT
1348632 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1348663 TGGAGATAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1352241 original size:17 final size:16
Alignment explanation
Indices: 1352213--1352249 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
1352203 TTGTTTTAAC
1352213 ATTT-TGGATGTTTGA
1 ATTTGTGGATGTTTGA
1352228 ATTTGTGGATTGTTTGA
1 ATTTGTGGA-TGTTTGA
1352245 ATTTG
1 ATTTG
1352250 GATGCTTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 4 0.20
16 4 0.20
17 12 0.60
ACGTcount: A:0.19, C:0.00, G:0.27, T:0.54
Consensus pattern (16 bp):
ATTTGTGGATGTTTGA
Found at i:1355270 original size:20 final size:21
Alignment explanation
Indices: 1355245--1355287 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 21
1355235 TTTATTGAAA
1355245 TTTTACTTTTCTTTCATT-TT
1 TTTTACTTTTCTTTCATTATT
1355265 TTTTACTTTTCTTTCATTATT
1 TTTTACTTTTCTTTCATTATT
1355286 TT
1 TT
1355288 CTTTTCACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTACTTTTCTTTCATTATT
Found at i:1362258 original size:22 final size:23
Alignment explanation
Indices: 1362233--1362283 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
1362223 ATAGTATATT
1362233 ATATTTTTAA-AATTATTAATAA
1 ATATTTTTAATAATTATTAATAA
* * *
1362255 ATATATTTTAATATTTTTTATTAA
1 ATAT-TTTTAATAATTATTAATAA
1362279 ATATT
1 ATATT
1362284 ATTAGACTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 4 0.17
23 7 0.29
24 13 0.54
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
ATATTTTTAATAATTATTAATAA
Found at i:1366801 original size:12 final size:12
Alignment explanation
Indices: 1366781--1366818 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
1366771 ATTATAACTA
1366781 ATAATATTAAAT
1 ATAATATTAAAT
*
1366793 ATTATATTAAAT
1 ATAATATTAAAT
1366805 A-AATATTAAAT
1 ATAATATTAAAT
1366816 ATA
1 ATA
1366819 TTTATGTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
ATAATATTAAAT
Found at i:1369825 original size:8 final size:8
Alignment explanation
Indices: 1369812--1369852 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1369802 CTCATTTTCA
1369812 GAGAATTT
1 GAGAATTT
1369820 GAGAATTT
1 GAGAATTT
*
1369828 -AGAGTTT
1 GAGAATTT
*
1369835 GGGAATTT
1 GAGAATTT
1369843 GAGAATTT
1 GAGAATTT
1369851 GA
1 GA
1369853 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:1370145 original size:126 final size:126
Alignment explanation
Indices: 1369920--1370397 Score: 913
Period size: 126 Copynumber: 3.8 Consensus size: 126
1369910 CTATAATCGG
* *
1369920 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGTGCGCCTTCCATTATTTCGTCAGTGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1369985 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
*
1370046 TTCACTATTCACATGAAGGTGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1370111 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
*
1370172 TTCACTATTCACATGAAGGCGCGTTCTCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1370237 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
1370298 TTCACTATTCACATGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1370362 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
1370398 ATAACTTAAA
Statistics
Matches: 346, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
125 72 0.21
126 274 0.79
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.32
Consensus pattern (126 bp):
TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
Found at i:1370846 original size:33 final size:34
Alignment explanation
Indices: 1370785--1370884 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 34
1370775 AAATTTAATG
*
1370785 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
1370819 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
1370852 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
1370885 AACATTTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.50
34 28 0.50
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:1371492 original size:21 final size:21
Alignment explanation
Indices: 1371404--1371495 Score: 125
Period size: 21 Copynumber: 4.4 Consensus size: 21
1371394 TATGGTATAA
*
1371404 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
1371425 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
1371446 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
1371467 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
1371488 AACCCTGC
1 AACCCTGC
1371496 AGAGATGGCA
Statistics
Matches: 67, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 61 0.91
22 3 0.04
ACGTcount: A:0.21, C:0.27, G:0.34, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:1371527 original size:21 final size:21
Alignment explanation
Indices: 1371501--1371548 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1371491 CCTGCAGAGA
*
1371501 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
1371522 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
1371543 GGGCAT
1 TGGCAT
1371549 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:1373344 original size:21 final size:19
Alignment explanation
Indices: 1373320--1373359 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
1373310 TAATATTTAC
1373320 ATAAATATTATATAAAAAATA
1 ATAAATATT-TA-AAAAAATA
*
1373341 ATAACTATTTAAAAAAATA
1 ATAAATATTTAAAAAAATA
1373360 CTAACATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 2 0.11
21 8 0.44
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
ATAAATATTTAAAAAAATA
Found at i:1373371 original size:33 final size:31
Alignment explanation
Indices: 1373301--1373374 Score: 78
Period size: 33 Copynumber: 2.3 Consensus size: 31
1373291 TATTATTTTA
* * * *
1373301 ATAAAAA-AATAATATTTACATAAATATTAT
1 ATAAAAATAATAATATTTAAAAAAATATAAC
1373331 ATAAAAAATAATAACTATTTAAAAAAATACTAAC
1 AT-AAAAATAATAA-TATTTAAAAAAATA-TAAC
1373365 ATAAAAATAA
1 ATAAAAATAA
1373375 ATTTCTTACC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 2 0.06
31 5 0.14
32 5 0.14
33 20 0.56
34 4 0.11
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (31 bp):
ATAAAAATAATAATATTTAAAAAAATATAAC
Found at i:1391562 original size:20 final size:20
Alignment explanation
Indices: 1391539--1391617 Score: 63
Period size: 20 Copynumber: 3.8 Consensus size: 20
1391529 ATTCGAGATT
1391539 ATTTTATAATATTTTAATAA
1 ATTTTATAATATTTTAATAA
* *
1391559 ATTTAATGATATATCTTTTA-AA
1 ATTTTAT-A-ATAT-TTTAATAA
*
1391581 ATTTTAATATTATTTTAATAA
1 ATTTT-ATAATATTTTAATAA
*
1391602 TTGTTTAT-ATATTTTA
1 AT-TTTATAATATTTTA
1391618 TCGTTAATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
20 17 0.37
21 9 0.20
22 14 0.30
23 6 0.13
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (20 bp):
ATTTTATAATATTTTAATAA
Found at i:1391920 original size:2 final size:2
Alignment explanation
Indices: 1391913--1391977 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
1391903 TATATGAAAT
1391913 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1391955 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
1391978 GCATATAAGT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1406822 original size:5 final size:5
Alignment explanation
Indices: 1406787--1406819 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
1406777 AATTATTTGG
*
1406787 ATTCA ATTCA ATTCA ATTCA ATTCA ATTTA ATT
1 ATTCA ATTCA ATTCA ATTCA ATTCA ATTCA ATT
1406820 TAAAATATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.39, C:0.15, G:0.00, T:0.45
Consensus pattern (5 bp):
ATTCA
Found at i:1406944 original size:33 final size:32
Alignment explanation
Indices: 1406887--1406975 Score: 99
Period size: 33 Copynumber: 2.7 Consensus size: 32
1406877 ATCTACCTAT
* *
1406887 TTTTATATATTATTTAATAATTTTATAGTATATG
1 TTTTATATATTATTTAAT--TTTTTTAATATATG
* *
1406921 TTTTATCT-TTATTTAATTTTTTTAATATATT
1 TTTTATATATTATTTAATTTTTTTAATATATG
*
1406952 TTTTAATATATTTTTTAATTTTTT
1 TTTT-ATATATTATTTAATTTTTT
1406976 AAATTTAAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
31 15 0.32
32 3 0.06
33 22 0.47
34 7 0.15
ACGTcount: A:0.29, C:0.01, G:0.02, T:0.67
Consensus pattern (32 bp):
TTTTATATATTATTTAATTTTTTTAATATATG
Found at i:1406953 original size:10 final size:11
Alignment explanation
Indices: 1406884--1406966 Score: 61
Period size: 11 Copynumber: 7.6 Consensus size: 11
1406874 TAGATCTACC
1406884 TATTTTT-ATA
1 TATTTTTAATA
1406894 TATTATTTAATA
1 TATT-TTTAATA
*
1406906 -ATTTTATAGTA
1 TATTTT-TAATA
*
1406917 TATGTTTT-ATC
1 TAT-TTTTAATA
1406928 T-TTATTTAAT-
1 TATT-TTTAATA
1406938 T-TTTTTAATA
1 TATTTTTAATA
1406948 TATTTTTTAATA
1 TA-TTTTTAATA
1406960 TATTTTT
1 TATTTTT
1406967 TAATTTTTTA
Statistics
Matches: 60, Mismatches: 3, Indels: 19
0.73 0.04 0.23
Matches are distributed among these distances:
9 7 0.12
10 14 0.23
11 19 0.32
12 17 0.28
13 3 0.05
ACGTcount: A:0.30, C:0.01, G:0.02, T:0.66
Consensus pattern (11 bp):
TATTTTTAATA
Found at i:1406955 original size:12 final size:12
Alignment explanation
Indices: 1406886--1406970 Score: 67
Period size: 12 Copynumber: 7.7 Consensus size: 12
1406876 GATCTACCTA
1406886 TTTTT-ATATAT
1 TTTTTAATATAT
*
1406897 TATTTAATA-AT
1 TTTTTAATATAT
* *
1406908 TTTATAGTATAT
1 TTTTTAATATAT
* *
1406920 GTTTT-ATCT-T
1 TTTTTAATATAT
*
1406930 TATTT-A-AT-T
1 TTTTTAATATAT
1406939 TTTTTAATATAT
1 TTTTTAATATAT
1406951 TTTTTAATATAT
1 TTTTTAATATAT
1406963 TTTTTAAT
1 TTTTTAAT
1406971 TTTTTAAATT
Statistics
Matches: 57, Mismatches: 12, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
9 6 0.11
10 6 0.11
11 16 0.28
12 29 0.51
ACGTcount: A:0.31, C:0.01, G:0.02, T:0.66
Consensus pattern (12 bp):
TTTTTAATATAT
Found at i:1412128 original size:176 final size:177
Alignment explanation
Indices: 1411818--1412586 Score: 1195
Period size: 176 Copynumber: 4.4 Consensus size: 177
1411808 TCAAGTGAGA
* *
1411818 TAAAAT-TTATTTGAAAACATCATGCACTGAAGGTCTTATGGATGGCCCGTTA-GACTTACAAAT
1 TAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCG-TAGGACTTACAAAT
* * * *
1411881 CAGGAAACCCTCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGACTTAGTTTCCT
65 CAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCT
* *
1411946 TTAACAGTTTTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTC
130 TTAACAGCTCTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTC
* *
1411994 TAAAATCTTATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGTAGGACTTGCAAATC
1 TAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGTAGGACTTACAAATC
* * * * *
1412059 AAGAAA-CCTCGAAGGTTTAGTTTTTTATTTGTCAAGAAACCCCTTTGTTAGGCTTAGCTTCCTT
66 AAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTT
*
1412123 TAACAGCTCTTTTGAGATAATTAGTAAACCCTCGAAGGCTTGGTTTC
131 TAACAGCTCTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTC
* * * ** *
1412170 TAAAATCTCATTTGAAAACATCCCGCATTGAAGGTCTTATAGATTTCTCGTAGGACTTACAAATC
1 TAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGTAGGACTTACAAATC
* *
1412235 AAGAAAGCCCCGAAGGCTTAGTTTCTCAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTT
66 AAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTT
* *
1412300 TAATAGCTTTTTTGAGATAATTAGTAAA-CCCCGAAGGCTTGGTTTC
131 TAACAGCTCTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTC
**
1412346 TAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCATGTAGGACTTACAAATC
1 TAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGTAGGACTTACAAATC
* * *
1412411 AAGAAACCCCCAAAGGCTTAGTTTATTAGTTGTCAAGGAACCCCTTTATTAGGCTTAGCTTCCTT
66 AAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTT
*
1412476 TAACAGCTCTTTTGAGATAATTAGTAAACCCCCGAAGGATTGGTTTC
131 TAACAGCTCTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTC
* *
1412523 TAAAATCTCATTTGAAAACATCTTGCACTAAAGGTCTTATGGATGGCCCGTAGGACTTACAAAT
1 TAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGTAGGACTTACAAAT
1412587 TTGGGAAATA
Statistics
Matches: 541, Mismatches: 48, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
176 328 0.61
177 213 0.39
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (177 bp):
TAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGTAGGACTTACAAATC
AAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTT
TAACAGCTCTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTC
Found at i:1412472 original size:353 final size:353
Alignment explanation
Indices: 1411818--1412586 Score: 1222
Period size: 353 Copynumber: 2.2 Consensus size: 353
1411808 TCAAGTGAGA
*
1411818 TAAAAT-TTATTTGAAAACATCATGCACTGAAGGTCTTATGGATGGCCCGTTA-GACTTACAAAT
1 TAAAATCTCATTTGAAAACATCATGCACTGAAGGTCTTATGGATGGCCCG-TAGGACTTACAAAT
* * *
1411881 CAGGAAACCCTCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGACTTAGTTTCCT
65 CAAGAAACCCTCGAAGGCTTAGTTTCTCAGTTGTCAAGGAACCCCTTTGTTAGACTTAGCTTCCT
* *
1411946 TTAACAGTTTTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTTATTTGAAA
130 TTAACAGCTTTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCATTTGAAA
* * * * *
1412011 ACATCCTGCACTGAAGGTCTTATGGATGGCCCGTAGGACTTGCAAATCAAGAAACCTCGAAGGTT
195 ACATCCTGCACTGAAGGTCTTATGGATGGCACGTAGGACTTACAAATCAAGAAACCCCAAAGGCT
* * *
1412076 TAGTTTTTTATTTGTCAAGAAACCCCTTTGTTAGGCTTAGCTTCCTTTAACAGCTCTTTTGAGAT
260 TAGTTTATTAGTTGTCAAGAAACCCCTTTATTAGGCTTAGCTTCCTTTAACAGCTCTTTTGAGAT
* *
1412141 AATTAGTAAACCCTCGAAGGCTTGGTTTC
325 AATTAGTAAACCCCCGAAGGATTGGTTTC
** * * ** *
1412170 TAAAATCTCATTTGAAAACATCCCGCATTGAAGGTCTTATAGATTTCTCGTAGGACTTACAAATC
1 TAAAATCTCATTTGAAAACATCATGCACTGAAGGTCTTATGGATGGCCCGTAGGACTTACAAATC
*
1412235 AAGAAAGCCC-CGAAGGCTTAGTTTCTCAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCT
66 AAGAAA-CCCTCGAAGGCTTAGTTTCTCAGTTGTCAAGGAACCCCTTTGTTAGACTTAGCTTCCT
*
1412299 TTAATAGCTTTTTTGAGATAATTAGTAAA-CCCCGAAGGCTTGGTTTCTAAAATCTCATTTGAAA
130 TTAACAGCTTTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCATTTGAAA
*
1412363 ACATCCTGCACTGAAGGTCTTATGGATGGCATGTAGGACTTACAAATCAAGAAACCCCCAAAGGC
195 ACATCCTGCACTGAAGGTCTTATGGATGGCACGTAGGACTTACAAATCAAGAAA-CCCCAAAGGC
*
1412428 TTAGTTTATTAGTTGTCAAGGAACCCCTTTATTAGGCTTAGCTTCCTTTAACAGCTCTTTTGAGA
259 TTAGTTTATTAGTTGTCAAGAAACCCCTTTATTAGGCTTAGCTTCCTTTAACAGCTCTTTTGAGA
1412493 TAATTAGTAAACCCCCGAAGGATTGGTTTC
324 TAATTAGTAAACCCCCGAAGGATTGGTTTC
* *
1412523 TAAAATCTCATTTGAAAACATCTTGCACTAAAGGTCTTATGGATGGCCCGTAGGACTTACAAAT
1 TAAAATCTCATTTGAAAACATCATGCACTGAAGGTCTTATGGATGGCCCGTAGGACTTACAAAT
1412587 TTGGGAAATA
Statistics
Matches: 378, Mismatches: 35, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
352 93 0.25
353 282 0.75
354 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (353 bp):
TAAAATCTCATTTGAAAACATCATGCACTGAAGGTCTTATGGATGGCCCGTAGGACTTACAAATC
AAGAAACCCTCGAAGGCTTAGTTTCTCAGTTGTCAAGGAACCCCTTTGTTAGACTTAGCTTCCTT
TAACAGCTTTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCATTTGAAAA
CATCCTGCACTGAAGGTCTTATGGATGGCACGTAGGACTTACAAATCAAGAAACCCCAAAGGCTT
AGTTTATTAGTTGTCAAGAAACCCCTTTATTAGGCTTAGCTTCCTTTAACAGCTCTTTTGAGATA
ATTAGTAAACCCCCGAAGGATTGGTTTC
Found at i:1413259 original size:22 final size:22
Alignment explanation
Indices: 1413234--1413307 Score: 98
Period size: 22 Copynumber: 3.4 Consensus size: 22
1413224 AATAAAGCTT
1413234 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
1413256 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
1413278 TCAT-TTT-TAAAGAATGAATCTA
1 TCATCTTTGAAAAG-A-GAATCTA
1413300 TCATCTTT
1 TCATCTTT
1413308 AAAGAATGTA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
20 3 0.07
21 4 0.09
22 36 0.78
23 3 0.07
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:1413308 original size:22 final size:22
Alignment explanation
Indices: 1413249--1413315 Score: 100
Period size: 22 Copynumber: 3.0 Consensus size: 22
1413239 TTTGAAAAGA
*
1413249 GAATCTATCATCTTTGAAGAGA-
1 GAATCTATCATCTTTAAAGA-AT
*
1413271 GAATCTATCATTTTTAAAGAAT
1 GAATCTATCATCTTTAAAGAAT
1413293 GAATCTATCATCTTTAAAGAAT
1 GAATCTATCATCTTTAAAGAAT
1413315 G
1 G
1413316 TAGATGTAGA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
21 1 0.02
22 40 0.98
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (22 bp):
GAATCTATCATCTTTAAAGAAT
Found at i:1413762 original size:54 final size:54
Alignment explanation
Indices: 1413677--1413838 Score: 207
Period size: 54 Copynumber: 3.0 Consensus size: 54
1413667 ATAATAAATG
* * *
1413677 GTTCGTAAAACATTTGACAATATATTTATCTTTTTATGTGGTTTCTGCACAGAT
1 GTTCGTAAAACATTTGACAATACATTCATCTTTTTATGTGGCTTCTGCACAGAT
* *
1413731 GTTCGTAAAACATTTGACAATACATTCATCTTTTTCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAATACATTCATCTTTTTATGTGGCTTCTGCACAGAT
* ** * ** * *
1413785 GCTCGTAAAACATTTGACAACGCATTCATCATTTCCTATGGCTTCTGCCCAGAT
1 GTTCGTAAAACATTTGACAATACATTCATCTTTTTATGTGGCTTCTGCACAGAT
1413839 TTCTCAATAA
Statistics
Matches: 96, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 96 1.00
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAATACATTCATCTTTTTATGTGGCTTCTGCACAGAT
Found at i:1417580 original size:24 final size:22
Alignment explanation
Indices: 1417553--1417610 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 22
1417543 ATGTGAAATA
1417553 ATGAAAGTGATTATATGTGTCCAT
1 ATGAAAGTGATTATATGT-T-CAT
* *
1417577 ATG-AAGTGAAATATATGTTTAT
1 ATGAAAGTG-ATTATATGTTCAT
1417599 ATGAAAAGTGAT
1 ATG-AAAGTGAT
1417611 GAAAAAGATG
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
22 5 0.18
23 7 0.25
24 16 0.57
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.36
Consensus pattern (22 bp):
ATGAAAGTGATTATATGTTCAT
Found at i:1423495 original size:90 final size:90
Alignment explanation
Indices: 1423331--1423510 Score: 292
Period size: 90 Copynumber: 2.0 Consensus size: 90
1423321 AAGAGGGCAA
* * *
1423331 AACAAAGGTGAGATTTCTTATAAGCTAATTGTTTGCTGAAATTTAAGTCTGGTTTTGTTGCTTTA
1 AACAAAGGTGAGATTTCTTATAAACTAATTGTTTGCTGAAATTTAAGTCTGGTTTTGATGCCTTA
1423396 AAGTAAATTAAGCTTATGGAAAGCT
66 AAGTAAATTAAGCTTATGGAAAGCT
1423421 AACAAAGGTGAGATTTCTTATAAACTAATTGTTTGCTGAAATTTAAGTCTGGTTTTGAT-CCTTA
1 AACAAAGGTGAGATTTCTTATAAACTAATTGTTTGCTGAAATTTAAGTCTGGTTTTGATGCCTTA
*
1423485 GATGCT-AATTAAGCTTATGGAAAGCT
66 -AAG-TAAATTAAGCTTATGGAAAGCT
1423511 TAATTTACTT
Statistics
Matches: 84, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
89 4 0.05
90 79 0.94
91 1 0.01
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.38
Consensus pattern (90 bp):
AACAAAGGTGAGATTTCTTATAAACTAATTGTTTGCTGAAATTTAAGTCTGGTTTTGATGCCTTA
AAGTAAATTAAGCTTATGGAAAGCT
Found at i:1424739 original size:18 final size:18
Alignment explanation
Indices: 1424716--1424788 Score: 92
Period size: 18 Copynumber: 3.9 Consensus size: 18
1424706 GTTCTTAAGG
1424716 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* * *
1424734 AGTGGTTCTTTGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
1424753 CAGTGGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
*
1424772 AGTGGTCCTTCAGGACA
1 AGTGGTCCTTCGGGACA
1424789 AATATTCAGT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
18 29 0.63
19 4 0.09
20 13 0.28
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:1426640 original size:26 final size:26
Alignment explanation
Indices: 1426610--1426688 Score: 68
Period size: 27 Copynumber: 3.0 Consensus size: 26
1426600 AAATGTAACT
1426610 ATGCAAAGATGCGAATGTAAATGCAA
1 ATGCAAAGATGCGAATGTAAATGCAA
* * * *
1426636 ATGCAAAAATGTGGATGTAAAATGAAA
1 ATGCAAAGATGCGAATGT-AAATGCAA
* * * *
1426663 ATACGAAGATGCAAAATGCAAATGCA
1 ATGCAAAGATGC-GAATGTAAATGCA
1426689 TGTATGAAAA
Statistics
Matches: 39, Mismatches: 12, Indels: 3
0.72 0.22 0.06
Matches are distributed among these distances:
26 15 0.38
27 21 0.54
28 3 0.08
ACGTcount: A:0.49, C:0.10, G:0.22, T:0.19
Consensus pattern (26 bp):
ATGCAAAGATGCGAATGTAAATGCAA
Found at i:1435521 original size:55 final size:55
Alignment explanation
Indices: 1435440--1435869 Score: 399
Period size: 55 Copynumber: 8.0 Consensus size: 55
1435430 ATACTTGAAA
* * *
1435440 AATCTTCAA-ATAACGGGTCTGCTCCCTTTTCTTTCAAGGAGTATAAGACTCGAAC
1 AATCTTCAACA-AACGTGTCTGCTCCCTATTCCTTCAAGGAGTATAAGACTCGAAC
** * * * *
1435495 AATCCTTGGA-AAATGTGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCAAAC
1 AAT-CTTCAACAAACGTGTCTGCTCCCTATTCCTTCAAGGAGTATAAGACTCGAAC
* * * *
1435550 AATCTTCAACAAACGTGTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTAGAAT
1 AATCTTCAACAAACGTGTCTGCTCCCTATTCCTTCAAGGAGTATAAGACTCGAAC
* *
1435605 AATCTTCAACAAACGGGTCCGCTCCCTATTCCTTC-AGAGAGTATAAGACTCG---
1 AATCTTCAACAAACGTGTCTGCTCCCTATTCCTTCAAG-GAGTATAAGACTCGAAC
* * * *
1435657 -ATCTTCAATAAACGTGTCCGCTCCCTATTCCTTC-AGAGAGTATAGGACTCAAAC
1 AATCTTCAACAAACGTGTCTGCTCCCTATTCCTTCAAG-GAGTATAAGACTCGAAC
* * * *
1435711 AATCTTCAACAAATGTGTCTGCTCCCTATTCGTTTAGGGAGTAT-AGAACTCGAAC
1 AATCTTCAACAAACGTGTCTGCTCCCTATTCCTTCAAGGAGTATAAG-ACTCGAAC
* * *
1435766 AATCTTCATA-AAAAGTGTCCGCTCTCTATTCCTTC-AGAGAGTAT-AGAACTCG---
1 AATCTTCA-ACAAACGTGTCTGCTCCCTATTCCTTCAAG-GAGTATAAG-ACTCGAAC
* * *
1435818 -ATCTTCAACAAACGTGTCCGCTCCATATTCCTTC-AGAGAGTATAGGACTCGA
1 AATCTTCAACAAACGTGTCTGCTCCCTATTCCTTCAAG-GAGTATAAGACTCGA
1435870 TCTTCATAAA
Statistics
Matches: 319, Mismatches: 42, Indels: 31
0.81 0.11 0.08
Matches are distributed among these distances:
50 1 0.00
51 90 0.28
52 1 0.00
54 7 0.02
55 213 0.67
56 7 0.02
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (55 bp):
AATCTTCAACAAACGTGTCTGCTCCCTATTCCTTCAAGGAGTATAAGACTCGAAC
Found at i:1435715 original size:106 final size:105
Alignment explanation
Indices: 1435441--1435879 Score: 394
Period size: 106 Copynumber: 4.1 Consensus size: 105
1435431 TACTTGAAAA
* * * * * **
1435441 ATCTTCAA-ATAACGGGTCTGCTCCCTTTTCTTTCA-AGGAGTATAAGACTCGAACAATCCTTGG
1 ATCTTCAATA-AACGTGTCCGCTCCCTATTCCTTCAGA-GAGTATAAGACT-AAACAAT-CTTCA
* * * * *
1435504 A-AAATGTGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCAAACA
62 ACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACT----CG
* * * * *
1435551 ATCTTCAACAAACGTGTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTAGAATAATCTTCAACA
1 ATCTTCAATAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTA-AACAATCTTCAACA
*
1435616 AACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCG
65 AACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCG
*
1435657 ATCTTCAATAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAAACAATCTTCAACA
1 ATCTTCAATAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACT-AAACAATCTTCAACA
* * * * *
1435722 AATGTGTCTGCTCCCTATTCGTTTAGGGAGTAT-AGAACTCG
65 AACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAG-ACTCG
* * *
1435763 AACAATCTTC-ATAAAAAGTGTCCGCTCTCTATTCCTTCAGAGAGTAT-AGAACT---CGATCTT
1 ----ATCTTCAAT-AAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAG-ACTAAACAATCTT
* *
1435823 CAACAAACGTGTCCGCTCCATATTCCTTCAGAGAGTATAGGACTCG
60 CAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCG
1435869 ATCTTC-ATAAA
1 ATCTTCAATAAA
1435880 ATAAGTTTGC
Statistics
Matches: 279, Mismatches: 37, Indels: 35
0.79 0.11 0.10
Matches are distributed among these distances:
101 3 0.01
102 8 0.03
105 2 0.01
106 133 0.48
107 2 0.01
109 7 0.03
110 123 0.44
111 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (105 bp):
ATCTTCAATAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTAAACAATCTTCAACAA
ACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCG
Found at i:1435722 original size:161 final size:159
Alignment explanation
Indices: 1435440--1435867 Score: 556
Period size: 161 Copynumber: 2.6 Consensus size: 159
1435430 ATACTTGAAA
* * * **
1435440 AATCTTCAAATAACGGGTCTGCTCCCTTTTCTTTCA-AGGAGTATAAGACTCGAACAATCCTTGG
1 AATCTTCAAA-AACGGGTCCGCTCCCTATTCCTTCAGA-GAGTATAAGACTCG----AT-CTTCA
* * * * *
1435504 AAAATGTGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCAAACAATCTTCAACAAACGTGTC
59 AAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAAACAATCTTCAACAAACGTGTC
*
1435569 TGCTCCCTATTCGTTCAGGGAGTATA-AGACTAGAAT
124 TGCTCCCTATTCGTTCAGGGAGTATAGA-ACTAGAAC
1435605 AATCTTCAACAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAATAAAC
1 AATCTTCAA-AAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAA-AAAC
*
1435670 GTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAAACAATCTTCAACAAATGTGTCTGCTC
64 GTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAAACAATCTTCAACAAACGTGTCTGCTC
* *
1435735 CCTATTCGTTTAGGGAGTATAGAACTCGAAC
129 CCTATTCGTTCAGGGAGTATAGAACTAGAAC
* * *
1435766 AATCTTCATAAAAAGTGTCCGCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGATCTTCAACAAA
1 AATCTTCA-AAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGATCTTCAA-AAA
*
1435830 CGTGTCCGCTCCATATTCCTTCAGAGAGTATAGGACTC
63 CGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTC
1435868 GATCTTCATA
Statistics
Matches: 238, Mismatches: 19, Indels: 16
0.87 0.07 0.06
Matches are distributed among these distances:
160 6 0.03
161 183 0.77
162 2 0.01
165 45 0.19
166 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.29
Consensus pattern (159 bp):
AATCTTCAAAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAAAAACGT
GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAAACAATCTTCAACAAACGTGTCTGCTCCC
TATTCGTTCAGGGAGTATAGAACTAGAAC
Found at i:1435927 original size:37 final size:37
Alignment explanation
Indices: 1435886--1435958 Score: 146
Period size: 37 Copynumber: 2.0 Consensus size: 37
1435876 TAAAATAAGT
1435886 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAC
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAC
1435923 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGA
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGA
1435959 ACTATTTCGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (37 bp):
TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAC
Found at i:1437258 original size:13 final size:14
Alignment explanation
Indices: 1437220--1437281 Score: 56
Period size: 14 Copynumber: 4.3 Consensus size: 14
1437210 TCTCTTTTTT
1437220 TTTTCATTTTTCTC
1 TTTTCATTTTTCTC
**
1437234 TTTTTGTTTTTCTC
1 TTTTCATTTTTCTC
1437248 -TTTCATTTTTCTTC
1 TTTTCATTTTTC-TC
1437262 TATTTTCCATTTTT-TC
1 --TTTT-CATTTTTCTC
1437278 TTTT
1 TTTT
1437282 TTTTTCTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
13 9 0.23
14 18 0.46
16 2 0.05
17 3 0.08
18 7 0.18
ACGTcount: A:0.06, C:0.18, G:0.02, T:0.74
Consensus pattern (14 bp):
TTTTCATTTTTCTC
Found at i:1437309 original size:18 final size:20
Alignment explanation
Indices: 1437288--1437330 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1437278 TTTTTTTTTC
1437288 TTTTCGTTTTTTC-CA-TCAT
1 TTTTC-TTTTTTCTCATTCAT
1437307 TTTTCTTTTTTCTCATTCAT
1 TTTTCTTTTTTCTCATTCAT
1437327 TTTT
1 TTTT
1437331 TTCTTCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.32
19 7 0.32
20 8 0.36
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTTCTTTTTTCTCATTCAT
Found at i:1437316 original size:19 final size:19
Alignment explanation
Indices: 1437250--1437330 Score: 59
Period size: 19 Copynumber: 4.4 Consensus size: 19
1437240 TTTTTCTCTT
1437250 TCATTTTTCTTCTATTTTCCA
1 TCATTTTTCTT-T-TTTTCCA
*
1437271 T--TTTTTCTTTTTTT--T
1 TCATTTTTCTTTTTTTCCA
*
1437286 TC--TTTTCGTTTTTTCCA
1 TCATTTTTCTTTTTTTCCA
1437303 TCATTTTTC-TTTTTTCTCA
1 TCATTTTTCTTTTTTTC-CA
1437322 TTCATTTTT
1 -TCATTTTT
1437331 TTCTTCTTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
15 12 0.24
17 6 0.12
18 8 0.16
19 15 0.30
20 8 0.16
21 1 0.02
ACGTcount: A:0.09, C:0.19, G:0.01, T:0.72
Consensus pattern (19 bp):
TCATTTTTCTTTTTTTCCA
Found at i:1437322 original size:16 final size:16
Alignment explanation
Indices: 1437219--1437356 Score: 65
Period size: 15 Copynumber: 8.3 Consensus size: 16
1437209 TTCTCTTTTT
*
1437219 TTTTTCATTTTTCTC-
1 TTTTTCTTTTTTCTCA
*
1437234 TTTTTGTTTTTCTCTTTCA
1 TTTTTCTTTTT-TC--TCA
1437253 TTTTTCTTCTATTT-TCCA
1 TTTTTCTT-T-TTTCT-CA
*
1437271 TTTTTTCTTTTTT-T-T
1 -TTTTTCTTTTTTCTCA
1437286 TCTTTTCGTTTTTTCCATCA
1 T-TTTTC-TTTTTT-C-TCA
1437306 TTTTTCTTTTTTCTCA
1 TTTTTCTTTTTTCTCA
**
1437322 TTCAT-TTTTTTCTTC-
1 TTTTTCTTTTTTC-TCA
*
1437337 TTTTTC-TTCTTCTCA
1 TTTTTCTTTTTTCTCA
1437352 TTTTT
1 TTTTT
1437357 ATTATTATTT
Statistics
Matches: 96, Mismatches: 10, Indels: 34
0.69 0.07 0.24
Matches are distributed among these distances:
14 3 0.03
15 34 0.35
16 16 0.17
17 6 0.06
18 11 0.11
19 21 0.22
20 3 0.03
21 2 0.02
ACGTcount: A:0.07, C:0.19, G:0.01, T:0.73
Consensus pattern (16 bp):
TTTTTCTTTTTTCTCA
Found at i:1446677 original size:45 final size:47
Alignment explanation
Indices: 1446610--1446699 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 47
1446600 CCATGCTTTG
1446610 TTATTCACAAAAATAAATCCTAACCACATGATATCTAATTCGCATAC
1 TTATTCACAAAAATAAATCCTAACCACATGATATCTAATTCGCATAC
* *
1446657 TTATTCA-AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCAT
1 TTATTCACAAAAATAAATCCTAACCACATGATATCTAATTCGCAT
1446700 GCATTTAATC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
45 25 0.61
46 9 0.22
47 7 0.17
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (47 bp):
TTATTCACAAAAATAAATCCTAACCACATGATATCTAATTCGCATAC
Found at i:1450927 original size:7 final size:7
Alignment explanation
Indices: 1450894--1450939 Score: 58
Period size: 7 Copynumber: 6.4 Consensus size: 7
1450884 CAAATATATA
1450894 AAAAATT
1 AAAAATT
*
1450901 AAATA-T
1 AAAAATT
1450907 AAAAATACT
1 AAAAAT--T
1450916 AAAAATT
1 AAAAATT
1450923 AAAAATT
1 AAAAATT
1450930 AAAAATT
1 AAAAATT
1450937 AAA
1 AAA
1450940 TTACTAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
6 5 0.15
7 22 0.65
9 7 0.21
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (7 bp):
AAAAATT
Found at i:1452001 original size:2 final size:2
Alignment explanation
Indices: 1451994--1452047 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1451984 TTTGTTACCA
1451994 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1452036 AT AT AT AT AT AT
1 AT AT AT AT AT AT
1452048 TGTTAAATGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1452457 original size:15 final size:16
Alignment explanation
Indices: 1452439--1452471 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1452429 TTTTTTATAC
1452439 ATAAATTTT-AATTTT
1 ATAAATTTTAAATTTT
*
1452454 ATAACTTTTAAATTTT
1 ATAAATTTTAAATTTT
1452470 AT
1 AT
1452472 TTTTTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
ATAAATTTTAAATTTT
Found at i:1461997 original size:33 final size:33
Alignment explanation
Indices: 1461960--1462029 Score: 106
Period size: 33 Copynumber: 2.1 Consensus size: 33
1461950 TTTGAAAAAA
*
1461960 CCGACCCGAATATCACAC-TTACAAAAACCAGAC
1 CCGACCCGAATATCAAACTTTA-AAAAACCAGAC
*
1461993 CCGACCCGAATATCAAACTTTAAAAAACCCGAC
1 CCGACCCGAATATCAAACTTTAAAAAACCAGAC
1462026 CCGA
1 CCGA
1462030 ACCTGAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 31 0.91
34 3 0.09
ACGTcount: A:0.41, C:0.36, G:0.10, T:0.13
Consensus pattern (33 bp):
CCGACCCGAATATCAAACTTTAAAAAACCAGAC
Found at i:1463223 original size:2 final size:2
Alignment explanation
Indices: 1463216--1463255 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1463206 TTTTCTAATC
1463216 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1463256 TTCTTCATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1463336 original size:21 final size:20
Alignment explanation
Indices: 1463289--1463338 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
1463279 TAATGTTATT
*
1463289 TAATA-TATTAAATATAATA
1 TAATATTATAAAATATAATA
* *
1463308 TAAAATTATAAAATATATTTA
1 TAATATTATAAAATATA-ATA
1463329 TAATATTATA
1 TAATATTATA
1463339 CTTCAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 4 0.16
20 10 0.40
21 11 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TAATATTATAAAATATAATA
Found at i:1464157 original size:14 final size:13
Alignment explanation
Indices: 1464138--1464176 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
1464128 TATATGGATA
1464138 TTTTATTCATTTAT
1 TTTTATT-ATTTAT
1464152 TTTTATTATTTAT
1 TTTTATTATTTAT
1464165 GTTATTATTATT
1 -TT-TTATTATT
1464177 ATATGTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 8 0.35
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (13 bp):
TTTTATTATTTAT
Found at i:1464175 original size:18 final size:17
Alignment explanation
Indices: 1464136--1464178 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1464126 ATTATATGGA
1464136 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
* *
1464152 TTTTATTATTTATGTTAT
1 TATTATTATTCAT-TTAT
1464170 TATTATTAT
1 TATTATTAT
1464179 ATGTATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:1464379 original size:2 final size:2
Alignment explanation
Indices: 1464374--1464398 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1464364 CTTATAACTT
1464374 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 T
1464399 TATTTTCGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1464681 original size:9 final size:9
Alignment explanation
Indices: 1464660--1464693 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
1464650 TTGTTTTTCC
1464660 TTTATCTTA-
1 TTTAT-TTAT
1464669 TTTATTTAT
1 TTTATTTAT
1464678 TTTATTTAT
1 TTTATTTAT
1464687 TTTATTT
1 TTTATTT
1464694 TTCCCTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 3 0.12
9 21 0.88
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTATTTAT
Found at i:1464682 original size:13 final size:14
Alignment explanation
Indices: 1464660--1464694 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
1464650 TTGTTTTTCC
*
1464660 TTTATCTTATTTA-
1 TTTATTTTATTTAT
1464673 TTTATTTTATTTAT
1 TTTATTTTATTTAT
1464687 TTTATTTT
1 TTTATTTT
1464695 TCCCTTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTATTTTATTTAT
Found at i:1466590 original size:22 final size:20
Alignment explanation
Indices: 1466553--1466597 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
1466543 TGCATTCTTG
* *
1466553 CATTTTTGCATCTTCATATA
1 CATTTTTGCATATTCATAAA
1466573 CATTTTTAAGCATATTCATAAA
1 CATTTTT--GCATATTCATAAA
1466595 CAT
1 CAT
1466598 GAAATTAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.33
22 14 0.67
ACGTcount: A:0.33, C:0.18, G:0.04, T:0.44
Consensus pattern (20 bp):
CATTTTTGCATATTCATAAA
Found at i:1467774 original size:20 final size:19
Alignment explanation
Indices: 1467735--1467789 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
1467725 AAGAAAAAAG
* *
1467735 AAAAGAAGAAAAAAAGGAA
1 AAAACAAGAAAAAAAAGAA
1467754 AAAACAAGAACAAAAAAGAA
1 AAAACAAGAA-AAAAAAGAA
*
1467774 AGAACAA-AAATAAAAA
1 AAAACAAGAAA-AAAAA
1467790 AAGGGACAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 1 0.03
19 16 0.52
20 14 0.45
ACGTcount: A:0.80, C:0.05, G:0.13, T:0.02
Consensus pattern (19 bp):
AAAACAAGAAAAAAAAGAA
Found at i:1467790 original size:20 final size:21
Alignment explanation
Indices: 1467744--1467790 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
1467734 GAAAAGAAGA
*
1467744 AAAAAAGGAAAAAACAAGAAC
1 AAAAAAGGAAAAAACAAAAAC
* *
1467765 AAAAAA-GAAAGAACAAAAAT
1 AAAAAAGGAAAAAACAAAAAC
1467785 AAAAAA
1 AAAAAA
1467791 AGGGACAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.81, C:0.06, G:0.11, T:0.02
Consensus pattern (21 bp):
AAAAAAGGAAAAAACAAAAAC
Found at i:1468419 original size:22 final size:22
Alignment explanation
Indices: 1468391--1468441 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
1468381 CCCCATCAAT
1468391 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
*
1468413 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCATCAAATACCAAA
1468435 CCTTTGA
1 CCTTTGA
1468442 CCAAACACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.25
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:1468864 original size:18 final size:18
Alignment explanation
Indices: 1468841--1468876 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1468831 TCAACATCAA
* *
1468841 ATATTGGGGCATTTTTGG
1 ATATTGAGGCATCTTTGG
1468859 ATATTGAGGCATCTTTGG
1 ATATTGAGGCATCTTTGG
1468877 GGATTCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.31, T:0.42
Consensus pattern (18 bp):
ATATTGAGGCATCTTTGG
Found at i:1469344 original size:36 final size:35
Alignment explanation
Indices: 1469304--1469637 Score: 202
Period size: 36 Copynumber: 9.5 Consensus size: 35
1469294 ACTCATGATT
* *
1469304 GTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGATC-
1 GTTTCTCTTAAAACAA-ATTTGTCTCTCTTGAGA-CA
* * **
1469340 GTTT-TCACTAAAAGAGTTTTGTCTCTCTTGAGACA
1 GTTTCTC-TTAAAACAAATTTGTCTCTCTTGAGACA
* *
1469375 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCTCTTAAAACAAA-TTTGTCTCTCTTGAGACA
*
1469411 GTTTCTCTTAAAACAAATTTCGTCTATCTTGAGACA
1 GTTTCTCTTAAAACAAATTT-GTCTCTCTTGAGACA
* * *
1469447 GTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACA
1 GTTTCTCTTAAAACAAA-TTTGTCTCTCTTGAGACA
* * * * *
1469483 GTTTCCCTTGAAACAAA-----ATAT-TTGA-ATA
1 GTTTCTCTTAAAACAAATTTGTCTCTCTTGAGACA
* ** * *
1469511 TGTTT-TCTTTGAAACAAATACCGTTTCCCTTGAGACA
1 -GTTTCTC-TTAAAACAAAT-TTGTCTCTCTTGAGACA
* ** *
1469548 GTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACA
1 GTTTCTCTTAAAAC-AA-ATTTGTCTCTCTTGAGACA
* * * *
1469585 GTTTCTCTTGAAACAATTTTCGGCTATCTTGAGACA
1 GTTTCTCTTAAAACAAATTT-GTCTCTCTTGAGACA
* *
1469621 GTTTCCCTTGAAACAAA
1 GTTTCTCTTAAAACAAA
1469638 ATCTTTGAAT
Statistics
Matches: 238, Mismatches: 40, Indels: 40
0.75 0.13 0.13
Matches are distributed among these distances:
28 3 0.01
29 18 0.08
30 2 0.01
34 1 0.00
35 34 0.14
36 146 0.61
37 33 0.14
38 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.40
Consensus pattern (35 bp):
GTTTCTCTTAAAACAAATTTGTCTCTCTTGAGACA
Found at i:1469406 original size:71 final size:72
Alignment explanation
Indices: 1469314--1469487 Score: 230
Period size: 72 Copynumber: 2.4 Consensus size: 72
1469304 GTTTTTCTTA
* * * * *
1469314 AAACAAGA-TTTGTCTCGCTTGAGATC-GTTT-TCACTAAAA-GAGTTTTGTCTCTCTTGAGACA
1 AAACAA-ATTTTGTCTCTCTTGAGA-CAGTTTCTC-CTAAAACAAATTTCGTCTATCTTGAGACA
1469375 GTTTCCCTTG
63 GTTTCCCTTG
*
1469385 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTAAAACAAATTTCGTCTATCTTGAGACAGTT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCCTAAAACAAATTTCGTCTATCTTGAGACAGTT
1469450 TCCCTTG
66 TCCCTTG
*
1469457 AAATAAATTTTGTCTCTCTTGAGACAGTTTC
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTC
1469488 CCTTGAAACA
Statistics
Matches: 92, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
70 2 0.02
71 30 0.33
72 60 0.65
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (72 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCCTAAAACAAATTTCGTCTATCTTGAGACAGTT
TCCCTTG
Found at i:1469465 original size:72 final size:72
Alignment explanation
Indices: 1469360--1469637 Score: 250
Period size: 72 Copynumber: 3.9 Consensus size: 72
1469350 AAAGAGTTTT
* *
1469360 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTAAAAC
1 GTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAAC
1469425 AAATTTC
66 AAATTTC
* *
1469432 GTCTATCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 GTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAAC
1469497 AAA----
66 AAATTTC
* * * * *** * * ** **
1469500 --ATAT-TTGA-ATATGTTTTCTTTGAAACAAATACCGTTTCCCTTGAGACAGTTTCTTTTGGAA
1 GTCTATCTTGAGACA-GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAA
* *
1469561 CTAAGTTTT
65 C-AAATTTC
* * * * *
1469570 GTCTCTCTTGAGACAGTTTCTCTTGAAAC-AATTTTCGGCTATCTTGAGACAGTTTCCCTTGAAA
1 GTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTT-GTCTCTCTTGAGACAGTTTCCCTTAAAA
1469634 CAAA
65 CAAA
1469638 ATCTTTGAAT
Statistics
Matches: 160, Mismatches: 35, Indels: 22
0.74 0.16 0.10
Matches are distributed among these distances:
64 2 0.01
65 43 0.27
66 5 0.03
72 71 0.44
73 37 0.23
74 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (72 bp):
GTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAAC
AAATTTC
Found at i:1469664 original size:138 final size:137
Alignment explanation
Indices: 1469396--1469700 Score: 369
Period size: 138 Copynumber: 2.2 Consensus size: 137
1469386 AACAAATTTT
*
1469396 GTCTCTCTTGAGACAGTTTCTCTTAAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAAT
1 GTCTCCCTTGAGACAGTTTCTCTTAAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAAT
* * * * ** *
1469461 AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCTTTGAAAC
66 AAATTTTGGCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATATTTCCCCTAAAAC
1469526 AAATACC
131 AAATACC
* * ** * * * *
1469533 GTTTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
1 GTCTCCCTTGAGACAGTTTCTCTTAAAAC-AAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAA
* * *
1469598 -CAATTTTCGGCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTCCCCTAAA
65 TAAATTTT-GGCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATATTTCCCCTAAA
***
1469662 ACAAATTTT
129 ACAAATACC
* *
1469671 GTCTCCCTTGAGACAGTTACTCTTGAAACA
1 GTCTCCCTTGAGACAGTTTCTCTTAAAACA
1469701 CAAAATCTTC
Statistics
Matches: 140, Mismatches: 26, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
137 31 0.22
138 109 0.78
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (137 bp):
GTCTCCCTTGAGACAGTTTCTCTTAAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAAT
AAATTTTGGCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATATTTCCCCTAAAAC
AAATACC
Found at i:1469729 original size:67 final size:68
Alignment explanation
Indices: 1469612--1469768 Score: 212
Period size: 68 Copynumber: 2.4 Consensus size: 68
1469602 TTTCGGCTAT
* ** *
1469612 CTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAATTTATTTCCCCTAAAACA-AATTTTGTC
1 CTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCCTAAAACATAAATTTGTC
1469674 TCC
66 TCC
* * *
1469677 CTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCTTAAAACATAAATTTGTT
1 CTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCCTAAAACATAAATTTGTC
1469742 TCC
66 TCC
* *
1469745 CTTGAGACCGTTTCTCATGAAACA
1 CTTGAGACAGTTTCTCTTGAAACA
1469769 ACAGATATCT
Statistics
Matches: 79, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
65 17 0.22
66 2 0.03
67 29 0.37
68 31 0.39
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.36
Consensus pattern (68 bp):
CTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCCTAAAACATAAATTTGTC
TCC
Found at i:1470743 original size:105 final size:105
Alignment explanation
Indices: 1470373--1471345 Score: 1401
Period size: 105 Copynumber: 9.3 Consensus size: 105
1470363 GCCATCCGCG
* * * * * * *
1470373 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACATCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * * *
1470438 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACCGCTGCTTGTCAAC-AACAACTTCCCAATCTCAGAGCCA
1470482 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * *
1470547 ACCGCTGGTTGTCAATAAACAATTTTCCCAATTTCAGAGCCA
66 ACCGCTGCTTGTCAA-CAACAA-CTTCCCAATCTCAGAGCCA
*
1470589 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
1470654 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
*
1470694 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
1470759 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
1470799 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
1470864 ACCGCTGCTTGTCAACAA-AA-TT-TC-AT-TCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
* ** *
1470899 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATACAAGTCCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
1470964 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
* *
1471004 ATTTCAACTTCACAACTAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
1471069 ACCGCTGTTTGTCAACAACAACTTCCCAATCCCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
*
1471109 ATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* **
1471174 ACCGCTGCTTGTCAACAA-AA-TT-TC-AT-TCAGATTCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
* * *
1471209 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * * **
1471274 ACGGCTGGTTGTCAATAAACAATTTCCCGGT-TCCAGAGCCA
66 ACCGCTGCTTGTCAA-CAACAACTTCCCAATCT-CAGAGCCA
* *
1471315 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
1471346 TGGAACAATG
Statistics
Matches: 795, Mismatches: 56, Indels: 29
0.90 0.06 0.03
Matches are distributed among these distances:
100 168 0.21
101 8 0.01
102 6 0.01
103 7 0.01
104 7 0.01
105 386 0.49
106 92 0.12
107 99 0.12
109 22 0.03
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.22
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
Found at i:1470987 original size:205 final size:209
Alignment explanation
Indices: 1470373--1471345 Score: 1433
Period size: 205 Copynumber: 4.6 Consensus size: 209
1470363 GCCATCCGCG
* * * * * * *
1470373 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACATCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
*
1470438 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
63 GGGACCGCTGGTTGTCAAC-AACAACTTCTCAA-TTCAGAGCCAATTTCAACTTCACAACGAAGG
* *
1470503 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
126 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAA-CAACA
* *
1470568 ATTTTCCCAATTTCAGAGCCA
190 ACTTT-CCAATCTCAGAGCCA
*
1470589 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
1470654 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
66 ACCGCTGGTTGTCAACAACAACTTCTCAAT-TCAGAGCCAATTTCAACTTCACAACGAAGGATAT
*
1470719 TGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTT
130 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTT
1470784 CCAATCTCAGAGCCA
195 CCAATCTCAGAGCCA
1470799 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
1470864 ACCGCTGCTTGTCAACAA-AA-TT-TC-ATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATT
66 ACCGCTGGTTGTCAACAACAACTTCTCAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATT
** *
1470925 GGACTCCAGACAATACAAGTCCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTC
131 GGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTC
1470990 CAATCTCAGAGCCA
196 CAATCTCAGAGCCA
* *
1471004 ATTTCAACTTCACAACTAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * *
1471069 ACCGCTGTTTGTCAACAACAACTTCCCAATCCCAGAGCCAATTTCAACTTCACAACGAAAGATAT
66 ACCGCTGGTTGTCAACAACAACTTCTCAAT-TCAGAGCCAATTTCAACTTCACAACGAAGGATAT
1471134 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TTT
130 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTT
**
1471197 -C-AT-TCAGATTCA
195 CCAATCTCAGAGCCA
* * *
1471209 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * * ** * *
1471274 ACGGCTGGTTGTCAATAAACAATTTCCCGGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATA
66 ACCGCTGGTTGTCAA-CAACAACTTCTCAATT-CAGAGCCAATTTCAACTTCACAACGAAGGATA
1471339 TTGGACT
129 TTGGACT
1471346 TGGAACAATG
Statistics
Matches: 702, Mismatches: 47, Indels: 26
0.91 0.06 0.03
Matches are distributed among these distances:
205 272 0.39
206 53 0.08
207 4 0.01
208 6 0.01
209 6 0.01
210 181 0.26
211 9 0.01
212 99 0.14
213 48 0.07
214 3 0.00
216 21 0.03
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.22
Consensus pattern (209 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGGTTGTCAACAACAACTTCTCAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATT
GGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTC
CAATCTCAGAGCCA
Found at i:1471027 original size:310 final size:310
Alignment explanation
Indices: 1470373--1471345 Score: 1475
Period size: 310 Copynumber: 3.1 Consensus size: 310
1470363 GCCATCCGCG
* * * * * * *
1470373 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACATCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * *
1470438 GGGACGGCTGGTTGTCAACAAACAAC-TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAG
63 GGGACCGCTGCTTGTCAAC-AACAACTTTC-CAATCTCAGAGCCAATTTCAACTTCACAACGAAG
* *
1470502 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAAC
126 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAA-CAA-
*
1470567 AATTTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
189 AA-TTT--C-A-TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACA
*
1470632 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
249 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTTCCAATCTCAGAGCCA
*
1470694 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1470759 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
66 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
1470824 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAAAATTTCA
131 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAAAATTTCA
* *
1470889 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATACAAGTCCAACTTCA
196 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCA
*
1470954 CGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCA
261 CGACGAAGGGACCGCTGGTTGTCAACAACAACTTTCCAATCTCAGAGCCA
* *
1471004 ATTTCAACTTCACAACTAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * *
1471069 ACCGCTGTTTGTCAACAACAACTTCCCAATCCCAGAGCCAATTTCAACTTCACAACGAAAGATAT
66 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
1471134 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAAAATTTCA
131 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAAAATTTCA
** * *
1471199 TTCAGATTCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCA
196 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCA
* * * **
1471264 CAACGAAGGGACGGCTGGTTGTCAATAAACAA-TTTCCCGGT-TCCAGAGCCA
261 CGACGAAGGGACCGCTGGTTGTCAA-CAACAACTTT-CCAATCT-CAGAGCCA
* *
1471315 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
1471346 TGGAACAATG
Statistics
Matches: 608, Mismatches: 40, Indels: 18
0.91 0.06 0.03
Matches are distributed among these distances:
310 383 0.63
311 45 0.07
312 1 0.00
314 3 0.00
315 2 0.00
316 2 0.00
317 98 0.16
318 49 0.08
319 3 0.00
321 22 0.04
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.22
Consensus pattern (310 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAAAATTTCA
TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCA
CGACGAAGGGACCGCTGGTTGTCAACAACAACTTTCCAATCTCAGAGCCA
Found at i:1472371 original size:14 final size:13
Alignment explanation
Indices: 1472352--1472390 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
1472342 TATATGGATA
1472352 TTTTATTCATTTAT
1 TTTTATT-ATTTAT
1472366 TTTTATTATTTAT
1 TTTTATTATTTAT
1472379 GTTATTATTATT
1 -TT-TTATTATT
1472391 ATATGTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 8 0.35
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (13 bp):
TTTTATTATTTAT
Found at i:1472389 original size:18 final size:17
Alignment explanation
Indices: 1472350--1472392 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1472340 ATTATATGGA
1472350 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
* *
1472366 TTTTATTATTTATGTTAT
1 TATTATTATTCAT-TTAT
1472384 TATTATTAT
1 TATTATTAT
1472393 ATGTATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:1472587 original size:2 final size:2
Alignment explanation
Indices: 1472582--1472608 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1472572 CTTATAACTT
1472582 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
1472609 TTTTTCGTTT
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:1472888 original size:9 final size:9
Alignment explanation
Indices: 1472867--1472900 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
1472857 TTGTTTTTCC
1472867 TTTATCTTA-
1 TTTAT-TTAT
1472876 TTTATTTAT
1 TTTATTTAT
1472885 TTTATTTAT
1 TTTATTTAT
1472894 TTTATTT
1 TTTATTT
1472901 TTCCCTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 3 0.12
9 21 0.88
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTATTTAT
Found at i:1472889 original size:13 final size:14
Alignment explanation
Indices: 1472867--1472901 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
1472857 TTGTTTTTCC
*
1472867 TTTATCTTATTTA-
1 TTTATTTTATTTAT
1472880 TTTATTTTATTTAT
1 TTTATTTTATTTAT
1472894 TTTATTTT
1 TTTATTTT
1472902 TCCCTTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTATTTTATTTAT
Found at i:1474031 original size:29 final size:29
Alignment explanation
Indices: 1473998--1474073 Score: 143
Period size: 29 Copynumber: 2.6 Consensus size: 29
1473988 CTTACCACAT
*
1473998 ATGAGAAATGAGTGTTATATCAAGAATTA
1 ATGAGCAATGAGTGTTATATCAAGAATTA
1474027 ATGAGCAATGAGTGTTATATCAAGAATTA
1 ATGAGCAATGAGTGTTATATCAAGAATTA
1474056 ATGAGCAATGAGTGTTAT
1 ATGAGCAATGAGTGTTAT
1474074 TTTGGTAAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (29 bp):
ATGAGCAATGAGTGTTATATCAAGAATTA
Found at i:1474843 original size:24 final size:25
Alignment explanation
Indices: 1474816--1474874 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
1474806 AATTGAAAAT
*
1474816 TTTTAATAATTTAAT-TATGTAGTA
1 TTTTAATAATTTAATGTATGTAATA
* *
1474840 TTTTTAT-ATTTAATGTATTTAATA
1 TTTTAATAATTTAATGTATGTAATA
*
1474864 TCTTAATAATT
1 TTTTAATAATT
1474875 GTTTATATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 7 0.25
24 18 0.64
25 3 0.11
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.58
Consensus pattern (25 bp):
TTTTAATAATTTAATGTATGTAATA
Found at i:1482760 original size:21 final size:21
Alignment explanation
Indices: 1482734--1482779 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
1482724 ATATGTAAAC
**
1482734 CGCATTGCGTTTTTCCAAATT
1 CGCATTGCAATTTTCCAAATT
1482755 CGCATTGCAATTTTCCAAATT
1 CGCATTGCAATTTTCCAAATT
1482776 CGCA
1 CGCA
1482780 ACGCAAATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.24, C:0.26, G:0.13, T:0.37
Consensus pattern (21 bp):
CGCATTGCAATTTTCCAAATT
Found at i:1482785 original size:21 final size:21
Alignment explanation
Indices: 1482744--1482785 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1482734 CGCATTGCGT
**
1482744 TTTTCCAAATTCGCATTGCAA
1 TTTTCCAAATTCGCAACGCAA
1482765 TTTTCCAAATTCGCAACGCAA
1 TTTTCCAAATTCGCAACGCAA
1482786 ATCTGTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (21 bp):
TTTTCCAAATTCGCAACGCAA
Found at i:1482804 original size:20 final size:20
Alignment explanation
Indices: 1482775--1482817 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
1482765 TTTTCCAAAT
1482775 TCGCAACGC-AAATCTGTAAA
1 TCGCAACGCAAAAT-TGTAAA
*
1482795 TCGCATCGCAAAATTGTAAA
1 TCGCAACGCAAAATTGTAAA
1482815 TCG
1 TCG
1482818 TAACACAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.23
Consensus pattern (20 bp):
TCGCAACGCAAAATTGTAAA
Found at i:1482840 original size:20 final size:20
Alignment explanation
Indices: 1482819--1482982 Score: 126
Period size: 20 Copynumber: 8.2 Consensus size: 20
1482809 TGTAAATCGT
*
1482819 AACACAGAAGTCAAATTCGT
1 AACACAGAAGTCAAATTCGC
* *
1482839 AACACAAAAGTCAAATTCAC
1 AACACAGAAGTCAAATTCGC
*
1482859 AACGC-GATAGTCAAATTCGC
1 AACACAGA-AGTCAAATTCGC
1482879 AACAC-GAA-TCTGTAAA-TCGC
1 AACACAGAAGTC---AAATTCGC
*
1482899 AACGC-GAATTTGT-AAA-TCGC
1 AACACAGAA---GTCAAATTCGC
1482919 AACACAGAAGTCAAATTCGC
1 AACACAGAAGTCAAATTCGC
*
1482939 AACACATAAGTCAAATTCGC
1 AACACAGAAGTCAAATTCGC
* * *
1482959 AACACTGAATTTGAAATTCGC
1 AACACAGAA-GTCAAATTCGC
1482980 AAC
1 AAC
1482983 TGAATTTCAA
Statistics
Matches: 118, Mismatches: 14, Indels: 23
0.76 0.09 0.15
Matches are distributed among these distances:
18 4 0.03
19 5 0.04
20 90 0.76
21 18 0.15
24 1 0.01
ACGTcount: A:0.43, C:0.23, G:0.14, T:0.20
Consensus pattern (20 bp):
AACACAGAAGTCAAATTCGC
Found at i:1482889 original size:100 final size:100
Alignment explanation
Indices: 1482770--1482961 Score: 303
Period size: 100 Copynumber: 1.9 Consensus size: 100
1482760 TGCAATTTTC
* * *
1482770 CAAATTCGCAACGCAAATCTGTAAATCGCATCGCAAAATTGTAAATCGTAACACAGAAGTCAAAT
1 CAAATTCGCAACACAAATCTGTAAATCGCAACGCAAAATTGTAAATCGCAACACAGAAGTCAAAT
*
1482835 TCGTAACACAAAAGTCAAATTCACAACGCGATAGT
66 TCGCAACACAAAAGTCAAATTCACAACGCGATAGT
* * *
1482870 CAAATTCGCAACACGAATCTGTAAATCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAAT
1 CAAATTCGCAACACAAATCTGTAAATCGCAACGCAAAATTGTAAATCGCAACACAGAAGTCAAAT
* *
1482935 TCGCAACACATAAGTCAAATTCGCAAC
66 TCGCAACACAAAAGTCAAATTCACAAC
1482962 ACTGAATTTG
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
100 83 1.00
ACGTcount: A:0.42, C:0.23, G:0.14, T:0.20
Consensus pattern (100 bp):
CAAATTCGCAACACAAATCTGTAAATCGCAACGCAAAATTGTAAATCGCAACACAGAAGTCAAAT
TCGCAACACAAAAGTCAAATTCACAACGCGATAGT
Found at i:1482893 original size:80 final size:79
Alignment explanation
Indices: 1482809--1482982 Score: 194
Period size: 80 Copynumber: 2.2 Consensus size: 79
1482799 ATCGCAAAAT
* * *
1482809 TGTAAATCGTAACACAGAA-GTCAAATTCGTAACACAAAAGTCAAATTCACAACGCGAT-AGTCA
1 TGTAAATCGCAACAC-GAATGT-AAA-TCGCAACACAAAAGTCAAATTCACAACAC-ATAAGTCA
1482872 AATTCGCAACAC-GAATC
62 AATTCGCAACACTGAATC
* * *
1482889 TGTAAATCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACACATAAGTCAAA
1 TGTAAATCGCAACACGAA--TGTAAATCGCAACACAAAAGTCAAATTCACAACACATAAGTCAAA
*
1482954 TTCGCAACACTGAATT
64 TTCGCAACACTGAATC
1482970 TG-AAATTCGCAAC
1 TGTAAA-TCGCAAC
1482983 TGAATTTCAA
Statistics
Matches: 81, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
79 5 0.06
80 58 0.72
81 16 0.20
82 2 0.02
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.21
Consensus pattern (79 bp):
TGTAAATCGCAACACGAATGTAAATCGCAACACAAAAGTCAAATTCACAACACATAAGTCAAATT
CGCAACACTGAATC
Found at i:1482960 original size:60 final size:60
Alignment explanation
Indices: 1482867--1482982 Score: 148
Period size: 60 Copynumber: 1.9 Consensus size: 60
1482857 ACAACGCGAT
** *
1482867 AGTCAAATTCGCAACACGAATCTGTAAATCGCAACGC-GAATTTGTAAA-TCGCAACACAGA
1 AGTCAAATTCGCAACAC-AATAAGTAAATCGCAACACTGAATTTG-AAATTCGCAACACAGA
1482927 AGTCAAATTCGCAACAC-ATAAGTCAAATTCGCAACACTGAATTTGAAATTCGCAAC
1 AGTCAAATTCGCAACACAATAAGT-AAA-TCGCAACACTGAATTTGAAATTCGCAAC
1482983 TGAATTTCAA
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
58 4 0.08
59 3 0.06
60 28 0.57
61 14 0.29
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.22
Consensus pattern (60 bp):
AGTCAAATTCGCAACACAATAAGTAAATCGCAACACTGAATTTGAAATTCGCAACACAGA
Found at i:1482993 original size:40 final size:40
Alignment explanation
Indices: 1482829--1483041 Score: 145
Period size: 40 Copynumber: 5.3 Consensus size: 40
1482819 AACACAGAAG
* * ** * * *
1482829 TCAAATTCGTAACACAAAAGTCAAATTCACAACGCG-ATAG
1 TCAAATTCGCAACACGAATTTCAAATTCGCAACACGAAT-T
*
1482869 TCAAATTCGCAACACGAATCTGT-AAA-TCGCAACGCGAATT
1 TCAAATTCGCAACACGAAT-T-TCAAATTCGCAACACGAATT
* * **
1482909 TGTAAA-TCGCAACACAGAA-GTCAAATTCGCAACAC-ATAAG
1 T-CAAATTCGCAACAC-GAATTTCAAATTCGCAACACGA-ATT
* *
1482949 TCAAATTCGCAACACTGAATTTGAAATTCGCAAC-TGAATT
1 TCAAATTCGCAACAC-GAATTTCAAATTCGCAACACGAATT
* * *
1482989 TCAAATTCGCAACTCGATTTTCTAATTCGCAACACGAATT
1 TCAAATTCGCAACACGAATTTCAAATTCGCAACACGAATT
*
1483029 T-AATTTCGCAACA
1 TCAAATTCGCAACA
1483042 GGTTTTAGTT
Statistics
Matches: 136, Mismatches: 25, Indels: 25
0.73 0.13 0.13
Matches are distributed among these distances:
38 1 0.01
39 32 0.24
40 78 0.57
41 24 0.18
42 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.25
Consensus pattern (40 bp):
TCAAATTCGCAACACGAATTTCAAATTCGCAACACGAATT
Found at i:1482993 original size:60 final size:58
Alignment explanation
Indices: 1482869--1483040 Score: 147
Period size: 60 Copynumber: 2.9 Consensus size: 58
1482859 AACGCGATAG
* * * *
1482869 TCAAATTCGCAACACGAATCTGT-AAA-TCGCAACGCGAATTTGTAAA-TCGCAACACAGAA-G
1 TCAAATTCGCAACACG-AT-AGTCAAATTCGCAACACGAA-TT-TAAATTCGC-A-ACTGAATT
1482929 TCAAATTCGCAACAC-ATAAGTCAAATTCGCAACACTGAATTTGAAATTCGCAACTGAATT
1 TCAAATTCGCAACACGAT-AGTCAAATTCGCAACAC-GAATTT-AAATTCGCAACTGAATT
* ** * *
1482989 TCAAATTCGCAACTCGATTTTCTAATTCGCAACACGAATTTAATTTCGCAAC
1 TCAAATTCGCAACACGATAGTCAAATTCGCAACACGAATTTAAATTCGCAAC
1483041 AGGTTTTAGT
Statistics
Matches: 95, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
58 14 0.15
59 15 0.16
60 57 0.60
61 9 0.09
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (58 bp):
TCAAATTCGCAACACGATAGTCAAATTCGCAACACGAATTTAAATTCGCAACTGAATT
Found at i:1482999 original size:80 final size:80
Alignment explanation
Indices: 1482829--1483001 Score: 219
Period size: 80 Copynumber: 2.2 Consensus size: 80
1482819 AACACAGAAG
* *
1482829 TCAAATTCGTAACACAAAAGTCAAATTCACAACGCGATAGTCAAATTCGCAACACGAATCTGTAA
1 TCAAATTCGCAACACAAAAGTCAAATTCACAACACGATAGTCAAATTCGCAACACGAATCTGTAA
1482894 ATCGCAACGCGAATT
66 ATCGCAACGCGAATT
* * * *
1482909 TGTAAA-TCGCAACACAGAAGTCAAATTCGCAACAC-ATAAGTCAAATTCGCAACACTGAATTTG
1 T-CAAATTCGCAACACAAAAGTCAAATTCACAACACGAT-AGTCAAATTCGCAACAC-GAATCTG
*
1482972 -AAATTCGCAAC-TGAATT
63 TAAA-TCGCAACGCGAATT
1482989 TCAAATTCGCAAC
1 TCAAATTCGCAAC
1483002 TCGATTTTCT
Statistics
Matches: 80, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
79 5 0.06
80 59 0.74
81 16 0.20
ACGTcount: A:0.41, C:0.23, G:0.13, T:0.23
Consensus pattern (80 bp):
TCAAATTCGCAACACAAAAGTCAAATTCACAACACGATAGTCAAATTCGCAACACGAATCTGTAA
ATCGCAACGCGAATT
Found at i:1483015 original size:20 final size:19
Alignment explanation
Indices: 1482949--1483040 Score: 96
Period size: 19 Copynumber: 4.7 Consensus size: 19
1482939 AACACATAAG
1482949 TCAAATTCGCAACACTGAATT
1 TCAAATTCGC-A-ACTGAATT
*
1482970 TGAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
1482989 TCAAATTCGCAACTCGATTT
1 TCAAATTCGCAACT-GAATT
* *
1483009 TCTAATTCGCAACACGAATT
1 TCAAATTCGCAAC-TGAATT
*
1483029 T-AATTTCGCAAC
1 TCAAATTCGCAAC
1483041 AGGTTTTAGT
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
19 30 0.49
20 22 0.36
21 9 0.15
ACGTcount: A:0.35, C:0.23, G:0.11, T:0.32
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:1483216 original size:14 final size:15
Alignment explanation
Indices: 1483197--1483234 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1483187 TCCCCATCTC
1483197 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
1483211 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
1483227 TAATTTTT
1 TAATTTTT
1483235 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:1484027 original size:24 final size:24
Alignment explanation
Indices: 1483976--1484029 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1483966 GTATTCAAAA
*
1483976 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
1484000 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
1484024 TTTGAT
1 TTTGAT
1484030 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:1484218 original size:9 final size:9
Alignment explanation
Indices: 1484204--1484239 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
1484194 ATATAACCCT
1484204 AAAGAAGAA
1 AAAGAAGAA
1484213 AAAGAAGAA
1 AAAGAAGAA
1484222 GAAA-AAGAA
1 -AAAGAAGAA
1484231 AAAGAAGAA
1 AAAGAAGAA
1484240 GTCCCCGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 3 0.12
9 19 0.76
10 3 0.12
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (9 bp):
AAAGAAGAA
Found at i:1484222 original size:12 final size:12
Alignment explanation
Indices: 1484205--1484236 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1484195 TATAACCCTA
1484205 AAGAAGAAAAAG
1 AAGAAGAAAAAG
1484217 AAGAAGAAAAAG
1 AAGAAGAAAAAG
*
1484229 AAAAAGAA
1 AAGAAGAA
1484237 GAAGTCCCCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (12 bp):
AAGAAGAAAAAG
Found at i:1484295 original size:24 final size:24
Alignment explanation
Indices: 1484263--1484320 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
1484253 AGAAAAAGAA
*
1484263 GAAAATGCCATGGGAGTATAATTG
1 GAAAATGCCACGGGAGTATAATTG
1484287 GAAAATGCCACGGGAGTATAATTG
1 GAAAATGCCACGGGAGTATAATTG
*
1484311 GAATATGCCA
1 GAAAATGCCA
1484321 GAATTATTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.38, C:0.12, G:0.28, T:0.22
Consensus pattern (24 bp):
GAAAATGCCACGGGAGTATAATTG
Found at i:1486366 original size:18 final size:18
Alignment explanation
Indices: 1486333--1486368 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1486323 AAACAAAAGG
**
1486333 AAATCAAAATTGCAATCA
1 AAATCAAAATCCCAATCA
1486351 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1486369 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:1486631 original size:14 final size:14
Alignment explanation
Indices: 1486593--1486631 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1486583 AAAGTCAAAT
1486593 TCGCAACGC-AAAA
1 TCGCAACGCGAAAA
1486606 TCGCAAAC-CGAAAA
1 TCGC-AACGCGAAAA
1486620 TCGCAACGCGAA
1 TCGCAACGCGAA
1486632 TTTGACTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 8 0.35
14 15 0.65
ACGTcount: A:0.44, C:0.31, G:0.18, T:0.08
Consensus pattern (14 bp):
TCGCAACGCGAAAA
Found at i:1486904 original size:14 final size:14
Alignment explanation
Indices: 1486885--1486918 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1486875 ATCAAATTAA
1486885 ACAAATAAACTTTT
1 ACAAATAAACTTTT
*
1486899 ACAAATCAACTTTT
1 ACAAATAAACTTTT
1486913 ACAAAT
1 ACAAAT
1486919 TAATTAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATAAACTTTT
Found at i:1487785 original size:24 final size:24
Alignment explanation
Indices: 1487734--1487787 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1487724 GTATTCAAAA
*
1487734 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
1487758 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
1487782 TTTGAT
1 TTTGAT
1487788 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:1490089 original size:18 final size:18
Alignment explanation
Indices: 1490056--1490091 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1490046 AAACAAAAGG
**
1490056 AAATCAAAATTGCAATCA
1 AAATCAAAATCCCAATCA
1490074 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1490092 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:1490354 original size:14 final size:14
Alignment explanation
Indices: 1490316--1490354 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1490306 AAAGTCAAAT
1490316 TCGCAACGC-AAAA
1 TCGCAACGCGAAAA
1490329 TCGCAAAC-CGAAAA
1 TCGC-AACGCGAAAA
1490343 TCGCAACGCGAA
1 TCGCAACGCGAA
1490355 TTTGACTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 8 0.35
14 15 0.65
ACGTcount: A:0.44, C:0.31, G:0.18, T:0.08
Consensus pattern (14 bp):
TCGCAACGCGAAAA
Found at i:1490620 original size:14 final size:14
Alignment explanation
Indices: 1490603--1490636 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
1490593 ATCAAATTAA
1490603 ACAAATCAACTTTT
1 ACAAATCAACTTTT
1490617 ACAAATCAACTTTT
1 ACAAATCAACTTTT
1490631 ACAAAT
1 ACAAAT
1490637 TAATTAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1490675 original size:79 final size:77
Alignment explanation
Indices: 1490538--1490692 Score: 249
Period size: 79 Copynumber: 2.0 Consensus size: 77
1490528 ATTTAAAACA
1490538 ACAAATCAACTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATTAA
1 ACAAATCAACTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATC-AATTAA
1490603 ACAAATCAACTTTT
65 AC-AATCAACTTTT
* * *
1490617 ACAAATCAACTTTTACAAATTAATTAAACAAGC-AAAAAATAATTCTTATTTCCTCATCAATTAA
1 ACAAATCAAC-TTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTAA
1490681 ACAATCAACTTT
65 ACAATCAACTTT
1490693 CAATGTAAAA
Statistics
Matches: 72, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
77 10 0.14
78 8 0.11
79 33 0.46
80 21 0.29
ACGTcount: A:0.50, C:0.18, G:0.01, T:0.31
Consensus pattern (77 bp):
ACAAATCAACTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTAAA
CAATCAACTTTT
Found at i:1492117 original size:21 final size:21
Alignment explanation
Indices: 1492039--1492155 Score: 89
Period size: 21 Copynumber: 5.7 Consensus size: 21
1492029 GTGAATCGAG
* *
1492039 CTCTTGAACGGTG-GAGGGAC
1 CTCTTGAACGATGAGAGGGGC
*
1492059 C-CATTGAACGATGACA-GGGC
1 CTC-TTGAACGATGAGAGGGGC
* * * * *
1492079 CTCTTAAAAGGTGGGAGGGGT
1 CTCTTGAACGATGAGAGGGGC
*
1492100 CTCTTGAACGATGAGAGGAGC
1 CTCTTGAACGATGAGAGGGGC
* *
1492121 CTATTGAACGAT-AGGAGGCGC
1 CTCTTGAACGATGA-GAGGGGC
1492142 CTCTTGAACGATGA
1 CTCTTGAACGATGA
1492156 CAGGTGAATC
Statistics
Matches: 73, Mismatches: 18, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
19 1 0.01
20 23 0.32
21 48 0.66
22 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.34, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGC
Found at i:1494369 original size:14 final size:14
Alignment explanation
Indices: 1494346--1494379 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1494336 TGCGATTTTC
1494346 ATTTTCGTGTTGCG
1 ATTTTCGTGTTGCG
*
1494360 ATTTTGGTGTTGCG
1 ATTTTCGTGTTGCG
1494374 ATTTTC
1 ATTTTC
1494380 ATTTTCGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.09, C:0.12, G:0.26, T:0.53
Consensus pattern (14 bp):
ATTTTCGTGTTGCG
Found at i:1494769 original size:22 final size:22
Alignment explanation
Indices: 1494742--1494795 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
1494732 GAGATAGACG
1494742 GATTTCGCCGGAGATGGGGACA
1 GATTTCGCCGGAGATGGGGACA
* * *
1494764 GATTTCGTCAGAGATGGGGACG
1 GATTTCGCCGGAGATGGGGACA
*
1494786 GATGTCGCCG
1 GATTTCGCCG
1494796 TAGAGAGTGA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.20, C:0.19, G:0.41, T:0.20
Consensus pattern (22 bp):
GATTTCGCCGGAGATGGGGACA
Done.