Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 128 of 316
Found at i:40665881 original size:14 final size:14
Alignment explanation
Indices: 40665862--40665889 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40665852 ATAACAACAT
40665862 CCATAAGAATTATC
1 CCATAAGAATTATC
40665876 CCATAAGAATTATC
1 CCATAAGAATTATC
40665890 TTACTACTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.29
Consensus pattern (14 bp):
CCATAAGAATTATC
Found at i:40665980 original size:16 final size:16
Alignment explanation
Indices: 40665961--40665991 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40665951 CTTCTGCACT
40665961 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
40665977 TACTTACTTACTTAA
1 TACTCACTTACTTAA
40665992 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:40665997 original size:20 final size:20
Alignment explanation
Indices: 40665958--40665997 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
40665948 AAACTTCTGC
* *
40665958 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
40665978 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
40665998 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:40678104 original size:11 final size:11
Alignment explanation
Indices: 40678088--40678113 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
40678078 ACTTTTTCAA
40678088 TCATCCCTCAT
1 TCATCCCTCAT
40678099 TCATCCCTCAT
1 TCATCCCTCAT
40678110 TCAT
1 TCAT
40678114 TCATCATTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.19, C:0.42, G:0.00, T:0.38
Consensus pattern (11 bp):
TCATCCCTCAT
Found at i:40679491 original size:25 final size:25
Alignment explanation
Indices: 40679463--40679534 Score: 81
Period size: 25 Copynumber: 2.9 Consensus size: 25
40679453 CCCTCTCTCG
** *
40679463 AGCCATATAATAGGAAGCTCATGTA
1 AGCCATATAACGGGAAGCTCATCTA
* *
40679488 AGCCATGTAACGGGAAGCACATCTA
1 AGCCATATAACGGGAAGCTCATCTA
* *
40679513 GGCTATATAACGGGAAGCTCAT
1 AGCCATATAACGGGAAGCTCAT
40679535 AAGAGCAATA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.21
Consensus pattern (25 bp):
AGCCATATAACGGGAAGCTCATCTA
Found at i:40679686 original size:23 final size:23
Alignment explanation
Indices: 40679642--40679691 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
40679632 GGATATCCAT
* * *
40679642 ATATTGGGAAGTTCAAGCGAGCA
1 ATATCGGGAAGCTCAAGAGAGCA
* *
40679665 ATATCGGGAAGCTCCAGAGAGCC
1 ATATCGGGAAGCTCAAGAGAGCA
40679688 ATAT
1 ATAT
40679692 AACAGGATGC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (23 bp):
ATATCGGGAAGCTCAAGAGAGCA
Found at i:40681382 original size:16 final size:15
Alignment explanation
Indices: 40681357--40681399 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
40681347 ATAATTATTT
40681357 AAAATATAAAAAATA
1 AAAATATAAAAAATA
40681372 AAAATTATAAAAAATA
1 AAAA-TATAAAAAATA
* *
40681388 AATATACAAAAA
1 AAAATATAAAAA
40681400 TTTAAACAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAATATAAAAAATA
Found at i:40681405 original size:23 final size:22
Alignment explanation
Indices: 40681353--40681405 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
40681343 TTTTATAATT
* *
40681353 ATTTAAAATATAAAAAATAAAA
1 ATTTAAAAAATAAAAAACAAAA
*
40681375 ATTATAAAAAATAAATATACAAAA
1 ATT-TAAAAAATAAA-AAACAAAA
40681399 ATTTAAA
1 ATTTAAA
40681406 CAAGTAGTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 3 0.12
23 14 0.54
24 9 0.35
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (22 bp):
ATTTAAAAAATAAAAAACAAAA
Found at i:40683702 original size:22 final size:22
Alignment explanation
Indices: 40683674--40683724 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
40683664 AAAGGGAATA
40683674 GTTAGTTGTTTTTGCATTCGAG
1 GTTAGTTGTTTTTGCATTCGAG
40683696 GTTAGTTGTTTTTGCATTCGAG
1 GTTAGTTGTTTTTGCATTCGAG
*
40683718 GTAAGTT
1 GTTAGTT
40683725 CGTGTGACAG
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:0.16, C:0.08, G:0.27, T:0.49
Consensus pattern (22 bp):
GTTAGTTGTTTTTGCATTCGAG
Found at i:40686101 original size:27 final size:27
Alignment explanation
Indices: 40686070--40686247 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
40686060 TAAATTGTAC
40686070 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
40686097 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
40686123 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
40686151 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
40686179 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
40686206 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
40686233 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40686248 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:40686184 original size:82 final size:81
Alignment explanation
Indices: 40686071--40686226 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
40686061 AAATTGTACA
* *
40686071 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
40686135 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
40686152 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
40686217 TGCGAGTTGA
65 TGCGAATTGA
40686227 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:40686238 original size:82 final size:81
Alignment explanation
Indices: 40686067--40686247 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
40686057 GATTAAATTG
* *
40686067 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
40686132 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
40686148 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
40686212 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
40686230 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
40686248 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:40694293 original size:27 final size:27
Alignment explanation
Indices: 40694262--40694439 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
40694252 TAAATTGTAC
*
40694262 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
40694289 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
40694315 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAATTGACTATGT
* *
40694343 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* * *
40694371 AGCACTAAGTGTGCGAGTTGATTACGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
40694398 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
40694425 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40694440 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:40694376 original size:82 final size:81
Alignment explanation
Indices: 40694263--40694418 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
40694253 AAATTGTACA
* *
40694263 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
40694327 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
40694344 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
40694409 TGCGAGTTGA
65 TGCGAATTGA
40694419 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:40694430 original size:82 final size:81
Alignment explanation
Indices: 40694259--40694439 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
40694249 GATTAAATTG
* *
40694259 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
40694324 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
40694340 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
40694404 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
40694422 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
40694440 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:40696291 original size:48 final size:48
Alignment explanation
Indices: 40696221--40696512 Score: 279
Period size: 48 Copynumber: 6.0 Consensus size: 48
40696211 AGACATTTGG
** *
40696221 TTGATATGTGTTCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCG
1 TTGATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
* *
40696269 TTGATATGTGTGCTAGTGTAAGACCATGTCTAGGACATGGCATCGGC-
1 TTGATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
* * * * * * *
40696316 CTCATTATGAGAACCAGTGTAAGACCATGTCTGGGACATGGCATTGGCC
1 TTGA-TATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
** * * *
40696365 TCAATATGTGAG-TCAGTGTAAGACTATGTTTGGAACATGGCATCGGCA
1 TTGATATGTGAGCT-AGTGTAAGACCATGTCTGGGACATGGCATCGGCA
* *
40696413 TTGTTATATGTG-TC-AGTGTAAGACCATGTCTAGGACATGGCATCGGCACCA
1 TTG--ATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGG---CA
* * * *
40696464 ATG-TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGTATCGGCA
1 TTGATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
40696511 TT
1 TT
40696513 TTACCCTTTT
Statistics
Matches: 199, Mismatches: 34, Indels: 23
0.78 0.13 0.09
Matches are distributed among these distances:
47 5 0.03
48 151 0.76
49 2 0.01
50 37 0.19
51 4 0.02
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.28
Consensus pattern (48 bp):
TTGATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
Found at i:40698270 original size:20 final size:20
Alignment explanation
Indices: 40698245--40698301 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 20
40698235 CGGGTAGAGG
40698245 ACACGGGCGTGTCCTGAGCC
1 ACACGGGCGTGTCCTGAGCC
*
40698265 ACAC-GG-GTG----GAG-G
1 ACACGGGCGTGTCCTGAGCC
40698278 ACACGGGCGTGTCCTGAGCC
1 ACACGGGCGTGTCCTGAGCC
40698298 ACAC
1 ACAC
40698302 AGGCTTGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 14
0.64 0.05 0.32
Matches are distributed among these distances:
13 4 0.14
14 5 0.18
15 3 0.11
18 3 0.11
19 5 0.18
20 8 0.29
ACGTcount: A:0.19, C:0.32, G:0.37, T:0.12
Consensus pattern (20 bp):
ACACGGGCGTGTCCTGAGCC
Found at i:40698278 original size:33 final size:33
Alignment explanation
Indices: 40698232--40698301 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
40698222 ACAGAGAATT
40698232 ACACGGGTAGAGGACACGGGCGTGTCCTGAGCC
1 ACACGGGTAGAGGACACGGGCGTGTCCTGAGCC
*
40698265 ACACGGGTGGAGGACACGGGCGTGTCCTGAGCC
1 ACACGGGTAGAGGACACGGGCGTGTCCTGAGCC
40698298 ACAC
1 ACAC
40698302 AGGCTTGTGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.21, C:0.29, G:0.39, T:0.11
Consensus pattern (33 bp):
ACACGGGTAGAGGACACGGGCGTGTCCTGAGCC
Found at i:40703899 original size:67 final size:64
Alignment explanation
Indices: 40703754--40703937 Score: 221
Period size: 64 Copynumber: 2.8 Consensus size: 64
40703744 ATATAGTTCG
* * * *
40703754 GCTCTCTTGTAC-ACATGGTGAACACTTAGTACCACCCATGTGACCTAGC--CAGTTTATCTCGT
1 GCTCTCTTGT-CTACATGGTGTACACTTAGTACCACCCATGCGACCTAGCTACA-TATATCCCGT
40703816 A
64 A
* * *
40703817 GCTCTCTTGTCTACATGGTGTCCTTCACTTAGAACCACGCATGCGACCTAGCTACATATATCCCG
1 GCTCTCTTGTCTACATGGTG---TACACTTAGTACCACCCATGCGACCTAGCTACATATATCCCG
40703882 TA
63 TA
* *
40703884 GCTCTCTTGTCTACATGGTGTACACATAGTATCACCCATGCGACCTAGCTACAT
1 GCTCTCTTGTCTACATGGTGTACACTTAGTACCACCCATGCGACCTAGCTACAT
40703938 CATAATGTCT
Statistics
Matches: 103, Mismatches: 12, Indels: 11
0.82 0.10 0.09
Matches are distributed among these distances:
62 1 0.01
63 18 0.17
64 29 0.28
66 24 0.23
67 29 0.28
68 2 0.02
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.30
Consensus pattern (64 bp):
GCTCTCTTGTCTACATGGTGTACACTTAGTACCACCCATGCGACCTAGCTACATATATCCCGTA
Found at i:40706491 original size:48 final size:47
Alignment explanation
Indices: 40706420--40706557 Score: 195
Period size: 48 Copynumber: 2.9 Consensus size: 47
40706410 CATTTGGTTT
***
40706420 ATATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTTG
1 ATATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC-CAC
40706468 ATATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCAC
1 ATATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCAC
* * * *
40706515 ATTATGAGAGCCAGTGTAAGACCATGTCTGGGACATGACATCG
1 A-TATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCG
40706558 CATTTTACCC
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
47 1 0.01
48 81 0.99
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (47 bp):
ATATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCAC
Found at i:40708000 original size:41 final size:41
Alignment explanation
Indices: 40707943--40708021 Score: 149
Period size: 41 Copynumber: 1.9 Consensus size: 41
40707933 TTTAAAAGTG
*
40707943 ACTAAATTAGTCTATGGATAGACCTTAGCATTAGTATGGTA
1 ACTAAATTAGTCTATGGATAGACCTTAGCATAAGTATGGTA
40707984 ACTAAATTAGTCTATGGATAGACCTTAGCATAAGTATG
1 ACTAAATTAGTCTATGGATAGACCTTAGCATAAGTATG
40708022 AAGTGTAAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (41 bp):
ACTAAATTAGTCTATGGATAGACCTTAGCATAAGTATGGTA
Found at i:40709581 original size:54 final size:54
Alignment explanation
Indices: 40709486--40709592 Score: 142
Period size: 54 Copynumber: 2.0 Consensus size: 54
40709476 TGAGTTAAAT
* * * *
40709486 AATTAAGCTTTATTAAAATATGAAATAGAATAAAAGGATAAAATACACTTGAAC
1 AATTAAACTGTATTAAAATATAAAATAGAATAAAAGAATAAAATACACTTGAAC
** * *
40709540 AATTAAACTGTATTAAAATATAAAATAGAATAGGAGAATAAAATGCCCTTGAA
1 AATTAAACTGTATTAAAATATAAAATAGAATAAAAGAATAAAATACACTTGAA
40709593 TGTGATTGAA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.53, C:0.07, G:0.12, T:0.27
Consensus pattern (54 bp):
AATTAAACTGTATTAAAATATAAAATAGAATAAAAGAATAAAATACACTTGAAC
Found at i:40711280 original size:11 final size:10
Alignment explanation
Indices: 40711239--40711286 Score: 60
Period size: 11 Copynumber: 4.6 Consensus size: 10
40711229 CAAAAAAAAA
40711239 TATTTTTTAC
1 TATTTTTTAC
*
40711249 TATTTTATTGC
1 TATTTT-TTAC
*
40711260 TGTTTTTTAC
1 TATTTTTTAC
40711270 TATTTTGTTAC
1 TATTTT-TTAC
40711281 TATTTT
1 TATTTT
40711287 CTTGTTGTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
10 14 0.44
11 18 0.56
ACGTcount: A:0.17, C:0.08, G:0.06, T:0.69
Consensus pattern (10 bp):
TATTTTTTAC
Found at i:40711286 original size:21 final size:21
Alignment explanation
Indices: 40711239--40711286 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
40711229 CAAAAAAAAA
*
40711239 TATTTTTTACTATTTTATTGC
1 TATTTTTTACTATTTTATTAC
* *
40711260 TGTTTTTTACTATTTTGTTAC
1 TATTTTTTACTATTTTATTAC
40711281 TATTTT
1 TATTTT
40711287 CTTGTTGTTT
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:0.17, C:0.08, G:0.06, T:0.69
Consensus pattern (21 bp):
TATTTTTTACTATTTTATTAC
Found at i:40713343 original size:198 final size:198
Alignment explanation
Indices: 40713005--40713396 Score: 712
Period size: 198 Copynumber: 2.0 Consensus size: 198
40712995 AGTACAGTTT
* *
40713005 ATTCATTAAAGGTTCCCATGTTTCACAGTTCAGCATACCTAACCTCTCTTCACTAAAAATAAATT
1 ATTCATTAAAGATTCCCATGTTTCACAGTTCAGCAGACCTAACCTCTCTTCACTAAAAATAAATT
*
40713070 ATCTCATTATGCAAAAATCGGATAATGTTTCTGTTTATTTCTAATGAAAATAGACTCACTAAGGA
66 ATCTCATTATGCAAAAATCAGATAATGTTTCTGTTTATTTCTAATGAAAATAGACTCACTAAGGA
*
40713135 ATCTATAAATATAAACTTTGACTTATAATTCTTTTTTTACAATTTCTAGTGATTTTCCAAATTTT
131 ATCTATAAATATAAACTTTGACTTATAATTCTTTTTTTAAAATTTCTAGTGATTTTCCAAATTTT
40713200 GAA
196 GAA
*
40713203 ATTCATTAAAGATTCCCCTGTTTCACAGTTCAGCAGACCTAACCTCTCTTCACTAAAAATAAATT
1 ATTCATTAAAGATTCCCATGTTTCACAGTTCAGCAGACCTAACCTCTCTTCACTAAAAATAAATT
* * *
40713268 ATCTCATTATGCAGAAATCAGATAATGTTTCTGTTTGTTTCTAATGAAAATATACTCACTAAGGA
66 ATCTCATTATGCAAAAATCAGATAATGTTTCTGTTTATTTCTAATGAAAATAGACTCACTAAGGA
40713333 ATCTATAAATATAAACTTTGACTTATAATTCTTTTTTTAAAATTTCTAGTGATTTTCCAAATTT
131 ATCTATAAATATAAACTTTGACTTATAATTCTTTTTTTAAAATTTCTAGTGATTTTCCAAATTT
40713397 GGAACAGGGG
Statistics
Matches: 186, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
198 186 1.00
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.40
Consensus pattern (198 bp):
ATTCATTAAAGATTCCCATGTTTCACAGTTCAGCAGACCTAACCTCTCTTCACTAAAAATAAATT
ATCTCATTATGCAAAAATCAGATAATGTTTCTGTTTATTTCTAATGAAAATAGACTCACTAAGGA
ATCTATAAATATAAACTTTGACTTATAATTCTTTTTTTAAAATTTCTAGTGATTTTCCAAATTTT
GAA
Found at i:40714193 original size:53 final size:53
Alignment explanation
Indices: 40714093--40714299 Score: 159
Period size: 53 Copynumber: 3.8 Consensus size: 53
40714083 TTCCTTTTTA
* * **
40714093 AACTTACCATTGCCATGTCTTGACATGGTCTTATGTGGTATCCTTGCCTTATG
1 AACTCACCATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATG
* *
40714146 AACTCACCATTGCCATGCCTTGGCATGGTCTTACATAGG-ATCTTTGCCTTATCG
1 AACTCACCATTGCCATGCCTTGACATGGTCTTACAT-GGTATCCTTGCCTTAT-G
** * * * * * * * * *
40714200 TAGTTTATCAATGTCATGTCTTGACATGGTCATACATGATTTCCTTGCCTCGTA-A
1 -AACTCACCATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCT--TATG
* * *
40714255 AACTTACCAATGCCATGCCTTGGCATGGTCTTAC-TGGGTATCCTT
1 AACTCACCATTGCCATGCCTTGACATGGTCTTACAT-GGTATCCTT
40714300 AAACCCTAAT
Statistics
Matches: 119, Mismatches: 28, Indels: 13
0.74 0.17 0.08
Matches are distributed among these distances:
53 44 0.37
54 38 0.32
55 35 0.29
57 2 0.02
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.37
Consensus pattern (53 bp):
AACTCACCATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATG
Found at i:40719650 original size:53 final size:53
Alignment explanation
Indices: 40719570--40719776 Score: 182
Period size: 53 Copynumber: 3.8 Consensus size: 53
40719560 TTCCTTTTTA
* * * * *
40719570 AACTTACCATTTCCAAGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTACG
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTTCCTTACG
* * * * * * **
40719623 AACTCACCATTGCCATGCCTTGGCATGGTCTTACGTGGGATTTTTTCCTTATCG
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTTCCTTA-CG
** * * * *
40719677 TAGTTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTTCCTTGTA-A
1 -AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTTCC-T-TACG
* *
40719732 AACTTACCAATGCCATGTCTTGGCATGGTCATACATGGTATCCTT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTT
40719777 AAACCCTAAT
Statistics
Matches: 120, Mismatches: 30, Indels: 7
0.76 0.19 0.04
Matches are distributed among these distances:
53 42 0.35
54 40 0.33
55 35 0.29
56 1 0.01
57 2 0.02
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (53 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTTCCTTACG
Found at i:40719725 original size:55 final size:52
Alignment explanation
Indices: 40719623--40719768 Score: 139
Period size: 55 Copynumber: 2.7 Consensus size: 52
40719613 TTGCCTTACG
* * * * **
40719623 AACTCACCATTGCCATGCCTTGGCATGGTCTTACGTGGGATTTTTTCCTTATCGT
1 AACTTACCAATGCCATGTCTTGGCATGGTCTTACAT--GATTTTTTCCTTAT-AA
** * * *
40719678 AGTTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTTCCTTGTAA
1 AACTTACCAATGCCATGTCTTGGCATGGTCTTACATGATTT--TTTCCTTATAA
*
40719732 AACTTACCAATGCCATGTCTTGGCATGGTCATACATG
1 AACTTACCAATGCCATGTCTTGGCATGGTCTTACATG
40719769 GTATCCTTAA
Statistics
Matches: 73, Mismatches: 16, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
53 5 0.07
54 32 0.44
55 36 0.49
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.38
Consensus pattern (52 bp):
AACTTACCAATGCCATGTCTTGGCATGGTCTTACATGATTTTTTCCTTATAA
Found at i:40719776 original size:54 final size:53
Alignment explanation
Indices: 40719553--40719776 Score: 173
Period size: 54 Copynumber: 4.2 Consensus size: 53
40719543 AGGATACACG
* * * * *
40719553 GGTA-CCTTTCCTTTTTAAACTTACCATTTCCAAGTCTTGACATGGTCTTACGT
1 GGTATCCTTTCC-TTTAAAACTTACCAATGCCATGTCTTGACATGGTCTTACAT
* * * * * * *
40719606 GGTATCCTTGCC-TTACGAACTCACCATTGCCATGCCTTGGCATGGTCTTACGT
1 GGTATCCTTTCCTTTA-AAACTTACCAATGCCATGTCTTGACATGGTCTTACAT
* ** ** ** *
40719659 GGGATTTTTTCCTTATCGTAGTTTATCAATGCCATGTCTTGACATGGTCTTACAT
1 GGTATCCTTTCCTT-T-AAAACTTACCAATGCCATGTCTTGACATGGTCTTACAT
* * * *
40719714 GATTTCCTTTCCTTGTAAAACTTACCAATGCCATGTCTTGGCATGGTCATACAT
1 GGTATCCTTTCCTT-TAAAACTTACCAATGCCATGTCTTGACATGGTCTTACAT
40719768 GGTATCCTT
1 GGTATCCTT
40719777 AAACCCTAAT
Statistics
Matches: 129, Mismatches: 37, Indels: 9
0.74 0.21 0.05
Matches are distributed among these distances:
52 2 0.02
53 43 0.33
54 45 0.35
55 39 0.30
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.39
Consensus pattern (53 bp):
GGTATCCTTTCCTTTAAAACTTACCAATGCCATGTCTTGACATGGTCTTACAT
Found at i:40720152 original size:14 final size:14
Alignment explanation
Indices: 40720133--40720166 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
40720123 AAAACTACGA
*
40720133 TTTTGCCCTTAAAC
1 TTTTGCCCCTAAAC
*
40720147 TTTTGCCCCTAAGC
1 TTTTGCCCCTAAAC
40720161 TTTTGC
1 TTTTGC
40720167 ATATTTACAC
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:0.15, C:0.29, G:0.12, T:0.44
Consensus pattern (14 bp):
TTTTGCCCCTAAAC
Found at i:40721167 original size:26 final size:26
Alignment explanation
Indices: 40721131--40721186 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
40721121 TGATACAAAT
40721131 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
40721157 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
40721183 TGAT
1 TGAT
40721187 GGGAATTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:40722850 original size:27 final size:26
Alignment explanation
Indices: 40722810--40722950 Score: 183
Period size: 27 Copynumber: 5.2 Consensus size: 26
40722800 AGGAAGCGTC
*
40722810 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
40722837 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
*
40722864 CTGGTGGCTATGCCACGATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
* *
40722891 CTGGTGGCTCTACCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
*
40722918 CTGGTGGCTCTGCCACAATATCTGTAT
1 CTGGTGGCTCTGCCACATTATCTG-AT
40722945 CTGGTG
1 CTGGTG
40722951 ACTTCGTCAC
Statistics
Matches: 100, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
26 10 0.10
27 88 0.88
28 2 0.02
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:40722892 original size:54 final size:53
Alignment explanation
Indices: 40722810--40722950 Score: 228
Period size: 54 Copynumber: 2.6 Consensus size: 53
40722800 AGGAAGCGTC
*
40722810 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCAC-ATTATCTGATCTGGTGGCTCTACCACATATATCTGTT
40722864 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTACCACATATATCTGTT
1 CTGGTGGCTATGCCAC-ATTATCTGATCTGGTGGCTCTACCACATATATCTGTT
* *
40722918 CTGGTGGCTCTGCCACAATATCTGTATCTGGTG
1 CTGGTGGCTATGCCACATTATCTG-ATCTGGTG
40722951 ACTTCGTCAC
Statistics
Matches: 82, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
53 7 0.09
54 75 0.91
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (53 bp):
CTGGTGGCTATGCCACATTATCTGATCTGGTGGCTCTACCACATATATCTGTT
Found at i:40742929 original size:23 final size:22
Alignment explanation
Indices: 40742899--40742956 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 22
40742889 ATAGTTGCTC
40742899 TTATATATACATGTATATTTCTT
1 TTATATATACATGTATATTTC-T
* * *
40742922 TTATATATAAATATATTTTTCT
1 TTATATATACATGTATATTTCT
* *
40742944 ATATATTTACATG
1 TTATATATACATG
40742957 CATACTTTTT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.55
Consensus pattern (22 bp):
TTATATATACATGTATATTTCT
Found at i:40743403 original size:5 final size:5
Alignment explanation
Indices: 40743389--40743417 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
40743379 ACATAAGTGC
40743389 TTTA- TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
40743418 ATTGTTTCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:40746390 original size:24 final size:24
Alignment explanation
Indices: 40746349--40746415 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
40746339 GGAAGCTTAT
* *
40746349 AAGAGCCATAATCGGGAAGTTCACA
1 AAGAACCAT-ATCAGGAAGTTCACA
* *
40746374 AAGAACCTTGTCAGGAAGTTCACA
1 AAGAACCATATCAGGAAGTTCACA
40746398 AAGAACCATATCAGGAAG
1 AAGAACCATATCAGGAAG
40746416 CTCCGGATAG
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
24 29 0.81
25 7 0.19
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.16
Consensus pattern (24 bp):
AAGAACCATATCAGGAAGTTCACA
Found at i:40760684 original size:33 final size:36
Alignment explanation
Indices: 40760614--40760687 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
40760604 ACATACAAAA
40760614 CAATAAAATAAAAAAATACAACAGCCCAAATCAAGGCC
1 CAATAAAAT-AAAAAATACAACAGCCCAAAT-AAGGCC
* *
40760652 CAATAAAAT-AAAAATACAA-AGGCCAGAT-AGGCC
1 CAATAAAATAAAAAATACAACAGCCCAAATAAGGCC
40760685 CAA
1 CAA
40760688 AGCATTGGGG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
33 8 0.24
35 7 0.21
36 10 0.29
38 9 0.26
ACGTcount: A:0.57, C:0.22, G:0.11, T:0.11
Consensus pattern (36 bp):
CAATAAAATAAAAAATACAACAGCCCAAATAAGGCC
Found at i:40761789 original size:18 final size:17
Alignment explanation
Indices: 40761762--40761795 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
40761752 AAAACACTAT
40761762 TATTCCTTATTTTTATA
1 TATTCCTTATTTTTATA
40761779 TATTACCTTATTTTTAT
1 TATT-CCTTATTTTTAT
40761796 GTGCATTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTCCTTATTTTTATA
Found at i:40764951 original size:39 final size:39
Alignment explanation
Indices: 40764906--40764985 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
40764896 AGATGTATAA
40764906 GCCAATGGTGTAAGTAGTTATCATGTAGTAGTATATACT
1 GCCAATGGTGTAAGTAGTTATCATGTAGTAGTATATACT
*
40764945 GCCAATGGTGTAAGTAGTTATCATGTATTAGTATATACT
1 GCCAATGGTGTAAGTAGTTATCATGTAGTAGTATATACT
40764984 GC
1 GC
40764986 TTTCTTTGGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.36
Consensus pattern (39 bp):
GCCAATGGTGTAAGTAGTTATCATGTAGTAGTATATACT
Found at i:40798604 original size:33 final size:32
Alignment explanation
Indices: 40798567--40798847 Score: 190
Period size: 33 Copynumber: 8.6 Consensus size: 32
40798557 TACCCAAATG
**
40798567 GTACAACTTGAAAAGGTTATGTACACTTTGTGT
1 GTAC-ACTTGAAAAGGAAATGTACACTTTGTGT
* *
40798600 GTACACTTGAAAAGGAAAGGTATACTTTGTGT
1 GTACACTTGAAAAGGAAATGTACACTTTGTGT
* * *
40798632 ATATCA-TATGAAAAGGAAATGTATACTTTGAGT
1 GTA-CACT-TGAAAAGGAAATGTACACTTTGTGT
* *
40798665 ATAC-CATATGAAAAGGAAATGTATACTTTGTGT
1 GTACAC-T-TGAAAAGGAAATGTACACTTTGTGT
* * *
40798698 ATACCACTTGAAAAGGAAAGGTACA-TTATATGT
1 GTA-CACTTGAAAAGGAAATGTACACTT-TGTGT
* * ** * * *
40798731 CTACATTTGAAAAGGTTATATGCACTTTGAGT
1 GTACACTTGAAAAGGAAATGTACACTTTGTGT
* ** *
40798763 GTACAAATTGAAAAGGGTATGTACTCTTTGTGT
1 GTAC-ACTTGAAAAGGAAATGTACACTTTGTGT
* * * * *
40798796 GTACCACTTGAAAAGGGAATGTGCACCTCGAGT
1 GTA-CACTTGAAAAGGAAATGTACACTTTGTGT
*
40798829 GTACAACTAGAAAAGGAAA
1 GTAC-ACTTGAAAAGGAAA
40798848 AGTCCATCGG
Statistics
Matches: 201, Mismatches: 36, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
32 52 0.26
33 145 0.72
34 3 0.01
35 1 0.00
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (32 bp):
GTACACTTGAAAAGGAAATGTACACTTTGTGT
Found at i:40798687 original size:98 final size:98
Alignment explanation
Indices: 40798568--40798811 Score: 278
Period size: 98 Copynumber: 2.5 Consensus size: 98
40798558 ACCCAAATGG
* * * *
40798568 TACAACTTGAAAAGGTTATGTACACTTTGTGTGTA-CACTTGAAAAGGAAAGGTATACTT-TGTG
1 TACAAATTGAAAAGGATATGTACACTTTGTGTGTACCACTTGAAAAGGAAAGGTACA-TTATATG
* *
40798631 TATATCATATGAAAAGGAAATGTATACTTTGAGTA
65 TATA-CATATGAAAAGGAAATATACACTTTGAGTA
* * * *
40798666 TAC-CATATGAAAAGGAAATGTATACTTTGTGTATACCACTTGAAAAGGAAAGGTACATTATATG
1 TACAAAT-TGAAAAGGATATGTACACTTTGTGTGTACCACTTGAAAAGGAAAGGTACATTATATG
* * ** * *
40798730 TCTACATTTGAAAAGGTTATATGCACTTTGAGTG
65 TATACATATGAAAAGGAAATATACACTTTGAGTA
* *
40798764 TACAAATTGAAAAGGGTATGTACTCTTTGTGTGTACCACTTGAAAAGG
1 TACAAATTGAAAAGGATATGTACACTTTGTGTGTACCACTTGAAAAGG
40798812 GAATGTGCAC
Statistics
Matches: 120, Mismatches: 22, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
97 1 0.01
98 91 0.76
99 28 0.23
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (98 bp):
TACAAATTGAAAAGGATATGTACACTTTGTGTGTACCACTTGAAAAGGAAAGGTACATTATATGT
ATACATATGAAAAGGAAATATACACTTTGAGTA
Found at i:40805343 original size:13 final size:13
Alignment explanation
Indices: 40805325--40805349 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40805315 GGTGGCAAGG
40805325 AAGAGGGAAGGGT
1 AAGAGGGAAGGGT
40805338 AAGAGGGAAGGG
1 AAGAGGGAAGGG
40805350 AAAGTTTGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.56, T:0.04
Consensus pattern (13 bp):
AAGAGGGAAGGGT
Found at i:40808317 original size:22 final size:22
Alignment explanation
Indices: 40808275--40808321 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
40808265 TAAAGAAAAG
*
40808275 TCATGTTTTCTTCATCAATTTCT
1 TCATGTTTTCTTCAACAATTT-T
40808298 TCAT-TTTTCTTCAA-ACATTTT
1 TCATGTTTTCTTCAACA-ATTTT
40808319 TCA
1 TCA
40808322 CCAAATGAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 5 0.23
22 13 0.59
23 4 0.18
ACGTcount: A:0.21, C:0.21, G:0.02, T:0.55
Consensus pattern (22 bp):
TCATGTTTTCTTCAACAATTTT
Found at i:40812658 original size:29 final size:28
Alignment explanation
Indices: 40812616--40812716 Score: 148
Period size: 29 Copynumber: 3.5 Consensus size: 28
40812606 CATGAAATTG
40812616 GCACTAAGTGTGCGGGTTCAATTTGTATA
1 GCACTAAGTGTGCGGGTTCAA-TTGTATA
40812645 GCACTAAGTGTGCGGGTTCAAGTTGTATA
1 GCACTAAGTGTGCGGGTTCAA-TTGTATA
* * *
40812674 GCACTAAGTGTGCGAGTTCGATTATATA
1 GCACTAAGTGTGCGGGTTCAATTGTATA
*
40812702 ACACTAAGTGTGCGG
1 GCACTAAGTGTGCGG
40812717 ACTTACTATA
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
28 19 0.29
29 47 0.71
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.31
Consensus pattern (28 bp):
GCACTAAGTGTGCGGGTTCAATTGTATA
Found at i:40820470 original size:29 final size:28
Alignment explanation
Indices: 40820428--40820528 Score: 148
Period size: 29 Copynumber: 3.5 Consensus size: 28
40820418 CATGAAATTG
40820428 GCACTAAGTGTGCGGGTTCAATTTGTATA
1 GCACTAAGTGTGCGGGTTCAA-TTGTATA
40820457 GCACTAAGTGTGCGGGTTCAAGTTGTATA
1 GCACTAAGTGTGCGGGTTCAA-TTGTATA
* * *
40820486 GCACTAAGTGTGCGAGTTCGATTATATA
1 GCACTAAGTGTGCGGGTTCAATTGTATA
*
40820514 ACACTAAGTGTGCGG
1 GCACTAAGTGTGCGG
40820529 ACTTACTATA
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
28 19 0.29
29 47 0.71
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.31
Consensus pattern (28 bp):
GCACTAAGTGTGCGGGTTCAATTGTATA
Found at i:40828535 original size:15 final size:15
Alignment explanation
Indices: 40828495--40828535 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 15
40828485 TTTTACTTAT
40828495 AATGTACATATATGAG
1 AATGT-CATATATGAG
*
40828511 AATATCATAT-T-AG
1 AATGTCATATATGAG
40828524 AATGTCATATAT
1 AATGTCATATAT
40828536 CAAGAAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 11 0.50
14 2 0.09
15 5 0.23
16 4 0.18
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (15 bp):
AATGTCATATATGAG
Found at i:40831152 original size:25 final size:25
Alignment explanation
Indices: 40831118--40831169 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
40831108 CAACCAGATT
40831118 GGAACTCCCAAATATTTATTAAAAG
1 GGAACTCCCAAATATTTATTAAAAG
40831143 GGAACTCCCAAATATTTATTAAAAG
1 GGAACTCCCAAATATTTATTAAAAG
40831168 GG
1 GG
40831170 TTAATTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (25 bp):
GGAACTCCCAAATATTTATTAAAAG
Found at i:40831664 original size:25 final size:25
Alignment explanation
Indices: 40831630--40831681 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
40831620 CAACCAGATT
40831630 GGAACTCCCAAATATTTATTAAAAG
1 GGAACTCCCAAATATTTATTAAAAG
40831655 GGAACTCCCAAATATTTATTAAAAG
1 GGAACTCCCAAATATTTATTAAAAG
40831680 GG
1 GG
40831682 TTAATTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (25 bp):
GGAACTCCCAAATATTTATTAAAAG
Found at i:40836795 original size:27 final size:26
Alignment explanation
Indices: 40836758--40836872 Score: 149
Period size: 27 Copynumber: 4.3 Consensus size: 26
40836748 AGCATGGCTG
* *
40836758 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
40836784 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
40836812 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
40836839 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
40836866 CCAGAAC
1 CCAGAAC
40836873 GCTTCCTCCA
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
26 5 0.06
27 58 0.73
28 17 0.21
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:40836822 original size:54 final size:54
Alignment explanation
Indices: 40836758--40836872 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
40836748 AGCATGGCTG
*
40836758 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * *
40836812 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
40836866 CCAGAAC
1 CCAGAAC
40836873 GCTTCCTCCA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:40837305 original size:16 final size:15
Alignment explanation
Indices: 40837284--40837313 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
40837274 AAAATACCGA
40837284 CTTTTCGGCATTTTGG
1 CTTTTCGGC-TTTTGG
40837300 CTTTTCGGCTTTTG
1 CTTTTCGGCTTTTG
40837314 CCAATCTAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.03, C:0.20, G:0.23, T:0.53
Consensus pattern (15 bp):
CTTTTCGGCTTTTGG
Found at i:40838588 original size:25 final size:26
Alignment explanation
Indices: 40838488--40838596 Score: 159
Period size: 26 Copynumber: 4.2 Consensus size: 26
40838478 CATGAAATTC
40838488 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
40838514 TTATCATGAAATATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
40838540 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
*
40838566 TTATCATTG-AACA-TTACCTAACCTA
1 TTATCA-TGAAACATTTACCTAACCCA
40838591 TTATCA
1 TTATCA
40838597 ATTTGTATCA
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
25 18 0.23
26 58 0.74
27 2 0.03
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:40843735 original size:23 final size:23
Alignment explanation
Indices: 40843691--40843735 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
40843681 ATCAATTTAA
*
40843691 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
40843714 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
40843736 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:40847448 original size:17 final size:18
Alignment explanation
Indices: 40847415--40847448 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
40847405 CGTCAAACTT
*
40847415 TTATGATTTATGTTAATG
1 TTATGATTTAAGTTAATG
40847433 TTATGA-TTAAGTTAAT
1 TTATGATTTAAGTTAAT
40847449 TTTAATTCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (18 bp):
TTATGATTTAAGTTAATG
Found at i:40848622 original size:9 final size:8
Alignment explanation
Indices: 40848598--40848641 Score: 54
Period size: 8 Copynumber: 5.4 Consensus size: 8
40848588 AATACAACCT
40848598 AAAAT-AA
1 AAAATAAA
40848605 AAAATAAA
1 AAAATAAA
40848613 AAAATAAA
1 AAAATAAA
40848621 AAAATGAAGA
1 AAAAT-AA-A
*
40848631 AAAAGAAA
1 AAAATAAA
40848639 AAA
1 AAA
40848642 CCTAATCTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
7 5 0.15
8 19 0.58
9 4 0.12
10 5 0.15
ACGTcount: A:0.84, C:0.00, G:0.07, T:0.09
Consensus pattern (8 bp):
AAAATAAA
Found at i:40848910 original size:5 final size:5
Alignment explanation
Indices: 40848884--40848934 Score: 52
Period size: 5 Copynumber: 10.2 Consensus size: 5
40848874 TTTGTTCATT
* *
40848884 TTTTA TTTTTCA TTTT- TGTTA TTTTA TTTTA TTTTA TTTT- CTTTA TTTTA
1 TTTTA -TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
40848934 T
1 T
40848935 ATATATACAT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
4 6 0.16
5 23 0.61
6 8 0.21
7 1 0.03
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:40849837 original size:19 final size:19
Alignment explanation
Indices: 40849813--40849850 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
40849803 TTGAGATTGC
*
40849813 CAACCTATTTGCTTGAAAT
1 CAACCTATTTGCCTGAAAT
40849832 CAACCTATTTGCCTGAAAT
1 CAACCTATTTGCCTGAAAT
40849851 TATTCATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.34
Consensus pattern (19 bp):
CAACCTATTTGCCTGAAAT
Found at i:40863760 original size:27 final size:27
Alignment explanation
Indices: 40863730--40863906 Score: 214
Period size: 27 Copynumber: 6.6 Consensus size: 27
40863720 ATATTGAGTC
* * * *
40863730 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
40863757 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40863784 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
* * *
40863812 CGCACACTTAGTGC-GCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
40863838 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
40863865 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40863892 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40863907 GTACAATTTA
Statistics
Matches: 132, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
26 15 0.11
27 101 0.77
28 16 0.12
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:40863844 original size:81 final size:80
Alignment explanation
Indices: 40863751--40863905 Score: 240
Period size: 81 Copynumber: 1.9 Consensus size: 80
40863741 TGCTATATAA
*
40863751 TCAACTCGCACACTTAGTGC-TACATAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGC
1 TCAACTCGCACACTTAGTGCAT-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGC
40863815 ACACTTAGTGCGCATGG
64 ACACTTAGTGCGCATGG
* * **
40863832 TCAATTCGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCAC
1 TCAACTCGCACACTTAGTGCATCATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
40863897 ACTTAGTGC
66 ACTTAGTGC
40863906 TGTACAATTT
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
80 15 0.22
81 52 0.76
82 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (80 bp):
TCAACTCGCACACTTAGTGCATCATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCGCATGG
Found at i:40871899 original size:27 final size:27
Alignment explanation
Indices: 40871866--40872043 Score: 187
Period size: 27 Copynumber: 6.6 Consensus size: 27
40871856 ATATTGAGTC
* *
40871866 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
40871893 CGTACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
40871920 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
40871948 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
40871975 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
40872002 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
40872029 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40872044 GTACAATTTA
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 105 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:40872006 original size:82 final size:81
Alignment explanation
Indices: 40871887--40872042 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
40871877 TGCTATATAA
* *
40871887 TCAACTCGTACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
40871952 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
40871969 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
40872033 CACTTAGTGC
65 CACTTAGTGC
40872043 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:40875159 original size:27 final size:24
Alignment explanation
Indices: 40875111--40875159 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 24
40875101 TCCAAGTTAG
40875111 ATAAAAAAAATAAAGAGAATAATT
1 ATAAAAAAAATAAAGAGAATAATT
*
40875135 ATAAATAAATAATAAATATGAATAA
1 ATAAA-AAA-AATAAAGA-GAATAA
40875160 AATAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 7 0.33
27 6 0.29
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.24
Consensus pattern (24 bp):
ATAAAAAAAATAAAGAGAATAATT
Found at i:40880256 original size:68 final size:67
Alignment explanation
Indices: 40880116--40880256 Score: 144
Period size: 68 Copynumber: 2.1 Consensus size: 67
40880106 CGGATTCTCA
* * * *
40880116 ATGTTGCCATGGTCGAACTATGGTTTTACAAATGATTGTCCCATGTTTAATGTCCTGGCGACCTC
1 ATGTTGCCATAGTCGAACTATGGTCTTAC-AACGATTGTCCCATGTTTAACGTCCTGGCGACCTC
* *
40880181 TCT
65 CCC
*
40880184 ATGTTGCCATAGTCGAGCTATGGTCTTAC-ACGA-TGTACCCATTGTTTAACGTCCTAGTG-GAC
1 ATGTTGCCATAGTCGAACTATGGTCTTACAACGATTGT-CCCA-TGTTTAACGTCCT-G-GCGAC
*
40880246 TTCCCC
62 CTCCCC
40880252 ATGTT
1 ATGTT
40880257 TACCGTCCCG
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
65 3 0.05
66 7 0.11
67 12 0.20
68 38 0.62
69 1 0.02
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (67 bp):
ATGTTGCCATAGTCGAACTATGGTCTTACAACGATTGTCCCATGTTTAACGTCCTGGCGACCTCC
CC
Found at i:40882857 original size:40 final size:40
Alignment explanation
Indices: 40882645--40882850 Score: 333
Period size: 40 Copynumber: 5.2 Consensus size: 40
40882635 AACCCAAGTA
* * *
40882645 CCTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
* *
40882684 CCTTCGGGACTTAGCCCGAATATAGTAACTAGCACAGATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
* *
40882724 CCTTCGAGACTTAGCCCGGATATAGTAACTAGAACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
40882764 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
*
40882804 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
40882844 CCTTCGG
1 CCTTCGG
40882851 ATCTTAGTCC
Statistics
Matches: 154, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 13 0.08
40 141 0.92
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
Found at i:40884244 original size:13 final size:13
Alignment explanation
Indices: 40884226--40884251 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40884216 ATTTTTATTT
40884226 TTAACATAAAATA
1 TTAACATAAAATA
40884239 TTAACATAAAATA
1 TTAACATAAAATA
40884252 ATTATAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
TTAACATAAAATA
Found at i:40886648 original size:38 final size:38
Alignment explanation
Indices: 40886596--40886771 Score: 208
Period size: 38 Copynumber: 4.6 Consensus size: 38
40886586 ATATTTGATA
* *
40886596 TATATCCGGTTTAAATCCCGCAGGCTTCGTACTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTAGTACTGGTAT
* * *
40886634 TATATCCGGGTTAAATCCCGCAGGCTTCGTAGTGGTAG
1 TATATCCGGGTTAAATCCCGCAGGCTTAGTACTGGTAT
* * *
40886672 TATATCCGGGTAAAATCCCGCAGGCTTAGTGCCGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTAGTACTGGTAT
** * *
40886710 TATATTAGGGTTAAATCCCGCAGGCTTAGTGCTGGTAC
1 TATATCCGGGTTAAATCCCGCAGGCTTAGTACTGGTAT
* *
40886748 TATATTCGAGCTTAAAGTCCCGCA
1 TATATCCG-GGTTAAA-TCCCGCA
40886772 AGTTTTGTGC
Statistics
Matches: 120, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
38 107 0.89
39 6 0.05
40 7 0.06
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.30
Consensus pattern (38 bp):
TATATCCGGGTTAAATCCCGCAGGCTTAGTACTGGTAT
Found at i:40887790 original size:48 final size:48
Alignment explanation
Indices: 40887720--40887949 Score: 198
Period size: 48 Copynumber: 5.0 Consensus size: 48
40887710 CATTAGGGTT
*
40887720 ATATGATATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCG
1 ATATGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCG
* * * *
40887768 ATATGAGATCCCATGTAAGACCATATCTAGGATATGGCATTGCCATCG
1 ATATGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCG
* ** *
40887816 ATATGTGATTTCGTGTAAGACCATGTCTGGGACATGGCA-T----T-G
1 ATATGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCG
* * *
40887858 ATATGAGA-CATCGTGTAAGACCATAG-CTGGG-C-T---ATCGGCATCG
1 ATATGAGATC-CCATGTAAGACCAT-GTCTGGGACATGGCATTGGCATCG
* * *
40887901 ATATGTGTGATCCCATGTAAGACCATATCTGGGATATGGCATTGGCATC
1 ATA--TGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC
40887950 TTACTATGTG
Statistics
Matches: 144, Mismatches: 21, Indels: 32
0.73 0.11 0.16
Matches are distributed among these distances:
37 1 0.01
40 1 0.01
41 1 0.01
42 28 0.19
43 6 0.04
45 21 0.15
46 1 0.01
47 2 0.01
48 75 0.52
50 8 0.06
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.28
Consensus pattern (48 bp):
ATATGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCG
Found at i:40892148 original size:22 final size:22
Alignment explanation
Indices: 40892120--40892242 Score: 67
Period size: 22 Copynumber: 5.3 Consensus size: 22
40892110 ACATGCATAT
40892120 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCCGAATGGCCA
* *
40892142 ATGTGATGAATGTG-AGCAT-G-CA
1 ATGTGAT-AA-G-GCCGAATGGCCA
40892164 TATGTGTGATAAGGCCGAATGGCCA
1 -A--TGTGATAAGGCCGAATGGCCA
* * *
40892189 ATGTGATGAATG-TGAACAT-GCATA
1 ATGTGAT-AAGGCCG-A-ATGGC-CA
40892213 TATGTGATAAGGCCGAATGGCCA
1 -ATGTGATAAGGCCGAATGGCCA
40892236 ATGTGAT
1 ATGTGAT
40892243 GAATGTGAAC
Statistics
Matches: 75, Mismatches: 10, Indels: 32
0.64 0.09 0.27
Matches are distributed among these distances:
22 24 0.32
23 17 0.23
24 17 0.23
25 17 0.23
ACGTcount: A:0.32, C:0.13, G:0.30, T:0.25
Consensus pattern (22 bp):
ATGTGATAAGGCCGAATGGCCA
Found at i:40892327 original size:47 final size:47
Alignment explanation
Indices: 40892048--40892312 Score: 424
Period size: 47 Copynumber: 5.6 Consensus size: 47
40892038 TTAGGATTTT
** * *
40892048 ATGTGATGAATGTGAATGTGTATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
40892095 ATGTGATGAATATGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
40892142 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
40892189 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
40892236 ATGTGATGAATGTGAACACGCATATATGTGATAAGGCAGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
40892283 ATGTGATGAATGTGAA-AGTGTATATATGTG
1 ATGTGATGAATGTGAACA-TGCATATATGTG
40892313 GCGAAGCCGA
Statistics
Matches: 203, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
46 1 0.00
47 202 1.00
ACGTcount: A:0.33, C:0.11, G:0.29, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:40892390 original size:46 final size:46
Alignment explanation
Indices: 40892306--40892394 Score: 115
Period size: 46 Copynumber: 1.9 Consensus size: 46
40892296 GAAAGTGTAT
* * *
40892306 ATATGTGGCGAAGCCGAATGGCTAATGCGAAACGTGTATGAGACGG
1 ATATGTGGCAAAGCCAAATGGCTAATGCGAAACATGTATGAGACGG
* * * *
40892352 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGA
1 ATATGTGGCAAAGCCAAATGGCTAATGCGAAACATGTATGAGA
40892395 TGTGTATATA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 36 1.00
ACGTcount: A:0.34, C:0.11, G:0.31, T:0.24
Consensus pattern (46 bp):
ATATGTGGCAAAGCCAAATGGCTAATGCGAAACATGTATGAGACGG
Found at i:40892650 original size:37 final size:37
Alignment explanation
Indices: 40892542--40892650 Score: 191
Period size: 37 Copynumber: 2.9 Consensus size: 37
40892532 GGAAATATAT
*
40892542 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
40892579 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* *
40892616 TCCGGGTAAGACCCGATGACTTCGTATGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
40892651 CGTCTGAGCT
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:40896910 original size:15 final size:15
Alignment explanation
Indices: 40896890--40896927 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
40896880 TAGGAAAGGG
40896890 AATGATCCTGATCTA
1 AATGATCCTGATCTA
*
40896905 AATGATCCTGATCTG
1 AATGATCCTGATCTA
40896920 AATGATCC
1 AATGATCC
40896928 ACTGAATCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.32
Consensus pattern (15 bp):
AATGATCCTGATCTA
Found at i:40904397 original size:13 final size:14
Alignment explanation
Indices: 40904379--40904407 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
40904369 AACCTGTAAT
40904379 AAACCATCAT-TTA
1 AAACCATCATGTTA
40904392 AAACCATCATGTTA
1 AAACCATCATGTTA
40904406 AA
1 AA
40904408 GGGAATCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.48, C:0.21, G:0.03, T:0.28
Consensus pattern (14 bp):
AAACCATCATGTTA
Found at i:40906425 original size:31 final size:31
Alignment explanation
Indices: 40906364--40906425 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 31
40906354 AATCCTAAAA
* *
40906364 AATAAATTATAAAAATAATTTATGTGTATTT
1 AATAAATTATAAAAATAAATTATATGTATTT
40906395 AATAAAGTTATAACAAA-AAATTATAT-TATTT
1 AATAAA-TTATAA-AAATAAATTATATGTATTT
40906426 CATTTTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 11 0.41
32 13 0.48
33 3 0.11
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (31 bp):
AATAAATTATAAAAATAAATTATATGTATTT
Found at i:40909869 original size:22 final size:22
Alignment explanation
Indices: 40909827--40909871 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
40909817 TATTGAGTTA
40909827 ATTAAATAATAATTTACATTTC
1 ATTAAATAATAATTTACATTTC
40909849 ATTAAA-AAT-ATTTCACAATTTC
1 ATTAAATAATAATTT-AC-ATTTC
40909871 A
1 A
40909872 CATTATCCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 4 0.19
21 5 0.24
22 12 0.57
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (22 bp):
ATTAAATAATAATTTACATTTC
Found at i:40910320 original size:35 final size:35
Alignment explanation
Indices: 40910274--40910344 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
40910264 GACAAAGTCA
40910274 AATAAGTTCCAAGACAGATTCCACAACAGTAGACT
1 AATAAGTTCCAAGACAGATTCCACAACAGTAGACT
40910309 AATAAGTTCCAAGACAGATTCCACAACAGTAGACT
1 AATAAGTTCCAAGACAGATTCCACAACAGTAGACT
40910344 A
1 A
40910345 TGACCATGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.44, C:0.23, G:0.14, T:0.20
Consensus pattern (35 bp):
AATAAGTTCCAAGACAGATTCCACAACAGTAGACT
Found at i:40914323 original size:5 final size:5
Alignment explanation
Indices: 40914315--40914343 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
40914305 ATTAAAGTAA
40914315 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
40914344 AATCACCACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:40934912 original size:25 final size:25
Alignment explanation
Indices: 40934878--40934932 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
40934868 GGATAAGGAG
40934878 GAGCTGTTCTAGGAACAAAGATTAA
1 GAGCTGTTCTAGGAACAAAGATTAA
40934903 GAGCTGTTCTAGGAACAAAGATTAA
1 GAGCTGTTCTAGGAACAAAGATTAA
40934928 GAGCT
1 GAGCT
40934933 AATTGGCTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.24
Consensus pattern (25 bp):
GAGCTGTTCTAGGAACAAAGATTAA
Found at i:40939448 original size:14 final size:14
Alignment explanation
Indices: 40939431--40939461 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
40939421 AGTAAAATGT
40939431 TTTCTGGAAAATAA
1 TTTCTGGAAAATAA
*
40939445 TTTCTGGAAAATGA
1 TTTCTGGAAAATAA
40939459 TTT
1 TTT
40939462 ACTTTTCTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.42
Consensus pattern (14 bp):
TTTCTGGAAAATAA
Found at i:40939477 original size:19 final size:20
Alignment explanation
Indices: 40939445--40939490 Score: 85
Period size: 19 Copynumber: 2.4 Consensus size: 20
40939435 TGGAAAATAA
40939445 TTTCTGGAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
40939465 TTTCTGG-AAATGATTTACT
1 TTTCTGGAAAATGATTTACT
40939484 TTTCTGG
1 TTTCTGG
40939491 TGTTTGGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.24, C:0.11, G:0.17, T:0.48
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:40942182 original size:25 final size:25
Alignment explanation
Indices: 40942147--40942194 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
40942137 AAGAGAATAT
*
40942147 GAAGAACGGAAGAAGGAAAAGGAAA
1 GAAGAACGGAAGAAAGAAAAGGAAA
* *
40942172 GAAGAATGGAAGAAAGAGAAGGA
1 GAAGAACGGAAGAAAGAAAAGGA
40942195 GCCTTACCTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.58, C:0.02, G:0.38, T:0.02
Consensus pattern (25 bp):
GAAGAACGGAAGAAAGAAAAGGAAA
Found at i:40942983 original size:75 final size:75
Alignment explanation
Indices: 40942889--40943053 Score: 303
Period size: 75 Copynumber: 2.2 Consensus size: 75
40942879 TGAAAGATCA
* * *
40942889 AAAAATGTAATTGAGAAAAATAGAAAGTAGGATGAAATCTTAAGATTTATCATGGTACACAGTTT
1 AAAAATCTAATTCAAAAAAATAGAAAGTAGGATGAAATCTTAAGATTTATCATGGTACACAGTTT
40942954 AGAAGACCAC
66 AGAAGACCAC
40942964 AAAAATCTAATTCAAAAAAATAGAAAGTAGGATGAAATCTTAAGATTTATCATGGTACACAGTTT
1 AAAAATCTAATTCAAAAAAATAGAAAGTAGGATGAAATCTTAAGATTTATCATGGTACACAGTTT
40943029 AGAAGACCAC
66 AGAAGACCAC
40943039 AAAAATCTAATTCAA
1 AAAAATCTAATTCAA
40943054 CCATAAATCT
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 87 1.00
ACGTcount: A:0.48, C:0.11, G:0.15, T:0.25
Consensus pattern (75 bp):
AAAAATCTAATTCAAAAAAATAGAAAGTAGGATGAAATCTTAAGATTTATCATGGTACACAGTTT
AGAAGACCAC
Found at i:40944520 original size:23 final size:23
Alignment explanation
Indices: 40944467--40944522 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
40944457 TTGCGATGAG
* *
40944467 TTTTTGGATGGGATCCAGACATT
1 TTTTTGGTTAGGATCCAGACATT
40944490 TTTTTGGTTAGGATCCAGACATT
1 TTTTTGGTTAGGATCCAGACATT
40944513 TTTTTGGTTA
1 TTTTTGGTTA
40944523 AGACATCTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.20, C:0.11, G:0.23, T:0.46
Consensus pattern (23 bp):
TTTTTGGTTAGGATCCAGACATT
Found at i:40946256 original size:16 final size:16
Alignment explanation
Indices: 40946235--40946265 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40946225 AACATTATGA
*
40946235 TTAATGGCAGACAATT
1 TTAATGGCAAACAATT
40946251 TTAATGGCAAACAAT
1 TTAATGGCAAACAAT
40946266 CCAAGTGGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (16 bp):
TTAATGGCAAACAATT
Found at i:40949089 original size:21 final size:21
Alignment explanation
Indices: 40949063--40949103 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
40949053 AGACGAGCGA
* *
40949063 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
40949084 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
40949104 TTGAGCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:40951042 original size:16 final size:16
Alignment explanation
Indices: 40951021--40951051 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40951011 AACATTATGA
*
40951021 TTAATGGCAGACAATT
1 TTAATGGCAAACAATT
40951037 TTAATGGCAAACAAT
1 TTAATGGCAAACAAT
40951052 CCAAGTGGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (16 bp):
TTAATGGCAAACAATT
Found at i:40953829 original size:112 final size:112
Alignment explanation
Indices: 40953632--40953857 Score: 425
Period size: 112 Copynumber: 2.0 Consensus size: 112
40953622 ATTTCTATAC
40953632 TCTATTCTTGAGCTCTGGGTCTAATGATTTTTCAAAGTGTTCACATGGTCAATATCGAGTTCTGA
1 TCTATTCTTGAGCTCTGGGTCTAATGATTTTTCAAAGTGTTCACATGGTCAATATCGAGTTCTGA
40953697 TGAGGATATTGTTAGCACCATTTACAAAGATGGAGATAAAGACTGGT
66 TGAGGATATTGTTAGCACCATTTACAAAGATGGAGATAAAGACTGGT
* *
40953744 TCTATTCTTGAGCTCTGGGTCTAATGATTTTTCAAAGTGTTCACATGTTCAATATCGAGTTTTGA
1 TCTATTCTTGAGCTCTGGGTCTAATGATTTTTCAAAGTGTTCACATGGTCAATATCGAGTTCTGA
*
40953809 TGAGGATATTGTTAGCACCATTTACAAAGATGGAGATAGAGACTGGT
66 TGAGGATATTGTTAGCACCATTTACAAAGATGGAGATAAAGACTGGT
40953856 TC
1 TC
40953858 AGTATGCATC
Statistics
Matches: 111, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
112 111 1.00
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (112 bp):
TCTATTCTTGAGCTCTGGGTCTAATGATTTTTCAAAGTGTTCACATGGTCAATATCGAGTTCTGA
TGAGGATATTGTTAGCACCATTTACAAAGATGGAGATAAAGACTGGT
Found at i:40965527 original size:19 final size:21
Alignment explanation
Indices: 40965485--40965528 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 21
40965475 CGGTTGAGTA
40965485 TGTCTCGAGACATATGACAAAT
1 TGTCTCGAGA-ATATGACAAAT
*
40965507 TGTCTCGAG-AT-TGACATAT
1 TGTCTCGAGAATATGACAAAT
40965526 TGT
1 TGT
40965529 GTATTGAGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 10 0.48
20 2 0.10
22 9 0.43
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (21 bp):
TGTCTCGAGAATATGACAAAT
Found at i:40969898 original size:47 final size:45
Alignment explanation
Indices: 40969786--40969912 Score: 134
Period size: 47 Copynumber: 2.7 Consensus size: 45
40969776 GGGTTATTGT
40969786 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGG-C-CATTATGAA
* * *
40969833 -ATCCAATGTAAGACCATGTCTGGGACATGACATCGG-CATTGA-GACGA
1 GAGCTAGTGTAAGA-CATGTCTGGGACATG-CATCGGCCATT-ATGA--A
*
40969880 GAGCTAGTGTAAGACATGTTTGGGACATGCATC
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATC
40969913 ATATAACACC
Statistics
Matches: 67, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
45 6 0.09
46 15 0.22
47 30 0.45
48 16 0.24
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.24
Consensus pattern (45 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCATTATGAA
Found at i:40982482 original size:41 final size:39
Alignment explanation
Indices: 40982415--40982494 Score: 133
Period size: 41 Copynumber: 2.0 Consensus size: 39
40982405 ATTTTTTGCT
40982415 AATGAAGAATATTAAAATATTTAATATTAAATTTAACAC
1 AATGAAGAATATTAAAATATTTAATATTAAATTTAACAC
*
40982454 AATGACAGAATCTTAAATATATTTAATATTAAATTTAACAC
1 AATGA-AGAATATTAAA-ATATTTAATATTAAATTTAACAC
40982495 TTACCATTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
39 5 0.13
40 10 0.26
41 23 0.61
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.36
Consensus pattern (39 bp):
AATGAAGAATATTAAAATATTTAATATTAAATTTAACAC
Found at i:40982614 original size:14 final size:15
Alignment explanation
Indices: 40982586--40982615 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
40982576 TTTTTATTTT
40982586 AAAAATAAATCTAGA
1 AAAAATAAATCTAGA
40982601 AAAAATAAAT-TAGA
1 AAAAATAAATCTAGA
40982615 A
1 A
40982616 CTTTTTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.70, C:0.03, G:0.07, T:0.20
Consensus pattern (15 bp):
AAAAATAAATCTAGA
Found at i:40982659 original size:11 final size:11
Alignment explanation
Indices: 40982639--40982687 Score: 66
Period size: 11 Copynumber: 4.5 Consensus size: 11
40982629 TTAACGGAGT
40982639 TTTGAGAGGAA
1 TTTGAGAGGAA
*
40982650 TTTAAGAGGAAA
1 TTTGAGAGG-AA
40982662 TTTGAGA-G-A
1 TTTGAGAGGAA
40982671 TTTGAGAGGAA
1 TTTGAGAGGAA
40982682 TTTGAG
1 TTTGAG
40982688 GAATATTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 8 0.24
10 1 0.03
11 16 0.48
12 8 0.24
ACGTcount: A:0.37, C:0.00, G:0.33, T:0.31
Consensus pattern (11 bp):
TTTGAGAGGAA
Found at i:40982678 original size:21 final size:22
Alignment explanation
Indices: 40982639--40982687 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
40982629 TTAACGGAGT
40982639 TTTGAGAGGAATTTAAGAGGAAA
1 TTTGAGAGGAATTTAAGAGG-AA
*
40982662 TTTGAGA-G-ATTTGAGAGGAA
1 TTTGAGAGGAATTTAAGAGGAA
40982682 TTTGAG
1 TTTGAG
40982688 GAATATTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 8 0.32
21 9 0.36
22 1 0.04
23 7 0.28
ACGTcount: A:0.37, C:0.00, G:0.33, T:0.31
Consensus pattern (22 bp):
TTTGAGAGGAATTTAAGAGGAA
Found at i:40982696 original size:21 final size:21
Alignment explanation
Indices: 40982644--40982696 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
40982634 GGAGTTTTGA
*
40982644 GAGGAATTTAAGAGGAAATTT
1 GAGGAATTTGAGAGGAAATTT
40982665 GA-GAGATTTGAGAGG-AATTT
1 GAGGA-ATTTGAGAGGAAATTT
40982685 GAGGAATATTGA
1 GAGGAAT-TTGA
40982697 AAGATTGAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
20 11 0.39
21 17 0.61
ACGTcount: A:0.40, C:0.00, G:0.32, T:0.28
Consensus pattern (21 bp):
GAGGAATTTGAGAGGAAATTT
Found at i:40988769 original size:19 final size:21
Alignment explanation
Indices: 40988741--40988784 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 21
40988731 GTCTCAATAC
40988741 ACAATATGTCA-A-TCTCGAG
1 ACAATATGTCATAGTCTCGAG
*
40988760 ACAATTTGTCATATGTCTCGAG
1 ACAATATGTCATA-GTCTCGAG
40988782 ACA
1 ACA
40988785 TACTCAACCG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 10 0.48
20 1 0.05
22 10 0.48
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (21 bp):
ACAATATGTCATAGTCTCGAG
Found at i:40992914 original size:16 final size:16
Alignment explanation
Indices: 40992881--40992914 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
40992871 CCTTTTTGTT
* *
40992881 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
40992897 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
40992913 AA
1 AA
40992915 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:41012106 original size:47 final size:45
Alignment explanation
Indices: 41011994--41012120 Score: 134
Period size: 47 Copynumber: 2.7 Consensus size: 45
41011984 GGGTTATTGT
41011994 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGG-C-CATTATGAA
* * *
41012041 -ATCCAATGTAAGACCATGTCTGGGACATGACATCGG-CATTGA-GACGA
1 GAGCTAGTGTAAGA-CATGTCTGGGACATG-CATCGGCCATT-ATGA--A
*
41012088 GAGCTAGTGTAAGACATGTTTGGGACATGCATC
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATC
41012121 ATATAACACC
Statistics
Matches: 67, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
45 6 0.09
46 15 0.22
47 30 0.45
48 16 0.24
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.24
Consensus pattern (45 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCATTATGAA
Found at i:41013822 original size:11 final size:11
Alignment explanation
Indices: 41013808--41013857 Score: 68
Period size: 11 Copynumber: 4.7 Consensus size: 11
41013798 TTTCAATATT
41013808 CTCTCAAATTC
1 CTCTCAAATTC
41013819 CTCTCAAA-T-
1 CTCTCAAATTC
*
41013828 CTCTCAAATTT
1 CTCTCAAATTC
*
41013839 CTCTTAAATTC
1 CTCTCAAATTC
41013850 CTCTCAAA
1 CTCTCAAA
41013858 ACTCTCGTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 8 0.24
10 2 0.06
11 24 0.71
ACGTcount: A:0.30, C:0.32, G:0.00, T:0.38
Consensus pattern (11 bp):
CTCTCAAATTC
Found at i:41013832 original size:20 final size:21
Alignment explanation
Indices: 41013800--41013857 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 21
41013790 CTTCAATCTT
41013800 TCAATATTCTCTCAAATTCCTC
1 TCAA-ATTCTCTCAAATTCCTC
*
41013822 TCAAA-TCTCTCAAATTTCTC
1 TCAAATTCTCTCAAATTCCTC
*
41013842 TTAAATTCCTCTCAAA
1 TCAAATT-CTCTCAAA
41013858 ACTCTCGTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 18 0.56
21 2 0.06
22 12 0.38
ACGTcount: A:0.31, C:0.29, G:0.00, T:0.40
Consensus pattern (21 bp):
TCAAATTCTCTCAAATTCCTC
Found at i:41014068 original size:44 final size:44
Alignment explanation
Indices: 41014005--41014092 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
41013995 CAAATGGTAA
41014005 GTGTTAAATTTAATATTTAATATTATTTAAGATTTCTGTCATTT
1 GTGTTAAATTTAATATTTAATATTATTTAAGATTTCTGTCATTT
*
41014049 GTGTTAAATTTAATATTTAATATTATTTAATATTTCTGTCATTT
1 GTGTTAAATTTAATATTTAATATTATTTAAGATTTCTGTCATTT
41014093 ATGCAAATTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.56
Consensus pattern (44 bp):
GTGTTAAATTTAATATTTAATATTATTTAAGATTTCTGTCATTT
Found at i:41016299 original size:79 final size:81
Alignment explanation
Indices: 41016163--41016347 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
41016153 TTGAATGATG
*
41016163 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
41016227 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
41016242 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
41016304 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
41016322 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
41016348 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:41016361 original size:40 final size:40
Alignment explanation
Indices: 41016164--41016347 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
41016154 TGAATGATGT
* * * *
41016164 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
41016204 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
41016244 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
41016282 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
41016323 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
41016348 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:41016369 original size:79 final size:79
Alignment explanation
Indices: 41016216--41016380 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
41016206 GGACTAAGAT
* **
41016216 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
41016281 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
41016295 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
41016358 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
41016374 CCGAAGG
1 CCGAAGG
41016381 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:41024199 original size:79 final size:81
Alignment explanation
Indices: 41024059--41024243 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
41024049 TTGAATGATG
*
41024059 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCAGGCTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCAGGCTAAGATCCGAAGGCATT
*
41024123 TGTTCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * * *
41024138 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCAGGCTAAGAT-CCGAAGGCA
*
41024200 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
41024218 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
41024244 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCAGGCTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:41024257 original size:40 final size:41
Alignment explanation
Indices: 41024059--41024243 Score: 222
Period size: 40 Copynumber: 4.6 Consensus size: 41
41024049 TTGAATGATG
* * *
41024059 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAT-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * * *
41024099 TCCAGGCTAAGAT-CCGAAGGCATTTGTTCGAGATACTA-AT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAA
41024139 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
41024178 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
41024219 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
41024244 AACGAGTAGC
Statistics
Matches: 125, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
39 34 0.27
40 82 0.66
41 9 0.07
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:41024274 original size:79 final size:79
Alignment explanation
Indices: 41024111--41024276 Score: 194
Period size: 79 Copynumber: 2.1 Consensus size: 79
41024101 CAGGCTAAGA
* * **
41024111 TCCGAAGGCATTTGTTCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTA
1 TCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTA
* *
41024176 AATCCGGGTTAAGT
66 AATCCGGATTAAAT
* * *
41024190 CCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAG
1 TCCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-
*
41024253 CTATATCC-GATTAAAT
63 CTAAATCCGGATTAAAT
41024269 TCCGAAGG
1 TCCGAAGG
41024277 TACGTGATTT
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
78 2 0.03
79 46 0.63
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.27
Consensus pattern (79 bp):
TCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTA
AATCCGGATTAAAT
Found at i:41028678 original size:126 final size:126
Alignment explanation
Indices: 41028144--41028670 Score: 799
Period size: 126 Copynumber: 4.2 Consensus size: 126
41028134 TTCAGAAAAC
*
41028144 ACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAATGCATCCTGCT
1 ACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAATGCATCCTGCT
* * * *
41028209 TGAAGCATTTTTGACACTATTTATGCAGACACATCTTCTCAAAATTA-TTTTTCAGAGACC
66 TGAAGCGTTTTTGACACTATTTACGCAGACACGTCTTCTCAAAATTATTTTTTCAGAGACT
* * * *
41028269 ATTGTAGCAAAAGAGCATCCACGTGGGAGTTTCTTCCAGTAATTTTGCTGAAAATGCATCCTGCT
1 ACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAATGCATCCTGCT
* *
41028334 TGAAGCGTTTTT-ACCACTATTTGCGCAGACACGTCTTCTTAAAATTATTTTTTCAGAGACT
66 TGAAGCGTTTTTGA-CACTATTTACGCAGACACGTCTTCTCAAAATTATTTTTTCAGAGACT
* * *
41028395 ACTGTAGCAAAAGAGCATCCAAGTGGAAGCTTCTTTCAGTACTTTTGCTGACAATGCATCCTGCT
1 ACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAATGCATCCTGCT
* * * *
41028460 TGAAGCGTTTTTTACACTATTTGCACAGACACGTCTTCTCAAAATTATTTTTTCAGATACT
66 TGAAGCGTTTTTGACACTATTTACGCAGACACGTCTTCTCAAAATTATTTTTTCAGAGACT
* *
41028521 ACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTTCAATACTTTTGCT-AACAATTCATCCTGC
1 ACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAA-AATGCATCCTGC
* *
41028585 TTGAAGCGTTTTTGACACTATTTACGCAGGCACGTCTTCTCAAATTTATTTTTTCAGAGACT
65 TTGAAGCGTTTTTGACACTATTTACGCAGACACGTCTTCTCAAAATTATTTTTTCAGAGACT
**
41028647 ACTGTAGCAAAAGAGTGTCCACGT
1 ACTGTAGCAAAAGAGCATCCACGT
41028671 AGAAGCTTTT
Statistics
Matches: 364, Mismatches: 34, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
124 1 0.00
125 101 0.28
126 261 0.72
127 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (126 bp):
ACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAATGCATCCTGCT
TGAAGCGTTTTTGACACTATTTACGCAGACACGTCTTCTCAAAATTATTTTTTCAGAGACT
Found at i:41028925 original size:96 final size:98
Alignment explanation
Indices: 41028728--41028954 Score: 282
Period size: 96 Copynumber: 2.3 Consensus size: 98
41028718 CCTAAACCCC
* * * * * *
41028728 AAACCCTAATTTATTTGAATTTTTTTCATAAATACCCTAAACCCTAAAATCCTAATCTATTTTTT
1 AAACCCTAATTTATTTG-ATTTTTTCCTTAAAAACCATAAACACTAAAATCCTAATCTATATTTT
* ** *
41028793 TTAAAATTTATAATTAATTTACTCAAGTAACCCT
65 TTAAAATTTATAATTAATTTAATCAACAAACACT
41028827 AAACCCTAATTTATTTGATTTTTTCCTTAAAAACCATAAACACT-AAA-CCATAATCTA-ATTTT
1 AAACCCTAATTTATTTGATTTTTTCCTTAAAAACCATAAACACTAAAATCC-TAATCTATATTTT
*
41028889 TTAAAA-TTAGTAATTAATTTAATTAACAAACACT
65 TTAAAATTTA-TAATTAATTTAATCAACAAACACT
* *
41028923 AAACCTTAATTTATTTAATTTTTTCCTTAAAA
1 AAACCCTAATTTATTTGATTTTTTCCTTAAAA
41028955 CCCTAAAATT
Statistics
Matches: 113, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
95 3 0.03
96 61 0.54
97 10 0.09
98 22 0.19
99 17 0.15
ACGTcount: A:0.40, C:0.16, G:0.02, T:0.42
Consensus pattern (98 bp):
AAACCCTAATTTATTTGATTTTTTCCTTAAAAACCATAAACACTAAAATCCTAATCTATATTTTT
TAAAATTTATAATTAATTTAATCAACAAACACT
Found at i:41028969 original size:15 final size:17
Alignment explanation
Indices: 41028948--41028992 Score: 67
Period size: 15 Copynumber: 2.8 Consensus size: 17
41028938 TAATTTTTTC
41028948 CTTAAAACCCTAAAA-T
1 CTTAAAACCCTAAAATT
*
41028964 -TTAAAAACCTAAAATT
1 CTTAAAACCCTAAAATT
41028980 CTTAAAACCCTAA
1 CTTAAAACCCTAA
41028993 CCCTAATTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 13 0.52
16 1 0.04
17 11 0.44
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (17 bp):
CTTAAAACCCTAAAATT
Found at i:41034712 original size:30 final size:30
Alignment explanation
Indices: 41034676--41034736 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
41034666 GTCCTTAATC
41034676 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
41034706 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
41034736 A
1 A
41034737 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:41040835 original size:40 final size:39
Alignment explanation
Indices: 41040770--41040901 Score: 126
Period size: 40 Copynumber: 3.4 Consensus size: 39
41040760 AGTTTGGCAC
*
41040770 CCAGTGCCTCATCGGATAATTCGAAGTAATAATTTGACA
1 CCAGTGCCTCATCGGATAATCCGAAGTAATAATTTGACA
* * * *
41040809 CCGAGTGTCTCATCGGCTAAACCGAAGT-A-AATTGGTAC-
1 CC-AGTGCCTCATCGGATAATCCGAAGTAATAATTTG-ACA
* * *
41040847 CCAGTGCCTCATCGAATTAATCCGAAGTAGTAAATTGACA
1 CCAGTGCCTCATCGGA-TAATCCGAAGTAATAATTTGACA
*
41040887 CCTAGTGTCTCATCG
1 CC-AGTGCCTCATCG
41040902 ACTCGAAGTT
Statistics
Matches: 73, Mismatches: 13, Indels: 12
0.74 0.13 0.12
Matches are distributed among these distances:
37 11 0.15
38 17 0.23
39 7 0.10
40 27 0.37
41 11 0.15
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (39 bp):
CCAGTGCCTCATCGGATAATCCGAAGTAATAATTTGACA
Found at i:41042730 original size:20 final size:20
Alignment explanation
Indices: 41042697--41042735 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41042687 TTGTACAGGG
* *
41042697 TTAATAAATTTATTTAAAAT
1 TTAATAAATATATTGAAAAT
*
41042717 TTAATTAATATATTGAAAA
1 TTAATAAATATATTGAAAA
41042736 ACTAATGTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (20 bp):
TTAATAAATATATTGAAAAT
Found at i:41043223 original size:15 final size:16
Alignment explanation
Indices: 41043190--41043224 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
41043180 TAAGCTTAAT
*
41043190 AATTTAATAATTATTA
1 AATTTAATAATTATAA
41043206 AATTTAAT-ATTATAA
1 AATTTAATAATTATAA
41043221 AATT
1 AATT
41043225 AAAAGTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AATTTAATAATTATAA
Found at i:41057773 original size:20 final size:20
Alignment explanation
Indices: 41057736--41057774 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41057726 TTCAACCATA
* *
41057736 TATTTTTACATTCGTTTATT
1 TATTTTTAAATTCATTTATT
*
41057756 TATTTTTAAATTTATTTAT
1 TATTTTTAAATTCATTTAT
41057775 GGGAATTTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.67
Consensus pattern (20 bp):
TATTTTTAAATTCATTTATT
Found at i:41060720 original size:24 final size:24
Alignment explanation
Indices: 41060693--41060744 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
41060683 TTAGTAAGTC
*
41060693 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
41060717 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
41060741 AAAT
1 AAAT
41060745 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:41062690 original size:24 final size:24
Alignment explanation
Indices: 41062663--41062714 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
41062653 TTAGTAAGTC
*
41062663 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
41062687 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
41062711 AAAT
1 AAAT
41062715 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:41069749 original size:32 final size:32
Alignment explanation
Indices: 41069711--41069775 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
41069701 ATTAATCAAT
* *
41069711 ATGAGTTATCAAATTAAATTAATTAATTTATA
1 ATGAGTTATCAAATTAAAGTAATCAATTTATA
** *
41069743 ATGAGTTATTGAATTCAAGTAATCAATTTATA
1 ATGAGTTATCAAATTAAAGTAATCAATTTATA
41069775 A
1 A
41069776 GTTTATGATG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.42
Consensus pattern (32 bp):
ATGAGTTATCAAATTAAAGTAATCAATTTATA
Found at i:41069894 original size:32 final size:32
Alignment explanation
Indices: 41069856--41069920 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
41069846 ATTAATCAAT
* *
41069856 ATGAGTTATCAAATTAAATTAATTAATTTATA
1 ATGAGTTATCAAATTAAAGTAATCAATTTATA
** *
41069888 ATGAGTTATTGAATTCAAGTAATCAATTTATA
1 ATGAGTTATCAAATTAAAGTAATCAATTTATA
41069920 A
1 A
41069921 GTTTATAATG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.42
Consensus pattern (32 bp):
ATGAGTTATCAAATTAAAGTAATCAATTTATA
Found at i:41069947 original size:145 final size:145
Alignment explanation
Indices: 41069681--41070087 Score: 687
Period size: 145 Copynumber: 2.8 Consensus size: 145
41069671 ATTATAAAGT
*
41069681 TCATAAATCTAACAAGCTCAATTAATCAATATGAGTTATCAAATTAAATTAATTAATTTATAATG
1 TCATAAATCTAACAGGCTCAATTAATCAATATGAGTTATCAAATTAAATTAATTAATTTATAATG
41069746 AGTTATTGAATTCAAGTAATCAATTTATAAGTTTATGATGTTCCGAATTCATAGTAGAATACATT
66 AGTTATTGAATTCAAGTAATCAATTTATAAGTTTATGATGTTCCGAATTCATAGTAGAATACATT
*
41069811 CTTACACATGATTAA
131 CTTACACATGATCAA
* *
41069826 TCCTAAATCTAGCAGGCTCAATTAATCAATATGAGTTATCAAATTAAATTAATTAATTTATAATG
1 TCATAAATCTAACAGGCTCAATTAATCAATATGAGTTATCAAATTAAATTAATTAATTTATAATG
* *
41069891 AGTTATTGAATTCAAGTAATCAATTTATAAGTTTATAATGTTCCGAATCCATAGTAGAATACATT
66 AGTTATTGAATTCAAGTAATCAATTTATAAGTTTATGATGTTCCGAATTCATAGTAGAATACATT
41069956 CTTACACATGATCAA
131 CTTACACATGATCAA
*
41069971 TCATAAATCTAACAGGCTCAATTAATCAGTATGAGTTATCAAATTAAATTAATTAA--T-T-ATG
1 TCATAAATCTAACAGGCTCAATTAATCAATATGAGTTATCAAATTAAATTAATTAATTTATAATG
* * * *
41070032 AGTTATTAAATTCAAGTAATCAATTTGTAAATTTATGATGTTCCAAATTCATAGTA
66 AGTTATTGAATTCAAGTAATCAATTTATAAGTTTATGATGTTCCGAATTCATAGTA
41070088 AAAATATTTA
Statistics
Matches: 247, Mismatches: 15, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
141 53 0.21
142 1 0.00
143 1 0.00
145 192 0.78
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.38
Consensus pattern (145 bp):
TCATAAATCTAACAGGCTCAATTAATCAATATGAGTTATCAAATTAAATTAATTAATTTATAATG
AGTTATTGAATTCAAGTAATCAATTTATAAGTTTATGATGTTCCGAATTCATAGTAGAATACATT
CTTACACATGATCAA
Found at i:41070051 original size:28 final size:28
Alignment explanation
Indices: 41070000--41070056 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
41069990 AATTAATCAG
* *
41070000 TATGAGTTATCAAATTAAATTAATTAAT
1 TATGAGTTATCAAATTAAAGTAATCAAT
* *
41070028 TATGAGTTATTAAATTCAAGTAATCAAT
1 TATGAGTTATCAAATTAAAGTAATCAAT
41070056 T
1 T
41070057 TGTAAATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (28 bp):
TATGAGTTATCAAATTAAAGTAATCAAT
Done.